Browsing by Subject "geenit"

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  • Vuorio, Kristiina; Mäki, Anita; Salmi, Pauliina; Aalto, Sanni L.; Tiirola, Marja (Frontiers Media S.A., 2020)
    Frontiers in Microbiology 11 (2020) 96
    The composition of phytoplankton community is the basis for environmental monitoring and assessment of the ecological status of aquatic ecosystems. Community composition studies of phytoplankton have been based on time-consuming and expertise-demanding light microscopy analyses. Molecular methods have the potential to replace microscopy, but the high copy number variation of ribosomal genes and the lack of universal primers for simultaneous amplification of prokaryotic and eukaryotic genes complicate data interpretation. In this study, we used our previously developed directional primer-independent high-throughput sequencing (HTS) approach to analyze 16S and 18S rRNA community structures. Comparison of 83 boreal lake samples showed that the relative abundances of eukaryotic phytoplankton at class level and prokaryotic cyanobacteria at order level were consistent between HTS and microscopy results. At the genus level, the results had low correspondence, mainly due to lack of sequences in the reference library. HTS was superior to identify genera that are extensively represented in the reference databases but lack specific morphological characteristics. Targeted metatranscriptomics proved to be a feasible method to complement the microscopy analysis. The metatranscriptomics can also be applied without linking the sequences to taxonomy. However, direct indexing of the sequences to their environmental indicator values needs collections of more comprehensive sample sets, as long as the coverage of molecular barcodes of eukaryotic species remains insufficient.
  • Schuster, Romina; Strehse, Jennifer S.; Ahvo, Aino; Turja, Raisa; Maser, Edmund; Bickmeyer, Ulf; Lehtonen, Kari K.; Brenner, Matthias (Elsevier, 2021)
    Marine Environmental Research 167 (2021), 105264
    Baltic mussels (Mytilus spp.) were exposed to the explosive trinitrotoluene (TNT) for 96 h (0.31–10.0 mg/L) and 21 d (0.31–2.5 mg/L). Bioaccumulation of TNT and its degradation products (2- and 4-ADNT) as well as biological effects ranging from the gene and cellular levels to behaviour were investigated. Although no mortality occurred in the concentration range tested, uptake and metabolism of TNT and responses in antioxidant enzymes and histochemical biomarkers were observed already at the lowest concentrations. The characteristic shell closure behaviour of bivalves at trigger concentrations led to complex exposure patterns and non-linear responses to the exposure concentrations. Conclusively, exposure to TNT exerts biomarker reponses in mussels already at 0.31 mg/L while effects are recorded also after a prolonged exposure although no mortality occurs. Finally, more attention should be paid on shell closure of bivalves in exposure studies since it plays a marked role in definining toxicity threshold levels.
  • Lehto, Markku (University of Helsinki, 1995)
  • Riskumäki, Matilda; Tessas, Ioannis; Ottman, Noora; Suomalainen, Alina; Werner, Paulina; Karisola, Piia; Lauerma, Antti; Ruokolainen, Lasse; Karkman, Antti; Wisgrill, Lukas; Sinkko, Hanna; Lehtimäki, Jenni; Alenius, Harri; Fyhrquist, Nanna (European Academy of Allergy and Clinical Immunology, 2021)
    Allergy 76: 4, 1280-1284
  • Virtanen, Suvi (Helsingfors universitet, 2016)
    Depression is a psychiatric disorder composed of several clusters of symptoms, which do not necessarily reflect common pathways of pathophysiological processes. Thus, a new conceptualization of depression has been proposed, which suggests that depression should be dissected to its key components instead of treating it as one homogeneous concept. Personality trait neuroticism is a risk factor that is consistently linked with depression. Several models have been suggested for the association between neuroticism and depression. One of them is a so-called common cause -model, which assumes that a shared etiology explains the co-occurrence of the two. Research from twin studies supports this notion, as neuroticism and depression have been found to share a large proportion of their genetic basis. However, earlier research has examined depression as a composite concept, and there are no studies to date which