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  • 1.
    Abelein, Axel
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Gräslund, Astrid
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Danielsson, Jens
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Zinc as chaperone-mimicking agent for retardation of amyloid beta peptide fibril formation2015In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 112, no 17, p. 5407-5412Article in journal (Refereed)
    Abstract [en]

    Metal ions have emerged to play a key role in the aggregation process of amyloid beta (A beta) peptide that is closely related to the pathogenesis of Alzheimer's disease. A detailed understanding of the underlying mechanistic process of peptide-metal interactions, however, has been challenging to obtain. By applying a combination of NMR relaxation dispersion and fluorescence kinetics methods we have investigated quantitatively the thermodynamic A beta-Zn2+ binding features as well as how Zn2+ modulates the nucleation mechanism of the aggregation process. Our results show that, under near-physiological conditions, substoichiometric amounts of Zn2+ effectively retard the generation of amyloid fibrils. A global kinetic profile analysis reveals that in the absence of zinc A beta(40) aggregation is driven by a monomer-dependent secondary nucleation process in addition to fibril-end elongation. In the presence of Zn2+, the elongation rate is reduced, resulting in reduction of the aggregation rate, but not a complete inhibition of amyloid formation. We show that Zn2+ transiently binds to residues in the N terminus of the monomeric peptide. A thermodynamic analysis supports a model where the N terminus is folded around the Zn2+ ion, forming a marginally stable, short-lived folded A beta(40) species. This conformation is highly dynamic and only a few percent of the peptide molecules adopt this structure at any given time point. Our findings suggest that the folded A beta(40)-Zn2+ complex modulates the fibril ends, where elongation takes place, which efficiently retards fibril formation. In this conceptual framework we propose that zinc adopts the role of a minimal antiaggregation chaperone for A beta(40).

  • 2.
    Acerbi, Alberto
    et al.
    Department of Psychology, University of Bologna.
    Enquist, Magnus
    Stockholm University, Faculty of Humanities, Centre for the Study of Cultural Evolution. Stockholm University, Faculty of Science, Department of Zoology, Department of Ethology.
    Ghirlanda, Stefano
    Stockholm University, Faculty of Humanities, Centre for the Study of Cultural Evolution.
    Cultural evolution and individual development of openness and conservatism2009In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 106, no 45, p. 18931-18935Article in journal (Refereed)
    Abstract [en]

    We present a model of cultural evolution in which an individual's propensity to engage in social learning is affected by social learning itself. We assume that individuals observe cultural traits displayed by others and decide whether to copy them based on their overall preference for the displayed traits. Preferences, too, can be transmitted between individuals. Our results show that such cultural dynamics tends to produce conservative individuals, i.e., individuals who are reluctant to copy new traits. Openness to new information, however, can be maintained when individuals need significant time to acquire the cultural traits that make them effective cultural models. We show that a gradual enculturation of young individuals by many models and a larger cultural repertoire to be acquired are favorable circumstances for the long-term maintenance of openness in individuals and groups. Our results agree with data about lifetime personality change, showing that openness to new information decreases with age. Our results show that cultural remodeling of cultural transmission is a powerful force in cultural evolution, i.e., that cultural evolution can change its own dynamics

  • 3. Ahn, Young O.
    et al.
    Mahinthichaichan, Paween
    Lee, Hyun Ju
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Ouyang, Hanlin
    Kaluka, Daniel
    Yeh, Syun-Ru
    Arjona, Davinia
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Rousseau, Denis L.
    Tajkhorshid, Emad
    Ädelroth, Pia
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Gennis, Robert B.
    Conformational coupling between the active site and residues within the K-C-channel of the Vibrio cholerae cbb(3)-type (C-family) oxygen reductase2014In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 111, no 42, p. E4419-E4428Article in journal (Refereed)
    Abstract [en]

    The respiratory chains of nearly all aerobic organisms are terminated by proton-pumping heme-copper oxygen reductases (HCOs). Previous studies have established that C-family HCOs contain a single channel for uptake from the bacterial cytoplasm of all chemical and pumped protons, and that the entrance of the K-C-channel is a conserved glutamate in subunit III. However, the majority of the K-C-channel is within subunit I, and the pathway from this conserved glutamate to subunit I is not evident. In the present study, molecular dynamics simulations were used to characterize a chain of water molecules leading from the cytoplasmic solution, passing the conserved glutamate in subunit III and extending into subunit I. Formation of the water chain, which controls the delivery of protons to the K-C-channel, was found to depend on the conformation of Y241(Vc), located in subunit I at the interface with subunit III. Mutations of Y241(Vc) (to A/F/H/S) in the Vibrio cholerae cbb(3) eliminate catalytic activity, but also cause perturbations that propagate over a 28-angstrom distance to the active site heme b(3). The data suggest a linkage between residues lining the KC-channel and the active site of the enzyme, possibly mediated by transmembrane helix alpha 7, which contains both Y241(Vc) and the active site crosslinked Y255(Vc), as well as two Cu-B histidine ligands. Other mutations of residues within or near helix alpha 7 also perturb the active site, indicating that this helix is involved in modulation of the active site of the enzyme.

  • 4.
    Almås, Ingvild
    et al.
    Stockholm University, Faculty of Social Sciences, Institute for International Economic Studies. Norwegian School of Economics, Norway.
    Cappelen, Alexander W.
    Sørensen, Erik Ø.
    Tungodden, Bertil
    Global evidence on the selfish rich inequality hypothesis2022In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 119, no 3, article id e2109690119Article in journal (Refereed)
    Abstract [en]

    We report on a study of whether people believe that the rich are richer than the poor because they have been more selfish in life, using data from more than 26,000 individuals in 60 countries. The findings show a strong belief in the selfish rich inequality hypothesis at the global level; in the majority of countries, the mode is to strongly agree with it. However, we also identify important between- and within-country variation. We find that the belief in selfish rich inequality is much stronger in countries with extensive corruption and weak institutions and less strong among people who are higher in the income distribution in their society. Finally, we show that the belief in selfish rich inequality is predictive of people’s policy views on inequality and redistribution: It is significantly positively associated with agreeing that inequality in their country is unfair, and it is significantly positively associated with agreeing that the government should aim to reduce inequality. These relationships are highly significant both across and within countries and robust to including country-level or individual-level controls and using Lasso-selected regressors. Thus, the data provide compelling evidence of people believing that the rich are richer because they have been more selfish in life and perceiving selfish behavior as creating unfair inequality and justifying equalizing policies.

  • 5. Alonso-Mori, Roberto
    et al.
    Kern, Jan
    Gildea, Richard J.
    Sokaras, Dimosthenis
    Weng, Tsu-Chien
    Lassalle-Kaiser, Benedikt
    Tran, Rosalie
    Hattne, Johan
    Laksmono, Hartawan
    Hellmich, Julia
    Glöckner, Carina
    Echols, Nathaniel
    Sierra, Raymond G.
    Schafer, Donald W.
    Sellberg, Jonas
    Stockholm University, Faculty of Science, Department of Physics. SLAC National Accelerator Laboratory, USA.
    Kenney, Christopher
    Herbst, Ryan
    Pines, Jack
    Hart, Philip
    Herrmann, Sven
    Grosse-Kunstleve, Ralf W.
    Latimer, Matthew J.
    Fry, Alan R.
    Messerschmidt, Marc M.
    Miahnahri, Alan
    Seibert, M. Marvin
    Zwart, Petrus H.
    White, William E.
    Adams, Paul D.
    Bogan, Michael J.
    Boutet, Sébastien
    Williams, Garth J.
    Zouni, Athina
    Messinger, Johannes
    Glatzel, Pieter
    Sauter, Nicholas K.
    Yachandra, Vittal K.
    Yano, Junko
    Bergmann, Uwe
    Energy-dispersive X-ray emission spectroscopy using an X-ray free-electron laser in a shot-by-shot mode2012In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 109, no 47, p. 19103-19107Article in journal (Refereed)
    Abstract [en]

    The ultrabright femtosecond X-ray pulses provided by X-ray free-electron lasers open capabilities for studying the structure and dynamics of a wide variety of systems beyond what is possible with synchrotron sources. Recently, this probe-before-destroy approach has been demonstrated for atomic structure determination by serial X-ray diffraction of microcrystals. There has been the question whether a similar approach can be extended to probe the local electronic structure by X-ray spectroscopy. To address this, we have carried out femtosecond X-ray emission spectroscopy (XES) at the Linac Coherent Light Source using redox-active Mn complexes. XES probes the charge and spin states as well as the ligand environment, critical for understanding the functional role of redox-active metal sites. K beta(1,3) XES spectra of Mn-II and Mn-2(III,IV) complexes at room temperature were collected using a wavelength dispersive spectrometer and femtosecond X-ray pulses with an individual dose of up to > 100 MGy. The spectra were found in agreement with undamaged spectra collected at low dose using synchrotron radiation. Our results demonstrate that the intact electronic structure of redox active transition metal compounds in different oxidation states can be characterized with this shot-by-shot method. This opens the door for studying the chemical dynamics of metal catalytic sites by following reactions under functional conditions. The technique can be combined with X-ray diffraction to simultaneously obtain the geometric structure of the overall protein and the local chemistry of active metal sites and is expected to prove valuable for understanding the mechanism of important metalloproteins, such as photosystem II.

