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  • 1.
    Ahrens, Johan
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Amselem, Elias
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Cabello, Adan
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum. University of Sevilla, Spain.
    Bourennane, Mohamed
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Two Fundamental Experimental Tests of Nonclassicality with Qutrits2013Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 3, artikkel-id 2170Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We report two fundamental experiments on three-level quantum systems (qutrits). The first one tests the simplest task for which quantum mechanics provides an advantage with respect to classical physics. The quantum advantage is certified by the violation of Wright's inequality, the simplest classical inequality violated by quantum mechanics. In the second experiment, we obtain contextual correlations by sequentially measuring pairs of compatible observables on a qutrit, and show the violation of Klyachko et al.'s inequality, the most fundamental noncontextuality inequality violated by qutrits. Our experiment tests exactly Klyachko et al.'s inequality, uses the same measurement procedure for each observable in every context, and implements the sequential measurements in any possible order.

  • 2. Altfeder, Igor
    et al.
    Voevodin, Andrey A.
    Check, Michael H.
    Eichfeld, Sarah M.
    Robinson, Joshua A.
    Balatsky, Alexander V.
    Stockholms universitet, Nordiska institutet för teoretisk fysik (Nordita). Los Alamos National Laboratory, USA.
    Scanning Tunneling Microscopy Observation of Phonon Condensate2017Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, artikkel-id 43214Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Using quantum tunneling of electrons into vibrating surface atoms, phonon oscillations can be observed on the atomic scale. Phonon interference patterns with unusually large signal amplitudes have been revealed by scanning tunneling microscopy in intercalated van der Waals heterostructures. Our results show that the effective radius of these phonon quasi-bound states, the real-space distribution of phonon standing wave amplitudes, the scattering phase shifts, and the nonlinear intermode coupling strongly depend on the presence of defect-induced scattering resonance. The observed coherence of these quasi-bound states most likely arises from phase-and frequency-synchronized dynamics of all phonon modes, and indicates the formation of many-body condensate of optical phonons around resonant defects. We found that increasing the strength of the scattering resonance causes the increase of the condensate droplet radius without affecting the condensate fraction inside it. The condensate can be observed at room temperature.

  • 3.
    Amselem, Elias
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Sadiq, Muhamad
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Bourennane, Mohamed
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Experimental bound entanglement through a Pauli channel2013Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 3, artikkel-id 1966Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Understanding the characteristics of a quantum systems when affected by noise is one of the biggest challenges for quantum technologies. The general Pauli error channel is an important lossless channel for quantum communication. In this work we consider the effects of a Pauli channel on a pure four-qubit state and simulate the Pauli channel experimentally by studying the action on polarization encoded entangled photons. When the noise channel acting on the photons is correlated, a set spanned by four orthogonal bound entangled states can be generated. We study this interesting case experimentally and demonstrate that products of Bell states can be brought into a bound entangled regime. We find states in the set of bound entangled states which experimentally violate the CHSH inequality while still possessing a positive partial transpose.

  • 4. Anderson, Bruce T.
    et al.
    Hassanzadeh, Pedram
    Caballero, Rodrigo
    Stockholms universitet, Naturvetenskapliga fakulteten, Meteorologiska institutionen (MISU).
    Persistent anomalies of the extratropical Northern Hemisphere wintertime circulation as an initiator of El Nino/Southern Oscillation events2017Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, artikkel-id 10145Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Climates across both hemispheres are strongly influenced by tropical Pacific variability associated with the El Nino/Southern Oscillation (ENSO). Conversely, extratropical variability also can affect the tropics. In particular, seasonal-mean alterations of near-surface winds associated with the North Pacific Oscillation (NPO) serve as a significant extratropical forcing agent of ENSO. However, it is still unclear what dynamical processes give rise to year-to-year shifts in these long-lived NPO anomalies. Here we show that intraseasonal variability in boreal winter pressure patterns over the Central North Pacific (CNP) imparts a significant signature upon the seasonal-mean circulations characteristic of the NPO. Further we show that the seasonal-mean signature results in part from year-to-year variations in persistent, quasi-stationary low-pressure intrusions into the subtropics of the CNP, accompanied by the establishment of persistent, quasi-stationary high-pressure anomalies over high latitudes of the CNP. Overall, we find that the frequency of these persistent extratropical anomalies (PEAs) during a given winter serves as a key modulator of intraseasonal variability in extratropical North Pacific circulations and, through their influence on the seasonal-mean circulations in and around the southern lobe of the NPO, the state of the equatorial Pacific 9-12 months later.

  • 5. Andriukonis, Eivydas
    et al.
    Gorokhova, Elena
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för miljövetenskap och analytisk kemi.
    Kinetic N-15-isotope effects on algal growth2017Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, artikkel-id 44181Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Stable isotope labeling is a standard technique for tracing material transfer in molecular, ecological and biogeochemical studies. The main assumption in this approach is that the enrichment with a heavy isotope has no effect on the organism metabolism and growth, which is not consistent with current theoretical and empirical knowledge on kinetic isotope effects. Here, we demonstrate profound changes in growth dynamics of the green alga Raphidocelis subcapitata grown in N-15-enriched media. With increasing N-15 concentration (0.37 to 50 at%), the lag phase increased, whereas maximal growth rate and total yield decreased; moreover, there was a negative relationship between the growth and the lag phase across the treatments. The latter suggests that a trade-off between growth rate and the ability to adapt to the high N-15 environment may exist. Remarkably, the lag-phase response at 3.5 at% N-15 was the shortest and deviated from the overall trend, thus providing partial support to the recently proposed Isotopic Resonance hypothesis, which predicts that certain isotopic composition is particularly favorable for living organisms. These findings confirm the occurrence of KIE in isotopically enriched algae and underline the importance of considering these effects when using stable isotope labeling in field and experimental studies.

  • 6.
    Arshamian, Artin
    et al.
    Stockholms universitet, Samhällsvetenskapliga fakulteten, Psykologiska institutionen, Perception och psykofysik. Karolinska Institutet, Sweden; Radboud University, The Netherlands.
    Laska, Matthias
    Gordon, Amy R.
    Norberg, Matilda
    Lahger, Christian
    Porada, Danja K.
    Jelvez Serra, Nadia
    Johansson, Emilia
    Schaefer, Martin
    Amundin, Mats
    Melin, Harald
    Olsson, Andreas
    Olsson, Mats J.
    Stensmyr, Marcus
    Lundström, Johan N.
    A mammalian blood odor component serves as an approach-avoidance cue across phylum border - from flies to humans2017Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, artikkel-id 13635Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Chemosignals are used by predators to localize prey and by prey to avoid predators. These cues vary between species, but the odor of blood seems to be an exception and suggests the presence of an evolutionarily conserved chemosensory cue within the blood odor mixture. A blood odor component, E2D, has been shown to trigger approach responses identical to those triggered by the full blood odor in mammalian carnivores and as such, is a key candidate as a food/alarm cue in blood. Using a multidisciplinary approach, we demonstrate that E2D holds the dual function of affecting both approach and avoidance behavior in a predator-prey predicted manner. E2D evokes approach responses in two taxonomically distant blood-seeking predators, Stable fly and Wolf, while evoking avoidance responses in the prey species Mouse. We extend this by demonstrating that this chemical cue is preserved in humans as well; E2D induces postural avoidance, increases physiological arousal, and enhances visual perception of affective stimuli. This is the first demonstration of a single chemical cue with the dual function of guiding both approach and avoidance in a predator-prey predicted manner across taxonomically distant species, as well as the first known chemosignal that affects both human and non-human animals alike.

  • 7. Ashraf, Batool
    et al.
    AghaKouchak, Amir
    Alizadeh, Amin
    Baygi, Mohammad Mousavi
    Moftakhari, Hamed R.
    Mirchi, Ali
    Anjileli, Hassan
    Madani, Kaveh
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för naturgeografi. Imperial College London, UK.
    Quantifying Anthropogenic Stress on Groundwater Resources2017Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, artikkel-id 12910Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    This study explores a general framework for quantifying anthropogenic influences on groundwater budget based on normalized human outflow (h(out)) and inflow (h(in)). The framework is useful for sustainability assessment of groundwater systems and allows investigating the effects of different human water abstraction scenarios on the overall aquifer regime (e.g., depleted, natural flow-dominated, and human flow-dominated). We apply this approach to selected regions in the USA, Germany and Iran to evaluate the current aquifer regime. We subsequently present two scenarios of changes in human water withdrawals and return flow to the system (individually and combined). Results show that approximately one-third of the selected aquifers in the USA, and half of the selected aquifers in Iran are dominated by human activities, while the selected aquifers in Germany are natural flow-dominated. The scenario analysis results also show that reduced human withdrawals could help with regime change in some aquifers. For instance, in two of the selected USA aquifers, a decrease in anthropogenic influences by similar to 20% may change the condition of depleted regime to natural flow-dominated regime. We specifically highlight a trending threat to the sustainability of groundwater in northwest Iran and California, and the need for more careful assessment and monitoring practices as well as strict regulations to mitigate the negative impacts of groundwater overexploitation.

  • 8. Baeza-Delgado, Carlos
    et al.
    von Heijne, Gunnar
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik. Stockholms universitet, Science for Life Laboratory (SciLifeLab).
    Marti-Renom, Marc A.
    Mingarro, Ismael
    Biological insertion of computationally designed short transmembrane segments2016Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, artikkel-id 23397Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The great majority of helical membrane proteins are inserted co-translationally into the ER membrane through a continuous ribosome-translocon channel. The efficiency of membrane insertion depends on transmembrane (TM) helix amino acid composition, the helix length and the position of the amino acids within the helix. In this work, we conducted a computational analysis of the composition and location of amino acids in transmembrane helices found in membrane proteins of known structure to obtain an extensive set of designed polypeptide segments with naturally occurring amino acid distributions. Then, using an in vitro translation system in the presence of biological membranes, we experimentally validated our predictions by analyzing its membrane integration capacity. Coupled with known strategies to control membrane protein topology, these findings may pave the way to de novo membrane protein design.

