Change search
Refine search result
2345 201 - 224 of 224
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Rows per page
  • 5
  • 10
  • 20
  • 50
  • 100
  • 250
Sort
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
  • Disputation date (earliest first)
  • Disputation date (latest first)
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
  • Disputation date (earliest first)
  • Disputation date (latest first)
Select
The maximal number of hits you can export is 250. When you want to export more records please use the Create feeds function.
  • 201.
    Vilhjálmsdóttir, Jóhanna
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Gennis, Robert B.
    Brzezinski, Peter
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    The electron distribution in the activated state of cytochrome c oxidase2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 7502Article in journal (Refereed)
    Abstract [en]

    Cytochrome c oxidase catalyzes reduction of O-2 to H2O at a catalytic site that is composed of a copper ion and heme group. The reaction is linked to translocation of four protons across the membrane for each O-2 reduced to water. The free energy associated with electron transfer to the catalytic site is unequal for the four electron-transfer events. Most notably, the free energy associated with reduction of the catalytic site in the oxidized cytochrome c oxidase (state O) is not sufficient for proton pumping across the energized membrane. Yet, this electron transfer is mechanistically linked to proton pumping. To resolve this apparent discrepancy, a high-energy oxidized state (denoted O-H) was postulated and suggested to be populated only during catalytic turnover. The difference between states O and O-H was suggested to be manifested in an elevated midpoint potential of Cu-B in the latter. This proposal predicts that one-electron reduction of cytochrome c oxidase after its oxidation would yield re-reduction of essentially only Cu-B. Here, we investigated this process and found similar to 5% and similar to 6% reduction of heme a(3) and Cu-B, respectively, i.e. the apparent redox potentials for heme a(3) and CuB are lower than that of heme a.

  • 202.
    Vilhjálmsdóttir, Jóhanna
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Johansson, Ann-Louise
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Brzezinski, Peter
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Structural Changes and Proton Transfer in Cytochrome c Oxidase2015In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 5, article id 12047Article in journal (Refereed)
    Abstract [en]

    In cytochrome c oxidase electron transfer from cytochrome c to O-2 is linked to transmembrane proton pumping, which contributes to maintaining a proton electrochemical gradient across the membrane. The mechanism by which cytochrome c oxidase couples the exergonic electron transfer to the endergonic proton translocation is not known, but it presumably involves local structural changes that control the alternating proton access to the two sides of the membrane. Such redox-induced structural changes have been observed in X-ray crystallographic studies at residues 423-425 ( in the R. sphaeroides oxidase), located near heme a. The aim of the present study is to investigate the functional effects of these structural changes on reaction steps associated with proton pumping. Residue Ser425 was modified using site-directed mutagenesis and time-resolved spectroscopy was used to investigate coupled electron-proton transfer upon reaction of the oxidase with O2. The data indicate that the structural change at position 425 propagates to the D proton pathway, which suggests a link between redox changes at heme a and modulation of intramolecular proton-transfer rates.

  • 203.
    Wallin, Cecilia
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Sholts, Sabrina B.
    Österlund, Nicklas
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry.
    Luo, Jinghui
    Jarvet, Jüri
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. The National Institute of Chemical Physics and Biophysics, Estonia.
    Roos, Per M.
    Ilag, Leopold
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry.
    Gräslund, Astrid
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Wärmländer, Sebastian K. T. S.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Alzheimer's disease and cigarette smoke components: effects of nicotine, PAHs, and Cd(II), Cr(III), Pb(II), Pb(IV) ions on amyloid-beta peptide aggregation2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 14423Article in journal (Refereed)
    Abstract [en]

    Cigarette smoking is a significant risk factor for Alzheimer’s disease (AD), which is associated with extracellular brain deposits of amyloid plaques containing aggregated amyloid-β (Aβ) peptides. Aβ aggregation occurs via multiple pathways that can be influenced by various compounds. Here, we used AFM imaging and NMR, fluorescence, and mass spectrometry to monitor in vitro how Aβ aggregation is affected by the cigarette-related compounds nicotine, polycyclic aromatic hydrocarbons (PAHs) with one to five aromatic rings, and the metal ions Cd(II), Cr(III), Pb(II), and Pb(IV). All PAHs and metal ions modulated the Aβ aggregation process. Cd(II), Cr(III), and Pb(II) ions displayed general electrostatic interactions with Aβ, whereas Pb(IV) ions showed specific transient binding coordination to the N-terminal Aβ segment. Thus, Pb(IV) ions are especially prone to interact with Aβ and affect its aggregation. While Pb(IV) ions affected mainly Aβ dimer and trimer formation, hydrophobic toluene mainly affected formation of larger aggregates such as tetramers. The uncharged and hydrophilic nicotine molecule showed no direct interactions with Aβ, nor did it affect Aβ aggregation. Our Aβ interaction results suggest a molecular rationale for the higher AD prevalence among smokers, and indicate that certain forms of lead in particular may constitute an environmental risk factor for AD.

