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  • 101.
    Kronqvist, Nina
    et al.
    Karolinska Institutet.
    Otikovs, Martins
    Latvian Institute of Organic Synthesis.
    Chmyrov, Volodymyr
    KTH, School of Engineering Sciences (SCI), Applied Physics, Experimental Biomolecular Physics. KTH, School of Biotechnology (BIO), Centres, Albanova VinnExcellence Center for Protein Technology, ProNova.
    Chen, Gefei
    Andersson, Marlene
    Sveriges lantbruksuniversitet.
    Nordling, Kerstin
    Karolinska Institutet.
    Landreh, Michael
    Sarr, Médoune
    Karolinska Institutet.
    Jörnvall, Hans
    Karolinska Institutet.
    Wennmalm, Stefan
    KTH, School of Engineering Sciences (SCI), Applied Physics, Experimental Biomolecular Physics. KTH, School of Biotechnology (BIO), Centres, Albanova VinnExcellence Center for Protein Technology, ProNova. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Widengren, Jerker
    KTH, School of Engineering Sciences (SCI), Applied Physics, Experimental Biomolecular Physics. KTH, School of Biotechnology (BIO), Centres, Albanova VinnExcellence Center for Protein Technology, ProNova.
    Meng, Qing
    Donghua University.
    Rising, Anna
    Sveriges lantbruksuniversitet.
    Otzen, Daniel Erik Rik
    Knight, Stefan
    Jaudzems, Kristaps
    Latvian Institute of Organic Synthesis.
    Johansson, Jan Ove
    Sequential pH-driven dimerization and stabilization of the N-terminal domain enables rapid spider silk formation2014In: Nature Communications, E-ISSN 2041-1723, Vol. 5, no 1, p. 3254-Article in journal (Refereed)
    Abstract [en]

    The mechanisms controlling the conversion of spider silk proteins into insoluble fibres, which happens in a fraction of a second and in a defined region of the silk glands, are still unresolved. The N-terminal domain changes conformation and forms a homodimer when pH is lowered from 7 to 6; however, the molecular details still remain to be determined. Here we investigate site-directed mutants of the N-terminal domain from Euprosthenops australis major ampullate spidroin 1 and find that the charged residues D40, R60 and K65 mediate intersubunit electrostatic interactions. Protonation of E79 and E119 is required for structural conversions of the subunits into a dimer conformation, and subsequent protonation of E84 around pH 5.7 leads to the formation of a fully stable dimer. These residues are highly conserved, indicating that the now proposed three-step mechanism prevents premature aggregation of spidroins and enables fast formation of spider silk fibres in general.

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  • 102. Kronqvist, Nina
    et al.
    Sarr, Medoune
    Lindqvist, Anton
    Nordling, Kerstin
    Otikovs, Martins
    Venturi, Luca
    Pioselli, Barbara
    Purhonen, Pasi
    Landreh, Michael
    Biverstal, Henrik
    Toleikis, Zigmantas
    Sjöberg, Lisa
    Robinson, Carol V.
    Pelizzi, Nicola
    Jornvall, Hans
    Hebert, Hans
    KTH, School of Technology and Health (STH), Basic Science and Biomedicine, Structural Biotechnology. Karolinska Institutet, Sverige.
    Jaudzems, Kristaps
    Curstedt, Tore
    Rising, Anna
    Johansson, Jan
    Efficient protein production inspired by how spiders make silk2017In: Nature Communications, E-ISSN 2041-1723, Vol. 8, article id 15504Article in journal (Refereed)
    Abstract [en]

    Membrane proteins are targets of most available pharmaceuticals, but they are difficult to produce recombinantly, like many other aggregation-prone proteins. Spiders can produce silk proteins at huge concentrations by sequestering their aggregation-prone regions in micellar structures, where the very soluble N-terminal domain (NT) forms the shell. We hypothesize that fusion to NT could similarly solubilize non-spidroin proteins, and design a charge-reversed mutant (NT star) that is pH insensitive, stabilized and hypersoluble compared to wildtype NT. NT star-transmembrane protein fusions yield up to eight times more of soluble protein in Escherichia coli than fusions with several conventional tags. NT star enables transmembrane peptide purification to homogeneity without chromatography and manufacture of low-cost synthetic lung surfactant that works in an animal model of respiratory disease. NT star also allows efficient expression and purification of non-transmembrane proteins, which are otherwise refractory to recombinant production, and offers a new tool for reluctant proteins in general.

  • 103.
    Kunnus, Kristjan
    et al.
    Stanford Univ, PULSE Inst, SLAC Natl Accelerator Lab, Menlo Pk, CA 94025 USA.
    Vacher, Morgane
    Uppsala universitet, Teoretisk kemi.
    Harlang, Tobias C. B.
    Lund Univ, Dept Chem Phys, POB 12, S-422100 Lund, Sweden;Tech Univ Denmark, Dept Phys, DK-2800 Lyngby, Denmark.
    Kjaer, Kasper S.
    Stanford Univ, PULSE Inst, SLAC Natl Accelerator Lab, Menlo Pk, CA 94025 USA;Lund Univ, Dept Chem Phys, POB 12, S-422100 Lund, Sweden;Tech Univ Denmark, Dept Phys, DK-2800 Lyngby, Denmark.
    Haldrup, Kristoffer
    Tech Univ Denmark, Dept Phys, DK-2800 Lyngby, Denmark.
    Biasin, Elisa
    Stanford Univ, PULSE Inst, SLAC Natl Accelerator Lab, Menlo Pk, CA 94025 USA;Tech Univ Denmark, Dept Phys, DK-2800 Lyngby, Denmark.
    van Driel, Tim B.
    SLAC Natl Accelerator Lab, LCLS, Menlo Pk, CA 94025 USA.
    Papai, Matyas
    Tech Univ Denmark, Dept Chem, Kemitorvet 207, DK-2800 Lyngby, Denmark.
    Chabera, Pavel
    Lund Univ, Dept Chem Phys, POB 12, S-422100 Lund, Sweden.
    Liu, Yizhu
    Lund Univ, Dept Chem Phys, POB 12, S-422100 Lund, Sweden;Lund Univ, Ctr Anal & Synth, Dept Chem, POB 12422100, Lund, Sweden.
    Tatsuno, Hideyuki
    Lund Univ, Dept Chem Phys, POB 12, S-422100 Lund, Sweden.
    Timm, Cornelia
    Lund Univ, Dept Chem Phys, POB 12, S-422100 Lund, Sweden.
    Källman, Erik
    Uppsala universitet, Teoretisk kemi.
    Delcey, Mickaël
    Uppsala universitet, Teoretisk kemi.
    Hartsock, Robert W.
    Stanford Univ, PULSE Inst, SLAC Natl Accelerator Lab, Menlo Pk, CA 94025 USA.
    Reinhard, Marco E.
    Stanford Univ, PULSE Inst, SLAC Natl Accelerator Lab, Menlo Pk, CA 94025 USA.
    Koroidov, Sergey
    Stanford Univ, PULSE Inst, SLAC Natl Accelerator Lab, Menlo Pk, CA 94025 USA.
    Laursen, Mads G.
    Tech Univ Denmark, Dept Phys, DK-2800 Lyngby, Denmark.
    Hansen, Frederik B.
    Tech Univ Denmark, Dept Phys, DK-2800 Lyngby, Denmark.
    Vester, Peter
    Tech Univ Denmark, Dept Phys, DK-2800 Lyngby, Denmark.
    Christensen, Morten
    Tech Univ Denmark, Dept Phys, DK-2800 Lyngby, Denmark.
    Sandberg, Lise
    Tech Univ Denmark, Dept Phys, DK-2800 Lyngby, Denmark;Univ Copenhagen, Niels Bohr Inst, Blegdamsvej 17, DK-2100 Copenhagen, Denmark.
    Nemeth, Zoltan
    Hungarian Acad Sci, Wigner Res Ctr Phys, POB 49, H-1525 Budapest, Hungary.
    Szemes, Dorottya Sarosine
    Hungarian Acad Sci, Wigner Res Ctr Phys, POB 49, H-1525 Budapest, Hungary.
    Bajnoczi, Eva
    Hungarian Acad Sci, Wigner Res Ctr Phys, POB 49, H-1525 Budapest, Hungary.
    Alonso-Mori, Roberto
    SLAC Natl Accelerator Lab, LCLS, Menlo Pk, CA 94025 USA.
    Glownia, James M.
    SLAC Natl Accelerator Lab, LCLS, Menlo Pk, CA 94025 USA.
    Nelson, Silke
    SLAC Natl Accelerator Lab, LCLS, Menlo Pk, CA 94025 USA.
    Sikorski, Marcin
    SLAC Natl Accelerator Lab, LCLS, Menlo Pk, CA 94025 USA.
    Sokaras, Dimosthenis
    SLAC Natl Accelerator Lab, SSRL, Menlo Pk, CA 94025 USA.
    Lemke, Henrik T.
    SLAC Natl Accelerator Lab, LCLS, Menlo Pk, CA 94025 USA.
    Canton, Sophie
    ELI HU Nonprofit Ltd, ELI ALPS, H-6720 Szeged, Hungary;DESY, Notkestr 85, D-22607 Hamburg, Germany.
    Moller, Klaus B.
    Tech Univ Denmark, Dept Chem, Kemitorvet 207, DK-2800 Lyngby, Denmark.
    Nielsen, Martin M.
    Tech Univ Denmark, Dept Phys, DK-2800 Lyngby, Denmark.
    Vank, Gyorgy
    Hungarian Acad Sci, Wigner Res Ctr Phys, POB 49, H-1525 Budapest, Hungary.
    Warnmark, Kenneth
    Lund Univ, Ctr Anal & Synth, Dept Chem, POB 12422100, Lund, Sweden.
    Sundstrom, Villy
    Lund Univ, Dept Chem Phys, POB 12, S-422100 Lund, Sweden.
    Persson, Petter
    Lund Univ, Theoret Chem Div, POB 12422100, Lund, Sweden.
    Lundberg, Marcus
    Uppsala universitet, Teoretisk kemi.
    Uhlig, Jens
    Lund Univ, Dept Chem Phys, POB 12, S-422100 Lund, Sweden.
    Gaffney, Kelly J.
    Stanford Univ, PULSE Inst, SLAC Natl Accelerator Lab, Menlo Pk, CA 94025 USA.
    Vibrational wavepacket dynamics in Fe carbene photosensitizer determined with femtosecond X-ray emission and scattering2020In: Nature Communications, E-ISSN 2041-1723, Vol. 11, no 1, article id 634Article in journal (Refereed)
    Abstract [en]

    The non-equilibrium dynamics of electrons and nuclei govern the function of photoactive materials. Disentangling these dynamics remains a critical goal for understanding photoactive materials. Here we investigate the photoinduced dynamics of the [Fe(bmip)2]2+ photosensitizer, where bmip = 2,6-bis(3-methyl-imidazole-1-ylidine)-pyridine, with simultaneous femtosecond-resolution Fe Kα and Kβ X-ray emission spectroscopy (XES) and X-ray solution scattering (XSS). This measurement shows temporal oscillations in the XES and XSS difference signals with the same 278 fs period oscillation. These oscillations originate from an Fe-ligand stretching vibrational wavepacket on a triplet metal-centered (3MC) excited state surface. This 3MC state is populated with a 110 fs time constant by 40% of the excited molecules while the rest relax to a 3MLCT excited state. The sensitivity of the Kα XES to molecular structure results from a 0.7% average Fe-ligand bond length shift between the 1 s and 2p core-ionized states surfaces.

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  • 104.
    Kvedaraite, Egle
    et al.
    Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden; Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden; Department of Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden.
    Jess, David Unnersjö
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Svensson, Mattias
    Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.
    et al.,
    Intestinal stroma guides monocyte differentiation to macrophages through GM-CSF2024In: Nature Communications, E-ISSN 2041-1723, Vol. 15, no 1, article id 1752Article in journal (Refereed)
    Abstract [en]

    Stromal cells support epithelial cell and immune cell homeostasis and play an important role in inflammatory bowel disease (IBD) pathogenesis. Here, we quantify the stromal response to inflammation in pediatric IBD and reveal subset-specific inflammatory responses across colon segments and intestinal layers. Using data from a murine dynamic gut injury model and human ex vivo transcriptomic, protein and spatial analyses, we report that PDGFRA+CD142−/low fibroblasts and monocytes/macrophages co-localize in the intestine. In primary human fibroblast-monocyte co-cultures, intestinal PDGFRA+CD142−/low fibroblasts foster monocyte transition to CCR2+CD206+ macrophages through granulocyte-macrophage colony-stimulating factor (GM-CSF). Monocyte-derived CCR2+CD206+ cells from co-cultures have a phenotype similar to intestinal CCR2+CD206+ macrophages from newly diagnosed pediatric IBD patients, with high levels of PD-L1 and low levels of GM-CSF receptor. The study describes subset-specific changes in stromal responses to inflammation and suggests that the intestinal stroma guides intestinal macrophage differentiation.

  • 105.
    Lacis, Ugis
    et al.
    KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Brosse, Nicolas
    KTH, School of Engineering Sciences (SCI), Solid Mechanics (Dept.). KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Ingremeau, F.
    Mazzino, A.
    Lundell, Fredrik
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Kellay, H.
    Bagheri, Shervin
    KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Passive appendages generate drift through symmetry breaking2014In: Nature Communications, E-ISSN 2041-1723, Vol. 5, p. 5310-Article in journal (Refereed)
    Abstract [en]

    Plants and animals use plumes, barbs, tails, feathers, hairs and fins to aid locomotion. Many of these appendages are not actively controlled, instead they have to interact passively with the surrounding fluid to generate motion. Here, we use theory, experiments and numerical simulations to show that an object with a protrusion in a separated flow drifts sideways by exploiting a symmetry-breaking instability similar to the instability of an inverted pendulum. Our model explains why the straight position of an appendage in a fluid flow is unstable and how it stabilizes either to the left or right of the incoming flow direction. It is plausible that organisms with appendages in a separated flow use this newly discovered mechanism for locomotion; examples include the drift of plumed seeds without wind and the passive reorientation of motile animals.

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  • 106.
    Legesse, Dagimhiwat H.
    et al.
    UT Southwestern Med Ctr, Dept Neurosci, Dallas, TX 75390 USA..
    Fan, Chen
    Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, Solna, Sweden..
    Teng, Jinfeng
    Univ Calif San Diego, Dept Neurobiol, La Jolla, CA 92093 USA..
    Zhuang, Yuxuan
    Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, Solna, Sweden..
    Howard, Rebecca J.
    Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, Solna, Sweden..
    Noviello, Colleen M.
    Univ Calif San Diego, Dept Neurobiol, La Jolla, CA 92093 USA..
    Lindahl, Erik
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics. Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, Solna, Sweden..
    Hibbs, Ryan E.
    UT Southwestern Med Ctr, Dept Neurosci, Dallas, TX 75390 USA.;Univ Calif San Diego, Dept Neurobiol, La Jolla, CA 92093 USA..
    Structural insights into opposing actions of neurosteroids on GABAA receptors2023In: Nature Communications, E-ISSN 2041-1723, Vol. 14, no 1Article in journal (Refereed)
    Abstract [en]

    γ-Aminobutyric acid type A (GABAA) receptors mediate fast inhibitory signaling in the brain and are targets of numerous drugs and endogenous neurosteroids. A subset of neurosteroids are GABAA receptor positive allosteric modulators; one of these, allopregnanolone, is the only drug approved specifically for treating postpartum depression. There is a consensus emerging from structural, physiological and photolabeling studies as to where positive modulators bind, but how they potentiate GABA activation remains unclear. Other neurosteroids are negative modulators of GABAA receptors, but their binding sites remain debated. Here we present structures of a synaptic GABAA receptor bound to allopregnanolone and two inhibitory sulfated neurosteroids. Allopregnanolone binds at the receptor-bilayer interface, in the consensus potentiator site. In contrast, inhibitory neurosteroids bind in the pore. MD simulations and electrophysiology support a mechanism by which allopregnanolone potentiates channel activity and suggest the dominant mechanism for sulfated neurosteroid inhibition is through pore block. 

