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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, 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, 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, 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.
    Ah-King, Malin
    Stockholm University, Faculty of Humanities, Department of Ethnology, History of Religions and Gender Studies.
    The history of sexual selection research provides insights as to why females are still understudied2022In: Nature Communications, E-ISSN 2041-1723, Vol. 13, article id 6976Article in journal (Refereed)
    Abstract [en]

    While it is widely acknowledged that Darwin’s descriptions of females were gender-biased, gender bias in current sexual selection research is less recognized. An examination of the history of sexual selection research shows prevalent male precedence—that research starts with male-centered investigations or explanations and thereafter includes female-centered equivalents. In comparison, the incidence of female precedence is low. Furthermore, a comparison between the volume of publications focusing on sexual selection in males versus in females shows that the former far outnumber the latter. This bias is not only a historical pattern; sexual selection theory and research are still male-centered—due to conspicuous traits, practical obstacles, and continued gender bias. Even the way sexual selection is commonly defined contributes to this bias. This history provides an illustrative example by which we can learn to recognize biases and identify gaps in knowledge. I conclude with a call for the scientific community to interrogate its own biases and suggest strategies for alleviating biases in this field and beyond.

  • 5. 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, 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.

  • 6. 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, 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.

  • 7.
    Akhoudas, Camille Hayatte
    et al.
    Stockholm University, Faculty of Science, Department of Geological Sciences. Stockholm University, Faculty of Science, The Bolin Centre for Climate Research (together with KTH & SMHI).
    Sallée, Jean-Baptiste
    Reverdin, Gilles
    Haumann, F. Alexander
    Pauthenet, Etienne
    Chapman, Christopher C.
    Margirier, Félix
    Lo Monaco, Claire
    Metzl, Nicolas
    Meilland, Julie
    Stranne, Christian
    Stockholm University, Faculty of Science, Department of Geological Sciences. Stockholm University, Faculty of Science, The Bolin Centre for Climate Research (together with KTH & SMHI).
    Isotopic evidence for an intensified hydrological cycle in the Indian sector of the Southern Ocean2023In: Nature Communications, E-ISSN 2041-1723, Vol. 14, article id 2763Article in journal (Refereed)
    Abstract [en]

    The hydrological cycle is expected to intensify in a warming climate. However, observational evidence of such changes in the Southern Ocean is difficult to obtain due to sparse measurements and a complex superposition of changes in precipitation, sea ice, and glacial meltwater. Here we disentangle these signals using a dataset of salinity and seawater oxygen isotope observations collected in the Indian sector of the Southern Ocean. Our results show that the atmospheric water cycle has intensified in this region between 1993 and 2021, increasing the salinity in subtropical surface waters by 0.06 ± 0.07 g kg−1 per decade, and decreasing the salinity in subpolar surface waters by -0.02 ± 0.01 g kg−1 per decade. The oxygen isotope data allow to discriminate the different freshwater processes showing that in the subpolar region, the freshening is largely driven by the increase in net precipitation (by a factor two) while the decrease in sea ice melt is largely balanced by the contribution of glacial meltwater at these latitudes. These changes extend the growing evidence for an acceleration of the hydrological cycle and a melting cryosphere that can be expected from global warming.

  • 8.
    Amann-Winkel, Katrin
    et al.
    Stockholm University, Faculty of Science, Department of Physics. Max Planck Institute for Polymer Research and Johannes Gutenberg University, Germany.
    Kim, Kyung Hwan
    Giovambattista, Nicolas
    Ladd-Parada, Marjorie
    Stockholm University, Faculty of Science, Department of Physics.
    Späh, Alexander
    Stockholm University, Faculty of Science, Department of Physics.
    Perakis, Fivos
    Stockholm University, Faculty of Science, Department of Physics.
    Pathak, Harshad
    Stockholm University, Faculty of Science, Department of Physics.
    Yang, Cheolhee
    Eklund, Tobias
    Stockholm University, Faculty of Science, Department of Physics.
    Lane, Thomas J.
    You, Seonju
    Jeong, Sangmin
    Lee, Jae Hyuk
    Eom, Intae
    Kim, Minseok
    Park, Jaeku
    Chun, Sae Hwan
    Poole, Peter H.
    Nilsson, Anders
    Stockholm University, Faculty of Science, Department of Physics.
    Liquid-liquid phase separation in supercooled water from ultrafast heating of low-density amorphous ice2023In: Nature Communications, E-ISSN 2041-1723, Vol. 14, no 1, article id 442Article in journal (Refereed)
    Abstract [en]

    Recent experiments continue to find evidence for a liquid-liquid phase transition (LLPT) in supercooled water, which would unify our understanding of the anomalous properties of liquid water and amorphous ice. These experiments are challenging because the proposed LLPT occurs under extreme metastable conditions where the liquid freezes to a crystal on a very short time scale. Here, we analyze models for the LLPT to show that coexistence of distinct high-density and low-density liquid phases may be observed by subjecting low-density amorphous (LDA) ice to ultrafast heating. We then describe experiments in which we heat LDA ice to near the predicted critical point of the LLPT by an ultrafast infrared laser pulse, following which we measure the structure factor using femtosecond x-ray laser pulses. Consistent with our predictions, we observe a LLPT occurring on a time scale < 100 ns and widely separated from ice formation, which begins at times >1 μs.