  • 204. Westerbom, Mats
    et al.
    Lappalainen, Antti
    Mustonen, Olli
    Norkko, Alf
    Stockholm University, Faculty of Science, Stockholm University Baltic Sea Centre. Tvärminne Zoological Station, Finland.
    Trophic overlap between expanding and contracting fish predators in a range margin undergoing change2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 7895Article in journal (Refereed)
    Abstract [en]

    Climate change is predicted to cause a freshening of the Baltic Sea, facilitating range expansions of freshwater species and contractions of marine. Resident marine flounders (Platichthys flesus) and expansive freshwater roach (Rutilus rutilus) are dominant consumers in the Baltic Sea sublittoral where they occur in partial sympatry. By comparing patterns of resource use by flounders and roach along a declining resource gradient of blue mussels (Mytilus trossulus) our aim was to explore predator functional responses and the degree of trophic overlap. Understanding the nature of density-dependent prey acquisition has important implications for predicting population dynamics of both predators and their shared prey. Results showed a highly specialized diet for both species, high reliance on blue mussels throughout the range, similar prey size preference and high trophic overlap. Highest overlap occurred where blue mussels were abundant but overlap was also high where they were scarce. Our results highlight the importance of a single food item - the blue mussel - for both species, likely promoting high population size and range expansion of roach. Findings also suggest that range expansion of roach may have a top-down structuring force on mussels that differ in severity and location from that originating from resident flounders.

  • 205. Wikström, Sverre
    et al.
    Lindh, Christian H.
    Shu, Huan
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry. Karlstad University, Sweden.
    Bornehag, Carl-Gustaf
    Early pregnancy serum levels of perfluoroalkyl substances and risk of preeclampsia in Swedish women2019In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, article id 9179Article in journal (Refereed)
    Abstract [en]

    Preeclampsia is a major cause of maternal and fetal morbidity. Emerging research shows an association with environmental exposures. The present aim was to investigate associations between early pregnancy serum levels of perfluoroalkyl substances (PFAS) and preeclampsia. Within the Swedish SELMA study, eight PFAS were measured at median 10 gestational weeks and cases of preeclampsia were postnatally identified from registers. Associations between individual PFAS and preeclampsia were assessed, adjusting for parity, age, weight and smoking. Out of 1,773 women in the study group, 64 ( 3.6%), developed preeclampsia. A doubling of PFOS and PFNA exposure, corresponding to an inter-quartile increase, was associated with an increased risk for preeclampsia of about 38-53% respectively. Serum PFOS within the highest quartile was associated with an odds ratio of 2.68 ( CI 95%: 1.17-6.12), equal to the increased risk associated with nulliparity, when compared to exposure in the first quartile. The same associations were identified, although with higher risk estimates, in analyses restricted to nulliparous women. For other PFAS, there were no associations. In conclusion and consistent with limited previous research only on PFOS, increasing serum levels of PFOS and PFNA during early pregnancy were associated with a clinically relevant risk of preeclampsia, adjusting for established confounders.

  • 206. Wild, Birgit
    et al.
    Gentsch, Norman
    Capek, Petr
    Diakova, Katerina
    Alves, Ricardo J. Eloy
    Barta, Jiri
    Gittel, Antje
    Hugelius, Gustaf
    Stockholm University, Faculty of Science, Department of Physical Geography.
    Knoltsch, Anna
    Kuhry, Peter
    Stockholm University, Faculty of Science, Department of Physical Geography.
    Lashchinskiy, Nikolay
    Mikutta, Robert
    Palmtag, Juri
    Stockholm University, Faculty of Science, Department of Physical Geography.
    Schleper, Christa
    Schnecker, Jörg
    Shibistova, Olga
    Takriti, Mounir
    Torsvik, Vigdis L.
    Urich, Tim
    Watzka, Margarete
    Santruckova, Hana
    Guggenberger, Georg
    Richter, Andreas
    Plant-derived compounds stimulate the decomposition of organic matter in arctic permafrost soils2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 25607Article in journal (Refereed)
    Abstract [en]

