Browsing by Subject "genetic variation"

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  • Vilander, Laura M.; Vaara, Suvi T.; Kaunisto, Mari A.; Pettilä, Ville; FINNAKI Study Grp; Laru-Sompa, Raili; Pulkkinen, Anni; Saarelainen, Minna; Reilama, Mikko; Tolmunen, Sinikka; Rantalainen, Ulla; Miettinen, Marja; Suvela, Markku; Pesola, Katrine; Saastamoinen, Pekka; Kauppinen, Sirpa; Kaukonen, Kirsi-Maija; Korhonen, Anna-Maija; Nisula, Sara; Vaara, Suvi; Suojaranta-Ylinen, Raili; Mildh, Leena; Haapio, Mikko; Nurminen, Laura; Sutinen, Sari; Pettilä, Leena; Laitinen, Helinä; Syrja, Heidi; Henttonen, Kirsi; Lappi, Elina; Boman, Hillevi; Varpula, Tero; Porkka, Päivi; Sivula, Mirka; Rahkonen, Mira; Tsurkka, Anne; Prittinen, Niina; Alaspaa, Ari; Salanto, Ville; Juntunen, Hanna; Sanisalo, Teija; Parviainen, Ilkka; Uusaro, Ari; Ruokonen, Esko; Bendel, Stepani; Rissanen, Niina; Lång, Maarit; Rahikainen, Sari; Rissanen, Saija; Ahonen, Merja; Halonen, Elina; Vaskelainen, Eija; Poukkanen, Meri; Lintula, Esa; Suominen, Sirpa; Heikkinen, Jorma; Lavander, Timo; Heinonen, Kirsi; Juopperi, Anne-Mari; Kaminski, Tadeusz; Gäddnäs, Fiia; Kuusela, Tuija; Roiko, Jane; Karlsson, Sari; Reinikainen, Matti; Surakka, Tero; Jyrkönen, Helena; Eiserbeck, Tanja; Kallinen, Jaana; Lund, Vesa; Tuominen, Päivi; Perkola, Pauliina; Tuominen, Riikka; Hietaranta, Marika; Johansson, Satu; Hovilehto, Seppo; Kirsi, Anne; Tiainen, Pekka; Myllärinen, Tuija; Leino, Pirjo; Toropainen, Anne; Kuitunen, Anne; Leppänen, Ilona; Levoranta, Markus; Hoppu, Sanna; Sauranen, Jukka; Tenhunen, Jyrki; Kukkurainen, Atte; Kortelainen, Samuli; Varila, Simo; Inkinen, Outi; Koivuviita, Niina; Kotamäki, Jutta; Laine, Anu; Ala-Kokko, Tero; Laurila, Jouko J.; Sälkiö, Sinikka; Koivisto, Simo-Pekka; Hautamäki, Raku; Skinnar, Maria (2019)
    Acute kidney injury (AKI) is a syndrome with high incidence among the critically ill. Because the clinical variables and currently used biomarkers have failed to predict the individual susceptibility to AKI, candidate gene variants for the trait have been studied. Studies about genetic predisposition to AKI have been mainly underpowered and of moderate quality. We report the association study of 27 genetic variants in a cohort of Finnish critically ill patients, focusing on the replication of associations detected with variants in genes related to inflammation, cell survival, or circulation. In this prospective, observational Finnish Acute Kidney Injury (FINNAKI) study, 2647 patients without chronic kidney disease were genotyped. We defined AKI according to Kidney Disease: Improving Global Outcomes (KDIGO) criteria. We compared severe AKI (Stages 2 and 3, n = 625) to controls (Stage 0, n = 1582). For genotyping we used iPLEX(TM) Assay (Agena Bioscience). We performed the association analyses with PLINK software, using an additive genetic model in logistic regression. Despite the numerous, although contradictory, studies about association between polymorphisms rs1800629 in TNFA and rs1800896 in IL10 and AKI, we found no association (odds ratios 1.06 (95% CI 0.89-1.28, p = 0.51) and 0.92 (95% CI 0.80-1.05, p = 0.20), respectively). Adjusting for confounders did not change the results. To conclude, we could not confirm the associations reported in previous studies in a cohort of critically ill patients.
  • Venhoranta, Heli; Pausch, Hubert; Wysocki, Michal; Szczerbal, Izabela; Hänninen, Reetta; Taponen, Juhani; Uimari, Pekka; Flisikowski, Krzysztof; Lohi, Hannes; Fries, Ruedi; Switonski, Marek; Andersson, Magnus (2013)
  • Pohjanmies, Tähti; Tack, Ayco J. M.; Pulkkinen, Pertti; Elshibli, Sakina; Vakkari, Pekka; Roslin, Tomas (2015)
    Host genetic diversity and genotypic identity have been reported to affect the abundance, species richness and species diversity of associated herbivore communities. Recent work, however, suggests that these effects are highly context-dependent and that the magnitude and direction of the effects may vary with e.g., spatial factors and the amount of genetic variation present in the host population. Here, we use observational data on a Finnish oak (Quercus robur) population to examine whether low genetic diversity within peripheral populations reduces the impact of host genotype on associated herbivore communities. We first compared measures of genetic variation within Finnish oak populations with those recorded in more central parts of the species' range, confirming that genetic variation within the Finnish populations is comparatively low. Despite this result, we found consistent imprints of host genetic diversity on herbivore communities: herbivore load, but not the species richness, increased with host genetic diversity in both years and both spatial scales examined. Spatial connectivity of hosts increased herbivore diversity as well as abundance. While the similarity of herbivore communities increased with the genetic similarity among hosts, the effect of geographic distance was stronger. Overall, our findings identify a major role for spatial context in structuring oak-associated herbivore communities-but we still trace detectable imprints of host genotype at multiple spatial scales even in this peripheral, genetically impoverished oak population.
  • Mäkitie, Sara (Helsingfors universitet, 2016)
    Numerous genome-wide association studies (GWAS), GWAS meta-analyses and mouse studies have demonstrated that Wingless-related integration site 16 (WNT16) is associated with BMD, cortical bone thickness and strength as well as fracture risk. Practically no data exists regarding the significance of WNT16 in childhood-onset osteoporosis and fractures. Mutations and genetic variation in WNT16 were hypothesized to explain the clinical characteristics of some of the patients in question. Therefore, in this study the WNT16 gene was screened by Sanger sequencing in 46 pediatric patients with early-onset osteoporosis and in 60 pediatric patients with multiple fractures. We found altogether 12 variants in WNT16, of which one was a novel change. Inspite of the large amount of genetic variation found in WNT16, no actual mutations were found. None of the changes were statistically significant. It is likely that WNT16 mutations do not play an important role in the development of childhood osteoporosis.
  • Kanduri, C.; Järvelä, I. (2017)
    Modern high-throughput studies often yield long lists of genes, a fraction of which are of high relevance to the phenotype of interest. To prioritize the candidate genes of complex genetic traits, our R/Bioconductor package GenRank ranks genes based on convergent evidence obtained from multiple layers of independent evidence. We implemented three methods to rank genes that integrate gene-level data generated from multiple layers of evidence: (a) the convergent evidence (CE) method aggregates evidence based on a weighted vote counting method; (b) the rank product (RP) method performs a meta-analysis of microarray-based gene expression data, and (c) the traditional method combines p-values. The methods are implemented in R and are available as a package in the Bioconductor repository. (http://bioconductor.org/packages/GenRank/). © 2017 Kanduri C and Järvelä I.
  • Salminen, Anniina (Helsingin yliopisto, 2022)
    Osteoporoosi on luuston sairaus, jossa luun rakenne on heikentynyt lisäten murtumariskiä. Perimällä on keskeinen rooli luuston kehityksessä. Osteoporoosin ajatellaan olevan polygeneettinen tauti, mutta on tunnistettu myös yksittäisiä geenejä, joiden muutokset voivat johtaa osteoporoosin. KIF26B-geenin on raportoitu olevan uusi luuston terveydelle merkittävä tekijä ja sen yhden nonsense-variantin (p.Q287X) on raportoitu aiheuttavan primaaria osteoporoosia. Tämän tutkimuksen tarkoituksena oli kuvata kattava kirjallisuuskatsaus luuston terveyteen vaikuttavista ja osteoporoosin kehittymiselle altistavista geneettisistä tekijöistä sekä kuvata KIF26B-geenin varianttien luonnetta ja yleisyyttä primaari osteopoorosipotilailla. Aineisto koostui yhteensä 21:stä primaari osteoporoosia sairastavasta potilaasta (10 miestä; ikäjakauma 8–71 v). Heiltä kaikilta Sanger-sekvensointiin koko KIF26B-geeni. Sekvensoinnissa havaittiin 17 varianttia, joista 14 sijaitsi eksonin alueella. Eksonin alueella sijainneista varianteista viisi oli missense-varianttia, aiheuttaen muutoksen kodonin koodaamassa aminohapossa. Varianttien tarkemman analysoinnin perusteella varianteista neljä viidestä oli beningnejä. Yksi varianteista (P.Pro1775Arg) voisi mahdollisesti olla proteiinin toiminnan kannalta haitallinen, mutta variantin mahdollinen patogeenisuus jäi avoimeksi tämän tutkimuksen puitteissa. Potilailta ei löytynyt aiemmin havaittua primaaria osteoporoosia aiheuttavaa nonsense-varianttia (p.Q287X). Tutkimuksessa ei löydetty muita potentiaalisia, patogeeniksi tutkittavia variantteja selittämään potilaiden primaaria osteoporoosia.
  • Lehmann, Laurent; Keller, Lukas F; Kokko, Hanna (2007)
    Female mate choice influences the maintenance of genetic variation by altering the mating success of males with different genotypes. The evolution of preferences themselves, on the other hand, depends on genetic variation present in the population. Few models have tracked this feedback between a choice gene and its effects on genetic variation, in particular when genes that determine offspring viability and attractiveness have dominance effects. Here we build a population genetic model that allows comparing the evolution of various choice rules in a single framework. We first consider preferences for good genes and show that focused preferences for homozygotes evolve more easily than broad preferences, which allow heterozygous males high mating success too. This occurs despite better maintenance of genetic diversity in the latter scenario, and we discuss why empirical findings of superior mating success of heterozygous males consequently do not immediately lead to a better understanding of the lek paradox. Our results thus suggest that the mechanisms that help maintain genetic diversity also have a flipside of making female choice an inaccurate means of producing the desired kind of offspring. We then consider preferences for heterozygosity per se, and show that these evolve only under very special conditions. Choice for compatible genotypes can evolve but its selective advantage diminishes quickly due to frequency-dependent selection. Finally, we show that our model reproduces earlier results on selfing, when the female choice strategy produces assortative mating. Overall, our model indicates that various forms of heterozygote-favouring (or variable) female choice pose a problem for the theory of sexual ornamentation based on indirect benefits, rather than a solution.
  • Johnsen, Øystein; Apeland, Inger (Suomen metsätieteellinen seura, 1988)
  • Rosa, Elena; van Nouhuys, Saskya; Saastamoinen, Marjo (2017)
    Aggregation can confer advantages in animal foraging, defense, and thermoregulation. There is a tight connection between the evolution of insect sociality and a highly effective immune system, presumably to inhibit rapid disease spread in a crowded environment. This connection is less evident for animals that spend only part of their life cycle in a social environment, such as noneusocial gregarious insects. Our aim was to elucidate the effects of group living by the gregarious larvae of the Glanville fritillary butterfly with respect to individual performance, immunity, and susceptibility to a parasitoid. We were also interested in the role of family relative to common postdiapause environment in shaping life-history traits. Larvae were reared at high or low density and then exposed to the pupal parasitoid wasp Pteromalus apum, either in presence or absence of a previous immune challenge that was used to measure the encapsulation immune response. Surviving adult butterflies were further tested for immunity. The wasp offspring from successfully parasitized butterfly pupae were counted and their brood sex ratios assessed. Larvae reared at high density grew larger and faster than those at low density. Despite high mortality due to parasitism, survival was greater among individuals with high pupal immunity in both density treatments. Moreover, butterfly pupae reared at high density were able to kill a larger fraction of individuals in the parasitoid broods, although this did not increase survival of the host. Finally, a larger proportion of variation observed in most of the traits was explained by butterfly family than by common postdiapause rearing environment, except for adult survival and immunity, for which this pattern was reversed. This gregarious butterfly clearly benefits from high conspecific density in terms of developmental performance and its ability to fight a parasitoid. These positive effects may be driven by cooperative interactions during feeding.