  • 6.
    Altmejd, Adam
    et al.
    Stockholm University, Faculty of Social Sciences, The Swedish Institute for Social Research (SOFI).
    Östergren, Olof
    Stockholm University, Faculty of Social Sciences, Department of Public Health Sciences.
    Björkegren, Evelina
    Stockholm University, Faculty of Social Sciences, Department of Economics.
    Persson, Torsten
    Stockholm University, Faculty of Social Sciences, Institute for International Economic Studies. London School of Economics, London, United Kingdon.
    Inequality and COVID-19 in Sweden: Relative risks of nine bad life events, by four social gradients, in pandemic vs. prepandemic years2023In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 120, no 46, article id e2303640120Article in journal (Refereed)
    Abstract [en]

    The COVID-19 pandemic struck societies directly and indirectly, not just challenging population health but disrupting many aspects of life. Different effects of the spreading virus—and the measures to fight it—are reported and discussed in different scientific fora, with hard-to-compare methods and metrics from different traditions. While the pandemic struck some groups more than others, it is difficult to assess the comprehensive impact on social inequalities. This paper gauges social inequalities using individual-level administrative data for Sweden’s entire population. We describe and analyze the relative risks for different social groups in four dimensions—gender, education, income, and world region of birth—to experience three types of COVID-19 incidence, as well as six additional negative life outcomes that reflect general health, access to medical care, and economic strain. During the pandemic, the overall population faced severe morbidity and mortality from COVID-19 and saw higher all-cause mortality, income losses and unemployment risks, as well as reduced access to medical care. These burdens fell more heavily on individuals with low income or education and on immigrants. Although these vulnerable groups experienced larger absolute risks of suffering the direct and indirect consequences of the pandemic, the relative risks in pandemic years (2020 and 2021) were conspicuously similar to those in prepandemic years (2016 to 2019)

  • 7. Antonelli, A
    et al.
    Nylander, Johan
    Stockholm University, Faculty of Science, Department of Botany.
    Persson, C
    Sanmartín, I
    Tracing the impact of the Andean uplift on Neotropical plant evolution: evidence from the coffee family2009In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 106, no 24, p. 9749-9754Article in journal (Refereed)
    Abstract [en]

    Recent phylogenetic studies have revealed the major role played by the uplift of the Andes in the extraordinary diversification of the Neotropical flora. These studies, however, have typically considered the Andean uplift as a single, time-limited event fostering the evolution of highland elements. This contrasts with geological reconstructions indicating that the uplift occurred in discrete periods from west to east and that it affected different regions at different times. We introduce an approach for integrating Andean tectonics with biogeographic reconstructions of Neotropical plants, using the coffee family (Rubiaceae) as a model group. The distribution of this family spans highland and montane habitats as well as tropical lowlands of Central and South America, thus offering a unique opportunity to study the influence of the Andean uplift on the entire Neotropical flora. Our results suggest that the Rubiaceae originated in the Paleotropics and used the boreotropical connection to reach South America. The biogeographic patterns found corroborate the existence of a long-lasting dispersal barrier between the Northern and Central Andes, the "Western Andean Portal.'' The uplift of the Eastern Cordillera ended this barrier, allowing dispersal of boreotropical lineages to the South, but gave rise to a huge wetland system ("Lake Pebas'') in western Amazonia that prevented in situ speciation and floristic dispersal between the Andes and Amazonia for at least 6 million years. Here, we provide evidence of these events in plants

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  • 8. Aze, Tracy
    et al.
    Ezard, Thomas H. G.
    Purvis, Andy
    Coxall, Helen K.
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Stewart, Duncan R. M.
    Wade, Bridget S.
    Pearson, Paul N.
    Identifying anagenesis cladogenesis in the fossil record2013In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 110, no 32, p. E2946-E2946Article in journal (Other academic)
  • 9. Bak-Coleman, Joseph B.
    et al.
    Alfano, Mark
    Barfuss, Wolfram
    Bergstrom, Carl T.
    Centeno, Miguel A.
    Couzin, Iain D.
    Donges, Jonathan F.
    Stockholm University, Faculty of Science, Stockholm Resilience Centre. Potsdam Institute for Climate Impact Research, Germany.
    Galesic, Mirta
    Gersick, Andrew S.
    Jacquet, Jennifer
    Kao, Albert B.
    Moran, Rachel E.
    Romanczuk, Pawel
    Rubenstein, Daniel
    Tombak, Kaia J.
    Van Bavel, Jay J.
    Weber, Elke U.
    Stewardship of global collective behavior2021In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 118, no 27, article id e2025764118Article in journal (Refereed)
    Abstract [en]

    Collective behavior provides a framework for understanding how the actions and properties of groups emerge from the way individuals generate and share information. In humans, information flows were initially shaped by natural selection yet are increasingly structured by emerging communication technologies. Our larger, more complex social networks now transfer high-fidelity information over vast distances at low cost. The digital age and the rise of social media have accelerated changes to our social systems, with poorly understood functional consequences. This gap in our knowledge represents a principal challenge to scientific progress, democracy, and actions to address global crises. We argue that the study of collective behavior must rise to a crisis discipline just as medicine, conservation, and climate science have, with a focus on providing actionable insight to policymakers and regulators for the stewardship of social systems.

  • 10.
    Balk, Lennart
    et al.
    Stockholm University, Faculty of Science, Department of Applied Environmental Science (ITM).
    Hägerroth, Per-Ake
    Stockholm University, Faculty of Science, Department of Applied Environmental Science (ITM).
    Åkerman, Gun
    Stockholm University, Faculty of Science, Department of Applied Environmental Science (ITM).
    Hanson, Marsha
    Stockholm University, Faculty of Science, Department of Applied Environmental Science (ITM).
    Tjärnlund, Ulla
    Stockholm University, Faculty of Science, Department of Applied Environmental Science (ITM).
    Hansson, Tomas
    Stockholm University, Faculty of Science, Department of Applied Environmental Science (ITM).
    Hallgrimsson, Gunnar Thor
    Zebühr, Yngve
    Stockholm University, Faculty of Science, Department of Applied Environmental Science (ITM).
    Broman, Dag
    Stockholm University, Faculty of Science, Department of Applied Environmental Science (ITM).
    Mörner, Torsten
    Sundberg, Henrik
    Wild birds of declining European species are dying from a thiamine deficiency syndrome.2009In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 106, no 29, p. 12001-12006Article in journal (Refereed)
    Abstract [en]

    Wild birds of several species are dying in large numbers from an idiopathic paralytic disease in the Baltic Sea area. Here, we demonstrate strong relationships between this disease, breeding failure, and thiamine (vitamin B(1)) deficiency in eggs, pulli, and full-grown individuals. Thiamine is essential for vertebrates, and its diphosphorylated form functions as a cofactor for several life sustaining enzymes, whereas the triphosphorylated form is necessary for the functioning of neuronal membranes. Paralyzed individuals were remedied by thiamine treatment. Moreover, thiamine deficiency and detrimental effects on thiamine-dependent enzymes were demonstrated in the yolk, liver, and brain. We propose that the mortality and breeding failure are part of a thiamine deficiency syndrome, which may have contributed significantly to declines in many bird populations during the last decades.

  • 11. Barfuss, Wolfra
    et al.
    Donges, Jonathan F.
    Stockholm University, Faculty of Science, Stockholm Resilience Centre. Potsdam Institute for Climate Impact Research, Germany.
    Vasconcelos, Vitor V.
    Kurths, Jürgen
    Levin, Simon A.
    Caring for the future can turn tragedy into comedy for long-term collective action under risk of collapse2020In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 117, no 23, p. 12915-12922Article in journal (Refereed)
    Abstract [en]

    We will need collective action to avoid catastrophic climate change, and this will require valuing the long term as well as the short term. Shortsightedness and uncertainty have hindered progress in resolving this collective action problem and have been recognized as important barriers to cooperation among humans. Here, we propose a coupled social-ecological dilemma to investigate the interdependence of three well-identified components of this cooperation problem: 1) timescales of collapse and recovery in relation to time preferences regarding future outcomes, 2) the magnitude of the impact of collapse, and 3) the number of actors in the collective. We find that, under a sufficiently severe and time-distant collapse, how much the actors care for the future can transform the game from a tragedy of the commons into one of coordination, and even into a comedy of the commons in which cooperation dominates. Conversely, we also find conditions under which even strong concern for the future still does not transform the problem from tragedy to comedy. For a large number of participating actors, we find that the critical collapse impact, at which these game regime changes happen, converges to a fixed value of collapse impact per actor that is independent of the enhancement factor of the public good, which is usually regarded as the driver of the dilemma. Our results not only call for experimental testing but also help explain why polarization in beliefs about human-caused climate change can threaten global cooperation agreements.

  • 12. Barrett, Scott
    et al.
    Dasgupta, Aisha
    Dasgupta, Partha
    Adger, W. Neil
    Anderies, John
    van den Bergh, Jeroen
    Bledsoe, Caroline
    Bongaarts, John
    Carpenter, Stephen
    Chapin, F. Stuart
    Crépin, Anne-Sophie
    Daily, Gretchen
    Ehrlich, Paul
    Folke, Carl
    Stockholm University, Faculty of Science, Stockholm Resilience Centre. Royal Swedish Academy of Sciences, Sweden.
    Kautsky, Nils
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Lambin, Eric F.
    Levin, Simon A.
    Mäler, Karl-Göran
    Naylor, Rosamond
    Nyborg, Karine
    Polasky, Stephen
    Scheffer, Marten
    Shogren, Jason
    Søgaard Jørgensen, Peter
    Stockholm University, Faculty of Science, Stockholm Resilience Centre. Royal Swedish Academy of Sciences, Sweden.
    Walker, Brian
    Wilen, James
    Social dimensions of fertility behavior and consumption patterns in the Anthropocene2020In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 117, no 12, p. 6300-6307Article in journal (Refereed)
    Abstract [en]

    We consider two aspects of the human enterprise that profoundly affect the global environment: population and consumption. We show that fertility and consumption behavior harbor a class of externalities that have not been much noted in the literature. Both are driven in part by attitudes and preferences that are not egoistic but socially embedded; that is, each household's decisions are influenced by the decisions made by others. In a famous paper, Garrett Hardin [G. Hardin, Science 162, 1243-1248 (1968)] drew attention to overpopulation and concluded that the solution lay in people abandoning the freedom to breed. That human attitudes and practices are socially embedded suggests that it is possible for people to reduce their fertility rates and consumption demands without experiencing a loss in wellbeing. We focus on fertility in sub-Saharan Africa and consumption in the rich world and argue that bottom-up social mechanisms rather than top-down government interventions are better placed to bring about those ecologically desirable changes.

