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  • 1. Abend, M.
    et al.
    Amundson, S. A.
    Badie, C.
    Brzoska, K.
    Hargitai, R.
    Kriehuber, R.
    Schüle, S.
    Kis, E.
    Ghandhi, S. A.
    Lumniczky, K.
    Morton, S. R.
    O'Brien, G.
    Oskamp, D.
    Ostheim, P.
    Siebenwirth, C.
    Shuryak, I.
    Szatmári, T.
    Unverricht-Yeboah, M.
    Ainsbury, E.
    Bassinet, C.
    Kulka, U.
    Oestreicher, U.
    Ristic, Y.
    Trompier, F.
    Wójcik, Andrzej
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för molekylär biovetenskap, Wenner-Grens institut.
    Waldner, L.
    Port, M.
    Inter-laboratory comparison of gene expression biodosimetry for protracted radiation exposures as part of the RENEB and EURADOS WG10 2019 exercise2021Inngår i: Scientific Reports, E-ISSN 2045-2322, Vol. 11, nr 1, artikkel-id 9756Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Large-scale radiation emergency scenarios involving protracted low dose rate radiation exposure (e.g. a hidden radioactive source in a train) necessitate the development of high throughput methods for providing rapid individual dose estimates. During the RENEB (Running the European Network of Biodosimetry) 2019 exercise, four EDTA-blood samples were exposed to an Iridium-192 source (1.36 TBq, Tech-Ops 880 Sentinal) at varying distances and geometries. This resulted in protracted doses ranging between 0.2 and 2.4 Gy using dose rates of 1.5-40 mGy/min and exposure times of 1 or 2.5 h. Blood samples were exposed in thermo bottles that maintained temperatures between 39 and 27.7 degrees C. After exposure, EDTA-blood samples were transferred into PAXGene tubes to preserve RNA. RNA was isolated in one laboratory and aliquots of four blinded RNA were sent to another five teams for dose estimation based on gene expression changes. Using an X-ray machine, samples for two calibration curves (first: constant dose rate of 8.3 mGy/min and 0.5-8 h varying exposure times; second: varying dose rates of 0.5-8.3 mGy/min and 4 h exposure time) were generated for distribution. Assays were run in each laboratory according to locally established protocols using either a microarray platform (one team) or quantitative real-time PCR (qRT-PCR, five teams). The qRT-PCR measurements were highly reproducible with coefficient of variation below 15% in >= 75% of measurements resulting in reported dose estimates ranging between 0 and 0.5 Gy in all samples and in all laboratories. Up to twofold reductions in RNA copy numbers per degree Celsius relative to 37 degrees C were observed. However, when irradiating independent samples equivalent to the blinded samples but increasing the combined exposure and incubation time to 4 h at 37 degrees C, expected gene expression changes corresponding to the absorbed doses were observed. Clearly, time and an optimal temperature of 37 degrees C must be allowed for the biological response to manifest as gene expression changes prior to running the gene expression assay. In conclusion, dose reconstructions based on gene expression measurements are highly reproducible across different techniques, protocols and laboratories. Even a radiation dose of 0.25 Gy protracted over 4 h (1 mGy/min) can be identified. These results demonstrate the importance of the incubation conditions and time span between radiation exposure and measurements of gene expression changes when using this method in a field exercise or real emergency situation.

  • 2. Acevedo, Nathalie
    et al.
    Benfeitas, Rui
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik. Stockholms universitet, Science for Life Laboratory (SciLifeLab).
    Katayama, Shintaro
    Bruhn, Sören
    Andersson, Anna
    Wikberg, Gustav
    Lundeberg, Lena
    Lindvall, Jessica M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik. Stockholms universitet, Science for Life Laboratory (SciLifeLab).
    Greco, Dario
    Kere, Juha
    Söderhäll, Cilla
    Scheynius, Annika
    Epigenetic alterations in skin homing CD4(+)CLA(+) T cells of atopic dermatitis patients2020Inngår i: Scientific Reports, E-ISSN 2045-2322, Vol. 10, nr 1, artikkel-id 18020Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    T cells expressing the cutaneous lymphocyte antigen (CLA) mediate pathogenic inflammation in atopic dermatitis (AD). The molecular alterations contributing to their dysregulation remain unclear. With the aim to elucidate putative altered pathways in AD we profiled DNA methylation levels and miRNA expression in sorted T cell populations -(CD4(+), -CD4(+)CD45RA(+) naive, -CD4(+)CLA(+), and -CD8(+)) from adult AD patients and healthy controls (HC). Skin homing -CD4(+)CLA(+) T cells from AD patients showed significant differences in DNA methylation in 40 genes compared to HC (p < 0.05). Reduced DNA methylation levels in the upstream region of the interleukin-13 gene (IL13) in -CD4(+)CLA(+) T cells from AD patients correlated with increased IL13 mRNA expression in these cells. Sixteen miRNAs showed differential expression in -CD4(+)CLA(+) T cells from AD patients targeting genes in 202 biological processes (p < 0.05). An integrated network analysis of miRNAs and CpG sites identified two communities of strongly interconnected regulatory elements with strong antagonistic behaviours that recapitulated the differences between AD patients and HC. Functional analysis of the genes linked to these communities revealed their association with key cytokine signaling pathways, MAP kinase signaling and protein ubiquitination. Our findings support that epigenetic mechanisms play a role in the pathogenesis of AD by affecting inflammatory signaling molecules in skin homing -CD4(+)CLA(+) T cells and uncover putative molecules participating in AD pathways.

  • 3. Afewerki, Samson
    et al.
    Franco, Ana
    Balu, Alina M.
    Tai, Cheuk-Wai
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Luque, Rafael
    Córdova, Armando
    Sustainable and recyclable heterogenous palladium catalysts from rice husk-derived biosilicates for Suzuki-Miyaura cross-couplings, aerobic oxidations and stereoselective cascade carbocyclizations2020Inngår i: Scientific Reports, E-ISSN 2045-2322, Vol. 10, artikkel-id 6407Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A new eco-friendly approach for the preparation of sustainable heterogeneous palladium catalysts from rice husk-derived biogenic silica (RHP-Si and RHU-Si). The designed heterogeneously supported palladium species (RHP-Si-NH2-Pd and RHU-Si-NH2-Pd) were fully characterized and successfully employed as catalysts for various chemical transformations (C–C bond-forming reactions, aerobic oxidations and carbocyclizations). Suzuki-Miyaura transformations were highly efficient in a green solvent system (H2O:EtOH (1:1) with excellent recyclability, providing the cross-coupling products with a wide range of functionalities in high isolated yields (up to 99%). Palladium species (Pd(0)-nanoparticles or Pd(II)) were also efficient catalysts in the green aerobic oxidation of an allylic alcohol and a co-catalytic stereoselective cascade carbocyclization transformation. In the latter case, a quaternary stereocenter was formed with excellent stereoselectivity (up to 27:1 dr).

  • 4.
    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, 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.

  • 5.
    Akhtar, Farid
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK). Luleå University of Technology, Sweden.
    Ogunwumi, Steven
    Bergström, Lennart
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Thin zeolite laminates for rapid and energy-efficient carbon capture2017Inngår i: Scientific Reports, E-ISSN 2045-2322, Vol. 7, artikkel-id 10988Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Thin, binder-less zeolite NaX laminates, with thicknesses ranging between 310 to 750 mu m and widths exceeding 50 mm and biaxial tensile strength in excess of 3 MPa, were produced by pulsed current processing. The NaX laminates displayed a high CO2 adsorption capacity and high binary CO2-over-N-2 and CO2-over-CH4 selectivity, suitable for CO2 capture from flue gas and upgrading of raw biogas. The thin laminates displayed a rapid CO2 uptake; NaX laminates with a thickness of 310 mu m were saturated to 40% of their CO2 capacity within 24 seconds. The structured laminates of 310 mu m thickness and 50 mm thickness would offer low pressure drop and efficient carbon capture performance in a laminate-based swing adsorption technology.

  • 6.
    Akuwudike, Pamela
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för molekylär biovetenskap, Wenner-Grens institut.
    López-Riego, Milagrosa
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för molekylär biovetenskap, Wenner-Grens institut.
    Dehours, Cloé
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för molekylär biovetenskap, Wenner-Grens institut. Polytech Angers l École d’Ingénieurs, France.
    Lundholm, Lovisa
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för molekylär biovetenskap, Wenner-Grens institut.
    Wojcik, Andrzej
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för molekylär biovetenskap, Wenner-Grens institut. Jan Kochanowski University, Poland.
    Impact of fractionated cisplatin and radiation treatment on cell growth and accumulation of DNA damage in two normal cell types differing in origin2023Inngår i: Scientific Reports, E-ISSN 2045-2322, Vol. 13, artikkel-id 14891Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Evidence on the impact of chemotherapy on radiotherapy-induced second malignant neoplasms is controversial. We estimated how cisplatin modulates the in vitro response of two normal cell types to fractionated radiation. AHH-1 lymphoblasts and VH10 fibroblasts were irradiated at 1 Gy/fraction 5 and 3 times per week during 12 and 19 days, respectively, and simultaneously treated with 0.1, 0.2, 0.4, 0.8, 1.7 and 3.3 µM of cisplatin twice a week. Cell growth during treatment was monitored. Cell growth/cell death and endpoints related to accumulation of DNA damage and, thus, carcinogenesis, were studied up to 21 days post treatment in cells exposed to radiation and the lowest cisplatin doses. Radiation alone significantly reduced cell growth. The impact of cisplatin alone below 3.3 µM was minimal. Except the lowest dose of cisplatin in VH10 cells, cisplatin reduced the inhibitory effect of radiation on cell growth. Delayed cell death was highest in the combination groups while the accumulation of DNA damage did not reveal a clear pattern. In conclusion, fractionated, concomitant exposure to radiation and cisplatin reduces the inhibitory effect of radiation on cell proliferation of normal cells and does not potentiate delayed effects resulting from accumulation of DNA damage.

  • 7. Al-Adwani, Salma
    et al.
    Wallin, Cecilia
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Balhuizen, Melanie D.
    Veldhuizen, Edwin J. A.
    Coorens, Maarten
    Landreh, Michael
    Végvári, Ákos
    Smith, Margaretha E.
    Qvarfordt, Ingemar
    Lindén, Anders
    Gräslund, Astrid
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Agerberth, Birgitta
    Bergman, Peter
    Studies on citrullinated LL-37: detection in human airways, antibacterial effects and biophysical properties2020Inngår i: Scientific Reports, E-ISSN 2045-2322, Vol. 10, nr 1, artikkel-id 2376Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Arginine residues of the antimicrobial peptide LL-37 can be citrullinated by peptidyl arginine deiminases, which reduce the positive charge of the peptide. Notably, citrullinated LL-37 has not yet been detected in human samples. In addition, functional and biophysical properties of citrullinated LL-37 are not fully explored. The aim of this study was to detect citrullinated LL-37 in human bronchoalveolar lavage (BAL) fluid and to determine antibacterial and biophysical properties of citrullinated LL-37. BAL fluid was obtained from healthy human volunteers after intra-bronchial exposure to lipopolysaccharide. Synthetic peptides were used for bacterial killing assays, transmission electron microscopy, isothermal titration calorimetry, mass-spectrometry and circular dichroism. Using targeted proteomics, we were able to detect both native and citrullinated LL-37 in BAL fluid. The citrullinated peptide did not kill Escherichia coli nor lysed human red blood cells. Both peptides had similar α-helical secondary structures but citrullinated LL-37 was more stable at higher temperatures, as shown by circular dichroism. In conclusion, citrullinated LL-37 is present in the human airways and citrullination impaired bacterial killing, indicating that a net positive charge is important for antibacterial and membrane lysing effects. It is possible that citrullination serves as a homeostatic regulator of AMP-function by alteration of key functions.

  • 8.
    Albert, Séréna
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Hedberg, Per
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Motwani, Nisha H.
    Sjöling, Sara
    Winder, Monika
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Nascimento, Francisco J. A.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik. Stockholms universitet, Naturvetenskapliga fakulteten, Stockholms universitets Östersjöcentrum.
    Phytoplankton settling quality has a subtle but significant effect on sediment microeukaryotic and bacterial communities2021Inngår i: Scientific Reports, E-ISSN 2045-2322, Vol. 11, nr 1, artikkel-id 24033Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In coastal aphotic sediments, organic matter (OM) input from phytoplankton is the primary food resource for benthic organisms. Current observations from temperate ecosystems like the Baltic Sea report a decline in spring bloom diatoms, while summer cyanobacteria blooms are becoming more frequent and intense. These climate-driven changes in phytoplankton communities may in turn have important consequences for benthic biodiversity and ecosystem functions, but such questions are not yet sufficiently explored experimentally. Here, in a 4-week experiment, we investigated the response of microeukaryotic and bacterial communities to different types of OM inputs comprising five ratios of two common phytoplankton species in the Baltic Sea, the diatom Skeletonema marinoi and filamentous cyanobacterium Nodularia spumigena. Metabarcoding analyses on 16S and 18S ribosomal RNA (rRNA) at the experiment termination revealed subtle but significant changes in diversity and community composition of microeukaryotes in response to settling OM quality. Sediment bacteria were less affected, although we observed a clear effect on denitrification gene expression (nirS and nosZ), which was positively correlated with increasing proportions of cyanobacteria. Altogether, these results suggest that future changes in OM input to the seafloor may have important effects on both the composition and function of microbenthic communities.

  • 9.
    Albertsson, Ingrid
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Sjöholm, Johannes
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik. Royal Institute of Technology (KTH), Sweden.
    ter Beek, Josy
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Watmough, Nicholas J.
    Widengren, Jerker
    Ädelroth, Pia
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Functional interactions between nitrite reductase and nitric oxide reductase from Paracoccus denitrificans2019Inngår i: Scientific Reports, E-ISSN 2045-2322, Vol. 9, artikkel-id 17234Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Denitrification is a microbial pathway that constitutes an important part of the nitrogen cycle on earth. Denitrifying organisms use nitrate as a terminal electron acceptor and reduce it stepwise to nitrogen gas, a process that produces the toxic nitric oxide (NO) molecule as an intermediate. In this work, we have investigated the possible functional interaction between the enzyme that produces NO; the cd(1) nitrite reductase (cd(1)NiR) and the enzyme that reduces NO; the c-type nitric oxide reductase (cNOR), from the model soil bacterium P. denitrificans. Such an interaction was observed previously between purified components from P. aeruginosa and could help channeling the NO (directly from the site of formation to the side of reduction), in order to protect the cell from this toxic intermediate. We find that electron donation to cNOR is inhibited in the presence of cd(1)NiR, presumably because cd(1)NiR binds cNOR at the same location as the electron donor. We further find that the presence of cNOR influences the dimerization of cd(1)NiR. Overall, although we find no evidence for a high-affinity, constant interaction between the two enzymes, our data supports transient interactions between cd(1)NiR and cNOR that influence enzymatic properties of cNOR and oligomerization properties of cd(1)NiR. We speculate that this could be of particular importance in vivo during metabolic switches between aerobic and denitrifying conditions.

  • 10. Alekseenko, Alisa
    et al.
    Barrett, Donal
    Pareja-Sanchez, Yerma
    Howard, Rebecca J.
    Stockholms universitet, Science for Life Laboratory (SciLifeLab). Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Strandback, Emilia
    Ampah-Korsah, Henry
    Rovšnik, Urška
    Stockholm Univ, Dept Biochem & Biophys, SciLifeLab, S-17121 Solna, Sweden.
    Zuniga-Veliz, Silvia
    Klenov, Alexander
    Malloo, Jayshna
    Ye, Shenglong
    Liu, Xiyang
    Reinius, Björn
    Elsässer, Simon J.
    Nyman, Tomas
    Sandh, Gustaf
    Yin, Xiushan
    Pelechano, Vicent
    Direct detection of SARS-CoV-2 using non-commercial RT-LAMP reagents on heat-inactivated samples2021Inngår i: Scientific Reports, E-ISSN 2045-2322, Vol. 11, nr 1, artikkel-id 1820Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    RT-LAMP detection of SARS-CoV-2 has been shown to be a valuable approach to scale up COVID-19 diagnostics and thus contribute to limiting the spread of the disease. Here we present the optimization of highly cost-effective in-house produced enzymes, and we benchmark their performance against commercial alternatives. We explore the compatibility between multiple DNA polymerases with high strand-displacement activity and thermostable reverse transcriptases required for RT-LAMP. We optimize reaction conditions and demonstrate their applicability using both synthetic RNA and clinical patient samples. Finally, we validate the optimized RT-LAMP assay for the detection of SARS-CoV-2 in unextracted heat-inactivated nasopharyngeal samples from 184 patients. We anticipate that optimized and affordable reagents for RT-LAMP will facilitate the expansion of SARS-CoV-2 testing globally, especially in sites and settings where the need for large scale testing cannot be met by commercial alternatives.

  • 11. Alsaffar, Z.
    et al.
    Pearman, J. K.
    Cúrdia, J.
    Ellis, J.
    Calleja, M. Ll
    Ruiz-Compean, P.
    Roth, Florian
    Stockholms universitet, Naturvetenskapliga fakulteten, Stockholms universitets Östersjöcentrum. King Abdullah University of Science and Technology (KAUST), Saudi Arabia; Tvärminne Zoological Station, Finland.
    Villalobos, R.
    Jones, B. H.
    Morán, X. A. G.
    Carvalho, S.
    The role of seagrass vegetation and local environmental conditions in shaping benthic bacterial and macroinvertebrate communities in a tropical coastal lagoon2020Inngår i: Scientific Reports, E-ISSN 2045-2322, Vol. 10, nr 1, artikkel-id 13550Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We investigated the influence of seagrass canopies on the benthic biodiversity of bacteria and macroinvertebrates in a Red Sea tropical lagoon. Changes in abundance, number of taxa and assemblage structure were analyzed in response to seagrass densities (low, SLD; high, SHD; seagrasses with algae, SA), and compared with unvegetated sediments. Biological and environmental variables were examined in these four habitats (hereafter called treatments), both in the underlaying sediments and overlaying waters, at three randomly picked locations in March 2017. Differences between treatments were more apparent in the benthic habitat than in the overlaying waters. The presence of vegetation (more than its cover) and changes in sedimentary features (grain size and metals) at local scales influenced the observed biological patterns, particularly for macroinvertebrates. Of note, the highest percentage of exclusive macroinvertebrate taxa (18% of the gamma diversity) was observed in the SHD treatment peaking in the SA for bacteria. Benthic macroinvertebrates and bacteria shared a generally low number of taxa across treatments and locations; approximately, 25% of the gamma diversity was shared among all treatments and locations for macrofauna, dropping to 11% for bacteria. Given the low overlap in the species distribution across the lagoon, sustaining the connectivity among heterogeneous soft sediment habitats appears to be essential for maintaining regional biodiversity. This study addresses a current scientific gap related to the relative contributions of vegetated and unvegetated habitats to biodiversity in tropical regions.

  • 12. 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, 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.

  • 13.
    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, 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.

  • 14. 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, 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.

  • 15.
    Andersson, August
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för miljövetenskap.
    Mechanisms for log normal concentration distributions in the environment2021Inngår i: Scientific Reports, E-ISSN 2045-2322, Vol. 11, nr 1, artikkel-id 16418Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Log normal-like concentration distributions are ubiquitously observed in the environment. However, the mechanistic origins are not well understood. In this paper, we show that first order exponential kinetics onsets log-normal concentration distributions, under certain assumptions. Given the ubiquity of exponential kinetics, e.g., source and sink processes, this model suggests an explanation for the frequent observation in the environment, and elsewhere. We compare this model to other mechanisms affecting concentration distributions, e.g., source mixing. Finally, we discuss possible implications for data analysis and modelling, e.g., log-normal rates and fluxes.

  • 16.
    Andersson, David
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum. Norwegian University of Science and Technology, Norway.
    Bratsberg, Sigrid
    Ringsmuth, Andrew K.
    Stockholms universitet, Naturvetenskapliga fakulteten, Stockholm Resilience Centre. Medical University of Vienna, Austria; University of Graz, Austria.
    de Wijn, Astrid S.
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum. Norwegian University of Science and Technology, Norway.
    Dynamics of collective action to conserve a large common-pool resource2021Inngår i: Scientific Reports, E-ISSN 2045-2322, Vol. 11, nr 1, artikkel-id 9208Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A pressing challenge for coming decades is sustainable and just management of large-scale common-pool resources including the atmosphere, biodiversity and public services. This poses a difficult collective action problem because such resources may not show signs that usage restraint is needed until tragedy is almost inevitable. To solve this problem, a sufficient level of cooperation with a pro-conservation behavioural norm must be achieved, within the prevailing sociopolitical environment, in time for the action taken to be effective. Here we investigate the transient dynamics of behavioural change in an agent-based model on structured networks that are also exposed to a global external influence. We find that polarisation emerges naturally, even without bounded confidence, but that for rationally motivated agents, it is temporary. The speed of convergence to a final consensus is controlled by the rate at which the polarised clusters are dissolved. This depends strongly on the combination of external influences and the network topology. Both high connectivity and a favourable environment are needed to rapidly obtain final consensus.

  • 17. 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, 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.

  • 18.
    Apostolopoulou Kalkavoura, Varvara
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Munier, Pierre
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Dlugozima, Lukasz
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Heuthe, Veit-Lorenz
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Bergström, Lennart
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Effect of density, phonon scattering and nanoporosity on the thermal conductivity of anisotropic cellulose nanocrystal foams2021Inngår i: Scientific Reports, E-ISSN 2045-2322, Vol. 11, nr 1, artikkel-id 18685Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Anisotropic cellulose nanocrystal (CNC) foams with densities between 25 and 130 kg m−3 (CNC25 –CNC130) were prepared by directional ice-templating of aqueous dispersions. Estimates of the solid and gas conduction contributions to the thermal conductivity of the foams using a parallel resistor model showed that the relatively small increase of the radial thermal conductivity with increasing foam density can be attributed to interfacial phonon scattering. The foam wall nanoporosity and, to a lesser extent, the orientation of the CNC particles and alignment of the columnar macropores, also influence the insulation performance of the foams. The insight on the importance of phonon scattering for the thermal insulation properties of nanocellulose foams provides useful guidelines for tailoring nanofibrillar foams for super-insulating applications.

  • 19. Arandia-Gorostidi, Nestor
    et al.
    Berthelot, Hugo
    Calabrese, Federica
    Stryhanyuk, Hryhoriy
    Klawonn, Isabell
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik. Leibniz Institute for Baltic Sea Research (IOW), Germany.
    Iversen, Morten
    Nahar, Nurun
    Grossart, Hans-Peter
    Ploug, Helle
    Musat, Niculina
    Efficient carbon and nitrogen transfer from marine diatom aggregates to colonizing bacterial groups2022Inngår i: Scientific Reports, E-ISSN 2045-2322, Vol. 12, nr 1, artikkel-id 14949Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Bacterial degradation of sinking diatom aggregates is key for the availability of organic matter in the deep-ocean. Yet, little is known about the impact of aggregate colonization by different bacterial taxa on organic carbon and nutrient cycling within aggregates. Here, we tracked the carbon (C) and nitrogen (N) transfer from the diatom Leptocylindrus danicus to different environmental bacterial groups using a combination of 13C and 15N isotope incubation (incubated for 72 h), CARD-FISH and nanoSIMS single-cell analysis. Pseudoalteromonas bacterial group was the first colonizing diatom-aggregates, succeeded by the Alteromonas group. Within aggregates, diatom-attached bacteria were considerably more enriched in 13C and 15N than non-attached bacteria. Isotopic mass balance budget indicates that both groups showed comparable levels of diatom C in their biomass, accounting for 19 ± 7% and 15 ± 11%, respectively. In contrast to C, bacteria of the Alteromonas groups showed significantly higher levels of N derived from diatoms (77 ± 28%) than Pseudoalteromonas (47 ± 17%), suggesting a competitive advantage for Alteromonas in the N-limiting environments of the deep-sea. Our results imply that bacterial succession within diatom aggregates may largely impact taxa-specific C and N uptake, which may have important consequences for the quantity and quality of organic matter exported to the deep ocean.

  • 20. Arnison, Tor
    et al.
    Schrooten, Martien G. S.
    Bauducco, Serena
    Jansson-Fröjmark, Markus
    Persson, Jonas
    Stockholms universitet, Samhällsvetenskapliga fakulteten, Centrum för forskning om äldre och åldrande (ARC), (tills m KI). Örebro University, Sweden.
    Sleep phase and pre-sleep arousal predicted co-developmental trajectories of pain and insomnia within adolescence2022Inngår i: Scientific Reports, E-ISSN 2045-2322, Vol. 12, nr 1, artikkel-id 4480Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The onset of both chronic pain and insomnia is high during adolescence. Although a bidirectional relationship between pain and insomnia has support, how pain and sleep co-develop throughout adolescence remains unknown. Sleep-wake patterns, pre-sleep behavior and pre-sleep arousal may influence the co-development of pain and insomnia. Four waves of longitudinal self-report data were used (N-baseline = 2767, Age(baseline) M = 13.65 years, SD = 0.65). Multidimensional growth mixture modeling was used to identify four subgroups of adolescents with different concurrent trajectories of pain and insomnia. The trajectories followed each other across time in all classes: one class of consistently low pain and insomnia (68.7%), one class with persistent high symptoms (4.9%), as well as one class of increasing (13.9%), and one of decreasing (12.5%), trajectories. Later sleep-wake patterns and more pre-sleep cognitive-emotional arousal predicted both increasing and decreasing trajectories of concurrent pain and insomnia. The current study showed that developmental trajectories of pain and insomnia follow each other within adolescents and across adolescence. Both sleep-phase focused interventions as well as psychological interventions that focus on pre-sleep cognitive-emotional arousal may prove beneficial for adolescents with comorbid pain and insomnia.

  • 21.
    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, 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.

  • 22. 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, 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.

  • 23.
    Attoff, Kristina
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Johansson, Ylva
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Cediel-Ulloa, Andrea
    Lundqvist, Jessica
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik. Karolinska Institutet, Sweden.
    Gupta, Rajinder
    Caiment, Florian
    Gliga, Anda
    Forsby, Anna
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik. Uppsala University, Sweden.
    Acrylamide alters CREB and retinoic acid signalling pathways during differentiation of the human neuroblastoma SH-SY5Y cell line2020Inngår i: Scientific Reports, E-ISSN 2045-2322, Vol. 10, nr 1, artikkel-id 16714Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Acrylamide (ACR) is a known neurotoxicant which crosses the blood-brain barrier, passes the placenta and has been detected in breast milk. Hence, early-life exposure to ACR could lead to developmental neurotoxicity. The aim of this study was to elucidate if non-cytotoxic concentrations of ACR alter neuronal differentiation by studying gene expression of markers significant for neurodevelopment in the human neuroblastoma SH-SY5Y cell model. Firstly, by using RNASeq we identified two relevant pathways that are activated during 9 days of retinoic acid (RA) induced differentiation i.e. RA receptor (RAR) activation and the cAMP response element-binding protein (CREB) signalling pathways. Next, by qPCR we showed that 1 and 70 mu M ACR after 9 days exposure alter the expression of 13 out of 36 genes in the RAR activation pathway and 18 out of 47 in the CREB signalling pathway. Furthermore, the expression of established neuronal markers i.e. BDNF, STXBP2, STX3, TGFB1 and CHAT were down-regulated. Decreased protein expression of BDNF and altered ratio of phosphorylated CREB to total CREB were confirmed by western blot. Our results reveal that micromolar concentrations of ACR sustain proliferation, decrease neurite outgrowth and interfere with signalling pathways involved in neuronal differentiation in the SH-SY5Y cell model.

  • 24. Avdic, Hanna Björlin
    et al.
    Strannegård, Claes
    Engberg, Hedvig
    Willfors, Charlotte
    Nordgren, Ida
    Frisen, Louise
    Hirschberg, Angelica Linden
    Guath, Mona
    Nordgren, Ann
    Kleberg, Johan L.
    Stockholms universitet, Samhällsvetenskapliga fakulteten, Psykologiska institutionen, Personlighets-, social- och utvecklingspsykologi.
    Reduced effects of social feedback on learning in Turner syndrome2023Inngår i: Scientific Reports, E-ISSN 2045-2322, Vol. 13, nr 1, artikkel-id 15858Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Turner syndrome is a genetic condition caused by a complete or partial loss of one of the X chromosomes. Previous studies indicate that Turner syndrome is associated with challenges in social skills, but the underlying mechanisms remain largely unexplored. A possible mechanism is a reduced social influence on learning. The current study examined the impact of social and non-social feedback on learning in women with Turner syndrome (n=35) and a sex- and age-matched control group (n=37). Participants were instructed to earn points by repeatedly choosing between two stimuli with unequal probabilities of resulting in a reward. Mastering the task therefore required participants to learn through feedback which of the two stimuli was more likely to be rewarded. Data were analyzed using computational modeling and analyses of choice behavior. Social feedback led to a more explorative choice behavior in the control group, resulting in reduced learning compared to non-social feedback. No effects of social feedback on learning were found in Turner syndrome. The current study thus indicates that women with Turner syndrome may be less sensitive to social influences on reinforcement learning, than the general population.

  • 25. Badinlou, Farzaneh
    et al.
    Forsström, David
    Stockholms universitet, Samhällsvetenskapliga fakulteten, Psykologiska institutionen, Klinisk psykologi. Stockholms universitet, Samhällsvetenskapliga fakulteten, Institutionen för folkhälsovetenskap.
    Jansson-Frojmark, Markus
    Abzhandadze, Tamar
    Lundgren, Tobias
    Impairments following COVID-19 infection: manifestations and investigations of related factors2023Inngår i: Scientific Reports, E-ISSN 2045-2322, Vol. 13, nr 1, artikkel-id 6564Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The COVID-19 pandemic had a major global impact on the health and wellbeing for many individuals. Even though the infection rates have gone down due to the availability of vaccines, the consequences of the disease are still present due to persistent symptoms among individuals. The aim of the current study was to map long-term impairments in individuals infected with COVID-19 by applying the framework of the World Health Organization's International Classification of Functioning, Disability and Health (ICF) and also investigate the factors related to the context of an individual's life influencing the impairments. A web-survey that targeted individuals that had been infected with COVID-19 was used. The survey included a range of measures covering contextual factors and factors related to body functions and structures and post-COVID impairments. A total of 501 individuals were included in the study (with a mean age of 47.6 years). 96% of the respondents reported at least one moderate-to-severe impairment due to COVID-19 infection and the most frequent one was fatigue. In that, 79.6% and 86.9% of the study sample reported moderate-to-severe brain fatigue and tiredness or lack of energy, respectively. Severity of COVID-19 infection appeared as the strongest risk factor for post-COVID impairments. Based on the results, interventions can be tailored to help individuals with post-COVID-19 condition. This could be one way lessening the effect of COVID-19 on health care and society as a whole.

  • 26. 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, 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.

  • 27. Balieiro, Laura Cristina Tibiletti
    et al.
    Gontijo, Cristiana Araújo
    Marot, Luisa Pereira
    Teixeira, Gabriela Pereira
    Fahmy, Walid Makin
    de Castro Moreno, Claudia Roberta
    Stockholms universitet, Samhällsvetenskapliga fakulteten, Psykologiska institutionen, Stressforskningsinstitutet. University of São Paulo, Brazil.
    Maia, Yara Cristina de Paiva
    Crispim, Cibele Aparecida
    Circadian misalignment measured by social jetlag from early to late pregnancy and its association with nutritional status: a longitudinal study2021Inngår i: Scientific Reports, E-ISSN 2045-2322, Vol. 11, nr 1, artikkel-id 18678Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A mismatch between circadian and social clocks leads to a circadian misalignment, which has been widely measured by social jetlag (SJL). There are several studies measuring SJL, but it has not been studied in pregnant women. Therefore, this study aimed to identify the occurrence of SJL throughout pregnancy and to verify whether there is an effect of pre-pregnancy body mass index (BMI) on SJL throughout pregnancy. The baseline of the present study was conducted with 205 1st trimester pregnant women of whom 100 were followed in their 2nd and 3rd trimester. SJL was calculated based on the absolute difference between mid-sleep time on workdays versus work-free days. The pre-pregnancy BMI and current BMI (kg/m2) were calculated. Linear regression and Generalised Estimating Equation (GEE) adjusted for confounders were used to determine the association between SJL and the gestational trimesters (time), and anthropometric variables. Most of the pregnant women (54.5%) presented SJL > 1 h in the first gestational trimester. We also found an isolated effect of the gestation trimester on the SJL mean. In this sense, pregnant women had a decrease in SJL from the second to the third trimester (1.33 ± 0.08 versus 1.12 ± 0.07, respectively; p = 0.012). GEE analyzes showed that pregnant women of a normal weight showed a decrease in SJL from the second to the third trimester (1.29 ± 0.11 and 0.93 ± 0.08, respectively, p = 0.032), but this was not found in the other groups of nutritional status (underweight, overweight and obesity). In addition, a positive association between SJL and pre-gestational BMI in the third trimester (β = 0.200, p = 0.046) was found. SJL is quite prevalent during the gestational period and excessive BMI both before and during pregnancy is associated with an increased risk of having SJL > 1 h in the third and second trimesters, respectively. In addition, pregnant women of normal weight—but not underweight or overweight—had decreased SJL from the second to the third trimester.

  • 28.
    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, 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.

  • 29.
    Balter, Leonie J. T.
    et al.
    Stockholms universitet, Samhällsvetenskapliga fakulteten, Psykologiska institutionen, Stressforskningsinstitutet.
    Sundelin, Tina
    Stockholms universitet, Samhällsvetenskapliga fakulteten, Psykologiska institutionen, Stressforskningsinstitutet. Karolinska Institutet, Sweden.
    Axelsson, John
    Stockholms universitet, Samhällsvetenskapliga fakulteten, Psykologiska institutionen, Stressforskningsinstitutet. Karolinska Institutet, Sweden.
    Sickness and sleep health predict frustration and affective responses to a frustrating trigger2021Inngår i: Scientific Reports, E-ISSN 2045-2322, Vol. 11, nr 1, artikkel-id 1542Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Fluctuations in health and sleep are common, but we know surprisingly little about how these daily life stressors affect one's level of frustration and sensitivity to becoming frustrated. In this pre-registered study, 517 participants (Mage = 30.4, SD = 10.4) reported their current sickness symptoms, health status, sleepiness, and sleep duration and quality the previous night. They also rated their general frustration and mood before and after a mild frustration-eliciting task. In the task, participants were instructed to copy geometric shapes onto a piece of paper, without lifting the pen from the paper. Participants were given three minutes to copy the eight shapes, but in order to induce frustration half of them were unsolvable. The study was subsequently repeated in an independent sample (N = 113). Frustration increased in response to the task; however, those with the worst sickness symptoms or sleep health reduced or did not change their frustration levels. Instead, across both studies, frustration was already high at baseline for these individuals. These findings indicate that being sick or having poor sleep is related to high general frustration, but resilience to further frustration due to mild frustrating situations.

  • 30. 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, 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.

  • 31.
    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, 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.

  • 32.
    Beer, Christian
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för miljövetenskap och analytisk kemi. University of Hamburg, Germany.
    Zimov, Nikita
    Olofsson, Johan
    Porada, Philipp
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för miljövetenskap och analytisk kemi. University of Hamburg, Germany.
    Zimov, Sergey
    Protection of Permafrost Soils from Thawing by Increasing Herbivore Density2020Inngår i: Scientific Reports, E-ISSN 2045-2322, Vol. 10, artikkel-id 4170Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Climate change will cause a substantial future greenhouse gas release from warming and thawing permafrost-affected soils to the atmosphere enabling a positive feedback mechanism. Increasing the population density of big herbivores in northern high-latitude ecosystems will increase snow density and hence decrease the insulation strength of snow during winter. As a consequence, theoretically 80% of current permafrost-affected soils (<10 m) is projected to remain until 2100 even when assuming a strong warming using the Representative Concentration Pathway 8.5. Importantly, permafrost temperature is estimated to remain below −4 °C on average after increasing herbivore population density. Such ecosystem management practices would be therefore theoretically an important additional climate change mitigation strategy. Our results also highlight the importance of new field experiments and observations, and the integration of fauna dynamics into complex Earth System models, in order to reliably project future ecosystem functions and climate.

  • 33. 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, 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.

  • 34.
    Bergfeldt, Nora
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen. Centre for Palaeogenetics, Sweden; Swedish Museum of Natural History, Sweden.
    Kirdök, Emrah
    Oskolkov, Nikolay
    Mirabello, Claudio
    Unneberg, Per
    Malmström, Helena
    Fraser, Magdalena
    Sanchez-Quinto, Federico
    Jorgensen, Roger
    Skar, Birgitte
    Lidén, Kerstin
    Stockholms universitet, Humanistiska fakulteten, Institutionen för arkeologi och antikens kultur.
    Jakobsson, Mattias
    Storå, Jan
    Stockholms universitet, Humanistiska fakulteten, Institutionen för arkeologi och antikens kultur.
    Götherström, Anders
    Stockholms universitet, Humanistiska fakulteten, Institutionen för arkeologi och antikens kultur. Centre for Palaeogenetics, Sweden.
    Identification of microbial pathogens in Neolithic Scandinavian humans2024Inngår i: Scientific Reports, E-ISSN 2045-2322, Vol. 14, nr 1, artikkel-id 5630Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    With the Neolithic transition, human lifestyle shifted from hunting and gathering to farming. This change altered subsistence patterns, cultural expression, and population structures as shown by the archaeological/zooarchaeological record, as well as by stable isotope and ancient DNA data. Here, we used metagenomic data to analyse if the transitions also impacted the microbiome composition in 25 Mesolithic and Neolithic hunter-gatherers and 13 Neolithic farmers from several Scandinavian Stone Age cultural contexts. Salmonella enterica, a bacterium that may have been the cause of death for the infected individuals, was found in two Neolithic samples from Battle Axe culture contexts. Several species of the bacterial genus Yersinia were found in Neolithic individuals from Funnel Beaker culture contexts as well as from later Neolithic context. Transmission of e.g. Y. enterocolitica may have been facilitated by the denser populations in agricultural contexts.

  • 35. 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, 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.

  • 36.
    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, 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.

  • 37.
    Berntsson, Elina
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik. Tallinn University of Technology, Estonia.
    Vosough, Faraz
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Svantesson, Teodor
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Pansieri, Jonathan
    Iashchishyn, Igor A.
    Ostojic, Lucija
    Dong, Xiaolin
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Paul, Suman
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Jarvet, Jüri
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik. Tallinn University of Technology, Estonia.
    Roos, Per M.
    Barth, Andreas
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Morozova-Roche, Ludmilla A.
    Gräslund, Astrid
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Wärmländer, Sebastian
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik. Stockholms universitet, Humanistiska fakulteten, Institutionen för arkeologi och antikens kultur.
    Residue-specific binding of Ni(II) ions influences the structure and aggregation of amyloid beta (Aβ) peptides2023Inngår i: Scientific Reports, E-ISSN 2045-2322, Vol. 13, nr 1, artikkel-id 3341Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Alzheimer's disease (AD) is the most common cause of dementia worldwide. AD brains display deposits of insoluble amyloid plaques consisting mainly of aggregated amyloid-beta (A beta) peptides, and A beta oligomers are likely a toxic species in AD pathology. AD patients display altered metal homeostasis, and AD plaques show elevated concentrations of metals such as Cu, Fe, and Zn. Yet, the metal chemistry in AD pathology remains unclear. Ni(II) ions are known to interact with A beta peptides, but the nature and effects of such interactions are unknown. Here, we use numerous biophysical methods-mainly spectroscopy and imaging techniques-to characterize A beta/Ni(II) interactions in vitro, for different A beta variants: A beta(1-40), A beta(1-40)(H6A, H13A, H14A), A beta(4-40), and A beta(1-42). We show for the first time that Ni(II) ions display specific binding to the N-terminal segment of full-length A beta monomers. Equimolar amounts of Ni(II) ions retard A beta aggregation and direct it towards non-structured aggregates. The His6, His13, and His14 residues are implicated as binding ligands, and the Ni(II)center dot A beta binding affinity is in the low mu M range. The redox-active Ni(II) ions induce formation of dityrosine cross-links via redox chemistry, thereby creating covalent A beta dimers. In aqueous buffer Ni(II) ions promote formation of beta sheet structure in A beta monomers, while in a membrane-mimicking environment (SDS micelles) coil-coil helix interactions appear to be induced. For SDS-stabilized A beta oligomers, Ni(II) ions direct the oligomers towards larger sizes and more diverse (heterogeneous) populations. All of these structural rearrangements may be relevant for the A beta aggregation processes that are involved in AD brain pathology.

  • 38.
    Björck, Markus L.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Vilhjálmsdóttir, Jóhanna
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Hartley, Andrew M.
    Meunier, Brigitte
    Näsvik Öjemyr, Linda
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Marechal, Amandine
    Brzezinski, Peter
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Proton-transfer pathways in the mitochondrial S. cerevisiae cytochrome c oxidase2019Inngår i: Scientific Reports, E-ISSN 2045-2322, Vol. 9, artikkel-id 20207Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In cytochrome c oxidase (CytcO) reduction of O-2 to water is linked to uptake of eight protons from the negative side of the membrane: four are substrate protons used to form water and four are pumped across the membrane. In bacterial oxidases, the substrate protons are taken up through the K and the D proton pathways, while the pumped protons are transferred through the D pathway. On the basis of studies with CytcO isolated from bovine heart mitochondria, it was suggested that in mitochondrial CytcOs the pumped protons are transferred though a third proton pathway, the H pathway, rather than through the D pathway. Here, we studied these reactions in S. cerevisiae CytcO, which serves as a model of the mammalian counterpart. We analyzed the effect of mutations in the D (Asn99Asp and Ile67Asn) and H pathways (Ser382Ala and Ser458Ala) and investigated the kinetics of electron and proton transfer during the reaction of the reduced CytcO with O-2. No effects were observed with the H pathway variants while in the D pathway variants the functional effects were similar to those observed with the R. sphaeroides CytcO. The data indicate that the S. cerevisiae CytcO uses the D pathway for proton uptake and presumably also for proton pumping.

  • 39.
    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, 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.

  • 40.
    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, 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.

    Fulltekst (pdf)
    Methane fluxes from coastal sediments are enhanced by macrofauna
  • 41. 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, 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.

  • 42.
    Bornscheuer, Lisa
    et al.
    Stockholms universitet, Samhällsvetenskapliga fakulteten, Institutionen för folkhälsovetenskap. Karolinska University Hospital, Sweden.
    Lundin, Andreas
    Forsell, Yvonne
    Lavebratt, Catharina
    Melas, Philippe A.
    The cannabinoid receptor-1 gene interacts with stressful life events to increase the risk for problematic alcohol use2022Inngår i: Scientific Reports, E-ISSN 2045-2322, Vol. 12, artikkel-id 4963Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Problematic alcohol use is a major contributor to the global burden of death and disabilities, and it represents a public health concern that has grown substantially following the COVID-19 pandemic. The available treatment options remain limited and to develop better pharmacotherapies for alcohol misuse we need to identify suitable biological targets. Previous research has implicated the brain’s endocannabinoid system (ECS) in psychiatric and stress-related outcomes, including substance use and habituation to repeated stress. Moreover, genetic variants in the cannabinoid-1 receptor gene (CNR1; CB1R) have been associated with personality traits, which are in turn predictors of substance use disorders. To date, however, no human genome-wide association study has provided evidence for an involvement of the ECS in substance use outcomes. One reason for this ECS-related “missing heritability” may be unexamined gene-environment interactions. To explore this possibility, we conducted cross-sectional analyses using DNA samples and stress-exposure data from a longitudinal Swedish population-based study (N = 2,915). Specifically, we genotyped rs2023239, a functional C/T single nucleotide polymorphism in CNR1, previously reported to be associated with CNR1 binding in the brain, subjective reward following alcohol intake, and alcohol cue-elicited brain activation. Our two outcomes of interest were (i) problematic alcohol use based on the Alcohol Use Disorders Identification Test (AUDIT), and (ii) personality trait scores based on the Five Factor Model. We found no baseline association between rs2023239 and problematic alcohol use or personality traits. However, there was a clear trend for interaction between rs2023239’s risk allele (C) and stressful life events (SLEs) in both childhood and adulthood, which predicted problematic alcohol use. Although not significant, there was also some indication that the risk allele interacted with child SLEs to increase scores on neuroticism. Our study supports the notion that the ECS can affect alcohol intake behaviors by interacting with life adversities and is—to the best of our knowledge—the first to focus on the interaction between CNR1 and stressors in both childhood and adulthood in humans. Further studies are warranted to confirm these findings.

  • 43. Braun, Cordula
    et al.
    Mereacre, Liuda
    Chen, Zheng
    Slabon, Adam
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Closing the yellow gap with Eu- and Tb-doped GaN: one luminescent host resulting in three colours2022Inngår i: Scientific Reports, E-ISSN 2045-2322, Vol. 12, nr 1, artikkel-id 2503Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Gallium nitride (GaN) is a key material when it comes to light-emitting diodes (LEDs) and has pushed the LED revolution in lighting and displays. The concept of down-conversion of a GaN-based blue LED offers the possibility to provide efficient generation of monochromatic, high-color purity light resulting in a highly efficient warm-white all-nitride phosphor-converted light emitting diode (pc-LED). Although the down conversion of blue light from InGaN LEDs has become a dominant technique for producing white light, there are still some technical challenges, e.g. the immiscibility of GaN and InN and the lattice mismatch between the substrate and InGaN, that have to be overcome. Here we demonstrate the doping of bulk GaN with europium, terbium and the combination of both resulting in intriguing luminescence properties, pushing the role of GaN:Eu,Tb as a chief component in future light emitting diodes. This colour tuning proves that one luminescence host can provide three colours (red, green and orange) and that even the so called “yellow gap” could be closed with a III-nitride. By using one material for all colours, it will be possible to overcome the technical challenges in building up LED devices, which will open up new capabilities for modern highly efficient phosphors.

  • 44. 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, 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.

  • 45. 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, 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.

  • 46.
    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, 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.

  • 47. Böhm, Anja
    et al.
    Keuper, Michaela
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för molekylär biovetenskap, Wenner-Grens institut. Eberhard Karls University Tübingen, Germany.
    Meile, Tobias
    Zdichavsky, Marty
    Fritsche, Andreas
    Häring, Hans-Ulrich
    Hrabe de Angelis, Martin
    Staiger, Harald
    Franko, Andras
    Increased mitochondrial respiration of adipocytes from metabolically unhealthy obese compared to healthy obese individuals2020Inngår i: Scientific Reports, E-ISSN 2045-2322, Vol. 10, nr 1, artikkel-id 12407Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Among obese subjects, metabolically healthy (MHO) and unhealthy obese (MUHO) subjects exist, the latter being characterized by whole-body insulin resistance, hepatic steatosis, and subclinical inflammation. Insulin resistance and obesity are known to associate with alterations in mitochondrial density, morphology, and function. Therefore, we assessed mitochondrial function in human subcutaneous preadipocytes as well as in differentiated adipocytes derived from well-matched donors. Primary subcutaneous preadipocytes from 4 insulin-resistant (MUHO) versus 4 insulin-sensitive (MHO), non-diabetic, morbidly obese Caucasians (BMI > 40 kg/m(2)), matched for sex, age, BMI, and percentage of body fat, were differentiated in vitro to adipocytes. Real-time cellular respiration was measured using an XF24 Extracellular Flux Analyzer (Seahorse). Lipolysis was stimulated by forskolin (FSK) treatment. Mitochondrial respiration was fourfold higher in adipocytes versus preadipocytes (p = 1.6*10(-9)). In adipocytes, a negative correlation of mitochondrial respiration with donors' insulin sensitivity was shown (p = 0.0008). Correspondingly, in adipocytes of MUHO subjects, an increased basal respiration (p = 0.002), higher proton leak (p = 0.04), elevated ATP production (p = 0.01), increased maximal respiration (p = 0.02), and higher spare respiratory capacity (p = 0.03) were found, compared to MHO. After stimulation with FSK, the differences in ATP production, maximal respiration and spare respiratory capacity were blunted. The differences in mitochondrial respiration between MUHO/MHO were not due to altered mitochondrial content, fuel switch, or lipid metabolism. Thus, despite the insulin resistance of MUHO, we could clearly show an elevated mitochondrial respiration of MUHO adipocytes. We suggest that the higher mitochondrial respiration reflects a compensatory mechanism to cope with insulin resistance and its consequences. Preserving this state of compensation might be an attractive goal for preventing or delaying the transition from insulin resistance to overt diabetes.

  • 48.
    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, 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.

  • 49. 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, 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.

  • 50.
    Castresana-Aguirre, Miguel
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik. Stockholms universitet, Science for Life Laboratory (SciLifeLab).
    Sonnhammer, Erik L. L.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik. Stockholms universitet, Science for Life Laboratory (SciLifeLab).
    Pathway-specific model estimation for improved pathway annotation by network crosstalk2020Inngår i: Scientific Reports, E-ISSN 2045-2322, Vol. 10, nr 1, artikkel-id 13585Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Pathway enrichment analysis is the most common approach for understanding which biological processes are affected by altered gene activities under specific conditions. However, it has been challenging to find a method that efficiently avoids false positives while keeping a high sensitivity. We here present a new network-based method ANUBIX based on sampling random gene sets against intact pathway. Benchmarking shows that ANUBIX is considerably more accurate than previous network crosstalk based methods, which have the drawback of modelling pathways as random gene sets. We demonstrate that ANUBIX does not have a bias for finding certain pathways, which previous methods do, and show that ANUBIX finds biologically relevant pathways that are missed by other methods.

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