Browsing by Subject "FATE"

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  • Laht, Mailis; Karkman, Antti; Voolaid, Veiko; Ritz, Christian; Tenson, Tanel; Virta, Marko; Kisand, Veljo (2014)
  • Danielsson, Rebecca; Lucas, Jane; Dahlberg, Josef; Ramin, Mohammad; Agenas, Sigrid; Bayat, Ali-Reza; Tapio, Ilma; Hammer, Tobin; Roslin, Tomas (2019)
    The use of antibiotics in livestock production may trigger ecosystem disservices, including increased emissions of greenhouse gases. To evaluate this, we conducted two separate animal experiments, administering two widely used antibiotic compounds (benzylpenicillin and tetracycline) to dairy cows over a 4- or 5-day period locally and/or systemically. We then recorded enteric methane production, total gas production from dung decomposing under aerobic versus anaerobic conditions, prokaryotic community composition in rumen and dung, and accompanying changes in nutrient intake, rumen fermentation, and digestibility resulting from antibiotic administration. The focal antibiotics had no detectable effect on gas emissions from enteric fermentation or dung in aerobic conditions, while they decreased total gas production from anaerobic dung. Microbiome-level effects of benzylpenicillin proved markedly different from those previously recorded for tetracycline in dung, and did not differ by the mode of administration (local or systemic). Antibiotic effects on gas production differed substantially between dung maintained under aerobic versus anaerobic conditions and between compounds. These findings demonstrate compound- and context-dependent impacts of antibiotics on methane emissions and underlying processes, and highlight the need for a global synthesis of data on agricultural antibiotic use before understanding their climatic impacts.
  • Helle, Inari; Mäkinen, Jussi Antti-Eerikki; Nevalainen, Maisa Katariina; Afenyo, Mawuli; Vanhatalo, Jarno (2020)
    Oil spills resulting from maritime accidents pose a poorly understood risk to the Arctic environment. We propose a novel probabilistic method to quantitatively assess these risks. Our method accounts for spatiotemporally varying population distributions, the spreading of oil, and seasonally varying species-specific exposure potential and sensitivity to oil. It quantifies risk with explicit uncertainty estimates, enables one to compare risks over large geographic areas, and produces information on a meaningful scale for decision-making. We demonstrate the method by assessing the short-term risks oil spills pose to polar bears, ringed seals, and walrus in the Kara Sea, the western part of the Northern Sea Route. The risks differ considerably between species, spatial locations, and seasons. Our results support current aspirations to ban heavy fuel oil in the Arctic but show that we should not underestimate the risks of lighter oils either, as these oils can pollute larger areas than heavier ones. Our results also highlight the importance of spatially explicit season-specific oil spill risk assessment in the Arctic and that environmental variability and the lack of data are a major source of uncertainty related to the oil spill impacts.
  • Akimov, Yevhen; Bulanova, Daria; Timonen, Sanna; Wennerberg, Krister; Aittokallio, Tero (2020)
    Abstract Cellular DNA barcoding has become a popular approach to study heterogeneity of cell populations and to identify clones with differential response to cellular stimuli. However, there is a lack of reliable methods for statistical inference of differentially responding clones. Here, we used mixtures of DNA-barcoded cell pools to generate a realistic benchmark read count dataset for modelling a range of outcomes of clone-tracing experiments. By accounting for the statistical properties intrinsic to the DNA barcode read count data, we implemented an improved algorithm that results in a significantly lower false-positive rate, compared to current RNA-seq data analysis algorithms, especially when detecting differentially responding clones in experiments with strong selection pressure. Building on the reliable statistical methodology, we illustrate how multidimensional phenotypic profiling enables one to deconvolute phenotypically distinct clonal subpopulations within a cancer cell line. The mixture control dataset and our analysis results provide a foundation for benchmarking and improving algorithms for clone-tracing experiments.
  • Morello, Francesca; Borshagovski, Daniel; Survila, Mantas; Tikker, Laura; Sadik-Ogli, Samir; Kirjavainen, Anna; Estartús, Nuri; Knaapi, Laura; Lahti, Laura; Törönen, Petri; Mazutis, Linas; Delogu, Alessio; Salminen, Marjo; Achim, Kaia; Partanen, Juha (2020)
    Tegmental nuclei in the ventral midbrain and anterior hindbrain control motivated behavior, mood, memory, and movement. These nuclei contain inhibitory GABAergic and excitatory glutamatergic neurons, whose molecular diversity and development remain largely unraveled. Many tegmental neurons originate in the embryonic ventral rhombomere 1 (r1), where GABAergic fate is regulated by the transcription factor (TF) Tal1. We used single-cell mRNA sequencing of the mouse ventral r1 to characterize the Tal1-dependent and independent neuronal precursors. We describe gene expression dynamics during bifurcation of the GABAergic and glutamatergic lineages and show how active Notch signaling promotes GABAergic fate selection in postmitotic precursors. We identify GABAergic precursor subtypes that give rise to distinct tegmental nuclei and demonstrate that Sox14 and Zfpm2, two TFs downstream of Tal1, are necessary for the differentiation of specific tegmental GABAergic neurons. Our results provide a framework for understanding the development of cellular diversity in the tegmental nuclei.