would have examined the shared genetic basis of specific symptoms of depression in relation with neuroticism. This study tests the common cause -model by estimating, whether the same genetic and environmental components are relevant in explaining the covariation between neuroticism and specific symptoms of depression. The data used in this study was from the Swedish Adoption/Twin Study (n = 1515, av. age = 62.0). Depression was measured with The Center for Epidemiological Studies - Depression Scale (CES-D), and separate analyses were conducted for three factors: somatic complaints, (lack of) positive affect and depressed affect. The results showed that all of the depressive symptoms shared the same genetic and environmental components when modeling the association with neuroticism, which supports the common cause -model. Over a half of the phenotypic correlation was explained by genetic influences between neuroticism and somatic complaints, as well as neuroticism and positive affect. Half of the co-variation between neuroticism and depressed affect was due to genetic influences. Findings of the current study suggest, that genetic and individual specific environmental influences are important in explaining the relationship in all of the symptoms. For future endeavors, it is suggested to search for concrete risk factors and neurobiological endophenotypes that are shared between specific symptoms and neuroticism. While the use of composite concept of depression was supported in this study, the research question has not been yet examined in molecular genetic studies. A twin model can only differentiate sources of variation, not concrete risk factors. Thus, the results presented here only apply in the context of twin modeling. Also, the robustness of the results should be tested by replicating the results among younger samples.
  • Miettinen, Hanna; Bomberg, Malin; Nyyssönen, Mari; Reunamo, Anna; Jørgensen, Kirsten S.; Vikman, Minna (PLoS ONE, 2019)
    PLoS ONE
    Two long-term potentially oil exposed Baltic Sea coastal sites near old oil refineries and harbours were compared to nearby less exposed sites in terms of bacterial, archaeal and fungal microbiomes and oil degradation potential. The bacterial, archaeal and fungal diversities were similar in oil exposed and less exposed sampling sites based on bacterial and archaeal 16S rRNA gene and fungal 5.8S rRNA gene amplicon sequencing from both DNA and RNA fractions. The number of genes participating in alkane degradation (alkB) or PAH-ring hydroxylation (PAH–RHDα) were detected by qPCR in all water and sediment samples. These numbers correlated with the number of bacterial 16S rRNA gene copies in sediment samples but not with the concentration of petroleum hydrocarbons or PAHs. This indicates that both the clean and the more polluted sites at the Baltic Sea coastal areas have a potential for petroleum hydrocarbon degradation. The active community (based on RNA) of the coastal Baltic Sea water differed largely from the total community (based on DNA). The most noticeable difference was seen in the bacterial community in the water samples were the active community was dominated by Cyanobacteria and Proteobacteria whereas in total bacterial community Actinobacteria was the most abundant phylum. The abundance, richness and diversity of Fungi present in water and sediment samples was in general lower than that of Bacteria and Archaea. Furthermore, the sampling location influenced the fungal community composition, whereas the bacterial and archaeal communities were not influenced. This may indicate that the fungal species that are adapted to the Baltic Sea environments are few and that Fungi are potentially more vulnerable to or affected by the Baltic Sea conditions than Bacteria and Archaea.
  • Timonen, Sari; Valkonen, Jari (Gaudeamus, 2018)
    Sienten biologia on ensimmäinen suomenkielinen yleisteos sienistä. Siitä selviävät perusasiat sienten monimuotoisuudesta, aineenvaihdunnasta, genetiikasta, toimintatavoista, ympäristövaikutuksista ja käytöstä ihmisen hyödyksi. Kirjan lukemista ja sienimaailman ymmärtämistä helpottaa kattava suomenkielinen sienitieteellinen sanasto. Kirja sopii luettavaksi niin opiskelijoille, tutkijoille, biologian opettajille kuin sieniharrastajillekin. Kirjoittajina ovat alansa parhaat suomalaiset asiantuntijat.
  • Määttä, Juha (University of Helsinki, 1993)