    Arctic ecosystems are warming rapidly, which is expected to promote soil organic matter (SOM) decomposition. In addition to the direct warming effect, decomposition can also be indirectly stimulated via increased plant productivity and plant-soil C allocation, and this so called priming effect might significantly alter the ecosystem C balance. In this study, we provide first mechanistic insights into the susceptibility of SOM decomposition in arctic permafrost soils to priming. By comparing 119 soils from four locations across the Siberian Arctic that cover all horizons of active layer and upper permafrost, we found that an increased availability of plant-derived organic C particularly stimulated decomposition in subsoil horizons where most of the arctic soil carbon is located. Considering the 1,035 Pg of arctic soil carbon, such an additional stimulation of decomposition beyond the direct temperature effect can accelerate net ecosystem C losses, and amplify the positive feedback to global warming.

  • 207. Wohlfarth, Carolin
    et al.
    Schmitteckert, Stefanie
    Härtle, Janina D.
    Houghton, Lesley A.
    Dweep, Harsh
    Fortea, Marina
    Assadi, Ghazaleh
    Braun, Alexander
    Mederer, Tanja
    Pöhner, Sarina
    Becker, Philip P.
    Fischer, Christine
    Granzow, Martin
    Mönnikes, Hubert
    Mayer, Emeran A.
    Sayuk, Gregory
    Boeckxstaens, Guy
    Wouters, Mira M.
    Simrén, Magnus
    Lindberg, Greger
    Ohlsson, Bodil
    Schmidt, Peter Thelin
    Dlugosz, Aldona
    Agreus, Lars
    Andreasson, Anna
    Stockholm University, Faculty of Social Sciences, Stress Research Institute. Karolinska Institutet, Sweden.
    D'Amato, Mauro
    Burwinkel, Barbara
    Bermejo, Justo Lorenzo
    Röth, Ralph
    Lasitschka, Felix
    Vicario, Maria
    Metzger, Marco
    Santos, Javier
    Rappold, Gudrun A.
    Martinez, Cristina
    Niesler, Beate
    miR-16 and miR-103 impact 5-HT4 receptor signalling and correlate with symptom profile in irritable bowel syndrome2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 14680Article in journal (Refereed)
    Abstract [en]

    Irritable bowel syndrome (IBS) is a gut-brain disorder involving alterations in intestinal sensitivity and motility. Serotonin 5-HT4 receptors are promising candidates in IBS pathophysiology since they regulate gut motor function and stool consistency, and targeted 5-HT4R selective drug intervention has been proven beneficial in subgroups of patients. We identified a single nucleotide polymorphism (SNP) (rs201253747) c.*61 T > C within the 5-HT4 receptor gene HTR4 to be predominantly present in diarrhoea-IBS patients (IBS-D). It affects a binding site for the miR-16 family and miR-103/miR-107 within the isoforms HTR4b/i and putatively impairs HTR4 expression. Subsequent miRNA-profiling revealed downregulation of miR-16 and miR-103 in the jejunum of IBS-D patients correlating with symptoms. In vitro assays confirmed expression regulation via three 3'UTR binding sites. The novel isoform HTR4b_2 lacking two of the three miRNA binding sites escapes miR-16/103/107 regulation in SNP carriers. We provide the first evidence that HTR4 expression is fine-tuned by miRNAs, and that this regulation is impaired either by the SNP c.*61 T > C or by diminished levels of miR-16 and miR-103 suggesting that HTR4 might be involved in the development of IBS-D.

  • 208. Wu, Zhendong
    et al.
    Hugelius, Gustaf
    Stockholm University, Faculty of Science, Department of Physical Geography. Stanford University, USA.
    Luo, Yiqi
    Smith, Benjamin
    Xia, Jianyang
    Fensholt, Rasmus
    Lehsten, Veiko
    Ahlström, Anders
    Approaching the potential of model-data comparisons of global land carbon storage2019In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, article id 3367Article in journal (Refereed)
    Abstract [en]

    Carbon storage dynamics in vegetation and soil are determined by the balance of carbon influx and turnover. Estimates of these opposing fluxes differ markedly among different empirical datasets and models leading to uncertainty and divergent trends. To trace the origin of such discrepancies through time and across major biomes and climatic regions, we used a model-data fusion framework. The framework emulates carbon cycling and its component processes in a global dynamic ecosystem model, LPJ-GUESS, and preserves the model-simulated pools and fluxes in space and time. Thus, it allows us to replace simulated carbon influx and turnover with estimates derived from empirical data, bringing together the strength of the model in representing processes, with the richness of observational data informing the estimations. The resulting vegetation and soil carbon storage and global land carbon fluxes were compared to independent empirical datasets. Results show model-data agreement comparable to, or even better than, the agreement between independent empirical datasets. This suggests that only marginal improvement in land carbon cycle simulations can be gained from comparisons of models with current-generation datasets on vegetation and soil carbon. Consequently, we recommend that model skill should be assessed relative to reference data uncertainty in future model evaluation studies.