  • Montanari, Martti P.; Tran, Ngan Vi; Shimmi, Osamu (2022)
    Bone morphogenetic proteins (BMPs), members of the transforming growth factor-ss (TGF-ss) family, have been shown to contribute to embryogenesis and organogenesis during animal development. Relevant studies provide support for the following concepts: (a) BMP signals are evolutionarily highly conserved as a genetic toolkit; (b) spatiotemporal distributions of BMP signals are precisely controlled at the post-translational level; and (c) the BMP signaling network has been co-opted to adapt to diversified animal development. These concepts originated from the historical findings of the Spemann-Mangold organizer and the subsequent studies about how this organizer functions at the molecular level. In this Commentary, we focus on two topics. First, we review how the BMP morphogen gradient is formed to sustain larval wing imaginal disc and early embryo growth and patterning in Drosophila. Second, we discuss how BMP signal is tightly controlled in a context-dependent manner, and how the signal and tissue dynamics are coupled to facilitate complex tissue structure formation. Finally, we argue how these concepts might be developed in the future for further understanding the significance of BMP signaling in animal development.
  • Aaltonen, Gisele; Carpelan-Holmström, Monika; Keränen, Ilona; Lepistö, Anna (2019)
    Purpose Crohn's colitis carries a risk for permanent stoma with extirpation of the rectum. We aimed to estimate the proctectomy rate and identify risk factors for proctectomy in patients with Crohn's colitis. Methods For this study, we retrospectively reviewed data from consecutive patients with Crohn's disease (CD) affecting the colon or anorectal region undergoing bowel resection in a reference colorectal centre between 2006 and 2016. The cumulative risk for proctectomy was calculated using the Kaplan-Meier curve. We used univariate and multivariate logistic regression analyses to determine independent risk factors for proctectomy. Outcomes after proctectomy concerning reoperation frequency and perineal wound healing are also described. ResultsIn total, this study included 125 patients. Proctectomy was performed in 36 patients (28.8%), of whom 14 patients (38.9%) experienced perineal wound healing problems. The rates of proctectomy were 5.6% and 32.0% 10 and 20 years after CD diagnosis, respectively. Female gender (odds ratio (OR) 3.375, 95% confidence interval (CI) 1.304-8.733, P=0.012), disease duration (OR 1.067, 95% CI 1.011-1.126, P=0.018) and history of perianal disease (OR 3.160, 95% CI 1.215-8.219, P=0.018) were independent risk factors for a proctectomy procedure, whereas thiopurine medication (OR 0.170, 95% CI 0.060-0.486, P=0.001) was an independent protective factor for proctectomy. Conclusions The duration of Crohn's disease, female gender and a history of perianal disease were significant risk factors for a proctectomy procedure. Future research should examine whether immunosuppressive and biological medications reduce the risk for proctectomy.
  • Pflugmacher, Stephan; Sulek, Amalia; Mader, Hannah; Heo, Jeongin; Noh, Ji Hyeon; Penttinen, Olli-Pekka; Kim, Youngjun; Kim, Sanghun; Esterhuizen, Maranda (2020)
    With the increase in environmental monitoring and assessing, we are gaining insight into the extent of microplastic pollution in our environment. The threat posed by microplastics to biota could come, e.g., from leached substances. As some plastic materials have been decaying in nature for extended periods already, the toxic effects of leaching compounds need to be investigated. It is furthermore essential to understand the adverse effects of new plastic and how these effects differ from the effects elicited by old plastic material. Therefore, in the present study, the effects of exposure to leachates from new and artificial aged polycarbonate as well as new and aged polycarbonate granules on various germination parameters of Lepidium sativum were studied. Germination, root, and shoot length, as well as the calculated germination rate index as a measure for germination speed, was negatively influenced in substrate-free and substrate containing exposures. From an ecological and agricultural point of view, this implies possible yield losses with less germinating seeds, slower plant germination speed, and smaller seedlings in general.