  • 9. 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, 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.

  • 10.
    Andersson, David
    et al.
    Stockholm University, Faculty of Science, Department of Physics. Norwegian University of Science and Technology (NTNU), Norway.
    de Wijn, Astrid S.
    Stockholm University, Faculty of Science, Department of Physics. Norwegian University of Science and Technology (NTNU), Norway.
    Understanding the friction of atomically thin layered materials2020In: Nature Communications, E-ISSN 2041-1723, Vol. 11, no 1, article id 420Article in journal (Refereed)
    Abstract [en]

    Friction is a ubiquitous phenomenon that greatly affects our everyday lives and is responsible for large amounts of energy loss in industrialised societies. Layered materials such as graphene have interesting frictional properties and are often used as (additives to) lubricants to reduce friction and protect against wear. Experimental Atomic Force Microscopy studies and detailed simulations have shown a number of intriguing effects such as frictional strengthening and dependence of friction on the number of layers covering a surface. Here, we propose a simple, fundamental, model for friction on thin sheets. We use our model to explain a variety of seemingly contradictory experimental as well as numerical results. This model can serve as a basis for understanding friction on thin sheets, and opens up new possibilities for ultimately controlling their friction and wear protection.

  • 11. Andresen, Camilla S.
    et al.
    Karlsson, Nanna B.
    Straneo, Fiammetta
    Schmidt, Sabine
    Andersen, Thorbjørn J.
    Eidam, Emily F.
    Bjørk, Anders A.
    Dartiguemalle, Nicolas
    Dyke, Laurence M.
    Vermassen, Flor
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Gundel, Ida E.
    Sediment discharge from Greenland's marine-terminating glaciers is linked with surface melt2024In: Nature Communications, E-ISSN 2041-1723, Vol. 15, no 1, article id 1332Article in journal (Refereed)
    Abstract [en]

    Sediment discharged from the Greenland Ice Sheet delivers nutrients to marine ecosystems around Greenland and shapes seafloor habitats. Current estimates of the total sediment flux are constrained by observations from land-terminating glaciers only. Addressing this gap, our study presents a budget derived from observations at 30 marine-margin locations. Analyzing sediment cores from nine glaciated fjords, we assess spatial deposition since 1950. A significant correlation is established between mass accumulation rates, normalized by surface runoff, and distance down-fjord. This enables calculating annual sediment flux at any fjord point based on nearby marine-terminating outlet glacier melt data. Findings reveal a total annual sediment flux of 1.324 + /- 0.79 Gt yr-1 over the period 2010-2020 from all marine-terminating glaciers to the fjords. These estimates are valuable for studies aiming to understand the basal ice sheet conditions and for studies predicting ecosystem changes in Greenland's fjords and offshore areas as the ice sheet melts and sediment discharge increase. 

  • 12. Ao, Hong
    et al.
    Dupont-Nivet, Guillaume
    Rohling, Eelco J.
    Zhang, Peng
    Ladant, Jean-Baptiste
    Roberts, Andrew P.
    Licht, Alexis
    Liu, Qingsong
    Liu, Zhonghui
    Dekkers, Mark J.
    Coxall, Helen K.
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Jin, Zhangdong
    Huang, Chunju
    Xiao, Guoqiao
    Poulsen, Christopher J.
    Barbolini, Natasha
    Meijer, Niels
    Sun, Qiang
    Qiang, Xiaoke
    Yao, Jiao
    An, Zhisheng
    Orbital climate variability on the northeastern Tibetan Plateau across the Eocene-Oligocene transition2020In: Nature Communications, E-ISSN 2041-1723, Vol. 11, no 1, article id 5249Article in journal (Refereed)
    Abstract [en]

