Recent Submissions

  • Aitamurto, Kaarina (E-International Relations Publishing, 2015)
    E-IR Edited Collections
  • 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)
  • Ito, Akira; Okamoto, Munehiro; Li, Tiaoying; Wandra, Toni; Dharmawan, Nyoman S; Swastika, Kadek I; Dekumyoy, Paron; Kusolsuk, Teera; Davvajav, Abmed; Davaasuren, Anu; Dorjsuren, Temuulen; Mekonnen, Sissay M; Negasi, Zerihun H; Yanagida, Tetsuya; Sako, Yasuhito; Nakao, Minoru; Nakaya, Kazuhiro; Lavikainen, Antti J; Nkouawa, Agathe; Mohammadzadeh, Tahereh (BioMed Central, 2011)
    Abstract The first workshop towards the control of cestode zoonoses in Asia and Africa was held in Asahikawa Medical University, Japan on 15 and 16 Feb 2011. This meeting was fully supported by the Asian Science and Technology Strategic Cooperation Promotion Programs sponsored by the Special Coordination Funds for Promoting Science and Technology, the Ministry of Education Japan (MEXT) for 3 years from 2010 to Akira Ito. A total of 24 researchers from 9 countries joined together and discussed the present situation and problems towards the control of cestode zoonoses. As the meeting was simultaneously for the establishment of joint international, either bilateral or multilateral collaboration projects, the main purposes were directed to 1) how to detect taeniasis/cysticercosis infected patients, 2) how to differentiate Taenia solium from two other human Taenia species, T. saginata and T. asiatica, 3) how to evaluate T. asiatica based on the evidence of hybrid and hybrid-derived adult tapeworms from Thailand and China, 4) how to evaluate T. solium and T. hyaenae and other Taenia species from the wild animals in Ethiopia, and 5) how to detect echinococcosis patients and 6) how to differentiate Echinococcus species worldwide. Such important topics are summarized in this meeting report.
  • 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.
  • Bien, Justyna; Näreaho, Anu; Varmanen, Pekka; Gozdzik, Katarzyna; Moskwa, Bozena; Cabaj, Wladyslaw; Nyman, Tuula A; Savijoki, Kirsi (BioMed Central, 2012)
    Abstract Background Trichinellosis is a zoonotic disease in humans caused by Trichinella spp. The present study was undertaken to discover excretory-secretory (E-S) proteins from T. spiralis and T. britovi muscle larvae (ML) that hold promise for species-specific diagnostics. To that end, the purified E-S proteins were analyzed by fluorescent two-dimensional difference gel electrophoresis (2-D DIGE) coupled with protein identification by liquid chromatography-tandem mass spectrometry (LC-MS/MS). To search for immunoreactive proteins that are specifically recognized by host antibodies the E-S proteins were subjected to two-dimensional (2-DE) immunoblotting with antisera derived from pigs experimentally infected with T. spiralis or T. britovi. Results According to 2-D DIGE analysis, a total of twenty-two proteins including potentially immunogenic proteins and proteins produced only by one of the two Trichinella species were subjected to LC-MS/MS for protein identification. From these proteins seventeen could be identified, of which many were identified in multiple spots, suggesting that they have undergone post-translational modification, possibly involving glycosylation and/or proteolysis. These proteins included 5'-nucleotidase, serine-type protease/proteinase, and p43 glycoprotein (gp43) as well as 49 kDa E-S protein (p49). Our findings also suggest that some of the commonly identified proteins were post-translationally modified to different extents, which in certain cases seemed to result in species-specific modification. Both commonly and specifically recognized immunoreactive proteins were identified by 2-DE immunoblotting; shared antigens were identified as gp43 and different protease variants, whereas those specific to T. britovi included multiple isoforms of the 5'-nucleotidase. Conclusions Both 2-D DIGE and 2-DE immunoblotting approaches indicate that T. spiralis and T. britovi produce somewhat distinctive antigen profiles, which contain E-S antigens with potential as species-specific diagnostic markers for Trichinella. Our results also demonstrate the value of 2-D DIGE as a versatile tool to compare secretomes of different Trichinella species for pinpointing factors contributing to the interaction with the host.