  • 209. Xi, Xinqiang
    et al.
    Yang, Yangheshan
    Yang, Xiaocheng
    Nylin, Soren
    Stockholm University, Faculty of Science, Department of Zoology.
    Eisenhauer, Nico
    Sun, Shucun
    Differential responses of body growth to artificial warming between parasitoids and hosts and the consequences for plant seed damage2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 15472Article in journal (Refereed)
    Abstract [en]

    Temperature increase may disrupt trophic interactions by differentially changing body growth of the species involved. In this study, we tested whether the response of body growth to artificial warming (similar to 2.2 degrees C) of a solitary koinobiont endo-parasitoid wasp (Pteromalus albipennis, Hymenoptera: Pteromalidae) differed from its main host tephritid fly (Tephritis femoralis, Diptera: Tephritidae; pre-dispersal seed predator), and whether the plant seed damage caused by wasp-parasitized and unparasitized maggots (larval flies) were altered by warming. In contrast to the significant and season-dependent effects of warming on body growth of the host tephritid fly reported in one of our previous studies, the effect of artificial warming on body growth was non-significant on the studied wasp. Moreover, the warming effect on seed damage due to unparasitized maggots was significant and varied with season, but the damage by parasitized maggots was not altered by warming. Distinct responses of body growth to warming between parasitoids studied here and hosts assessed in a previous study indicate that temperature increase may differentially affect life history traits of animals along food chains, which is likely to affect trophic interactions.

  • 210. Xie, Xueshu
    et al.
    Backman, Daniel
    Lebedev, Albert T.
    Artaev, Viatcheslav B.
    Jiang, Liying
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry.
    Ilag, Leopold L.
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry.
    Zubarev, Roman A.
    Primordial soup was edible: abiotically produced Miller-Urey mixture supports bacterial growth2015In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 5, article id 14338Article in journal (Refereed)
    Abstract [en]

    Sixty years after the seminal Miller-Urey experiment that abiotically produced a mixture of racemized amino acids, we provide a definite proof that this primordial soup, when properly cooked, was edible for primitive organisms. Direct admixture of even small amounts of Miller-Urey mixture strongly inhibits E. coli bacteria growth due to the toxicity of abundant components, such as cyanides. However, these toxic compounds are both volatile and extremely reactive, while bacteria are highly capable of adaptation. Consequently, after bacterial adaptation to a mixture of the two most abundant abiotic amino acids, glycine and racemized alanine, dried and reconstituted MU soup was found to support bacterial growth and even accelerate it compared to a simple mixture of the two amino acids. Therefore, primordial Miller-Urey soup was perfectly suitable as a growth media for early life forms.

  • 211.
    Yahia, Salwa Haj
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). University of Gabes, Tunisia.
    Lee, Kian Keat
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Ayed, Brahim
    Hedin, Niklas
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Church, Tamara L.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Activated Carbons from Hydrochars Prepared in Milk2019In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, article id 16956Article in journal (Refereed)
    Abstract [en]

    Hydrothermal carbonization converts organics in aqueous suspension to a mixture of liquid components and carbon-rich solids (hydrochars), which in turn can be processed into activated carbons. We investigated whether milk could be used as a medium for hydrothermal carbonization, and found that hydrochars prepared from milk, with or without an added fibrous biomass, contained more carbon (particularly aliphatic carbon), less oxygen, and more mineral components than those prepared from fibrous biomass in water. Activated carbons produced from hydrochars generated in milk had lower specific surface areas and CO2 capacities than those from hydrochars formed in water; however, these differences disappeared upon normalizing to the combustible mass of the solid. Thus, in the context of N-2 and CO2 uptake on activated carbons, the primary effect of using milk rather than water to form the hydrochar precursor was to contribute inorganic mass that adsorbed little CO2. Nevertheless, some of the activated carbons generated from hydrochars formed in milk had specific CO2 uptake capacities in the normal range for activated carbons prepared by activation in CO2 (here, up to 1.6 mmol g(-1) CO2 at 15 kPa and 0 degrees C). Thus, hydrothermal carbonization could be used to convert waste milk to hydrochars and activated carbons.

