Publications by authors named "Tuomas Nurmi"

9 Publications

  • Page 1 of 1

Characterization of nucleic acids from extracellular vesicle-enriched human sweat.

BMC Genomics 2021 Jun 9;22(1):425. Epub 2021 Jun 9.

Faculty of Biochemistry and Molecular Medicine, Disease Networks Research Unit, Laboratory of Developmental Biology, Kvantum Institute, Infotech Oulu, University of Oulu, 90014 University of Oulu, Oulu, Finland.

Background: The human sweat is a mixture of secretions from three types of glands: eccrine, apocrine, and sebaceous. Eccrine glands open directly on the skin surface and produce high amounts of water-based fluid in response to heat, emotion, and physical activity, whereas the other glands produce oily fluids and waxy sebum. While most body fluids have been shown to contain nucleic acids, both as ribonucleoprotein complexes and associated with extracellular vesicles (EVs), these have not been investigated in sweat. In this study we aimed to explore and characterize the nucleic acids associated with sweat particles.

Results: We used next generation sequencing (NGS) to characterize DNA and RNA in pooled and individual samples of EV-enriched sweat collected from volunteers performing rigorous exercise. In all sequenced samples, we identified DNA originating from all human chromosomes, but only the mitochondrial chromosome was highly represented with 100% coverage. Most of the DNA mapped to unannotated regions of the human genome with some regions highly represented in all samples. Approximately 5 % of the reads were found to map to other genomes: including bacteria (83%), archaea (3%), and virus (13%), identified bacteria species were consistent with those commonly colonizing the human upper body and arm skin. Small RNA-seq from EV-enriched pooled sweat RNA resulted in 74% of the trimmed reads mapped to the human genome, with 29% corresponding to unannotated regions. Over 70% of the RNA reads mapping to an annotated region were tRNA, while misc. RNA (18,5%), protein coding RNA (5%) and miRNA (1,85%) were much less represented. RNA-seq from individually processed EV-enriched sweat collection generally resulted in fewer percentage of reads mapping to the human genome (7-45%), with 50-60% of those reads mapping to unannotated region of the genome and 30-55% being tRNAs, and lower percentage of reads being rRNA, LincRNA, misc. RNA, and protein coding RNA.

Conclusions: Our data demonstrates that sweat, as all other body fluids, contains a wealth of nucleic acids, including DNA and RNA of human and microbial origin, opening a possibility to investigate sweat as a source for biomarkers for specific health parameters.
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http://dx.doi.org/10.1186/s12864-021-07733-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8188706PMC
June 2021

A fugacity model assessment of ibuprofen, diclofenac, carbamazepine, and their transformation product concentrations in an aquatic environment.

Environ Sci Pollut Res Int 2019 Jan 5;26(1):328-341. Epub 2018 Nov 5.

Department of Chemistry, University of Jyvaskyla, P.O. Box 35, FI-40014, Jyväskylä, Finland.

An updated version of FATEMOD, a multimedia fugacity model for environmental fate of organic chemicals, was set up to assess environmental behaviour of three pharmaceuticals in northern Lake Päijänne, Finland. Concentrations of ibuprofen, diclofenac, and carbamazepine were estimated at various depths at two sites: near a wastewater treatment plant and 3.5 km downstream the plant. When compared with environmental sampling data from corresponding depths and sites, the predicted concentrations, ranging from nanograms to hundreds of nanograms per litre, were found to be in good agreement. Weather data were utilised with the model to rationalise the effects of various environmental parameters on the sampling results, and, e.g. the roles of various properties of lake dynamics and photodegradation were identified. The new model also enables simultaneous assessment of transformation products. Environmentally formed transformation product concentrations were estimated to be at highest an order of magnitude lower than those of the parent compounds, and unlikely to reach a detectable level. However, a possibility that conjugates of ibuprofen are present at higher levels than the parent compound was identified. Simulation results suggest that environmental degradation half-lives of the inspected contaminants under stratified lake conditions are in the range of some weeks to months.
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http://dx.doi.org/10.1007/s11356-018-3485-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6318256PMC
January 2019

Joint evolution of dispersal propensity and site selection in structured metapopulation models.

J Theor Biol 2018 05 13;444:50-72. Epub 2018 Feb 13.

Department of Biology, FIN-20014 University of Turku, Finland.

