Change search
Refine search result
1 - 5 of 5
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Rows per page
  • 5
  • 10
  • 20
  • 50
  • 100
  • 250
Sort
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
  • Disputation date (earliest first)
  • Disputation date (latest first)
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
  • Disputation date (earliest first)
  • Disputation date (latest first)
Select
The maximal number of hits you can export is 250. When you want to export more records please use the Create feeds function.
  • 1.
    Agaton, Charlotta
    et al.
    KTH, Superseded Departments, Biotechnology.
    Unneberg, Per
    KTH, Superseded Departments, Biotechnology.
    Sievertzon, Maria
    KTH, Superseded Departments, Biotechnology.
    Holmberg, Anders
    KTH, Superseded Departments, Biotechnology.
    Ehn, Maria
    KTH, Superseded Departments, Biotechnology.
    Larsson, Magnus
    KTH, Superseded Departments, Biotechnology.
    Odeberg, Jacob
    KTH, Superseded Departments, Biotechnology.
    Uhlén, Mathias
    KTH, Superseded Departments, Biotechnology.
    Lundeberg, Joakim
    KTH, Superseded Departments, Biotechnology.
    Gene expression analysis by signature pyrosequencing2002In: Gene, ISSN 0378-1119, E-ISSN 1879-0038, Vol. 289, no 1-2, p. 31-39Article in journal (Refereed)
    Abstract [en]

     We describe a novel method for transcript profiling based on high-throughput parallel sequencing of signature tags using a non-gel-based microtiter plate format. The method relies on the identification of cDNA clones by pyrosequencing of the region corresponding to the 3'-end of the mRNA preceding the poly(A) tail. Simultaneously, the method can be used for gene discovery, since tags corresponding to unknown genes can be further characterized by extended sequencing. The protocol was validated using a model system for human atherosclerosis. Two 3'-tagged cDNA libraries, representing macrophages and foam cells, which are key components in the development of atherosclerotic plaques, were constructed using a solid phase approach. The libraries were analyzed by pyrosequencing, giving on average 25 bases. As a control, conventional expressed sequence tag (EST) sequencing using slab gel electrophoresis was performed. Homology searches were used to identify the genes corresponding to each tag. Comparisons with EST sequencing showed identical, unique matches in the majority of cases when the pyrosignature was at least 18 bases. A visualization tool was developed to facilitate differential analysis using a virtual chip format. The analysis resulted in identification of genes with possible relevance for development of atherosclerosis. The use of the method for automated massive parallel signature sequencing is discussed.

  • 2.
    Bertilson, Michael
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
    von Hofsten, Olov
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
    Vogt, Ulrich
    Holmberg, Anders
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
    Christakou, Athanasia
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
    Jerlström-Hultqvist, J.
    Svärd, S.
    Hertz, Hans M.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
    Laboratory Soft X-Ray Cryo TomographyManuscript (preprint) (Other academic)
    Abstract [en]

    X-rays allow quantitative high-spatial-resolution three-dimensional (3D) imaging of intact unstained cells. Such 3D imaging is provided by soft x-ray lens-based methods (water-window cryo tomography) and hard x-ray lens-less methods (coherent diffraction imaging) are emerging. However, both methods rely on high-brightness synchrotron-radiation sources, which limit the accessibility of a wider scientific community. Here we show 3D water-window cryo tomography with a laboratory-source-based microscope arrangement. The system relies on a λ=2.48-nm liquid-jet laser-plasma source, normal- incidence multilayer condenser optics, 30-nm zone-plate optics, and a cryo sample chamber. We demonstrate imaging of intact unstained yeast, protozoan parasites and mammalian cells. 3D images show noise-limited features close to ~100 nm and intra-cellular structure is classified based on the local absorption coefficient. A comprehensive theoretical model of the tomographic imaging system allows optimization of system parameters and a quantitative estimate of the 3D imaging accuracy. The model includes issues such as non-geometric projections of the thick samples and stray light, and is applicable to laboratory as well as synchrotron-based x-ray microscopes. The model shows that laboratory x-ray cryo tomography will allow quantitative 3D imaging with ~30-nm (half-period) resolution over a full 5 µm object.