  • 212. Yan, Caiqing
    et al.
    Zheng, Mei
    Bosch, Carme
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry.
    Andersson, August
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry.
    Desyaterik, Yury
    Sullivan, Amy P.
    Collett, Jeffrey L.
    Zhao, Bin
    Wang, Shuxiao
    He, Kebin
    Gustafsson, Örjan
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry.
    Important fossil source contribution to brown carbon in Beijing during winter2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 43182Article in journal (Refereed)
    Abstract [en]

    Organic aerosol (OA) constitutes a substantial fraction of fine particles and affects both human health and climate. It is becoming clear that OA absorbs light substantially (hence termed Brown Carbon, BrC), adding uncertainties to global aerosol radiative forcing estimations. The few current radiative-transfer and chemical-transport models that include BrC primarily consider sources from biogenic and biomass combustion. However, radiocarbon fingerprinting here clearly indicates that light-absorbing organic carbon in winter Beijing, the capital of China, is mainly due to fossil sources, which contribute the largest part to organic carbon (OC, 67 +/- 3%) and its sub-constituents (water-soluble OC, WSOC: 54 +/- 4%, and water-insoluble OC, WIOC: 73 +/- 3%). The dual-isotope (Delta C-14/delta C-13) signatures, organic molecular tracers and Beijing-tailored emission inventory identify that this fossil source is primarily from coal combustion activities in winter, especially from the residential sector. Source testing on Chinese residential coal combustion provides direct evidence that intensive coal combustion could contribute to increased light-absorptivity of ambient BrC in Beijing winter. Coal combustion is an important source to BrC in regions such as northern China, especially during the winter season. Future modeling of OA radiative forcing should consider the importance of both biomass and fossil sources.

  • 213. Yang, Cheng-En
    et al.
    Mao, Jiafu
    Hoffman, Forrest M.
    Ricciuto, Daniel M.
    Fu, Joshua S.
    Jones, Chris D.
    Thurner, Martin
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry.
    Uncertainty Quantification of Extratropical Forest Biomass in CMIP5 Models over the Northern Hemisphere2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 10962Article in journal (Refereed)
    Abstract [en]

    Simplified representations of processes influencing forest biomass in Earth system models (ESMs) contribute to large uncertainty in projections. We evaluate forest biomass from eight ESMs outputs archived in the Coupled Model Intercomparison Project Phase 5 (CMIP5) using the biomass data synthesized from radar remote sensing and ground-based observations across northern extratropical latitudes. ESMs exhibit large biases in the forest distribution, forest fraction, and mass of carbon pools that contribute to uncertainty in forest total biomass (biases range from -20 Pg C to 135 Pg C). Forest total biomass is primarily positively correlated with precipitation variations, with surface temperature becoming equally important at higher latitudes, in both simulations and observations. Relatively small differences in forest biomass between the pre-industrial period and the contemporary period indicate uncertainties in forest biomass were introduced in the pre-industrial model equilibration (spin-up), suggesting parametric or structural model differences are a larger source of uncertainty than differences in transient responses. Our findings emphasize the importance of improved (1) models of carbon allocation to biomass compartments, (2) distribution of vegetation types in models, and (3) reproduction of pre-industrial vegetation conditions, in order to reduce the uncertainty in forest biomass simulated by ESMs.

  • 214. Yang, Haijun
    et al.
    Zhao, Yingying
    Liu, Zhengyu
    Li, Qing
    He, Feng
    Zhang, Qiong
    Stockholm University, Faculty of Science, Department of Physical Geography.
    Heat Transport Compensation in Atmosphere and Ocean over the Past 22,000 Years2015In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 5, article id 16661Article in journal (Refereed)
    Abstract [en]

    The Earth's climate has experienced dramatic changes over the past 22,000 years; however, the total meridional heat transport (MHT) of the climate system remains stable. A 22,000-year-long simulation using an ocean-atmosphere coupled model shows that the changes in atmosphere and ocean MHT are significant but tend to be out of phase in most regions, mitigating the total MHT change, which helps to maintain the stability of the Earth's overall climate. A simple conceptual model is used to understand the compensation mechanism. The simple model can reproduce qualitatively the evolution and compensation features of the MHT over the past 22,000 years. We find that the global energy conservation requires the compensation changes in the atmosphere and ocean heat transports. The degree of compensation is mainly determined by the local climate feedback between surface temperature and net radiation flux at the top of the atmosphere. This study suggests that an internal mechanism may exist in the climate system, which might have played a role in constraining the global climate change over the past 22,000 years.