  • 13. Bastos, André M.
    et al.
    Lundqvist, Mikael
    Stockholm University, Faculty of Social Sciences, Department of Psychology, Biological psychology. Massachusetts Institute of Technology, USA.
    Waite, Ayan S.
    Kopell, Nancy
    Miller, Earl K.
    Layer and rhythm specificity for predictive routing2020In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 117, no 49, p. 31459-31469Article in journal (Refereed)
    Abstract [en]

    In predictive coding, experience generates predictions that attenuate the feeding forward of predicted stimuli while passing forward unpredicted “errors.” Different models have suggested distinct cortical layers, and rhythms implement predictive coding. We recorded spikes and local field potentials from laminar electrodes in five cortical areas (visual area 4 [V4], lateral intraparietal [LIP], posterior parietal area 7A, frontal eye field [FEF], and prefrontal cortex [PFC]) while monkeys performed a task that modulated visual stimulus predictability. During predictable blocks, there was enhanced alpha (8 to 14 Hz) or beta (15 to 30 Hz) power in all areas during stimulus processing and prestimulus beta (15 to 30 Hz) functional connectivity in deep layers of PFC to the other areas. Unpredictable stimuli were associated with increases in spiking and in gamma-band (40 to 90 Hz) power/connectivity that fed forward up the cortical hierarchy via superficial-layer cortex. Power and spiking modulation by predictability was stimulus specific. Alpha/beta power in LIP, FEF, and PFC inhibited spiking in deep layers of V4. Area 7A uniquely showed increases in high-beta (∼22 to 28 Hz) power/connectivity to unpredictable stimuli. These results motivate a conceptual model, predictive routing. It suggests that predictive coding may be implemented via lower-frequency alpha/beta rhythms that “prepare” pathways processing-predicted inputs by inhibiting feedforward gamma rhythms and associated spiking.

  • 14. Baym, Gordons
    et al.
    Pethick, Christopher J.
    Stockholm University, Nordic Institute for Theoretical Physics (Nordita). University of Copenhagen, Denmark.
    Ben Mottelson: Codeveloper of the unified theory of the structure and dynamics of atomic nuclei2022In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 119, no 40, article id e2214052119Article in journal (Other academic)
  • 15. Bergelson, Elika
    et al.
    Soderstrom, Melanie
    Schwarz, Iris-Corinna
    Stockholm University, Faculty of Humanities, Department of Linguistics, Phonetics. Stockholm University, Faculty of Social Sciences, Department of Special Education.
    Rowland, Caroline F.
    Ramírez-Esparza, Nairán
    R. Hamrick, Lisa
    Marklund, Ellen
    Stockholm University, Faculty of Humanities, Department of Linguistics, Phonetics.
    Kalashnikova, Marina
    Guez, Ava
    Casillas, Marisa
    Benetti, Lucia
    Alphen, Petra van
    Cristia, Alejandrina
    Everyday language input and production in 1,001 children from six continents2023In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 120, no 52Article in journal (Refereed)
    Abstract [en]

    Language is a universal human ability, acquired readily by young children, who otherwise struggle with many basics of survival. And yet, language ability is variable across individuals. Naturalistic and experimental observations suggest that children’s linguistic skills vary with factors like socioeconomic status and children’s gender. But which factors really influence children’s day-to-day language use? Here, we leverage speech technology in a big-data approach to report on a unique cross-cultural and diverse data set: >2,500 d-long, child-centered audio-recordings of 1,001 2- to 48-mo-olds from 12 countries spanning six continents across urban, farmer-forager, and subsistence-farming contexts. As expected, age and language-relevant clinical risks and diagnoses predicted how much speech (and speech-like vocalization) children produced. Critically, so too did adult talk in children’s environments: Children who heard more talk from adults produced more speech. In contrast to previous conclusions based on more limited sampling methods and a different set of language proxies, socioeconomic status (operationalized as maternal education) was not significantly associated with children’s productions over the first 4y of life, and neither were gender or multilingualism. These findings from large-scale naturalistic data advance our understanding of which factors are robust predictors of variability in the speech behaviors of young learners in a wide range of everyday contexts.

  • 16. Berger, Thor
    et al.
    Engzell, Per
    Stockholm University, Faculty of Social Sciences, The Swedish Institute for Social Research (SOFI). University of Oxford, United Kingdom.
    American geography of opportunity reveals European origins2019In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 116, no 13, p. 6045-6050Article in journal (Refereed)
    Abstract [en]

    A large literature documents how intergenerational mobility-the degree to which (dis)advantage is passed on from parents to children-varies across and within countries. Less is known about the origin or persistence of such differences. We show that US areas populated by descendants to European immigrants have similar levels of income equality and mobility as the countries their forebears came from: highest in areas dominated by descendants to Scandinavian and German immigrants, lower in places with French or Italian heritage, and lower still in areas with British roots. Similar variation in mobility is found for the black population and when analyzing causal place effects, suggesting that mobility differences arise at the community level and extend beyond descendants of European immigrant groups. Our findings indicate that the geography of US opportunity may have deeper historical roots than previously recognized.

  • 17. Bergh, Johan
    et al.
    Zetterstrom, Per
    Andersen, Peter M.
    Brannstrom, Thomas
    Graffmo, Karin S.
    Jonsson, P. Andreas
    Lang, Lisa
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Danielsson, Jens
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Oliveberg, Mikael
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Marklund, Stefan L.
    Structural and kinetic analysis of protein-aggregate strains in vivo using binary epitope mapping2015In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 112, no 14, p. 4489-4494Article in journal (Refereed)
    Abstract [en]

    Despite considerable progress in uncovering the molecular details of protein aggregation in vitro, the cause and mechanism of protein-aggregation disease remain poorly understood. One reason is that the amount of pathological aggregates in neural tissue is exceedingly low, precluding examination by conventional approaches. We present here a method for determination of the structure and quantity of aggregates in small tissue samples, circumventing the above problem. The method is based on binary epitope mapping using anti-peptide antibodies. We assessed the usefulness and versatility of the method in mice modeling the neurodegenerative disease amyotrophic lateral sclerosis, which accumulate intracellular aggregates of superoxide dismutase-1. Two strains of aggregates were identified with different structural architectures, molecular properties, and growth kinetics. Both were different from superoxide dismutase-1 aggregates generated in vitro under a variety of conditions. The strains, which seem kinetically under fragmentation control, are associated with different disease progressions, complying with and adding detail to the growing evidence that seeding, infectivity, and strain dependence are unifying principles of neurodegenerative disease.

  • 18.
    Bernsel, Andreas
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Viklund, Håkan
    Falk, Jenny
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Lindahl, Erik
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    von Heijne, Gunnar
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Elofsson, Arne
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Prediction of membrane-protein topology from first principles2008In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 105, no 20, p. 7177-7181Article in journal (Refereed)
  • 19. Berrah, Nora
    et al.
    Fang, Li
    Murphy, Brendan
    Osipov, Timur
    Ueda, Kiyoshi
    Kukk, Edwin
    Feifel, Raimund
    van der Meulen, Peter
    Stockholm University, Faculty of Science, Department of Physics.
    Salén, Peter
    Stockholm University, Faculty of Science, Department of Physics.
    Schmidt, Henning T.
    Stockholm University, Faculty of Science, Department of Physics.
    Thomas, Richard D.
    Stockholm University, Faculty of Science, Department of Physics.
    Larsson, Mats
    Stockholm University, Faculty of Science, Department of Physics.
    Richter, Robert
    Prince, Kevin C.
    Bozek, John D.
    Bostedt, Christoph
    Wada, Shin-ichi
    Piancastelli, Maria N.
    Tashiro, Motomichi
    Ehara, Masahiro
    Double-core-hole spectroscopy for chemical analysis with an intense X-ray femtosecond laser2011In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 108, no 41, p. 16912-16915Article in journal (Refereed)
    Abstract [en]

    Theory predicts that double-core-hole (DCH) spectroscopy can provide a new powerful means of differentiating between similar chemical systems with a sensitivity not hitherto possible. Although DCH ionization on a single site in molecules was recently measured with double-and single-photon absorption, double-core holes with single vacancies on two different sites, allowing unambiguous chemical analysis, have remained elusive. Here we report that direct observation of double-core holes with single vacancies on two different sites produced via sequential two-photon absorption, using short, intense X-ray pulses from the Linac Coherent Light Source free-electron laser and compare it with theoretical modeling. The observation of DCH states, which exhibit a unique signature, and agreement with theory proves the feasibility of the method. Our findings exploit the ultrashort pulse duration of the free-electron laser to eject two core electrons on a time scale comparable to that of Auger decay and demonstrate possible future X-ray control of physical inner-shell processes.