  • 9.
    Balk, Lennart
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för miljövetenskap och analytisk kemi.
    Hägerroth, Per-Åke
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för miljövetenskap och analytisk kemi.
    Gustavsson, Hanna
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för miljövetenskap och analytisk kemi.
    Sigg, Lisa
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för miljövetenskap och analytisk kemi.
    Åkerman, Gun
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för miljövetenskap och analytisk kemi.
    Ruiz Munoz, Yolanda
    Honeyfield, Dale C.
    Tjärnlund, Ulla
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för miljövetenskap och analytisk kemi.
    Oliveira, Kenneth
    Ström, Karin
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för miljövetenskap och analytisk kemi.
    McCormick, Stephen D.
    Karlsson, Simon
    Ström, Marika
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för miljövetenskap och analytisk kemi. Karolinska Institutet, Sweden.
    van Manen, Mathijs
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för miljövetenskap och analytisk kemi. Utrecht University, Germany.
    Berg, Anna-Lena
    Halldorsson, Halldor P.
    Strömquist, Jennie
    Collier, Tracy K.
    Börjeson, Hans
    Mörner, Torsten
    Hansson, Tomas
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för miljövetenskap och analytisk kemi.
    Widespread episodic thiamine deficiency in Northern Hemisphere wildlife2016Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, artikkel-id 38821Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Many wildlife populations are declining at rates higher than can be explained by known threats to biodiversity. Recently, thiamine (vitamin B-1) deficiency has emerged as a possible contributing cause. Here, thiamine status was systematically investigated in three animal classes: bivalves, ray-finned fishes, and birds. Thiamine diphosphate is required as a cofactor in at least five life-sustaining enzymes that are required for basic cellular metabolism. Analysis of different phosphorylated forms of thiamine, as well as of activities and amount of holoenzyme and apoenzyme forms of thiaminedependent enzymes, revealed episodically occurring thiamine deficiency in all three animal classes. These biochemical effects were also linked to secondary effects on growth, condition, liver size, blood chemistry and composition, histopathology, swimming behaviour and endurance, parasite infestation, and reproduction. It is unlikely that the thiamine deficiency is caused by impaired phosphorylation within the cells. Rather, the results point towards insufficient amounts of thiamine in the food. By investigating a large geographic area, by extending the focus from lethal to sublethal thiamine deficiency, and by linking biochemical alterations to secondary effects, we demonstrate that the problem of thiamine deficiency is considerably more widespread and severe than previously reported.

  • 10. Barrientos-Somarribas, Mauricio
    et al.
    Messina, David N.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik. Stockholms universitet, Science for Life Laboratory (SciLifeLab).
    Pou, Christian
    Lysholm, Fredrik
    Bjerkner, Annelie
    Allander, Tobias
    Andersson, Bjorn
    Sonnhammer, Erik L. L.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik. Stockholms universitet, Science for Life Laboratory (SciLifeLab).
    Discovering viral genomes in human metagenomic data by predicting unknown protein families2018Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, artikkel-id 28Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Massive amounts of metagenomics data are currently being produced, and in all such projects a sizeable fraction of the resulting data shows no or little homology to known sequences. It is likely that this fraction contains novel viruses, but identification is challenging since they frequently lack homology to known viruses. To overcome this problem, we developed a strategy to detect ORFan protein families in shotgun metagenomics data, using similarity-based clustering and a set of filters to extract bona fide protein families. We applied this method to 17 virus-enriched libraries originating from human nasopharyngeal aspirates, serum, feces, and cerebrospinal fluid samples. This resulted in 32 predicted putative novel gene families. Some families showed detectable homology to sequences in metagenomics datasets and protein databases after reannotation. Notably, one predicted family matches an ORF from the highly variable Torque Teno virus (TTV). Furthermore, follow-up from a predicted ORFan resulted in the complete reconstruction of a novel circular genome. Its organisation suggests that it most likely corresponds to a novel bacteriophage in the microviridae family, hence it was named bacteriophage HFM.

  • 11.
    Baumgarten, Thomas
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Schlegel, Susan
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Wagner, Samuel
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Löw, Mirjam
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Eriksson, Jonas
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Bonde, Ida
    Herrgård, Markus J.
    Heipieper, Hermann J.
    Nørholm, Morten H. H.
    Slotboom, Dirk Jan
    de Gier, Jan-Willem
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Isolation and characterization of the E. coli membrane protein production strain Mutant56(DE3)2017Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, artikkel-id 45089Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Membrane protein production is usually toxic to E. coli. However, using genetic screens strains can be isolated in which the toxicity of membrane protein production is reduced, thereby improving production yields. Best known examples are the C41(DE3) and C43(DE3) strains, which are both derived from the T7 RNA polymerase (P)-based BL21(DE3) protein production strain. In C41(DE3) and C43(DE3) mutations lowering t7rnap expression levels result in strongly reduced T7 RNAP accumulation levels. As a consequence membrane protein production stress is alleviated in the C41(DE3) and C43(DE3) strains, thereby increasing membrane protein yields. Here, we isolated Mutant56(DE3) from BL21(DE3) using a genetic screen designed to isolate BL21(DE3)-derived strains with mutations alleviating membrane protein production stress other than the ones in C41(DE3) and C43(DE3). The defining mutation of Mutant56(DE3) changes one amino acid in its T7 RNAP, which weakens the binding of the T7 RNAP to the T7 promoter governing target gene expression rather than lowering T7 RNAP levels. For most membrane proteins tested yields in Mutant56(DE3) were considerably higher than in C41(DE3) and C43(DE3). Thus, the isolation of Mutant56(DE3) shows that the evolution of BL21(DE3) can be promoted towards further enhanced membrane protein production.

  • 12. Begun, Alexander
    et al.
    Molochkov, Alexander
    Niemi, Antti J.
    Stockholms universitet, Nordiska institutet för teoretisk fysik (Nordita). Far Eastern Federal University, Russia; Institut Denis Poisson, France; Beijing Institute of Technology, People’s Republic of China.
    Protein tertiary structure and the myoglobin phase diagram2019Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, artikkel-id 10819Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We develop an effective theory approach to investigate the phase properties of globular proteins. Instead of interactions between individual atoms or localized interaction centers, the approach builds directly on the tertiary structure of a protein. As an example we construct the phase diagram of (apo) myoglobin with temperature (T) and acidity (pH) as the thermodynamical variables. We describe how myoglobin unfolds from the native folded state to a random coil when temperature and acidity increase. We confirm the presence of two molten globule folding intermediates, and we predict an abrupt transition between the two when acidity changes. When temperature further increases we find that the abrupt transition line between the two molten globule states terminates at a tricritical point, where the helical structures fade away. Our results also suggest that the ligand entry and exit is driven by large scale collective motions that destabilize the myoglobin F-helix.

  • 13. Bermudez, J. Rafael
    et al.
    Riebesell, Ulf
    Larsen, Aud
    Winder, Monika
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik. GEOMAR, Helmholtz Centre for Ocean Research Kiel, Germany.
    Ocean acidification reduces transfer of essential biomolecules in a natural plankton community2016Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, artikkel-id 27749Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Ocean acidification (OA), a process of increasing seawater acidity caused by the uptake of anthropogenic carbon dioxide (CO2) by the ocean, is expected to change surface ocean pH to levels unprecedented for millions of years, affecting marine food web structures and trophic interactions. Using an in situ mesocosm approach we investigated effects of OA on community composition and trophic transfer of essential fatty acids (FA) in a natural plankton assemblage. Elevated pCO(2) favored the smallest phytoplankton size class in terms of biomass, primarily picoeukaryotes, at the expense of chlorophyta and haptophyta in the nano-plankton size range. This shift in community composition and size structure was accompanied by a decline in the proportion of polyunsaturated FA (PUFA) to total FA content in the nano- and picophytoplankton size fractions. This decline was mirrored in a continuing reduction in the relative PUFA content of the dominant copepod, Calanus finmarchicus, which primarily fed on the nano-size class. Our results demonstrate that a shift in phytoplankton community composition and biochemical composition in response to rising CO2 can affect the transfer of essential compounds to higher trophic levels, which rely on their prey as a source for essential macromolecules.

  • 14.
    Berntell, Ellen
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för naturgeografi.
    Zhang, Qiong
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för naturgeografi.
    Chafik, Léon
    Körnich, Heiner
    Representation of Multidecadal Sahel Rainfall Variability in 20th Century Reanalyses2018Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, artikkel-id 10937Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Summer rainfall in the Sahel region has exhibited strong multidecadal variability during the 20th century causing dramatic human and socio-economic impacts. Studies have suggested that the variability is linked to the Atlantic multidecadal variability; a spatially persistent pattern of warm/cold sea surface temperatures in the North Atlantic. In the last few years, several promising century-long reanalysis datasets have been made available, opening up for further studies into the dynamics inducing the observed low-frequency rainfall variability in Sahel. We find that although three of the 20th century ECMWF reanalyses show clear multidecadal rainfall variability with extended wet and dry periods, the timing of the multidecadal variability in two of these reanalyses is found to exhibit almost anti-phase features for a large part of the 20th century when compared to observations. The best representation of the multidecadal rainfall variability is found in the ECMWF reanalysis that, unlike the other reanalyses (including NOAA's 20th century), do not assimilate any observations and may well be a critical reason for this mismatch, as discussed herein. This reanalysis, namely ERA-20CM, is thus recommended for future studies on the dynamics driving the multidecadal rainfall variability in Sahel and its linkages to the low-frequency North Atlantic oceanic temperatures.