  • 215. Yasui, Takao
    et al.
    Ogawa, Kensuke
    Kaji, Noritada
    Nilsson, Mats
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Ajiri, Taiga
    Tokeshi, Manabu
    Horiike, Yasuhiro
    Baba, Yoshinobu
    Label-free detection of real-time DNA amplification using a nanofluidic diffraction grating2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 31642Article in journal (Refereed)
    Abstract [en]

    Quantitative DNA amplification using fluorescence labeling has played an important role in the recent, rapid progress of basic medical and molecular biological research. Here we report a label-free detection of real-time DNA amplification using a nanofluidic diffraction grating. Our detection system observed intensity changes during DNA amplification of diffracted light derived from the passage of a laser beam through nanochannels embedded in a microchannel. Numerical simulations revealed that the diffracted light intensity change in the nanofluidic diffraction grating was attributed to the change of refractive index. We showed the first case reported to date for label-free detection of real-time DNA amplification, such as specific DNA sequences from tubercle bacilli (TB) and human papillomavirus (HPV). Since our developed system allows quantification of the initial concentration of amplified DNA molecules ranging from 1 fM to 1 pM, we expect that it will offer a new strategy for developing fundamental techniques of medical applications.

  • 216. Yman, Victor
    et al.
    White, Michael T.
    Rono, Josea
    Arca, Bruno
    Osier, Faith H.
    Troye-Blomberg, Marita
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Boström, Stephanie
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Ronca, Raffaele
    Rooth, Ingegerd
    Färnert, Anna
    Antibody acquisition models: A new tool for serological surveillance of malaria transmission intensity2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 19472Article in journal (Refereed)
    Abstract [en]

    Serology has become an increasingly important tool for the surveillance of a wide range of infectious diseases. It has been particularly useful to monitor malaria transmission in elimination settings where existing metrics such as parasite prevalence and incidence of clinical cases are less sensitive. Seroconversion rates, based on antibody prevalence to Plasmodium falciparum asexual blood-stage antigens, provide estimates of transmission intensity that correlate with entomological inoculation rates but lack precision in settings where seroprevalence is still high. Here we present a new and widely applicable method, based on cross-sectional data on individual antibody levels. We evaluate its use as a sero-surveillance tool in a Tanzanian setting with declining malaria prevalence. We find that the newly developed mathematical models produce more precise estimates of transmission patterns, are robust in high transmission settings and when sample sizes are small, and provide a powerful tool for serological evaluation of malaria transmission intensity.

  • 217.
    Yuan, Ning
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). Swedish University of Agricultural Sciences, Sweden.
    Church, Tamara L.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Brandt, Erik G.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Hedin, Niklas
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Zou, Xiaodong
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Bernin, Diana
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). Chalmers University, Sweden.
    Insights into Functionalization of Metal-Organic Frameworks Using In Situ NMR Spectroscopy2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 17530Article in journal (Refereed)
    Abstract [en]

    Postsynthetic reactions of metal-organic frameworks (MOFs) are versatile tools for producing functional materials, but the methods of evaluating these reactions are cumbersome and destructive. Here we demonstrate and validate the use of in situ NMR spectroscopy of species in the liquid state to examine solvent-assisted ligand exchange (SALE) and postsynthetic modification (PSM) reactions of metal-organic frameworks. This technique allows functionalization to be monitored over time without decomposing the product for analysis, which simplifies reaction screening. In the case of SALE, both the added ligand and the ligand leaving the framework can be observed. We demonstrate this in situ method by examining SALE and PSM reactions of the robust zirconium MOF UiO-67 as well as SALE with the aluminum MOF DUT-5. In situ NMR spectroscopy provided insights into the reactions studied, and we expect that future studies using this method will permit the examination of a variety of MOF-solute reactions.

  • 218. Zaghlool, Ammar
    et al.
    Ameur, Adam
    Wu, Chenglin
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Orzechowski Westholm, Jakub
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Niazi, Adnan
    Manivannan, Manimozhi
    Bramlett, Kelli
    Nilsson, Mats
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab). Uppsala University, Sweden.
    Feuk, Lars
    Expression profiling and in situ screening of circular RNAs in human tissues2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 16953Article in journal (Refereed)
    Abstract [en]

    Circular RNAs (circRNAs) were recently discovered as a class of widely expressed noncoding RNA and have been implicated in regulation of gene expression. However, the function of the majority of circRNAs remains unknown. Studies of circRNAs have been hampered by a lack of essential approaches for detection, quantification and visualization. We therefore developed a target-enrichment sequencing method suitable for screening of circRNAs and their linear counterparts in large number of samples. We also applied padlock probes and in situ sequencing to visualize and determine circRNA localization in human brain tissue at subcellular levels. We measured circRNA abundance across different human samples and tissues. Our results highlight the potential of this RNA class to act as a specific diagnostic marker in blood and serum, by detection of circRNAs from genes exclusively expressed in the brain. The powerful and scalable tools we present will enable studies of circRNA function and facilitate screening of circRNA as diagnostic biomarkers.