  • Koli, Raika; Köhler, Klaus; Tonteri, Elina; Peltonen, Juha; Tikkanen, Heikki; Fogelholm, Mikael (BioMed Central, 2015)
    Abstract Background Several studies have shown that cocoa and cocoa-containing foods have the potential to lower blood pressure and improve endothelial function. Most of the studies reporting the beneficial effects of dark chocolate on blood pressure have been short (≤ 4 weeks). The aim of the present 8-wks (weeks) study was to assess the effects of regular consumption of dark chocolate during a reduced snack consumption intervention on blood pressure and other cardiovascular risk factors in mildly hypertensive individuals. Design This was a randomized, controlled, cross-over trial involving 22 adults (8 women, 14 men), aged 33–64 y, BMI 27.7 ± 3.7 kg/m2 with mild hypertension. During the intervention period (8-wks) the participants reduced the intake of habitual snacks and replaced them with dark chocolate (49 g/day). In the control period, they only reduced the snacks without any added chocolate. Data (blood lipid profile, glucose, insulin, 24 h blood pressure) was collected in the beginning and end of both periods (intervention and control), and some variables also in the run-in and run-out periods (weight, body fat percentage, blood pressure, arterial stiffness index, diet and physical activity). Results Daily consumption of dark chocolate had no effects on 24 h blood pressure, resting blood pressure (mean ± SD, pre 142 ± 11.5/89 ± 8.4 mmHg vs. post 142 ± 14.2/88 ± 9.4 mmHg in systolic and diastolic blood pressure, respectively) or arterial stiffness (mean ± SD, pre 7.68 ± 0.88 vs. post 7.76 ± 0.89). Weight was reduced by 1.0 ± 2.2 kg during the control (reduced snack only) period, but was unchanged while eating chocolate (p < 0.027 between the treatments). Conclusion The data collected in this study indicates that inclusion of dark chocolate daily in the diet had no significant effects on blood pressure or other cardiovascular risk factors during a reduced snack period. Trial registration identifier NCT02130141
  • Antonios, Gregory; Saiepour, Nasrin; Bouter, Yvonne; Richard, Bernhard C; Paetau, Anders; Verkkoniemi-Ahola, Auli; Lannfelt, Lars; Ingelsson, Martin; Kovacs, Gabor G; Pillot, Thierry; Wirths, Oliver; Bayer, Thomas A (BioMed Central, 2013)
    Abstract Background The amyloid hypothesis in Alzheimer disease (AD) considers amyloid β peptide (Aβ) deposition causative in triggering down-stream events like neurofibrillary tangles, cell loss, vascular damage and memory decline. In the past years N-truncated Aβ peptides especially N-truncated pyroglutamate AβpE3-42 have been extensively studied. Together with full-length Aβ1–42 and Aβ1–40, N-truncated AβpE3-42 and Aβ4–42 are major variants in AD brain. Although Aβ4–42 has been known for a much longer time, there is a lack of studies addressing the question whether AβpE3-42 or Aβ4–42 may precede the other in Alzheimer’s disease pathology. Results Using different Aβ antibodies specific for the different N-termini of N-truncated Aβ, we discovered that Aβ4-x preceded AβpE3-x intraneuronal accumulation in a transgenic mouse model for AD prior to plaque formation. The novel Aβ4-x immunoreactive antibody NT4X-167 detected high molecular weight aggregates derived from N-truncated Aβ species. While NT4X-167 significantly rescued Aβ4–42 toxicity in vitro no beneficial effect was observed against Aβ1–42 or AβpE3-42 toxicity. Phenylalanine at position four of Aβ was imperative for antibody binding, because its replacement with alanine or proline completely prevented binding. Although amyloid plaques were observed using NT4X-167 in 5XFAD transgenic mice, it barely reacted with plaques in the brain of sporadic AD patients and familial cases with the Arctic, Swedish and the presenilin-1 PS1Δ9 mutation. A consistent staining was observed in blood vessels in all AD cases with cerebral amyloid angiopathy. There was no cross-reactivity with other aggregates typical for other common neurodegenerative diseases showing that NT4X-167 staining is specific for AD. Conclusions Aβ4-x precedes AβpE3-x in the well accepted 5XFAD AD mouse model underlining the significance of N-truncated species in AD pathology. NT4X-167 therefore is the first antibody reacting with Aβ4-x and represents a novel tool in Alzheimer research.
  • Syrjänen, Leo; Valanne, Susanna; Kuuslahti, Marianne; Tuomela, Tea; Sriram, Ashwin; Sanz, Alberto; Jacobs, Howard T; Rämet, Mika; Parkkila, Seppo (BioMed Central, 2015)
    Abstract Background Carbonic anhydrases (CAs, EC are ubiquitous enzymes that catalyze the reversible hydration reaction of carbon dioxide. CAs are present as six structurally divergent enzyme families: α, β, γ, δ, ζ and η. β-CAs have a wide distribution across different species including invertebrates. Previously, we showed that Drosophila melanogaster β-CA is a highly active mitochondrial enzyme. In this study, we investigated the function of Drosophila β-CA by silencing the expression of the β-CA gene using UAS/GAL4-based RNA interference (RNAi) in Drosophila in vivo. Results Crossing β-CA RNAi lines over ubiquitous Actin driver flies did not produce any viable progeny, indicating that β-CA expression is required for fly development. RNAi silencing of β-CA ubiquitously in adult flies did not affect their survival rate or function of mitochondrial electron transport chain. Importantly, β-CA RNAi led to impaired reproduction. All β-CA knockdown females were sterile, and produced few or no eggs. Whole ovaries of knockdown females looked normal but upon cadherin staining, there was an apparent functional defect in migration of border cells, which are considered essential for normal fertilization. Conclusions These results indicate that although Drosophila β-CA is dispensable for survival of adult flies, it is essential for female fertility.
  • 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.