  • 15.
    Björkander, Sophia
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för molekylär biovetenskap, Wenner-Grens institut.
    Hell, Lena
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för molekylär biovetenskap, Wenner-Grens institut.
    Johansson, Maria A.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för molekylär biovetenskap, Wenner-Grens institut.
    Mata Forsberg, Manuel
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för molekylär biovetenskap, Wenner-Grens institut.
    Lasaviciute, Gintare
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för molekylär biovetenskap, Wenner-Grens institut.
    Roos, Stefan
    Holmlund, Ulrika
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för molekylär biovetenskap, Wenner-Grens institut.
    Sverremark-Ekström, Eva
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för molekylär biovetenskap, Wenner-Grens institut.
    Staphylococcus aureus-derived factors induce IL-10, IFN-gamma and IL-17A-expressing FOXP3(+)CD161(+) T-helper cells in a partly monocyte-dependent manner2016Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, artikkel-id 22083Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Staphylococcus aureus (S. aureus) is a human pathogen as well as a frequent colonizer of skin and mucosa. This bacterium potently activates conventional T-cells through superantigens and it is suggested to induce T-cell cytokine-production as well as to promote a regulatory phenotype in T-cells in order to avoid clearance. This study aimed to investigate how S. aureus impacts the production of regulatory and pro-inflammatory cytokines and the expression of CD161 and HELIOS by peripheral CD4(+)FOXP3(+) T-cells. Stimulation of PBMC with S. aureus 161:2-cell free supernatant (CFS) induced expression of IL-10, IFN-gamma and IL-17A in FOXP3(+) cells. Further, CD161 and HELIOS separated the FOXP3(+) cells into four distinct populations regarding cytokine-expression. Monocyte-depletion decreased S. aureus 161:2-induced activation of FOXP3(+) cells while pre-stimulation of purified monocytes with S. aureus 161:2-CFS and subsequent co-culture with autologous monocyte-depleted PBMC was sufficient to mediate activation of FOXP3(+) cells. Together, these data show that S. aureus potently induces FOXP3(+) cells and promotes a diverse phenotype with expression of regulatory and pro-inflammatory cytokines connected to increased CD161-expression. This could indicate potent regulation or a contribution of FOXP3(+) cells to inflammation and repression of immune-suppression upon encounter with S. aureus.

  • 16.
    Bonaglia, Stefano
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Brüchert, Volker
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för geologiska vetenskaper.
    Callac, Nolwenn
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för geologiska vetenskaper.
    Vicenzi, Alessandra
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för geologiska vetenskaper.
    Chi Fru, Ernest
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för geologiska vetenskaper. Cardiff University, UK.
    Nascimento, Francisco J. A.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Methane fluxes from coastal sediments are enhanced by macrofauna2017Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, nr 1, artikkel-id 13145Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Methane and nitrous oxide are potent greenhouse gases (GHGs) that contribute to climate change. Coastal sediments are important GHG producers, but the contribution of macrofauna (benthic invertebrates larger than 1 mm) inhabiting them is currently unknown. Through a combination of trace gas, isotope, and molecular analyses, we studied the direct and indirect contribution of two macrofaunal groups, polychaetes and bivalves, to methane and nitrous oxide fluxes from coastal sediments. Our results indicate that macrofauna increases benthic methane efflux by a factor of up to eight, potentially accounting for an estimated 9.5% of total emissions from the Baltic Sea. Polychaetes indirectly enhance methane efflux through bioturbation, while bivalves have a direct effect on methane release. Bivalves host archaeal methanogenic symbionts carrying out preferentially hydrogenotrophic methanogenesis, as suggested by analysis of methane isotopes. Low temperatures (8 °C) also stimulate production of nitrous oxide, which is consumed by benthic denitrifying bacteria before it reaches the water column. We show that macrofauna contributes to GHG production and that the extent is dependent on lineage. Thus, macrofauna may play an important, but overlooked role in regulating GHG production and exchange in coastal sediment ecosystems.

  • 17. Boratynski, Zbyszek
    et al.
    Lehmann, Philipp
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen. University of Jyvaskyla, Finland.
    Mappes, Tapio
    Mousseau, Timothy A.
    Moller, Anders Pape
    Increased radiation from Chernobyl decreases the expression of red colouration in natural populations of bank voles (Myodes glareolus)2014Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 4, s. 7141-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Pheomelanin is a pink to red version of melanin pigment deposited in skin and hair. Due to its bright colour, pheomelanin plays a crucial function in signalling, in particular sexual signalling. However, production of pheomelanin, as opposed to its dark alternative, eumelanin, bears costs in terms of consumption of antioxidants important for protection of DNA against naturally produced reactive oxidative species. Therefore, decreased expression of pheomelanin is expected in organisms exposed to severe oxidative stress such as that caused by exposure to chronic ionizing radiation. We tested if variable exposure to radiation among natural populations of bank voles Myodes glareolus in Chernobyl affected expression of red colouration in their dorsal fur. The relative redness of dorsal fur was positively correlated with weight, but also negatively correlated with the level of background radiation. These results suggest that the development of the natural red colouration in adult bank voles is affected by ionizing background radiation, and potentially causing elevated levels of oxidative stress. Reduced production of pheomelanin allows more antioxidants to mitigate the oxidative stress caused by radiation. However, changing natural animal colouration for physiological reasons can have ecological costs, if e.g. it causes mismatch with habitat colouration and conspicuousness for predators.

  • 18. Braun, Stefan
    et al.
    Mhatre, Snehit S.
    Jaussi, Marion
    Roy, Hans
    Kjeldsen, Kasper U.
    Pearce, Christof
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för geologiska vetenskaper. Aarhus University, Denmark.
    Seidenkrantz, Marit-Solveig
    Jorgensen, Bo Barker
    Lomstein, Bente Aa.
    Microbial turnover times in the deep seabed studied by amino acid racemization modelling2017Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, artikkel-id 5680Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The study of active microbial populations in deep, energy-limited marine sediments has extended our knowledge of the limits of life on Earth. Typically, microbial activity in the deep biosphere is calculated by transport-reaction modelling of pore water solutes or from experimental measurements involving radiotracers. Here we modelled microbial activity from the degree of D: L-aspartic acid racemization in microbial necromass (remains of dead microbial biomass) in sediments up to ten million years old. This recently developed approach (D: L-amino acid modelling) does not require incubation experiments and is highly sensitive in stable, low-activity environments. We applied for the first time newly established constraints on several important input parameters of the D: L-amino acid model, such as a higher aspartic acid racemization rate constant and a lower cell-specific carbon content of sub-seafloor microorganisms. Our model results show that the pool of necromass amino acids is turned over by microbial activity every few thousand years, while the turnover times of vegetative cells are in the order of years to decades. Notably, microbial turnover times in million-year-old sediment from the Peru Margin are up to 100-fold shorter than previous estimates, highlighting the influence of microbial activities on element cycling over geologic time scales.

  • 19. Brizuela, F.
    et al.
    Heyl, C. M.
    Rudawski, P.
    Kroon, D.
    Rading, L.
    Dahlström, J. Marcus
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Mauritsson, J.
    Johnsson, P.
    Arnold, C. L.
    L'Huillier, A.
    Efficient high order harmonic generation boosted by below threshold harmonics2013Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 3, artikkel-id 1410Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    High-order harmonic generation (HHG) in gases has been established as an important technique for the generation of coherent extreme ultraviolet (XUV) pulses at ultrashort time scales. Its main drawback, however, is the low conversion efficiency, setting limits for many applications, such as ultrafast coherent imaging, nonlinear processes in the XUV range, or seeded free electron lasers. Here we introduce a novel scheme based on using below-threshold harmonics, generated in a seeding cell, to boost the HHG process in a generation cell, placed further downstream in the focused laser beam. By modifying the fundamental driving field, these low-order harmonics alter the ionization step of the nonlinear HHG process. Our dual-cell scheme enhances the conversion efficiency of HHG, opening the path for the realization of robust intense attosecond XUV sources.

  • 20.
    Bäckman, Lars
    et al.
    Stockholms universitet, Samhällsvetenskapliga fakulteten, Centrum för forskning om äldre och åldrande (ARC), (tills m KI).
    Waris, Otto
    Johansson, Jarkko
    Andersson, Micael
    Rinne, Juha O.
    Alakurtti, Kati
    Soveri, Anna
    Laine, Matti
    Nyberg, Lars
    Increased dopamine release after working-memory updating training: Neurochemical correlates of transfer2017Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, artikkel-id 7160Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Previous work demonstrates that working-memory (WM) updating training results in improved performance on a letter-memory criterion task, transfers to an untrained n-back task, and increases striatal dopamine (DA) activity during the criterion task. Here, we sought to replicate and extend these findings by also examining neurochemical correlates of transfer. Four positron emission tomography (PET) scans using the radioligand raclopride were performed. Two of these assessed DAD2 binding (letter memory; n-back) before 5 weeks of updating training, and the same two scans were performed post training. Key findings were (a) pronounced training-related behavioral gains in the lettermemory criterion task, (b) altered striatal DAD2 binding potential after training during letter-memory performance, suggesting training-induced increases in DA release, and (c) increased striatal DA activity also during the n-back transfer task after the intervention, but no concomitant behavioral transfer. The fact that the training-related DA alterations during the transfer task were not accompanied by behavioral transfer suggests that increased DA release may be a necessary, but not sufficient, condition for behavioral transfer to occur.

