Recent Submissions

  • Pihlatie, Mari; Rannik, Ullar; Haapanala, Sami; Peltola, Olli; Shurpali, Narasinha; Martikainen, Pertti J.; Lind, Saara; Hyvönen, Niina; Virkajärvi, Perttu; Zahniser, Mark; Mammarella, Ivan (COPERNICUS GESELLSCHAFT MBH, 2016)
    Carbon monoxide (CO) is an important reactive trace gas in the atmosphere, while its sources and sinks in the biosphere are poorly understood. Soils are generally considered as a sink of CO due to microbial oxidation processes, while emissions of CO have been reported from a wide range of soil-plant systems. We measured CO fluxes using the micrometeorological eddy covariance method from a bioenergy crop (reed canary grass) in eastern Finland from April to November 2011. Continuous flux measurements allowed us to assess the seasonal and diurnal variability and to compare the CO fluxes to simultaneously measured net ecosystem exchange of CO2, N2O and heat fluxes as well as to relevant meteorological, soil and plant variables in order to investigate factors driving the CO exchange. The reed canary grass (RCG) crop was a net source of CO from mid-April to mid-June and a net sink throughout the rest of the measurement period from mid-June to November 2011, excluding a measurement break in July. CO fluxes had a distinct diurnal pattern with a net CO uptake in the night and a net CO emission during the daytime with a maximum emission at noon. This pattern was most pronounced in spring and early summer. During this period the most significant relationships were found between CO fluxes and global radiation, net radiation, sensible heat flux, soil heat flux, relative humidity, N2O flux and net ecosystem exchange. The strong positive correlation between CO fluxes and radiation suggests abiotic CO production processes, whereas the relationship between CO fluxes and net ecosystem exchange of CO2, and night-time CO fluxes and N2O emissions indicate biotic CO formation and microbial CO uptake respectively. The study shows a clear need for detailed process studies accompanied by continuous flux measurements of CO exchange to improve the understanding of the processes associated with CO exchange.
  • Pentinsaari, Mikko; Salmela, Heli; Mutanen, Marko; Roslin, Tomas (NATURE PUBLISHING GROUP, 2016)
  • Knight, Anna K.; Craig, Jeffrey M.; Theda, Christiane; Baekvad-Hansen, Marie; Bybjerg-Grauholm, Jonas; Hansen, Christine S.; Hollegaard, Mads V.; Hougaard, David M.; Mortensen, Preben B.; Weinsheimer, Shantel M.; Werge, Thomas M.; Brennan, Patricia A.; Cubells, Joseph F.; Newport, D. Jeffrey; Stowe, Zachary N.; Cheong, Jeanie L. Y.; Dalach, Philippa; Doyle, Lex W.; Loke, Yuk J.; Baccarelli, Andrea A.; Just, Allan C.; Wright, Robert O.; Tellez-Rojo, Mara M.; Svensson, Katherine; Trevisi, Letizia; Kennedy, Elizabeth M.; Binder, Elisabeth B.; Iurato, Stella; Räikkönen, Katri; Lahti, Jari M. T.; Pesonen, Anu-Katriina; Kajantie, Eero; Villa, Pia M.; Laivuori, Hannele; Hämäläinen, Esa; Park, Hea Jin; Bailey, Lynn B.; Parets, Sasha E.; Kilaru, Varun; Menon, Ramkumar; Horvath, Steve; Bush, Nicole R.; LeWinn, Kaja Z.; Tylavsky, Frances A.; Conneely, Karen N.; Smith, Alicia K. (BioMed Central, 2016)
    Background: Gestational age is often used as a proxy for developmental maturity by clinicians and researchers alike. DNA methylation has previously been shown to be associated with age and has been used to accurately estimate chronological age in children and adults. In the current study, we examine whether DNA methylation in cord blood can be used to estimate gestational age at birth. Results: We find that gestational age can be accurately estimated from DNA methylation of neonatal cord blood and blood spot samples. We calculate a DNA methylation gestational age using 148 CpG sites selected through elastic net regression in six training datasets. We evaluate predictive accuracy in nine testing datasets and find that the accuracy of the DNA methylation gestational age is consistent with that of gestational age estimates based on established methods, such as ultrasound. We also find that an increased DNA methylation gestational age relative to clinical gestational age is associated with birthweight independent of gestational age, sex, and ancestry. Conclusions: DNA methylation can be used to accurately estimate gestational age at or near birth and may provide additional information relevant to developmental stage. Further studies of this predictor are warranted to determine its utility in clinical settings and for research purposes. When clinical estimates are available this measure may increase accuracy in the testing of hypotheses related to developmental age and other early life circumstances.
  • Paloniitty née Korvela, Tiina (Edward Elgar Publishing, 2015)
  • Hytönen, Marjo K.; Arumilli, Meharji; Lappalainen, Anu K.; Owczarek-Lipska, Marta; Jagannathan, Vidhya; Hundi, Sruthi; Salmela, Elina; Venta, Patrick; Sarkiala, Eva; Jokinen, Tarja; Gorgas, Daniela; Kere, Juha; Nieminen, Pekka; Drögemüller, Cord; Lohi, Hannes (PUBLIC LIBRARY OF SCIENCE, 2016)
  • Selonen, Vesa; Wistbacka, Ralf; Santangeli, Andrea (BioMed Central, 2016)
    Background: Reproductive strategies and evolutionary pressures differ between males and females. This often results in size differences between the sexes, and also in sex-specific seasonal variation in body mass. Seasonal variation in body mass is also affected by other factors, such as weather. Studies on sex-specific body mass patterns may contribute to better understand the mating system of a species. Here we quantify patterns underlying sex-specific body mass variation using a long-term dataset on body mass in the Siberian flying squirrel, Pteromys volans. Results: We show that female flying squirrels were larger than males based on body mass and other body measures. Males had lowest body mass after the breeding season, whereas female body mass was more constant between seasons, when the pregnancy period was excluded. Male body mass did not increase before the mating season, despite the general pattern that males with higher body mass are usually dominant in squirrel species. Seasonal body mass variation was linked to weather factors, but this relationship was not straightforward to interpret, and did not clearly affect the trend in body mass observed over the 22 years of study. Conclusions: Our study supports the view that arboreal squirrels often deviate from the general pattern found in mammals for larger males than females. The mating system seems to be the main driver of sex-specific seasonal body mass variation in flying squirrels, and conflicting selective pressure may occur for males to have low body mass to facilitate gliding versus high body mass to facilitate dominance.
  • Teramura-Gronblad, Mariko; Raivio, Minna; Savikko, Niina; Muurinen, Seija; Soini, Helena; Suominen, Merja; Pitkala, Kaisu (TAYLOR & FRANCIS LTD, 2016)
    Objective: This study aims to assess potentially severe class D drug-drug interactions (DDDIs) in residents 65 years or older in assisted living facilities with the use of a Swedish and Finnish drug-drug interaction database (SFINX). Design: A cross-sectional study of residents in assisted living facilities in Helsinki, Finland. Setting: A total of 1327 residents were assessed in this study. Drugs were classified according to the Anatomical Therapeutic Chemical (ATC) classification system and DDDIs were coded according to the SFINX. Main outcome measures: Prevalence of DDDIs, associated factors and 3-year mortality among residents. Results: Of the participants (mean age was 82.7 years, 78.3% were females), 5.9% (N=78) are at risk for DDDIs, with a total of 86 interactions. Participants with DDDIs had been prescribed a higher number of drugs (10.8 (SD 3.8) vs. 7.9 (SD 3.7), p Conclusions: Of the residents in assisted living, 5.9% were exposed to DDDIs associated with the use of a higher number of drugs. Physicians should be trained to find safer alternatives to drugs associated with DDDIs.
  • Horne, Hisani N.; Chung, Charles C.; Zhang, Han; Yu, Kai; Prokunina-Olsson, Ludmila; Michailidou, Kyriaki; Bolla, Manjeet K.; Wang, Qin; Dennis, Joe; Hopper, John L.; Southey, Melissa C.; Schmidt, Marjanka K.; Broeks, Annegien; Muir, Kenneth; Lophatananon, Artitaya; Fasching, Peter A.; Beckmann, Matthias W.; Fletcher, Olivia; Johnson, Nichola; Sawyer, Elinor J.; Tomlinson, Ian; Burwinkel, Barbara; Marme, Frederik; Guenel, Pascal; Truong, Therese; Bojesen, Stig E.; Flyger, Henrik; Benitez, Javier; Gonzalez-Neira, Anna; Anton-Culver, Hoda; Neuhausen, Susan L.; Brenner, Hermann; Arndt, Volker; Meindl, Alfons; Schmutzler, Rita K.; Brauch, Hiltrud; Hamann, Ute; Nevanlinna, Heli; Khan, Sofia; Matsuo, Keitaro; Iwata, Hiroji; Dork, Thilo; Bogdanova, Natalia V.; Lindblom, Annika; Margolin, Sara; Mannermaa, Arto; Kosma, Veli-Matti; Chenevix-Trench, Georgia; Wu, Anna H.; den Berg, David Ven; Smeets, Ann; Zhao, Hui; Chang-Claude, Jenny; Rudolph, Anja; Radice, Paolo; Barile, Monica; Couch, Fergus J.; Vachon, Celine; Giles, Graham G.; Milne, Roger L.; Haiman, Christopher A.; Le Marchand, Loic; Goldberg, Mark S.; Teo, Soo H.; Taib, Nur A. M.; Kristensen, Vessela; Borresen-Dale, Anne-Lise; Zheng, Wei; Shrubsole, Martha; Winqvist, Robert; Jukkola-Vuorinen, Arja; Andrulis, Irene L.; Knight, Julia A.; Devilee, Peter; Seynaeve, Caroline; Garcia-Closas, Montserrat; Czene, Kamila; Darabi, Hatef; Hollestelle, Antoinette; Martens, John W. M.; Li, Jingmei; Lu, Wei; Shu, Xiao-Ou; Cox, Angela; Cross, Simon S.; Blot, William; Cai, Qiuyin; Shah, Mitul; Luccarini, Craig; Baynes, Caroline; Harrington, Patricia; Kang, Daehee; Choi, Ji-Yeob; Hartman, Mikael; Chia, Kee Seng; Kabisch, Maria; Torres, Diana; Jakubowska, Anna; Lubinski, Jan; Sangrajrang, Suleeporn; Brennan, Paul; Slager, Susan; Yannoukakos, Drakoulis; Shen, Chen-Yang; Hou, Ming-Feng; Swerdlow, Anthony; Orr, Nick; Simard, Jacques; Hall, Per; Pharoah, Paul D. P.; Easton, Douglas F.; Chanock, Stephen J.; Dunning, Alison M.; Figueroa, Jonine D.; kConFab AOCS Investigators (PUBLIC LIBRARY OF SCIENCE, 2016)
    The Cancer Genetic Markers of Susceptibility genome-wide association study (GWAS) originally identified a single nucleotide polymorphism (SNP) rs11249433 at 1p11.2 associated with breast cancer risk. To fine-map this locus, we genotyped 92 SNPs in a 900kb region (120,505,799-121,481,132) flanking rs11249433 in 45,276 breast cancer cases and 48,998 controls of European, Asian and African ancestry from 50 studies in the Breast Cancer Association Consortium. Genotyping was done using iCOGS, a custom-built array. Due to the complicated nature of the region on chr1p11.2: 120,300,000-120,505,798, that lies near the centromere and contains seven duplicated genomic segments, we restricted analyses to 429 SNPs excluding the duplicated regions (42 genotyped and 387 imputed). Perallelic associations with breast cancer risk were estimated using logistic regression models adjusting for study and ancestry-specific principal components. The strongest association observed was with the original identified index SNP rs11249433 (minor allele frequency (MAF) 0.402; per-allele odds ratio (OR) = 1.10, 95% confidence interval (CI) 1.08-1.13, P = 1.49 x 10(-21)). The association for rs11249433 was limited to ER-positive breast cancers (test for heterogeneity P
  • Skog, Maria S; Nystedt, Johanna; Korhonen, Matti; Anderson, Heidi; Lehti, Timo A; Pajunen, Maria I; Finne, Jukka (BioMed Central, 2016)
    BACKGROUND: In order to develop novel clinical applications and to gain insights into possible therapeutic mechanisms, detailed molecular characterization of human bone marrow-derived mesenchymal stromal cells (hBM-MSCs) is needed. Neural cell adhesion molecule (NCAM, CD56) is a transmembrane glycoprotein modulating cell–cell and cell–matrix interactions. An additional post-translational modification of NCAM is the α2,8-linked polysialic acid (polySia). Because of its background, NCAM is often considered a marker of neural lineage commitment. Generally, hBM-MSCs are considered to be devoid of NCAM expression, but more rigorous characterization is needed. METHODS: We have studied NCAM and polySia expression in five hBM-MSC lines at mRNA and protein levels. Cell surface localization was confirmed by immunofluorescence staining and expression frequency in the donor-specific lines by flow cytometry. For the detection of poorly immunogenic polySia, a fluorochrome-tagged catalytically defective enzyme was employed. RESULTS: All five known NCAM isoforms are expressed in these cells at mRNA level and the three main isoforms are present at protein level. Both polysialyltransferases, generally responsible for NCAM polysialylation, are expressed at mRNA level, but only very few cells express polySia at the cell surface. CONCLUSIONS: Our results underline the need for a careful control of methods and conditions in the characterization of MSCs. This study shows that, against the generally held view, clinical-grade hBM-MSCs do express NCAM. In contrast, although both polysialyltransferase genes are transcribed in these cells, very few express polySia at the cell surface. NCAM and polySia represent new candidate molecules for influencing MSC interactions.
  • Jäppinen, Luke; Jalkanen, Tero; Sieber, Brigitte; Addad, Ahmed; Heinonen, Markku; Kukk, Edwin; Radevici, Ivan; Paturi, Petriina; Peurla, Markus; Shahbazi, Mohammad-Ali; Santos, Hélder A.; Boukherroub, Rabah; Santos, Hellen; Lastusaari, Mika; Salonen, Jarno (Springer, 2016)
    Zinc oxide (ZnO) nanorods were manufactured using the aqueous chemical growth (ACG) method, and the effect of thermal acetylene treatment on their morphology, chemical composition, and optical properties was investigated. Changes in the elemental content of the treated rods were found to be different than in previous reports, possibly due to the different defect concentrations in the samples, highlighting the importance of synthesis method selection for the process. Acetylene treatment resulted in a significant improvement of the ultraviolet photoluminescence of the rods. The greatest increase in emission intensity was recorded on ZnO rods treated at the temperature of 825 degrees C. The findings imply that the changes brought on by the treatment are limited to the surface of the ZnO rods.
  • Livingstone, Katherine M.; Celis-Morales, Carlos; Papandonatos, George D.; Erar, Bahar; Florez, Jose C.; Jablonski, Kathleen A.; Razquin, Cristina; Marti, Amelia; Heianza, Yoriko; Huang, Tao; Sacks, Frank M.; Svendstrup, Mathilde; Sui, Xuemei; Church, Timothy S.; Jääskeläinen, Tiina; Lindstrom, Jaana; Tuomilehto, Jaakko; Uusitupa, Matti; Rankinen, Tuomo; Saris, Wim H. M.; Hansen, Torben; Pedersen, Oluf; Astrup, Arne; Sorensen, Thorkild I. A.; Qi, Lu; Bray, George A.; Martinez-Gonzalez, Miguel A.; Martinez, J. Alfredo; Franks, Paul W.; McCaffery, Jeanne M.; Lara, Jose; Mathers, John C. (BMJ PUBLISHING GROUP, 2016)
    OBJECTIVE To assess the effect of the FTO genotype on weight loss after dietary, physical activity, or drug based interventions in randomised controlled trials. DESIGN Systematic review and random effects meta-analysis of individual participant data from randomised controlled trials. DATA SOURCES Ovid Medline, Scopus, Embase, and Cochrane from inception to November 2015. ELIGIBILITY CRITERIA FOR STUDY SELECTION Randomised controlled trials in overweight or obese adults reporting reduction in body mass index, body weight, or waist circumference by FTO genotype (rs9939609 or a proxy) after dietary, physical activity, or drug based interventions. Gene by treatment interaction models were fitted to individual participant data from all studies included in this review, using allele dose coding for genetic effects and a common set of covariates. Study level interactions were combined using random effect models. Metaregression and subgroup analysis were used to assess sources of study heterogeneity. RESULTS We identified eight eligible randomised controlled trials for the systematic review and meta-analysis (n=9563). Overall, differential changes in body mass index, body weight, and waist circumference in response to weight loss intervention were not significantly different between FTO genotypes. Sensitivity analyses indicated that differential changes in body mass index, body weight, and waist circumference by FTO genotype did not differ by intervention type, intervention length, ethnicity, sample size, sex, and baseline body mass index and age category. CONCLUSIONS We have observed that carriage of the FTO minor allele was not associated with differential change in adiposity after weight loss interventions. These findings show that individuals carrying the minor allele respond equally well to dietary, physical activity, or drug based weight loss interventions and thus genetic predisposition to obesity associated with the FTO minor allele can be at least partly counteracted through such interventions.
  • Jokihaara, Jarkko; Porsti, Ilkka H.; Sievanen, Harri; Koobi, Peeter; Kannus, Pekka; Niemela, Onni; Turner, Russell T.; Iwaniec, Urszula T.; Järvinen, Teppo L. N. (PUBLIC LIBRARY OF SCIENCE, 2016)
    Introduction Phosphate binding with sevelamer can ameliorate detrimental histomorphometric changes of bone in chronic renal insufficiency (CRI). Here we explored the effects of sevelamer-HCl treatment on bone strength and structure in experimental CRI. Methods Forty-eight 8-week-old rats were assigned to surgical 5/6 nephrectomy (CRI) or renal decapsulation (Sham). After 14 weeks of disease progression, the rats were allocated to untreated and sevelamer-treated (3% in chow) groups for 9 weeks. Then the animals were sacrificed, plasma samples collected, and femora excised for structural analysis (biomechanical testing, quantitative computed tomography). Results Sevelamer-HCl significantly reduced blood pH, and final creatinine clearance in the CRI groups ranged 30%-50% of that in the Sham group. Final plasma phosphate increased 2.4- to 2.9-fold, and parathyroid hormone 13- to 21-fold in CRI rats, with no difference between sevelamer-treated and untreated animals. In the femoral midshaft, CRI reduced cortical bone mineral density (-3%) and breaking load (-15%) (p Conclusions In this model of stage 3-4 CRI, sevelamer-HCl treatment ameliorated the decreases in femoral midshaft and neck mineral density, and restored bone strength despite prevailing acidosis. Therefore, treatment with sevelamer can efficiently preserve mechanical competence of bone in CRI.
  • Nissinen, T. A.; Degerman, J.; Räsänen, M.; Poikonen, A. R.; Koskinen, S.; Mervaala, E.; Pasternack, A.; Ritvos, O.; Kivela, R.; Hulmi, J. J. (NATURE PUBLISHING GROUP, 2016)
    Doxorubicin is a widely used and effective chemotherapy drug. However, cardiac and skeletal muscle toxicity of doxorubicin limits its use. Inhibiting myostatin/activin signalling can prevent muscle atrophy, but its effects in chemotherapy-induced muscle wasting are unknown. In the present study we investigated the effects of doxorubicin administration alone or combined with activin receptor ligand pathway blockade by soluble activin receptor IIB (sACVR2B-Fc). Doxorubicin administration decreased body mass, muscle size and bone mineral density/content in mice. However, these effects were prevented by sACVR2B-Fc administration. Unlike in many other wasting situations, doxorubicin induced muscle atrophy without markedly increasing typical atrogenes or protein degradation pathways. Instead, doxorubicin decreased muscle protein synthesis which was completely restored by sACVR2B-Fc. Doxorubicin administration also resulted in impaired running performance without effects on skeletal muscle mitochondrial capacity/function or capillary density. Running performance and mitochondrial function were unaltered by sACVR2B-Fc administration. Tumour experiment using Lewis lung carcinoma cells demonstrated that sACVR2B-Fc decreased the cachectic effects of chemotherapy without affecting tumour growth. These results demonstrate that blocking ACVR2B signalling may be a promising strategy to counteract chemotherapy-induced muscle wasting without damage to skeletal muscle oxidative capacity or cancer treatment.
  • Shubin, Mikhail; Schaufler, Katharina; Tedin, Karsten; Vehkala, Minna; Corander, Jukka (PUBLIC LIBRARY OF SCIENCE, 2016)
    Biolog Phenotype Microarray (PM) is a technology allowing simultaneous screening of the metabolic behaviour of bacteria under a large number of different conditions. Bacteria may often undergo several cycles of metabolic activity during a Biolog experiment. We introduce a novel algorithm to identify these metabolic cycles in PM experimental data, thus increasing the potential of PM technology in microbiology. Our method is based on a statistical decomposition of the time-series measurements into a set of growth models. We show that the method is robust to measurement noise and captures accurately the biologically relevant signals from the data. Our implementation is made freely available as a part of an R package for PM data analysis and can be found at
  • Leikkilä, Jaana; Faehnle, Maija Elina; Galanakis, Michail (URBAN UND FISCHER VERLAG, 2013)
    Immigration in Finland has increased significantly in the last decades. The integration of immigrants and autochthonous Finns poses new challenges to the society. Nevertheless, the resulting cultural diversity creates opportunities for intercultural social development. According to previous studies, urban nature can benefit human well-being and it can also play a role in integration processes. However, the role urban nature can potentially play in integration is largely overlooked, and immigrants are rarely involved in the planning of urban nature. This paper presents the main results of a qualitative study carried out in Helsinki metropolitan area, Finland. The aim was to understand the role of urban nature in integration, and to address how the planning of urban nature can support integration and interculturalism. We found that using urban nature helps immigrants feel comfortable and enjoy their living environment. The inter- viewed immigrants were interested in getting information on urban planning, especially in their own neighbourhood, and many of them wanted to participate in planning, although they were unsure of their right to do so, and access to planning processes appeared problematic in many ways. To support integration and interculturalism, urban planning should take the opportunity to enhance intercultural understanding. Adhering to culturally sensitive processes, and developing trust with local residents by taking their views seriously, can do this. Nature has the potential to inspire people to connect with one another.