  • 107.
    Leo, Isabelle Rose
    et al.
    Karolinska Inst, Dept Oncol Pathol, Clin Prote Mass Spectrometry, Sci Life Lab, Tomtebodavagen 23A, S-17165 Solna, Sweden..
    Aswad, Luay
    Karolinska Inst, Dept Oncol Pathol, Clin Prote Mass Spectrometry, Sci Life Lab, Tomtebodavagen 23A, S-17165 Solna, Sweden..
    Stahl, Matthias
    Karolinska Inst, Dept Oncol Pathol, Clin Prote Mass Spectrometry, Sci Life Lab, Tomtebodavagen 23A, S-17165 Solna, Sweden..
    Kunold, Elena
    Karolinska Inst, Dept Oncol Pathol, Clin Prote Mass Spectrometry, Sci Life Lab, Tomtebodavagen 23A, S-17165 Solna, Sweden..
    Post, Frederik
    Karolinska Inst, Dept Oncol Pathol, Clin Prote Mass Spectrometry, Sci Life Lab, Tomtebodavagen 23A, S-17165 Solna, Sweden.;Univ Munster, Inst Plant Biol & Biotechnol, Schlosspl 7, D-48149 Munster, Germany..
    Erkers, Tom
    Karolinska Inst, Sci Life Lab, Dept Oncol Pathol, Mol Precis Med, Tomtebodavagen 23A, S-17165 Solna, Sweden..
    Struyf, Nona
    Karolinska Inst, Sci Life Lab, Dept Oncol Pathol, Mol Precis Med, Tomtebodavagen 23A, S-17165 Solna, Sweden..
    Mermelekas, Georgios
    Karolinska Inst, Dept Oncol Pathol, Clin Prote Mass Spectrometry, Sci Life Lab, Tomtebodavagen 23A, S-17165 Solna, Sweden..
    Joshi, Rubin Narayan
    Karolinska Inst, Dept Oncol Pathol, Clin Prote Mass Spectrometry, Sci Life Lab, Tomtebodavagen 23A, S-17165 Solna, Sweden..
    Villacampa, Eva Gracia
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Ostling, Paivi
    Karolinska Inst, Sci Life Lab, Dept Oncol Pathol, Mol Precis Med, Tomtebodavagen 23A, S-17165 Solna, Sweden..
    Kallioniemi, Olli P.
    Karolinska Inst, Sci Life Lab, Dept Oncol Pathol, Mol Precis Med, Tomtebodavagen 23A, S-17165 Solna, Sweden..
    Tamm, Katja Pokrovskaja
    Karolinska Inst, BioClinicum J6 140, Dept Oncol Pathol, Akad Straket 1, S-17164 Solna, Sweden..
    Siavelis, Ioannis
    Karolinska Inst, Dept Oncol Pathol, Clin Prote Mass Spectrometry, Sci Life Lab, Tomtebodavagen 23A, S-17165 Solna, Sweden..
    Lehtio, Janne
    Karolinska Inst, Dept Oncol Pathol, Clin Prote Mass Spectrometry, Sci Life Lab, Tomtebodavagen 23A, S-17165 Solna, Sweden..
    Vesterlund, Mattias
    Karolinska Inst, Dept Oncol Pathol, Clin Prote Mass Spectrometry, Sci Life Lab, Tomtebodavagen 23A, S-17165 Solna, Sweden..
    Jafari, Rozbeh
    Karolinska Inst, Dept Oncol Pathol, Clin Prote Mass Spectrometry, Sci Life Lab, Tomtebodavagen 23A, S-17165 Solna, Sweden..
    Integrative multi-omics and drug response profiling of childhood acute lymphoblastic leukemia cell lines2022In: Nature Communications, E-ISSN 2041-1723, Vol. 13, no 1, article id 1691Article in journal (Refereed)
    Abstract [en]

    Acute lymphoblastic leukemia (ALL) is the most common childhood cancer. Although standard-of-care chemotherapeutics are sufficient for most ALL cases, there are subsets of patients with poor response who relapse in disease. The biology underlying differences between subtypes and their response to therapy has only partially been explained by genetic and transcriptomic profiling. Here, we perform comprehensive multi-omic analyses of 49 readily available childhood ALL cell lines, using proteomics, transcriptomics, and pharmacoproteomic characterization. We connect the molecular phenotypes with drug responses to 528 oncology drugs, identifying drug correlations as well as lineage-dependent correlations. We also identify the diacylglycerol-analog bryostatin-1 as a therapeutic candidate in the MEF2D-HNRNPUL1 fusion high-risk subtype, for which this drug activates pro-apoptotic ERK signaling associated with molecular mediators of pre-B cell negative selection. Our data is the foundation for the interactive online Functional Omics Resource of ALL (FORALL) with navigable proteomics, transcriptomics, and drug sensitivity profiles at https://proteomics.se/fora.

  • 108.
    Li, Cong
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Materials and Nanophysics. Department of Applied Physics, Stanford University, Stanford, CA, 94305, USA.
    Zhang, Jianfeng
    Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.
    Wang, Yang
    KTH, School of Engineering Sciences (SCI), Applied Physics, Materials and Nanophysics.
    Liu, Hongxiong
    Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.
    Guo, Qinda
    KTH, School of Engineering Sciences (SCI), Applied Physics, Materials and Nanophysics.
    Rienks, Emile
    Helmholtz-Zentrum Berlin für Materialien und Energie, Elektronenspeicherring BESSY II, Albert-Einstein-Straße 15, 12489, Berlin, Germany.
    Chen, Wanyu
    KTH, School of Engineering Sciences (SCI), Applied Physics, Materials and Nanophysics.
    Bertran, Francois
    Synchrotron SOLEIL, L’Orme des Merisiers, Départementale 128, 91190, Saint-Aubin, France.
    Yang, Huancheng
    Department of Physics and Beijing Key Laboratory of Opto-electronic Functional Materials & Micro-nano Devices, Renmin University of China, Beijing, 100872, China.
    Phuyal, Dibya
    KTH, School of Engineering Sciences (SCI), Applied Physics, Materials and Nanophysics.
    Fedderwitz, Hanna
    MAX IV Laboratory, Lund University, 22100, Lund, Sweden.
    Thiagarajan, Balasubramanian
    MAX IV Laboratory, Lund University, 22100, Lund, Sweden.
    Dendzik, Maciej
    KTH, School of Engineering Sciences (SCI), Applied Physics, Materials and Nanophysics.
    Berntsen, Magnus H.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Materials and Nanophysics.
    Shi, Youguo
    Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.
    Xiang, Tao
    Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.
    Tjernberg, Oscar
    KTH, School of Engineering Sciences (SCI), Applied Physics, Materials and Nanophysics.
    Emergence of Weyl fermions by ferrimagnetism in a noncentrosymmetric magnetic Weyl semimetal2023In: Nature Communications, E-ISSN 2041-1723, Vol. 14, no 1, article id 7185Article in journal (Refereed)
    Abstract [en]

    Condensed matter physics has often provided a platform for investigating the interplay between particles and fields in cases that have not been observed in high-energy physics. Here, using angle-resolved photoemission spectroscopy, we provide an example of this by visualizing the electronic structure of a noncentrosymmetric magnetic Weyl semimetal candidate NdAlSi in both the paramagnetic and ferrimagnetic states. We observe surface Fermi arcs and bulk Weyl fermion dispersion as well as the emergence of new Weyl fermions in the ferrimagnetic state. Our results establish NdAlSi as a magnetic Weyl semimetal and provide an experimental observation of ferrimagnetic regulation of Weyl fermions in condensed matter.

  • 109.
    Li, Jian
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology, Fibre Technology. College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, 100871, China.
    Lin, C.
    Ma, T.
    Sun, J.
    Atomic-resolution structures from polycrystalline covalent organic frameworks with enhanced cryo-cRED2022In: Nature Communications, E-ISSN 2041-1723, Vol. 13, no 1, article id 4016Article in journal (Refereed)
    Abstract [en]

    The pursuit of atomic precision structure of porous covalent organic frameworks (COFs) is the key to understanding the relationship between structures and properties, and further developing new materials with superior performance. Yet, a challenge of how to determine their atomic structures has always existed since the first COFs reported seventeen years ago. Here, we present a universal method for ab initio structure determination of polycrystalline three-dimensional (3D) COFs at atomic level using enhanced cryo-continuous rotation electron diffraction (cryo-cRED), which combines hierarchical cluster analysis with cryo-EM technique. The high-quality datasets possess not only up to 0.79-angstrom resolution but more than 90% completeness, leading to unambiguous solution and precise refinement with anisotropic temperature factors. With such a powerful method, the dynamic structures with flexible linkers, degree of interpenetration, position of functional groups, and arrangement of ordered guest molecules are successfully revealed with atomic precision in five 3D COFs, which are almost impossible to be obtained without atomic resolution structure solution. This study demonstrates a practicable strategy for determining the structures of polycrystalline COFs and other beam-sensitive materials and to help in the future discovery of novel materials on the other.

  • 110.
    Li, Junhao
    et al.
    Huazhong Univ Sci & Technol, Wuhan Natl Lab Optoelect, Wuhan 430074, Peoples R China.;Huazhong Univ Sci & Technol, Sch Opt & Elect Informat, Wuhan 430074, Peoples R China..
    Hu, Guangwei
    Natl Univ Singapore, Dept Elect & Comp Engn, 4 Engn Dr 3, Singapore 117583, Singapore..
    Shi, Lina
    Chinese Acad Sci, Inst Microelect, Key Lab Microelect Devices & Integrated Technol, Beijing 100029, Peoples R China..
    He, Nan
    Zhejiang Univ, Ctr Opt & Electromagnet Res, Zhejiang Prov Key Lab Sensing Technol, JORCEP, Hangzhou 310058, Peoples R China..
    Li, Daqian
    Huazhong Univ Sci & Technol, Wuhan Natl Lab Optoelect, Wuhan 430074, Peoples R China.;Huazhong Univ Sci & Technol, Sch Opt & Elect Informat, Wuhan 430074, Peoples R China..
    Shang, Qiuyu
    Peking Univ, Sch Mat Sci & Engn, Beijing 100871, Peoples R China..
    Zhang, Qing
    Peking Univ, Sch Mat Sci & Engn, Beijing 100871, Peoples R China..
    Fu, Huange
    Huazhong Univ Sci & Technol, Wuhan Natl Lab Optoelect, Wuhan 430074, Peoples R China.;Huazhong Univ Sci & Technol, Sch Opt & Elect Informat, Wuhan 430074, Peoples R China..
    Zhou, Linlin
    Huazhong Univ Sci & Technol, Wuhan Natl Lab Optoelect, Wuhan 430074, Peoples R China.;Huazhong Univ Sci & Technol, Sch Opt & Elect Informat, Wuhan 430074, Peoples R China..
    Xiong, Wei
    Huazhong Univ Sci & Technol, Wuhan Natl Lab Optoelect, Wuhan 430074, Peoples R China.;Huazhong Univ Sci & Technol, Sch Opt & Elect Informat, Wuhan 430074, Peoples R China..
    Guan, Jianguo
    Wuhan Univ Technol, State Key Lab Adv Technol Mat Synth & Proc, Wuhan 430074, Peoples R China..
    Wang, Jian
    Huazhong Univ Sci & Technol, Wuhan Natl Lab Optoelect, Wuhan 430074, Peoples R China.;Huazhong Univ Sci & Technol, Sch Opt & Elect Informat, Wuhan 430074, Peoples R China..
    He, Sailing
    KTH, School of Electrical Engineering and Computer Science (EECS), Electrical Engineering, Electromagnetic Engineering. Zhejiang Univ, Ctr Opt & Electromagnet Res, Zhejiang Prov Key Lab Sensing Technol, JORCEP, Hangzhou 310058, Peoples R China..
    Chen, Lin
    Huazhong Univ Sci & Technol, Wuhan Natl Lab Optoelect, Wuhan 430074, Peoples R China.;Huazhong Univ Sci & Technol, Sch Opt & Elect Informat, Wuhan 430074, Peoples R China..
    Full-color enhanced second harmonic generation using rainbow trapping in ultrathin hyperbolic metamaterials2021In: Nature Communications, E-ISSN 2041-1723, Vol. 12, no 1, article id 6425Article in journal (Refereed)
    Abstract [en]

    Though metamaterials enhance nonlinear light-matter interactions due to their resonant features, these materials typically show a narrow spectral bandwidth. Here, the authors report broadband enhanced second-harmonic generation in patterned multilayer hyperbolic metamaterial arrays. Metasurfaces have provided a promising approach to enhance the nonlinearity at subwavelength scale, but usually suffer from a narrow bandwidth as imposed by sharp resonant features. Here, we counterintuitively report a broadband, enhanced second-harmonic generation, in nanopatterned hyperbolic metamaterials. The nanopatterning allows the direct access of the mode with large momentum, rendering the rainbow light trapping, i.e. slow light in a broad frequency, and thus enhancing the local field intensity for boosted nonlinear light-matter interactions. For a proof-of-concept demonstration, we fabricated a nanostructured Au/ZnO multilayer, and enhanced second harmonic generation can be observed within the visible wavelength range (400-650 nm). The enhancement factor is over 50 within the wavelength range of 470-650 nm, and a maximum conversion efficiency of 1.13x10(-6) is obtained with a pump power of only 8.80 mW. Our results herein offer an effective and robust approach towards the broadband metasurface-based nonlinear devices for various important technologies.

  • 111.
    Li, Qizhao
    et al.
    East China Univ Sci & Technol, Feringa Nobel Prize Scientist Joint Res Ctr, Frontiers Sci Ctr Mat & Dynam Chem, Sch Chem & Mol Engn,Key Lab Adv Mat, 130 Meilong Rd, Shanghai 200237, Peoples R China.;East China Univ Sci & Technol, Feringa Nobel Prize Scientist Joint Res Ctr, Frontiers Sci Ctr Mat & Dynam Chem, Sch Chem & Mol Engn,Joint Int Res Lab Precision C, 130 Meilong Rd, Shanghai 200237, Peoples R China..
    Li, Chengjie
    East China Univ Sci & Technol, Feringa Nobel Prize Scientist Joint Res Ctr, Frontiers Sci Ctr Mat & Dynam Chem, Sch Chem & Mol Engn,Key Lab Adv Mat, 130 Meilong Rd, Shanghai 200237, Peoples R China.;East China Univ Sci & Technol, Feringa Nobel Prize Scientist Joint Res Ctr, Frontiers Sci Ctr Mat & Dynam Chem, Sch Chem & Mol Engn,Joint Int Res Lab Precision C, 130 Meilong Rd, Shanghai 200237, Peoples R China..
    Baryshnikov, Gleb V.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Ding, Yubin
    East China Univ Sci & Technol, Feringa Nobel Prize Scientist Joint Res Ctr, Frontiers Sci Ctr Mat & Dynam Chem, Sch Chem & Mol Engn,Key Lab Adv Mat, 130 Meilong Rd, Shanghai 200237, Peoples R China.;East China Univ Sci & Technol, Feringa Nobel Prize Scientist Joint Res Ctr, Frontiers Sci Ctr Mat & Dynam Chem, Sch Chem & Mol Engn,Joint Int Res Lab Precision C, 130 Meilong Rd, Shanghai 200237, Peoples R China..
    Zhao, Chengxi
    East China Univ Sci & Technol, Feringa Nobel Prize Scientist Joint Res Ctr, Frontiers Sci Ctr Mat & Dynam Chem, Sch Chem & Mol Engn,Key Lab Adv Mat, 130 Meilong Rd, Shanghai 200237, Peoples R China.;East China Univ Sci & Technol, Feringa Nobel Prize Scientist Joint Res Ctr, Frontiers Sci Ctr Mat & Dynam Chem, Sch Chem & Mol Engn,Joint Int Res Lab Precision C, 130 Meilong Rd, Shanghai 200237, Peoples R China..
    Gu, Tingting
    Jiangsu Univ, Sch Chem & Chem Engn, Zhenjiang 212013, Jiangsu, Peoples R China..
    Sha, Feng
    East China Univ Sci & Technol, Feringa Nobel Prize Scientist Joint Res Ctr, Frontiers Sci Ctr Mat & Dynam Chem, Sch Chem & Mol Engn,Key Lab Adv Mat, 130 Meilong Rd, Shanghai 200237, Peoples R China.;East China Univ Sci & Technol, Feringa Nobel Prize Scientist Joint Res Ctr, Frontiers Sci Ctr Mat & Dynam Chem, Sch Chem & Mol Engn,Joint Int Res Lab Precision C, 130 Meilong Rd, Shanghai 200237, Peoples R China..
    Liang, Xu
    Jiangsu Univ, Sch Chem & Chem Engn, Zhenjiang 212013, Jiangsu, Peoples R China..
    Zhu, Weihua
    Jiangsu Univ, Sch Chem & Chem Engn, Zhenjiang 212013, Jiangsu, Peoples R China..
    Wu, Xinyan
    East China Univ Sci & Technol, Feringa Nobel Prize Scientist Joint Res Ctr, Frontiers Sci Ctr Mat & Dynam Chem, Sch Chem & Mol Engn,Key Lab Adv Mat, 130 Meilong Rd, Shanghai 200237, Peoples R China.;East China Univ Sci & Technol, Feringa Nobel Prize Scientist Joint Res Ctr, Frontiers Sci Ctr Mat & Dynam Chem, Sch Chem & Mol Engn,Joint Int Res Lab Precision C, 130 Meilong Rd, Shanghai 200237, Peoples R China..
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Centres, Albanova VinnExcellence Center for Protein Technology, ProNova. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Sessler, Jonathan L.
    Univ Texas Austin, Dept Chem, Austin, TX 78712 USA..
    Xie, Yongshu
    East China Univ Sci & Technol, Feringa Nobel Prize Scientist Joint Res Ctr, Frontiers Sci Ctr Mat & Dynam Chem, Sch Chem & Mol Engn,Key Lab Adv Mat, 130 Meilong Rd, Shanghai 200237, Peoples R China.;East China Univ Sci & Technol, Feringa Nobel Prize Scientist Joint Res Ctr, Frontiers Sci Ctr Mat & Dynam Chem, Sch Chem & Mol Engn,Joint Int Res Lab Precision C, 130 Meilong Rd, Shanghai 200237, Peoples R China..
    Twisted-Planar-Twisted expanded porphyrinoid dimer as a rudimentary reaction-based methanol indicator2020In: Nature Communications, E-ISSN 2041-1723, Vol. 11, no 1, article id 5289Article in journal (Refereed)
    Abstract [en]

    Directly linked porphyrin dimers have attracted considerable attention because of their intriguing electronic features. Most emphasis has been placed on either dimers with large dihedral angles between the constituent planar monomeric subunits or those with overall planarity, referred to as "Planar-Twisted-Planar" and "Planar-Planar-Planar", respectively. Herein, we report a "Twisted-Planar-Twisted" framework, the hexaphyrin dimer D that exists in a trans configuration. Treatment of D with MeOH affords two isomeric dimers, MD1 and MD2, both of which incorporate a methoxy moiety and exist in cis orientations with respect to the tethering linkage. The methanol-promoted conversion is accompanied by a readily discernible color change from green to brown and is not induced to an appreciable level by other alcohols. Dimer D thus acts as a rudimentary, albeit highly selective, reaction-based methanol indicator. This work provides a promising approach for constructing reaction-based chemosensors using porphyrinoid dimers of nonplanar subunits with biased reactivity. Directly linked porphyrin dimers show intriguing electronic features but emphasis has been placed on planar monomeric units. Here, the authors report a Twisted-Planar-Twisted framework which can undergo a cis-trans transformation accompanied by a colour change in presence of methanol, making this framework applicable as a methanol sensor.

  • 112. Li, W. Y.
    et al.
    Graham, D. B.
    Khotyaintsev, Y. V.
    Vaivads, Andris
    KTH, School of Electrical Engineering and Computer Science (EECS), Electrical Engineering, Space and Plasma Physics.
    André, M.
    Min, K.
    Liu, K.
    Tang, B. B.
    Wang, C.
    Fujimoto, K.
    Norgren, C.
    Toledo-Redondo, S.
    Lindqvist, Per-Arne
    KTH, School of Electrical Engineering and Computer Science (EECS), Electrical Engineering, Space and Plasma Physics.
    Ergun, R. E.
    Torbert, R. B.
    Rager, A. C.
    Dorelli, J. C.
    Gershman, D. J.
    Giles, B. L.
    Lavraud, B.
    Plaschke, F.
    Magnes, W.
    Le Contel, O.
    Russell, C. T.
    Burch, J. L.
    Electron Bernstein waves driven by electron crescents near the electron diffusion region2020In: Nature Communications, E-ISSN 2041-1723, Vol. 11, no 1, article id 141Article in journal (Refereed)
    Abstract [en]

    The Magnetospheric Multiscale (MMS) spacecraft encounter an electron diffusion region (EDR) of asymmetric magnetic reconnection at Earth’s magnetopause. The EDR is characterized by agyrotropic electron velocity distributions on both sides of the neutral line. Various types of plasma waves are produced by the magnetic reconnection in and near the EDR. Here we report large-amplitude electron Bernstein waves (EBWs) at the electron-scale boundary of the Hall current reversal. The finite gyroradius effect of the outflow electrons generates the crescent-shaped agyrotropic electron distributions, which drive the EBWs. The EBWs propagate toward the central EDR. The amplitude of the EBWs is sufficiently large to thermalize and diffuse electrons around the EDR. The EBWs contribute to the cross-field diffusion of the electron-scale boundary of the Hall current reversal near the EDR.

  • 113.
    Li, Wenlong
    et al.
    Dalian Univ Technol, DUT KTH Joint Educ & Res Ctr Mol Devices, Inst Artificial Photosynth, State Key Lab Fine Chem,Inst Energy Sci & Technol, Dalian 116024, Peoples R China..
    Li, Fusheng
    Dalian Univ Technol, DUT KTH Joint Educ & Res Ctr Mol Devices, Inst Artificial Photosynth, State Key Lab Fine Chem,Inst Energy Sci & Technol, Dalian 116024, Peoples R China..
    Yang, Hao
    Dalian Univ Technol, DUT KTH Joint Educ & Res Ctr Mol Devices, Inst Artificial Photosynth, State Key Lab Fine Chem,Inst Energy Sci & Technol, Dalian 116024, Peoples R China..
    Wu, Xiujuan
    Dalian Univ Technol, DUT KTH Joint Educ & Res Ctr Mol Devices, Inst Artificial Photosynth, State Key Lab Fine Chem,Inst Energy Sci & Technol, Dalian 116024, Peoples R China..
    Zhang, Peili
    Dalian Univ Technol, DUT KTH Joint Educ & Res Ctr Mol Devices, Inst Artificial Photosynth, State Key Lab Fine Chem,Inst Energy Sci & Technol, Dalian 116024, Peoples R China..
    Shan, Yu
    Dalian Univ Technol, DUT KTH Joint Educ & Res Ctr Mol Devices, Inst Artificial Photosynth, State Key Lab Fine Chem,Inst Energy Sci & Technol, Dalian 116024, Peoples R China..
    Sun, Licheng
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry.
    A bio-inspired coordination polymer as outstanding water oxidation catalyst via second coordination sphere engineering2019In: Nature Communications, E-ISSN 2041-1723, Vol. 10, article id 5074Article in journal (Refereed)
    Abstract [en]

    First-row transition metal-based catalysts have been developed for the oxygen evolution reaction (OER) during the past years, however, such catalysts typically operate at overpotentials (eta) significantly above thermodynamic requirements. Here, we report an iron/ nickel terephthalate coordination polymer on nickel form (NiFeCP/NF) as catalyst for OER, in which both coordinated and uncoordinated carboxylates were maintained after electrolysis. NiFeCP/NF exhibits outstanding electro-catalytic OER activity with a low overpotential of 188 mV at 10 mA cm(-2) in 1.0 KOH, with a small Tafel slope and excellent stability. The pH-independent OER activity of NiFeCP/NF on the reversible hydrogen electrode scale suggests that a concerted proton-coupled electron transfer (c-PET) process is the rate-determining step (RDS) during water oxidation. Deuterium kinetic isotope effects, proton inventory studies and atom-proton-transfer measurements indicate that the uncoordinated carboxylates are serving as the proton transfer relays, with a similar function as amino acid residues in photosystem II (PSII), accelerating the proton-transfer rate.

  • 114.
    Li, Xuping
    et al.
    Fudan Univ, Dept Macromol Sci, State Key Lab Mol Engn Polymers, Shanghai 200438, Peoples R China..
    Baryshnikov, Gleb V.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Deng, Chao
    Zhejiang Univ, Dept Polymer Sci & Engn, MOE Key Lab Macromol Synth & Functionalizat, Hangzhou 310027, Zhejiang, Peoples R China..
    Bao, Xiaoyan
    Fudan Univ, Dept Macromol Sci, State Key Lab Mol Engn Polymers, Shanghai 200438, Peoples R China..
    Wu, Bin
    Fudan Univ, Dept Macromol Sci, State Key Lab Mol Engn Polymers, Shanghai 200438, Peoples R China..
    Zhou, Yunyun
    Fudan Univ, Dept Macromol Sci, State Key Lab Mol Engn Polymers, Shanghai 200438, Peoples R China..
    Ågren, Hans
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Zhu, Liangliang
    Fudan Univ, Dept Macromol Sci, State Key Lab Mol Engn Polymers, Shanghai 200438, Peoples R China..
    A three-dimensional ratiometric sensing strategy on unimolecular fluorescence-thermally activated delayed fluorescence dual emission2019In: Nature Communications, E-ISSN 2041-1723, Vol. 10, article id 731Article in journal (Refereed)
    Abstract [en]

    Visualized sensing through fluorescence signals is a powerful method for chemical and physical detection. However, the utilization of fluorescent molecular probes still suffers from lack of precise signal self-calibration in practical use. Here we show that fluorescence and thermally activated delayed fluorescence can be simultaneously produced at the single-molecular level. The thermally activated delayed fluorescence serves as a sensing signal with its wavelength and lifetime both altered correlating to polarity, whereas the fluorescence always remains unchanged as an internal reference. Upon the establishment of a three-dimensional working curve upon the ratiometric wavelength and photoluminescence lifetime vs. polarity, disturbance factors during a relevant sensing process can be largely minimized by such a multiple self-calibration. This strategy was further applied into a precise detection of the microenvironmental polarity variation in complex phospholipid systems, towards providing new insights for convenient and accurate diagnosis of membrane lesions.

  • 115. Li, Y.
    et al.
    Zakharov, D.
    Zhao, S.
    Tappero, R.
    Jung, U.
    Elsen, A.
    Baumann, Ph.
    Nuzzo, Ralph G.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Surface and Corrosion Science.
    Stach, E. A.
    Frenkel, A. I.
    Complex structural dynamics of nanocatalysts revealed in Operando conditions by correlated imaging and spectroscopy probes2015In: Nature Communications, E-ISSN 2041-1723, Vol. 6, article id 7583Article in journal (Refereed)
    Abstract [en]

    Understanding how heterogeneous catalysts change size, shape and structure during chemical reactions is limited by the paucity of methods for studying catalytic ensembles in working state, that is, in operando conditions. Here by a correlated use of synchrotron X-ray absorption spectroscopy and scanning transmission electron microscopy in operando conditions, we quantitatively describe the complex structural dynamics of supported Pt catalysts exhibited during an exemplary catalytic reaction-ethylene hydrogenation. This work exploits a microfabricated catalytic reactor compatible with both probes. The results demonstrate dynamic transformations of the ensemble of Pt clusters that spans a broad size range throughout changing reaction conditions. This method is generalizable to quantitative operando studies of complex systems using a wide variety of X-ray and electron-based experimental probes.

  • 116.
    Li, Yuanyuan
    et al.
    SUNY Stony Brook, Dept Mat Sci & Chem Engn, Stony Brook, NY 11794 USA..
    Kottwitz, Matthew
    Univ Illinois, Dept Chem, Urbana, IL 61801 USA..
    Vincent, Joshua L.
    Arizona State Univ, Sch Engn Matter Transport & Energy, Tempe, AZ 85287 USA..
    Enright, Michael J.
    Univ Illinois, Dept Chem, Urbana, IL 61801 USA..
    Liu, Zongyuan
    Brookhaven Natl Lab, Chem Div, Upton, NY 11973 USA..
    Zhang, Lihua
    Brookhaven Natl Lab, Ctr Funct Nanomat, Upton, NY 11973 USA..
    Huang, Jiahao
    SUNY Stony Brook, Dept Mat Sci & Chem Engn, Stony Brook, NY 11794 USA..
    Senanayake, Sanjaya D.
    Brookhaven Natl Lab, Chem Div, Upton, NY 11973 USA..
    Yang, Wei-Chang D.
    NIST, Phys Measurement Lab, Gaithersburg, MD 20899 USA.;Univ Maryland, Inst Res Elect & Appl Phys, College Pk, MD 20742 USA.;Univ Maryland, Maryland NanoCtr, College Pk, MD 20742 USA..
    Crozier, Peter A.
    Arizona State Univ, Sch Engn Matter Transport & Energy, Tempe, AZ 85287 USA..
    Nuzzo, Ralph G.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Surface and Corrosion Science. Univ Illinois, Dept Chem, Urbana, IL 61801 USA..
    Frenkel, Anatoly, I
    SUNY Stony Brook, Dept Mat Sci & Chem Engn, Stony Brook, NY 11794 USA.;Brookhaven Natl Lab, Chem Div, Upton, NY 11973 USA..
    Dynamic structure of active sites in ceria-supported Pt catalysts for the water gas shift reaction2021In: Nature Communications, E-ISSN 2041-1723, Vol. 12, no 1, article id 914Article in journal (Refereed)
    Abstract [en]

    Oxide-supported noble metal catalysts have been extensively studied for decades for the water gas shift (WGS) reaction, a catalytic transformation central to a host of large volume processes that variously utilize or produce hydrogen. There remains considerable uncertainty as to how the specific features of the active metal-support interfacial bonding-perhaps most importantly the temporal dynamic changes occurring therein-serve to enable high activity and selectivity. Here we report the dynamic characteristics of a Pt/CeO2 system at the atomic level for the WGS reaction and specifically reveal the synergistic effects of metal-support bonding at the perimeter region. We find that the perimeter Pt-0-O vacancy-Ce3+ sites are formed in the active structure, transformed at working temperatures and their appearance regulates the adsorbate behaviors. We find that the dynamic nature of this site is a key mechanistic step for the WGS reaction. Revealing the structure and dynamics of active sites is essential to understand catalytic mechanisms. Here the authors demonstrate the dynamic nature of perimeter Pt-0-O vacancy-Ce3+ sites in Pt/CeO2 and the key effects of their dynamics on the mechanism of the water gas shift reaction.

  • 117.
    Li, Zhongyu
    et al.
    Fudan Univ, Dept Macromol Sci, State Key Lab Mol Engn Polymers, Shanghai, Peoples R China..
    Wang, Yanjie
    Fudan Univ, Dept Macromol Sci, State Key Lab Mol Engn Polymers, Shanghai, Peoples R China..
    Baryshnikov, Gleb V.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Tomsk State Univ, Tomsk, Russia..
    Shen, Shen
    Fudan Univ, Dept Macromol Sci, State Key Lab Mol Engn Polymers, Shanghai, Peoples R China..
    Zhang, Man
    Fudan Univ, Dept Macromol Sci, State Key Lab Mol Engn Polymers, Shanghai, Peoples R China..
    Zou, Qi
    Shanghai Univ Elect Power, Shanghai Key Lab Mat Protect & Adv Mat Elect Powe, Shanghai, Peoples R China..
    Ågren, Hans
    Tomsk State Univ, Tomsk, Russia.;Uppsala Univ, Dept Phys & Astron, Uppsala, Sweden..
    Zhu, Liangliang
    Fudan Univ, Dept Macromol Sci, State Key Lab Mol Engn Polymers, Shanghai, Peoples R China..
    Lighting up solid states using a rubber2021In: Nature Communications, E-ISSN 2041-1723, Vol. 12, no 1, article id 908Article in journal (Refereed)
    Abstract [en]

    It is crucial and desirable to develop green and high-efficient strategies to regulate solid-state structures and their related material properties. However, relative to solution, it is more difficult to break and generate chemical bonds in solid states. In this work, a rubbing-induced photoluminescence on the solid states of ortho-pyridinil phenol family was achieved. This rubbing response relied on an accurately designed topochemical tautomerism, where a negative charge, exactly provided by the triboelectric effect of a rubber, can induce a proton transfer in a double H-bonded dimeric structure. This process instantaneously led to a bright-form tautomer that can be stabilized in the solid-state settings, leading to an up to over 450-fold increase of the fluorescent quantum yield of the materials. The property can be repeatedly used due to the reversibility of the tautomerism, enabling encrypted applications. Moreover, a further modification to the structure can be accomplished to achieve different properties, opening up more possibilities for the design of new-generation smart materials. Changes in molecular properties due to stimuli response are critically important for the development of new materials. However, most processes are slow or inefficient in the solid state. Here the authors demonstrate property switching in the solid state using a rubbing-induced tautomerism in multiple hydrogen-bonded donor-acceptor couples.

  • 118. Libanori, Rafael
    et al.
    Erb, Randall M.
    Reiser, Alain
    Complex Materials, Department of Materials, ETH Zurich, 8093 Zurich, Switzerland.
    Le Ferrand, Hortense
    Süess, Martin J.
    Spolenak, Ralph
    Studart, André R.
    Stretchable heterogeneous composites with extreme mechanical gradients2012In: Nature Communications, E-ISSN 2041-1723, Vol. 3, no 1Article in journal (Refereed)
    Abstract [en]

    Heterogeneous composite materials with variable local stiffness are widespread in nature, but are far less explored in engineering structural applications. The development of heterogeneous synthetic composites with locally tuned elastic properties would allow us to extend the lifetime of functional devices with mechanically incompatible interfaces, and to create new enabling materials for applications ranging from flexible electronics to regenerative medicine. Here we show that heterogeneous composites with local elastic moduli tunable over five orders of magnitude can be prepared through the site-specific reinforcement of an entangled elastomeric matrix at progressively larger length scales. Using such a hierarchical reinforcement approach, we designed and produced composites exhibiting regions with extreme soft-to-hard transitions, while still being reversibly stretchable up to 350%. The implementation of the proposed methodology in a mechanically challenging application is illustrated here with the development of locally stiff and globally stretchable substrates for flexible electronics. 

  • 119.
    Lu, San
    et al.
    Univ Calif Los Angeles, Dept Earth Planetary & Space Sci, Los Angeles, CA USA.;Univ Calif Los Angeles, Inst Geophys & Planetary Phys, Los Angeles, CA 90024 USA..
    Wang, Rongsheng
    Univ Sci & Technol China, CAS Key Lab Geospace Environm, Dept Geophys & Planetary Sci, Hefei, Anhui, Peoples R China.;CAS Ctr Excellence Comparat Planetol, Hefei, Anhui, Peoples R China..
    Lu, Quanming
    Univ Sci & Technol China, CAS Key Lab Geospace Environm, Dept Geophys & Planetary Sci, Hefei, Anhui, Peoples R China.;CAS Ctr Excellence Comparat Planetol, Hefei, Anhui, Peoples R China..
    Angelopoulos, V.
    Univ Calif Los Angeles, Dept Earth Planetary & Space Sci, Los Angeles, CA USA.;Univ Calif Los Angeles, Inst Geophys & Planetary Phys, Los Angeles, CA 90024 USA..
    Nakamura, R.
    Austrian Acad Sci, Space Res Inst, Graz, Austria..
    Artemyev, A. V.
    Univ Calif Los Angeles, Dept Earth Planetary & Space Sci, Los Angeles, CA USA.;Univ Calif Los Angeles, Inst Geophys & Planetary Phys, Los Angeles, CA 90024 USA.;Russian Acad Sci, Space Res Inst, Moscow, Russia..
    Pritchett, P. L.
    Univ Calif Los Angeles, Dept Phys & Astron, Los Angeles, CA USA..
    Liu, T. Z.
    Univ Calif Los Angeles, Dept Earth Planetary & Space Sci, Los Angeles, CA USA.;Univ Calif Los Angeles, Inst Geophys & Planetary Phys, Los Angeles, CA 90024 USA..
    Zhang, X. -J
    Baumjohann, W.
    Austrian Acad Sci, Space Res Inst, Graz, Austria..
    Gonzalez, W.
    Inst Nacl Pesquisas Espaciais, China Brazil Joint Lab Space Weather, Sao Jose Dos Campos, SP, Brazil..
    Rager, A. C.
    Catholic Univ Amer, Dept Phys, Washington, DC 20064 USA..
    Torbert, R. B.
    Univ New Hampshire, Main Campus, Durham, NH 03824 USA..
    Giles, B. L.
    NASA, Heliophys Sci Div, Goddard Space Flight Ctr, Greenbelt, MD USA..
    Gershman, D. J.
    NASA, Heliophys Sci Div, Goddard Space Flight Ctr, Greenbelt, MD USA..
    Russell, C. T.
    Univ Calif Los Angeles, Dept Earth Planetary & Space Sci, Los Angeles, CA USA.;Univ Calif Los Angeles, Inst Geophys & Planetary Phys, Los Angeles, CA 90024 USA..
    Strangeway, R. J.
    Univ Calif Los Angeles, Dept Earth Planetary & Space Sci, Los Angeles, CA USA.;Univ Calif Los Angeles, Inst Geophys & Planetary Phys, Los Angeles, CA 90024 USA..
    Qi, Y.
    Univ Calif Los Angeles, Dept Earth Planetary & Space Sci, Los Angeles, CA USA.;Univ Calif Los Angeles, Inst Geophys & Planetary Phys, Los Angeles, CA 90024 USA..
    Ergun, R. E.
    Univ Colorado, Dept Astrophys & Planetary Sci, Boulder, CO 80309 USA..
    Lindqvist, Per-Arne
    KTH, School of Electrical Engineering and Computer Science (EECS), Electrical Engineering, Space and Plasma Physics.
    Burch, J. L.
    Southwest Res Inst, San Antonio, TX USA..
    Wang, Shui
    Univ Sci & Technol China, CAS Key Lab Geospace Environm, Dept Geophys & Planetary Sci, Hefei, Anhui, Peoples R China.;CAS Ctr Excellence Comparat Planetol, Hefei, Anhui, Peoples R China..
    Magnetotail reconnection onset caused by electron kinetics with a strong external driver2020In: Nature Communications, E-ISSN 2041-1723, Vol. 11, no 1, article id 5049Article in journal (Refereed)
    Abstract [en]

    Magnetotail reconnection plays a crucial role in explosive energy conversion in geospace. Because of the lack of in-situ spacecraft observations, the onset mechanism of magnetotail reconnection, however, has been controversial for decades. The key question is whether magnetotail reconnection is externally driven to occur first on electron scales or spontaneously arising from an unstable configuration on ion scales. Here, we show, using spacecraft observations and particle-in-cell (PIC) simulations, that magnetotail reconnection starts from electron reconnection in the presence of a strong external driver. Our PIC simulations show that this electron reconnection then develops into ion reconnection. These results provide direct evidence for magnetotail reconnection onset caused by electron kinetics with a strong external driver.

  • 120.
    Lundqvist, Mikael
    et al.
    Division of Psychology, Department of Clinical Neuroscience, Karolinska Institute, Stockholm, Sweden; The Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, 43 Vassar Street, Cambridge, MA, 02139, USA, 43 Vassar Street.
    Brincat, Scott L.
    The Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, 43 Vassar Street, Cambridge, MA, 02139, USA, 43 Vassar Street.
    Rose, Jonas
    The Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, 43 Vassar Street, Cambridge, MA, 02139, USA, 43 Vassar Street; Faculty of Psychology, Neural Basis of Learning, Ruhr University Bochum, 44801, Bochum, Germany.
    Warden, Melissa R.
    The Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, 43 Vassar Street, Cambridge, MA, 02139, USA, 43 Vassar Street; Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, USA.
    Buschman, Timothy J.
    The Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, 43 Vassar Street, Cambridge, MA, 02139, USA, 43 Vassar Street; Princeton Neuroscience Institute, Princeton University, Washington Rd., Princeton, NJ, 08540, USA, Washington Rd..
    Miller, Earl K.
    The Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, 43 Vassar Street, Cambridge, MA, 02139, USA, 43 Vassar Street.
    Herman, Pawel
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Working memory control dynamics follow principles of spatial computing2023In: Nature Communications, E-ISSN 2041-1723, Vol. 14, no 1, article id 1429Article in journal (Refereed)
    Abstract [en]

    Working memory (WM) allows us to remember and selectively control a limited set of items. Neural evidence suggests it is achieved by interactions between bursts of beta and gamma oscillations. However, it is not clear how oscillations, reflecting coherent activity of millions of neurons, can selectively control individual WM items. Here we propose the novel concept of spatial computing where beta and gamma interactions cause item-specific activity to flow spatially across the network during a task. This way, control-related information such as item order is stored in the spatial activity independent of the detailed recurrent connectivity supporting the item-specific activity itself. The spatial flow is in turn reflected in low-dimensional activity shared by many neurons. We verify these predictions by analyzing local field potentials and neuronal spiking. We hypothesize that spatial computing can facilitate generalization and zero-shot learning by utilizing spatial component as an additional information encoding dimension.

  • 121. Lundqvist, Mikael
    et al.
    Herman, Pawel
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Warden, Melissa R.
    Brincat, Scott L.
    Miller, Earl K.
    Gamma and beta bursts during working memory readout suggest roles in its volitional control2018In: Nature Communications, E-ISSN 2041-1723, Vol. 9, article id 394Article in journal (Refereed)
    Abstract [en]

    Working memory (WM) activity is not as stationary or sustained as previously thought. There are brief bursts of gamma (similar to 50-120 Hz) and beta (similar to 20-35 Hz) oscillations, the former linked to stimulus information in spiking. We examined these dynamics in relation to readout and control mechanisms of WM. Monkeys held sequences of two objects in WM to match to subsequent sequences. Changes in beta and gamma bursting suggested their distinct roles. In anticipation of having to use an object for the match decision, there was an increase in gamma and spiking information about that object and reduced beta bursting. This readout signal was only seen before relevant test objects, and was related to premotor activity. When the objects were no longer needed, beta increased and gamma decreased together with object spiking information. Deviations from these dynamics predicted behavioral errors. Thus, beta could regulate gamma and the information in WM.

  • 122. Maccaferri, Nicolo
    et al.
    Gregorczyk, Keith E.
    de Oliveira, Thales V. A. G.
    Kataja, Mikko
    van Dijken, Sebastiaan
    Pirzadeh, Zhaleh
    Dmitriev, Alexandre
    Akerman, Johan
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Material Physics, MF. Department of Physics, University of Gothenburg, Sweden .
    Knez, Mato
    Vavassori, Paolo
    Ultrasensitive and label-free molecular-level detection enabled by light phase control in magnetoplasmonic nanoantennas2015In: Nature Communications, E-ISSN 2041-1723, Vol. 6, article id 6150Article in journal (Refereed)
    Abstract [en]

    Systems allowing label-free molecular detection are expected to have enormous impact on biochemical sciences. Research focuses on materials and technologies based on exploiting localized surface plasmon resonances in metallic nanostructures. The reason for this focused attention is their suitability for single-molecule sensing, arising from intrinsically nanoscopic sensing volume and the high sensitivity to the local environment. Here we propose an alternative route, which enables radically improved sensitivity compared with recently reported plasmon-based sensors. Such high sensitivity is achieved by exploiting the control of the phase of light in magnetoplasmonic nanoantennas. We demonstrate a manifold improvement of refractometric sensing figure-of-merit. Most remarkably, we show a raw surface sensitivity (that is, without applying fitting procedures) of two orders of magnitude higher than the current values reported for nanoplasmonic sensors. Such sensitivity corresponds to a mass of similar to 0.8 ag per nanoantenna of polyamide-6.6 (n = 1.51), which is representative for a large variety of polymers, peptides and proteins.

  • 123. Madru, ClEment
    et al.
    Henneke, Ghislaine
    Raia, Pierre
    Hugonneau-Beaufet, Ines
    Pehau-Arnaudet, Gerard
    England, Patrick
    Lindahl, Erik
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics.
    Delarue, Marc
    Carroni, Marta
    Sauguet, Ludovic
    Structural basis for the increased processivity of D-family DNA polymerases in complex with PCNA2020In: Nature Communications, E-ISSN 2041-1723, Vol. 11, no 1, article id 1591Article in journal (Refereed)
    Abstract [en]

    Replicative DNA polymerases (DNAPs) have evolved the ability to copy the genome with high processivity and fidelity. In Eukarya and Archaea, the processivity of replicative DNAPs is greatly enhanced by its binding to the proliferative cell nuclear antigen (PCNA) that encircles the DNA. We determined the cryo-EM structure of the DNA-bound PolD-PCNA complex from Pyrococcus abyssi at 3.77 angstrom. Using an integrative structural biology approach - combining cryo-EM, X-ray crystallography, protein-protein interaction measurements, and activity assays - we describe the molecular basis for the interaction and cooperativity between a replicative DNAP and PCNA. PolD recruits PCNA via a complex mechanism, which requires two different PIP-boxes. We infer that the second PIP-box, which is shared with the eukaryotic Pol alpha replicative DNAP, plays a dual role in binding either PCNA or primase, and could be a master switch between an initiation and a processive phase during replication.

  • 124.
    Man, Gabriel J.
    et al.
    Uppsala Univ, Div Xray Photon Sci, Dept Phys & Astron, Condensed Matter Phys Energy Mat, Box 516, S-75121 Uppsala, Sweden.;GJM Sci Consulting, Ft Lee, NJ 07024 USA..
    Kamal, Chinnathambi
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, S-10691 Stockholm, Sweden.;Raja Ramanna Ctr Adv Technol, Theory & Simulat Lab, HRDS, Indore 452013, India.;Homi Bhabha Natl Inst, Training Sch Complex, Mumbai 400094, Maharashtra, India..
    Kalinko, Aleksandr
    Deutsch Elektronen Synchrotron DESY, Notkestr 85, D-22607 Hamburg, Germany..
    Phuyal, Dibya
    KTH, School of Engineering Sciences (SCI), Applied Physics, Materials and Nanophysics.
    Acharya, Joydev
    Tata Inst Fundamental Res, Hyderabad 500046, India..
    Mukherjee, Soham
    Uppsala Univ, Div Xray Photon Sci, Dept Phys & Astron, Condensed Matter Phys Energy Mat, Box 516, S-75121 Uppsala, Sweden..
    Nayak, Pabitra K.
    Tata Inst Fundamental Res, Hyderabad 500046, India..
    Rensmo, Håkan
    Uppsala Univ, Div Xray Photon Sci, Dept Phys & Astron, Condensed Matter Phys Energy Mat, Box 516, S-75121 Uppsala, Sweden..
    Odelius, Michael
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, S-10691 Stockholm, Sweden..
    Butorin, Sergei M.
    Uppsala Univ, Div Xray Photon Sci, Dept Phys & Astron, Condensed Matter Phys Energy Mat, Box 516, S-75121 Uppsala, Sweden..
    A-site cation influence on the conduction band of lead bromide perovskites2022In: Nature Communications, E-ISSN 2041-1723, Vol. 13, no 1, article id 3839Article in journal (Refereed)
    Abstract [en]

    Hot carrier solar cells hold promise for exceeding the Shockley-Queisser limit. Slow hot carrier cooling is one of the most intriguing properties of lead halide perovskites and distinguishes this class of materials from competing materials used in solar cells. Here we use the element selectivity of high-resolution X-ray spectroscopy and density functional theory to uncover a previously hidden feature in the conduction band states, the sigma-pi energy splitting, and find that it is strongly influenced by the strength of electronic coupling between the A-cation and bromide-lead sublattice. Our finding provides an alternative mechanism to the commonly discussed polaronic screening and hot phonon bottleneck carrier cooling mechanisms. Our work emphasizes the optoelectronic role of the A-cation, provides a comprehensive view of A-cation effects in the crystal and electronic structures, and outlines a broadly applicable spectroscopic approach for assessing the impact of chemical alterations of the A-cation on perovskite electronic structure. The A-cation influence on the mechanism of slow hot carrier cooling in perovskites is controversial. Here, Man et al. resolve a debated issue regarding A-cation influence on the electronic structure of lead halide perovskites.

  • 125. Mardinoglu, Adil
    et al.
    Ågren, Rasmus
    Kampf, Caroline
    Asplund, Anna
    Uhlén, Mathias
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Nielsen, Jens
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Genome-scale metabolic modelling of hepatocytes reveals serine deficiency in patients with non-alcoholic fatty liver disease2014In: Nature Communications, E-ISSN 2041-1723, Vol. 5, p. 3083-Article in journal (Refereed)
    Abstract [en]

    Several liver disorders result from perturbations in the metabolism of hepatocytes, and their underlying mechanisms can be outlined through the use of genome-scale metabolic models (GEMs). Here we reconstruct a consensus GEM for hepatocytes, which we call iHepatocytes2322, that extends previous models by including an extensive description of lipid metabolism. We build iHepatocytes2322 using Human Metabolic Reaction 2.0 database and proteomics data in Human Protein Atlas, which experimentally validates the incorporated reactions. The reconstruction process enables improved annotation of the proteomics data using the network centric view of iHepatocytes2322. We then use iHepatocytes2322 to analyse transcriptomics data obtained from patients with non-alcoholic fatty liver disease. We show that blood concentrations of chondroitin and heparan sulphates are suitable for diagnosing non-alcoholic steatohepatitis and for the staging of non-alcoholic fatty liver disease. Furthermore, we observe serine deficiency in patients with NASH and identify PSPH, SHMT1 and BCAT1 as potential therapeutic targets for the treatment of non-alcoholic steatohepatitis.

  • 126.
    Marino, Raffaele
    et al.
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST). KTH, Centres, Nordic Institute for Theoretical Physics NORDITA.
    Parisi, G.
    Ricci-Tersenghi, F.
    The backtracking survey propagation algorithm for solving random K-SAT problems2016In: Nature Communications, E-ISSN 2041-1723, Vol. 7, article id 12996Article in journal (Refereed)
    Abstract [en]

    Discrete combinatorial optimization has a central role in many scientific disciplines, however, for hard problems we lack linear time algorithms that would allow us to solve very large instances. Moreover, it is still unclear what are the key features that make a discrete combinatorial optimization problem hard to solve. Here we study random K-satisfiability problems with K=3,4, which are known to be very hard close to the SAT-UNSAT threshold, where problems stop having solutions. We show that the backtracking survey propagation algorithm, in a time practically linear in the problem size, is able to find solutions very close to the threshold, in a region unreachable by any other algorithm. All solutions found have no frozen variables, thus supporting the conjecture that only unfrozen solutions can be found in linear time, and that a problem becomes impossible to solve in linear time when all solutions contain frozen variables.

  • 127.
    Marking, Ulrika
    et al.
    Department of Clinical Sciences, Karolinska Institutet Danderyd Hospital, Stockholm, Sweden.
    Havervall, Sebastian
    Department of Clinical Sciences, Karolinska Institutet Danderyd Hospital, Stockholm, Sweden.
    Norin, Nina Greilert
    Department of Clinical Sciences, Karolinska Institutet Danderyd Hospital, Stockholm, Sweden.
    Bladh, Oscar
    Department of Clinical Sciences, Karolinska Institutet Danderyd Hospital, Stockholm, Sweden.
    Christ, Wanda
    Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden.
    Gordon, Max
    Department of Clinical Sciences, Karolinska Institutet Danderyd Hospital, Stockholm, Sweden.
    Ng, Henry
    Department of Medical Cell Biology and SciLifeLab, Uppsala University, Uppsala, Sweden.
    Blom, Kim
    Department of Clinical Sciences, Karolinska Institutet Danderyd Hospital, Stockholm, Sweden.
    Phillipson, Mia
    Department of Medical Cell Biology and SciLifeLab, Uppsala University, Uppsala, Sweden.
    Mangsbo, Sara
    Department of Pharmacy and SciLifeLab, Uppsala University, Uppsala, Sweden.
    Alm, Jessica J.
    Department of Microbiology, Tumor and Cell Biology & National Pandemic Center, Karolinska Institutet, Solna, Sweden.
    Smed-Sörensen, Anna
    Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.
    Nilsson, Peter
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Affinity Proteomics.
    Hober, Sophia
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Protein Technology.
    Åberg, Mikael
    Department of Medical Sciences, Clinical Chemistry and SciLifeLab, Uppsala University, Uppsala, Sweden.
    Klingström, Jonas
    Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden; Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden.
    Thålin, Charlotte
    Department of Clinical Sciences, Karolinska Institutet Danderyd Hospital, Stockholm, Sweden.
    Correlates of protection and viral load trajectories in omicron breakthrough infections in triple vaccinated healthcare workers2023In: Nature Communications, E-ISSN 2041-1723, Vol. 14, no 1, article id 1577Article in journal (Refereed)
    Abstract [en]

    Vaccination offers protection against severe COVID-19 caused by SARS-CoV-2 omicron but is less effective against infection. Characteristics such as serum antibody titer correlation to protection, viral abundance and clearance of omicron infection in vaccinated individuals are scarce. We present a 4-week twice-weekly SARS-CoV-2 qPCR screening in 368 triple vaccinated healthcare workers. Spike-specific IgG levels, neutralization titers and mucosal spike-specific IgA-levels were determined at study start and qPCR-positive participants were sampled repeatedly for two weeks. 81 (cumulative incidence 22%) BA.1, BA.1.1 and BA.2 infections were detected. High serum antibody titers are shown to be protective against infection (p < 0.01), linked to reduced viral load (p < 0.01) and time to viral clearance (p < 0.05). Pre-omicron SARS-CoV-2 infection is independently associated to increased protection against omicron, largely mediated by mucosal spike specific IgA responses (nested models lr test p = 0.02 and 0.008). Only 10% of infected participants remain asymptomatic through the course of their infection. We demonstrate that high levels of vaccine-induced spike-specific WT antibodies are linked to increased protection against infection and to reduced viral load if infected, and suggest that the additional protection offered by pre-omicron SARS-CoV-2 infection largely is mediated by mucosal spike-specific IgA.

  • 128.
    Marklund, Maja
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Schultz, Niklas
    Karolinska Inst, Div Translat Med & Chem Biol, Sci Life Lab, Solna, Sweden..
    Friedrich, Stefanie
    Stockholm Univ, Dept Biochem & Biophys, Sci Lab, Solna, Sweden..
    Berglund, Emelie
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Tarish, Firas
    Karolinska Inst, Div Translat Med & Chem Biol, Sci Life Lab, Solna, Sweden..
    Tanoglidi, Anna
    Evangelismos Gen Hosp, Dept Pathol, 45-47 Ipsilantou Str, Athens, Greece..
    Liu, Yao
    Karolinska Inst, Div Translat Med & Chem Biol, Sci Life Lab, Solna, Sweden..
    Bergenstråhle, Ludvig
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Erickson, Andrew
    Univ Oxford, Nuffield Dept Surg Sci, Oxford, England..
    Helleday, Thomas
    Karolinska Inst, Div Translat Med & Chem Biol, Sci Life Lab, Solna, Sweden..
    Lamb, Alastair D.
    Univ Oxford, Nuffield Dept Surg Sci, Oxford, England..
    Sonnhammer, Erik
    Stockholm Univ, Dept Biochem & Biophys, Sci Lab, Solna, Sweden..
    Lundeberg, Joakim
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Spatio-temporal analysis of prostate tumors in situ suggests pre-existence of treatment-resistant clones2022In: Nature Communications, E-ISSN 2041-1723, Vol. 13, no 1, article id 5475Article in journal (Refereed)
    Abstract [en]

    The molecular mechanisms underlying lethal castration-resistant prostate cancer remain poorly understood, with intratumoral heterogeneity a likely contributing factor. To examine the temporal aspects of resistance, we analyze tumor heterogeneity in needle biopsies collected before and after treatment with androgen deprivation therapy. By doing so, we are able to couple clinical responsiveness and morphological information such as Gleason score to transcriptome-wide data. Our data-driven analysis of transcriptomes identifies several distinct intratumoral cell populations, characterized by their unique gene expression profiles. Certain cell populations present before treatment exhibit gene expression profiles that match those of resistant tumor cell clusters, present after treatment. We confirm that these clusters are resistant by the localization of active androgen receptors to the nuclei in cancer cells post-treatment. Our data also demonstrates that most stromal cells adjacent to resistant clusters do not express the androgen receptor, and we identify differentially expressed genes for these cells. Altogether, this study shows the potential to increase the power in predicting resistant tumors. Spatial heterogeneity in prostate cancer can contribute to its resistance to androgen deprivation therapy (ADT). Here, the authors analyse prostate cancer samples before and after ADT using Spatial Transcriptomics, and find heterogeneous pre-treatment tumour cell populations and stromal cells that are associated with resistance.

  • 129.
    Massier, Lucas
    et al.
    Karolinska Univ Hosp Huddinge, Karolinska Inst, Dept Med Huddinge H7, SE-14183 Huddinge, Sweden..
    Jalkanen, Jutta
    Karolinska Univ Hosp Huddinge, Karolinska Inst, Dept Med Huddinge H7, SE-14183 Huddinge, Sweden..
    Elmastas, Merve
    Karolinska Univ Hosp Huddinge, Karolinska Inst, Dept Med Huddinge H7, SE-14183 Huddinge, Sweden..
    Zhong, Jiawei
    Karolinska Univ Hosp Huddinge, Karolinska Inst, Dept Med Huddinge H7, SE-14183 Huddinge, Sweden..
    Wang, Tongtong
    Swiss Fed Inst Technol, Dept Hlth Sci & Technol, Inst Food Nutr & Hlth, Lab Translat Nutr Biol, Schwerzenbach, Switzerland..
    Nankam, Pamela A. Nono A.
    Univ Leipzig, Helmholtz Inst Metab Obes & Vasc Res HI MAG, Helmholtz Zentrum Munchen, Leipzig, Germany.;Univ Hosp Leipzig, Leipzig, Germany..
    Frendo-Cumbo, Scott
    Karolinska Univ Hosp Huddinge, Karolinska Inst, Dept Med Huddinge H7, SE-14183 Huddinge, Sweden..
    Backdahl, Jesper
    Karolinska Univ Hosp Huddinge, Karolinska Inst, Dept Med Huddinge H7, SE-14183 Huddinge, Sweden..
    Subramanian, Narmadha
    Karolinska Univ Hosp Huddinge, Karolinska Inst, Dept Med Huddinge H7, SE-14183 Huddinge, Sweden..
    Sekine, Takuya
    Karolinska Univ Hosp Huddinge, Karolinska Inst, Ctr Infect Med, Dept Med Huddinge H7, SE-14152 Huddinge, Sweden..
    Kerr, Alastair G. G.
    Karolinska Univ Hosp Huddinge, Karolinska Inst, Dept Med Huddinge H7, SE-14183 Huddinge, Sweden..
    Tseng, Ben T. P.
    Karolinska Univ Hosp Huddinge, Karolinska Inst, Dept Med Huddinge H7, SE-14183 Huddinge, Sweden..
    Laurencikiene, Jurga
    Karolinska Univ Hosp Huddinge, Karolinska Inst, Dept Med Huddinge H7, SE-14183 Huddinge, Sweden..
    Buggert, Marcus
    Karolinska Univ Hosp Huddinge, Karolinska Inst, Ctr Infect Med, Dept Med Huddinge H7, SE-14152 Huddinge, Sweden..
    Lourda, Magda
    Karolinska Univ Hosp Huddinge, Karolinska Inst, Ctr Infect Med, Dept Med Huddinge H7, SE-14152 Huddinge, Sweden.;Karolinska Inst, Dept Womens & Childrens Hlth, Childhood Canc Res Unit, SE-17177 Stockholm, Sweden..
    Kublickiene, Karolina
    Karolinska Univ Hosp Huddinge, Karolinska Inst, Dept Clin Sci Intervent & Technol CLINTEC, Unit Renal Med, SE-14186 Huddinge, Sweden..
    Bhalla, Nayanika
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Andersson, Alma
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Valsesia, Armand
    Nestle Res, Nestle Inst Hlth Sci, Dept Metab Hlth, Lausanne, Switzerland..
    Astrup, Arne
    Novo Nord Fdn, Dept Obes & Nutr Sci, Hellerup, Denmark..
    Blaak, Ellen E. E.
    Maastricht Univ Med Ctr, NUTRIM Sch Nutr & Translat Res Metab, Dept Human Biol, Maastricht, Netherlands. Univ Toulouse III Paul Sabatier UPS, Univ Toulouse, Inst Metab & Cardiovasc Dis I2MC, Inserm,UMR1297, Toulouse, France. Charles Univ Prague, Fac Med 3, Franco Czech Lab Clin Res Obes, Prague, Czech Republic..
    Ståhl, Patrik
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Viguerie, Nathalie
    Univ Toulouse III Paul Sabatier UPS, Toulouse, France. Ctr Hosp Univ Toulouse, Lab Biochim, Toulouse, France. Inst Univ France IUF, Paris, France. Univ Leipzig, Med Dept 3 Endocrinol Nephrol Rheumatol, Med Ctr, Leipzig, Germany..
    Langin, Dominique
    Univ Toulouse III Paul Sabatier UPS, Toulouse, France. Ctr Hosp Univ Toulouse, Lab Biochim, Toulouse, France. Inst Univ France IUF, Paris, France. Univ Leipzig, Med Dept 3 Endocrinol Nephrol Rheumatol, Med Ctr, Leipzig, Germany..
    Wolfrum, Christian
    Swiss Fed Inst Technol, Dept Hlth Sci & Technol, Inst Food Nutr & Hlth, Lab Translat Nutr Biol, Schwerzenbach, Switzerland..
    Blueher, Matthias
    Univ Leipzig, Helmholtz Inst Metab Obes & Vasc Res HI MAG, Helmholtz Zentrum Munchen, Leipzig, Germany.;Univ Hosp Leipzig, Leipzig, Germany..
    Ryden, Mikael
    Karolinska Univ Hosp Huddinge, Karolinska Inst, Dept Med Huddinge H7, SE-14183 Huddinge, Sweden..
    Mejhert, Niklas
    Karolinska Univ Hosp Huddinge, Karolinska Inst, Dept Med Huddinge H7, SE-14183 Huddinge, Sweden..
    An integrated single cell and spatial transcriptomic map of human white adipose tissue2023In: Nature Communications, E-ISSN 2041-1723, Vol. 14, no 1, article id 1438Article in journal (Refereed)
    Abstract [en]

    Single-cell studies of human white adipose tissue (WAT) provide insights into the specialized cell types in the tissue. Here the authors combine publicly available and newly generated high-resolution and bulk transcriptomic results from multiple human datasets to provide a comprehensive cellular map of white adipose tissue. To date, single-cell studies of human white adipose tissue (WAT) have been based on small cohort sizes and no cellular consensus nomenclature exists. Herein, we performed a comprehensive meta-analysis of publicly available and newly generated single-cell, single-nucleus, and spatial transcriptomic results from human subcutaneous, omental, and perivascular WAT. Our high-resolution map is built on data from ten studies and allowed us to robustly identify >60 subpopulations of adipocytes, fibroblast and adipogenic progenitors, vascular, and immune cells. Using these results, we deconvolved spatial and bulk transcriptomic data from nine additional cohorts to provide spatial and clinical dimensions to the map. This identified cell-cell interactions as well as relationships between specific cell subtypes and insulin resistance, dyslipidemia, adipocyte volume, and lipolysis upon long-term weight changes. Altogether, our meta-map provides a rich resource defining the cellular and microarchitectural landscape of human WAT and describes the associations between specific cell types and metabolic states.

  • 130.
    Masullo, Luciano A.
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Boden, Andreas
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Pennacchietti, Francesca
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Coceano, Giovanna
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Ratz, Michael
    Karolinska Inst, Dept Cell & Mol Biol, S-17176 Stockholm, Sweden..
    Testa, Ilaria
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Enhanced photon collection enables four dimensional fluorescence nanoscopy of living systems2018In: Nature Communications, E-ISSN 2041-1723, Vol. 9, article id 3281Article in journal (Refereed)
    Abstract [en]

    The theoretically unlimited spatial resolution of fluorescence nanoscopy often comes at the expense of time, contrast and increased dose of energy for recording. Here, we developed MoNaLISA, for Molecular Nanoscale Live Imaging with Sectioning Ability, a nanoscope capable of imaging structures at a scale of 45-65 nm within the entire cell volume at low light intensities (W-kW cm(-2)). Our approach, based on reversibly switchable fluorescent proteins, features three distinctly modulated illumination patterns crafted and combined to gain fluorescence ON-OFF switching cycles and image contrast. By maximizing the detected photon flux, MoNaLISA enables prolonged (40-50 frames) and large (50 x 50 mu m(2)) recordings at 0.3-1.3 Hz with enhanced optical sectioning ability. We demonstrate the general use of our approach by 4D imaging of organelles and fine structures in epithelial human cells, colonies of mouse embryonic stem cells, brain cells, and organotypic tissues.

  • 131. Matlashov, M. E.
    et al.
    Shcherbakova, D. M.
    Alvelid, Jonatan
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics.
    Baloban, M.
    Pennacchietti, Francesca
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics.
    Shemetov, A. A.
    Testa, Ilaria
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics.
    Verkhusha, V. V.
    A set of monomeric near-infrared fluorescent proteins for multicolor imaging across scales2020In: Nature Communications, E-ISSN 2041-1723, Vol. 11, no 1, article id 239Article in journal (Refereed)
    Abstract [en]

    Bright monomeric near-infrared (NIR) fluorescent proteins (FPs) are in high demand as protein tags for multicolor microscopy and in vivo imaging. Here we apply rational design to engineer a complete set of monomeric NIR FPs, which are the brightest genetically encoded NIR probes. We demonstrate that the enhanced miRFP series of NIR FPs, which combine high effective brightness in mammalian cells and monomeric state, perform well in both nanometer-scale imaging with diffraction unlimited stimulated emission depletion (STED) microscopy and centimeter-scale imaging in mice. In STED we achieve ~40 nm resolution in live cells. In living mice we detect ~105 fluorescent cells in deep tissues. Using spectrally distinct monomeric NIR FP variants, we perform two-color live-cell STED microscopy and two-color imaging in vivo. Having emission peaks from 670 nm to 720 nm, the next generation of miRFPs should become versatile NIR probes for multiplexed imaging across spatial scales in different modalities.

  • 132. Matt, C. E.
    et al.
    Sutter, D.
    Cook, A. M.
    Sassa, Y.
    Månsson, Martin
    KTH, School of Engineering Sciences (SCI), Applied Physics, Material Physics, MF.
    Tjernberg, Oscar
    KTH, School of Engineering Sciences (SCI), Applied Physics, Material Physics, MF.
    Das, L.
    Horio, M.
    Destraz, D.
    Fatuzzo, C. G.
    Hauser, K.
    Shi, M.
    Kobayashi, M.
    Strocov, V. N.
    Schmitt, T.
    Dudin, P.
    Hoesch, M.
    Pyon, S.
    Takayama, T.
    Takagi, H.
    Lipscombe, O. J.
    Hayden, S. M.
    Kurosawa, T.
    Momono, N.
    Oda, M.
    Neupert, T.
    Chang, J.
    Direct observation of orbital hybridisation in a cuprate superconductor2018In: Nature Communications, E-ISSN 2041-1723, Vol. 9, article id 972Article in journal (Refereed)
    Abstract [en]

    The minimal ingredients to explain the essential physics of layered copper-oxide (cuprates) materials remains heavily debated. Effective low-energy single-band models of the copper-oxygen orbitals are widely used because there exists no strong experimental evidence supporting multi-band structures. Here, we report angle-resolved photoelectron spectroscopy experiments on La-based cuprates that provide direct observation of a two-band structure. This electronic structure, qualitatively consistent with density functional theory, is parametrised by a two-orbital (d(x2-y2) and d(z2)) tight-binding model. We quantify the orbital hybridisation which provides an explanation for the Fermi surface topology and the proximity of the van-Hove singularity to the Fermi level. Our analysis leads to a unification of electronic hopping parameters for single-layer cuprates and we conclude that hybridisation, restraining d-wave pairing, is an important optimisation element for superconductivity.

  • 133. Miron, Catalin
    et al.
    Miao, Quan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Nicolas, Christophe
    Bozek, John D.
    Andralojc, Witold
    Patanen, Minna
    Simoes, Grazieli
    Travnikova, Oksana
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Gel'mukhanov, Faris
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Site-selective photoemission from delocalized valence shells induced by molecular rotation2014In: Nature Communications, E-ISSN 2041-1723, Vol. 5, p. 3816-Article in journal (Refereed)
    Abstract [en]

    Due to the generally delocalized nature of molecular valence orbitals, valence-shell spectroscopies do not usually allow to specifically target a selected atom in a molecule. However, in X-ray electron spectroscopy, the photoelectron momentum is large and the recoil angular momentum transferred to the molecule is larger when the photoelectron is ejected from a light atom compared with a heavy one. This confers an extreme sensitivity of the rotational excitation to the ionization site. Here we show that, indeed, the use of high-energy photons to photoionize valence-shell electrons of hydrogen chloride offers an unexpected way to decrypt the atomic composition of the molecular orbitals due to the rotational dependence of the photoionization profiles. The analysis of the site-specific rotational envelopes allows us to disentangle the effects of the two main mechanisms of rotational excitation, based on angular momentum exchange between the molecule and either the incoming photon or the emitted electron.

  • 134.
    Mirzazadeh, Reza
    et al.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Andrusivova, Zaneta
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Larsson, Ludvig
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Newton, Phillip T
    Department of Women’s and Children’s Health, Karolinska Institute, Solna, Sweden and Astrid Lindgren Children’s Hospital, Karolinska University Hospital, Solna, Sweden.
    Galicia, Leire Alonso
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Abalo, Xesús M
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Avijgan, Mahtab
    Department of Women’s and Children’s Health, Karolinska Institute, Solna, Sweden and Astrid Lindgren Children’s Hospital, Karolinska University Hospital, Solna, Sweden.
    Kvastad, Linda
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Denadai-Souza, Alexandre
    Department of Chronic Diseases and Metabolism, Katholieke Universiteit te Leuven, Leuven, Belgium.
    Stakenborg, Nathalie
    Department of Chronic Diseases and Metabolism, Katholieke Universiteit te Leuven, Leuven, Belgium.
    Firsova, Alexandra B
    Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, Science for Life Laboratory, Stockholm, Sweden.
    Shamikh, Alia
    Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden.
    Jurek, Alexandra
    10x Genomics, Stockholm, Sweden.
    Schultz, Niklas
    Department of Oncology-Pathology, Karolinska Institutet, BioClinicum, Karolinska University Hospital, Stockholm, Sweden.
    Nistér, Monica
    Department of Oncology-Pathology, Karolinska Institutet, BioClinicum, Karolinska University Hospital, Stockholm, Sweden.
    Samakovlis, Christos
    Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, Science for Life Laboratory, Stockholm, Sweden.
    Boeckxstaens, Guy
    Department of Chronic Diseases and Metabolism, Katholieke Universiteit te Leuven, Leuven, Belgium.
    Lundeberg, Joakim
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Spatially resolved transcriptomic profiling of degraded and challenging fresh frozen samples2023In: Nature Communications, E-ISSN 2041-1723, Vol. 14, no 1Article in journal (Refereed)
    Abstract [en]

    Spatially resolved transcriptomics has enabled precise genome-wide mRNA expression profiling within tissue sections. The performance of methods targeting the polyA tails of mRNA relies on the availability of specimens with high RNA quality. Moreover, the high cost of currently available spatial resolved transcriptomics assays requires a careful sample screening process to increase the chance of obtaining high-quality data. Indeed, the upfront analysis of RNA quality can show considerable variability due to sample handling, storage, and/or intrinsic factors. We present RNA-Rescue Spatial Transcriptomics (RRST), a workflow designed to improve mRNA recovery from fresh frozen specimens with moderate to low RNA quality. First, we provide a benchmark of RRST against the standard Visium spatial gene expression protocol on high RNA quality samples represented by mouse brain and prostate cancer samples. Then, we test the RRST protocol on tissue sections collected from five challenging tissue types, including human lung, colon, small intestine, pediatric brain tumor, and mouse bone/cartilage. In total, we analyze 52 tissue sections and demonstrate that RRST is a versatile, powerful, and reproducible protocol for fresh frozen specimens of different qualities and origins. 

  • 135.
    Mälarstig, Anders
    et al.
    Pfizer Worldwide Res Dev & Med, Stockholm, Sweden.
    Grassmann, Felix
    Karolinska Inst, Dept Med Epidemiol & Biostat, Stockholm, Sweden; Hlth & Med Univ, Inst Clin Res & Syst Med, Potsdam, Germany.
    Dahl, Leo
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Affinity Proteomics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Dimitriou, Marios
    Karolinska Inst, Dept Med Epidemiol & Biostat, Stockholm, Sweden; Pfizer Worldwide Res Dev & Med, Stockholm, Sweden.
    McLeod, Dianna
    Karolinska Inst, Dept Med Epidemiol & Biostat, Stockholm, Sweden.
    Gabrielson, Marike
    Karolinska Inst, Dept Med Epidemiol & Biostat, Stockholm, Sweden.
    Smith-Byrne, Karl
    Univ Oxford, Nuffield Dept Populat Hlth, Canc Epidemiol Unit, Oxford, England.
    Thomas, Cecilia Engel
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Affinity Proteomics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Huang, Tzu Hsuan
    Pfizer Inc, Canc Immunol Discovery, San Diego, CA USA.
    Forsberg, Simon K.G.
    Olink Prote AB, Uppsala, Sweden.
    Eriksson, Per
    Olink Prote AB, Uppsala, Sweden.
    Ulfstedt, Mikael
    Olink Prote AB, Uppsala, Sweden.
    Johansson, Mattias
    Int Agcy Res Canc IARC WHO, Genom Epidemiol Branch, Lyon, France.
    Sokolov, Aleksandr V.
    Uppsala Univ, Dept Surg Sci Funct Pharmacol & Neurosci, Uppsala, Sweden.
    Schiöth, Helgi B.
    Uppsala Univ, Dept Surg Sci Funct Pharmacol & Neurosci, Uppsala, Sweden.
    Hall, Per
    Karolinska Inst, Dept Med Epidemiol & Biostat, Stockholm, Sweden; Södersjukhuset, Dept Oncol, Stockholm, Sweden.
    Schwenk, Jochen M.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Affinity Proteomics.
    Czene, Kamila
    Karolinska Inst, Dept Med Epidemiol & Biostat, Stockholm, Sweden.
    Hedman, Åsa K.
    Karolinska Inst, Dept Med Epidemiol & Biostat, Stockholm, Sweden; Pfizer Worldwide Res Dev & Med, Stockholm, Sweden.
    Evaluation of circulating plasma proteins in breast cancer using Mendelian randomisation2023In: Nature Communications, E-ISSN 2041-1723, Vol. 14, no 1, article id 7680Article in journal (Refereed)
    Abstract [en]

    Biomarkers for early detection of breast cancer may complement population screening approaches to enable earlier and more precise treatment. The blood proteome is an important source for biomarker discovery but so far, few proteins have been identified with breast cancer risk. Here, we measure 2929 unique proteins in plasma from 598 women selected from the Karolinska Mammography Project to explore the association between protein levels, clinical characteristics, and gene variants, and to identify proteins with a causal role in breast cancer. We present 812 cis-acting protein quantitative trait loci for 737 proteins which are used as instruments in Mendelian randomisation analyses of breast cancer risk. Of those, we present five proteins (CD160, DNPH1, LAYN, LRRC37A2 and TLR1) that show a potential causal role in breast cancer risk with confirmatory results in independent cohorts. Our study suggests that these proteins should be further explored as biomarkers and potential drug targets in breast cancer.

  • 136.
    Natesan, Dinesh
    et al.
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST). Manipal Academy of Higher Education, Manipal, 576104, India; National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK campus, Bellary road, Bangalore, 560065, India .
    Saxena, Nitesh
    Tata Inst Fundamental Res, Natl Ctr Biol Sci, GKVK Campus,Bellary Rd, Bangalore 560065, Karnataka, India..
    Ekeberg, Örjan
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Sane, Sanjay P.
    Tata Inst Fundamental Res, Natl Ctr Biol Sci, GKVK Campus,Bellary Rd, Bangalore 560065, Karnataka, India..
    Tuneable reflexes control antennal positioning in flying hawkmoths2019In: Nature Communications, E-ISSN 2041-1723, Vol. 10, article id 5593Article in journal (Refereed)
    Abstract [en]

    Complex behaviours may be viewed as sequences of modular actions, each elicited by specific sensory cues in their characteristic timescales. From this perspective, we can construct models in which unitary behavioural modules are hierarchically placed in context of related actions. Here, we analyse antennal positioning reflex in hawkmoths as a tuneable behavioural unit. Mechanosensory feedback from two antennal structures, Bohm's bristles (BB) and Johnston's organs (JO), determines antennal position. At flight onset, antennae attain a specific position, which is maintained by feedback from BB. Simultaneously, JO senses deflections in flagellum-pedicel joint due to frontal airflow, to modulate its steady-state position. Restricting JO abolishes positional modulation but maintains stability against perturbations. Linear feedback models are sufficient to predict antennal dynamics at various set-points. We modelled antennal positioning as a hierarchical neural-circuit in which fast BB feedback maintains instantaneous set-point, but slow JO feedback modulates it, thereby elucidating mechanisms underlying its robustness and flexibility.

  • 137.
    Nielsen, Jakob Toudahl
    et al.
    Center for Insoluble Protein Structures (inSPIN), and Interdisciplinary Nanoscience Center (iNANO) Department of Chemistry and Department of Chemistry, Aarhus C DK-8000, Denmark .
    Kulminskaya, Natalia V
    Center for Insoluble Protein Structures (inSPIN), and Interdisciplinary Nanoscience Center (iNANO) Department of Chemistry and Department of Chemistry, Aarhus C DK-8000, Denmark.
    Bjerring, Morten
    Center for Insoluble Protein Structures (inSPIN), and Interdisciplinary Nanoscience Center (iNANO) Department of Chemistry and Department of Chemistry, Aarhus C DK-8000, Denmark.
    Linnanto, Juha M
    Institute of Physics, University of Tartu, Estonia.
    Rätsep, Margus
    Institute of Physics, University of Tartu, Estonia.
    Pedersen, Marie Østergaard
    Center for Insoluble Protein Structures (inSPIN), and Novo Nordisk a/s, Novo Nordisk Park, Denmark .
    Lambrev, Petar H
    Hungarian Academy of Sciences, Biological Research Centre, Szeged, Hungary.
    Dorogi, Márta
    Hungarian Academy of Sciences, Biological Research Centre, Szeged, Hungary.
    Garab, Győző
    Hungarian Academy of Sciences, Biological Research Centre, Szeged, Hungary.
    Thomsen, Karen
    Interdisciplinary Nanoscience Center (iNANO), Aarhus University.
    Jegerschöld, Caroline
    Karolinska Institutet, Biovetenskaper och Nutrition, samt Strukturell Bioteknik, KTH.
    Frigaard, Niels-Ulrik
    Section for Marine Biology, Department of Biology, University of Copenhagen.
    Lindahl, Martin
    Karolinska Institutet, Biovetenskaper och Nutrition, samt Strukturell Bioteknik, KTH.
    Nielsen, Niels Chr
    Center for Insoluble Protein Structures (inSPIN), and Interdisciplinary Nanoscience Center (iNANO) Department of Chemistry and Department of Chemistry, Aarhus C DK-8000, Denmark.
    In situ high-resolution structure of the baseplate antenna complex in Chlorobaculum tepidum.2016In: Nature Communications, E-ISSN 2041-1723, Vol. 7, article id 12454Article in journal (Refereed)
    Abstract [en]

    Photosynthetic antenna systems enable organisms harvesting light and transfer the energy to the photosynthetic reaction centre, where the conversion to chemical energy takes place. One of the most complex antenna systems, the chlorosome, found in the photosynthetic green sulfur bacterium Chlorobaculum (Cba.) tepidum contains a baseplate, which is a scaffolding super-structure, formed by the protein CsmA and bacteriochlorophyll a. Here we present the first high-resolution structure of the CsmA baseplate using intact fully functional, light-harvesting organelles from Cba. tepidum, following a hybrid approach combining five complementary methods: solid-state NMR spectroscopy, cryo-electron microscopy, isotropic and anisotropic circular dichroism and linear dichroism. The structure calculation was facilitated through development of new software, GASyCS for efficient geometry optimization of highly symmetric oligomeric structures. We show that the baseplate is composed of rods of repeated dimers of the strongly amphipathic CsmA with pigments sandwiched within the dimer at the hydrophobic side of the helix.

  • 138.
    Nijsse, Femke J. M. M.
    et al.
    Univ Exeter, Global Syst Inst, Dept Geog, Exeter, England..
    Mercure, Jean-Francois
    Univ Exeter, Global Syst Inst, Dept Geog, Exeter, England.;Univ Cambridge, Cambridge Ctr Energy Environm & Nat Resource Gover, Cambridge, England.;World Bank, Washington, DC USA..
    Ameli, Nadia
    UCL, Inst Sustainable Resources, London, England..
    Larosa, Francesca
    KTH, School of Engineering Sciences (SCI), Engineering Mechanics, Fluid Mechanics and Engineering Acoustics. KTH, School of Industrial Engineering and Management (ITM), Centres, KTH Climate Action Centre, CAC. UCL, Inst Sustainable Resources, London, England.
    Kothari, Sumit
    UCL, Inst Sustainable Resources, London, England..
    Rickman, Jamie
    UCL, Inst Sustainable Resources, London, England..
    Vercoulen, Pim
    Univ Exeter, Global Syst Inst, Dept Geog, Exeter, England.;Cambridge Econometr, Cambridge, England..
    Pollitt, Hector
    Univ Cambridge, Cambridge Ctr Energy Environm & Nat Resource Gover, Cambridge, England.;World Bank, Washington, DC USA..
    The momentum of the solar energy transition2023In: Nature Communications, E-ISSN 2041-1723, Vol. 14, no 1, article id 6542Article in journal (Refereed)
    Abstract [en]

    Decarbonisation plans across the globe require zero-carbon energy sources to be widely deployed by 2050 or 2060. Solar energy is the most widely available energy resource on Earth, and its economic attractiveness is improving fast in a cycle of increasing investments. Here we use data-driven conditional technology and economic forecasting modelling to establish which zero carbon power sources could become dominant worldwide. We find that, due to technological trajectories set in motion by past policy, a global irreversible solar tipping point may have passed where solar energy gradually comes to dominate global electricity markets, without any further climate policies. Uncertainties arise, however, over grid stability in a renewables-dominated power system, the availability of sufficient finance in underdeveloped economies, the capacity of supply chains and political resistance from regions that lose employment. Policies resolving these barriers may be more effective than price instruments to accelerate the transition to clean energy.

  • 139. Nozière, Barbara
    et al.
    Baduel, Christine
    Jaffrezo, Jean-Luc
    The dynamic surface tension of atmospheric aerosol surfactants reveals new aspects of cloud activation2014In: Nature Communications, E-ISSN 2041-1723, Vol. 5, no 1, article id 3335Article in journal (Refereed)
    Download full text (pdf)
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  • 140.
    Nyström, Gustav
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology.
    Marais, Andrew
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology.
    Karabulut, Erdem
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology.
    Wågberg, Lars
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology.
    Cui, Yi
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology.
    Hamedi, Mahiar
    Self-assembled three-dimensional and compressible interdigitated thin-film supercapacitors and batteries2015In: Nature Communications, E-ISSN 2041-1723, Vol. 6, p. 7259-Article in journal (Refereed)
    Abstract [en]

    Traditional thin-film energy-storage devices consist of stacked layers of active films on two-dimensional substrates and do not exploit the third dimension. Fully three-dimensional thin-film devices would allow energy storage in bulk materials with arbitrary form factors and with mechanical properties unique to bulk materials such as compressibility. Here we show three-dimensional energy-storage devices based on layer-by-layer self-assembly of interdigitated thin films on the surface of an open-cell aerogel substrate. We demonstrate a reversibly compressible three-dimensional supercapacitor with carbon nanotube electrodes and a three-dimensional hybrid battery with a copper hexacyanoferrate ion intercalating cathode and a carbon nanotube anode. The three-dimensional supercapacitor shows stable operation over 400 cycles with a capacitance of 25â €‰Fâ €‰g â '1 and is fully functional even at compressions up to 75%. Our results demonstrate that layer-by-layer self-assembly inside aerogels is a rapid, precise and scalable route for building high-surface-area 3D thin-film devices.

  • 141.
    Ohlsson, Tommy
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical Particle Physics.
    Zhou, Shun
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical Particle Physics. Chinese Acad Sci,China.
    Renormalization group running of neutrino parameters2014In: Nature Communications, E-ISSN 2041-1723, Vol. 5, p. 5153-Article, review/survey (Refereed)
    Abstract [en]

    Neutrinos are the most elusive particles in our Universe. They have masses at least one million times smaller than the electron mass, carry no electric charge and very weakly interact with other particles, meaning that they are rarely captured in terrestrial detectors. Tremendous efforts in the past two decades have revealed that neutrinos can transform from one type to another as a consequence of neutrino oscillations-a quantum mechanical effect over macroscopic distances-yet the origin of neutrino masses remains puzzling. The physical evolution of neutrino parameters with respect to energy scale may help elucidate the mechanism for their mass generation.

  • 142.
    Oliaei, Erfan
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology, Biocomposites. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Centres, Wallenberg Wood Science Center. RISE Bioeconomy and health, Stockholm, Sweden.
    Olsén, Peter
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology, Biocomposites. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Centres, Wallenberg Wood Science Center.
    Lindström, Tom
    RISE Bioecon & Hlth, Stockholm, Sweden..
    Berglund, Lars A.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology, Biocomposites. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Centres, Wallenberg Wood Science Center.
    Highly reinforced and degradable lignocellulose biocomposites by polymerization of new polyester oligomers2022In: Nature Communications, E-ISSN 2041-1723, Vol. 13, no 1, article id 5666Article in journal (Refereed)
    Abstract [en]

    Unbleached wood fibers and nanofibers are environmentally friendly bio-based candidates for material production, in particular, as reinforcements in polymer matrix biocomposites due to their low density and potential as carbon sink during the materials production phase. However, producing high reinforcement content biocomposites with degradable or chemically recyclable matrices is troublesome. Here, we address this issue with a new concept for facile and scalable in-situ polymerization of polyester matrices based on functionally balanced oligomers in pre-formed lignocellulosic networks. The idea enabled us to create high reinforcement biocomposites with well-dispersed mechanically undamaged fibers or nanocellulose. These degradable biocomposites have much higher mechanical properties than analogs in the literature. Reinforcement geometry (fibers at 30 mu m or fibrils at 10-1000 nm diameter) influenced the polymerization and degradation of the polyester matrix. Overall, this work opens up new pathways toward environmentally benign materials in the context of a circular bioeconomy. Cellulose biocomposites from nanocellulose or plant fibers with polymer matrix are often not degradable and suffer from insufficient mechanical properties to replace established materials. Here, the authors demonstrate the fabrication of hydrolytically degradable polymers through in-situ polymerization of new functionally balanced oligomers within high-content lignocellulose reinforcement networks.

  • 143.
    Ollech, Dirk
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Pflasterer, Tim
    Shellard, Adam
    Zambarda, Chiara
    Spatz, Joachim Pius
    Marcq, Philippe
    Mayor, Roberto
    Wombacher, Richard
    Cavalcanti-Adam, Elisabetta Ada
    Correction: An optochemical tool for light-induced dissociation of adherens junctions to control mechanical coupling between cells (vol 11, 472, 2020)2020In: Nature Communications, E-ISSN 2041-1723, Vol. 11, no 1, article id 1681Article in journal (Refereed)
  • 144.
    Ollech, Dirk
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Pflästerer, T.
    Shellard, A.
    Zambarda, C.
    Spatz, J. P.
    Marcq, P.
    Mayor, R.
    Wombacher, R.
    Cavalcanti-Adam, E. A.
    An optochemical tool for light-induced dissociation of adherens junctions to control mechanical coupling between cells2020In: Nature Communications, E-ISSN 2041-1723, Vol. 11, no 1, article id 472Article in journal (Refereed)
    Abstract [en]

    The cadherin-catenin complex at adherens junctions (AJs) is essential for the formation of cell-cell adhesion and epithelium integrity; however, studying the dynamic regulation of AJs at high spatio-temporal resolution remains challenging. Here we present an optochemical tool which allows reconstitution of AJs by chemical dimerization of the force bearing structures and their precise light-induced dissociation. For the dimerization, we reconstitute acto-myosin connection of a tailless E-cadherin by two ways: direct recruitment of α-catenin, and linking its cytosolic tail to the transmembrane domain. Our approach enables a specific ON-OFF switch for mechanical coupling between cells that can be controlled spatially on subcellular or tissue scale via photocleavage. The combination with cell migration analysis and traction force microscopy shows a wide-range of applicability and confirms the mechanical contribution of the reconstituted AJs. Remarkably, in vivo our tool is able to control structural and functional integrity of the epidermal layer in developing Xenopus embryos.

  • 145. Orellana, Laura
    et al.
    Yoluk, Özge
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Carrillo, Oliver
    Orozco, Modesto
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Prediction and Validation of Protein Intermediate States from Structurally Rich Ensembles and Coarse-Grained Simulations2016In: Nature Communications, E-ISSN 2041-1723, Vol. 7Article in journal (Refereed)
    Abstract [en]

    Protein conformational changes are at the heart of cell functions, from signaling to ion transport. However, the transient nature of the intermediates along transition pathways hampers their experimental detection, making the underlying mechanisms elusive. Here, we retrieve dynamic information on the actual transition routes from Principal Component Analysis (PCA) of structurally-rich ensembles and, in combination with coarse-grained simulations, explore the conformational landscapes of five well-studied proteins. Modeling them as elastic networks in a hybrid Elastic-Network Brownian Dynamics simulation (eBDIMS), we generate trajectories connecting stable end-states that spontaneously sample the crystallographic motions, predicting the structures of known intermediates along thepaths. We also show that the explored non-linear routes can delimit the lowest energy passages between end-states sampled by atomistic molecular dynamics. The integrative methodology presented here provides a powerful framework to extract and expand dynamic pathway information from the Protein Data Bank, as well as to validate sampling methods in general. 

  • 146.
    Parigi, Sara M.
    et al.
    Karolinska Inst & Univ Hosp, Dept Med Solna, Div Immunol & Allergy, Stockholm, Sweden.;Ctr Mol Med, Stockholm, Sweden..
    Larsson, Ludvig
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Das, Srustidhar
    Karolinska Inst & Univ Hosp, Dept Med Solna, Div Immunol & Allergy, Stockholm, Sweden.;Ctr Mol Med, Stockholm, Sweden..
    Flores, Ricardo O. Ramirez
    Heidelberg Univ, Fac Med, Heidelberg, Germany.;Heidelberg Univ Hosp, Inst Computat Biomed, Bioquant, Heidelberg, Germany..
    Frede, Annika
    Karolinska Inst & Univ Hosp, Dept Med Solna, Div Immunol & Allergy, Stockholm, Sweden.;Ctr Mol Med, Stockholm, Sweden..
    Tripathi, Kumar P.
    Karolinska Inst & Univ Hosp, Dept Med Solna, Div Immunol & Allergy, Stockholm, Sweden.;Ctr Mol Med, Stockholm, Sweden..
    Diaz, Oscar E.
    Karolinska Inst & Univ Hosp, Dept Med Solna, Div Immunol & Allergy, Stockholm, Sweden.;Ctr Mol Med, Stockholm, Sweden..
    Selin, Katja
    Karolinska Inst & Univ Hosp, Dept Med Solna, Div Immunol & Allergy, Stockholm, Sweden.;Ctr Mol Med, Stockholm, Sweden..
    Morales, Rodrigo A.
    Karolinska Inst & Univ Hosp, Dept Med Solna, Div Immunol & Allergy, Stockholm, Sweden.;Ctr Mol Med, Stockholm, Sweden..
    Luo, Xinxin
    Karolinska Inst & Univ Hosp, Dept Med Solna, Div Immunol & Allergy, Stockholm, Sweden.;Ctr Mol Med, Stockholm, Sweden..
    Monasterio, Gustavo
    Karolinska Inst & Univ Hosp, Dept Med Solna, Div Immunol & Allergy, Stockholm, Sweden.;Ctr Mol Med, Stockholm, Sweden..
    Engblom, Camilla
    Karolinska Inst, Dept Cell & Mol Biol, Stockholm, Sweden..
    Gagliani, Nicola
    Karolinska Inst & Univ Hosp, Dept Med Solna, Div Immunol & Allergy, Stockholm, Sweden.;Ctr Mol Med, Stockholm, Sweden.;Univ Med Ctr Hamburg Eppendorf, Dept Med, Hamburg, Germany.;Univ Med Ctr Hamburg Eppendorf, Dept Gen Visceral & Thorac Surg, Hamburg, Germany..
    Saez-Rodriguez, Julio
    Heidelberg Univ, Fac Med, Heidelberg, Germany.;Heidelberg Univ Hosp, Inst Computat Biomed, Bioquant, Heidelberg, Germany..
    Lundeberg, Joakim
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Villablanca, Eduardo J.
    Karolinska Inst & Univ Hosp, Dept Med Solna, Div Immunol & Allergy, Stockholm, Sweden.;Ctr Mol Med, Stockholm, Sweden..
    The spatial transcriptomic landscape of the healing mouse intestine following damage2022In: Nature Communications, E-ISSN 2041-1723, Vol. 13, no 1, article id 828Article in journal (Refereed)
    Abstract [en]

    The colon is comprised of specialized cells that interact with each other to function, however, the molecular regionalization of the colon is incompletely understood. Here, the authors use spatial transcriptomics to generate a publicly available resource defining the transcriptomic regionalization of the colon during steady state and mucosal healing. The intestinal barrier is composed of a complex cell network defining highly compartmentalized and specialized structures. Here, we use spatial transcriptomics to define how the transcriptomic landscape is spatially organized in the steady state and healing murine colon. At steady state conditions, we demonstrate a previously unappreciated molecular regionalization of the colon, which dramatically changes during mucosal healing. Here, we identified spatially-organized transcriptional programs defining compartmentalized mucosal healing, and regions with dominant wired pathways. Furthermore, we showed that decreased p53 activation defined areas with increased presence of proliferating epithelial stem cells. Finally, we mapped transcriptomics modules associated with human diseases demonstrating the translational potential of our dataset. Overall, we provide a publicly available resource defining principles of transcriptomic regionalization of the colon during mucosal healing and a framework to develop and progress further hypotheses.

  • 147.
    Park, Tae-Eun
    et al.
    Harvard Univ, Wyss Inst Biol Inspired Engn, Boston, MA 02115 USA.;UNIST, UNIST Gil 50, Ulsan 44919, South Korea..
    Mustafaoglu, Nur
    Harvard Univ, Wyss Inst Biol Inspired Engn, Boston, MA 02115 USA..
    Herland, Anna
    KTH, School of Electrical Engineering and Computer Science (EECS), Intelligent systems, Micro and Nanosystems. Harvard Univ, USA ;Karolinska Inst, Swedish Med Nanosci Ctr, Dept Neurosci, Stockholm, Sweden..
    Hasselkus, Ryan
    Harvard Univ, Wyss Inst Biol Inspired Engn, Boston, MA 02115 USA..
    Mannix, Robert
    Harvard Univ, Wyss Inst Biol Inspired Engn, Boston, MA 02115 USA.;Harvard Med Sch, Boston, MA 02115 USA.;Boston Childrens Hosp, Vasc Biol Program, Boston, MA 02115 USA.;Boston Childrens Hosp, Dept Surg, Boston, MA 02115 USA..
    FitzGerald, Edward A.
    Harvard Univ, Wyss Inst Biol Inspired Engn, Boston, MA 02115 USA..
    Prantil-Baun, Rachelle
    Harvard Univ, Wyss Inst Biol Inspired Engn, Boston, MA 02115 USA..
    Watters, Alexander
    Harvard Univ, Wyss Inst Biol Inspired Engn, Boston, MA 02115 USA..
    Henry, Olivier
    Harvard Univ, Wyss Inst Biol Inspired Engn, Boston, MA 02115 USA..
    Benz, Maximilian
    Harvard Univ, Wyss Inst Biol Inspired Engn, Boston, MA 02115 USA..
    Sanchez, Henry
    Harvard Univ, Wyss Inst Biol Inspired Engn, Boston, MA 02115 USA..
    McCrea, Heather J.
    Boston Childrens Hosp, Dept Neurosurg, Boston, MA 02115 USA.;Harvard Med Sch, Boston, MA 02115 USA..
    Goumnerova, Liliana Christova
    Boston Childrens Hosp, Dept Neurosurg, Boston, MA 02115 USA.;Harvard Med Sch, Boston, MA 02115 USA..
    Song, Hannah W.
    Univ Wisconsin, Dept Chem & Biol Engn, Madison, WI 53706 USA..
    Palecek, Sean P.
    Univ Wisconsin, Dept Chem & Biol Engn, Madison, WI 53706 USA..
    Shusta, Eric
    Univ Wisconsin, Dept Chem & Biol Engn, Madison, WI 53706 USA..
    Ingber, Donald E.
    Harvard Univ, Wyss Inst Biol Inspired Engn, Boston, MA 02115 USA.;Harvard Med Sch, Boston, MA 02115 USA.;Harvard Univ, Harvard John A Paulson Sch Engn & Appl Sci, Cambridge, MA 02138 USA.;Boston Childrens Hosp, Vasc Biol Program, Boston, MA 02115 USA.;Boston Childrens Hosp, Dept Surg, Boston, MA 02115 USA..
    Hypoxia-enhanced Blood-Brain Barrier Chip recapitulates human barrier function and shuttling of drugs and antibodies2019In: Nature Communications, E-ISSN 2041-1723, Vol. 10, article id 2621Article in journal (Refereed)
    Abstract [en]

    The high selectivity of the human blood-brain barrier (BBB) restricts delivery of many pharmaceuticals and therapeutic antibodies to the central nervous system. Here, we describe an in vitro microfluidic organ-on-a-chip BBB model lined by induced pluripotent stem cell-derived human brain microvascular endothelium interfaced with primary human brain astrocytes and pericytes that recapitulates the high level of barrier function of the in vivo human BBB for at least one week in culture. The endothelium expresses high levels of tight junction proteins and functional efflux pumps, and it displays selective transcytosis of peptides and antibodies previously observed in vivo. Increased barrier functionality was accomplished using a developmentally-inspired induction protocol that includes a period of differentiation under hypoxic conditions. This enhanced BBB Chip may therefore represent a new in vitro tool for development and validation of delivery systems that transport drugs and therapeutic antibodies across the human BBB.

  • 148.
    Pathak, Anuj
    et al.
    Karolinska Inst, Dept Microbiol Tumor & Cell Biol, SE-17177 Stockholm, Sweden..
    Bergstrand, Jan
    KTH, School of Engineering Sciences (SCI), Applied Physics, Quantum and Biophotonics.
    Sender, Vicky
    Karolinska Inst, Dept Microbiol Tumor & Cell Biol, SE-17177 Stockholm, Sweden..
    Spelmink, Laura
    Karolinska Inst, Dept Microbiol Tumor & Cell Biol, SE-17177 Stockholm, Sweden..
    Aschtgen, Marie-Stephanie
    Karolinska Inst, Dept Microbiol Tumor & Cell Biol, SE-17177 Stockholm, Sweden..
    Muschiol, Sandra
    Karolinska Inst, Dept Microbiol Tumor & Cell Biol, SE-17177 Stockholm, Sweden..
    Widengren, Jerker
    KTH, School of Engineering Sciences (SCI), Applied Physics, Quantum and Biophotonics.
    Henriques-Normark, Birgitta
    Karolinska Inst, Dept Microbiol Tumor & Cell Biol, SE-17177 Stockholm, Sweden.;Nanyang Technol Univ, Lee Kong Chian Sch Med LKC, Singapore 639798, Singapore.;Nanyang Technol Univ, Singapore Ctr Environm Life Sci Engn SCELSE, Singapore 639798, Singapore.;Karolinska Univ Hosp, Dept Clin Microbiol, SE-17176 Stockholm, Sweden..
    Factor H binding proteins protect division septa on encapsulated Streptococcus pneumoniae against complement C3b deposition and amplification2018In: Nature Communications, E-ISSN 2041-1723, Vol. 9, article id 3398Article in journal (Refereed)
    Abstract [en]

    Streptococcus pneumoniae evades C3-mediated opsonization and effector functions by expressing an immuno-protective polysaccharide capsule and Factor H (FH)-binding proteins. Here we use super-resolution microscopy, mutants and functional analysis to show how these two defense mechanisms are functionally and spatially coordinated on the bacterial cell surface. We show that the pneumococcal capsule is less abundant at the cell wall septum, providing C3/C3b entry to underlying nucleophilic targets. Evasion of C3b deposition at division septa and lateral amplification underneath the capsule requires localization of the FH-binding protein PspC at division sites. Most pneumococcal strains have one PspC protein, but successful lineages in colonization and disease may have two, PspC1 and PspC2, that we show affect virulence differently. We find that spatial localization of these FH-recruiting proteins relative to division septa and capsular layer is instrumental for pneumococci to resist complement-mediated opsonophagocytosis, formation of membrane-attack complexes, and for the function as adhesins.

  • 149.
    Paulraj, Thomas
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology.
    Wennmalm, Stefan
    KTH, School of Engineering Sciences (SCI), Applied Physics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Wieland, D. C.F.
    Riazanova, Anastasia
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology.
    Dèdinaitè, Andra A.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Surface and Corrosion Science. RISE Research Institutes of Sweden, Division of Bioscience and Materials, Stockholm, 114 86, Sweden.
    Günther Pomorski, T.
    Cárdenas, M.
    Svagan, Anna Justina
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology.
    Primary cell wall inspired micro containers as a step towards a synthetic plant cell2020In: Nature Communications, E-ISSN 2041-1723, Vol. 11, no 1, article id 958Article in journal (Refereed)
    Abstract [en]

    The structural integrity of living plant cells heavily relies on the plant cell wall containing a nanofibrous cellulose skeleton. Hence, if synthetic plant cells consist of such a cell wall, they would allow for manipulation into more complex synthetic plant structures. Herein, we have overcome the fundamental difficulties associated with assembling lipid vesicles with cellulosic nanofibers (CNFs). We prepare plantosomes with an outer shell of CNF and pectin, and beneath this, a thin layer of lipids (oleic acid and phospholipids) that surrounds a water core. By exploiting the phase behavior of the lipids, regulated by pH and Mg2+ ions, we form vesicle-crowded interiors that change the outer dimension of the plantosomes, mimicking the expansion in real plant cells during, e.g., growth. The internal pressure enables growth of lipid tubules through the plantosome cell wall, which paves the way to the development of hierarchical plant structures and advanced synthetic plant cell mimics.

  • 150.
    Peng, Bo
    et al.
    Univ Cambridge, Cavendish Lab, TCM Grp, JJ Thomson Ave, Cambridge CB3 0HE, England..
    Bouhon, Adrien
    Nordita SU; Stockholm Univ, Hannes Alfvens Vag 12, SE-10691 Stockholm, Sweden.
    Monserrat, Bartomeu
    Univ Cambridge, Cavendish Lab, TCM Grp, JJ Thomson Ave, Cambridge CB3 0HE, England.;Univ Cambridge, Dept Mat Sci & Met, 27 Charles Babbage Rd, Cambridge CB3 0FS, England..
    Slager, Robert-Jan
    Univ Cambridge, Cavendish Lab, TCM Grp, JJ Thomson Ave, Cambridge CB3 0HE, England..
    Phonons as a platform for non-Abelian braiding and its manifestation in layered silicates2022In: Nature Communications, E-ISSN 2041-1723, Vol. 13, no 1, article id 423Article in journal (Refereed)
    Abstract [en]

    Multi-gap topology is a new avenue in topological phases of matter but it remains difficult to verify in real materials. Here, the authors predict multi-gap topologies and associated phase transitions driven by braiding processes in the phonon spectra of monolayer silicates, providing clear signatures for experimental verification. Topological phases of matter have revolutionised the fundamental understanding of band theory and hold great promise for next-generation technologies such as low-power electronics or quantum computers. Single-gap topologies have been extensively explored, and a large number of materials have been theoretically proposed and experimentally observed. These ideas have recently been extended to multi-gap topologies with band nodes that carry non-Abelian charges, characterised by invariants that arise by the momentum space braiding of such nodes. However, the constraints placed by the Fermi-Dirac distribution to electronic systems have so far prevented the experimental observation of multi-gap topologies in real materials. Here, we show that multi-gap topologies and the accompanying phase transitions driven by braiding processes can be readily observed in the bosonic phonon spectra of known monolayer silicates. The associated braiding process can be controlled by means of an electric field and epitaxial strain, and involves, for the first time, more than three bands. Finally, we propose that the band inversion processes at the Gamma point can be tracked by following the evolution of the Raman spectrum, providing a clear signature for the experimental verification of the band inversion accompanied by the braiding process.

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