  • 21.
    Callac, Nolwenn
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för geologiska vetenskaper.
    Posth, Nicole R.
    Rattray, Jayne E.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för geologiska vetenskaper.
    Yamoah, Kweku K. Y.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för geologiska vetenskaper.
    Wiech, Alan
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för geologiska vetenskaper.
    Ivarsson, Magnus
    Hemmingsson, Christoffer
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för geologiska vetenskaper.
    Kilias, Stephanos P.
    Argyraki, Ariadne
    Broman, Curt
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för geologiska vetenskaper.
    Skogby, Henrik
    Smittenberg, Rienk H.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för geologiska vetenskaper.
    Chi Fru, Ernest
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för geologiska vetenskaper.
    Modes of carbon fixation in an arsenic and CO2-rich shallow hydrothermal ecosystem2017Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, artikkel-id 14708Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The seafloor sediments of Spathi Bay, Milos Island, Greece, are part of the largest arsenic-CO2-rich shallow submarine hydrothermal ecosystem on Earth. Here, white and brown deposits cap chemically distinct sediments with varying hydrothermal influence. All sediments contain abundant genes for autotrophic carbon fixation used in the Calvin-Benson-Bassham (CBB) and reverse tricaboxylic acid (rTCA) cycles. Both forms of RuBisCO, together with ATP citrate lyase genes in the rTCA cycle, increase with distance from the active hydrothermal centres and decrease with sediment depth. Clustering of RuBisCO Form II with a highly prevalent Zetaproteobacteria 16S rRNA gene density infers that ironoxidizing bacteria contribute significantly to the sediment CBB cycle gene content. Three clusters form from different microbial guilds, each one encompassing one gene involved in CO2 fixation, aside from sulfate reduction. Our study suggests that the microbially mediated CBB cycle drives carbon fixation in the Spathi Bay sediments that are characterized by diffuse hydrothermal activity, high CO2, As emissions and chemically reduced fluids. This study highlights the breadth of conditions influencing the biogeochemistry in shallow CO2-rich hydrothermal systems and the importance of coupling highly specific process indicators to elucidate the complexity of carbon cycling in these ecosystems.

  • 22. Campeau, Audrey
    et al.
    Wallin, Marcus B.
    Giesler, Reiner
    Löfgren, Stefan
    Mörth, Carl-Magnus
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för geologiska vetenskaper.
    Schiff, Sherry
    Venkiteswaran, Jason J.
    Bishop, Kevin
    Multiple sources and sinks of dissolved inorganic carbon across Swedish streams, refocusing the lens of stable C isotopes2017Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, artikkel-id 9158Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    It is well established that stream dissolved inorganic carbon (DIC) fluxes play a central role in the global C cycle, yet the sources of stream DIC remain to a large extent unresolved. Here, we explore large-scale patterns in delta C-13-DIC from streams across Sweden to separate and further quantify the sources and sinks of stream DIC. We found that stream DIC is governed by a variety of sources and sinks including biogenic and geogenic sources, CO2 evasion, as well as in-stream processes. Although soil respiration was the main source of DIC across all streams, a geogenic DIC influence was identified in the northernmost region. All streams were affected by various degrees of atmospheric CO2 evasion, but residual variance in delta C-13-DIC also indicated a significant influence of in-stream metabolism and anaerobic processes. Due to those multiple sources and sinks, we emphasize that simply quantifying aquatic DIC fluxes will not be sufficient to characterise their role in the global C cycle.

  • 23. Cattaneo, Alberto Maria
    et al.
    Gonzalez, Francisco
    Bengtsson, Jonas M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Corey, Elizabeth A.
    Jacquin-Joly, Emmanuelle
    Montagné, Nicolas
    Salvagnin, Umberto
    Walker, William B.
    Witzgall, Peter
    Anfora, Gianfranco
    Bobkov, Yuriy V.
    Candidate pheromone receptors of codling moth Cydia pomonella respond to pheromones and kairomones2017Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, artikkel-id 41105Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Olfaction plays a dominant role in the mate-finding and host selection behaviours of the codling moth (Cydia pomonella), an important pest of apple, pear and walnut orchards worldwide. Antennal transcriptome analysis revealed a number of abundantly expressed genes related to the moth olfactory system, including those encoding the olfactory receptors (ORs) CpomOR1, CpomOR3 and CpomOR6a, which belong to the pheromone receptor (PR) lineage, and the co-receptor (CpomOrco). Using heterologous expression, in both Drosophila olfactory sensory neurones and in human embryonic kidney cells, together with electrophysiological recordings and calcium imaging, we characterize the basic physiological and pharmacological properties of these receptors and demonstrate that they form functional ionotropic receptor channels. Both the homomeric CpomOrco and heteromeric CpomOrco + OR complexes can be activated by the common Orco agonists VUAA1 and VUAA3, as well as inhibited by the common Orco antagonists amiloride derivatives. CpomOR3 responds to the plant volatile compound pear ester ethyl-(E, Z)-2,4-decadienoate, while CpomOR6a responds to the strong pheromone antagonist codlemone acetate (E, E)-8,10-dodecadien-1-yl acetate. These findings represent important breakthroughs in the deorphanization of codling moth pheromone receptors, as well as more broadly into insect ecology and evolution and, consequently, for the development of sustainable pest control strategies based on manipulating chemosensory communication.

  • 24. Cebula, Marcus
    et al.
    Turan, Ilke Simsek
    Sjödin, Birgitta
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för neurokemi.
    Thulasingam, Madhuranayaki
    Brock, Joseph
    Chmyrov, Volodymyr
    Widengren, Jerker
    Abe, Hiroshi
    Mannervik, Bengt
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för neurokemi.
    Haeggström, Jesper Z.
    Rinaldo-Matthis, Agnes
    Akkaya, Engin U.
    Morgenstern, Ralf
    Catalytic Conversion of Lipophilic Substrates by Phase constrained Enzymes in the Aqueous or in the Membrane Phase2016Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, artikkel-id 38316Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Both soluble and membrane-bound enzymes can catalyze the conversion of lipophilic substrates. The precise substrate access path, with regard to phase, has however, until now relied on conjecture from enzyme structural data only (certainly giving credible and valuable hypotheses). Alternative methods have been missing. To obtain the first experimental evidence directly determining the access paths (of lipophilic substrates) to phase constrained enzymes we here describe the application of a BODIPY-derived substrate (PS1). Using this tool, which is not accessible to cytosolic enzymes in the presence of detergent and, by contrast, not accessible to membrane embedded enzymes in the absence of detergent, we demonstrate that cytosolic and microsomal glutathione transferases (GSTs), both catalyzing the activation of PS1, do so only within their respective phases. This approach can serve as a guideline to experimentally validate substrate access paths, a fundamental property of phase restricted enzymes. Examples of other enzyme classes with members in both phases are xenobiotic-metabolizing sulphotransferases/UDP-glucuronosyl transferases or epoxide hydrolases. Since specific GSTs have been suggested to contribute to tumor drug resistance, PS1 can also be utilized as a tool to discriminate between phase constrained members of these enzymes by analyzing samples in the absence and presence of Triton X-100.

  • 25.
    Chafik, Léon
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Meteorologiska institutionen (MISU). University of Bergen, Norway; Bjerknes Centre for Climate Research, Norway.
    Øie Nilsen, Jan Even
    Dangendorf, Sönke
    Reverdin, Gilles
    Frederikse, Thomas
    North Atlantic Ocean Circulation and Decadal Sea Level Change During the Altimetry Era2019Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, artikkel-id 1041Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Regional sea-level rise is characterized by decadal acceleration and deceleration periods that typically stem from oceanic climate variability. Here, we investigate decadal sea-level trends during the altimetry era and pin down the associated ocean circulation changes. We find that decadal subpolar gyre cooling (warming), strengthening (weakening), widening (shrinking) since the mid-2000s (early 1990s) resulted in negative (positive) sea level trends of −7.1 mm/yr ± 1.3 mm/yr (3.9 mm/yr ± 1.5 mm/yr). These large-scale changes further coincide with steric sea-level trends, and are driven by decadal-scale ocean circulation variability. Sea level on the European shelf, however, is found to correlate well with along-slope winds (R = 0.78), suggesting it plays a central role in driving the associated low-frequency dynamic sea level variability. Furthermore, when the North Atlantic is in a cooling (warming) period, the winds along the eastern boundary are predominantly from the North (South), which jointly drive a slowdown (rapid increase) in shelf and coastal sea level rise. Understanding the mechanisms that produce these connections may be critical for interpreting future regional sea-level trends.

  • 26. Chauvin, M.
    et al.
    Florén, Hans-Gustav
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för astronomi.
    Friis, M.
    Jackson, M.
    Kamae, T.
    Kataoka, J.
    Kawano, T.
    Kiss, M.
    Mikhalev, V.
    Mizuno, T.
    Ohashi, N.
    Stana, T.
    Tajima, H.
    Takahashi, H.
    Uchida, N.
    Pearce, M.
    Shedding new light on the Crab with polarized X-rays2017Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, artikkel-id 7816Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Strong magnetic fields, synchrotron emission, and Compton scattering are omnipresent in compact celestial X-ray sources. Emissions in the X-ray energy band are consequently expected to be linearly polarized. X-ray polarimetry provides a unique diagnostic to study the location and fundamental mechanisms behind emission processes. The polarization of emissions from a bright celestial X-ray source, the Crab, is reported here for the first time in the hard X-ray band (similar to 20-160 keV). The Crab is a complex system consisting of a central pulsar, a diffuse pulsar wind nebula, as well as structures in the inner nebula including a jet and torus. Measurements are made by a purpose-built and calibrated polarimeter, PoGO+. The polarization vector is found to be aligned with the spin axis of the pulsar for a polarization fraction, PF = (20.9 +/- 5.0)%. This is higher than that of the optical diffuse nebula, implying a more compact emission site, though not as compact as, e.g., the synchrotron knot. Contrary to measurements at higher energies, no significant temporal evolution of phase-integrated polarisation parameters is observed. The polarization parameters for the pulsar itself are measured for the first time in the X-ray energy band and are consistent with observations at optical wavelengths.

