Browsing by Subject "FATE"

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Now showing items 1-13 of 13
  • 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.
  • Ares, Feanor Reuben; Henriksson, Oscar; Hindmarsh, Mark; Hoyos, Carlos; Jokela, Niko (2022)
    We discuss the computation of the quantum effective action of strongly interacting field theories using holographic duality and its use to determine quasiequilibrium parameters of first-order phase transitions relevant for gravitational wave production. A particularly simple holographic model is introduced, containing only the metric and a free massive scalar field. Despite the simplicity, the model contains a rich phase diagram, including first-order phase transitions at nonzero temperature, due to various multitrace deformations. We obtain the leading terms in the effective action from homogeneous black brane solutions in the gravity dual and linearized perturbations around them. We then employ the effective action to construct bubble and domain wall solutions in the field theory side and study their properties. In particular, we show how the scaling of the effective action with the effective number of degrees of freedom of the quantum field theory determines the corresponding scaling of gravitational wave parameters.
  • Balboa, Diego; Barsby, Tom; Lithovius, Väinö; Saarimäki-Vire, Jonna; Omar-Hmeadi, Muhmmad; Dyachok, Oleg; Montaser, Hossam; Lund, Per-Eric; Yang, Mingyu; Ibrahim, Hazem; Näätänen, Anna; Chandra, Vikash; Vihinen, Helena; Jokitalo, Eija; Kvist, Jouni; Ustinov, Jarkko; Nieminen, Anni; Kuuluvainen, Emilia; Hietakangas, Ville; Katajisto, Pekka; Lau, Joey; Carlsson, Per-Ola; Barg, Sebastian; Tengholm, Anders; Otonkoski, Timo (2022)
    Transplantation of pancreatic islet cells derived from human pluripotent stem cells is a promising treatment for diabetes. Despite progress in the generation of stem-cell-derived islets (SC-islets), no detailed characterization of their functional properties has been conducted. Here, we generated functionally mature SC-islets using an optimized protocol and benchmarked them comprehensively against primary adult islets. Biphasic glucose-stimulated insulin secretion developed during in vitro maturation, associated with cytoarchitectural reorganization and the increasing presence of alpha cells. Electrophysiology, signaling and exocytosis of SC-islets were similar to those of adult islets. Glucose-responsive insulin secretion was achieved despite differences in glycolytic and mitochondrial glucose metabolism. Single-cell transcriptomics of SC-islets in vitro and throughout 6 months of engraftment in mice revealed a continuous maturation trajectory culminating in a transcriptional landscape closely resembling that of primary islets. Our thorough evaluation of SC-islet maturation highlights their advanced degree of functionality and supports their use in further efforts to understand and combat diabetes. Pancreatic islets derived from stem cells are benchmarked against primary cells.
  • 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.
  • Scopetani, Costanza; Chelazzi, David; Mikola, Juha; Leinio, Ville; Heikkinen, Reijo; Cincinelli, Alesandra; Pellinen, Jukka (2020)
  • 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.
  • Abugessaisa, Imad; Hasegawa, Akira; Noguchi, Shuhei; Cardon, Melissa; Watanabe, Kazuhide; Takahashi, Masataka; Suzuki, Harukazu; Katayama, Shintaro; Kere, Juha; Kasukawa, Takeya (2022)
    The analysis and interpretation of single-cell RNA sequencing (scRNA-seq) experiments are compromised by the presence of poor-quality cells. For meaningful analyses, such poor-quality cells should be excluded as they introduce noise in the data. We introduce SkewC, a quality-assessment tool, to identify skewed cells in scRNA-seq experiments. The tool's methodology is based on the assessment of gene coverage for each cell, and its skewness as a quality measure; the gene body coverage is a unique characteristic for each protocol, and different protocols yield highly different coverage profiles. This tool is designed to avoid misclustering or false clusters by identifying, isolating, and removing cells with skewed gene body coverage profiles. SkewC is capable of processing any type of scRNA-seq dataset, regardless of the protocol. We envision SkewC as a distinctive QC method to be incorporated into scRNA-seq QC processing to preclude the possibility of scRNA-seq data misinterpretation.
  • 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.
  • Gould, Oliver; Sukuvaara, Satumaaria; Weir, David (2021)
    We comprehensively study the effects of bubble wall thickness and speed on the gravitational wave emission spectrum of collisions of two vacuum bubbles. We numerically simulate a large dynamical range, making use of symmetry to reduce the dimensionality. The high-frequency slope of the gravitational wave spectrum is shown to depend on the thickness of the bubble wall, becoming steeper for thick-wall bubbles, in agreement with recent fully 3 + 1 dimensional lattice simulations of many-bubble collisions. This dependence is present, even for highly relativistic bubble wall collisions. We use the reduced dimensionality as an opportunity to investigate dynamical phenomena which may underlie the observed differences in the gravitational wave spectra. These phenomena include "trapping," which occurs most for thin-wall bubbles, and oscillations behind the bubble wall, which occur for thick-wall bubbles.