We propose a novel mathematical model for a metapopulation in which dispersal occurs on two levels: juvenile dispersal from the natal site is mandatory but it may take place either locally within the natal patch or globally between patches. Within each patch, individuals live in sites. Each site can be inhabited by at most one individual at a time and it may be of high or low quality. A disperser immigrates into a high-quality site whenever it obtains one, but it immigrates into a low-quality site only with a certain probability that depends on the time within the dispersal season. The vector of these low-quality-site-acceptance probabilities is the site-selection strategy of an individual. We derive a proxy for the invasion fitness in this model and study the joint evolution of long-distance-dispersal propensity and site-selection strategy. We focus on the way different ecological changes affect the evolutionary dynamics and study the interplay between global patch-to-patch dispersal and local site-selection. We show that ecological changes affect site-selection mainly via the severeness of competition for sites, which often leads to effects that may appear counterintuitive. Moreover, the metapopulation structure may result in extremely complex site-selection strategies and even in evolutionary cycles. The propensity for long-distance dispersal is mainly determined by the metapopulation-level ecological factors. It is, however, also strongly affected by the winter-survival of the site-holders within patches, which results in surprising non-monotonous effects in the evolution of site-selection due to interplay with long-distance dispersal. Altogether, our results give new additional support to the recent general conclusion that evolution of site-selection is often dominated by the indirect factors that take place via density-dependence, which means that evolutionary responses can rarely be predicted by intuition.
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http://dx.doi.org/10.1016/j.jtbi.2018.02.011DOI Listing
May 2018

Role of the extracellular matrix-located Mac-2 binding protein as an interactor of the Wnt proteins.

Biochem Biophys Res Commun 2017 09 26;491(4):953-957. Epub 2017 Jul 26.

Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, FIN-90220 Oulu, Finland.

The Wnt proteins constitute a conserved family of secreted palmitoleate-containing signaling proteins that play important roles in development and tissue homeostasis. Their hydrophobic nature has raised the question of how the proteins are transported outside the cells. Accumulating evidence suggests that several different mechanisms, including transport by lipoprotein particles and exosomes, may contribute to this process. Here, we expressed epitope-tagged Wnt4 in HEK293 cells, and identified Mac-2 binding protein (Mac-2BP) as its binding partner in the serum-free conditioned medium. Serine-to-alanine substitution at the conserved fatty acid-conjugation site did not affect Mac-2BP binding. Subsequent studies showed that Mac-2BP may be a general Wnt interactor. It is found in the extracellular matrix (ECM) of various tissues, where it forms unusual oligomeric ring-like structures. Its functions appear to include interactions with cells and certain ECM components. Intriguingly, both Wnt signaling and Mac-2BP expression are upregulated in many types of cancer. Our studies on the four-domain Mac-2BP indicate a crucial role in Wnt binding for the C-terminal domain that bears no sequence similarity to any other protein. Mac-2BP may have a role in regulating the extracellular spreading and storage of the Wnts, thereby modulating their bioavailability and stability.
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http://dx.doi.org/10.1016/j.bbrc.2017.07.141DOI Listing
September 2017

The evolution of site-selection strategy during dispersal.

J Theor Biol 2017 07 4;425:11-22. Epub 2017 May 4.

Department of Biology, University of Turku, FIN-20014, Finland.

We propose a mathematical model that enables the evolutionary analysis of site-selection process of dispersing individuals that encounter sites of high or low quality. Since each site can be inhabited by at most one individual, all dispersers are not able to obtain a high-quality site. We study the evolutionary dynamics of the low-quality-site acceptance as a function of the time during the dispersal season using adaptive dynamics. We show that environmental changes affect the evolutionary dynamics in two ways: directly and indirectly via density-dependent factors. Direct evolutionary effects usually follow intuition, whereas indirect effects are often counter-intuitive and hence difficult to predict without mechanistic modeling. Therefore, the mechanistic derivation of the fitness function, with careful attention on density- and frequency dependence, is essential for predicting the consequences of environmental changes to site selection. For example, increasing fecundity in high-quality sites makes them more tempting for dispersers and hence the direct effect of this ecological change delays the acceptance of low-quality sites. However, increasing fecundity in high-quality sites also increases the population size, which makes the competition for sites more severe and thus, as an indirect effect, forces evolution to favor less picky individuals. Our results indicate that the indirect effects often dominate the intuitive effects, which emphasizes the need for mechanistic models of the immigration process.
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http://dx.doi.org/10.1016/j.jtbi.2017.05.002DOI Listing
July 2017

Evolution of specialization under non-equilibrium population dynamics.

J Theor Biol 2013 Mar 7;321:63-77. Epub 2013 Jan 7.

Department of Mathematics, University of Turku, Turku, Finland.

We analyze the evolution of specialization in resource utilization in a mechanistically underpinned discrete-time model using the adaptive dynamics approach. We assume two nutritionally equivalent resources that in the absence of consumers grow sigmoidally towards a resource-specific carrying capacity. The consumers use resources according to the law of mass-action with rates involving trade-off. The resulting discrete-time model for the consumer population has over-compensatory dynamics. We illuminate the way non-equilibrium population dynamics affect the evolutionary dynamics of the resource consumption rates, and show that evolution to the trimorphic coexistence of a generalist and two specialists is possible due to asynchronous non-equilibrium population dynamics of the specialists. In addition, various forms of cyclic evolutionary dynamics are possible. Furthermore, evolutionary suicide may occur even without Allee effects and demographic stochasticity.
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http://dx.doi.org/10.1016/j.jtbi.2012.12.018DOI Listing
March 2013

Joint evolution of specialization and dispersal in structured metapopulations.

J Theor Biol 2011 Apr 31;275(1):78-92. Epub 2011 Jan 31.

Department of Mathematics, University of Turku, FIN-20014, Finland.

We study the joint evolution of dispersal and specialization concerning resource usage in a mechanistically underpinned structured discrete-time metapopulation model. We show that dispersal significantly affects the evolution of specialization and that specialization is a key factor that determines the possibility of evolutionary branching in dispersal propensity. Allowing both dispersal propensity and specialization to evolve as a consequence of natural selection is necessary in order to understand the evolutionary dynamics. The joint evolution of dispersal and specialization forms a natural evolutionary path leading to the coexistence of generalists and specialists. We show that in this process, the number of different patch types and the resource distribution are essential.
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http://dx.doi.org/10.1016/j.jtbi.2011.01.023DOI Listing
April 2011

Evolution of specialization in resource utilization in structured metapopulations.

J Biol Dyn 2008 Jul;2(3):297-322

Department of Mathematics, University of Turku, FIN-20014, Turku, Finland.

We study the evolution of resource utilization in a structured discrete-time metapopulation model with an infinite number of patches, prone to local catastrophes. The consumer faces a trade-off in the abilities to consume two resources available in different amounts in each patch. We analyse how the evolution of specialization in the utilization of the resources is affected by different ecological factors: migration, local growth, local catastrophes, forms of the trade-off and distribution of the resources in the patches. Our modelling approach offers a natural way to include more than two patch types into the models. This has not been usually possible in the previous spatially heterogeneous models focusing on the evolution of specialization.
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http://dx.doi.org/10.1080/17513750701769907DOI Listing
July 2008

On the evolution of specialization with a mechanistic underpinning in structured metapopulations.

Theor Popul Biol 2008 Mar 15;73(2):222-43. Epub 2007 Dec 15.

Department of Mathematics, FIN-20014, University of Turku, Finland.

We analyze the evolution of specialization in resource utilization in a discrete-time metapopulation model using the adaptive dynamics approach. The local dynamics in the metapopulation are based on the Beverton-Holt model with mechanistic underpinnings. The consumer faces a trade-off in the abilities to consume two resources that are spatially heterogeneously distributed to patches that are prone to local catastrophes. We explore the factors favoring the spread of generalist or specialist strategies. Increasing fecundity or decreasing catastrophe probability favors the spread of the generalist strategy and increasing environmental heterogeneity enlarges the parameter domain where the evolutionary branching is possible. When there are no catastrophes, increasing emigration diminishes the parameter domain where the evolutionary branching may occur. Otherwise, the effect of emigration on evolutionary dynamics is non-monotonous: both small and large values of emigration probability favor the spread of the specialist strategies whereas the parameter domain where evolutionary branching may occur is largest when the emigration probability has intermediate values. We compare how different forms of spatial heterogeneity and different models of local growth affect the evolutionary dynamics. We show that even small changes in the resource dynamics may have outstanding evolutionary effects to the consumers.
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http://dx.doi.org/10.1016/j.tpb.2007.12.002DOI Listing
March 2008
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