    The first major build-up of Antarctic glaciation occurred in two consecutive stages across the Eocene-Oligocene transition (EOT): the EOT-1 cooling event at similar to 34.1-33.9Ma and the Oi-1 glaciation event at similar to 33.8-33.6Ma. Detailed orbital-scale terrestrial environmental responses to these events remain poorly known. Here we present magnetic and geochemical climate records from the northeastern Tibetan Plateau margin that are dated precisely from similar to 35.5 to 31Ma by combined magneto- and astro-chronology. These records suggest a hydroclimate transition at similar to 33.7Ma from eccentricity dominated cycles to oscillations paced by a combination of eccentricity, obliquity, and precession, and confirm that major Asian aridification and cooling occurred at Oi-1. We conclude that this terrestrial orbital response transition coincided with a similar transition in the marine benthic delta O-18 record for global ice volume and deep-sea temperature variations. The dramatic reorganization of the Asian climate system coincident with Oi-1 was, thus, a response to coeval atmospheric CO2 decline and continental-scale Antarctic glaciation. Marine records indicate a greenhouse to icehouse climate transition at similar to 34 million years ago, but how the climate changed within continental interiors at this time is less well known. Here, the authors show an orbital climate response shift with aridification on the northeastern Tibetan Plateau during this time.

  • 13. 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, 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.

  • 14. Arndt, Tina
    et al.
    Jaudzems, Kristaps
    Shilkova, Olga
    Francis, Juanita
    Johansson, Mathias
    Laity, Peter R.
    Sahin, Cagla
    Chatterjee, Urmimala
    Kronqvist, Nina
    Barajas-Ledesma, Edgar
    Kumar, Rakesh
    Chen, Gefei
    Strömberg, Roger
    Abelein, Axel
    Langton, Maud
    Landreh, Michael
    Barth, Andreas
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Holland, Chris
    Johansson, Jan
    Rising, Anna
    Spidroin N-terminal domain forms amyloid-like fibril based hydrogels and provides a protein immobilization platform2022In: Nature Communications, E-ISSN 2041-1723, Vol. 13, article id 4695Article in journal (Refereed)
    Abstract [en]

    Recombinant spider silk proteins (spidroins) have multiple potential applications in development of novel biomaterials, but their multimodal and aggregation-prone nature have complicated production and straightforward applications. Here, we report that recombinant miniature spidroins, and importantly also the N-terminal domain (NT) on its own, rapidly form self-supporting and transparent hydrogels at 37 °C. The gelation is caused by NT α-helix to β-sheet conversion and formation of amyloid-like fibrils, and fusion proteins composed of NT and green fluorescent protein or purine nucleoside phosphorylase form hydrogels with intact functions of the fusion moieties. Our findings demonstrate that recombinant NT and fusion proteins give high expression yields and bestow attractive properties to hydrogels, e.g., transparency, cross-linker free gelation and straightforward immobilization of active proteins at high density.

  • 15. 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, 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.

  • 16.
    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, 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.

  • 17.
    B. Araujo, Rafael
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Rodrigues, Gabriel Libânio Silva
    Stockholm University, Faculty of Science, Department of Physics.
    Campos dos Santos, Egon
    Stockholm University, Faculty of Science, Department of Physics.
    Pettersson, Lars Gunnar Moody
    Stockholm University, Faculty of Science, Department of Physics.
    Adsorption energies on transition metal surfaces: towards an accurate and balanced description2022In: Nature Communications, E-ISSN 2041-1723, Vol. 13, article id 6853Article in journal (Refereed)
    Abstract [en]

    Density functional theory predictions of binding energies and reaction barriers provide invaluable data for analyzing chemical transformations in heterogeneous catalysis. For high accuracy, effects of band structure and coverage, as well as the local bond strength in both covalent and non-covalent interactions, must be reliably described and much focus has been put on improving functionals to this end. Here, we show that a correction from higher-level calculations on small metal clusters can be applied to improve periodic band structure adsorption energies and barriers. We benchmark against 38 reliable experimental covalent and non-covalent adsorption energies and five activation barriers with mean absolute errors of 2.2 kcal mol−1, 2.7 kcal mol−1, and 1.1 kcal mol−1, respectively, which are lower than for functionals widely used and tested for surface science evaluations, such as BEEF-vdW and RPBE.

  • 18. Baccarini, Andrea
    et al.
    Karlsson, Linn
    Stockholm University, Faculty of Science, Department of Environmental Science.
    Dommen, Josef
    Duplessis, Patrick
    Vüllers, Jutta
    Brooks, Ian M.
    Saiz-Lopez, Alfonso
    Salter, Matthew
    Stockholm University, Faculty of Science, Department of Environmental Science.
    Tjernström, Michael
    Stockholm University, Faculty of Science, Department of Meteorology .
    Baltensperger, Urs
    Zieger, Paul
    Stockholm University, Faculty of Science, Department of Environmental Science.
    Schmale, Julia
    Frequent new particle formation over the high Arctic pack ice by enhanced iodine emissions2020In: Nature Communications, E-ISSN 2041-1723, Vol. 11, no 1, article id 4924Article in journal (Refereed)
    Abstract [en]