     

  • 3.
    Hertz, Hans
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
    von Hofsten, Olov
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
    Bertilson, Mikael
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
    Vogt, Ulrich
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
    Holmberg, Anders
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
    Reinspach, Julia Antonia
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
    Martz, Dale
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
    Selin, Mårten
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
    Christakou, Athanasia
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
    Jerlström-Hultqvist, J
    Svärd, S
    Laboratory cryo soft X-ray microscopy2012In: Journal of Structural Biology, ISSN 1047-8477, E-ISSN 1095-8657, Vol. 177, no 2, p. 267-272Article in journal (Refereed)
    Abstract [en]

    Lens-based water-window X-ray microscopy allows two- and three-dimensional (2D and 3D) imaging of intact unstained cells in their near-native state with unprecedented contrast and resolution. Cryofixation is essential to avoid radiation damage to the sample. Present cryo X-ray microscopes rely on synchrotron radiation sources, thereby limiting the accessibility for a wider community of biologists. In the present paper we demonstrate water-window cryo X-ray microscopy with a laboratory-source-based arrangement. The microscope relies on a lambda = 2.48-nm liquid-jet high-brightness laser-plasma source, normal-incidence multilayer condenser optics, 30-nm zone-plate optics, and a cryo sample chamber. We demonstrate 2D imaging of test patterns, and intact unstained yeast, protozoan parasites and mammalian cells. Overview 3D information is obtained by stereo imaging while complete 3D microscopy is provided by full tomographic reconstruction. The laboratory microscope image quality approaches that of the synchrotron microscopes, but with longer exposure times. The experimental image quality is analyzed from a numerical wave-propagation model of the imaging system and a path to reach synchrotron-like exposure times in laboratory microscopy is outlined.

  • 4.
    Holmberg, Anders
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
    Reinspach, Julia
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
    Lindblom, Magnus
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
    Chubarova, Elena
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
    Bertilson, Michael
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
    von Hofsten, Olov
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
    Nilsson, Daniel
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
    Selin, Mårten
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
    Larsson, Daniel
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
    Skoglund Lindberg, Peter
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
    Lundstrom, Ulf
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
    Takman, Per
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
    Vogt, Ulrich
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
    Hertz, Hans
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
    Towards 10-nm Soft X-Ray Zone Plate Fabrication2011Conference paper (Refereed)
    Abstract [en]

    In this paper the latest efforts to improve our nanofabrication process for soft x‐ray zone plates is presented. The resolving power, which is proportional to the smallest outermost zone width of the zone plate, is increased by introducing cold development of the electron beam resist that is used for the patterning. With this process we have fabricated Ni zone plates with 13‐nm outermost zone and shown potential for making 11‐nm half‐pitch lines in the electron beam resist. Maintaining the diffraction efficiency of the zone plate is a great concern when the outermost zone width is decreased. To resolve this problem we have developed the so‐called Ni‐Ge zone plate in which the zone plate is build up by Ni and Ge, resulting in an increase of the diffraction efficiency. In a proof‐of‐principle experiment with 25‐nm Ni‐Ge zone plates, we have shown a doubling of the diffraction efficiency. When combined with cold development, the Ni‐Ge process has been shown to work down to 16‐nm half‐pitch. It is plausible that further refinement of the process will make it possible to go to 10‐nm outermost zone widths.

  • 5.
    Westberg, Joakim
    et al.
    KTH, Superseded Departments, Biotechnology.
    Persson, Anja
    KTH, Superseded Departments, Biotechnology.
    Holmberg, Anders H.
    KTH, Superseded Departments, Biotechnology.
    Goesmann, A.
    Lundeberg, Joakim
    KTH, Superseded Departments, Biotechnology.
    Johansson, K. E.
    Pettersson, Bertil
    KTH, Superseded Departments, Biotechnology.
    Uhlén, Mathias
    KTH, Superseded Departments, Biotechnology.
    The genome sequence of Mycoplasma mycoides subsp mycoides SC type strain PG1(T), the causative agent of contagious bovine pleuropneumonia (CBPP)2004In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 14, no 2, p. 221-227Article in journal (Refereed)
    Abstract [en]

    Mycoplasma mycoides subsp. mycoidesSC (MmymySC) is the etiological agent of contagious bovine pleuropneumonia (CBPP), a highly contagious respiratory disease in cattle. The genome of Mmymy SC type strain PUT has been sequenced to map all the genes and to facilitate further studies regarding the cell function of the organism and CBPP. The genome is characterized by a single circular chromosome of 1,211,703 bp with the lowest G+C content (24 mole%) and the highest density of insertion sequences (13% of the genome size) of all sequenced bacterial genomes. The genome contains 985 putative genes, of which 72 are part of insertion sequences and encode transposases. Anomalies in the GC-skew pattern and the presence of large repetitive sequences indicate a high genomic plasticity. A variety of potential virulence factors was identified, including genes encoding putative variable surface proteins and enzymes and transport proteins responsible for the production of hydrogen peroxide and the capsule, which is believed to have toxic effects on the animal.

1 - 5 of 5
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf