Recent Submissions

  • Shiraishi, Yutaro; Natsume, Mei; Kofuku, Yutaka; Imai, Shunsuke; Nakata, Kunio; Mizukoshi, Toshimi; Ueda, Takumi; Iwai, Hideo; Shimada, Ichio (2018)
    The C-terminal region of G-protein-coupled receptors (GPCRs), stimulated by agonist binding, is phosphorylated by GPCR kinases, and the phosphorylated GPCRs bind to arrestin, leading to the cellular responses. To understand the mechanism underlying the formation of the phosphorylated GPCR-arrestin complex, we performed NMR analyses of the phosphorylated beta(2)-adrenoceptor (beta(2)AR) and the phosphorylated beta(2)AR-beta-arrestin 1 complex, in the lipid bilayers of nanodisc. Here we show that the phosphorylated C-terminal region adheres to either the intracellular side of the transmembrane region or lipids, and that the phosphorylation of the C-terminal region allosterically alters the conformation around M215(5.54) and M279(6.41), located on transemembrane helices 5 and 6, respectively. In addition, we found that the conformation induced by the phosphorylation is similar to that corresponding to the beta-arrestin-bound state. The phosphorylation-induced structures revealed in this study propose a conserved structural motif of GPCRs that enables beta-arrestin to recognize dozens of GPCRs.
  • Nordlund, Kai Henrik (2018)
    Using energy degrading foils to slow down antiprotons is of interest for producing antihydrogen atoms. I consider here the slowing down of 100 keV antiprotons, that will be produced in the ELENA storage ring under construction at CERN, to energies below 10 keV. At these low energies, they are suitable for efficient antihydrogen production. I simulate the antihydrogen motion and slowing down in Al foils using a recently developed molecular dynamics approach. The results show that the optimal Al foil thickness for slowing down the antiprotons to below 5 keV is 910 nm, and to below 10 keV is 840 nm. Also the lateral spreading of the transmitted antiprotons is reported and the uncertainties discussed.
  • Humisto, Anu Karoliina; Jokela, Jouni Kalevi; Liu, Liwei; Wahlsten, Matti Per-Vilhelm; Wang, Hao; Permi, Perttu Esko Ilari; Machado, João Paulo; Antunes, Agostinho; Fewer, David Peter; Sivonen, Anna Kaarina (2018)
    Swinholides are 42-carbon ring polyketides with a 2-fold axis of symmetry. They are potent cytotoxins that disrupt the actin cytoskeleton. Swinholides were discovered from the marine sponge Theonella sp. and were long suspected to be produced by symbiotic bacteria. Misakinolide, a structural variant of swinholide, was recently demonstrated to be the product of a symbiotic heterotrophic proteobacterium. Here, we report the production of swinholide A by an axenic strain of the terrestrial cyanobacterium Nostoc sp. strain UHCC 0450. We located the 85-kb trans-AT polyketide synthase (PKS) swinholide biosynthesis gene cluster from a draft genome of Nostoc sp. UHCC 0450. The swinholide and misakinolide biosynthesis gene clusters share an almost identical order of catalytic domains, with 85% nucleotide sequence identity, and they group together in phylogenetic analysis. Our results resolve speculation around the true producer of swinholides and demonstrate that bacteria belonging to two distantly related phyla both produce structural variants of the same natural product. In addition, we described a biosynthesis cluster from Anabaena sp. strain UHCC 0451 for the synthesis of the cytotoxic and antifungal scytophycin. All of these biosynthesis gene clusters were closely related to each other and created a group of cytotoxic macrolide compounds produced by trans-AT PKSs of cyanobacteria and proteobacteria.
  • Baibuz, Ekaterina; Vigonski, Simon; Lahtinen, Jyri Kalevi; Zhao, Junlei; Jansson, Ville Bernt Christian; Zadin, Vahur; Djurabekova, Flyura Gatifovna (2018)
    Atomistic rigid lattice Kinetic Monte Carlo (KMC) is an efficient method for simulating nano-objects and surfaces at timescales much longer than those accessible by molecular dynamics. A laborious and non-trivial part of constructing any KMC model is, however, to calculate all migration barriers that are needed to give the probabilities for any atom jump event to occur in the simulations. We have calculated three data sets of migration barriers for Cu self-diffusion with two different methods. The data sets were specifically calculated for rigid lattice KMC simulations of copper self-diffusion on arbitrarily rough surfaces, but can be used for KMC simulations of bulk diffusion as well.
  • Yan, Lijuan; Yu, Dan; Hui, Nan; Naanuri, Eve; Viggor, Signe; Gafarov, Arslan; Sokolov, Sergei L; Heinaru, Ain; Romantschuk, Martin L. (2018)
    The Baltic Sea is vulnerable to environmental changes. With the increasing shipping activities, the risk of oil spills remains high. Archaea are widely distributed in many environments. However, the distribution and the response of archaeal communities to oil contamination have rarely been investigated in brackish habitats. Hence, we conducted a survey to investigate the distribution, diversity, composition, and species interactions of indigenous archaeal communities at oil-contaminated sites along the coast of the Gulf of Finland (GoF) using high-throughput sequencing. Surface water and littoral sediment samples were collected at presumably oil-contaminated (oil distribution facilities) and clean sites along the coastline of the GoF in the winter 2015 and the summer 2016. Another three samples of open sea surface water were taken as offshore references. Of Archaea, Euryarchaeota dominated in the surface water and the littoral sediment of the coast of the GoF, followed by Crenarchaeota (including Thaumarchaeota, Thermoprotei, and Korarchaeota based on the Greengenes database used). The unclassified sequences accounted for 5.62% of the total archaeal sequences. Our study revealed a strong dependence of the archaeal community composition on environmental variables (e.g., salinity, pH, oil concentration, TOM, electrical conductivity, and total DNA concentration) in both littoral sediment and coastal water in the GoF. The composition of archaeal communities was season and ecosystem dependent. Archaea was highly diverse in the three ecosystems (littoral sediment, coastal water, and open sea water). Littoral sediment harbored the highest diversity of archaea. Oil was often detected in the littoral sediment but rarely detected in water at those presumably contaminated sites. Although the composition of archaeal community in the littoral sediment was sensitive to low-input oil contamination, the unchanged putative functional profiles and increased interconnectivity of the archaeal core species network plausibly revealed resilience and the potential for oil degradation. Halobacteriaceae and putative cytochrome P450 pathways were significantly enriched in the oil-contaminated littoral sediment.The archaeal taxa formed highly interconnected and interactive networks, in which Halobacteriaceae, Thermococcus, and methanogens were the main components, implying a potential relevant trophic connection between hydrocarbon degradation, methanogenesis, sulfate reduction, and/or fermentative growth.
  • Veijola, Anna; Rantala, Jukka Tapani (2018)
    This article presents a study examining the historical literacy skills of Finnish (N=86) and Californian (N=131) high school students. Our goal was to discover how students read and subsequently interpret historical documents. For this purpose we created a document-based task. We analysed the data by surveying how students interpreted the documents and used them in their texts. The students were capable of identifying the content of each document and most crafted coherent conclusions based on the given sources. The most problematic aspect of historical literacy in our study was contextualising documents. However, there were differences in the results for the groups. Among the Finnish high school students, the variation was great. Those students who mastered historical content knowledge also mastered historical literacy; those whose historical content knowledge or Finnish language skills were weak also had weak historical literacy. This polarization was not evident among the Californian students we examined. However, their disciplinary literacy skills were reduced to generic text skills; students took the document-based interpretation task as a reading comprehension task and did not evaluate the authors’ intentions.
  • Reunanen, Justus; Kainulainen, Veera; Huuskonen, Laura; Ottman, Noora; Belzer, Clara; Huhtinen, Heikki; de Vos, Willem M.; Satokari, Reetta (2015)
    Akkermansia muciniphila is a Gram-negative mucin-degrading bacterium that resides in the gastrointestinal tracts of humans and animals. A. muciniphila has been linked with intestinal health and improved metabolic status in obese and type 2 diabetic subjects. Specifically, A. muciniphila has been shown to reduce high-fat-diet-induced endotoxemia, which develops as a result of an impaired gut barrier. Despite the accumulating evidence of the health-promoting effects of A. muciniphila, the mechanisms of interaction of the bacterium with the host have received little attention. In this study, we used several in vitro models to investigate the adhesion of A. muciniphila to the intestinal epithelium and its interaction with the host mucosa. We found that A. muciniphila adheres strongly to the Caco-2 and HT-29 human colonic cell lines but not to human colonic mucus. In addition, A. muciniphila showed binding to the extracellular matrix protein laminin but not to collagen I or IV, fibronectin, or fetuin. Importantly, A. muciniphila improved enterocyte monolayer integrity, as shown by a significant increase in the transepithelial electrical resistance (TER) of cocultures of Caco-2 cells with the bacterium. Further, A. muciniphila induced interleukin 8 (IL-8) production by enterocytes at cell concentrations 100-fold higher than those for Escherichia coli, suggesting a very low level of proinflammatory activity in the epithelium. In conclusion, our results demonstrate that A. muciniphila adheres to the intestinal epithelium and strengthens enterocyte monolayer integrity in vitro, suggesting an ability to fortify an impaired gut barrier. These results support earlier associative in vivo studies and provide insights into the interaction of A. muciniphila with the host.
  • Ottman, Noora; Smidt, Hauke; Vos de, Willem M.; Belzer, Clara (2012)
    Current meta-omics developments provide a portal into the functional potential and activity of the intestinal microbiota. The comparative and functional meta-omics approaches have made it possible to get a molecular snap shot of microbial function at a certain time and place. To this end, metagenomics is a DNA-based approach, metatranscriptomics studies the total transcribed RNA, metaproteomics focuses on protein levels and metabolomics describes metabolic profiles. Notably, the metagenomic toolbox is rapidly expanding and has been instrumental in the generation of draft genome sequences of over 1000 human associated microorganisms as well as an astonishing 3.3 million unique microbial genes derived from the intestinal tract of over 100 European adults. Remarkably, it appeared that there are at least 3 clusters of co-occurring microbial species, termed enterotypes, that characterize the intestinal microbiota throughout various continents. The human intestinal microbial metagenome further revealed unique functions carried out in the intestinal environment and provided the basis for newly discovered mechanisms for signaling, vitamin production and glycan, amino-acid and xenobiotic metabolism. The activity and composition of the microbiota is affected by genetic background, age, diet, and health status of the host. In its turn the microbiota composition and activity influence host metabolism and disease development. Exemplified by the differences in microbiota composition and activity between breast- as compared to formula-fed babies, healthy and malnourished infants, elderly and centenarians as compared to youngsters, humans that are either lean or obese and healthy or suffering of inflammatory bowel diseases (IBD). In this review we will focus on our current understanding of the functionality of the human intestinal microbiota based on all available metagenome, metatranscriptome, and metaproteome results
  • Qiao, Jixin; Lagerkvist, Petra; Rodushkin, Ilia; Salminen-Paatero, Marke Susanna; Roos, Per; Lierhagen, Syverin; Jensen, Karl Andreas; Engström, Emma; Skipperud, Lindis (NKS Secretariat, 2018)
    NKS report series
    Inductively coupled plasma (ICP) spectrometry techniques are widely used in the fields related to environmental monitoring, nuclear waste disposal and management, radioecology and tracer studies, as well as nuclear forensics and nuclear emergency preparedness. Especially ICP mass spectrometry (ICP-MS) is playing an important role for determination of low-level long-lived radionuclides and their isotopic ratios. ICP optical emission spectrometry (ICP-OES) is commonly used for determining stable elements (Al, Fe, Ca, etc.) and cannot perform isotopic ratio measurement with desirable precision and at low analyte concentrations. Therefore ICP-OES is often used as a supplementary technique to ICP-MS in the analysis, for instance, to screen the matrix composition of a sample, or to determine Sr and Y chemical yield in the Sr-90 analysis, etc. Among the Nordic countries, there are probably less than 20 ICP-MS instruments which are currently applied in the nuclear field for the measurement of radionuclides and their isotopic ratios. Due to different application purposes and technical background of the analysts, each ICP lab has different set-ups and experiences in running these instruments. More efficient application of ICP-MS will be achieved when these experiences are well shared among these labs. Also, for newly established ICP labs or scientists/students in the Nordic countries to quickly build up the competence in operating their instruments in practice, hands-on experience is very valuable. Therefore, within the Nordic-ICP project, an inter-comparison exercise was performed during 2016, which was focused on the measurement of uranium and plutonium isotopes in certified reference material by ICP-MS in combination with radiochemical separation. This report summarizes the results and conclusions obtained base on this inter-comparison exercise.
  • Villnäs, Anna; Norkko, Joanna; Hietanen, Susanna; Josefson, Alf; Lukkari, Kaarina; Norkko, Alf (2013)
    Ecosystem functioning is threatened by an increasing number of anthropogenic stressors, creating a legacy of disturbance that undermines ecosystem resilience. However, few empirical studies have assessed to what extent an ecosystem can tolerate repeated disturbances and sustain its multiple functions. By inducing increasingly recurring hypoxic disturbances to a sedimentary ecosystem, we show that the majority of individual ecosystem functions experience gradual degradation patterns in response to repetitive pulse disturbances. The degradation in overall ecosystem functioning was, however, evident at an earlier stage than for single ecosystem functions and was induced after a short pulse of hypoxia (i.e., three days), which likely reduced ecosystem resistance to further hypoxic perturbations. The increasing number of repeated pulse disturbances gradually moved the system closer to a press response. In addition to the disturbance regime, the changes in benthic trait composition as well as habitat heterogeneity were important for explaining the variability in overall ecosystem functioning. Our results suggest that disturbance-induced responses across multiple ecosystem functions can serve as a warning signal for losses of the adaptive capacity of an ecosystem, and might at an early stage provide information to managers and policy makers when remediation efforts should be initiated.
  • Roine, Ulrika; Salmi, Juha; Roine, Timo; Nieminen-von Wendt, Taina; Leppämäki, Sami; Rintahaka, Pertti; Tani, Pekka; Leemans, Alexander; Sams, Mikko (2015)
  • Roine, Ulrika; Roine, Timo; Salmi, Juha; Nieminen-von Wendt, Taina; Tani, Pekka; Leppämäki, Sami; Rintahaka, Pertti; Caeyenberghs, Karen; Leemans, Alexander; Sams, Mikko (2015)
    Background: Recent brain imaging findings suggest that there are widely distributed abnormalities affecting the brain connectivity in individuals with autism spectrum disorder (ASD). Using graph theoretical analysis, it is possible to investigate both global and local properties of brain's wiring diagram, i.e., the connectome. Methods: We acquired diffusion-weighted magnetic resonance imaging data from 14 adult males with high-functioning ASD and 19 age-, gender-, and IQ-matched controls. As with diffusion tensor imaging-based tractography, it is not possible to detect complex (e.g., crossing) fiber configurations, present in 60-90 % of white matter voxels; we performed constrained spherical deconvolution-based whole brain tractography. Unweighted and weighted structural brain networks were then reconstructed from these tractography data and analyzed with graph theoretical measures. Results: In subjects with ASD, global efficiency was significantly decreased both in the unweighted and the weighted networks, normalized characteristic path length was significantly increased in the unweighted networks, and strength was significantly decreased in the weighted networks. In the local analyses, betweenness centrality of the right caudate was significantly increased in the weighted networks, and the strength of the right superior temporal pole was significantly decreased in the unweighted networks in subjects with ASD. Conclusions: Our findings provide new insights into understanding ASD by showing that the integration of structural brain networks is decreased and that there are abnormalities in the connectivity of the right caudate and right superior temporal pole in subjects with ASD.
  • Nicolle, Marie; Debret, Maxime; Massei, Nicolas; Colin, Christophe; deVernal, Anne; Divine, Dmitri; Werner, Jojannes P.; Hormes, Anne; Korhola, Atte Antero; Linderholm, Hans W. (2018)
    To put recent climate change in perspective, it is necessary to extend the instrumental climate records with proxy data from paleoclimate archives. Arctic climate variability for the last 2 millennia has been investigated using statistical and signal analyses from three regionally averaged records from the North Atlantic, Siberia and Alaska based on many types of proxy data archived in the Arctic 2k database v1.1.1. In the North Atlantic and Alaska, the major climatic trend is characterized by long-term cooling interrupted by recent warming that started at the beginning of the 19th century. This cooling is visible in the Siberian region at two sites, warming at the others. The cooling of the Little Ice Age (LIA) was identified from the individual series, but it is characterized by wide-range spatial and temporal expression of climate variability, in contrary to the Medieval Climate Anomaly. The LIA started at the earliest by around AD1200 and ended at the latest in the middle of the 20th century. The widespread temporal coverage of the LIA did not show regional consistency or particular spatial distribution and did not show a relationship with archive or proxy type either. A focus on the last 2 centuries shows a recent warming characterized by a well-marked warming trend parallel with increasing greenhouse gas emissions. It also shows a multidecadal variability likely due to natural processes acting on the internal climate system on a regional scale. A 16–30-year cycle is found in Alaska and seems to be linked to the Pacific Decadal Oscillation, whereas 20–30- and 50–90-year periodicities characterize the North Atlantic climate variability, likely in relation with the Atlantic Multidecadal Oscillation. These regional features are probably linked to the sea ice cover fluctuations through ice–temperature positive feedback.
  • Snelgrove, Paul V.R.; Soetaert, Karline; Solan, Martin; Thrush, Simon; Wei, Chih-Lin; Danovaro, Roberto; Fulweiler, Robinson W.; Kitazato, Hiroshi; Ingole, Baban; Norkko, Alf; Parkes, R. John; Volkenborn, Nils (2018)
    Diverse biological communities mediate the transformation, transport, and storage of elements fundamental to life on Earth, including carbon, nitrogen, and oxygen. However, global biogeochemical model outcomes can vary by orders of magnitude, compromising capacity to project realistic ecosystem responses to planetary changes, including ocean productivity and climate. Here, we compare global carbon turnover rates estimated using models grounded in biological versus geochemical theory and argue that the turnover estimates based on each perspective yield divergent outcomes. Importantly, empirical studies that include sedimentary biological activity vary less than those that ignore it. Improving the relevance of model projections and reducing uncertainty associated with the anticipated consequences of global change requires reconciliation of these perspectives, enabling better societal decisions on mitigation and adaptation.
  • Huttunen, Niko Ilari (Suomen eksegeettinen seura, 2016)
    Suomen Eksegeettisen Seuran julkaisuja