  • 27. Cheon, Jae Yeong
    et al.
    Kim, Taeyoung
    Choi, YongMan
    Jeong, Hu Young
    Kim, Min Gyu
    Sa, Young Jin
    Kim, Jaesik
    Lee, Zonghoon
    Yang, Tae-Hyun
    Kwon, Kyungjung
    Terasaki, Osamu
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för oorganisk kemi och strukturkemi. Korea Advanced Institute of Science and Technology, Republic of Korea.
    Park, Gu-Gon
    Adzic, Radoslav R.
    Joo, Sang Hoon
    Ordered mesoporous porphyrinic carbons with very high electrocatalytic activity for the oxygen reduction reaction2013Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 3, s. 2715-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The high cost of the platinum-based cathode catalysts for the oxygen reduction reaction (ORR) has impeded the widespread application of polymer electrolyte fuel cells. We report on a new family of non-precious metal catalysts based on ordered mesoporous porphyrinic carbons (M-OMPC; M = Fe, Co, or FeCo) with high surface areas and tunable pore structures, which were prepared by nanocasting mesoporous silica templates with metalloporphyrin precursors. The FeCo-OMPC catalyst exhibited an excellent ORR activity in an acidic medium, higher than other non-precious metal catalysts. It showed higher kinetic current at 0.9 V than Pt/C catalysts, as well as superior long-term durability and MeOH-tolerance. Density functional theory calculations in combination with extended X-ray absorption fine structure analysis revealed a weakening of the interaction between oxygen atom and FeCo-OMPC compared to Pt/C. This effect and high surface area of FeCo-OMPC appear responsible for its significantly high ORR activity.

  • 28. Chernobrovkin, Alexey
    et al.
    Marin-Vicente, Consuelo
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för molekylär biovetenskap, Wenner-Grens institut. Karolinska Institutet, Sweden .
    Visa, Neus
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för molekylär biovetenskap, Wenner-Grens institut.
    Zubarev, Roman A.
    Functional Identification of Target by Expression Proteomics (FITExP) reveals protein targets and highlights mechanisms of action of small molecule drugs2015Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 5, artikkel-id 11176Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Phenomenological screening of small molecule libraries for anticancer activity yields potentially interesting candidate molecules, with a bottleneck in the determination of drug targets and the mechanism of anticancer action. We have found that, for the protein target of a small-molecule drug, the abundance change in late apoptosis is exceptional compared to the expectations based on the abundances of co-regulated proteins. Based on this finding, a novel method to drug target deconvolution is proposed. In a proof of principle experiment, the method yielded known targets of several common anticancer agents among a few (often, just one) likely candidates identified in an unbiased way from cellular proteome comprising more than 4,000 proteins. A validation experiment with a different set of cells and drugs confirmed the findings. As an additional benefit, mapping most specifically regulated proteins on known protein networks highlighted the mechanism of drug action. The new method, if proven to be general, can significantly shorten drug target identification, and thus facilitate the emergence of novel anticancer treatments.

  • 29.
    Chi Fru, Ernest
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för geologiska vetenskaper. Swedish Museum of Natural History, Sweden.
    Arvestal, Emma
    Callac, Nolwenn
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för geologiska vetenskaper.
    El Albani, Abderrazak
    Kilias, Stephanos
    Argyraki, Ariadne
    Jakobsson, Martin
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för geologiska vetenskaper.
    Arsenic stress after the Proterozoic glaciations2015Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 5, artikkel-id 17789Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Protection against arsenic damage in organisms positioned deep in the tree of life points to early evolutionary sensitization. Here, marine sedimentary records reveal a Proterozoic arsenic concentration patterned to glacial-interglacial ages. The low glacial and high interglacial sedimentary arsenic concentrations, suggest deteriorating habitable marine conditions may have coincided with atmospheric oxygen decline after similar to 2.1 billion years ago. A similar intensification of near continental margin sedimentary arsenic levels after the Cryogenian glaciations is also associated with amplified continental weathering. However, interpreted atmospheric oxygen increase at this time, suggests that the marine biosphere had widely adapted to the reorganization of global marine elemental cycles by glaciations. Such a glacially induced biogeochemical bridge would have produced physiologically robust communities that enabled increased oxygenation of the ocean-atmosphere system and the radiation of the complex Ediacaran-Cambrian life.

  • 30. Chiba, Mitsuru
    et al.
    Monzen, Satoru
    Iwaya, Chihiro
    Kashiwagi, Yuri
    Yamada, Sunao
    Hosokawa, Yoichiro
    Mariya, Yasushi
    Nakamura, Toshiya
    Wojcik, Andrzej
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för molekylär biovetenskap, Wenner-Grens institut. Jan Kochanowski University, Poland.
    Serum miR-375-3p increase in mice exposed to a high dose of ionizing radiation2018Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, artikkel-id 1302Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Exposure to high-doses of ionizing radiation (IR) leads to development of a strong acute radiation syndrome (ARS) in mammals. ARS manifests after a latency period and it is important to develop fast prognostic biomarkers for its early detection and assessment. Analysis of chromosomal aberrations in peripheral blood lymphocytes is the gold standard of biological dosimetry, but it fails after high doses of IR. Therefore, it is important to establish novel biomarkers of exposure that are fast and reliable also in the high dose range. Here, we investigated the applicability of miRNA levels in mouse serum. We found significantly increased levels of miR-375-3p following whole body exposure to 7 Gy of X-rays. In addition, we analyzed their levels in various organs of control mice and found them to be especially abundant in the pancreas and the intestine. Following a dose of 7 Gy, extensive cell death occurred in these tissues and this correlated negatively with the levels of miR-375-3p in the organs. We conclude that high expressing tissues of miR-375-3p may secrete this miRNA in serum following exposure to 7 Gy. Therefore, elevated miR-375-3p in serum may be a predictor of tissue damage induced by exposure to a high radiation dose.

  • 31.
    Chiruvella, Kishore K.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för molekylär biovetenskap, Wenner-Grens institut.
    Rajaei, Naghmeh
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för molekylär biovetenskap, Wenner-Grens institut.
    Jonna, Venkateswara Rao
    Hofer, Anders
    Åström, Stefan U.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för molekylär biovetenskap, Wenner-Grens institut.
    Biochemical Characterization of Kat1: a Domesticated hAT-Transposase that Induces DNA Hairpin Formation and MAT-Switching2016Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, artikkel-id 21671Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Kluyveromyces lactis hAT-transposase 1 (Kat1) generates hairpin-capped DNA double strand breaks leading to MAT-switching (MATa to MAT alpha). Using purified Kat1, we demonstrate the importance of terminal inverted repeats and subterminal repeats for its endonuclease activity. Kat1 promoted joining of the transposon end into a target DNA molecule in vitro, a biochemical feature that ties Kat1 to transposases. Gas-phase Electrophoretic Mobility Macromolecule analysis revealed that Kat1 can form hexamers when complexed with DNA. Kat1 point mutants were generated in conserved positions to explore structure-function relationships. Mutants of predicted catalytic residues abolished both DNA cleavage and strand-transfer. Interestingly, W576A predicted to be impaired for hairpin formation, was active for DNA cleavage and supported wild type levels of mating-type switching. In contrast, the conserved CXXH motif was critical for hairpin formation because Kat1 C402A/H405A completely blocked hairpinning and switching, but still generated nicks in the DNA. Mutations in the BED zinc-finger domain (C130A/C133A) resulted in an unspecific nuclease activity, presumably due to nonspecific DNA interaction. Kat1 mutants that were defective for cleavage in vitro were also defective for mating-type switching. Collectively, this study reveals Kat1 sharing extensive biochemical similarities with cut and paste transposons despite being domesticated and evolutionary diverged from active transposons.

  • 32. Ch'ng, Jun-Hong
    et al.
    Sirel, Madle
    Zandian, Arash
    del Pilar Quintana, Maria
    Chan, Sherwin Chun Leung
    Moll, Kirsten
    Tellgren-Roth, Åsa
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Nilsson, IngMarie
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Nilsson, Peter
    Qundos, Ulrika
    Wahlgren, Mats
    Epitopes of anti-RIFIN antibodies and characterization of rif-expressing Plasmodium falciparum parasites by RNA sequencing2017Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, artikkel-id 43190Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Variable surface antigens of Plasmodium falciparum have been a major research focus since they facilitate parasite sequestration and give rise to deadly malaria complications. Coupled with its potential use as a vaccine candidate, the recent suggestion that the repetitive interspersed families of polypeptides (RIFINs) mediate blood group A rosetting and influence blood group distribution has raised the research profile of these adhesins. Nevertheless, detailed investigations into the functions of this highly diverse multigene family remain hampered by the limited number of validated reagents. In this study, we assess the specificities of three promising polyclonal anti-RIFIN antibodies that were IgG-purified from sera of immunized animals. Their epitope regions were mapped using a 175,000-peptide microarray holding overlapping peptides of the P. falciparum variable surface antigens. Through immunoblotting and immunofluorescence imaging, we show that different antibodies give varying results in different applications/assays. Finally, we authenticate the antibody-based detection of RIFINs in two previously uncharacterized non-rosetting parasite lines by identifying the dominant rif transcripts using RNA sequencing.