  • 219. Zapata, Luis
    et al.
    Susak, Hana
    Drechsel, Oliver
    Friedländer, Marc R.
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute. Stockholm University, Science for Life Laboratory (SciLifeLab). The Barcelona Institute of Science and Technology, Spain; Universitat Pompeu Fabra (UPF), Spain.
    Estivill, Xavier
    Ossowski, Stephan
    Signatures of positive selection reveal a universal role of chromatin modifiers as cancer driver genes2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 13124Article in journal (Refereed)
    Abstract [en]

    Tumors are composed of an evolving population of cells subjected to tissue-specific selection, which fuels tumor heterogeneity and ultimately complicates cancer driver gene identification. Here, we integrate cancer cell fraction, population recurrence, and functional impact of somatic mutations as signatures of selection into a Bayesian model for driver prediction. We demonstrate that our model, cDriver, outperforms competing methods when analyzing solid tumors, hematological malignancies, and pan-cancer datasets. Applying cDriver to exome sequencing data of 21 cancer types from 6,870 individuals revealed 98 unreported tumor type-driver gene connections. These novel connections are highly enriched for chromatin-modifying proteins, hinting at a universal role of chromatin regulation in cancer etiology. Although infrequently mutated as single genes, we show that chromatin modifiers are altered in a large fraction of cancer patients. In summary, we demonstrate that integration of evolutionary signatures is key for identifying mutational driver genes, thereby facilitating the discovery of novel therapeutic targets for cancer treatment.

  • 220. Zeng, Lunjie
    et al.
    Tran, Dung Trung
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Tai, Cheuk-Wai
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Svensson, Gunnar
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Olsson, Eva
    Atomic structure and oxygen deficiency of the ultrathin aluminium oxide barrier in Al/AlOx/Al Josephson junctions2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 29679Article in journal (Refereed)
    Abstract [en]

    Al/AlOx/Al Josephson junctions are the building blocks of a wide range of superconducting quantum devices that are key elements for quantum computers, extremely sensitive magnetometers and radiation detectors. The properties of the junctions and the superconducting quantum devices are determined by the atomic structure of the tunnel barrier. The nanoscale dimension and disordered nature of the barrier oxide have been challenges for the direct experimental investigation of the atomic structure of the tunnel barrier. Here we show that the miniaturized dimension of the barrier and the interfacial interaction between crystalline Al and amorphous AlOx give rise to oxygen deficiency at the metal/oxide interfaces. In the interior of the barrier, the oxide resembles the atomic structure of bulk aluminium oxide. Atomic defects such as oxygen vacancies at the interfaces can be the origin of the two-level systems and contribute to decoherence and noise in superconducting quantum circuits.

  • 221.
    Zguna, Nadezda
    et al.
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry.
    Karlson, Agnes M. L.
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry. Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Ilag, Leopold L.
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry.
    Garbaras, Andrius
    Gorokhova, Elena
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry.
    Insufficient evidence for BMAA transfer in the pelagic and benthic food webs in the Baltic Sea2019In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, article id 10406Article in journal (Refereed)
    Abstract [en]

    The evidence regarding BMAA occurrence in the Baltic Sea is contradictory, with benthic sources appearing to be more important than pelagic ones. The latter is counterintuitive considering that the identified sources of this compound in the food webs are pelagic primary producers, such as diatoms, dinoflagellates, and cyanobacteria. To elucidate BMAA distribution, we analyzed BMAA in the pelagic and benthic food webs in the Northern Baltic Proper. As potential sources, phytoplankton communities were used. Pelagic food chain was represented by zooplankton, mysids and zooplanktivorous fish, whereas benthic invertebrates and benthivorous fish comprised the benthic chain. The trophic structure of the system was confirmed by stable isotope analysis. Contrary to the reported ubiquitous occurrence of BMAA in the Baltic food webs, only phytoplankton, zooplankton and mysids tested positive, whereas no measurable levels of this compound occurred in the benthic invertebrates and any of the tested fish species. These findings do not support the widely assumed occurrence and transfer of BMAA to the top consumers in the Baltic food webs. More controlled experiments and field observations are needed to understand the transfer and possible transformation of BMAA in the food web under various environmental settings.

