Articles from TUHAT CRIS

 

Kokoelma sisältää TUHAT-tutkimustietojäjestelmän kautta tallennetut Open Access-artikkelit.

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

This collection contains Open Access articles deposited from the University of Helsinki TUHAT CRIS

Recent Submissions

  • Aitamurto, Kaarina (E-International Relations Publishing, 2015)
  • Saarinen, Risto (Centre d'études Istina, 2014)
  • Salonen, Minna K.; Wasenius, Niko; Kajantie, Eero; Lano, Aulikki; Lahti, Jari; Heinonen, Kati; Räikkönen, Katri; Eriksson, Johan G. (Public Library of Science, 2015)
    Objective Low physical activity (PA) is a major risk factor for cardiovascular and metabolic disorders in all age groups. We measured intensity and volume of PA and examined the associations between PA and the metabolic syndrome (MS), its components and body composition among young Finnish adults. Research Design and Methods The study comprises 991 men and women born 1985-86, who participated in a clinical study during the years 2009-11 which included assessments of metabolism, body composition and PA. Objectively measured (SenseWear Armband) five-day PA data was available from 737 participants and was expressed in metabolic equivalents of task (MET). Results The prevalence of MS ranged between 8-10%. Higher total mean volume (MET-hours) or intensity (MET) were negatively associated with the risk of MS and separate components of MS, while the time spent at sedentary level of PA was positively associated with MS. Conclusions MS was prevalent in approximately every tenth of the young adults at the age of 24 years. Higher total mean intensity and volume rates as well as longer duration spent at moderate and vigorous PA level had a beneficial impact on the risk of MS. Longer time spent at the sedentary level of PA increased the risk of MS.
  • Cousminer, Diana L.; Leinonen, Jaakko T.; Sarin, Antti-Pekka; Chheda, Himanshu; Surakka, Ida; Wehkalampi, Karoliina; Ellonen, Pekka; Ripatti, Samuli; Dunkel, Leo; Palotie, Aarno; Widen, Elisabeth (Public Library of Science, 2015)
    Constitutional delay of growth and puberty (CDGP) is the most common cause of pubertal delay. CDGP is defined as the proportion of the normal population who experience pubertal onset at least 2 SD later than the population mean, representing 2.3% of all adolescents. While adolescents with CDGP spontaneously enter puberty, they are at risk for short stature, decreased bone mineral density, and psychosocial problems. Genetic factors contribute heavily to the timing of puberty, but the vast majority of CDGP cases remain biologically unexplained, and there is no definitive test to distinguish CDGP from pathological absence of puberty during adolescence. Recently, we published a study identifying significant linkage between a locus at the pericentromeric region of chromosome 2 (chr 2) and CDGP in Finnish families. To investigate this region for causal variation, we sequenced chr 2 between the genomic coordinates of 79-124 Mb (genome build GRCh37) in the proband and affected parent of the 13 families contributing most to this linkage signal. One gene, DNAH6, harbored 6 protein-altering low-frequency variants (<6% in the Finnish population) in 10 of the CDGP probands. We sequenced an additional 135 unrelated Finnish CDGP subjects and utilized the unique Sequencing Initiative Suomi (SISu) population reference exome set to show that while 5 of these variants were present in the CDGP set, they were also present in the Finnish population at similar frequencies. Additional variants in the targeted region could not be prioritized for follow-up, possibly due to gaps in sequencing coverage or lack of functional knowledge of non-genic genomic regions. Thus, despite having a well-characterized sample collection from a genetically homogeneous population with a large population-based reference sequence dataset, we were unable to pinpoint variation in the linked region predisposing delayed puberty. This study highlights the difficulties of detecting genetic variants under linkage regions for complex traits and suggests that advancements in annotation of gene function and regulatory regions of the genome will be critical for solving the genetic background of complex phenotypes like CDGP.
  • Ruokanen, Miikka (VANDENHOECK UND RUPRECHT, 2013)
  • Ruokanen, Miikka; Chen, Yongtao; Liu, Ruomin (World Council of Churches, 2015)
  • Kaasalainen, Ulla; Olsson, Sanna Elina; Rikkinen, Jouko Kalevi (Public Library of Science, 2015)
    The group I intron interrupting the tRNALeu UAA gene (trnL) is present in most cyanobacterial genomes as well as in the plastids of many eukaryotic algae and all green plants. In lichen symbiotic Nostoc, the P6b stem-loop of trnL intron always involves one of two different repeat motifs, either Class I or Class II, both with unresolved evolutionary histories. Here we attempt to resolve the complex evolution of the two different trnL P6b region types. Our analysis indicates that the Class II repeat motif most likely appeared first and that independent and unidirectional shifts to the Class I motif have since taken place repeatedly. In addition, we compare our results with those obtained with other genetic markers and find strong evidence of recombination in the 16S rRNA gene, a marker widely used in phylogenetic studies on Bacteria. The congruence of the different genetic markers is successfully evaluated with the recently published software Saguaro, which has not previously been utilized in comparable studies.
  • Kohonen, Jukka; Corander, Jukka (TAYLOR & FRANCIS INC., 2015)
    An exponential-time exact algorithm is provided for the task of clustering n items of data into k clusters. Instead of seeking one partition, posterior probabilities are computed for summary statistics: the number of clusters, and pairwise co-occurrence. The method is based on subset convolution, and yields the posterior distribution for the number of clusters in O(n 3^n) operations, or O(n^3 2^n) using fast subset convolution. Pairwise co-occurrence probabilities are then obtained in O(n^3 2^n) operations. This is considerably faster than exhaustive enumeration of all partitions.
  • Heinonen, Jussi S.; Kurz, Mark D. (ELSEVIER BV, 2015)
    The massive outpourings of Karoo and Ferrar continental flood basalts (CFBs) ~180 Ma ago mark the initial Jurassic rifting stages of the Gondwana supercontinent. The origin and sources of these eruptions have been debated for decades, largely due to difficulties in defining their parental melt and mantle source characteristics. Recent findings of Fe- and Mg-rich dikes (depleted ferropicrite suite) from Vestfjella, western Dronning Maud Land, Antarctica, have shed light on the composition of the deep sub-Gondwanan mantle: these magmas have been connected to upper mantle sources presently sampled by the Southwest Indian Ocean mid-ocean ridge basalts (SWIR MORBs) or to high 3He/4He plume-entrained non-chondritic primitive mantle sources formed early in Earth’s history. In an attempt to determine their He isotopic composition and relative contributions from magmatic, cosmogenic, and radiogenic He sources, we performed in-vacuo stepwise crushing and melting analyses of olivine mineral separates, some of which were abraded to remove the outer layer. The best estimate for the mantle isotopic composition is given by a sample with the highest amount of He released (> 50%) during the first crushing step of an abraded coarse fraction. It has a 3He/4He of 7.03 ± 0.23 (2σ) times the atmospheric ratio (Ra), which is indistinguishable from those measured from SWIR MORBs (6.3‒7.3 Ra; source 3He/4He ~6.4–7.6 Ra at 180 Ma) and notably lower than in the most primitive lavas from the North Atlantic Igneous Province (up to 50 Ra), considered to represent the epitome magmas from non-chondritic primitive mantle sources. Previously published trace element and isotopic (Sr, Nd, and Pb) compositions do not suggest a direct genetic link to any modern hotspot of Indian or southern Atlantic Oceans. Although influence of a mantle plume cannot be ruled out, the high magma temperatures and SWIR MORB-like geochemistry of the suite are best explained by supercontinent insulation of a precursory Indian Ocean upper mantle source. Such a model is also supported by the majority of the recent studies on the structure, geochronology, and petrology of the Karoo CFBs.
  • Heinonen, Jussi S.; Jennings, Eleanor S.; Riley, Teal R. (ELSEVIER BV, 2015)
    Calculating reliable temperatures of Mg-rich magmas is problematic because melt composition and KD(Fe-Mg)ol-liq, the key parameters of many traditional thermometers, are difficult to constrain precisely. The recently developed Al-in-olivine thermometer [Coogan, L.A., Saunders, A.D., Wilson, R.N., 2014. Aluminum-in-olivine thermometry of primitive basalts: Evidence of an anomalously hot mantle source for large igneous provinces. Chemical Geology 368, 1–10] circumvents these problems by relying on the temperature-dependent exchange of Al between olivine and spinel crystallising in equilibrium with each other. This thermometer is used to re-evaluate the crystallisation temperatures of the most Mg-rich magma type identified from the Karoo large igneous province (LIP), known as the Vestfjella depleted ferropicrite suite. Previous temperature estimates for the suite were based on olivine-melt equilibria and indicated anomalously high crystallisation temperatures in excess of 1600 °C. We also present crystallisation temperatures for another Antarctic Karoo magma type, Group 3 dykes from Ahlmannryggen, which are derived from a pyroxene-rich mantle source. Our high-precision analysis of Al in olivine-spinel pairs indicate crystallisation temperatures from 1391±42 °C to 1481±35 °C for the Vestfjella depleted ferropicrite suite (Fo88–92) and from 1253±64 °C to 1303±40 °C for the Group 3 dykes (Fo79–82). Although the maximum temperature estimates for the former are over 100 °C lower than the previously presented estimates, they are still ~200 °C higher than those calculated for mid-ocean ridge basalts using the same method. Although exact mantle potential temperatures are difficult to estimate, the presented results support elevated sub-Gondwanan upper mantle temperatures (generated by a mantle plume or internal mantle heating) during the generation of the Karoo LIP.
  • Hella, Lauri; Väänänen, Jouko (de Gruyter, 2015)
    We introduce a refinement of the usual Ehrenfeucht-Fra\"{\i}ss\'e game. The new game will help us make finer distinctions than the traditional one. In particular, it can be used to measure the size formulas needed for expressing a given property. We will give two versions of the game: the first version characterizes the size of formulas in propositional logic, and the second version works for first-order predicate logic.
  • Du, Mian; Pierce, Matthew; Pivovarova, Lidia; Yangarber, Roman (2015)
  • Bourdais, Gildas; Burdiak, Pawel; Gauthier, Adrien Guy Bernard; Nitsch, Lisette; Salojärvi, Jarkko Tapani; Rayapuram, Channabasavangowda; Idänheimo, Niina Johanna; Hunter, Kerri Alyssa; Kimura, Sachie; Merilo, Ebe; Vaattovaara, Aleksia Fanni Maria; Oracz, Krystyna; Kaufholdt, David; Pallon, Andres; Anggoro, Damar Tri; Glow, Dawid; Lowe, Jennifer; Zhou, Ji; Mohammadi, Omid; Puukko, Tuomas; Albert, Andreas; Lang, Hans; Ernst, Dieter; Kollist, Hannes; Brosche, Mikael Johan; Durner, Jörg; Borst, Jan Willem; Collinge, David B.; Karpinski, Stanislaw; Lyngkjaer, Michael F.; Robatzek, Silke; Wrzaczek, Michael Alois; Kangasjärvi, Jaakko Sakari (PUBLIC LIBRARY OF SCIENCE, 2015)
    Cysteine-rich receptor-like kinases (CRKs) are transmembrane proteins characterized by the presence of two domains of unknown function 26 (DUF26) in their ectodomain. The CRKs form one of the largest groups of receptor-like protein kinases in plants, but their biological functions have so far remained largely uncharacterized. We conducted a large-scale phenotyping approach of a nearly complete crk T-DNA insertion line collection showing that CRKs control important aspects of plant development and stress adaptation in response to biotic and abiotic stimuli in a non-redundant fashion. In particular, the analysis of reactive oxygen species (ROS)-related stress responses, such as regulation of the stomatal aperture, suggests that CRKs participate in ROS/redox signalling and sensing. CRKs play general and fine-tuning roles in the regulation of stomatal closure induced by microbial and abiotic cues. Despite their great number and high similarity, large-scale phenotyping identified specific functions in diverse processes for many CRKs and indicated that CRK2 and CRK5 play predominant roles in growth regulation and stress adaptation, respectively. As a whole, the CRKs contribute to specificity in ROS signalling. Individual CRKs control distinct responses in an antagonistic fashion suggesting future potential for using CRKs in genetic approaches to improve plant performance and stress tolerance.
  • Ayvaz, Muavviz; Guven, Avni; Fagerstedt, Kurt Valter (DIAGNOSIS PRESS LTD., 2015)