  • 33.
    Ciftci, Sibel
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik. Stockholms universitet, Science for Life Laboratory (SciLifeLab).
    Neumann, Felix
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik. Stockholms universitet, Science for Life Laboratory (SciLifeLab).
    Hernández-Neuta, Iván
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik. Stockholms universitet, Science for Life Laboratory (SciLifeLab).
    Hakhverdyan, Mikhayil
    Bálint, Ádám
    Herthnek, David
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik. Stockholms universitet, Science for Life Laboratory (SciLifeLab).
    Madaboosi, Narayanan
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik. Stockholms universitet, Science for Life Laboratory (SciLifeLab).
    Nilsson, Mats
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik. Stockholms universitet, Science for Life Laboratory (SciLifeLab).
    A novel mutation tolerant padlock probe design for multiplexed detection of hypervariable RNA viruses2019Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, artikkel-id 2872Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The establishment of a robust detection platform for RNA viruses still remains a challenge in molecular diagnostics due to their high mutation rates. Newcastle disease virus (NDV) is one such RNA avian virus with a hypervariable genome and multiple genotypes. Classical approaches like virus isolation, serology, immunoassays and RT-PCR are cumbersome, and limited in terms of specificity and sensitivity. Padlock probes (PLPs) are known for allowing the detection of multiple nucleic acid targets with high specificity, and in combination with Rolling circle amplification (RCA) have permitted the development of versatile pathogen detection assays. In this work, we aimed to detect hypervariable viruses by developing a novel PLP design strategy capable of tolerating mutations while preserving high specificity by targeting several moderately conserved regions and using degenerate bases. For this, we designed nine padlock probes based on the alignment of 335 sequences covering both Class I and II NDV. Our PLP design showed high coverage and specificity for the detection of eight out of ten reported genotypes of Class II NDV field isolated strains, yielding a detection limit of less than ten copies of viral RNA. Further taking advantage of the multiplex capability of PLPs, we successfully extended the assay for the simultaneous detection of three poultry RNA viruses (NDV, IBV and AIV) and combined it with a paper based microfluidic enrichment read-out for digital quantification. In summary, our novel PLP design addresses the current issue of tolerating mutations of highly emerging virus strains with high sensitivity and specificity.

  • 34. Clausson, Carl-Magnus
    et al.
    Arngården, Linda
    Ishaq, Omer
    Klaesson, Axel
    Kühnemund, Malte
    Grannas, Karin
    Koos, Björn
    Qian, Xiaoyan
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik. Stockholms universitet, Science for Life Laboratory (SciLifeLab).
    Ranefall, Petter
    Krzywkowski, Tomasz
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik. Stockholms universitet, Science for Life Laboratory (SciLifeLab).
    Brismar, Hjalmar
    Nilsson, Mats
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik. Stockholms universitet, Science for Life Laboratory (SciLifeLab).
    Wählby, Carolina
    Söderberg, Ola
    Compaction of rolling circle amplification products increases signal integrity and signal-to-noise ratio2015Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 5, artikkel-id 12317Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Rolling circle amplification (RCA) for generation of distinct fluorescent signals in situ relies upon the self-collapsing properties of single-stranded DNA in commonly used RCA-based methods. By introducing a cross-hybridizing DNA oligonucleotide during rolling circle amplification, we demonstrate that the fluorophore-labeled RCA products (RCPs) become smaller. The reduced size of RCPs increases the local concentration of fluorophores and as a result, the signal intensity increases together with the signal-to-noise ratio. Furthermore, we have found that RCPs sometimes tend to disintegrate and may be recorded as several RCPs, a trait that is prevented with our cross-hybridizing DNA oligonucleotide. These effects generated by compaction of RCPs improve accuracy of visual as well as automated in situ analysis for RCA based methods, such as proximity ligation assays (PLA) and padlock probes.

  • 35. Conti, Luca
    et al.
    Renhorn, Jakob
    Gabrielsson, Anders
    Turesson, Fredrik
    Liin, Sara I.
    Lindahl, Erik
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik. Stockholms universitet, Science for Life Laboratory (SciLifeLab). KTH Royal Institute of Technology, Sweden.
    Elinder, Fredrik
    Reciprocal voltage sensor-to-pore coupling leads to potassium channel C-type inactivation2016Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, artikkel-id 27562Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Voltage-gated potassium channels open at depolarized membrane voltages. A prolonged depolarization causes a rearrangement of the selectivity filter which terminates the conduction of ions - a process called slow or C-type inactivation. How structural rearrangements in the voltage-sensor domain (VSD) cause alteration in the selectivity filter, and vice versa, are not fully understood. We show that pulling the pore domain of the Shaker potassium channel towards the VSD by a Cd2+ bridge accelerates C-type inactivation. Molecular dynamics simulations show that such pulling widens the selectivity filter and disrupts the K+ coordination, a hallmark for C-type inactivation. An engineered Cd2+ bridge within the VSD also affect C-type inactivation. Conversely, a pore domain mutation affects VSD gating-charge movement. Finally, C-type inactivation is caused by the concerted action of distant amino acid residues in the pore domain. All together, these data suggest a reciprocal communication between the pore domain and the VSD in the extracellular portion of the channel.

  • 36.
    Dalerum, Fredrik
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen. University of Oviedo, Spain; University of Pretoria, South Africa.
    Miranda, Maria
    Game auction prices are not related to biodiversity contributions of southern African ungulates and large carnivores2016Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, artikkel-id 21922Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    There is an urgent need for human societies to become environmentally sustainable. Because public policy is largely driven by economic processes, quantifications of the relationship between market prices and environmental values can provide important information for developing strategies towards sustainability. Wildlife in southern Africa is often privately owned and traded at game auctions to be utilized for commercial purposes mostly related to tourism. This market offers an interesting opportunity to evaluate how market prices relate to biologically meaningful species characteristics. In this market, prices were not correlated with species contributions to either phylogenetic or functional diversity, and species contributions to phylogenetic or functional diversity did not influence the trends in prices over time for the past 20 years. Since this economic market did not seem to appreciate evolutionary or ecologically relevant characteristics, we question if the game tourism market may contribute towards biodiversity conservation in southern Africa. We suggest that market prices in general may have limited values as guides for directing conservation and environmental management. We further suggest that there is a need to evaluate what humans value in biological organisms, and how potentially necessary shifts in such values can be instigated.

  • 37.
    Daley, Daniel O.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Skoglund, Ulf
    Söderström, Bill
    FtsZ does not initiate membrane constriction at the onset of division2016Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, artikkel-id 33138Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The source of constriction required for division of a bacterial cell remains enigmatic. FtsZ is widely believed to be a key player, because in vitro experiments indicate that it can deform liposomes when membrane tethered. However in vivo evidence for such a role has remained elusive as it has been challenging to distinguish the contribution of FtsZ from that of peptidoglycan-ingrowth. To differentiate between these two possibilities we studied the early stages of division in Escherichia coli, when FtsZ is present at the division site but peptidoglycan synthesizing enzymes such as FtsI and FtsN are not. Our approach was to use correlative cryo-fluorescence and cryo-electron microscopy (cryo-CLEM) to monitor the localization of fluorescently labeled FtsZ, FtsI or FtsN correlated with the septal ultra-structural geometry in the same cell. We noted that the presence of FtsZ at the division septum is not sufficient to deform membranes. This observation suggests that, although FtsZ can provide a constrictive force, the force is not substantial at the onset of division. Conversely, the presence of FtsN always correlated with membrane invagination, indicating that allosteric activation of peptidoglycan ingrowth is the trigger for constriction of the cell envelope during cell division in E. coli.

  • 38. Dall' Osto, M.
    et al.
    Beddows, D. C. S.
    Tunved, Peter
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för miljövetenskap och analytisk kemi.
    Krejci, Radovan
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för miljövetenskap och analytisk kemi.
    Ström, Johan
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för miljövetenskap och analytisk kemi.
    Hansson, Hans-Christen
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för miljövetenskap och analytisk kemi.
    Yoon, Y. J.
    Park, Ki-Tae
    Becagli, S.
    Udisti, R.
    Onasch, T.
    O'Dowd, C. D.
    Simo, R.
    Harrison, Roy M.
    Arctic sea ice melt leads to atmospheric new particle formation2017Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, artikkel-id 3318Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Atmospheric new particle formation (NPF) and growth significantly influences climate by supplying new seeds for cloud condensation and brightness. Currently, there is a lack of understanding of whether and how marine biota emissions affect aerosol-cloud-climate interactions in the Arctic. Here, the aerosol population was categorised via cluster analysis of aerosol size distributions taken at Mt Zeppelin (Svalbard) during a 11 year record. The daily temporal occurrence of NPF events likely caused by nucleation in the polar marine boundary layer was quantified annually as 18%, with a peak of 51% during summer months. Air mass trajectory analysis and atmospheric nitrogen and sulphur tracers link these frequent nucleation events to biogenic precursors released by open water and melting sea ice regions. The occurrence of such events across a full decade was anti-correlated with sea ice extent. New particles originating from open water and open pack ice increased the cloud condensation nuclei concentration background by at least ca. 20%, supporting a marine biosphere-climate link through sea ice melt and low altitude clouds that may have contributed to accelerate Arctic warming. Our results prompt a better representation of biogenic aerosol sources in Arctic climate models.

  • 39. Dall'Osto, M.
    et al.
    Beddows, D. C. S.
    Asmi, A.
    Poulain, L.
    Hao, L.
    Freney, E.
    Allan, J. D.
    Canagaratna, M.
    Crippa, M.
    Bianchi, F.
    de Leeuw, G.
    Eriksson, A.
    Swietlicki, E.
    Hansson, Hans Christen
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för miljövetenskap och analytisk kemi.
    Henzing, J. S.
    Granier, C.
    Zemankova, K.
    Laj, P.
    Onasch, T.
    Prevot, A.
    Putaud, J. P.
    Sellegri, K.
    Vidal, M.
    Virtanen, A.
    Simo, R.
    Worsnop, D.
    O'Dowd, C.
    Kulmala, M.
    Harrison, Roy M.
    Novel insights on new particle formation derived from a pan-european observing system2018Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, artikkel-id 1482Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The formation of new atmospheric particles involves an initial step forming stable clusters less than a nanometre in size (<similar to 1 nm), followed by growth into quasi-stable aerosol particles a few nanometres (similar to 1-10 nm) and larger (>similar to 10 nm). Although at times, the same species can be responsible for both processes, it is thought that more generally each step comprises differing chemical contributors. Here, we present a novel analysis of measurements from a unique multi-station ground-based observing system which reveals new insights into continental-scale patterns associated with new particle formation. Statistical cluster analysis of this unique 2-year multi-station dataset comprising size distribution and chemical composition reveals that across Europe, there are different major seasonal trends depending on geographical location, concomitant with diversity in nucleating species while it seems that the growth phase is dominated by organic aerosol formation. The diversity and seasonality of these events requires an advanced observing system to elucidate the key processes and species driving particle formation, along with detecting continental scale changes in aerosol formation into the future.