  • 222. Zhang, Huan
    et al.
    Werner, Johannes P.
    García-Bustamante, Elena
    González-Rouco, Fidel
    Wagner, Sebastian
    Zorita, Eduardo
    Fraedrich, Klaus
    Jungclaus, Johann H.
    Charpentier Ljungqvist, Fredrik
    Stockholm University, Faculty of Humanities, Department of History.
    Zhu, Xiuhua
    Xoplaki, Elena
    Chen, Fahu
    Duan, Jianping
    Ge, Quansheng
    Hao, Zhixin
    Ivanov, Martin
    Schneider, Lea
    Talento, Stefanie
    Wang, Jianglin
    Yang, Bao
    Luterbacher, Jürg
    East Asian warm season temperature variations over the past two millennia2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 7702Article in journal (Refereed)
    Abstract [en]

    East Asia has experienced strong warming since the 1960s accompanied by an increased frequency of heat waves and shrinking glaciers over the Tibetan Plateau and the Tien Shan. Here, we place the recent warmth in a long-term perspective by presenting a new spatially resolved warm-season (May-September) temperature reconstruction for the period 1-2000 CE using 59 multiproxy records from a wide range of East Asian regions. Our Bayesian Hierarchical Model (BHM) based reconstructions generally agree with earlier shorter regional temperature reconstructions but are more stable due to additional temperature sensitive proxies. We find a rather warm period during the first two centuries CE, followed by a multi-century long cooling period and again a warm interval covering the 900-1200 CE period (Medieval Climate Anomaly, MCA). The interval from 1450 to 1850 CE (Little Ice Age, LIA) was characterized by cooler conditions and the last 150 years are characterized by a continuous warming until recent times. Our results also suggest that the 1990s were likely the warmest decade in at least 1200 years. The comparison between an ensemble of climate model simulations and our summer reconstructions since 850 CE shows good agreement and an important role of internal variability and external forcing on multi-decadal time-scales.

  • 223. Zhang, Zhaohui
    et al.
    Smittenberg, Rienk H.
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Bradley, Raymond S.
    GDGT distribution in a stratified lake and implications for the application of TEX86 in paleoenvironmental reconstructions2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 34465Article in journal (Refereed)
    Abstract [en]

    We investigated the relationship between distributions of GDGTs, GDGT-based proxies and environmental factors in a stratified lake in northwestern Norway. More than 90% of isoGDGTs were produced at the bottom of the oxycline, indicating a predominance of ammonia-oxidizing Group I.1a of Thaumarchaeota, supported by high crenarchaeol/caldarchaeol ratios. Dissolved oxygen content, rather than temperature, exercised a primary control on TEX86 values. In spite of low BIT value in surface sediment, the reconstructed lake surface temperature was cold biased. MBT values in streams and lake surface water were significantly smaller than those in the catchment soil, suggesting in situ production of brGDGTs in streams. A rapid transition of MBT vs. temperature/pH relationships occurring at the bottom of oxycline indicated the differential production of various brGDGTs with D.O. and depths. Only within the oxycline were CBT-based pH values close to in situ pH. Our results confirm earlier studies calling for caution in applying TEX86 as a surface temperature proxy, or MBT and/or CBT for reconstructing pH, in anoxic or euxinic lakes, estuaries and ocean basins. We propose that caldarchaeol/crenarchaeol ratio, an indicator of contributions from methanogenic archaea, together with the BIT and TEX86 proxies, can help reconstruct past levels of stratification.

  • 224. Zhao, Jing
    et al.
    Lee, Sang Hoon
    Huss, Mikael
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Holme, Petter
    The Network Organization of Cancer-associated Protein Complexes in Human Tissues2013In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 3, article id 1583Article in journal (Refereed)
    Abstract [en]

    Differential gene expression profiles for detecting disease genes have been studied intensively in systems biology. However, it is known that various biological functions achieved by proteins follow from the ability of the protein to form complexes by physically binding to each other. In other words, the functional units are often protein complexes rather than individual proteins. Thus, we seek to replace the perspective of disease-related genes by disease-related complexes, exemplifying with data on 39 human solid tissue cancers and their original normal tissues. To obtain the differential abundance levels of protein complexes, we apply an optimization algorithm to genome-wide differential expression data. From the differential abundance of complexes, we extract tissue- and cancer-selective complexes, and investigate their relevance to cancer. The method is supported by a clustering tendency of bipartite cancer-complex relationships, as well as a more concrete and realistic approach to disease-related proteomics.

2345 201 - 224 of 224
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf