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  • 1. Abrahamsson, S.
    et al.
    Blom, Hans
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Agostinho, A.
    Jans, Daniel
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Jost, A.
    Müller, M.
    Nilsson, Linnea
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Bernhem, K.
    Lambert, T. J.
    Heintzmann, R.
    Brismar, Hjalmar
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Multifocus structured illumination microscopy for fast volumetric super-resolution imaging2017In: Biomedical Optics Express, ISSN 2156-7085, E-ISSN 2156-7085, Vol. 8, no 9, p. 4135-4140, article id #294866Article in journal (Refereed)
    Abstract [en]

    We here report for the first time the synergistic implementation of structured illumination microscopy (SIM) and multifocus microscopy (MFM). This imaging modality is designed to alleviate the problem of insufficient volumetric acquisition speed in superresolution biological imaging. SIM is a wide-field super-resolution technique that allows imaging with visible light beyond the classical diffraction limit. Employing multifocus diffractive optics we obtain simultaneous wide-field 3D imaging capability in the SIM acquisition sequence, improving volumetric acquisition speed by an order of magnitude. Imaging performance is demonstrated on biological specimens.

  • 2.
    Guala, Dimitri
    et al.
    Stockholm Univ, Dept Biochem & Biophys, Stockholm Bioinformat Ctr, Sci Life Lab, Box 1031, S-17121 Solna, Sweden..
    Bernhem, Kristoffer
    KTH, School of Engineering Sciences (SCI), Applied Physics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Blal, Hammou Ait
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Biotechnology (BIO).
    Jans, Daniel
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences (SCI), Applied Physics.
    Lundberg, Emma
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Biotechnology (BIO).
    Brismar, Hjalmar
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences (SCI), Applied Physics.
    Sonnhammer, Erik L. L.
    Stockholm Univ, Dept Biochem & Biophys, Stockholm Bioinformat Ctr, Sci Life Lab, Box 1031, S-17121 Solna, Sweden..
    Experimental validation of predicted cancer genes using FRET2018In: METHODS AND APPLICATIONS IN FLUORESCENCE, ISSN 2050-6120, Vol. 6, no 3, article id 035007Article in journal (Refereed)
    Abstract [en]

    Huge amounts of data are generated in genome wide experiments, designed to investigate diseases with complex genetic causes. Follow up of all potential leads produced by such experiments is currently cost prohibitive and time consuming. Gene prioritization tools alleviate these constraints by directing further experimental efforts towards the most promising candidate targets. Recently a gene prioritization tool called MaxLink was shown to outperform other widely used state-of-the-art prioritization tools in a large scale in silico benchmark. An experimental validation of predictions made by MaxLink has however been lacking. In this study we used Fluorescence Resonance Energy Transfer, an established experimental technique for detection of protein-protein interactions, to validate potential cancer genes predicted by MaxLink. Our results provide confidence in the use of MaxLink for selection of new targets in the battle with polygenic diseases.