  • 40. De Palma, Adriana
    et al.
    Abrahamczyk, Stefan
    Aizen, Marcelo A.
    Albrecht, Matthias
    Basset, Yves
    Bates, Adam
    Blake, Robin J.
    Boutin, Celine
    Bugter, Rob
    Connop, Stuart
    Cruz-Lopez, Leopoldo
    Cunningham, Saul A.
    Darvill, Ben
    Diekoetter, Tim
    Dorn, Silvia
    Downing, Nicola
    Entling, Martin H.
    Farwig, Nina
    Felicioli, Antonio
    Fonte, Steven J.
    Fowler, Robert
    Franzen, Markus
    Goulson, Dave
    Grass, Ingo
    Hanley, Mick E.
    Hendrix, Stephen D.
    Herrmann, Farina
    Herzog, Felix
    Holzschuh, Andrea
    Jauker, Birgit
    Kessler, Michael
    Knight, M. E.
    Kruess, Andreas
    Lavelle, Patrick
    Le Feon, Violette
    Lentini, Pia
    Malone, Louise A.
    Marshall, Jon
    Pachon, Eliana Martinez
    McFrederick, Quinn S.
    Morales, Carolina L.
    Mudri-Stojnic, Sonja
    Nates-Parra, Guiomar
    Nilsson, Sven G.
    Ockinger, Erik
    Osgathorpe, Lynne
    Parra-H, Alejandro
    Peres, Carlos A.
    Persson, Anna S.
    Petanidou, Theodora
    Poveda, Katja
    Power, Eileen F.
    Quaranta, Marino
    Quintero, Carolina
    Rader, Romina
    Richards, Miriam H.
    Roulston, T'ai
    Rousseau, Laurent
    Sadler, Jonathan P.
    Samnegård, Ulrika
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Schellhorn, Nancy A.
    Schuepp, Christof
    Schweiger, Oliver
    Smith-Pardo, Allan H.
    Steffan-Dewenter, Ingolf
    Stout, Jane C.
    Tonietto, Rebecca K.
    Tscharntke, Teja
    Tylianakis, Jason M.
    Verboven, Hans A. F.
    Vergara, Carlos H.
    Verhulst, Jort
    Westphal, Catrin
    Yoon, Hyung Joo
    Purvis, Andy
    Predicting bee community responses to land-use changes: Effects of geographic and taxonomic biases2016Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, artikkel-id 31153Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Land-use change and intensification threaten bee populations worldwide, imperilling pollination services. Global models are needed to better characterise, project, and mitigate bees' responses to these human impacts. The available data are, however, geographically and taxonomically unrepresentative; most data are from North America and Western Europe, overrepresenting bumblebees and raising concerns that model results may not be generalizable to other regions and taxa. To assess whether the geographic and taxonomic biases of data could undermine effectiveness of models for conservation policy, we have collated from the published literature a global dataset of bee diversity at sites facing land-use change and intensification, and assess whether bee responses to these pressures vary across 11 regions (Western, Northern, Eastern and Southern Europe; North, Central and South America; Australia and New Zealand; South East Asia; Middle and Southern Africa) and between bumblebees and other bees. Our analyses highlight strong regionally-based responses of total abundance, species richness and Simpson's diversity to land use, caused by variation in the sensitivity of species and potentially in the nature of threats. These results suggest that global extrapolation of models based on geographically and taxonomically restricted data may underestimate the true uncertainty, increasing the risk of ecological surprises.

  • 41.
    Deiana, Luca
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Afewerki, Samson
    Palo-Nieto, Carlos
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Verho, Oscar
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Johnston, Eric V.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Cordova, Armando
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi. Mid Sweden University.
    Highly Enantioselective Cascade Transformations by Merging Heterogeneous Transition Metal Catalysis with Asymmetric Aminocatalysis2012Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 2, s. 851-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The concept of combining heterogeneous transition metal and amine catalysis for enantioselective cascade reactions has not yet been realized. This is of great advantage since it would allow for the recycling of expensive and non-environmentally friendly transition metals. We disclose that the use of a heterogeneous Pd-catalyst in combination with a simple chiral amine co-catalyst allows for highly enantioselective cascade transformations. The preparative power of this process has been demonstrated in the context of asymmetric cascade Michael/carbocyclization transformations that delivers cyclopentenes bearing an all carbon quaternary stereocenters in high yields with up to 30: 1 dr and 99% ee. Moreover, a variety of highly enantioselective cascade hetero-Michael/carbocyclizations were developed for the one-pot synthesis of valuable dihydrofurans and pyrrolidines (up to 98% ee) by using bench-stable heterogeneous Pd and chiral amines as co-catalysts.

  • 42. Del Giudice, Marco
    et al.
    Bosia, Carla
    Grigolon, Silvia
    Bo, Stefano
    Stockholms universitet, Nordiska institutet för teoretisk fysik (Nordita).
    Stochastic sequestration dynamics: a minimal model with extrinsic noise for bimodal distributions and competitors correlation2018Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, artikkel-id 10387Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Many biological processes are known to be based on molecular sequestration. This kind of dynamics involves two types of molecular species, namely targets and sequestrants, that bind to form a complex. In the simple framework of mass-action law, key features of these systems appear to be threshold-like profiles of the amounts of free molecules as a function of the parameters determining their possible maximum abundance. However, biochemical processes are probabilistic and take place in stochastically fluctuating environments. How these different sources of noise affect the final outcome of the network is not completely characterised yet. In this paper we specifically investigate the effects induced by a source of extrinsic noise onto a minimal stochastic model of molecular sequestration. We analytically show how bimodal distributions of the targets can appear and characterise them as a result of noise filtering mediated by the threshold response. We then address the correlations between target species induced by the sequestrant and discuss how extrinsic noise can turn the negative correlation caused by competition into a positive one. Finally, we consider the more complex scenario of competitive inhibition for enzymatic kinetics and discuss the relevance of our findings with respect to applications.

  • 43. Diodato, Nazzareno
    et al.
    Charpentier Ljungqvist, Fredrik
    Stockholms universitet, Humanistiska fakulteten, Historiska institutionen. University of Cambridge, United Kingdom.
    Bellocchi, Gianni
    A millennium-long reconstruction of damaging hydrological events across Italy2019Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, artikkel-id 9963Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Damaging hydrological events are extreme phenomena with potentially severe impacts on human societies. Here, we present the hitherto longest reconstruction of damaging hydrological events for Italy, and for the whole Mediterranean region, revealing 674 such events over the period 800-2017. For any given year, we established a severity index based on information in historical documentary records, facilitating the transformation of the data into a continuous time-series. Episodes of hydrological extremes disrupted ecosystems during the more severe events by changing landforms. The frequency and severity of damaging hydrological events across Italy were likely influenced by the mode of the Atlantic Multidecadal Variability (AMV), with relatively few events during the warm Medieval Climate Anomaly dominated by a positive phase of the AMV. More frequent and heavier storms prevailed during the cold Little Ice Age, dominated by a more negative phase of the AMV. Since the mid-19th century, a decreasing occurrence of exceptional hydrological events is evident, especially during the most recent decades, but this decrease is not yet unprecedented in the context of the past twelve centuries.

  • 44. Dlugosz, Aldona
    et al.
    Winckler, Björn
    Lundin, Elin
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Zakikhany, Katherina
    Sandström, Gunnar
    Ye, Weimin
    Engstrand, Lars
    Lindberg, Greger
    No difference in small bowel microbiota between patients with irritable bowel syndrome and healthy controls2015Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 5, artikkel-id 8508Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Several studies have indicated that colonic microbiota may exhibit important differences between patients with irritable bowel syndrome (IBS) and healthy controls. Less is known about the microbiota of the small bowel. We used massive parallel sequencing to explore the composition of small bowel mucosa-associated microbiota in patients with IBS and healthy controls. We analysed capsule biopsies from the jejunum of 35 patients (26 females) with IBS aged 18-(36)-57 years and 16 healthy volunteers (11 females) aged 20-(32)-48 years. Sequences were analysed based on taxonomic classification. The phyla with the highest total abundance across all samples were: Firmicutes (43%), Proteobacteria (23%), Bacteroidetes (15%), Actinobacteria (9.3%) and Fusobacteria (7.0%). The most abundant genera were: Streptococcus (19%), Veillonella (13%), Prevotella (12%), Rothia (6.4%), Haemophilus (5.7%), Actinobacillus (5.5%), Escherichia (4.6%) and Fusobacterium (4.3%). We found no difference among major phyla or genera between patients with IBS and controls. We identified a cluster of samples in the small bowel microbiota dominated by Prevotella, which may represent a common enterotype of the upper small intestine. The remaining samples formed a gradient, dominated by Streptococcus at one end and Escherichia at the other.