  • 20.
    Berry, Bruce W.
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. University of Pennsylvania, USA.
    Martinez-Rivera, Melissa C.
    Tommos, Cecilia
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. University of Pennsylvania, USA.
    Reversible voltammograms and a Pourbaix diagram for a protein tyrosine radical2012In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 109, no 25, p. 9739-9743Article in journal (Refereed)
    Abstract [en]

    Reversible voltammograms and a voltammetry half-wave potential versus solution pH diagram are described for a protein tyrosine radical. This work required a de novo designed tyrosine-radical protein displaying a unique combination of structural and electrochemical properties. The alpha Y-3 protein is structurally stable across a broad pH range. The redox-active tyrosine Y32 resides in a desolvated and well-structured environment. Y32 gives rise to reversible square-wave and differential pulse voltammograms at alkaline pH. The formal potential of the Y32-O-center dot/Y32-OH redox couple is determined to 918 +/- 2 mV versus the normal hydrogen electrode at pH 8.40 +/- 0.01. The observation that Y32 gives rise to fully reversible voltammograms translates into an estimated lifetime of >= 30 ms for the Y32-O-center dot state. This illustrates the range of tyrosine-radical stabilization that a structured protein can offer. Y32 gives rise to quasireversible square-wave and differential pulse voltammograms at acidic pH. These voltammograms represent the Y32 species at the upper edge of the quasirevesible range. The square-wave net potential closely approximates the formal potential of the Y32-O center dot/Y32-OH redox couple to 1,070 +/- 1 mV versus the normal hydrogen electrode at pH 5.52 +/- 0.01. The differential pulse voltammetry half-wave potential of the Y32-O-center dot/Y32-OH redox pair is measured between pH 4.7 and 9.0. These results are described and analyzed.

  • 21.
    Berthold, Catrine L.
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Wang, He
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Nordlund, Stefan
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Högbom, Martin
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Mechanism of ADP-ribosylation removal revealed by the structure and ligand complexes of the dimanganese mono-ADP-ribosylhydrolase DraG2009In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 106, no 34, p. 14247-14252Article in journal (Refereed)
    Abstract [en]

    ADP-ribosylation is a ubiquitous regulatory posttranslational modification involved in numerous key processes such as DNA repair, transcription, cell differentiation, apoptosis, and the pathogenic mechanism of certain bacterial toxins. Despite the importance of this reversible process, very little is known about the structure and mechanism of the hydrolases that catalyze removal of the ADP-ribose moiety. In the phototrophic bacterium Rhodospirillum rubrum, dinitrogenase reductase-activating glycohydrolase (DraG), a dimanganese enzyme that reversibly associates with the cell membrane, is a key player in the regulation of nitrogenase activity. DraG has long served as a model protein for ADP-ribosylhydrolases. Here, we present the crystal structure of DraG in the holo and ADP-ribose bound forms. We also present the structure of a reaction intermediate analogue and propose a detailed catalytic mechanism for protein de-ADP-ribosylation involving ring opening of the substrate ribose. In addition, the particular manganese coordination in DraG suggests a rationale for the enzyme's preference for manganese over magnesium, although not requiring a redox active metal for the reaction.

  • 22. Blöcher, Jens
    et al.
    Brami, Maxime
    Feinauer, Isabelle Sofie
    Stockholm University, Faculty of Science, Department of Zoology. Johannes Gutenberg University, Germany; Centre for Palaeogenetics, Sweden; Swedish Museum of Natural History, Sweden.
    Stolarczyk, Eliza
    Diekmann, Yoan
    Vetterdietz, Lisa
    Karapetian, Marina
    Winkelbach, Laura
    Kokot, Vanessa
    Vallini, Leonardo
    Stobbe, Astrid
    Haak, Wolfgang
    Papageorgopoulou, Christina
    Krause, Rüdiger
    Sharapova, Svetlana
    Burger, Joachim
    Descent, marriage, and residence practices of a 3,800-year-old pastoral community in Central Eurasia2023In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 120, no 36, article id e2303574120Article in journal (Refereed)
    Abstract [en]

    Our understanding of prehistoric societal organization at the family level is still limited. Here, we generated genome data from 32 individuals from an approximately 3,800-y-old burial mound attributed to the Bronze Age Srubnaya-Alakul cultural tradition at the site of Nepluyevsky, located in the Southern Ural region of Central Eurasia. We found that life expectancy was generally very low, with adult males living on average 8 y longer than females. A total of 35 first-degree, 40 second-degree, and 48 third-degree biological relationships connected 23 of the studied individuals, allowing us to propose a family tree spanning three generations with six brothers at its center. The oldest of these brothers had eight children with two women and the most children overall, whereas the other relationships were monogamous. Notably, related female children above the age of five were completely absent from the site, and adult females were more genetically diverse than males. These results suggest that biological relationships between male siblings played a structural role in society and that descent group membership was based on patrilineality. Women originated from a larger mating network and moved to join the men, with whom they were buried. Finally, the oldest brother likely held a higher social position, which was expressed in terms of fertility.

  • 23. Bohutínská, Magdalena
    et al.
    Vlček, Jakub
    Yair, Sivan
    Laenen, Benjamin
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Konečná, Veronika
    Fracassetti, Marco
    Stockholm University, Science for Life Laboratory (SciLifeLab). Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Slotte, Tanja
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Kolář, Filip
    Genomic basis of parallel adaptation varies with divergence in Arabidopsis and its relatives2021In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 118, no 21, article id e2022713118Article in journal (Refereed)
    Abstract [en]

    Parallel adaptation provides valuable insight into the predictability of evolutionary change through replicated natural experiments. A steadily increasing number of studies have demonstrated genomic parallelism, yet the magnitude of this parallelism varies depending on whether populations, species, or genera are compared. This led us to hypothesize that the magnitude of genomic parallelism scales with genetic divergence between lineages, but whether this is the case and the underlying evolutionary processes remain unknown. Here, we resequenced seven parallel lineages of two Arabidopsis species, which repeatedly adapted to challenging alpine environments. By combining genome-wide divergence scans with model-based approaches, we detected a suite of 151 genes that show parallel signatures of positive selection associated with alpine colonization, involved in response to cold, high radiation, short season, herbivores, and pathogens. We complemented these parallel candidates with published gene lists from five additional alpine Brassicaceae and tested our hypothesis on a broad scale spanning ∼0.02 to 18 My of divergence. Indeed, we found quantitatively variable genomic parallelism whose extent significantly decreased with increasing divergence between the compared lineages. We further modeled parallel evolution over the Arabidopsis candidate genes and showed that a decreasing probability of repeated selection on the same standing or introgressed alleles drives the observed pattern of divergence-dependent parallelism. We therefore conclude that genetic divergence between populations, species, and genera, affecting the pool of shared variants, is an important factor in the predictability of genome evolution.

  • 24.
    Boija, Ann
    et al.
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Mannervik, Mattias
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Initiation of diverse epigenetic states during nuclear programming of the Drosophila body plan2016In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 113, no 31, p. 8735-8740Article in journal (Refereed)
    Abstract [en]

    Epigenetic patterns of histone modifications contribute to the maintenance of tissue-specific gene expression. Here, we show that such modifications also accompany the specification of cell identities by the NF-kappa B transcription factor Dorsal in the precellular Drosophila embryo. We provide evidence that the maternal pioneer factor, Zelda, is responsible for establishing poised RNA polymerase at Dorsal target genes before Dorsal-mediated zygotic activation. At the onset of cell specification, Dorsal recruits the CBP/p300 coactivator to the regulatory regions of defined target genes in the presumptive neuroectoderm, resulting in their histone acetylation and transcriptional activation. These genes are inactive in the mesoderm due to transcriptional quenching by the Snail repressor, which precludes recruitment of CBP and prevents histone acetylation. By contrast, inactivation of the same enhancers in the dorsal ectoderm is associated with Polycomb-repressed H3K27me3 chromatin. Thus, the Dorsal morphogen gradient produces three distinct histone signatures including two modes of transcriptional repression, active repression (hypoacetylation), and inactivity (H3K27me3). Whereas histone hypoacetylation is associated with a poised polymerase, H3K27me3 displaces polymerase from chromatin. Our results link different modes of RNA polymerase regulation to separate epigenetic patterns and demonstrate that developmental determinants orchestrate differential chromatin states, providing new insights into the link between epigenetics and developmental patterning.

  • 25. Brace, Selina
    et al.
    Palkopoulou, Eleftheria
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of National History, Sweden.
    Dalén, Love
    Lister, Adrian M.
    Miller, Rebecca
    Otte, Marcel
    Germonpre, Mietje
    Blockley, Simon P. E.
    Stewart, John R.
    Barnes, Ian
    Serial population extinctions in a small mammal indicate Late Pleistocene ecosystem instability2012In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 109, no 50, p. 20532-20536Article in journal (Refereed)
    Abstract [en]

    The Late Pleistocene global extinction of many terrestrial mammal species has been a subject of intensive scientific study for over a century, yet the relative contributions of environmental changes and the global expansion of humans remain unresolved. A defining component of these extinctions is a bias toward large species, with the majority of small-mammal taxa apparently surviving into the present. Here, we investigate the population-level history of a key tundra-specialist small mammal, the collared lemming (Dicrostonyx torquatus), to explore whether events during the Late Pleistocene had a discernible effect beyond the large mammal fauna. Using ancient DNA techniques to sample across three sites in North-West Europe, we observe a dramatic reduction in genetic diversity in this species over the last 50,000 y. We further identify a series of extinction-recolonization events, indicating a previously unrecognized instability in Late Pleistocene small-mammal populations, which we link with climatic fluctuations. Our results reveal climate-associated, repeated regional extinctions in a keystone prey species across the Late Pleistocene, a pattern likely to have had an impact on the wider steppe-tundra community, and one that is concordant with environmental change as a major force in structuring Late Pleistocene biodiversity.

  • 26. Brand, Stephen K.
    et al.
    Schmidt, Joel E.
    Deem, Michael W.
    Daeyaert, Frits
    Ma, Yanhang
    Terasaki, Osamu
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). ShanghaiTech University, China.
    Orazov, Marat
    Davis, Mark E.
    Enantiomerically enriched, polycrystalline molecular sieves2017In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 114, no 20, p. 5101-5106Article in journal (Refereed)
    Abstract [en]

    Zeolite and zeolite-like molecular sieves are being used in a large number of applications such as adsorption and catalysis. Achievement of the long-standing goal of creating a chiral, polycrystalline molecular sieve with bulk enantioenrichment would enable these materials to perform enantioselective functions. Here, we report the synthesis of enantiomerically enriched samples of a molecular sieve. Enantiopure organic structure directing agents are designed with the assistance of computational methods and used to synthesize enantioenriched, polycrystalline molecular sieve samples of either enantiomer. Computational results correctly predicted which enantiomer is obtained, and enantiomeric enrichment is proven by high-resolution transmission electron microscopy. The enantioenriched and racemic samples of the molecular sieves are tested as adsorbents and heterogeneous catalysts. The enantioenriched molecular sieves show enantioselectivity for the ring opening reaction of epoxides and enantioselective adsorption of 2-butanol (the R enantiomer of the molecular sieve shows opposite and approximately equal enantioselectivity compared with the S enantiomer of the molecular sieve, whereas the racemic sample of the molecular sieve shows no enantioselectivity).

  • 27. Braun, Tatjana
    et al.
    Orlova, Albina
    Valegård, Karin
    Lindås, Ann-Christin
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Schröder, Gunnar F.
    Egelman, Edward H.
    Archaeal actin from a hyperthermophile forms a single-stranded filament2015In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 112, no 30, p. 9340-9345Article in journal (Refereed)
    Abstract [en]

    The prokaryotic origins of the actin cytoskeleton have been firmly established, but it has become clear that the bacterial actins form a wide variety of different filaments, different both from each other and from eukaryotic F-actin. We have used electron cryomicroscopy (cryo-EM) to examine the filaments formed by the protein crenactin (a crenarchaeal actin) from Pyrobaculum calidifontis, an organism that grows optimally at 90 degrees C. Although this protein only has similar to 20% sequence identity with eukaryotic actin, phylogenetic analyses have placed it much closer to eukaryotic actin than any of the bacterial homologs. It has been assumed that the crenactin filament is double-stranded, like F-actin, in part because it would be hard to imagine how a single-stranded filament would be stable at such high temperatures. We show that not only is the crenactin filament single-stranded, but that it is remarkably similar to each of the two strands in F-actin. A large insertion in the crenactin sequence would prevent the formation of an F-actin-like double-stranded filament. Further, analysis of two existing crystal structures reveals six different subunit-subunit interfaces that are filament-like, but each is different from the others in terms of significant rotations. This variability in the subunit-subunit interface, seen at atomic resolution in crystals, can explain the large variability in the crenactin filaments observed by cryo-EM and helps to explain the variability in twist that has been observed for eukaryotic actin filaments.

  • 28. Budhavant, Krishnakant
    et al.
    Andersson, August
    Stockholm University, Faculty of Science, Department of Environmental Science. Stockholm University, Faculty of Science, The Bolin Centre for Climate Research (together with KTH & SMHI).
    Holmstrand, Henry
    Stockholm University, Faculty of Science, Department of Environmental Science. Stockholm University, Faculty of Science, The Bolin Centre for Climate Research (together with KTH & SMHI).
    Satheesh, S. K.
    Gustafsson, Örjan
    Stockholm University, Faculty of Science, Department of Environmental Science. Stockholm University, Faculty of Science, The Bolin Centre for Climate Research (together with KTH & SMHI).
    Black carbon aerosols over Indian Ocean have unique source fingerprint and optical characteristics during monsoon season2023In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 120, no 8, article id e2210005120Article in journal (Refereed)
    Abstract [en]

    Effects of aerosols such as black carbon (BC) on climate and buildup of the monsoon over the Indian Ocean are insufficiently quantified. Uncertain contributions from various natural and anthropogenic sources impede our understanding. Here, we use observations over 5 y of BC and its isotopes at a remote island observatory in northern Indian Ocean to constrain loadings and sources during little-studied monsoon season. Carbon-14 data show a highly variable yet largely fossil (65 ± 15%) source mixture. Combining carbon-14 with carbon-13 reveals the impact of African savanna burning, which occasionally approach 50% (48 ± 9%) of the total BC loadings. The BC mass-absorption cross-section for this regime is 7.6 ± 2.6 m2/g, with higher values during savanna fire input. Taken together, the combustion sources, longevity, and optical properties of BC aerosols over summertime Indian Ocean are different than the more-studied winter aerosol, with implications for chemical transport and climate model simulations of the Indian monsoon.

  • 29. Butt, Edward W.
    et al.
    Baker, Jessica C. A.
    Bezerra, Francisco G. Silva
    von Randow, Celso
    Aguiar, Ana Paula D.
    Stockholm University, Faculty of Science, Stockholm Resilience Centre. INPE - Instituto Nacional de Pesquisas Espaciais, Brazil.
    Sprackle, Dominick
    Amazon deforestation causes strong regional warming2023In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 120, no 45, article id e2309123120Article in journal (Refereed)
    Abstract [en]

    Tropical deforestation impacts the climate through complex land-atmosphere interactions causing local and regional warming. However, whilst the impacts of deforestation on local temperature are well understood, the regional (nonlocal) response is poorly quantified. Here, we used remote-sensed observations of forest loss and dry season land-surface temperature during the period 2001 to 2020 to demonstrate that deforestation of the Amazon caused strong warming at distances up to 100 km away from the forest loss. We apply a machine learning approach to show nonlocal warming due to forest loss at 2-100 km length scales increases the warming due to deforestation by more than a factor 4, from 0.16 K to 0.71 K for each 10-percentage points of forest loss. We estimate that rapid future deforestation under a strong inequality scenario could cause dry season warming of 0.96 K across Mato Grosso state in southern Brazil over the period 2020 to 2050. Reducing deforestation could reduce future warming caused by forest loss to 0.4 K. Our results demonstrate the contribution of tropical deforestation to regional climate warming and the potential for reduced deforestation to deliver regional climate adaptation and resilience with important implications for sustainable management of the Amazon.

  • 30.
    Caballero, Rodrigo
    et al.
    Stockholm University, Faculty of Science, Department of Meteorology .
    Huber, Matthew
    State-dependent climate sensitivity in past warm climates and its implications for future climate projections2013In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 110, no 35, p. 14162-14167Article in journal (Refereed)
    Abstract [en]

    Projections of future climate depend critically on refined estimates of climate sensitivity. Recent progress in temperature proxies dramatically increases the magnitude of warming reconstructed from early Paleogene greenhouse climates and demands a close examination of the forcing and feedback mechanisms that maintained this warmth and the broad dynamic range that these paleoclimate records attest to. Here, we show that several complementary resolutions to these questions are possible in the context of model simulations using modern and early Paleogene configurations. We find that (i) changes in boundary conditions representative of slow Earth system feedbacks play an important role in maintaining elevated early Paleogene temperatures, (ii) radiative forcing by carbon dioxide deviates significantly from pure logarithmic behavior at concentrations relevant for simulation of the early Paleogene, and (iii) fast or Charney climate sensitivity in this model increases sharply as the climate warms. Thus, increased forcing and increased slow and fast sensitivity can all play a substantial role in maintaining early Paleogene warmth. This poses an equifinality problem: The same climate can be maintained by a different mix of these ingredients; however, at present, the mix cannot be constrained directly from climate proxy data. The implications of strongly state-dependent fast sensitivity reach far beyond the early Paleogene. The study of past warm climates may not narrow uncertainty in future climate projections in coming centuries because fast climate sensitivity may itself be state-dependent, but proxies and models are both consistent with significant increases in fast sensitivity with increasing temperature.

  • 31. Calabrese, Salvatore
    et al.
    Chakrawal, Arjun
    Stockholm University, Faculty of Science, Department of Physical Geography.
    Manzoni, Stefano
    Stockholm University, Faculty of Science, Department of Physical Geography.
    Van Cappellen, Philippe
    Energetic scaling in microbial growth2021In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 118, no 47, article id e2107668118Article in journal (Refereed)
    Abstract [en]

    Microbial growth is a clear example of organization and structure arising in nonequilibrium conditions. Due to the complexity of the microbial metabolic network, elucidating the fundamental principles governing microbial growth remains a challenge. Here, we present a systematic analysis of microbial growth thermodynamics, leveraging an extensive dataset on energy-limited monoculture growth. A consistent thermodynamic framework based on reaction stoichiometry allows us to quantify how much of the available energy microbes can efficiently convert into new biomass while dissipating the remaining energy into the environment and producing entropy. We show that dissipation mechanisms can be linked to the electron donor uptake rate, a fact leading to the central result that the thermodynamic efficiency is related to the electron donor uptake rate by the scaling law eta proportional to M-1/2 ED and to the growth yield by eta proportional to Y4/5. These findings allow us to rederive the Pirt equation from a thermodynamic perspective, providing a means to compute its coefficients, as well as a deeper understanding of the relationship between growth rate and yield. Our results provide rather general insights into the relation between mass and energy conversion in microbial growth with potentially wide application, especially in ecology and biotechnology.

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  • 32.
    Carlberg, Inger
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Hansson, Maria
    Kieselbach, Thomas
    Schröder, Wolfgang P
    Andersson, Bertil
    Vener, Alexander V
    A novel plant protein undergoing light-induced phosphorylation and release from the photosynthetic thylakoid membranes2003In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 100, no 2, p. 757-62Article in journal (Refereed)
    Abstract [en]

    The characteristics of a phosphoprotein with a relative electrophoretic mobility of 12 kDa have been unknown during two decades of studies on redox-dependent protein phosphorylation in plant photosynthetic membranes. Digestion of this protein from spinach thylakoid membranes with trypsin and subsequent tandem nanospray-quadrupole-time-of-flight mass spectrometry of the peptides revealed a protein sequence that did not correspond to any previously known protein. Sequencing of the corresponding cDNA uncovered a gene for a precursor protein with a transit peptide followed by a strongly basic mature protein with a molecular mass of 8,640 Da. Genes encoding homologous proteins were found on chromosome 3 of Arabidopsis and rice as well as in ESTs from 20 different plant species, but not from any other organisms. The protein can be released from the membrane with high salt and is also partially released in response to light-induced phosphorylation of thylakoids, in contrast to all other known thylakoid phosphoproteins, which are integral to the membrane. On the basis of its properties, this plant-specific protein is named thylakoid soluble phosphoprotein of 9 kDa (TSP9). Mass spectrometric analyses revealed the existence of non-, mono-, di-, and triphosphorylated forms of TSP9 and phosphorylation of three distinct threonine residues in the central part of the protein. The phosphorylation and release of TSP9 from the photosynthetic membrane on illumination favor participation of this basic protein in cell signaling and regulation of plant gene expression in response to changing light conditions.

  • 33. Carpenter, Stephen R.
    et al.
    Brock, William A.
    Folke, Carl
    Stockholm University, Faculty of Science, Stockholm Resilience Centre. Royal Swedish Academy of Sciences, Sweden.
    van Nes, Egbert H.
    Scheffer, Marten
    Allowing variance may enlarge the safe operating space for exploited ecosystems2015In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 112, no 46, p. 14384-14389Article in journal (Refereed)
    Abstract [en]

    Variable flows of food, water, or other ecosystem services complicate planning. Management strategies that decrease variability and increase predictability may therefore be preferred. However, actions to decrease variance over short timescales (2-4 y), when applied continuously, may lead to long-term ecosystem changes with adverse consequences. We investigated the effects of managing short-term variance in three well-understood models of ecosystem services: lake eutrophication, harvest of a wild population, and yield of domestic herbivores on a rangeland. In all cases, actions to decrease variance can increase the risk of crossing critical ecosystem thresholds, resulting in less desirable ecosystem states. Managing to decrease short-term variance creates ecosystem fragility by changing the boundaries of safe operating spaces, suppressing information needed for adaptive management, cancelling signals of declining resilience, and removing pressures that may build tolerance of stress. Thus, the management of variance interacts strongly and inseparably with the management of resilience. By allowing for variation, learning, and flexibility while observing change, managers can detect opportunities and problems as they develop while sustaining the capacity to deal with them.

  • 34. Carrière, Yves
    et al.
    Brown, Zachary
    Aglasan, Serkan
    Dutilleul, Pierre
    Carroll, Matthew
    Head, Graham
    Tabashnik, Bruce E.
    Søgaard Jørgensen, Peter
    Stockholm University, Faculty of Science, Stockholm Resilience Centre.
    Carroll, Scott P.
    Crop rotation mitigates impacts of corn rootworm resistance to transgenic Bt corn2020In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 117, no 31, p. 18385-18392Article in journal (Refereed)
    Abstract [en]

    Transgenic crops that produce insecticidal proteins from Bacillus thuringiensis (Bt) can suppress pests and reduce insecticide sprays, but their efficacy is reduced when pests evolve resistance. Although farmers plant refuges of non-Bt host plants to delay pest resistance, this tactic has not been sufficient against the western corn rootworm, Diabrotica virgifera virgifera. In the United States, some populations of this devastating pest have rapidly evolved practical resistance to Cry3 toxins and Cry34/35Ab, the only Bt toxins in commercially available corn that kill rootworms. Here, we analyzed data from 2011 to 2016 on Bt corn fields producing Cry3Bb alone that were severely damaged by this pest in 25 cropreporting districts of Illinois, Iowa, and Minnesota. The annual mean frequency of these problem fields was 29 fields (range 7 to 70) per million acres of Cry3Bb corn in 2011 to 2013, with a cost of $163 to $227 per damaged acre. The frequency of problem fields declined by 92% in 2014 to 2016 relative to 2011 to 2013 and was negatively associated with rotation of corn with soybean. The effectiveness of corn rotation for mitigating Bt resistance problems did not differ significantly between crop-reporting districts with versus without prevalent rotation-resistant rootworm populations. In some analyses, the frequency of problem fields was positively associated with planting of Cry3 corn and negatively associated with planting of Bt corn producing both a Cry3 toxin and Cry34/35Ab. The results highlight the central role of crop rotation for mitigating impacts of D. v. virgifera resistance to Bt corn.

  • 35. Carstensen, Jacob
    et al.
    Andersen, Jesper H.
    Gustafsson, Bo G.
    Stockholm University, Faculty of Science, Stockholm University Baltic Sea Centre, Baltic Nest Institute.
    Conley, Daniel J.
    Deoxygenation of the Baltic Sea during the last century2014In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 111, no 15, p. 5628-5633Article in journal (Refereed)
    Abstract [en]

    Deoxygenation is a global problem in coastal and open regions of the ocean, and has led to expanding areas of oxygen minimum zones and coastal hypoxia. The recent expansion of hypoxia in coastal ecosystems has been primarily attributed to global warming and enhanced nutrient input from land and atmosphere. The largest anthropogenically induced hypoxic area in the world is the Baltic Sea, where the relative importance of physical forcing versus eutrophication is still debated. We have analyzed water column oxygen and salinity profiles to reconstruct oxygen and stratification conditions over the last 115 y and compare the influence of both climate and anthropogenic forcing on hypoxia. We report a 10-fold increase of hypoxia in the Baltic Sea and show that this is primarily linked to increased inputs of nutrients from land, although increased respiration from higher temperatures during the last two decades has contributed to worsening oxygen conditions. Although shifts in climate and physical circulation are important factors modulating the extent of hypoxia, further nutrient reductions in the Baltic Sea will be necessary to reduce the ecosystems impacts of deoxygenation.

  • 36.
    Carter, Sidney D.
    et al.
    Stockholm University, Faculty of Science, The Wenner-Gren Institute.
    Vigasova, Dana
    Chen, Jiang
    Stockholm University, Faculty of Science, The Wenner-Gren Institute.
    Chovanec, Miroslav
    Åström, Stefan U.
    Stockholm University, Faculty of Science, The Wenner-Gren Institute.
    Nej1 recruits the Srs2 helicase to DNA double-strand breaks and supports repair by a single-strand annealing-like mechanism2009In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 106, no 29, p. 12037-12042Article in journal (Refereed)
    Abstract [en]

    Double-strand breaks (DSBs) represent the most severe DNA lesion a cell can suffer, as they pose the risk of inducing loss of genomic integrity and promote oncogenesis in mammals. Two pathways repair DSBs, nonhomologous end joining (NHEJ) and homologous recombination (HR). With respect to mechanism and genetic requirements, characterization of these pathways has revealed a large degree of functional separation between the two. Nej1 is a cell-type specific regulator essential to NHEJ in Saccharomyces cerevisiae. Srs2 is a DNA helicase with multiple roles in HR. In this study, we show that Nej1 physically interacts with Srs2. Furthermore, mutational analysis of Nej1 suggests that the interaction was strengthened by Dun1-dependent phosphorylation of Nej1 serines 297/298. Srs2 was previously shown to be recruited to replication forks, where it promotes translesion DNA synthesis. We demonstrate that Srs2 was also efficiently recruited to DSBs generated by the HO endonuclease. Additionally, efficient Srs2 recruitment to this DSB was dependent on Nej1, but independent of mechanisms facilitating Srs2 recruitment to replication forks. Functionally, both Nej1 and Srs2 were required for efficient repair of DSBs with 15-bp overhangs, a repair event reminiscent of a specific type of HR called single-strand annealing (SSA). Moreover, absence of Rad51 suppressed the SSA-defect in srs2 and nej1 strains. We suggest a model in which Nej1 recruits Srs2 to DSBs to promote NHEJ/SSA-like repair by dismantling inappropriately formed Rad51 nucleoprotein filaments. This unexpected link between NHEJ and HR components may represent cross-talk between DSB repair pathways to ensure efficient repair.

  • 37. Casini, Michele
    et al.
    Blenckner, Thorsten
    Stockholm University, Stockholm Resilience Centre, Baltic Nest Institute.
    Moellmann, Christian
    Gardmark, Anna
    Lindegren, Martin
    Llope, Marcos
    Kornilovs, Georgs
    Plikshs, Maris
    Stenseth, Nils Christian
    Predator transitory spillover induces trophic cascades in ecological sinks2012In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 109, no 21, p. 8185-8189Article in journal (Refereed)
    Abstract [en]

    Understanding the effects of cross-system fluxes is fundamental in ecosystem ecology and biological conservation. Source-sink dynamics and spillover processes may link adjacent ecosystems by movement of organisms across system boundaries. However, effects of temporal variability in these cross-system fluxes on a whole marine ecosystem structure have not yet been presented. Here we show, using 35 y of multitrophic data series from the Baltic Sea, that transitory spillover of the top-predator cod from its main distribution area produces cascading effects in the whole food web of an adjacent and semi-isolated ecosystem. At varying population size, cod expand/contract their distribution range and invade/retreat from the neighboring Gulf of Riga, thereby affecting the local prey population of herring and, indirectly, zooplankton and phytoplankton via top-down control. The Gulf of Riga can be considered for cod a true sink habitat, where in the absence of immigration from the source areas of the central Baltic Sea the cod population goes extinct due to the absence of suitable spawning grounds. Our results add a metaecosystem perspective to the ongoing intense scientific debate on the key role of top predators in structuring natural systems. The integration of regional and local processes is central to predict species and ecosystem responses to future climate changes and ongoing anthropogenic disturbances.

  • 38.
    Chi Fru, Ernest
    et al.
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Rodriguez, Nathalie P.
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Partin, Camille A.
    Lalonde, Stefan V.
    Andersson, Per
    Weiss, Dominik J.
    El Albani, Abderrazak
    Rodushkin, Ilia
    Konhauser, Kurt O.
    Cu isotopes in marine black shales record the Great Oxidation Event2016In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 113, no 18, p. 4941-4946Article in journal (Refereed)
    Abstract [en]

    The oxygenation of the atmosphere similar to 2.45-2.32 billion years ago (Ga) is one of the most significant geological events to have affected Earth's redox history. Our understanding of the timing and processes surrounding this key transition is largely dependent on the development of redox-sensitive proxies, many of which remain unexplored. Here we report a shift from negative to positive copper isotopic compositions (delta Cu-65(ERM-AE633)) in organic carbon-rich shales spanning the period 2.66-2.08 Ga. We suggest that, before 2.3 Ga, a muted oxidative supply of weathering-derived copper enriched in Cu-65, along with the preferential removal of Cu-65 by iron oxides, left seawater and marine biomass depleted in Cu-65 but enriched in Cu-63. As banded iron formation deposition waned and continentally sourced Cu became more important, biomass sampled a dissolved Cu reservoir that was progressively less fractionated relative to the continental pool. This evolution toward heavy delta Cu-65 values coincides with a shift to negative sedimentary delta Fe-56 values and increased marine sulfate after the Great Oxidation Event (GOE), and is traceable through Phanerozoic shales to modern marine settings, where marine dissolved and sedimentary delta Cu-65 values are universally positive. Our finding of an important shift in sedimentary Cu isotope compositions across the GOE provides new insights into the Precambrian marine cycling of this critical micronutrient, and demonstrates the proxy potential for sedimentary Cu isotope compositions in the study of biogeochemical cycles and oceanic redox balance in the past.

  • 39. Chu, Olivia J.
    et al.
    Donges, Jonathan
    Stockholm University, Faculty of Science, Stockholm Resilience Centre. Potsdam Institute for Climate Impact Research, Germany.
    Robertson, Graeme B.
    Pop-Eleches, Grigore
    The microdynamics of spatial polarization: A model and an application to survey data from Ukraine2021In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 118, no 50, article id e2104194118Article in journal (Refereed)
    Abstract [en]

    Although spatial polarization of attitudes is extremely common around the world, we understand little about the mechanisms through which polarization on divisive issues rises and falls over time. We develop a theory that explains how political shocks can have different effects in different regions of a country depending upon local dynamics generated by the preexisting spatial distribution of attitudes and discussion networks. Where opinions were previously divided, attitudinal diversity is likely to persist after the shock. Meanwhile, where a clear precrisis majority exists on key issues, opinions should change in the direction of the predominant view. These dynamics result in greater local homogeneity in attitudes but at the same time exacerbate geographic polarization across regions and sometimes even within regions. We illustrate our theory by developing a modified version of the adaptive voter model, an adaptive network model of opinion dynamics, to study changes in attitudes toward the European Union (EU) in Ukraine in the context of the Euromaidan Revolution of 2013 to 2014. Using individual-level panel data from surveys fielded before and after the Euromaidan Revolution, we show that EU support increased in areas with high prior public support for EU integration but declined further where initial public attitudes were opposed to the EU, thereby increasing the spatial polarization of EU attitudes in Ukraine. Our tests suggest that the predictive power of both network and regression models increases significantly when we incorporate information about the geographic location of network participants, which highlights the importance of spatially rooted social networks.

  • 40. Chung, J S
    et al.
    Dircksen, Henrich
    Institute of Zoophysiology, University of Bonn, Germany.
    Webster, S G
    A remarkable, precisely timed release of hyperglycemic hormone from endocrine cells in the gut is associated with ecdysis in the crab Carcinus maenas1999In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 96, no 23, p. 13103-7Article in journal (Refereed)
    Abstract [en]

    Molting or ecdysis is the most fundamentally important process in arthropod life history, because shedding of the exoskeleton is an absolute prerequisite for growth and metamorphosis. Although the hormonal mechanisms driving ecdysis in insects have been studied extensively, nothing is known about these processes in crustaceans. During late premolt and during ecdysis in the crab Carcinus maenas, we observed a precise and reproducible surge in hemolymph hyperglycemic hormone (CHH) levels, which was over 100-fold greater than levels seen in intermolt animals. The source of this hormone surge was not from the eyestalk neurosecretory tissues but from previously undescribed endocrine cells (paraneurons), in defined areas of the foregut and hindgut. During premolt (the only time when CHH is expressed by these tissues), the gut is the largest endocrine tissue in the crab. The CHH surge, which is a result of an unusual, almost complete discharge of the contents of the gut endocrine cell, regulates water and ion uptake during molting, thus allowing the swelling necessary for successful ecdysis and the subsequent increase in size during postmolt. This study defines an endocrine brain/gut axis in the arthropods. We propose that the ionoregulatory process controlled by CHH may be common to arthropods, in that, for insects, a similar mechanism seems to be involved in antidiuresis. It also seems likely that a cascade of very precisely coordinated release of (neuro) hormones controls ecdysis.

  • 41. Cinner, Joshua E.
    et al.
    McClanahan, Tim R.
    MacNeil, M. Aaron
    Graham, Nicholas A. J.
    Daw, Tim M.
    Stockholm University, Stockholm Resilience Centre.
    Mukminin, Ahmad
    Feary, David A.
    Rabearisoa, Ando L.
    Wamukota, Andrew
    Jiddawi, Narriman
    Campbell, Stuart J.
    Baird, Andrew H.
    Januchowski-Hartley, Fraser A.
    Hamed, Salum
    Lahari, Rachael
    Morove, Tau
    Kuange, John
    Comanagement of coral reef social ecological systems2012In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 109, no 14, p. 5219-5222Article in journal (Refereed)
    Abstract [en]

    In an effort to deliver better outcomes for people and the ecosystems they depend on, many governments and civil society groups are engaging natural resource users in collaborative management arrangements (frequently called comanagement). However, there are few empirical studies demonstrating the social and institutional conditions conducive to successful comanagement outcomes, especially in small-scale fisheries. Here, we evaluate 42 comanagement arrangements across five countries and show that: (i) comanagement is largely successful at meeting social and ecological goals; (ii) comanagement tends to benefit wealthier resource users; (iii) resource overexploitation is most strongly influenced by market access and users' dependence on resources; and (iv) institutional characteristics strongly influence livelihood and compliance outcomes, yet have little effect on ecological conditions.

  • 42. Cintron-Colon, Rigo
    et al.
    Sanchez-Alavez, Manuel
    Nguyen, William
    Mori, Simone
    Gonzalez-Rivera, Ruben
    Lien, Tiffany
    Bartfai, Tamas
    Stockholm University, Faculty of Science, Department of Neurochemistry.
    Aid, Saba
    Francois, Jean-Christophe
    Holzenbergerf, Martin
    Conti, Bruno
    Insulin-like growth factor 1 receptor regulates hypothermia during calorie restriction2017In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 114, no 36, p. 9731-9736Article in journal (Refereed)
    Abstract [en]

    When food resources are scarce, endothermic animals can lower core body temperature (Tb). This phenomenon is believed to be part of an adaptive mechanism that may have evolved to conserve energy until more food becomes available. Here, we found in the mouse that the insulin-like growth factor 1 receptor (IGF-1R) controls this response in the central nervous system. Pharmacological or genetic inhibition of IGF-1R enhanced the reduction of temperature and of energy expenditure during calorie restriction. Full blockade of IGF-1R affected female and male mice similarly. In contrast, genetic IGF-1R dosage was effective only in females, where it also induced transient and estrusspecific hypothermia in animals fed ad libitum. These effects were regulated in the brain, as only central, not peripheral, pharmacological activation of IGF-1R prevented hypothermia during calorie restriction. Targeted IGF-1R knockout selectively in forebrain neurons revealed that IGF signaling also modulates calorie restriction-dependent Tb regulation in regions rostral of the canonical hypothalamic nuclei involved in controlling body temperature. In aggregate, these data identify central IGF-1R as a mediator of the integration of nutrient and temperature homeostasis. They also show that calorie restriction, IGF-1R signaling, and body temperature, three of the main regulators of metabolism, aging, and longevity, are components of the same pathway.

  • 43. Cosens, Barbara
    et al.
    Ruhl, J. B.
    Soininen, Niko
    Gunderson, Lance
    Belinskij, Antti
    Blenckner, Thorsten
    Stockholm University, Faculty of Science, Stockholm Resilience Centre.
    Camacho, Alejandro E.
    Chaffin, Brian C.
    Craig, Robin Kundis
    Doremus, Holly
    Glicksman, Robert
    Heiskanen, Anna-Stiina
    Larson, Rhett
    Similä, Jukka
    Governing complexity: Integrating science, governance, and law to manage accelerating in the commons2021In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 118, no 36, article id e2102798118Article in journal (Refereed)
    Abstract [en]

    The speed and uncertainty of environmental change in the Anthropocene challenge the capacity of coevolving social-ecological-technological systems (SETs) to adapt or transform to these changes. Formal government and legal structures further constrain the adaptive capacity of our SETs. However, new, selforganized forms of adaptive governance are emerging at multiple scales in natural resource-based SETs. Adaptive governance involves the private and public sectors as well as formal and informal institutions, self-organized to fill governance gaps in the traditional roles of states. While new governance forms are emerging, they are not yet doing so rapidly enough to match the pace of environmental change. Furthermore, they do not yet possess the legitimacy or capacity needed to address disparities between the winners and losers from change. These emergent forms of adaptive governance appear to be particularly effective in managing complexity. We explore governance and SETs as coevolving complex systems, focusing on legal systems to understand the potential pathways and obstacles to equitable adaptation. We explore how governments may facilitate the emergence of adaptive governance and promote legitimacy in both the process of governance despite the involvement of nonstate actors, and its adherence to democratic values of equity and justice. To manage the contextual nature of the results of change in complex systems, we propose the establishment of long-term study initiatives for the coproduction of knowledge, to accelerate learning and synergize interactions between science and governance and to foster public science and epistemic communities dedicated to navigating transitions to more just, sustainable, and resilient futures.

  • 44.
    Cymer, Florian
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    von Heijne, Gunnar
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Cotranslational folding of membrane proteins probed by arrest-peptide-mediated force measurements2013In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 110, no 36, p. 14640-14645Article in journal (Refereed)
    Abstract [en]

    Polytopic membrane proteins are inserted cotranslationally into target membranes by ribosome-translocon complexes. It is, however, unclear when during the insertion process specific interactions between the transmembrane helices start to form. Here, we use a recently developed in vivo technique to measure pulling forces acting on transmembrane helices during their cotranslational insertion into the inner membrane of Escherichia coli to study the earliest steps of tertiary folding of five polytopic membrane proteins. We find that interactions between residues in a C-terminally located transmembrane helix and in more N-terminally located helices can be detected already at the point when the C-terminal helix partitions from the translocon into the membrane. Our findings pinpoint the earliest steps of tertiary structure formation and open up possibilities to study the cotranslational folding of polytopic membrane proteins.

  • 45. Dacke, Marie
    et al.
    Bell, Adrian T. A.
    Foster, James J.
    Baird, Emily J.
    Stockholm University, Faculty of Science, Department of Zoology.
    Strube-Bloss, Martin F.
    Byrne, Marcus J.
    el Jundi, Basil
    Multimodal cue integration in the dung beetle compass2019In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 116, no 28, p. 14248-14253Article in journal (Refereed)
    Abstract [en]

    South African ball-rolling dung beetles exhibit a unique orientation behavior to avoid competition for food: after forming a piece of dung into a ball, they efficiently escape with it from the dung pile along a straight-line path. To keep track of their heading, these animals use celestial cues, such as the sun, as an orientation reference. Here we show that wind can also be used as a guiding cue for the ball-rolling beetles. We demonstrate that this mechanosensory compass cue is only used when skylight cues are difficult to read, i.e., when the sun is close to the zenith. This raises the question of how the beetles combine multimodal orientation input to obtain a robust heading estimate. To study this, we performed behavioral experiments in a tightly controlled indoor arena. This revealed that the beetles register directional information provided by the sun and the wind and can use them in a weighted manner. Moreover, the directional information can be transferred between these 2 sensory modalities, suggesting that they are combined in the spatial memory network in the beetle's brain. This flexible use of compass cue preferences relative to the prevailing visual and mechanosensory scenery provides a simple, yet effective, mechanism for enabling precise compass orientation at any time of the day.

  • 46. Dahl, Tais W.
    et al.
    Hammarlund, Emma U.
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Anbar, Ariel D.
    Bond, David P. G.
    Gill, Benjamin C.
    Gordon, Gwyneth W.
    Knoll, Andrew H.
    Canfield, Donald E.
    Reply to Butterfield: The Devonian radiation of large predatory fish coincided with elevated athospheric oxygen levels2011In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 108, no 9, p. E29-Article in journal (Refereed)
    Abstract [en]

    We welcome this opportunity to clarify the conclusions and implications of our recent publication in PNAS. Butterfield (1) raises four issues regarding the oxygenation of the Paleozoic Earth's surface and its correlation to animal evolution. Our geochemical and paleontological data supported ocean oxygenation in the Silurian-Early Devonian (2), a critical transition in Earth history that influenced biogeochemical cycles and biological systems.

    First, Butterfield suggests that evidence of charcoal in late Silurian rocks is incompatible with our claim that the earlier Paleozoic atmosphere had oxygen levels below 50% PAL (present-day atmospheric level). This counterargument rests on the assumption that the “fire window” of 62–166% PAL oxygen is well defined, but this is not the case (3).

  • 47. Dahl, Tais W.
    et al.
    Hammarlund, Emma U.
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Anbar, Ariel D.
    Bond, David P. G.
    Gill, Benjamin C.
    Gordon, Gwyneth W.
    Knoll, Andrew H.
    Nielsen, Arne T.
    Schovsbo, Niels H.
    Canfield, Donald E.
    Devonian rise in atmospheric oxygen correlated to the radiations of terrestrial plants and large predatory fish2010In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 107, no 42, p. 17911-17915Article in journal (Refereed)
    Abstract [en]

    The evolution of Earth's biota is intimately linked to the oxygenation of the oceans and atmosphere. We use the isotopic composition and concentration of molybdenum (Mo) in sedimentary rocks to explore this relationship. Our results indicate two episodes of global ocean oxygenation. The first coincides with the emergence of the Ediacaran fauna, including large, motile bilaterian animals, ca. 550-560 million year ago (Ma), reinforcing previous geochemical indications that Earth surface oxygenation facilitated this radiation. The second, perhaps larger, oxygenation took place around 400 Ma, well after the initial rise of animals and, therefore, suggesting that early metazoans evolved in a relatively low oxygen environment. This later oxygenation correlates with the diversification of vascular plants, which likely contributed to increased oxygenation through the enhanced burial of organic carbon in sediments. It also correlates with a pronounced radiation of large predatory fish, animals with high oxygen demand. We thereby couple the redox history of the atmosphere and oceans to major events in animal evolution.

  • 48. Dalou, Celia
    et al.
    Füri, Evelyn
    Deligny, Cécile
    Piani, Laurette
    Caumon, Marie-Camille
    Laumonier, Mickael
    Boulliung, Julien
    Edén, Mattias
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Redox control on nitrogen isotope fractionation during planetary core formation2019In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 116, no 29, p. 14485-14494Article in journal (Refereed)
    Abstract [en]

    The present-day nitrogen isotopic compositions of Earth's surficial (N-15-enriched) and deep reservoirs (N-15-depleted) differ significantly. This distribution can neither be explained by modern mantle degassing nor recycling via subduction zones. As the effect of planetary differentiation on the behavior of N isotopes is poorly understood, we experimentally determined N-isotopic fractionations during metal-silicate partitioning (analogous to planetary core formation) over a large range of oxygen fugacities (Delta IW -3.1 < logfO(2) <Delta IW -0.5, where Delta IW is the logarithmic difference between experimental oxygen fugacity [fO(2)] conditions and that imposed by the coexistence of iron and wustite) at 1 GPa and 1,400 degrees C. We developed an in situ analytical method to measure the N-elemental and -isotopic compositions of experimental run products composed of Fe-C-N metal alloys and basaltic melts. Our results show substantial N-isotopic fractionations between metal alloys and silicate glasses, i.e., from -257 +/- 22% to -49 +/- 1% over 3 log units of fO(2). These large fractionations under reduced conditions can be explained by the large difference between N bonding in metal alloys (Fe-N) and in silicate glasses (as molecular N-2 and NH complexes). We show that the delta N-15 value of the silicate mantle could have increased by similar to 20 parts per thousand during core formation due to N segregation into the core.

  • 49.
    Dalén, Love
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Nyström, Veronica
    Stockholm University, Faculty of Science, Department of Zoology.
    Valdiosera, Cristina
    Germonpre, Mietje
    Sablin, Mikhail
    Turner, Elaine
    Angerbjörn, Anders
    Stockholm University, Faculty of Science, Department of Zoology.
    Arsuaga, Juan Luis
    Götherström, Anders
    Ancient DNA reveals lack of postglacial habitat tracking in the arctic fox2007In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 104, no 16, p. 6726-6729Article in journal (Refereed)
    Abstract [en]

    How species respond to an increased availability of habitat, for example at the end of the last glaciation, has been well established. In contrast, little is known about the opposite process, when the amount of habitat decreases. The hypothesis of habitat tracking predicts that species should be able to track both increases and decreases in habitat availability. The alternative hypothesis is that populations outside refugia become extinct during periods of unsuitable climate. To test these hypotheses, we used ancient DNA techniques to examine genetic variation in the arctic fox (Alopex lagopus) through an expansion/contraction cycle. The results show that the arctic fox in midlatitude Europe became extinct at the end of the Pleistocene and did not track the habitat when it shifted to the north. Instead, a high genetic similarity between the extant populations in Scandinavia and Siberia suggests an eastern origin for the Scandinavian population at the end of the last glaciation. These results provide new insights into how species respond to climate change, since they suggest that populations are unable to track decreases in habitat avaliability. This implies that arctic species may be particularly vulnerable to increases in global temperatures.

  • 50. d'Amour, Christopher Bren
    et al.
    Reitsma, Femke
    Baiocchi, Giovanni
    Barthel, Stephan
    Stockholm University, Faculty of Science, Stockholm Resilience Centre. University of Gävle, Sweden.
    Guneralp, Burak
    Erb, Karl-Heinz
    Haberl, Helmut
    Creutzig, Felix
    Seto, Karen C.
    Future urban land expansion and implications for global croplands2017In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 114, no 34, p. 8939-8944Article in journal (Refereed)
    Abstract [en]

    Urban expansion often occurs on croplands. However, there is little scientific understanding of how global patterns of future urban expansion will affect the world's cultivated areas. Here, we combine spatially explicit projections of urban expansion with datasets on global croplands and crop yields. Our results show that urban expansion will result in a 1.8-2.4% loss of global croplands by 2030, with substantial regional disparities. About 80% of global cropland loss from urban expansion will take place in Asia and Africa. In both Asia and Africa, much of the cropland that will be lost is more than twice as productive as national averages. Asia will experience the highest absolute loss in cropland, whereas African countries will experience the highest percentage loss of cropland. Globally, the croplands that are likely to be lost were responsible for 3-4% of worldwide crop production in 2000. Urban expansion is expected to take place on cropland that is 1.77 times more productive than the global average. The loss of cropland is likely to be accompanied by other sustainability risks and threatens livelihoods, with diverging characteristics for different megaurban regions. Governance of urban area expansion thus emerges as a key area for securing livelihoods in the agrarian economies of the Global South.

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