    In the central Arctic Ocean the formation of clouds and their properties are sensitive to the availability of cloud condensation nuclei (CCN). The vapors responsible for new particle formation (NPF), potentially leading to CCN, have remained unidentified since the first aerosol measurements in 1991. Here, we report that all the observed NPF events from the Arctic Ocean 2018 expedition are driven by iodic acid with little contribution from sulfuric acid. Iodic acid largely explains the growth of ultrafine particles (UFP) in most events. The iodic acid concentration increases significantly from summer towards autumn, possibly linked to the ocean freeze-up and a seasonal rise in ozone. This leads to a one order of magnitude higher UFP concentration in autumn. Measurements of cloud residuals suggest that particles smaller than 30nm in diameter can activate as CCN. Therefore, iodine NPF has the potential to influence cloud properties over the Arctic Ocean. Which vapors are responsible for new particle formation in the Arctic is largely unknown. Here, the authors show that the formation of new particles at the central Arctic Ocean is mainly driven by iodic acid and that particles smaller than 30nm in diameter can activate as cloud condensation nuclei.

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  • 19. Baker, C. J.
    et al.
    Bertsche, W.
    Capra, A.
    Cesar, C. L.
    Charlton, M.
    Cridland Mathad, A.
    Eriksson, S.
    Evans, A.
    Evetts, N.
    Fabbri, S.
    Fajans, J.
    Friesen, T.
    Fujiwara, M. C.
    Grandemange, P.
    Granum, P.
    Hangst, J. S.
    Hayden, M. E.
    Hodgkinson, D.
    Isaac, C. A.
    Johnson, M. A.
    Jones, J. M.
    Jones, S. A.
    Jonsell, Svante
    Stockholm University, Faculty of Science, Department of Physics.
    Kurchaninov, L.
    Madsen, N.
    Maxwell, D.
    McKenna, J. T. K.
    Menary, S.
    Momose, T.
    Mullan, P.
    Olchanski, K.
    Olin, A.
    Peszka, J.
    Powell, A.
    Pusa, P.
    Rasmussen, C. Ø.
    Robicheaux, F.
    Sacramento, R. L.
    Sameed, M.
    Sarid, E.
    Silveira, D. M.
    Stutter, G.
    So, C.
    Tharp, T. D.
    Thompson, R.
    van der Werf, D. P.
    Wurtele, J. S.
    Sympathetic cooling of positrons to cryogenic temperatures for antihydrogen production2021In: Nature Communications, E-ISSN 2041-1723, Vol. 12, no 1, article id 6139Article in journal (Refereed)
    Abstract [en]

    The positron, the antiparticle of the electron, predicted by Dirac in 1931 and discovered by Anderson in 1933, plays a key role in many scientific and everyday endeavours. Notably, the positron is a constituent of antihydrogen, the only long-lived neutral antimatter bound state that can currently be synthesized at low energy, presenting a prominent system for testing fundamental symmetries with high precision. Here, we report on the use of laser cooled Be+ ions to sympathetically cool a large and dense plasma of positrons to directly measured temperatures below 7 K in a Penning trap for antihydrogen synthesis. This will likely herald a significant increase in the amount of antihydrogen available for experimentation, thus facilitating further improvements in studies of fundamental symmetries. Positrons are key to the production of cold antihydrogen. Here the authors report the sympathetic cooling of positrons by interacting them with laser-cooled Be+ ions resulting in a three-fold reduction of the temperature of positrons for antihydrogen synthesis.

  • 20.
    Banerjee, Ambar
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Coates, Michael R.
    Stockholm University, Faculty of Science, Department of Physics.
    Kowalewski, Markus
    Stockholm University, Faculty of Science, Department of Physics.
    Wikmark, Hampus
    Jay, Raphael M.
    Wernet, Philippe
    Odelius, Michael
    Stockholm University, Faculty of Science, Department of Physics.
    Photoinduced bond oscillations in ironpentacarbonyl give delayed synchronous bursts of carbonmonoxide release2022In: Nature Communications, E-ISSN 2041-1723, Vol. 13, no 1, article id 1337Article in journal (Refereed)
    Abstract [en]

    Early excited state dynamics in the photodissociation of transition metal carbonyls determines the chemical nature of short-lived catalytically active reaction intermediates. However, time-resolved experiments have not yet revealed mechanistic details in the sub-picosecond regime. Hence, in this study the photoexcitation of ironpentacarbonyl Fe(CO)5 is simulated with semi-classical excited state molecular dynamics. We find that the bright metal-to-ligand charge-transfer (MLCT) transition induces synchronous Fe-C oscillations in the trigonal bipyramidal complex leading to periodically reoccurring release of predominantly axial CO. Metaphorically the photoactivated Fe(CO)5 acts as a CO geyser, as a result of dynamics in the potential energy landscape of the axial Fe-C distances and non-adiabatic transitions between manifolds of bound MLCT and dissociative metal-centered (MC) excited states. The predominant release of axial CO ligands and delayed release of equatorial CO ligands are explained in a unified mechanism based on the σ*(Fe-C) anti-bonding character of the receiving orbital in the dissociative MC states.

  • 21. 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, 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.

  • 22. 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, 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.

  • 23. 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, 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.

  • 24. Baumgart, Mona
    et al.
    Röpke, Michael
    Mühlbauer, Max E.
    Asami, Sam
    Mader, Sophie L.
    Fredriksson, Kai
    Groll, Michael
    Gamiz-Hernandez, Ana P.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Technische Universität München, Germany.
    Kaila, Ville R. I.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Technische Universität München, Germany.
    Design of buried charged networks in artificial proteins2021In: Nature Communications, E-ISSN 2041-1723, Vol. 12, no 1, article id 1895Article in journal (Refereed)
    Abstract [en]

    Soluble proteins are universally packed with a hydrophobic core and a polar surface that drive the protein folding process. Yet charged networks within the central protein core are often indispensable for the biological function. Here, we show that natural buried ion-pairs are stabilised by amphiphilic residues that electrostatically shield the charged motif from its surroundings to gain structural stability. To explore this effect, we build artificial proteins with buried ion-pairs by combining directed computational design and biophysical experiments. Our findings illustrate how perturbation in charged networks can introduce structural rearrangements to compensate for desolvation effects. We validate the physical principles by resolving high-resolution atomic structures of the artificial proteins that are resistant towards unfolding at extreme temperatures and harsh chemical conditions. Our findings provide a molecular understanding of functional charged networks and how point mutations may alter the protein's conformational landscape.

  • 25. 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, 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.

  • 26. Bellec, Maëlle
    et al.
    Dufourt, Jérémy
    Hunt, George
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Lenden-Hasse, Hélène
    Trullo, Antonio
    El Aabidine, Amal Zine
    Lamarque, Marie
    Gaskill, Marissa M.
    Faure-Gautron, Heloïse
    Mannervik, Mattias
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Harrison, Melissa M.
    Andrau, Jean-Christophe
    Favard, Cyril
    Radulescu, Ovidiu
    Lagha, Mounia
    The control of transcriptional memory by stable mitotic bookmarking2022In: Nature Communications, E-ISSN 2041-1723, Vol. 13, no 1, article id 1176Article in journal (Refereed)
    Abstract [en]

    To maintain cellular identities during development, gene expression profiles must be faithfully propagated through cell generations. The reestablishment of gene expression patterns upon mitotic exit is mediated, in part, by transcription factors (TF) mitotic bookmarking. However, the mechanisms and functions of TF mitotic bookmarking during early embryogenesis remain poorly understood. In this study, taking advantage of the naturally synchronized mitoses of Drosophila early embryos, we provide evidence that GAGA pioneer factor (GAF) acts as a stable mitotic bookmarker during zygotic genome activation. We show that, during mitosis, GAF remains associated to a large fraction of its interphase targets, including at cis-regulatory sequences of key developmental genes with both active and repressive chromatin signatures. GAF mitotic targets are globally accessible during mitosis and are bookmarked via histone acetylation (H4K8ac). By monitoring the kinetics of transcriptional activation in living embryos, we report that GAF binding establishes competence for rapid activation upon mitotic exit.

  • 27. 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, 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.

  • 28. 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, 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.

  • 29.
    Berglund, Sara
    et al.
    Stockholm University, Faculty of Science, Department of Meteorology .
    Döös, Kristofer
    Stockholm University, Faculty of Science, Department of Meteorology .
    Groeskamp, Sjoerd
    McDougall, Trevor J.
    The downward spiralling nature of the North Atlantic Subtropical Gyre2022In: Nature Communications, E-ISSN 2041-1723, Vol. 13, no 1, article id 2000Article in journal (Refereed)
    Abstract [en]

    The Atlantic Meridional Overturning Circulation (AMOC) regulates the heat distribution and climate of Earth. Here we identify a new feature of the circulation within the North Atlantic Subtropical Gyre that is associated with the northward flowing component of the AMOC. We find that 70% of the water that flows northwards as part of the AMOC circulates the Gyre at least once before it can continue northwards. These circuits are needed to achieve an increase of density and depth through a combination of air-sea interaction and interior mixing processes, before water can escape the latitudes of the Gyre and join the northern upper branch of the AMOC. This points towards an important role of the Gyre circulation in determining the strength and variability of the AMOC and the northward heat transport. Understanding this newly identified role of the North Atlantic Subtropical Gyre is needed to properly represent future changes of the AMOC.

  • 30.
    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, 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.

  • 31. 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, 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.

  • 32.
    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, 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.

  • 33.
    Blichner, Sara M.
    et al.
    Stockholm University, Faculty of Science, Department of Environmental Science. Stockholm University, Faculty of Science, The Bolin Centre for Climate Research (together with KTH & SMHI).
    Yli-Juuti, Taina
    Mielonen, Tero
    Pöhlker, Christopher
    Holopainen, Eemeli
    Heikkinen, Liine
    Stockholm University, Faculty of Science, Department of Environmental Science. Stockholm University, Faculty of Science, The Bolin Centre for Climate Research (together with KTH & SMHI).
    Mohr, Claudia
    Stockholm University, Faculty of Science, Department of Environmental Science. Stockholm University, Faculty of Science, The Bolin Centre for Climate Research (together with KTH & SMHI).
    Artaxo, Paulo
    Carbone, Samara
    Meller, Bruno Backes
    Dias-Júnior, Cléo Quaresma
    Kulmala, Markku
    Petäjä, Tuukka
    Scott, Catherine E.
    Svenhag, Carl
    Nieradzik, Lars
    Sporre, Moa
    Partridge, Daniel G.
    Tovazzi, Emanuele
    Virtanen, Annele
    Kokkola, Harri
    Riipinen, Ilona
    Stockholm University, Faculty of Science, Department of Environmental Science. Stockholm University, Faculty of Science, The Bolin Centre for Climate Research (together with KTH & SMHI).
    Process-evaluation of forest aerosol-cloud-climate feedback shows clear evidence from observations and large uncertainty in models2024In: Nature Communications, E-ISSN 2041-1723, Vol. 15, article id 969Article in journal (Refereed)
    Abstract [en]

    Natural aerosol feedbacks are expected to become more important in the future, as anthropogenic aerosol emissions decrease due to air quality policy. One such feedback is initiated by the increase in biogenic volatile organic compound (BVOC) emissions with higher temperatures, leading to higher secondary organic aerosol (SOA) production and a cooling of the surface via impacts on cloud radiative properties. Motivated by the considerable spread in feedback strength in Earth System Models (ESMs), we here use two long-term observational datasets from boreal and tropical forests, together with satellite data, for a process-based evaluation of the BVOC-aerosol-cloud feedback in four ESMs. The model evaluation shows that the weakest modelled feedback estimates can likely be excluded, but highlights compensating errors making it difficult to draw conclusions of the strongest estimates. Overall, the method of evaluating along process chains shows promise in pin-pointing sources of uncertainty and constraining modelled aerosol feedbacks.

  • 34.
    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, 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.

  • 35. Bondarenko, Vasyl
    et al.
    Wells, Marta M.
    Chen, Qiang
    Tillman, Tommy S.
    Singewald, Kevin
    Lawless, Matthew J.
    Caporoso, Joel
    Brandon, Nicole
    Coleman, Jonathan A.
    Saxena, Sunil
    Lindahl, Erik
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab). KTH Royal Institute of Technology, Sweden.
    Xu, Yan
    Tang, Pei
    Structures of highly flexible intracellular domain of human α7 nicotinic acetylcholine receptor2022In: Nature Communications, E-ISSN 2041-1723, Vol. 13, article id 793Article in journal (Refereed)
    Abstract [en]

    The intracellular domain (ICD) of Cys-loop receptors mediates diverse functions. To date, no structure of a full-length ICD is available due to challenges stemming from its dynamic nature. Here, combining nuclear magnetic resonance (NMR) and electron spin resonance experiments with Rosetta computations, we determine full-length ICD structures of the human α7 nicotinic acetylcholine receptor in a resting state. We show that ~57% of the ICD residues are in highly flexible regions, primarily in a large loop (loop L) with the most mobile segment spanning ~50 Å from the central channel axis. Loop L is anchored onto the MA helix and virtually forms two smaller loops, thereby increasing its stability. Previously known motifs for cytoplasmic binding, regulation, and signaling are found in both the helices and disordered flexible regions, supporting the essential role of the ICD conformational plasticity in orchestrating a broad range of biological processes. 

  • 36.
    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+δ mesa structures2017In: Nature Communications, E-ISSN 2041-1723, Vol. 8, article id 1742Article in journal (Refereed)
    Abstract [en]

    Mesa structures made of Bi2Sr2CaCu2O8+δ 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 ~ 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. 

  • 37.
    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, 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.

  • 38.
    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, 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.

  • 39. Bridges, Hannah R.
    et al.
    Fedor, Justin G.
    Blaza, James N.
    Di Luca, Andrea
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Technische Universität München, Germany.
    Jussupow, Alexander
    Jarman, Owen D.
    Wright, John J.
    Agip, Ahmed-Noor A.
    Gamiz-Hernandez, Ana P.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Technische Universität München, Germany.
    Roessler, Maxie M.
    Kaila, Ville R. I.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Technische Universität München, Germany.
    Hirst, Judy
    Structure of inhibitor-bound mammalian complex I2020In: Nature Communications, E-ISSN 2041-1723, Vol. 11, no 1, article id 5261Article in journal (Refereed)
    Abstract [en]

    Respiratory complex I (NADH:ubiquinone oxidoreductase) captures the free energy from oxidising NADH and reducing ubiquinone to drive protons across the mitochondrial inner membrane and power oxidative phosphorylation. Recent cryo-EM analyses have produced near-complete models of the mammalian complex, but leave the molecular principles of its long-range energy coupling mechanism open to debate. Here, we describe the 3.0-Ao resolution cryo-EM structure of complex I from mouse heart mitochondria with a substrate-like inhibitor, piericidin A, bound in the ubiquinone-binding active site. We combine our structural analyses with both functional and computational studies to demonstrate competitive inhibitor binding poses and provide evidence that two inhibitor molecules bind end-to-end in the long substrate binding channel. Our findings reveal information about the mechanisms of inhibition and substrate reduction that are central for understanding the principles of energy transduction in mammalian complex I. The respiratory complex I (NADH:ubiquinone oxidoreductase) is a large redox-driven proton pump that initiates respiration in mitochondria. Here, the authors present the 3.0 angstrom cryo-EM structure of complex I from mouse heart mitochondria with the ubiquinone-analogue inhibitor piericidin A bound in the active site and with kinetic measurements and MD simulations they further show that this inhibitor acts competitively against the native ubiquinone-10 substrate.

  • 40.
    Bryant, Patrick
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Pozzati, Gabriele
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Elofsson, Arne
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Improved prediction of protein-protein interactions using AlphaFold22022In: Nature Communications, E-ISSN 2041-1723, Vol. 13, no 1, article id 1265Article in journal (Refereed)
    Abstract [en]

    Predicting the structure of interacting protein chains is a fundamental step towards understanding protein function. Unfortunately, no computational method can produce accurate structures of protein complexes. AlphaFold2, has shown unprecedented levels of accuracy in modelling single chain protein structures. Here, we apply AlphaFold2 for the prediction of heterodimeric protein complexes. We find that the AlphaFold2 protocol together with optimised multiple sequence alignments, generate models with acceptable quality (DockQ >= 0.23) for 63% of the dimers. From the predicted interfaces we create a simple function to predict the DockQ score which distinguishes acceptable from incorrect models as well as interacting from non-interacting proteins with state-of-art accuracy. We find that, using the predicted DockQ scores, we can identify 51% of all interacting pairs at 1% FPR. Predicting the structure of protein complexes is extremely difficult. Here, authors apply AlphaFold2 with optimized multiple sequence alignments to model complexes of interacting proteins, enabling prediction of both if and how proteins interact with state-of-art accuracy.

  • 41.
    Bryant, Patrick
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Pozzati, Gabriele
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Zhu, Wensi
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Shenoy, Aditi
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Kundrotas, Petras
    Elofsson, Arne
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Predicting the structure of large protein complexes using AlphaFold and Monte Carlo tree search2022In: Nature Communications, E-ISSN 2041-1723, Vol. 13, no 1, article id 6028Article in journal (Refereed)
    Abstract [en]

    AlphaFold can predict the structure of single- and multiple-chain proteins with very high accuracy. However, the accuracy decreases with the number of chains, and the available GPU memory limits the size of protein complexes which can be predicted. Here we show that one can predict the structure of large complexes starting from predictions of subcomponents. We assemble 91 out of 175 complexes with 10–30 chains from predicted subcomponents using Monte Carlo tree search, with a median TM-score of 0.51. There are 30 highly accurate complexes (TM-score ≥0.8, 33% of complete assemblies). We create a scoring function, mpDockQ, that can distinguish if assemblies are complete and predict their accuracy. We find that complexes containing symmetry are accurately assembled, while asymmetrical complexes remain challenging. The method is freely available and accesible as a Colab notebook https://colab.research.google.com/github/patrickbryant1/MoLPC/blob/master/MoLPC.ipynb.

  • 42.
    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, 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.

  • 43.
    Bunge, Anne Charlotte
    et al.
    Stockholm University, Faculty of Science, Stockholm Resilience Centre.
    Mazac, Rachel
    Stockholm University, Faculty of Science, Stockholm Resilience Centre. University of Helsinki, Finland.
    Clark, Michael
    Wood, Amanda
    Stockholm University, Faculty of Science, Stockholm Resilience Centre.
    Gordon, Line
    Stockholm University, Faculty of Science, Stockholm Resilience Centre.
    Sustainability benefits of transitioning from current diets to plant-based alternatives or whole-food diets in Sweden2024In: Nature Communications, E-ISSN 2041-1723, Vol. 15, article id 951Article in journal (Refereed)
    Abstract [en]

    Plant-based alternatives (PBAs) are increasingly becoming part of diets. Here, we investigate the environmental, nutritional, and economic implications of replacing animal-source foods (ASFs) with PBAs or whole foods (WFs) in the Swedish diet. Utilising two functional units (mass and energy), we model vegan, vegetarian, and flexitarian scenarios, each based on PBAs or WFs. Our results demonstrate that PBA-rich diets substantially reduce greenhouse gas emissions (30–52%), land use (20–45%), and freshwater use (14–27%), with the vegan diet showing the highest reduction potential. We observe comparable environmental benefits when ASFs are replaced with WFs, underscoring the need to reduce ASF consumption. PBA scenarios meet most Nordic Nutrition Recommendations, except for vitamin B12, vitamin D and selenium, while enhancing iron, magnesium, folate, and fibre supply and decreasing saturated fat. Daily food expenditure slightly increases in the PBA scenarios (3–5%) and decreases in the WF scenarios (4–17%), with PBA diets being 10–20% more expensive than WF diets. Here we show, that replacing ASFs with PBAs can reduce the environmental impact of current Swedish diets while meeting most nutritional recommendations, but slightly increases food expenditure. We recommend prioritising ASF reduction and diversifying WFs and healthier PBAs to accommodate diverse consumer preferences during dietary transitions.

  • 44. 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, 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.

  • 45. Büntgen, Ulf
    et al.
    Allen, Kathy
    Anchukaitis, Kevin J.
    Arseneault, Dominique
    Boucher, Étienne
    Bräuning, Achim
    Chatterjee, Snigdhansu
    Cherubini, Paolo
    Churakova, Olga
    Corona, Christophe
    Gennaretti, Fabio
    Grießinger, Jussi
    Guillet, Sebastian
    Guiot, Joel
    Gunnarson, Björn
    Stockholm University, Faculty of Science, Department of Physical Geography.
    Helama, Samuli
    Hochreuther, Philipp
    Hughes, Malcolm K.
    Huybers, Peter
    Kirdyanov, Alexander
    Krusic, Paul J.
    Stockholm University, Faculty of Science, Department of Physical Geography. University of Cambridge, UK.
    Ludescher, Josef
    Meier, Wolfgang J.-H.
    Myglan, Vladimir S.
    Nicolussi, Kurt
    Oppenheimer, Clive
    Reinig, Frederick
    Salzer, Matthew W.
    Seftigen, Kristina
    Stine, Alexander R.
    Stoffel, Markus
    St. George, Scott
    Tejedor, Ernesto
    Trevino, Aleyda
    Trouet, Valerie
    Wang, Jianglin
    Wilson, Rob
    Yang, Bao
    Xu, Guobao B.
    Esper, Jan
    The influence of decision-making in tree ring-based climate reconstructions2021In: Nature Communications, E-ISSN 2041-1723, Vol. 12, no 1, article id 3411Article in journal (Refereed)
    Abstract [en]

    Tree-ring chronologies underpin the majority of annually-resolved reconstructions of Common Era climate. However, they are derived using different datasets and techniques, the ramifications of which have hitherto been little explored. Here, we report the results of a double-blind experiment that yielded 15 Northern Hemisphere summer temperature reconstructions from a common network of regional tree-ring width datasets. Taken together as an ensemble, the Common Era reconstruction mean correlates with instrumental temperatures from 1794-2016 CE at 0.79 (p<0.001), reveals summer cooling in the years following large volcanic eruptions, and exhibits strong warming since the 1980s. Differing in their mean, variance, amplitude, sensitivity, and persistence, the ensemble members demonstrate the influence of subjectivity in the reconstruction process. We therefore recommend the routine use of ensemble reconstruction approaches to provide a more consensual picture of past climate variability. Tree rings are a crucial archive for Common Era climate reconstructions, but the degree to which methodological decisions influence outcomes is not well known. Here, the authors show how different approaches taken by 15 different groups influence the ensemble temperature reconstruction from the same data.

  • 46. 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, 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.

  • 47. 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, 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.

  • 48. 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, 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.

  • 49. 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, 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.

  • 50.
    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, 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.

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