  • 3.
    Johansson, Henrik J.
    et al.
    Karolinska Inst, Dept Oncol Pathol, Sci Life Lab, S-17121 Solna, Sweden..
    Socciarelli, Fabio
    Karolinska Inst, Dept Oncol Pathol, Sci Life Lab, S-17121 Solna, Sweden..
    Vacanti, Nathaniel M.
    Karolinska Inst, Dept Oncol Pathol, Sci Life Lab, S-17121 Solna, Sweden.;Cornell Univ, Div Nutrit Sci, Ithaca, NY 14853 USA..
    Haugen, Mads H.
    Oslo Univ Hosp, Inst Canc Res, Dept Tumor Biol, N-0424 Oslo, Norway.;Oslo Univ Hosp, Inst Canc Res, Dept Canc Genet, N-0424 Oslo, Norway..
    Zhu, Yafeng
    Karolinska Inst, Dept Oncol Pathol, Sci Life Lab, S-17121 Solna, Sweden..
    Siavelis, Ioannis
    Karolinska Inst, Dept Oncol Pathol, Sci Life Lab, S-17121 Solna, Sweden..
    Fernandez-Woodbridge, Alejandro
    Karolinska Inst, Dept Oncol Pathol, Sci Life Lab, S-17121 Solna, Sweden..
    Aure, Miriam R.
    Oslo Univ Hosp, Inst Canc Res, Dept Canc Genet, N-0424 Oslo, Norway..
    Sennblad, Bengt
    Uppsala Univ, Sci Life Lab, Dept Cell & Mol Biol, Natl Bioinformat Infrastruct Sweden, S-75237 Uppsala, Sweden..
    Vesterlund, Mattias
    Karolinska Inst, Dept Oncol Pathol, Sci Life Lab, S-17121 Solna, Sweden..
    Branca, Rui M.
    Karolinska Inst, Dept Oncol Pathol, Sci Life Lab, S-17121 Solna, Sweden..
    Orre, Lukas M.
    Karolinska Inst, Dept Oncol Pathol, Sci Life Lab, S-17121 Solna, Sweden..
    Huss, Mikael
    Stockholm Univ, Sci Life Lab, Dept Biochem & Biophys, Natl Bioinformat Infrastruct Sweden, S-17121 Solna, Sweden..
    Fredlund, Erik
    Karolinska Inst, Dept Oncol Pathol, Sci Life Lab, S-17121 Solna, Sweden..
    Beraki, Elsa
    Oslo Univ Hosp, Dept Pathol, N-0424 Oslo, Norway..
    Garred, Oystein
    Oslo Univ Hosp, Dept Pathol, N-0424 Oslo, Norway..
    Boekel, Jorrit
    Karolinska Inst, Dept Oncol Pathol, Sci Life Lab, S-17121 Solna, Sweden..
    Sauer, Torill
    Akershus Univ Hosp, Dept Pathol, N-1478 Lorenskog, Norway.;Univ Oslo, Inst Clin Med, N-0318 Oslo, Norway..
    Zhao, Wei
    Univ Texas MD Anderson Canc Ctr, Dept Syst Biol, Houston, TX 77230 USA..
    Nord, Silje
    Oslo Univ Hosp, Inst Canc Res, Dept Canc Genet, N-0424 Oslo, Norway..
    Hoglander, Elen K.
    Oslo Univ Hosp, Inst Canc Res, Dept Canc Genet, N-0424 Oslo, Norway..
    Jans, Daniel C.
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Brismar, Hjalmar
    KTH, School of Engineering Sciences (SCI), Applied Physics. Karolinska Inst, Dept Womenss & Childrens Hlth, S-17121 Solna, Sweden..
    Haukaas, Tonje H.
    Norwegian Univ Sci & Technol NTNU, Dept Circulat & Med Imaging, N-7491 Trondheim, Norway..
    Bathen, Tone F.
    Norwegian Univ Sci & Technol NTNU, Dept Circulat & Med Imaging, N-7491 Trondheim, Norway..
    Schlichting, Ellen
    Oslo Univ Hosp, Dept Canc, Sect Breast & Endocrine Surg, Div Surg Canc & Transplantat Med, N-0424 Oslo, Norway..
    Naume, Bjorn
    Univ Oslo, Inst Clin Med, N-0318 Oslo, Norway.;Oslo Univ Hosp, Div Surg & Canc & Transplantat Med, Dept Oncol, N-0424 Oslo, Norway..
    Geisler, Juergen
    Univ Oslo, Inst Clin Med, N-0318 Oslo, Norway.;Akershus Univ Hosp, Dept Oncol, N-1478 Lorenskog, Norway.;Akershus Univ Hosp, Div Med, N-1478 Lorenskog, Norway..
    Hofvind, Solveig
    Canc Registry Norway, N-0379 Oslo, Norway.;Oslo & Akershus Univ, Coll Appl Sci, Fac Hlth Sci, N-0130 Oslo, Norway..
    Engebraten, Olav
    Univ Oslo, Inst Clin Med, N-0318 Oslo, Norway.;Oslo Univ Hosp, Div Surg & Canc & Transplantat Med, Dept Oncol, N-0424 Oslo, Norway.;Oslo Univ Hosp, Inst Canc Res, Dept Tumor Biol, N-0379 Oslo, Norway..
    Geitvik, Gry Aarum
    Oslo Univ Hosp, Norwegian Radium Hosp, Inst Canc Res, Dept Canc Genet, N-0379 Oslo, Norway..
    Langerod, Anita
    Oslo Univ Hosp, Norwegian Radium Hosp, Inst Canc Res, Dept Canc Genet, N-0379 Oslo, Norway..
    Karesen, Rolf
    Univ Oslo, Inst Clin Med, N-0318 Oslo, Norway.;Oslo Univ Hosp, Div Surg Canc & Transplantat, Dept Breast & Endocrine Surg, N-0379 Oslo, Norway..
    Maelandsmo, Gunhild Mari
    Oslo Univ Hosp, Inst Canc Res, Dept Tumor Biol, N-0379 Oslo, Norway.;Univ Tromso, Fac Hlth Sci, Dept Pharm, N-9010 Tromso, Norway..
    Sorlie, Therese
    Oslo Univ Hosp, Norwegian Radium Hosp, Inst Canc Res, Dept Canc Genet, N-0379 Oslo, Norway..
    Skjerven, Helle Kristine
    Vestre Viken Hosp Trust, Dept Breast & Endocrine Surg, Breast & Endocrine Surg, N-3004 Drammen, Norway..
    Park, Daehoon
    Vestre Viken Hosp Trust, Dept Pathol, N-3004 Drammen, Norway..
    Hartman-Johnsen, Olaf-Johan
    Ostfold Hosp, N-1714 Ostfold, Norway..
    Luders, Torben
    Univ Oslo, Inst Clin Med, N-0318 Oslo, Norway.;Akershus Univ Hosp, Div Med, Dept Clin Mol Biol & Lab Sci EpiGen, N-1478 Lorenskog, Norway..
    Borgen, Elin
    Oslo Univ Hosp, Dept Pathol, N-0424 Oslo, Norway..
    Kristensen, Vessela N.
    Oslo Univ Hosp, Inst Canc Res, Dept Canc Genet, N-0424 Oslo, Norway.;Univ Oslo, Inst Clin Med, N-0318 Oslo, Norway.;Akershus Univ Hosp, Div Med, Dept Clin Mol Biol & Lab Sci EpiGen, N-1478 Lorenskog, Norway..
    Russnes, Hege G.
    Oslo Univ Hosp, Inst Canc Res, Dept Canc Genet, N-0424 Oslo, Norway..
    Lingjaerde, Ole Christian
    Oslo Univ Hosp, Inst Canc Res, Dept Canc Genet, N-0424 Oslo, Norway.;Univ Oslo, Ctr Canc Biomed, N-0424 Oslo, Norway..
    Mills, Gordon B.
    Univ Texas MD Anderson Canc Ctr, Dept Syst Biol, Houston, TX 77230 USA..
    Sahlberg, Kristine K.
    Oslo Univ Hosp, Inst Canc Res, Dept Canc Genet, N-0424 Oslo, Norway.;Vestre Viken Hosp Trust, Dept Res, N-3004 Drammen, Norway..
    Borresen-Dale, Anne-Lise
    Oslo Univ Hosp, Inst Canc Res, Dept Canc Genet, N-0424 Oslo, Norway.;Univ Oslo, Inst Clin Med, N-0318 Oslo, Norway..
    Lehtio, Janne
    Karolinska Inst, Dept Oncol Pathol, Sci Life Lab, S-17121 Solna, Sweden..
    Breast cancer quantitative proteome and proteogenomic landscape2019In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 10, article id 1600Article in journal (Refereed)
    Abstract [en]

