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  • 1. Aben, Ralf C. H.
    et al.
    Barros, Nathan
    van Donk, Ellen
    Frenken, Thijs
    Hilt, Sabine
    Kazanjian, Garabet
    Lamers, Leon P. M.
    Peeters, Edwin T. H. M.
    Roelofs, Jan G. M.
    de Senerpont Domis, Lisette N.
    Stephan, Susanne
    Velthuis, Mandy
    Van de Waal, Dedmer B.
    Wik, Martin
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Thornton, Brett F.
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Wilkinson, Jeremy
    DelSontro, Tonya
    Kosten, Sarian
    Cross continental increase in methane ebullition under climate change2017In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 8, article id 1682Article in journal (Refereed)
    Abstract [en]

    Methane (CH4) strongly contributes to observed global warming. As natural CH4 emissions mainly originate from wet ecosystems, it is important to unravel how climate change may affect these emissions. This is especially true for ebullition (bubble flux from sediments), a pathway that has long been underestimated but generally dominates emissions. Here we show a remarkably strong relationship between CH4 ebullition and temperature across a wide range of freshwater ecosystems on different continents using multi-seasonal CH4 ebullition data from the literature. As these temperature-ebullition relationships may have been affected by seasonal variation in organic matter availability, we also conducted a controlled year-round mesocosm experiment. Here 4 degrees C warming led to 51% higher total annual CH4 ebullition, while diffusion was not affected. Our combined findings suggest that global warming will strongly enhance freshwater CH4 emissions through a disproportional increase in ebullition (6-20% per 1 degrees C increase), contributing to global warming.

  • 2.
    Abreu-Vieira, Gustavo
    et al.
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Fischer, Alexander W.
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute. University of Hamburg, Germany.
    Mattsson, Charlotte
    de Jong, Jasper M. A.
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Shabalina, Irina G.
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Ryden, Mikael
    Laurencikiene, Jurga
    Arner, Peter
    Cannon, Barbara
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Nedergaard, Jan
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Petrovic, Natasa
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Cidea improves the metabolic profile through expansion of adipose tissue2015In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 6, article id 7433Article in journal (Refereed)
    Abstract [en]

    In humans, Cidea (cell death-inducing DNA fragmentation factor alpha-like effector A) is highly but variably expressed in white fat, and expression correlates with metabolic health. Here we generate transgenic mice expressing human Cidea in adipose tissues (aP2-hCidea mice) and show that Cidea is mechanistically associated with a robust increase in adipose tissue expandability. Under humanized conditions (thermoneutrality, mature age and prolonged exposure to high-fat diet), aP2-hCidea mice develop a much more pronounced obesity than their wild-type littermates. Remarkably, the malfunctioning of visceral fat normally caused by massive obesity is fully overcome-perilipin 1 and Akt expression are preserved, tissue degradation is prevented, macrophage accumulation is decreased and adiponectin expression remains high. Importantly, the aP2-hCidea mice display enhanced insulin sensitivity. Our data establish a functional role for Cidea and suggest that, in humans, the association between Cidea levels in white fat and metabolic health is not only correlative but also causative.

  • 3. Adamczyk, Bartosz
    et al.
    Sietio, Outi-Maaria
    Strakoya, Petra
    Prommer, Judith
    Wild, Birgit
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry. University of Vienna, Austria; University of Gothenburg, Sweden.
    Hagner, Marleena
    Pihlatie, Mari
    Fritze, Hannu
    Richter, Andreas
    Heinonsalo, Jussi
    Plant roots increase both decomposition and stable organic matter formation in boreal forest soil2019In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 10, article id 3982Article in journal (Refereed)
    Abstract [en]

    Boreal forests are ecosystems with low nitrogen (N) availability that store globally significant amounts of carbon (C), mainly in plant biomass and soil organic matter (SOM). Although crucial for future climate change predictions, the mechanisms controlling boreal C and N pools are not well understood. Here, using a three-year field experiment, we compare SOM decomposition and stabilization in the presence of roots, with exclusion of roots but presence of fungal hyphae and with exclusion of both roots and fungal hyphae. Roots accelerate SOM decomposition compared to the root exclusion treatments, but also promote a different soil N economy with higher concentrations of organic soil N compared to inorganic soil N accompanied with the build-up of stable SOM-N. In contrast, root exclusion leads to an inorganic soil N economy (i.e., high level of inorganic N) with reduced stable SOM-N buildup. Based on our findings, we provide a framework on how plant roots affect SOM decomposition and stabilization.

  • 4. Ahmadi, M.
    et al.
    Alves, B. X. R.
    Baker, C. J.
    Bertsche, W.
    Butler, E.
    Capra, A.
    Carruth, C.
    Cesar, C. L.
    Charlton, M.
    Cohen, S.
    Collister, R.
    Eriksson, S.
    Evans, A.
    Evetts, N.
    Fajans, J.
    Friesen, T.
    Fujiwara, M. C.
    Gill, D. R.
    Gutierrez, A.
    Hangst, J. S.
    Hardy, W. N.
    Hayden, M. E.
    Isaac, C. A.
    Ishida, A.
    Johnson, M. A.
    Jones, S. A.
    Jonsell, Svante
    Stockholm University, Faculty of Science, Department of Physics.
    Kurchaninov, L.
    Madsen, N.
    Mathers, M.
    Maxwell, D.
    McKenna, J. T. K.
    Menary, S.
    Michan, J. M.
    Momose, T.
    Munich, J. J.
    Nolan, P.
    Olchanski, K.
    Olin, A.
    Pusa, P.
    Rasmussen, C. Ø.
    Robicheaux, F.
    Sacramento, R. L.
    Sameed, M.
    Sarid, E.
    Silveira, D. M.
    Stracka, S.
    Stutter, G.
    So, C.
    Tharp, T. D.
    Thompson, J. E.
    Thompson, R. I.
    van der Werf, D. P.
    Wurtele, J. S.
    Antihydrogen accumulation for fundamental symmetry tests2017In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 8, article id 681Article in journal (Refereed)
    Abstract [en]

    Antihydrogen, a positron bound to an antiproton, is the simplest anti-atom. Its structure and properties are expected to mirror those of the hydrogen atom. Prospects for precision comparisons of the two, as tests of fundamental symmetries, are driving a vibrant programme of research. In this regard, a limiting factor in most experiments is the availability of large numbers of cold ground state antihydrogen atoms. Here, we describe how an improved synthesis process results in a maximum rate of 10.5 +/- 0.6 atoms trapped and detected per cycle, corresponding to more than an order of magnitude improvement over previous work. Additionally, we demonstrate how detailed control of electron, positron and antiproton plasmas enables repeated formation and trapping of antihydrogen atoms, with the simultaneous retention of atoms produced in previous cycles. We report a record of 54 detected annihilation events from a single release of the trapped anti-atoms accumulated from five consecutive cycles.

  • 5. Ahola, Virpi
    et al.
    Lehtonen, Rainer
    Somervuo, Panu
    Salmela, Leena
    Koskinen, Patrik
    Rastas, Pasi
    Valimaki, Niko
    Paulin, Lars
    Kvist, Jouni
    Wahlberg, Niklas
    Tanskanen, Jaakko
    Hornett, Emily A.
    Ferguson, Laura C.
    Luo, Shiqi
    Cao, Zijuan
    de Jong, Maaike A.
    Duplouy, Anne
    Smolander, Olli-Pekka
    Vogel, Heiko
    McCoy, Rajiv C.
    Qian, Kui
    Chong, Wong Swee
    Zhang, Qin
    Ahmad, Freed
    Haukka, Jani K.
    Joshi, Aruj
    Salojarvi, Jarkko
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, Department of Zoology.
    Grosse-Wilde, Ewald
    Hughes, Daniel
    Katainen, Riku
    Pitkanen, Esa
    Ylinen, Johannes
    Waterhouse, Robert M.
    Turunen, Mikko
    Vaharautio, Anna
    Ojanen, Sami P.
    Schulman, Alan H.
    Taipale, Minna
    Lawson, Daniel
    Ukkonen, Esko
    Makinen, Veli
    Goldsmith, Marian R.
    Holm, Liisa
    Auvinen, Petri
    Frilander, Mikko J.
    Hanski, Ilkka
    The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera2014In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 5, p. 4737-Article in journal (Refereed)
    Abstract [en]

    Previous studies have reported that chromosome synteny in Lepidoptera has been well conserved, yet the number of haploid chromosomes varies widely from 5 to 223. Here we report the genome (393 Mb) of the Glanville fritillary butterfly (Melitaea cinxia; Nymphalidae), a widely recognized model species in metapopulation biology and eco-evolutionary research, which has the putative ancestral karyotype of n = 31. Using a phylogenetic analyses of Nymphalidae and of other Lepidoptera, combined with orthologue-level comparisons of chromosomes, we conclude that the ancestral lepidopteran karyotype has been n = 31 for at least 140 My. We show that fusion chromosomes have retained the ancestral chromosome segments and very few rearrangements have occurred across the fusion sites. The same, shortest ancestral chromosomes have independently participated in fusion events in species with smaller karyotypes. The short chromosomes have higher rearrangement rate than long ones. These characteristics highlight distinctive features of the evolutionary dynamics of butterflies and moths.

  • 6. Amole, C.
    et al.
    Ashkezari, M. D.
    Baquero-Ruiz, M.
    Bertsche, W.
    Butler, E.
    Capra, A.
    Cesar, C. L.
    Charlton, M.
    Eriksson, S.
    Fajans, J.
    Friesen, T.
    Fujiwara, M. C.
    Gill, D. R.
    Gutierrez, A.
    Hangst, J. S.
    Hardy, W. N.
    Hayden, M. E.
    Isaac, C. A.
    Jonsell, Svante
    Stockholm University, Faculty of Science, Department of Physics.
    Kurchaninov, L.
    Little, A.
    Madsen, N.
    McKenna, J. T. K.
    Menary, S.
    Napoli, S. C.
    Nolan, P.
    Olchanski, K.
    Olin, A.
    Povilus, A.
    Pusa, P.
    Rasmussen, C. O.
    Robicheaux, F.
    Sarid, E.
    Silveira, D. M.
    So, C.
    Tharp, T. D.
    Thompson, R. I.
    van der Werf, D. P.
    Vendeiro, Z.
    Wurtele, J. S.
    Zhmoginov, A. I.
    Charman, A. E.
    An experimental limit on the charge of antihydrogen2014In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 5, p. 3955-Article in journal (Refereed)
    Abstract [en]

    The properties of antihydrogen are expected to be identical to those of hydrogen, and any differences would constitute a profound challenge to the fundamental theories of physics. The most commonly discussed antiatom- based tests of these theories are searches for antihydrogen- hydrogen spectral differences (tests of CPT (charge- parity- time) invariance) or gravitational differences (tests of the weak equivalence principle). Here we, the ALPHA Collaboration, report a different and somewhat unusual test of CPT and of quantum anomaly cancellation. A retrospective analysis of the influence of electric fields on antihydrogen atoms released from the ALPHA trap finds a mean axial deflection of 4.1 +/- 3.4mm for an average axial electric field of 0.51Vmm1. Combined with extensive numerical modelling, this measurement leads to a bound on the charge Qe of antihydrogen of Q (+/- 1.3 +/- 1.1 +/- 0.4)10 8. Here, e is the unit charge, and the errors are from statistics and systematic effects.

  • 7. Aragão, Luiz E. O. C.
    et al.
    Anderson, Liana O.
    Fonseca, Marisa G.
    Rosan, Thais M.
    Vedovato, Laura B.
    Wagner, Fabien H.
    Silva, Camila V. J.
    Silva Junior, Celso H. L.
    Arai, Egidio
    Aguiar, Ana P.
    Stockholm University, Faculty of Science, Stockholm Resilience Centre. National Institute for Space Research, Brazil.
    Barlow, Jos
    Berenguer, Erika
    Deeter, Merritt N.
    Domingues, Lucas G.
    Gatti, Luciana
    Gloor, Manuel
    Malhi, Yadvinder
    Marengo, Jose A.
    Miller, John B.
    Phillips, Oliver L.
    Saatchi, Sassan
    21st Century drought-related fires counteract the decline of Amazon deforestation carbon emissions2018In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, article id 536Article in journal (Refereed)
    Abstract [en]

    Tropical carbon emissions are largely derived from direct forest clearing processes. Yet, emissions from drought-induced forest fires are, usually, not included in national-level carbon emission inventories. Here we examine Brazilian Amazon drought impacts on fire incidence and associated forest fire carbon emissions over the period 2003-2015. We show that despite a 76% decline in deforestation rates over the past 13 years, fire incidence increased by 36% during the 2015 drought compared to the preceding 12 years. The 2015 drought had the largest ever ratio of active fire counts to deforestation, with active fires occurring over an area of 799,293 km(2). Gross emissions from forest fires (989 +/- 504 Tg CO2 year(-1)) alone are more than half as great as those from old-growth forest deforestation during drought years. We conclude that carbon emission inventories intended for accounting and developing policies need to take account of substantial forest fire emissions not associated to the deforestation process.

  • 8. Artiglia, Luca
    et al.
    Edebeli, Jacinta
    Orlando, Fabrizio
    Chen, Shuzhen
    Lee, Ming-Tao
    Stockholm University, Faculty of Science, Department of Physics. Paul Scherrer Institut, Switzerland.
    Arroyo, Pablo Corral
    Gilgen, Anina
    Bartels-Rausch, Thorsten
    Kleibert, Armin
    Vazdar, Mario
    Carignano, Marcelo Andres
    Francisco, Joseph S.
    Shepson, Paul B.
    Gladich, Ivan
    Ammann, Markus
    A surface-stabilized ozonide triggers bromide oxidation at the aqueous solution-vapour interface2017In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 8, article id 700Article in journal (Refereed)
    Abstract [en]

    Oxidation of bromide in aqueous environments initiates the formation of molecular halogen compounds, which is important for the global tropospheric ozone budget. In the aqueous bulk, oxidation of bromide by ozone involves a [Br center dot OOO-] complex as intermediate. Here we report liquid jet X-ray photoelectron spectroscopy measurements that provide direct experimental evidence for the ozonide and establish its propensity for the solution-vapour interface. Theoretical calculations support these findings, showing that water stabilizes the ozonide and lowers the energy of the transition state at neutral pH. Kinetic experiments confirm the dominance of the heterogeneous oxidation route established by this precursor at low, atmospherically relevant ozone concentrations. Taken together, our results provide a strong case of different reaction kinetics and mechanisms of reactions occurring at the aqueous phase-vapour interface compared with the bulk aqueous phase.

  • 9.
    Auffret, Alistair G.
    et al.
    Stockholm University, Faculty of Science, Department of Physical Geography. Swedish University of Agricultural Sciences, Sweden; University of York, UK.
    Kimberley, Adam
    Stockholm University, Faculty of Science, Department of Physical Geography.
    Plue, Jan
    Stockholm University, Faculty of Science, Department of Physical Geography. Södertörn University, Sweden.
    Waldén, Emelie
    Stockholm University, Faculty of Science, Department of Physical Geography.
    Super-regional land-use change and effects on the grassland specialist flora2018In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, article id 3464Article in journal (Refereed)
    Abstract [en]

    Habitat loss through land-use change is the most pressing threat to biodiversity worldwide. European semi-natural grasslands have suffered an ongoing decline since the early twentieth century, but we have limited knowledge of how grassland loss has affected biodiversity across large spatial scales. We quantify land-use change over 50-70 years across a 175,000 km(2) super-region in southern Sweden, identifying a widespread loss of open cover and a homogenisation of landscape structure, although these patterns vary considerably depending on the historical composition of the landscape. Analysing species inventories from 46,796 semi-natural grasslands, our results indicate that habitat loss and degradation have resulted in a decline in grassland specialist plant species. Local factors are the best predictors of specialist richness, but the historical landscape predicts present-day richness better than the contemporary landscape. This supports the widespread existence of time-lagged biodiversity responses, indicating that further species losses could occur in the future.

  • 10. Barfuss, Wolfram
    et al.
    Donges, Jonathan F.
    Stockholm University, Faculty of Science, Stockholm Resilience Centre. Potsdam Institute for Climate Impact Research, Germany.
    Lade, Steven J.
    Stockholm University, Faculty of Science, Stockholm Resilience Centre. The Australian National University, Australia.
    Kurths, Jürgen
    When optimization for governing human-environment tipping elements is neither sustainable nor safe2018In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, article id 2354Article in journal (Refereed)
    Abstract [en]

    Optimizing economic welfare in environmental governance has been criticized for delivering short-term gains at the expense of long-term environmental degradation. Different from economic optimization, the concepts of sustainability and the more recent safe operating space have been used to derive policies in environmental governance. However, a formal comparison between these three policy paradigms is still missing, leaving policy makers uncertain which paradigm to apply. Here, we develop a better understanding of their interrelationships, using a stylized model of human-environment tipping elements. We find that no paradigm guarantees fulfilling requirements imposed by another paradigm and derive simple heuristics for the conditions under which these trade-offs occur. We show that the absence of such a master paradigm is of special relevance for governing real-world tipping systems such as climate, fisheries, and farming, which may reside in a parameter regime where economic optimization is neither sustainable nor safe.

  • 11. Barnes, Michele L.
    et al.
    Bodin, Örjan
    Stockholm University, Faculty of Science, Stockholm Resilience Centre.
    McClanahan, Tim R.
    Kittinger, John N.
    Hoey, Andrew S.
    Gaoue, Orou G.
    Graham, Nicholas A. J.
    Social-ecological alignment and ecological conditions in coral reefs2019In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 10, article id 2039Article in journal (Refereed)
    Abstract [en]

    Complex social-ecological interactions underpin many environmental problems. To help capture this complexity, we advance an interdisciplinary network modeling framework to identify important relationships between people and nature that can influence environmental conditions. Drawing on comprehensive social and ecological data from five coral reef fishing communities in Kenya; including interviews with 648 fishers, underwater visual census data of reef ecosystem condition, and time-series landings data; we show that positive ecological conditions are associated with 'social-ecological network closure' - i.e., fully linked and thus closed network structures between social actors and ecological resources. Our results suggest that when fishers facing common dilemmas form cooperative communication ties with direct resource competitors, they may achieve positive gains in reef fish biomass and functional richness. Our work provides key empirical insight to a growing body of research on social-ecological alignment, and helps to advance an integrative framework that can be applied empirically in different social-ecological contexts.

  • 12. Bassett, Andrew R.
    et al.
    Azzam, Ghows
    Wheatley, Lucy
    Tibbit, Charlotte
    Rajakumar, Timothy
    McGowan, Simon
    Stanger, Nathan
    Ewels, Philip Andrew
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Taylor, Stephen
    Ponting, Chris P.
    Liu, Ji-Long
    Sauka-Spengler, Tatjana
    Fulga, Tudor A.
    Understanding functional miRNA-target interactions in vivo by site-specific genome engineering2014In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 5, p. 4640-Article in journal (Refereed)
    Abstract [en]

    MicroRNA (miRNA) target recognition is largely dictated by short 'seed' sequences, and single miRNAs therefore have the potential to regulate a large number of genes. Understanding the contribution of specific miRNA-target interactions to the regulation of biological processes in vivo remains challenging. Here we use transcription activator-like effector nuclease (TALEN) and clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 technologies to interrogate the functional relevance of predicted miRNA response elements (MREs) to post-transcriptional silencing in zebrafish and Drosophila. We also demonstrate an effective strategy that uses CRISPR-mediated homology-directed repair with short oligonucleotide donors for the assessment of MRE activity in human cells. These methods facilitate analysis of the direct phenotypic consequences resulting from blocking specific miRNA-MRE interactions at any point during development.

  • 13. Bañó-Polo, Manuel
    et al.
    Baeza-Delgado, Carlos
    Tamborero, Silvia
    Hazel, Anthony
    Grau, Brayan
    Nilsson, IngMarie
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Whitley, Paul
    Gumbart, James C.
    von Heijne, Gunnar
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Mingarro, Ismael
    Transmembrane but not soluble helices fold inside the ribosome tunnel2018In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, article id 5246Article in journal (Refereed)
    Abstract [en]

    Integral membrane proteins are assembled into the ER membrane via a continuous ribosome-translocon channel. The hydrophobicity and thickness of the core of the membrane bilayer leads to the expectation that transmembrane (TM) segments minimize the cost of harbouring polar polypeptide backbones by adopting a regular pattern of hydrogen bonds to form a-helices before integration. Co-translational folding of nascent chains into an a-helical conformation in the ribosomal tunnel has been demonstrated previously, but the features governing this folding are not well understood. In particular, little is known about what features influence the propensity to acquire a-helical structure in the ribosome. Using in vitro translation of truncated nascent chains trapped within the ribosome tunnel and molecular dynamics simulations, we show that folding in the ribosome is attained for TM helices but not for soluble helices, presumably facilitating SRP (signal recognition particle) recognition and/or a favourable conformation for membrane integration upon translocon entry.

  • 14. Bergkvist, Johanna
    et al.
    Klawonn, Isabell
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Whitehouse, Martin J.
    Stockholm University, Faculty of Science, Department of Geological Sciences. Swedish Museum of Natural History, Sweden.
    Lavik, Gaute
    Brüchert, Volker
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Ploug, Helle
    Turbulence simultaneously stimulates small-and large-scale CO2 sequestration by chain-forming diatoms in the sea2018In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, article id 3046Article in journal (Refereed)
    Abstract [en]

    Chain-forming diatoms are key CO2-fixing organisms in the ocean. Under turbulent conditions they form fast-sinking aggregates that are exported from the upper sunlit ocean to the ocean interior. A decade-old paradigm states that primary production in chain-forming diatoms is stimulated by turbulence. Yet, direct measurements of cell-specific primary production in individual field populations of chain-forming diatoms are poorly documented. Here we measured cell-specific carbon, nitrate and ammonium assimilation in two field populations of chain-forming diatoms (Skeletonema and Chaetoceros) at low-nutrient concentrations under still conditions and turbulent shear using secondary ion mass spectrometry combined with stable isotopic tracers and compared our data with those predicted by mass transfer theory. Turbulent shear significantly increases cell-specific C assimilation compared to still conditions in the cells/chains that also form fast-sinking, aggregates rich in carbon and ammonium. Thus, turbulence simultaneously stimulates small-scale biological CO2 assimilation and large-scale biogeochemical C and N cycles in the ocean.

  • 15. Berglund, Emelie
    et al.
    Maaskola, Jonas
    Schultz, Niklas
    Friedrich, Stefanie
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Marklund, Maja
    Bergenstråhle, Joseph
    Tarish, Firas
    Tanoglidi, Anna
    Vickovic, Sanja
    Larsson, Ludvig
    Salmén, Fredrik
    Ogris, Christoph
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Wallenborg, Karolina
    Lagergren, Jens
    Ståhl, Patrik
    Sonnhammer, Erik
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Helleday, Thomas
    Lundeberg, Joakim
    Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity2018In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, article id 2419Article in journal (Refereed)
    Abstract [en]

    Intra-tumor heterogeneity is one of the biggest challenges in cancer treatment today. Here we investigate tissue-wide gene expression heterogeneity throughout a multifocal prostate cancer using the spatial transcriptomics (ST) technology. Utilizing a novel approach for deconvolution, we analyze the transcriptomes of nearly 6750 tissue regions and extract distinct expression profiles for the different tissue components, such as stroma, normal and PIN glands, immune cells and cancer. We distinguish healthy and diseased areas and thereby provide insight into gene expression changes during the progression of prostate cancer. Compared to pathologist annotations, we delineate the extent of cancer foci more accurately, interestingly without link to histological changes. We identify gene expression gradients in stroma adjacent to tumor regions that allow for re-stratification of the tumor microenvironment. The establishment of these profiles is the first step towards an unbiased view of prostate cancer and can serve as a dictionary for future studies.

  • 16.
    Berntsson, Ronnie P. A.
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Peng, Lisheng
    Dong, Min
    Stenmark, Pål
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Structure of dual receptor binding to botulinum neurotoxin B2013In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 4, p. 2058-Article in journal (Refereed)
    Abstract [en]

    Botulinum neurotoxins are highly toxic, and bind two receptors to achieve their high affinity and specificity for neurons. Here we present the first structure of a botulinum neurotoxin bound to both its receptors. We determine the 2.3-angstrom structure of a ternary complex of botulinum neurotoxin type B bound to both its protein receptor synaptotagmin II and its ganglioside receptor GD1a. We show that there is no direct contact between the two receptors, and that the binding affinity towards synaptotagmin II is not influenced by the presence of GD1a. The interactions of botulinum neurotoxin type B with the sialic acid 5 moiety of GD1a are important for the ganglioside selectivity. The structure demonstrates that the protein receptor and the ganglioside receptor occupy nearby but separate binding sites, thus providing two independent anchoring points.

  • 17. Biskaborn, Boris K.
    et al.
    Smith, Sharon L.
    Noetzli, Jeannette
    Matthes, Heidrun
    Vieira, Goncalo
    Streletskiy, Dmitry A.
    Schoeneich, Philippe
    Romanovsky, Vladimir E.
    Lewkowicz, Antoni G.
    Abramov, Andrey
    Allard, Michel
    Boike, Julia
    Cable, William L.
    Christiansen, Hanne H.
    Delaloye, Reynald
    Diekmann, Bernhard
    Drozdov, Dmitry
    Etzelmüller, Bernd
    Grosse, Guido
    Guglielmin, Mauro
    Ingeman-Nielsen, Thomas
    Isaksen, Ketil
    Ishikawa, Mamoru
    Johansson, Margareta
    Johannsson, Halldor
    Joo, Anseok
    Kaverin, Dmitry
    Kholodov, Alexander
    Konstantinov, Pavel
    Kröger, Tim
    Lambiel, Christophe
    Lanckman, Jean-Pierre
    Luo, Dongliang
    Malkova, Galina
    Meiklejohn, Ian
    Moskalenko, Natalia
    Oliva, Marc
    Phillips, Marcia
    Ramos, Miguel
    Sannel, A. Britta K.
    Stockholm University, Faculty of Science, Department of Physical Geography.
    Sergeev, Dmitrii
    Seybold, Cathy
    Skryabin, Pavel
    Vasiliev, Alexander
    Wu, Qingbai
    Yoshikawa, Kenji
    Zheleznyak, Mikhail
    Lantuit, Hugues
    Permafrost is warming at a global scale2019In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 10, article id 264Article in journal (Refereed)
    Abstract [en]

    Permafrost warming has the potential to amplify global climate change, because when frozen sediments thaw it unlocks soil organic carbon. Yet to date, no globally consistent assessment of permafrost temperature change has been compiled. Here we use a global data set of permafrost temperature time series from the Global Terrestrial Network for Permafrost to evaluate temperature change across permafrost regions for the period since the International Polar Year (2007-2009). During the reference decade between 2007 and 2016, ground temperature near the depth of zero annual amplitude in the continuous permafrost zone increased by 0.39 +/- 0.15 degrees C. Over the same period, discontinuous permafrost warmed by 0.20 +/- 0.10 degrees C. Permafrost in mountains warmed by 0.19 +/- 0.05 degrees C and in Antarctica by 0.37 +/- 0.10 degrees C. Globally, permafrost temperature increased by 0.29 +/- 0.12 degrees C. The observed trend follows the Arctic amplification of air temperature increase in the Northern Hemisphere. In the discontinuous zone, however, ground warming occurred due to increased snow thickness while air temperature remained statistically unchanged.

  • 18.
    Björck, Markus L.
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Brzezinski, Peter
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Control of transmembrane charge transfer in cytochrome c oxidase by the membrane potential2018In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, article id 3187Article in journal (Refereed)
    Abstract [en]

    The respiratory chain in mitochondria is composed of membrane-bound proteins that couple electron transfer to proton translocation across the inner membrane. These charge-transfer reactions are regulated by the proton electrochemical gradient that is generated and maintained by the transmembrane charge transfer. Here, we investigate this feedback mechanism in cytochrome c oxidase in intact inner mitochondrial membranes upon generation of an electrochemical potential by hydrolysis of ATP. The data indicate that a reaction step that involves proton uptake to the catalytic site and presumably proton translocation is impaired by the potential, but electron transfer is not affected. These results define the order of electron and proton-transfer reactions and suggest that the proton pump is regulated by the transmembrane electrochemical gradient through control of internal proton transfer rather than by control of electron transfer.

  • 19.
    Bonaglia, Stefano
    et al.
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Nascimento, Francisco J. A.
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Bartoli, M.
    Klawonn, Isabell
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Bruchert, Volker
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Meiofauna increases bacterial denitrification in marine sediments2014In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 5, p. 5133-Article in journal (Refereed)
    Abstract [en]

    Denitrification is a critical process that can alleviate the effects of excessive nitrogen availability in aquatic ecosystems subject to eutrophication. An important part of denitrification occurs in benthic systems where bioturbation by meiofauna (invertebrates <1mm) and its effect on element cycling are still not well understood. Here we study the quantitative impact of meiofauna populations of different abundance and diversity, in the presence and absence of macrofauna, on nitrate reduction, carbon mineralization and methane fluxes. In sediments with abundant and diverse meiofauna, denitrification is double that in sediments with low meiofauna, suggesting that meiofauna bioturbation has a stimulating effect on nitrifying and denitrifying bacteria. However, high meiofauna densities in the presence of bivalves do not stimulate denitrification, while dissimilatory nitrate reduction to ammonium rate and methane efflux are significantly enhanced. We demonstrate that the ecological interactions between meio-, macrofauna and bacteria are important in regulating nitrogen cycling in soft-sediment ecosystems.

  • 20.
    Bonetti, Stefano
    et al.
    Stanford University, USA; SLAC National Accelerator Laboratory, USA.
    Kukreja, R.
    Chen, Z.
    Macià, F.
    Hernàndez, J. M.
    Eklund, A.
    Backes, D.
    Frisch, J.
    Katine, J.
    Malm, G.
    Urazhdin, S.
    Kent, A. D.
    Stöhr, J.
    Ohldag, H.
    Dürr, H. A.
    Direct observation and imaging of a spin-wave soliton with p-like symmetry2015In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 6, article id 8889Article in journal (Refereed)
    Abstract [en]

    Spin waves, the collective excitations of spins, can emerge as nonlinear solitons at the nanoscale when excited by an electrical current from a nanocontact. These solitons are expected to have essentially cylindrical symmetry (that is, s-like), but no direct experimental observation exists to confirm this picture. Using a high-sensitivity time-resolved magnetic X-ray microscopy with 50 ps temporal resolution and 35 nm spatial resolution, we are able to create a real-space spin-wave movie and observe the emergence of a localized soliton with a nodal line, that is, with p-like symmetry. Micromagnetic simulations explain the measurements and reveal that the symmetry of the soliton can be controlled by magnetic fields. Our results broaden the understanding of spin-wave dynamics at the nanoscale, with implications for the design of magnetic nanodevices.

  • 21.
    Borodianskyi, Evgenii A.
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Krasnov, Vladimir M.
    Stockholm University, Faculty of Science, Department of Physics.
    Josephson emission with frequency span 1-11 THz from small Bi2Sr2CaCu2O8+delta mesa structures2017In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 8, article id 1742Article in journal (Refereed)
    Abstract [en]

    Mesa structures made of Bi2Sr2CaCu2O8+delta high-temperature superconductor represent stacks of atomic scale intrinsic Josephson junctions. They can be used for generation of high-frequency electromagnetic waves. Here we analyze Josephson emission from small-but-high mesas (with a small area, but containing many stacked junctions). We have found strong evidence for tunable terahertz emission with a good efficacy in a record high-frequency span 1-11 THz, approaching the theoretical upper limit for this superconductor. Emission maxima correspond to in-phase cavity modes in the mesas, indicating coherent superradiant nature of the emission. We conclude that terahertz emission requires a threshold number of junctions N similar to 100. The threshold behavior is not present in the classical description of stacked Josephson junctions and suggests importance of laser-like cascade amplification of the photon number in the cavity.

  • 22.
    Bourgeois, Quentin
    et al.
    Stockholm University, Faculty of Science, Department of Meteorology .
    Ekman, Annica M. L.
    Stockholm University, Faculty of Science, Department of Meteorology .
    Igel, Matthew R.
    Krejci, Radovan
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry.
    Ubiquity and impact of thin mid-level clouds in the tropics2016In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 7, article id 12432Article in journal (Refereed)
    Abstract [en]

    Clouds are crucial for Earth's climate and radiation budget. Great attention has been paid to low, high and vertically thick tropospheric clouds such as stratus, cirrus and deep convective clouds. However, much less is known about tropospheric mid-level clouds as these clouds are challenging to observe in situ and difficult to detect by remote sensing techniques. Here we use Cloud-Aerosol Lidar with Orthogonal Polarization (CALIOP) satellite observations to show that thin mid-level clouds (TMLCs) are ubiquitous in the tropics. Supported by high-resolution regional model simulations, we find that TMLCs are formed by detrainment from convective clouds near the zero-degree isotherm. Calculations using a radiative transfer model indicate that tropical TMLCs have a cooling effect on climate that could be as large in magnitude as the warming effect of cirrus. We conclude that more effort has to be made to understand TMLCs, as their influence on cloud feedbacks, heat and moisture transport, and climate sensitivity could be substantial.

  • 23.
    Braga, Mariana P.
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Guimarães Jr, Paulo R.
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, Department of Zoology.
    Nylin, Sören
    Stockholm University, Faculty of Science, Department of Zoology.
    Janz, Niklas
    Stockholm University, Faculty of Science, Department of Zoology.
    Unifying host-associated diversification processes using butterfly-plant networks2018In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, article id 5155Article in journal (Refereed)
    Abstract [en]

    Explaining the exceptional diversity of herbivorous insects is an old problem in evolutionary ecology. Here we focus on the two prominent hypothesised drivers of their diversification, radiations after major host switch or variability in host use due to continuous probing of new hosts. Unfortunately, current methods cannot distinguish between these hypotheses, causing controversy in the literature. Here we present an approach combining network and phylogenetic analyses, which directly quantifies support for these opposing hypotheses. After demonstrating that each hypothesis produces divergent network structures, we then investigate the contribution of each to diversification in two butterfly families: Pieridae and Nymphalidae. Overall, we find that variability in host use is essential for butterfly diversification, while radiations following colonisation of a new host are rare but can produce high diversity. Beyond providing an important reconciliation of alternative hypotheses for butterfly diversification, our approach has potential to test many other hypotheses in evolutionary biology.

  • 24.
    Bröder, Lisa
    et al.
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry.
    Tesi, Tommaso
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry. Institute of Marine Sciences - National Research Council, Italy.
    Andersson, August
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry.
    Semiletov, Igor
    Gustafsson, Örjan
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry.
    Bounding cross-shelf transport time and degradation in Siberian-Arctic land-ocean carbon transfer2018In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, article id 806Article in journal (Refereed)
    Abstract [en]

    The burial of terrestrial organic carbon (terrOC) in marine sediments contributes to the regulation of atmospheric CO2 on geological timescales and may mitigate positive feedback to present-day climate warming. However, the fate of terrOC in marine settings is debated, with uncertainties regarding its degradation during transport. Here, we employ compound-specific radiocarbon analyses of terrestrial biomarkers to determine cross-shelf transport times. For the World's largest marginal sea, the East Siberian Arctic shelf, transport requires 3600 +/- 300 years for the 600 km from the Lena River to the Laptev Sea shelf edge. TerrOC was reduced by similar to 85% during transit resulting in a degradation rate constant of 2.4 +/- 0.6 kyr(-1). Hence, terrOC degradation during cross-shelf transport constitutes a carbon source to the atmosphere over millennial time. For the contemporary carbon cycle on the other hand, slow terrOC degradation brings considerable attenuation of the decadal-centennial permafrost carbon-climate feedback caused by global warming.

  • 25. Burlacu, Elena
    et al.
    Lackmann, Fredrik
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Aguilar, Lisbeth-Carolina
    Belikov, Sergey
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    van Nues, Rob
    Trahan, Christian
    Hector, Ralph D.
    Dominelli-Whiteley, Nicholas
    Cockroft, Scott L.
    Wieslander, Lars
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Oeffinger, Marlene
    Granneman, Sander
    High-throughput RNA structure probing reveals critical folding events during early 60S ribosome assembly in yeast2017In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 8, article id 714Article in journal (Refereed)
    Abstract [en]

    While the protein composition of various yeast 60S ribosomal subunit assembly intermediates has been studied in detail, little is known about ribosomal RNA (rRNA) structural rearrangements that take place during early 60S assembly steps. Using a high-throughput RNA structure probing method, we provide nucleotide resolution insights into rRNA structural rearrangements during nucleolar 60S assembly. Our results suggest that many rRNA-folding steps, such as folding of 5.8S rRNA, occur at a very specific stage of assembly, and propose that downstream nuclear assembly events can only continue once 5.8S folding has been completed. Our maps of nucleotide flexibility enable making predictions about the establishment of protein-rRNA interactions, providing intriguing insights into the temporal order of protein-rRNA as well as long-range inter-domain rRNA interactions. These data argue that many distant domains in the rRNA can assemble simultaneously during early 60S assembly and underscore the enormous complexity of 60S synthesis.

  • 26. Büntgen, Ulf
    et al.
    Krusic, Paul J.
    Stockholm University, Faculty of Science, Department of Physical Geography. University of Cambridge, UK.
    Piermattei, Alma
    Coomes, David A.
    Esper, Jan
    Myglan, Vladimir S.
    Kirdyanov, Alexander
    Julio Camarero, J.
    Crivellaro, Alan
    Körner, Christian
    Limited capacity of tree growth to mitigate the global greenhouse effect under predicted warming2019In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 10, article id 2171Article in journal (Refereed)
    Abstract [en]

    It is generally accepted that animal heartbeat and lifespan are often inversely correlated, however, the relationship between productivity and longevity has not yet been described for trees growing under industrial and pre-industrial climates. Using 1768 annually resolved and absolutely dated ring width measurement series from living and dead conifers that grew in undisturbed, high-elevation sites in the Spanish Pyrenees and the Russian Altai over the past 2000 years, we test the hypothesis of grow fast-die young. We find maximum tree ages are significantly correlated with slow juvenile growth rates. We conclude, the interdependence between higher stem productivity, faster tree turnover, and shorter carbon residence time, reduces the capacity of forest ecosystems to store carbon under a climate warming-induced stimulation of tree growth at policy-relevant timescales.

  • 27. Büntgen, Ulf
    et al.
    Wacker, Lukas
    Galvan, J. Diego
    Arnold, Stephanie
    Arseneault, Dominique
    Baillie, Michael
    Beer, Jurg
    Bernabei, Mauro
    Bleicher, Niels
    Boswijk, Gretel
    Brauning, Achim
    Carrer, Marco
    Charpentier Ljungqvist, Fredrik
    Stockholm University, Faculty of Humanities, Department of History. University of Cambridge, UK.
    Cherubini, Paolo
    Christl, Marcus
    Christie, Duncan A.
    Clark, Peter W.
    Cook, Edward R.
    D'Arrigo, Rosanne
    Davi, Nicole
    Eggertsson, Olafur
    Esper, Jan
    Fowler, Anthony M.
    Gedalof, Ze'ev
    Gennaretti, Fabio
    Griessinger, Jussi
    Grissino-Mayer, Henri
    Grudd, Hakan
    Gunnarson, Björn E.
    Stockholm University, Faculty of Science, Department of Physical Geography.
    Hantemirov, Rashit
    Herzig, Franz
    Hessl, Amy
    Heussner, Karl-Uwe
    Jull, A. J. Timothy
    Kukarskih, Vladimir
    Kirdyanov, Alexander
    Kolar, Tomas
    Krusic, Paul J.
    Stockholm University, Faculty of Science, Department of Physical Geography. University of Cambridge, UK; Navarino Environmental Observatory, Greece.
    Kyncl, Tomas
    Lara, Antonio
    LeQuesne, Carlos
    Linderholm, Hans W.
    Loader, Neil J.
    Luckman, Brian
    Miyake, Fusa
    Myglan, Vladimir S.
    Nicolussi, Kurt
    Oppenheimer, Clive
    Palmer, Jonathan
    Panyushkina, Irina
    Pederson, Neil
    Rybnicek, Michal
    Schweingruber, Fritz H.
    Seim, Andrea
    Sigl, Michael
    Churakova (Sidorova), Olga
    Speer, James H.
    Synal, Hans-Arno
    Tegel, Willy
    Treydte, Kerstin
    Villalba, Ricardo
    Wiles, Greg
    Wilson, Rob
    Winship, Lawrence J.
    Wunder, Jan
    Yang, Bao
    Young, Giles H. F.
    Tree rings reveal globally coherent signature of cosmogenic radiocarbon events in 774 and 993 CE2018In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, article id 3605Article in journal (Refereed)
    Abstract [en]

    Though tree-ring chronologies are annually resolved, their dating has never been independently validated at the global scale. Moreover, it is unknown if atmospheric radiocarbon enrichment events of cosmogenic origin leave spatiotemporally consistent fingerprints. Here we measure the C-14 content in 484 individual tree rings formed in the periods 770-780 and 990-1000 CE. Distinct C-14 excursions starting in the boreal summer of 774 and the boreal spring of 993 ensure the precise dating of 44 tree-ring records from five continents. We also identify a meridional decline of 11-year mean atmospheric radiocarbon concentrations across both hemispheres. Corroborated by historical eye-witness accounts of red auroras, our results suggest a global exposure to strong solar proton radiation. To improve understanding of the return frequency and intensity of past cosmic events, which is particularly important for assessing the potential threat of space weather on our society, further annually resolved C-14 measurements are needed.

  • 28. Carow, Berit
    et al.
    Hauling, Thomas
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Qian, Xiaoyan
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Kramnik, Igor
    Nilsson, Mats
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Rottenberg, Martin E.
    Spatial and temporal localization of immune transcripts defines hallmarks and diversity in the tuberculosis granuloma2019In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 10, article id 1823Article in journal (Refereed)
    Abstract [en]

    Granulomas are the pathological hallmark of tuberculosis (TB) and the niche where bacilli can grow and disseminate or the immunological microenvironment in which host cells interact to prevent bacterial dissemination. Here we show 34 immune transcripts align to the morphology of lung sections from Mycobacterium tuberculosis-infected mice at cellular resolution. Colocalizing transcript networks at <10 mu m in C57BL/6 mouse granulomas increase complexity with time after infection. B-cell clusters develop late after infection. Transcripts from activated macrophages are enriched at subcellular distances from M. tuberculosis. Encapsulated C3HeB/FeJ granulomas show necrotic centers with transcripts associated with immunosuppression (Foxp3, Il10), whereas those in the granuloma rims associate with activated T cells and macrophages. We see highly diverse networks with common interactors in similar lesions. Different immune landscapes of M. tuberculosis granulomas depending on the time after infection, the histopathological features of the lesion, and the proximity to bacteria are here defined.

  • 29. Carreras-Puigvert, Jordi
    et al.
    Zitnik, Marinka
    Jemth, Ann-Sofie
    Carter, Megan
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Unterlass, Judith E.
    Hallström, Björn
    Loseva, Olga
    Karem, Zhir
    Calderón-Montaño, José Manuel
    Lindskog, Cecilia
    Edqvist, Per-Henrik
    Matuszewski, Damian J.
    Blal, Hammou Ait
    Berntsson, Ronnie P. A.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Häggblad, Maria
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Martens, Ulf
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Studham, Matthew
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Lundgren, Bo
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Wählby, Carolina
    Sonnhammer, Erik L. L.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Lundberg, Emma
    Stenmark, Pål
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Zupan, Blaz
    Helleday, Thomas
    A comprehensive structural, biochemical and biological profiling of the human NUDIX hydrolase family2017In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 8, article id 1541Article in journal (Refereed)
    Abstract [en]

    The NUDIX enzymes are involved in cellular metabolism and homeostasis, as well as mRNA processing. Although highly conserved throughout all organisms, their biological roles and biochemical redundancies remain largely unclear. To address this, we globally resolve their individual properties and inter-relationships. We purify 18 of the human NUDIX proteins and screen 52 substrates, providing a substrate redundancy map. Using crystal structures, we generate sequence alignment analyses revealing four major structural classes. To a certain extent, their substrate preference redundancies correlate with structural classes, thus linking structure and activity relationships. To elucidate interdependence among the NUDIX hydrolases, we pairwise deplete them generating an epistatic interaction map, evaluate cell cycle perturbations upon knockdown in normal and cancer cells, and analyse their protein and mRNA expression in normal and cancer tissues. Using a novel FUSION algorithm, we integrate all data creating a comprehensive NUDIX enzyme profile map, which will prove fundamental to understanding their biological functionality.

  • 30.
    Carter, Megan
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Jemth, Ann-Sofie
    Hagenkort, Anna
    Page, Brent D. G.
    Gustafsson, Robert
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Griese, Julia J.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Gad, Helge
    Valerie, Nicholas C. K.
    Desroses, Matthieu
    Boström, Johan
    Berglund, Ulrika Warpman
    Helleday, Thomas
    Stenmark, Pål
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Crystal structure, biochemical and cellular activities demonstrate separate functions of MTH1 and MTH22015In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 6, article id 7871Article in journal (Refereed)
    Abstract [en]

    Deregulated redox metabolism in cancer leads to oxidative damage to cellular components including deoxyribonucleoside triphosphates (dNTPs). Targeting dNTP pool sanitizing enzymes, such as MTH1, is a highly promising anticancer strategy. The MTH2 protein, known as NUDT15, is described as the second human homologue of bacterial MutT with 8-oxo-dGTPase activity. We present the first NUDT15 crystal structure and demonstrate that NUDT15 prefers other nucleotide substrates over 8-oxo-dGTP. Key structural features are identified that explain different substrate preferences for NUDT15 and MTH1. We find that depletion of NUDT15 has no effect on incorporation of 8-oxo-dGTP into DNA and does not impact cancer cell survival in cell lines tested. NUDT17 and NUDT18 were also profiled and found to have far less activity than MTH1 against oxidized nucleotides. We show that NUDT15 is not a biologically relevant 8-oxo-dGTPase, and that MTH1 is the most prominent sanitizer of the cellular dNTP pool known to date.

  • 31. Charman, A. E.
    et al.
    Amole, C.
    Jonsell, Svante
    Stockholm University, Faculty of Science, Department of Physics.
    Zhmoginov, A. I.
    Description and first application of a new technique to measure the gravitational mass of antihydrogen2013In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 4, article id 1785Article in journal (Refereed)
    Abstract [en]

    Physicists have long wondered whether the gravitational interactions between matter and antimatter might be different from those between matter and itself. Although there are many indirect indications that no such differences exist and that the weak equivalence principle holds, there have been no direct, free-fall style, experimental tests of gravity on antimatter. Here we describe a novel direct test methodology; we search for a propensity for anti-hydrogen atoms to fall downward when released from the ALPHA antihydrogen trap. In the absence of systematic errors, we can reject ratios of the gravitational to inertial mass of antihydrogen 475 at a statistical significance level of 5%; worst-case systematic errors increase the minimum rejection ratio to 110. A similar search places somewhat tighter bounds on a negative gravitational mass, that is, on antigravity. This methodology, coupled with ongoing experimental improvements, should allow us to bound the ratio within the more interesting near equivalence regime.

  • 32. Chen, Geng
    et al.
    Aharon, Nati
    Sun, Yong-Nan
    Zhang, Zi-Huai
    Zhang, Wen-Hao
    He, De-Yong
    Tang, Jian-Shun
    Xu, Xiao-Ye
    Kedem, Yaron
    Stockholm University, Faculty of Science, Department of Physics.
    Li, Chuan-Feng
    Guo, Guang-Can
    Heisenberg-scaling measurement of the single-photon Kerr non-linearity using mixed states2018In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, article id 93Article in journal (Refereed)
    Abstract [en]

    Improving the precision of measurements is a significant scientific challenge. Previous works suggest that in a photon-coupling scenario the quantum fisher information shows a quantum-enhanced scaling of N-2, which in theory allows a better-than-classical scaling in practical measurements. In this work, utilizing mixed states with a large uncertainty and a post-selection of an additional pure system, we present a scheme to extract this amount of quantum fisher information and experimentally attain a practical Heisenberg scaling. We performed a measurement of a single-photon's Kerr non-linearity with a Heisenberg scaling, where an ultra-small Kerr phase of. 6 x 10(-8) rad was observed with a precision of similar or equal to 3.6 x 10(-10) rad. From the use of mixed states, the upper bound of quantum fisher information is improved to 2N(2). Moreover, by using an imaginary weak-value the scheme is robust to noise originating from the self-phase modulation.

  • 33. Chi Fru, Ernest
    et al.
    Ivarsson, Magnus
    Kilias, Stephanos P.
    Bengtson, Stefan
    Belivanova, Veneta
    Marone, Federica
    Fortin, Danielle
    Broman, Curt
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Stampanoni, Marco
    Fossilized iron bacteria reveal a pathway to the biological origin of banded iron formation2013In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 4, p. 2050-Article in journal (Refereed)
    Abstract [en]

    Debates on the formation of banded iron formations in ancient ferruginous oceans are dominated by a dichotomy between abiotic and biotic iron cycling. This is fuelled by difficulties in unravelling the exact processes involved in their formation. Here we provide fossil environmental evidence for anoxygenic photoferrotrophic deposition of analogue banded iron rocks in shallow marine waters associated with an Early Quaternary hydrothermal vent field on Milos Island, Greece. Trace metal, major and rare earth elemental compositions suggest that the deposited rocks closely resemble banded iron formations of Precambrian origin. Well-preserved microbial fossils in combination with chemical data imply that band formation was linked to periodic massive encrustation of anoxygenic phototrophic biofilms by iron oxyhydroxide alternating with abiotic silica precipitation. The data implicate cyclic anoxygenic photoferrotrophy and their fossilization mechanisms in the construction of microskeletal fabrics that result in the formation of characteristic banded iron formation bands of varying silica and iron oxide ratios.

  • 34. Cirelli, Claudio
    et al.
    Marante, Carlos
    Heuser, Sebastian
    Petersson, C. L. M.
    Jiménez Galán, Álvaro
    Argenti, Luca
    Zhong, Shiyang
    Busto, David
    Isinger, Marcus
    Nandi, Saikat
    Maclot, Sylvain
    Rading, Linnea
    Johnsson, Per
    Gisselbrecht, Mathieu
    Lucchini, Matteo
    Gallmann, Lukas
    Dahlström, J. Marcus
    Stockholm University, Faculty of Science, Department of Physics.
    Lindroth, Eva
    Stockholm University, Faculty of Science, Department of Physics.
    L'Huillier, Anne
    Martin, Fernando
    Keller, Ursula
    Anisotropic photoemission time delays close to a Fano resonance2018In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, article id 955Article in journal (Refereed)
    Abstract [en]

    Electron correlation and multielectron effects are fundamental interactions that govern many physical and chemical processes in atomic, molecular and solid state systems. The process of autoionization, induced by resonant excitation of electrons into discrete states present in the spectral continuum of atomic and molecular targets, is mediated by electron correlation. Here we investigate the attosecond photoemission dynamics in argon in the 20-40 eV spectral range, in the vicinity of the 3s(-1)np autoionizing resonances. We present measurements of the differential photoionization cross section and extract energy and angle-dependent atomic time delays with an attosecond interferometric method. With the support of a theoretical model, we are able to attribute a large part of the measured time delay anisotropy to the presence of autoionizing resonances, which not only distort the phase of the emitted photoelectron wave packet but also introduce an angular dependence.

  • 35. Cliffe, Matthew J.
    et al.
    Wan, Wei
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Zou, Xiaodong
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Chater, Philip A.
    Kleppe, Annette K.
    Tucker, Matthew G.
    Wilhelm, Heribert
    Funnell, Nicholas P.
    Coudert, Francois-Xavier
    Goodwin, Andrew L.
    Correlated defect nanoregions in a metal-organic framework2014In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 5, p. 4176-Article in journal (Refereed)
    Abstract [en]

    Throughout much of condensed matter science, correlated disorder is a key to material function. While structural and compositional defects are known to exist within a variety of metal-organic frameworks (MOFs), the prevailing understanding is that these defects are only ever included in a random manner. Here we show-using a combination of diffuse scattering, electron microscopy, anomalous X-ray scattering and pair distribution function measurements-that correlations between defects can in fact be introduced and controlled within a hafnium terephthalate MOF. The nanoscale defect structures that emerge are an analogue of correlated Schottky vacancies in rocksalt-structured transition metal monoxides and have implications for storage, transport, optical and mechanical responses. Our results suggest how the diffraction behaviour of some MOFs might be reinterpreted, and establish a strategy of exploiting correlated nanoscale disorder as a targetable and desirable motif in MOF design.

  • 36. Contreras, Estefania
    et al.
    Masuyer, Geoffrey
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Qureshi, Nadia
    Chawla, Swati
    Dhillon, Harpal S.
    Lee, Han Lim
    Chen, Jianwu
    Stenmark, Pål
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Lund University, Sweden.
    Gill, Sarjeet S.
    A neurotoxin that specifically targets Anopheles mosquitoes2019In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 10, article id 2869Article in journal (Refereed)
    Abstract [en]

    Clostridial neurotoxins, including tetanus and botulinum neurotoxins, generally target vertebrates. We show here that this family of toxins has a much broader host spectrum, by identifying PMP1, a clostridial-like neurotoxin that selectively targets anopheline mosquitoes. Isolation of PMP1 from Paraclostridium bifermentans strains collected in anopheline endemic areas on two continents indicates it is widely distributed. The toxin likely evolved from an ancestral form that targets the nervous system of similar organisms, using a common mechanism that disrupts SNARE-mediated exocytosis. It cleaves the mosquito syntaxin and employs a unique receptor recognition strategy. Our research has an important impact on the study of the evolution of clostridial neurotoxins and provides the basis for the use of P. bifermentans strains and PMP1 as innovative, environmentally friendly approaches to reduce malaria through anopheline control.

  • 37. Couto, Rafael C.
    et al.
    Cruz, Vinicius V.
    Ertan, Emelie
    Stockholm University, Faculty of Science, Department of Physics.
    Eckert, Sebastian
    Fondell, Mattis
    Dantz, Marcus
    Kennedy, Brian
    Schmitt, Thorsten
    Pietzsch, Annette
    Guimarães, Freddy F.
    Ågren, Hans
    Gel'mukhanov, Faris
    Odelius, Michael
    Stockholm University, Faculty of Science, Department of Physics.
    Kimberg, Victor
    Föhlisch, Alexander
    Selective gating to vibrational modes through resonant X-ray scattering2017In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 8, article id 14165Article in journal (Refereed)
    Abstract [en]

    The dynamics of fragmentation and vibration of molecular systems with a large number of coupled degrees of freedom are key aspects for understanding chemical reactivity and properties. Here we present a resonant inelastic X-ray scattering (RIXS) study to show how it is possible to break down such a complex multidimensional problem into elementary components. Local multimode nuclear wave packets created by X-ray excitation to different core-excited potential energy surfaces (PESs) will act as spatial gates to selectively probe the particular ground-state vibrational modes and, hence, the PES along these modes. We demonstrate this principle by combining ultra-high resolution RIXS measurements for gas-phase water with state-of-the-art simulations.

  • 38. Croft, B.
    et al.
    Wentworth, G. R.
    Martin, R. V.
    Leaitch, W. R.
    Murphy, J. G.
    Murphy, Benjamin N.
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry. U.S. Environmental Protection Agency, USA.
    Kodros, J. K.
    Abbatt, J. P. D.
    Pierce, J. R.
    Contribution of Arctic seabird-colony ammonia to atmospheric particles and cloud-albedo radiative effect2016In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 7, article id 13444Article in journal (Refereed)
    Abstract [en]

    The Arctic region is vulnerable to climate change and able to affect global climate. The summertime Arctic atmosphere is pristine and strongly influenced by natural regional emissions, which have poorly understood climate impacts related to atmospheric particles and clouds. Here we show that ammonia from seabird-colony guano is a key factor contributing to bursts of newly formed particles, which are observed every summer in the near-surface atmosphere at Alert, Nunavut, Canada. Our chemical-transport model simulations indicate that the pan-Arctic seabird-influenced particles can grow by sulfuric acid and organic vapour condensation to diameters sufficiently large to promote pan-Arctic cloud-droplet formation in the clean Arctic summertime. We calculate that the resultant cooling tendencies could be large (about -0.5Wm(-2) pan-Arctic-mean cooling), exceeding -1Wm(-2) near the largest seabird colonies due to the effects of seabird-influenced particles on cloud albedo. These coupled ecological-chemical processes may be susceptible to Arctic warming and industrialization.

  • 39. da Cruz, Vinícius Vaz
    et al.
    Gel'mukhanov, Faris
    Eckert, Sebastian
    Iannuzzi, Marcella
    Ertan, Emelie
    Stockholm University, Faculty of Science, Department of Physics.
    Pietzsch, Annette
    Couto, Rafael C.
    Niskanen, Johannes
    Fondell, Mattis
    Dantz, Marcus
    Schmitt, Thorsten
    Lu, Xingye
    McNally, Daniel
    Jay, Raphael M.
    Kimberg, Victor
    Föhlisch, Alexander
    Odelius, Michael
    Stockholm University, Faculty of Science, Department of Physics.
    Probing hydrogen bond strength in liquid water by resonant inelastic X-ray scattering2019In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 10, article id 1013Article in journal (Refereed)
    Abstract [en]

    Local probes of the electronic ground state are essential for understanding hydrogen bonding in aqueous environments. When tuned to the dissociative core-excited state at the O1s pre-edge of water, resonant inelastic X-ray scattering back to the electronic ground state exhibits a long vibrational progression due to ultrafast nuclear dynamics. We show how the coherent evolution of the OH bonds around the core-excited oxygen provides access to high vibrational levels in liquid water. The OH bonds stretch into the long-range part of the potential energy curve, which makes the X-ray probe more sensitive than infra-red spectroscopy to the local environment. We exploit this property to effectively probe hydrogen bond strength via the distribution of intramolecular OH potentials derived from measurements. In contrast, the dynamical splitting in the spectral feature of the lowest valence-excited state arises from the short-range part of the OH potential curve and is rather insensitive to hydrogen bonding.

  • 40. Dabral, Swati
    et al.
    Muecke, Christian
    Valasarajan, Chanil
    Schmoranzer, Mario
    Wietelmann, Astrid
    Semenza, Gregg L.
    Meister, Michael
    Muley, Thomas
    Seeger-Nukpezah, Tamina
    Samakovlis, Christos
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute. Max-Planck-Institute for Heart and Lung Research, Germany.
    Weissmann, Norbert
    Grimminger, Frich
    Seeger, Werner
    Savai, Rajkumar
    Pullamsetti, Soni S.
    A RASSF1A-HIF1 alpha loop drives Warburg effect in cancer and pulmonary hypertension2019In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 10, article id 2130Article in journal (Refereed)
    Abstract [en]

    Hypoxia signaling plays a major role in non-malignant and malignant hyperproliferative diseases. Pulmonary hypertension (PH), a hypoxia-driven vascular disease, is characterized by a glycolytic switch similar to the Warburg effect in cancer. Ras association domain family 1A (RASSF1A) is a scaffold protein that acts as a tumour suppressor. Here we show that hypoxia promotes stabilization of RASSF1A through NOX-1- and protein kinase C- dependent phosphorylation. In parallel, hypoxia inducible factor-1 alpha (HIF-1 alpha) activates RASSF1A transcription via HIF-binding sites in the RASSF1A promoter region. Vice versa, RASSF1A binds to HIF-1 alpha, blocks its prolyl-hydroxylation and proteasomal degradation, and thus enhances the activation of the glycolytic switch. We find that this mechanism operates in experimental hypoxia-induced PH, which is blocked in RASSF1A knockout mice, in human primary PH vascular cells, and in a subset of human lung cancer cells. We conclude that RASSF1A-HIF-1 alpha forms a feedforward loop driving hypoxia signaling in PH and cancer.

  • 41. Das, Tanmoy
    et al.
    Balatsky, Alexander V.
    Stockholm University, Nordic Institute for Theoretical Physics (Nordita). Los Alamos National Laboratory .
    Engineering three-dimensional topological insulators in Rashba-type spin-orbit coupled heterostructures2013In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 4, p. 1972-Article in journal (Refereed)
    Abstract [en]

    Topological insulators represent a new class of quantum phase defined by invariant symmetries and spin-orbit coupling that guarantees metallic Dirac excitations at its surface. The discoveries of these states have sparked the hope of realizing non-trivial excitations and novel effects such as a magnetoelectric effect and topological Majorana excitations. Here we develop a theoretical formalism to show that a three-dimensional topological insulator can be designed artificially via stacking bilayers of two-dimensional Fermi gases with opposite Rashba-type spin-orbit coupling on adjacent layers, and with interlayer quantum tunneling. We demonstrate that in the stack of bilayers grown along a (001)-direction, a non-trivial topological phase transition occurs above a critical number of Rashba bilayers. In the topological phase, we find the formation of a single spin-polarized Dirac cone at the G-point. This approach offers an accessible way to design artificial topological insulators in a set up that takes full advantage of the atomic layer deposition approach. This design principle is tunable and also allows us to bypass limitations imposed by bulk crystal geometry.

  • 42. Davies, Gail
    et al.
    Lam, Max
    Harris, Sarah E.
    Trampush, Joey W.
    Luciano, Michelle
    Hill, W. David
    Hagenaars, Saskia P.
    Ritchie, Stuart J.
    Marioni, Riccardo E.
    Fawns-Ritchie, Chloe
    Liewald, David C. M.
    Okely, Judith A.
    Ahola-Olli, Ari V.
    Barnes, Catriona L. K.
    Bertram, Lars
    Bis, Joshua C.
    Burdick, Katherine E.
    Christoforou, Andrea
    DeRosse, Pamela
    Djurovic, Srdjan
    Espeseth, Thomas
    Giakoumaki, Stella
    Giddaluru, Sudheer
    Gustavson, Daniel E.
    Hayward, Caroline
    Hofer, Edith
    Ikram, M. Arfan
    Karlsson, Robert
    Knowles, Emma
    Lahti, Jari
    Leber, Markus
    Li, Shuo
    Mather, Karen A.
    Melle, Ingrid
    Morris, Derek
    Oldmeadow, Christopher
    Palviainen, Teemu
    Payton, Antony
    Pazoki, Raha
    Petrovic, Katja
    Reynolds, Chandra A.
    Sargurupremraj, Muralidharan
    Scholz, Markus
    Smith, Jennifer A.
    Smith, Albert V.
    Terzikhan, Natalie
    Thalamuthu, Anbupalam
    Trompet, Stella
    van der Lee, Sven J.
    Ware, Erin B.
    Windham, B. Gwen
    Wright, Margaret J.
    Yang, Jingyun
    Yu, Jin
    Ames, David
    Amin, Najaf
    Amouyel, Philippe
    Andreassen, Ole A.
    Armstrong, Nicola J.
    Assareh, Amelia A.
    Attia, John R.
    Attix, Deborah
    Avramopoulos, Dimitrios
    Bennett, David A.
    Boehmer, Anne C.
    Boyle, Patricia A.
    Brodaty, Henry
    Campbell, Harry
    Cannon, Tyrone D.
    Cirulli, Elizabeth T.
    Congdon, Eliza
    Conley, Emily Drabant
    Corley, Janie
    Cox, Simon R.
    Dale, Anders M.
    Dehghan, Abbas
    Dick, Danielle
    Dickinson, Dwight
    Eriksson, Johan G.
    Evangelou, Evangelos
    Faul, Jessica D.
    Ford, Ian
    Freimer, Nelson A.
    Gao, He
    Giegling, Ina
    Gillespie, Nathan A.
    Gordon, Scott D.
    Gottesman, Rebecca F.
    Griswold, Michael E.
    Gudnason, Vilmundur
    Harris, Tamara B.
    Hartmann, Annette M.
    Hatzimanolis, Alex
    Heiss, Gerardo
    Holliday, Elizabeth G.
    Joshi, Peter K.
    Kahonen, Mika
    Kardia, Sharon L. R.
    Karlsson, Ida
    Kleineidam, Luca
    Knopman, David S.
    Kochan, Nicole A.
    Konte, Bettina
    Kwok, John B.
    Le Hellard, Stephanie
    Lee, Teresa
    Lehtimaki, Terho
    Li, Shu-Chen
    Liu, Tian
    Koini, Marisa
    London, Edythe
    Longstreth, Will T.
    Lopez, Oscar L.
    Loukola, Anu
    Luck, Tobias
    Lundervold, Astri J.
    Lundquist, Anders
    Lyytikainen, Leo-Pekka
    Martin, Nicholas G.
    Montgomery, Grant W.
    Murray, Alison D.
    Need, Anna C.
    Noordam, Raymond
    Nyberg, Lars
    Ollier, William
    Papenberg, Göran
    Stockholm University, Faculty of Social Sciences, Aging Research Center (ARC), (together with KI). Max Planck Institute for Human Development, Germany.
    Pattie, Alison
    Polasek, Ozren
    Poldrack, Russell A.
    Psaty, Bruce M.
    Reppermund, Simone
    Riedel-Heller, Steffi G.
    Rose, Richard J.
    Rotter, Jerome I.
    Roussos, Panos
    Rovio, Suvi P.
    Saba, Yasaman
    Sabb, Fred W.
    Sachdev, Perminder S.
    Satizabal, Claudia L.
    Schmid, Matthias
    Scott, Rodney J.
    Scult, Matthew A.
    Simino, Jeannette
    Slagboom, P. Eline
    Smyrnis, Nikolaos
    Soumare, Aicha
    Stefanis, Nikos C.
    Stott, David J.
    Straub, Richard E.
    Sundet, Kjetil
    Taylor, Adele M.
    Taylor, Kent D.
    Tzoulaki, Ioanna
    Tzourio, Christophe
    Uitterlinden, Andre
    Vitart, Veronique
    Voineskos, Aristotle N.
    Kaprio, Jaakko
    Wagner, Michael
    Wagner, Holger
    Weinhold, Leonie
    Wen, K. Hoyan
    Widen, Elisabeth
    Yang, Qiong
    Zhao, Wei
    Adams, Hieab H. H.
    Arking, Dan E.
    Bilder, Robert M.
    Bitsios, Panos
    Boerwinkle, Eric
    Chiba-Falek, Ornit
    Corvin, Aiden
    De Jager, Philip L.
    Debette, Stephanie
    Donohoe, Gary
    Elliott, Paul
    Fitzpatrick, Annette L.
    Gill, Michael
    Glahn, David C.
    Hagg, Sara
    Hansell, Narelle K.
    Hariri, Ahmad R.
    Ikram, M. Kamran
    Jukema, J. Wouter
    Vuoksimaa, Eero
    Keller, Matthew C.
    Kremen, William S.
    Launer, Lenore
    Lindenberger, Ulman
    Palotie, Aarno
    Pedersen, Nancy L.
    Pendleton, Neil
    Porteous, David J.
    Raikkonen, Katri
    Raitakari, Olli T.
    Ramirez, Alfredo
    Reinvang, Ivar
    Rudan, Igor
    Rujescu, Dan
    Schmidt, Reinhold
    Schmidt, Helena
    Schofield, Peter W.
    Schofield, Peter R.
    Starr, John M.
    Steen, Vidar M.
    Trollor, Julian N.
    Turner, Steven T.
    Van Duijn, Cornelia M.
    Villringer, Arno
    Weinberger, Daniel R.
    Weir, David R.
    Wilson, James F.
    Malhotra, Anil
    McIntosh, Andrew M.
    Gale, Catharine R.
    Seshadri, Sudha
    Mosley, Thomas H.
    Bressler, Jan
    Lencz, Todd
    Deary, Ian J.
    Study of 300,486 individuals identifies 148 independent genetic loci influencing general cognitive function2018In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, article id 2098Article in journal (Refereed)
    Abstract [en]

    General cognitive function is a prominent and relatively stable human trait that is associated with many important life outcomes. We combine cognitive and genetic data from the CHARGE and COGENT consortia, and UK Biobank (total N = 300,486; age 16-102) and find 148 genome-wide significant independent loci (P < 5 x 10(-8)) associated with general cognitive function. Within the novel genetic loci are variants associated with neurodegenerative and neurodevelopmental disorders, physical and psychiatric illnesses, and brain structure. Gene-based analyses find 709 genes associated with general cognitive function. Expression levels across the cortex are associated with general cognitive function. Using polygenic scores, up to 4.3% of variance in general cognitive function is predicted in independent samples. We detect significant genetic overlap between general cognitive function, reaction time, and many health variables including eyesight, hypertension, and longevity. In conclusion we identify novel genetic loci and pathways contributing to the heritability of general cognitive function.

  • 43. Dellantonio, Luca
    et al.
    Kyriienko, Oleksandr
    Stockholm University, Nordic Institute for Theoretical Physics (Nordita). University of Copenhagen, Denmark.
    Marquardt, Florian
    Sørensen, Anders S.
    Quantum nondemolition measurement of mechanical motion quanta2018In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, article id 3621Article in journal (Refereed)
    Abstract [en]

    The fields of optomechanics and electromechanics have facilitated numerous advances in the areas of precision measurement and sensing, ultimately driving the studies of mechanical systems into the quantum regime. To date, however, the quantization of the mechanical motion and the associated quantum jumps between phonon states remains elusive. For optomechanical systems, the coupling to the environment was shown to make the detection of the mechanical mode occupation difficult, typically requiring the single-photon strong coupling regime. Here, we propose and analyse an electromechanical setup, which allows us to overcome this limitation and resolve the energy levels of a mechanical oscillator. We found that the heating of the membrane, caused by the interaction with the environment and unwanted couplings, can be suppressed for carefully designed electromechanical systems. The results suggest that phonon number measurement is within reach for modern electromechanical setups.

  • 44. Ding, Huimin
    et al.
    Li, Jian
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). Peking University, China.
    Xie, Guohua
    Lin, Guiqing
    Chen, Rufan
    Peng, Zhengkang
    Yang, Chuluo
    Wang, Baoshan
    Sun, Junliang
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). Peking University, China.
    Wang, Cheng
    An AIEgen-based 3D covalent organic framework for white light-emitting diodes2018In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, article id 5234Article in journal (Refereed)
    Abstract [en]

    The design and synthesis of three-dimensional covalent organic frameworks (3D COFs) have still been considered as a big challenge. Here we report the design and synthesis of an AIEgen-based 3D COF (3D-TPE-COF), with a high surface area (1084 m(2)g(-1)). According to powder X-ray diffraction and continuous rotation electron diffraction analyses, 3D-TPE-COF is identified to adopt a seven-fold interpenetrated pts topology. Interestingly, 3D-TPE-COF emits yellow fluorescence upon excitation, with a photoluminescence quantum yield of 20%. Moreover, by simply coating 3D-TPE-COF onto a commercial blue light-emitting diode (LED), a prototype white LED (WLED) under continuously driving without degradation for 1200 h was demonstrated. The present work suggests the possibility of using COF materials for stable WLEDs, which will greatly inspire us to design and synthesize fluorescent 3D COFs and facilitate the development of COF-based WLEDs in future.

  • 45.
    Domingo-Prim, Judit
    et al.
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Endara-Coll, Martin
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Bonath, Franziska
    Stockholm University, Science for Life Laboratory (SciLifeLab). Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Jimeno, Sonia
    Prados-Carvaja, Rosario
    Friedländer, Marc R.
    Stockholm University, Science for Life Laboratory (SciLifeLab). Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Huertas, Pablo
    Visa, Neus
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    EXOSC10 is required for RPA assembly and controlled DNA end resection at DNA double-strand breaks2019In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 10, article id 2135Article in journal (Refereed)
    Abstract [en]

    The exosome is a ribonucleolytic complex that plays important roles in RNA metabolism. Here we show that the exosome is necessary for the repair of DNA double-strand breaks (DSBs) in human cells and that RNA clearance is an essential step in homologous recombination. Transcription of DSB-flanking sequences results in the production of damage-induced long non-coding RNAs (dilncRNAs) that engage in DNA-RNA hybrid formation. Depletion of EXOSC10, an exosome catalytic subunit, leads to increased dilncRNA and DNA-RNA hybrid levels. Moreover, the targeting of the ssDNA-binding protein RPA to sites of DNA damage is impaired whereas DNA end resection is hyper-stimulated in EXOSC10-depleted cells. The DNA end resection deregulation is abolished by transcription inhibitors, and RNase H1 overexpression restores the RPA recruitment defect caused by EXOSC10 depletion, which suggests that RNA clearance of newly synthesized dilncRNAs is required for RPA recruitment, controlled DNA end resection and assembly of the homologous recombination machinery.

  • 46. Drake, Henrik
    et al.
    Roberts, Nick M. W.
    Heim, Christine
    Whitehouse, Martin J.
    Siljeström, Sandra
    Kooijman, Ellen
    Broman, Curt
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Ivarsson, Magnus
    Åström, Mats E.
    Timing and origin of natural gas accumulation in the Siljan impact structure, Sweden2019In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 10, article id 4736Article in journal (Refereed)
    Abstract [en]

    Fractured rocks of impact craters may be suitable hosts for deep microbial communities on Earth and potentially other terrestrial planets, yet direct evidence remains elusive. Here, we present a study of the largest crater of Europe, the Devonian Siljan structure, showing that impact structures can be important unexplored hosts for long-term deep microbial activity. Secondary carbonate minerals dated to 80 +/- 5 to 22 +/- 3 million years, and thus postdating the impact by more than 300 million years, have isotopic signatures revealing both microbial methanogenesis and anaerobic oxidation of methane in the bedrock. Hydrocarbons mobilized from matured shale source rocks were utilized by subsurface microorganisms, leading to accumulation of microbial methane mixed with a thermogenic and possibly a minor abiotic gas fraction beneath a sedimentary cap rock at the crater rim. These new insights into crater hosted gas accumulation and microbial activity have implications for understanding the astrobiological consequences of impacts.

  • 47. Drake, Henrik
    et al.
    Åström, Mats E.
    Heim, Christine
    Broman, Curt
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Åström, Jan
    Whitehouse, Martin
    Ivarsson, Magnus
    Siljeström, Sandra
    Sjövall, Peter
    Extreme C-13 depletion of carbonates formed during oxidation of biogenic methane in fractured granite2015In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 6, article id 7020Article in journal (Refereed)
    Abstract [en]

    Precipitation of exceptionally C-13-depleted authigenic carbonate is a result of, and thus a tracer for, sulphate-dependent anaerobic methane oxidation, particularly in marine sediments. Although these carbonates typically are less depleted in C-13 than in the source methane, because of incorporation of C also from other sources, they are far more depleted in C-13 (delta C-13 as light as - 69% V-PDB) than in carbonates formed where no methane is involved. Here we show that oxidation of biogenic methane in carbon-poor deep groundwater in fractured granitoid rocks has resulted in fracture-wall precipitation of the most extremely C-13-depleted carbonates ever reported, delta C-13 down to - 125% V-PDB. A microbial consortium of sulphate reducers and methane oxidizers has been involved, as revealed by biomarker signatures in the carbonates and S-isotope compositions of co-genetic sulphide. Methane formed at shallow depths has been oxidized at several hundred metres depth at the transition to a deep-seated sulphate-rich saline water. This process is so far an unrecognized terrestrial sink of methane.

  • 48. Dremov, Viacheslav V.
    et al.
    Grebenchuk, Sergey Yu.
    Shishkin, Andrey G.
    Baranov, Denis S.
    Hovhannisyan, Razmik A.
    Skryabina, Olga V.
    Golovchanskiy, Igor A.
    Chichkov, Vladimir I.
    Brun, Chritophe
    Cren, Tristan
    Krasnov, Vladimir M.
    Stockholm University, Faculty of Science, Department of Physics. Moscow Institute of Physics and Technology, Russia.
    Golubov, Alexander A.
    Roditchev, Dimitri
    Stolyarov, Vasily S.
    Local Josephson vortex generation and manipulation with a Magnetic Force Microscope2019In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 10, article id 4009Article in journal (Refereed)
    Abstract [en]

    Josephson vortices play an essential role in superconducting quantum electronics devices. Often seen as purely conceptual topological objects, 2 pi-phase singularities, their observation and manipulation are challenging. Here we show that in Superconductor-Normal metal- Superconductor lateral junctions Josephson vortices have a peculiar magnetic fingerprint that we reveal in Magnetic Force Microscopy (MFM) experiments. Based on this discovery, we demonstrate the possibility of the Josephson vortex generation and manipulation by the magnetic tip of a MFM, thus paving a way for the remote inspection and control of individual nano-components of superconducting quantum circuits.

  • 49. Erttmann, Saskia F.
    et al.
    Gekara, Nelson O.
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute. Umeå University, Sweden.
    Hydrogen peroxide release by bacteria suppresses inflammasome-dependent innate immunity2019In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 10, article id 3493Article in journal (Refereed)
    Abstract [en]

    Hydrogen peroxide (H2O2) has a major function in host-microbial interactions. Although most studies have focused on the endogenous H2O2 produced by immune cells to kill microbes, bacteria can also produce H2O2. How microbial H2O2 influences the dynamics of host-microbial interactions is unclear. Here we show that H2O2 released by Streptococcus pneumoniae inhibits inflammasomes, key components of the innate immune system, contributing to the pathogen colonization of the host. We also show that the oral commensal H2O2-producing bacteria Streptococcus oralis can block inflammasome activation. This study uncovers an unexpected role of H2O2 in immune suppression and demonstrates how, through this mechanism, bacteria might restrain the immune system to co-exist with the host.

  • 50. Estrader, M.
    et al.
    Lopez-Ortega, A.
    Estrade, S.
    Golosovsky, I. V.
    Salazar-Alvarez, German
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Vasilakaki, M.
    Trohidou, K. N.
    Varela, M.
    Stanley, D. C.
    Sinko, M.
    Pechan, M. J.
    Keavney, D. J.
    Peiro, F.
    Surinach, S.
    Baro, M. D.
    Nogués, J.
    Robust antiferromagnetic coupling in hard-soft bi-magnetic core/shell nanoparticles2013In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 4, article id 2960Article in journal (Refereed)
    Abstract [en]

    The growing miniaturization demand of magnetic devices is fuelling the recent interest in bi-magnetic nanoparticles as ultimate small components. One of the main goals has been to reproduce practical magnetic properties observed so far in layered systems. In this context, although useful effects such as exchange bias or spring magnets have been demonstrated in core/shell nanoparticles, other interesting key properties for devices remain elusive. Here we show a robust antiferromagnetic (AFM) coupling in core/shell nanoparticles which, in turn, leads to the foremost elucidation of positive exchange bias in bi-magnetic hard-soft systems and the remarkable regulation of the resonance field and amplitude. The AFM coupling in iron oxide-manganese oxide based, soft/hard and hard/soft, core/shell nanoparticles is demonstrated by magnetometry, ferromagnetic resonance and X-ray magnetic circular dichroism. Monte Carlo simulations prove the consistency of the AFM coupling. This unique coupling could give rise to more advanced applications of bi-magnetic core/shell nanoparticles.

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