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Helsingin yliopiston tutkijoiden julkaisemia artikkeleja.

Helsingin yliopiston tutkijat voivat rinnakkaistallentaa tutkimusjulkaisujansa HELDAan liittämällä kokotekstin julkaisuun TUHAT-tutkimustietojärjestelmässä. (Toimintaohje tutkijalle)

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Uusimmat julkaisut

  • Toivonen, Marjaana; Huusela-Veistola, Erja; Herzon, Irina (2018)
    Fallow strips are promoted through agri-climate-environment schemes to enhance farmland biodiversity, but their effects on biodiversity-mediated ecosystem services remain poorly studied in different cropping systems. The effects of fallow strips on biological control of bird cherry-oat aphids in spring barley were examined in a field experiment in Finland in 2014–2016. Two types of sown perennial fallow strips – grass strip and wildflower strip – were compared. The relative efficiency of biological pest control was tested by monitoring the number of experimentally added aphids in the fallow strips and in the adjacent barley fields at different distances from the strips. Data were also collected on the densities of naturally occurring aphids and ground-dwelling natural enemies. The effects of the fallow strips differed between years. When aphid pressure was high, the proximity of the strips slowed the growth of aphid population. In the year of low aphid abundance, the fallow strips sustained more aphids than the adjacent barley fields, but did not constitute a risk for pest control. In the second and third years, especially wildflower strips supported high activity density of ground-dwelling predators. The activity densities were particularly high in the both fallow strip types in early summer, highlighting the role of the perennial strips as refuges for natural enemies. The results suggest that perennial fallow strips, and especially those sown with diverse wildflower mixtures, can promote pest control in spring cereals, thus contributing to ecological intensification in agriculture.
  • Schmale, Julia; Henning, Silvia; Decesari, Stefano; Henzing, Bas; Keskinen, Helmi; Sellegri, Karine; Ovadnevaite, Jurgita; Poehlker, Mira L.; Brito, Joel; Bougiatioti, Aikaterini; Kristensson, Adam; Kalivitis, Nikos; Stavroulas, Iasonas; Carbone, Samara; Jefferson, Anne; Park, Minsu; Schlag, Patrick; Iwamoto, Yoko; Aalto, Pasi; Äijälä, Mikko; Bukowiecki, Nicolas; Ehn, Mikael; Frank, Goran; Frohlich, Roman; Frumau, Arnoud; Herrmann, Erik; Herrmann, Hartmut; Holzinger, Rupert; Kos, Gerard; Kulmala, Markku; Mihalopoulos, Nikolaos; Nenes, Athanasios; O'Dowd, Colin; Petäjä, Tuukka; Picard, David; Poehlker, Christopher; Poeschl, Ulrich; Poulain, Laurent; Prevot, Andre Stephan Henry; Swietlicki, Erik; Andreae, Meinrat O.; Artaxo, Paulo; Wiedensohler, Alfred; Ogren, John; Matsuki, Atsushi; Yum, Seong Soo; Stratmann, Frank; Baltensperger, Urs; Gysel, Martin (2018)
    Aerosol-cloud interactions (ACI) constitute the single largest uncertainty in anthropogenic radiative forcing. To reduce the uncertainties and gain more confidence in the simulation of ACI, models need to be evaluated against observations, in particular against measurements of cloud condensation nuclei (CCN). Here we present a data set - ready to be used for model validation - of long-term observations of CCN number concentrations, particle number size distributions and chemical composition from 12 sites on 3 continents. Studied environments include coastal background, rural background, alpine sites, remote forests and an urban surrounding. Expectedly, CCN characteristics are highly variable across site categories. However, they also vary within them, most strongly in the coastal background group, where CCN number concentrations can vary by up to a factor of 30 within one season. In terms of particle activation behaviour, most continental stations exhibit very similar activation ratios (relative to particles > 20 nm) across the range of 0.1 to 1.0% supersaturation. At the coastal sites the transition from particles being CCN inactive to becoming CCN active occurs over a wider range of the supersaturation spectrum. Several stations show strong seasonal cycles of CCN number concentrations and particle number size distributions, e. g. at Barrow (Arctic haze in spring), at the alpine stations (stronger influence of polluted boundary layer air masses in summer), the rain forest (wet and dry season) or Finokalia (wildfire influence in autumn). The rural background and urban sites exhibit relatively little variability throughout the year, while short-term variability can be high especially at the urban site. The average hygroscopicity parameter, kappa, calculated from the chemical composition of submicron particles was highest at the coastal site of Mace Head (0.6) and lowest at the rain forest station ATTO (0.2-0.3). We performed closure studies based on kappa-Kohler theory to predict CCN number concentrations. The ratio of predicted to measured CCN concentrations is between 0.87 and 1.4 for five different types of kappa. The temporal variability is also well captured, with Pearson correlation coefficients exceeding 0.87. Information on CCN number concentrations at many locations is important to better characterise ACI and their radiative forcing. But long-term comprehensive aerosol particle characterisations are labour intensive and costly. Hence, we recommend operating "migrating-CCNCs" to conduct collocated CCN number concentration and particle number size distribution measurements at individual locations throughout one year at least to derive a seasonally resolved hygroscopicity parameter. This way, CCN number concentrations can only be calculated based on continued particle number size distribution information and greater spatial coverage of longterm measurements can be achieved.
  • Haldorsen, Bjorg; Giske, Christian G.; Hansen, Dennis S.; Helgason, Kristjan Orri; Kahlmeter, Gunnar; Lohr, Iren H.; Matuschek, Erika; Osterblad, Monica; Rantakokko-Jalava, Kaisu; Wang, Mikala; Smabrekke, Lars; Samuelsen, Orjan; Sundsfjord, Arnfinn; Kärpänoja, Pauliina (2018)
    Objectives: To examine performance of EUCAST disc diffusion and supplementary MIC methods for detection of Enterobacteriaceae with reduced susceptibility to meropenem using EUCAST screening recommendations. Methods: Sixty-one Nordic laboratories delivered data on EUCAST disc diffusion (n = 61), semi-automated meropenem MIC (n = 23; VITEK2, n = 20 and Phoenix, n = 3) and gradient meropenem MIC (n = 58) methods: The strains (n - 27) included the major carbapenemase classes (A, n - 4; B, n - 9; D, n - 6) involved in the global spread of carbapenemase-producing Enterobacteriaceae (CPE) and non-CPE strains (n = 8) covering a range of broth microdilution (BMD) meropenem MICs. Results: A triplicate Klebsiella vanicola (meropenem MIC >= 0,5 mg/L) harbouring OXA-48 and Escherichia coli ATCC 25922 showed an overall good precision. Meropenem zone diameters below the EUCAST screening cut-off (= 1 mg/L (n = 21), irrespective of resistance mechanism. For three strains (MIC - 0.5 mg/L) with OXA-481-181, eight laboratories provided meropenem zone diameters above the screening cut-off, Very major errors (VMEs) were not observed. The overall distributions of major errors (MEs) and minor errors (mEs) were 9% and 36% (disc diffusion), 26% and 18% (VITEK2) and 7% and 20% (gradient MIC), respectively, Differences in ME and mE distributions between disc diffusion and MIC gradient tests compared with semi-automated methods were significant (P <0,0001), using BMD MICs as a reference for categorization, Conclusions: The EUCAST disc diffusion method is a robust method to screen for CPE but isolates with meropenem MICs
  • Pietarinen, Jaakko; Muuttoranta, Kirsi; Mäki-Tanila, Asko Vilhelm (2018)
  • Boom, Devin H. A.; Ehlers, Andreas W.; Nieger, Martin; Devillard, Marc; Bouhadir, Ghenwa; Bourissou, Didier; Slootweg, J. Chris (2018)
    In this work, we explored the coordination properties of the geminal phosphinoborane tBu(2)PCH(2)BPh(2) (2) toward different gold(I) precursors. The reaction of 2 with an equimolar amount of the sulfur-based complex (Me2S) AuCl resulted in displacement of the SMe2 ligand and formation of linear phosphine gold(I) chloride 3. Using an excess of ligand 2, bisligated complex 4 was formed and showed dynamic behavior at room temperature. Changing the gold(I) metal precursor to the phosphorus-based complex, (Ph3P) AuCl impacted the coordination behavior of ligand 2. Namely, the reaction of ligand 2 with (Ph3P) AuCl led to the heterolytic cleavage of the gold-chloride bond, which is favored over PPh3 ligand displacement. To the best of our knowledge, 2 is the first example of a P/Bambiphilic ligand capable of cleaving the gold-chloride bond. The coordination chemistry of 2 was further analyzed by density functional theory calculations.
  • Tietäväinen, Aino; Kuvaldina, Maria; Haeggström, Edward (2018)
    Sleep deprivation may cause accidents, and it has deteriorating effects on health. A measurement of postural steadiness by a portable and affordable Nintendo Wii Fit balance board can be used to quantify a person's alertness. At work, people are under the influence of their environment-often other peopledthat may affect their alertness. This work investigates whether sleep deprivation among people is "contagious," as quantified by sway measures. We measured 21 volunteers' postural steadiness while alert and sleep deprived. During the measurements, a screen placed in front of the participants showed a footage of either alert or sleep-deprived faces. We found a significant difference between the day time and night time steadiness, but found no effect resulting from watching footage of sleep-deprived people. This finding shows that a posturographic sleepiness tester quantifies physiological sleep deprivation, and is insensitive to the influence of social factors. (C) 2017 Occupational Safety and Health Research Institute, Published by Elsevier Korea LLC.
  • Päivänen, Eero Juhani (2018)
  • Lees, John A.; Harris, Simon R.; Tonkin-Hill, Gerry; Gladstone, Rebecca A.; Lo, Stephanie W.; Weiser, Jeffrey N.; Corander, Jukka; Bentley, Stephen D.; Croucher, Nicholas J. (2019)
    The routine use of genomics for disease surveillance provides the opportunity for high-resolution bacterial epidemiology. Current whole-genome clustering and multilocus typing approaches do not fully exploit core and accessory genomic variation, and they cannot both automatically identify, and subsequently expand, clusters of significantly similar isolates in large data sets spanning entire species. Here, we describe PopPUNK (Population Partitioning Using Nucleotide K-mers), a software implementing scalable and expandable annotation-and alignment-free methods for population analysis and clustering. Variable-length k-mer comparisons are used to distinguish isolates' divergence in shared sequence and gene content, which we demonstrate to be accurate over multiple orders of magnitude using data from both simulations and genomic collections representing 10 taxonomically widespread species. Connections between closely related isolates of the same strain are robustly identified, despite interspecies variation in the pairwise distance distributions that reflects species' diverse evolutionary patterns. PopPUNK can process 10(3)-10(4) genomes in a single batch, with minimal memory use and runtimes up to 200-fold faster than existing model-based methods. Clusters of strains remain consistent as new batches of genomes are added, which is achieved without needing to reanalyze all genomes de novo. This facilitates real-time surveillance with consistent cluster naming between studies and allows for outbreak detection using hundreds of genomes in minutes. Interactive visualization and online publication is streamlined through the automatic output of results to multiple platforms. PopPUNK has been designed as a flexible platform that addresses important issues with currently used whole-genome clustering and typing methods, and has potential uses across bacterial genetics and public health research.
  • Päivänen, Eero Juhani (2018)
  • Salmi-Niklander, Kirsti; Tähtinen, Juhani (2018)
  • Martens, Helge; Tillmann, Urban; Harju, Kirsi; Dell'Aversano, Carmela; Tartaglione, Luciana; Krock, Bernd (2017)
    Alexandrium ostenfeldii is a toxic dinoflagellate that has recently bloomed in Ouwerkerkse Kreek, The Netherlands, and which is able to cause a serious threat to shellfish consumers and aquacultures. We used a large set of 68 strains to the aim of fully characterizing the toxin profiles of the Dutch A. ostenfeldii in consideration of recent reports of novel toxins. Alexandrium ostenfeldii is known as a causative species of paralytic shellfish poisoning, and consistently in the Dutch population we determined the presence of several paralytic shellfish toxins (PST) including saxitoxin (STX), GTX2/3 (gonyautoxins), B1 and C1/C2. We also examined the production of spiroimine toxins by the Dutch A. ostenfeldii strains. An extensive liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis revealed a high intraspecific variability of spirolides (SPX) and gymnodimines (GYM). Spirolides included 13-desMethyl-spirolide C generally as the major compound and several other mostly unknown SPX-like compounds that were detected and characterized. Besides spirolides, the presence of gymnodimine A and 12-Methyl-gymnodimine A was confirmed, together with two new gymnodimines. One of these was tentatively identified as an analogue of gymnodimine D and was the most abundant gymnodimine (calculated cell quota up to 274 pg cell(-1), expressed as GYM A equivalents). Our multi-clonal approach adds new analogues to the increasing number of compounds in these toxin classes and revealed a high strain variability in cell quota and in toxin profile of toxic compounds within a single population.
  • Biferale, L.; Khomenko, D.; L'vov, V.; Pomyalov, A.; Procaccia, I.; Sahoo, G. (2017)
  • Polianskyte-Prause, Zydrune; Tolvanen, Tuomas A.; Lindfors, Sonja; Dumont, Vincent; Van, Mervi; Wang, Hong; Dash, Surjya N.; Berg, Mika; Naams, Jette-Britt; Hautala, Laura C.; Nisen, Harry; Mirtti, Tuomas; Groop, Per-Henrik; Wähälä, Kristiina; Tienari, Jukka; Lehtonen, Sanna (2019)
    Metformin, the first-line drug to treat type 2 diabetes (T2D), inhibits mitochondrial glycerolphosphate dehydrogenase in the liver to suppress gluconeogenesis. However, the direct target and the underlying mechanisms by which metformin increases glucose uptake in peripheral tissues remain uncharacterized. Lipid phosphatase Src homology 2 domain-containing inositol-5-phosphatase 2 (SHIP2) is upregulated in diabetic rodent models and suppresses insulin signaling by reducing Akt activation, leading to insulin resistance and diminished glucose uptake. Here, we demonstrate that metformin directly binds to and reduces the catalytic activity of the recombinant SHIP2 phosphatase domain in vitro. Metformin inhibits SHIP2 in cultured cells and in skeletal muscle and kidney of db/db mice. In SHIP2-overexpressing myotubes, metformin ameliorates reduced glucose uptake by slowing down glucose transporter 4 endocytosis. SHIP2 overexpression reduces Akt activity and enhances podocyte apoptosis, and both are restored to normal levels by metformin. SHIP2 activity is elevated in glomeruli of patients with T2D receiving nonmetformin medication, but not in patients receiving metformin, compared with people without diabetes. Furthermore, podocyte loss in kidneys of metformin-treated T2D patients is reduced compared with patients receiving nonmetformin medication. Our data unravel a novel molecular mechanism by which metformin enhances glucose uptake and acts renoprotectively by reducing SHIP2 activity.Polianskyte-Prause, Z., Tolvanen, T. A., Lindfors, S., Dumont, V., Van, M., Wang, H., Dash, S. N., Berg, M., Naams, J.-B., Hautala, L. C., Nisen, H., Mirtti, T., Groop, P.-H., Wahala, K., Tienari, J., Lehtonen, S. Metformin increases glucose uptake and acts renoprotectively by reducing SHIP2 activity.
  • Trémion, Virginie; Dervin, Fred (2018)
    This article aims to identify aspects of telecollaboration that could have a positive influence on the development of ‘renewed’ intercultural encounters. The authors also discuss the strategies needed to construct new knowledge about such encounters. The starting point is a review of a ‘classic’ model of online intercultural telecollaboration, Cultura. As a contrast, the way(s) the intercultural is constructed, negotiated and problematised in a MOOC about intercultural communication. Through their specific aspects, can MOOCs allow participants to look into the intercultural from a dialogical, critical and reflexive angle, which are signs of a much needed ‘renewed’ interculturality in education?
  • Tamm, Aile; Kalam, Kristjan; Seemen, Helina; Kozlova, Jekaterina; Kukli, Kaupo; Aarik, Jaan; Link, Joosep; Stern, Raivo; Duenas, Salvador; Castan, Helena (2017)
    Mixed films of a high-permittivity oxide, Er2O3, and a magnetic material, Fe2O3, were grown by atomic layer deposition on silicon and titanium nitride at 375 degrees C using erbium diketonate, ferrocene, and ozone as precursors. Crystalline phases of erbium and iron oxides were formed. Growth into three-dimensional trenched structures was demonstrated. A structure deposited using tens to hundreds subsequent cycles for both constituent metal oxide layers promoted both charge polarization and saturative magnetization compared to those in the more homogeneously mixed films.
  • Pryazhnikov, Evgeny; Mugantseva, Ekaterina; Casarotto, Plinio; Kolikova, Julia; Fred, Senem Merve; Toptunov, Dmytro; Afzalov, Ramil; Hotulainen, Pirta; Voikar, Vootele; Terry-Lorenzo, Ryan; Engel, Sharon; Kirov, Sergei; Castren, Eero; Khiroug, Leonard (2018)
    Ketamine, a well-known anesthetic, has recently attracted renewed attention as a fast-acting antidepressant. A single dose of ketamine induces rapid synaptogenesis, which may underlie its antidepressant effect. To test whether repeated exposure to ketamine triggers sustained synaptogenesis, we administered a sub-anesthetic dose of ketamine (10 mg/kg i.p.) once-daily for 5 days, and repeatedly imaged dendritic spines of the YFP-expressing pyramidal neurons in somatosensory cortex of awake female mice using in vivo two-photon microscopy. We found that the spine formation rate became significantly higher at 72-132 h after the first ketamine injection (but not at 6-24 h), while the rate of elimination of pre-existing spines remained unchanged. In contrast to the net gain of spines observed in ketamine-treated mice, the vehicle-injected control mice exhibited a net loss typical for young-adult animals undergoing synapse pruning. Ketamine-induced spinogenesis was correlated with increased PSD-95 and phosphorylated actin, consistent with formation of new synapses. Moreover, structural synaptic plasticity caused by ketamine was paralleled by a significant improvement in the nest building behavioral assay. Taken together, our data show that subchronic low-dose ketamine induces a sustained shift towards spine formation.
  • Guirado, Ramon; Carceller, Hector; Castillo-Gomez, Esther; Castren, Eero; Nacher, Juan (2018)
    The quantification of the expression of different molecules is a key question in both basic and applied sciences. While protein quantification through molecular techniques leads to the loss of spatial information and resolution, immunohistochemistry is usually associated with time-consuming image analysis and human bias. In addition, the scarce automatic software analysis is often proprietary and expensive and relies on a fixed threshold binarization. Here we describe and share a set of macros ready for automated fluorescence analysis of large batches of fixed tissue samples using FIJI/ImageJ. The quantification of the molecules of interest are based on an automatic threshold analysis of immunofluorescence images to automatically identify the top brightest structures of each image. These macros measure several parameters commonly quantified in basic neuroscience research, such as neuropil density and fluorescence intensity of synaptic puncta, perisomatic innervation and col-localization of different molecules and analysis of the neurochemical phenotype of neuronal subpopulations. In addition, these same macro functions can be easily modified to improve similar analysis of fluorescent probes in human biopsies for diagnostic purposes based on the expression patterns of several molecules.

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