    In the preceding decades, molecular characterization has revolutionized breast cancer (BC) research and therapeutic approaches. Presented herein, an unbiased analysis of breast tumor proteomes, inclusive of 9995 proteins quantified across all tumors, for the first time recapitulates BC subtypes. Additionally, poor-prognosis basal-like and luminal B tumors are further subdivided by immune component infiltration, suggesting the current classification is incomplete. Proteome-based networks distinguish functional protein modules for breast tumor groups, with co-expression of EGFR and MET marking ductal carcinoma in situ regions of normal-like tumors and lending to a more accurate classification of this poorly defined subtype. Genes included within prognostic mRNA panels have significantly higher than average mRNA-protein correlations, and gene copy number alterations are dampened at the protein-level; underscoring the value of proteome quantification for prognostication and phenotypic classification. Furthermore, protein products mapping to non-coding genomic regions are identified; highlighting a potential new class of tumor-specific immunotherapeutic targets.

  • 4.
    Stoldt, Stefan
    et al.
    Max Planck Inst Biophys Chem, Dept NanoBiophoton, D-37077 Gottingen, Germany..
    Stephan, Till
    Max Planck Inst Biophys Chem, Dept NanoBiophoton, D-37077 Gottingen, Germany..
    Jans, Daniel C.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences (SCI), Applied Physics. Univ Med Ctr Gottingen, Clin Neurol, D-37075 Gottingen, Germany..
    Brueser, Christian
    Max Planck Inst Biophys Chem, Dept NanoBiophoton, D-37077 Gottingen, Germany..
    Lange, Felix
    Max Planck Inst Biophys Chem, Dept NanoBiophoton, D-37077 Gottingen, Germany..
    Keller-Findeisen, Jan
    Max Planck Inst Biophys Chem, Dept NanoBiophoton, D-37077 Gottingen, Germany..
    Riedel, Dietmar
    Max Planck Inst Biophys Chem, Lab Electron Microscopy, D-37077 Gottingen, Germany..
    Hell, Stefan W.
    Max Planck Inst Biophys Chem, Dept NanoBiophoton, D-37077 Gottingen, Germany..
    Jakobs, Stefan
    Max Planck Inst Biophys Chem, Dept NanoBiophoton, D-37077 Gottingen, Germany.;Univ Med Ctr Gottingen, Clin Neurol, D-37075 Gottingen, Germany..
    Mic60 exhibits a coordinated clustered distribution along and across yeast and mammalian mitochondria2019In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 116, no 20, p. 9853-9858Article in journal (Refereed)
    Abstract [en]

    Mitochondria are tubular double-membrane organelles essential for eukaryotic life. They form extended networks and exhibit an intricate inner membrane architecture. The MICOS (mitochondrial contact site and cristae organizing system) complex, crucial for proper architecture of the mitochondrial inner membrane, is localized primarily at crista junctions. Harnessing superresolution fluorescence microscopy, we demonstrate that Mic60, a subunit of the MICOS complex, as well as several of its interaction partners are arranged into intricate patterns in human and yeast mitochondria, suggesting an ordered distribution of the crista junctions. We show that Mic60 forms clusters that are preferentially localized in the inner membrane at two opposing sides of the mitochondrial tubules so that they form extended opposing distribution bands. These Mic60 distribution bands can be twisted, resulting in a helical arrangement. Focused ion beam milling-scanning electron microscopy showed that in yeast the twisting of the opposing distribution bands is echoed by the folding of the inner membrane. We show that establishment of the Mic60 distribution bands is largely independent of the cristae morphology. We suggest that Mic60 is part of an extended multiprotein interaction network that scaffolds mitochondria.

  • 5.
    Wurm, Christian A.
    et al.
    Max Planck Inst Biophys Chem, Dept NanoBiophoton, Gottingen, Germany.;Abberior Instruments GmbH, Gottingen, Germany..
    Schwarz, Heinz
    Max Planck Inst Dev Biol, Tubingen, Germany..
    Jans, Daniel C.
    KTH, School of Engineering Sciences (SCI), Applied Physics. KTH, Centres, Science for Life Laboratory, SciLifeLab. Max Planck Inst Biophys Chem, Dept NanoBiophoton, Gottingen, Germany.;Univ Med Ctr Gottingen, Clin Neurol, Gottingen, Germany.
    Riedel, Dietmar
    Max Planck Inst Biophys Chem, Lab Electron Microscopy, D-37077 Gottingen, Germany..
    Humbel, Bruno M.
    Univ Lausanne, Electron Microscopy Facil, Lausanne, Switzerland.;Okinawa Inst Sci & Technol, Imaging, Onna Son, Okinawa, Japan..
    Jakobs, Stefan
    Max Planck Inst Biophys Chem, Dept NanoBiophoton, Gottingen, Germany.;Univ Med Ctr Gottingen, Clin Neurol, Gottingen, Germany..
    Correlative STED super-resolution light and electron microscopy on resin sections2019In: Journal of Physics D: Applied Physics, ISSN 0022-3727, E-ISSN 1361-6463, Vol. 52, no 37, article id 374003Article in journal (Refereed)
    Abstract [en]

    Correlative light and electron microscopy approaches can reveal the localisation of specific proteins while providing detailed information on the cellular context, thereby combining the strengths of both imaging modalities. The major challenge in combining fluorescence microscopy with electron microscopy is the different sample preparation requirements necessary for obtaining high quality data from both modalities. To overcome this limitation, we combined conventional sample preparation protocols for electron microscopy with post-embedding labelling on ultra-thin sections using antibodies and other specific ligands. We successfully employed STED super-resolution microscopy to image the subcellular distribution of several targets in various specimen including E. coli, T brucei, S. cerevisiae, human cancer cells and bovine sperm. Thus, we present widely applicable methods facilitating the use of antibodies for correlative super-resolution light and electron microscopy of post-embedding labelled targets.

  • 6.
    Yu, Yang
    et al.
    Karolinska Inst, Ctr Alzheimer Res, Div Neurogeriatr, Dept Neurobiol Care Sci & Soc, Huddinge, Sweden..
    Jans, Daniel C.
    KTH, School of Engineering Sciences (SCI), Applied Physics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Winblad, Bengt
    Karolinska Inst, Ctr Alzheimer Res, Div Neurogeriatr, Dept Neurobiol Care Sci & Soc, Huddinge, Sweden..
    Tjernberg, Lars O.
    Karolinska Inst, Ctr Alzheimer Res, Div Neurogeriatr, Dept Neurobiol Care Sci & Soc, Huddinge, Sweden..
    Schedin-Weiss, Sophia
    Karolinska Inst, Ctr Alzheimer Res, Div Neurogeriatr, Dept Neurobiol Care Sci & Soc, Huddinge, Sweden..
    Neuronal A beta 42 is enriched in small vesicles at the presynaptic side of synapses2018In: LIFE SCIENCE ALLIANCE, ISSN 2575-1077, Vol. 1, no 3, article id e201800028Article in journal (Refereed)
    Abstract [en]

    The amyloid beta-peptide (A beta) is a physiological ubiquitously expressed peptide suggested to be involved in synaptic function, long-term potentiation, and memory function. The 42 amino acid-long variant (A beta 42) forms neurotoxic oligomers and amyloid plaques and plays a key role in the loss of synapses and other pathogenic events of Alzheimer disease. Still, the exact localization of A beta 42 in neurons and at synapses has not been reported. Here, we used super-resolution microscopy and show that A beta 42 was present in small vesicles in presynaptic compartments, but not in postsynaptic compartments, in the neurites of hippocampal neurons. Some of these vesicles appeared to lack synaptophysin, indicating that they differ from the synaptic vesicles responsible for neurotransmitter release. The A beta 42-containing vesicles existed in presynapses connected to stubby spines and mushroom spines, and were also present in immature presynapses. These vesicleswere scarce inother parts of the neurites, where A beta 42 was instead present in large, around 200-600 nm, vesicular structures. Three-dimensional super-resolution microscopy confirmed that A beta 42 was present in the presynapse and absent in the postsynapse.

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