  • 45. Donovan, Mary K.
    et al.
    Friedlander, Alan M.
    Lecky, Joey
    Jouffray, Jean-Baptiste
    Stockholms universitet, Naturvetenskapliga fakulteten, Stockholm Resilience Centre. Royal Swedish Academy of Sciences, Sweden.
    Williams, Gareth J.
    Wedding, Lisa M.
    Crowder, Larry B.
    Erickson, Ashley L.
    Graham, Nick A. J.
    Gove, Jamison M.
    Kappel, Carrie V.
    Karr, Kendra
    Kittinger, John N.
    Norström, Albert V.
    Stockholms universitet, Naturvetenskapliga fakulteten, Stockholm Resilience Centre.
    Nyström, Magnus
    Stockholms universitet, Naturvetenskapliga fakulteten, Stockholm Resilience Centre.
    Oleson, Kirsten L. L.
    Stamoulis, Kostantinos A.
    White, Crow
    Williams, Ivor D.
    Selkoe, Kimberly A.
    Combining fish and benthic communities into multiple regimes reveals complex reef dynamics2018Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, artikkel-id 16943Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Coral reefs worldwide face an uncertain future with many reefs reported to transition from being dominated by corals to macroalgae. However, given the complexity and diversity of the ecosystem, research on how regimes vary spatially and temporally is needed. Reef regimes are most often characterised by their benthic components; however, complex dynamics are associated with losses and gains in both fish and benthic assemblages. To capture this complexity, we synthesised 3,345 surveys from Hawai'i to define reef regimes in terms of both fish and benthic assemblages. Model-based clustering revealed five distinct regimes that varied ecologically, and were spatially heterogeneous by island, depth and exposure. We identified a regime characteristic of a degraded state with low coral cover and fish biomass, one that had low coral but high fish biomass, as well as three other regimes that varied significantly in their ecology but were previously considered a single coral dominated regime. Analyses of time series data reflected complex system dynamics, with multiple transitions among regimes that were a function of both local and global stressors. Coupling fish and benthic communities into reef regimes to capture complex dynamics holds promise for monitoring reef change and guiding ecosystem-based management of coral reefs.

  • 46.
    Dowaidar, Moataz
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för neurokemi.
    Abdelhamid, Hani Nasser
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Hällbrink, Mattias
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för neurokemi.
    Freimann, Krista
    Kurrikof, Kaido
    Zou, Xiaodong
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Langel, Ülo
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för neurokemi. University of Tartu, Estonia.
    Magnetic Nanoparticle Assisted Self-assembly of Cell Penetrating Peptides-Oligonucleotides Complexes for Gene Delivery2017Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, artikkel-id 9159Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Magnetic nanoparticles (MNPs, Fe3O4) incorporated into the complexes of cell penetrating peptides (CPPs)-oligonucleotides (ONs) promoted the cell transfection for plasmid transfection, splice correction, and gene silencing efficiencies. Six types of cell penetrating peptides (CPPs; PeptFect220 (denoted PF220), PF221, PF222, PF223, PF224 and PF14) and three types of gene therapeutic agents (plasmid (pGL3), splicing correcting oligonucleotides (SCO), and small interfering RNA (siRNA) were investigated. Magnetic nanoparticles incorporated into the complexes of CPPs-pGL3, CPPs-SCO, and CPPs-siRNA showed high cell biocompatibility and efficiently transfected the investigated cells with pGL3, SCO, and siRNA, respectively. Gene transfer vectors formed among PF14, SCO, and MNPs (PF14-SCO-MNPs) showed a superior transfection efficiency (up to 4-fold) compared to the noncovalent PF14-SCO complex, which was previously reported with a higher efficiency compared to commercial vector called Lipofectamine™2000. The high transfection efficiency of the new complexes (CPPs-SCO-MNPs) may be attributed to the morphology, low cytotoxicity, and the synergistic effect of MNPs and CPPs. PF14-pDNA-MNPs is an efficient complex for in vivo gene delivery upon systemic administration. The conjugation of CPPs-ONs with inorganic magnetic nanoparticles (Fe3O4) may open new venues for selective and efficient gene therapy.

  • 47.
    Dowaidar, Moataz
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för neurokemi.
    Gestin, Maxime
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för neurokemi.
    Cerrato, Carmine Pasquale
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för neurokemi.
    Jafferali, Mohammed Hakim
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för neurokemi.
    Margus, Helerin
    Kivistik, Paula Ann
    Ezzat, Kariem
    Hallberg, Einar
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för neurokemi.
    Pooga, Margus
    Hällbrink, Mattias
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för neurokemi.
    Langel, Ülo
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för neurokemi. University of Tartu, Estonia.
    Role of autophagy in cell-penetrating peptide transfection model2017Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, artikkel-id 12635Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Cell-penetrating peptides (CPPs) uptake mechanism is still in need of more clarification to have a better understanding of their action in the mediation of oligonucleotide transfection. In this study, the effect on early events (1 h treatment) in transfection by PepFect14 (PF14), with or without oligonucleotide cargo on gene expression, in HeLa cells, have been investigated. The RNA expression profile was characterized by RNA sequencing and confirmed by qPCR analysis. The gene regulations were then related to the biological processes by the study of signaling pathways that showed the induction of autophagy-related genes in early transfection. A ligand library interfering with the detected intracellular pathways showed concentration-dependent effects on the transfection efficiency of splice correction oligonucleotide complexed with PepFect14, proving that the autophagy process is induced upon the uptake of complexes. Finally, the autophagy induction and colocalization with autophagosomes have been confirmed by confocal microscopy and transmission electron microscopy. We conclude that autophagy, an inherent cellular response process, is triggered by the cellular uptake of CPP-based transfection system. This finding opens novel possibilities to use autophagy modifiers in future gene therapy.

  • 48. Drobyshev, Igor
    et al.
    Bergeron, Yves
    de Vernal, Anne
    Moberg, Anders
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för naturgeografi.
    Ali, Adam A.
    Niklasson, Mats
    Atlantic SSTs control regime shifts in forest fire activity of Northern Scandinavia2016Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, artikkel-id 22532Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Understanding the drivers of the boreal forest fire activity is challenging due to the complexity of the interactions driving fire regimes. We analyzed drivers of forest fire activity in Northern Scandinavia (above 60 N) by combining modern and proxy data over the Holocene. The results suggest that the cold climate in northern Scandinavia was generally characterized by dry conditions favourable to periods of regionally increased fire activity. We propose that the cold conditions over the northern North Atlantic, associated with low SSTs, expansion of sea ice cover, and the southward shift in the position of the subpolar gyre, redirect southward the precipitation over Scandinavia, associated with the westerlies. This dynamics strengthens high pressure systems over Scandinavia and results in increased regional fire activity. Our study reveals a previously undocumented teleconnection between large scale climate and ocean dynamics over the North Atlantic and regional boreal forest fire activity in Northern Scandinavia. Consistency of the pattern observed annually through millennium scales suggests that a strong link between Atlantic SST and fire activity on multiple temporal scales over the entire Holocene is relevant for understanding future fire activity across the European boreal zone.

  • 49.
    Eriksson, Kimmo
    et al.
    Stockholms universitet, Humanistiska fakulteten, Institutionen för arkeologi och antikens kultur, Centrum för evolutionär kulturforskning. Mälardalen University, Sweden.
    Cownden, Daniel
    Stockholms universitet, Humanistiska fakulteten, Institutionen för arkeologi och antikens kultur, Centrum för evolutionär kulturforskning. INgrooves, Canada.
    Strimling, Pontus
    Stockholms universitet, Humanistiska fakulteten, Institutionen för arkeologi och antikens kultur, Centrum för evolutionär kulturforskning. Institute for Futures Studies, Sweden.
    Social learning may lead to population level conformity without individual level frequency bias2017Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, artikkel-id 17341Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A requirement of culture, whether animal or human, is some degree of conformity of behavior within populations. Researchers of gene-culture coevolution have suggested that population level conformity may result from frequency-biased social learning: individuals sampling multiple role models and preferentially adopting the majority behavior in the sample. When learning from a single role model, frequency-bias is not possible. We show why a population-level trend, either conformist or anticonformist, may nonetheless be almost inevitable in a population of individuals that learn through social enhancement, that is, using observations of others' behavior to update their own probability of using a behavior in the future. The exact specification of individuals' updating rule determines the direction of the trend. These results offer a new interpretation of previous findings from simulations of social enhancement in combination with reinforcement learning, and demonstrate how results of dynamical models may strongly depend on seemingly innocuous choices of model specifications, and how important it is to obtain empirical data on which to base such choices.

  • 50.
    Fang, Wenzheng
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för miljövetenskap och analytisk kemi.
    Andersson, August
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för miljövetenskap och analytisk kemi.
    Zheng, Mei
    Lee, Meehye
    Holmstrand, Henry
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för miljövetenskap och analytisk kemi.
    Kim, Sang-Woo
    Du, Ke
    Gustafsson, Örjan
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för miljövetenskap och analytisk kemi.
    Divergent Evolution of Carbonaceous Aerosols during Dispersal of East Asian Haze2017Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, artikkel-id 10422Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Wintertime East Asia is plagued by severe haze episodes, characterized by large contributions of carbonaceous aerosols. However, the sources and atmospheric transformations of these major components are poorly constrained, hindering development of efficient mitigation strategies and detailed modelling of effects. Here we present dual carbon isotope (delta C-13 and Delta C-14) signatures for black carbon (BC), organic carbon (OC) and water-soluble organic carbon (WSOC) aerosols collected in urban (Beijing and BC for Shanghai) and regional receptors (e.g., Korea Climate Observatory at Gosan) during January 2014. Fossil sources (>50%) dominate BC at all sites with most stemming from coal combustion, except for Shanghai, where liquid fossil source is largest. During source-to-receptor transport, the delta C-13 fingerprint becomes enriched for WSOC but depleted for water-insoluble OC (WIOC). This reveals that the atmospheric processing of these two major pools are fundamentally different. The photochemical aging (e.g., photodissociation, photooxidation) during formation and transport can release CO2/CO or short-chain VOCs with lighter carbon, whereas the remaining WSOC becomes increasingly enriched in delta C-13. On the other hand, several processes, e.g., secondary formation, rearrangement reaction in the particle phase, and photooxidation can influence WIOC. Taken together, this study highlights high fossil contributions for all carbonaceous aerosol sub-compartments in East Asia, and suggests different transformation pathways for different classes of carbonaceous aerosols.

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