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  • O'Sullivan, Ronan James; Aykanat, Tutku; Johnston, Susan E.; Rogan, Ger; Poole, Russell; Prodohl, Paulo A.; de Eyto, Elvira; Primmer, Craig R.; McGinnity, Philip; Reed, Thomas Eric (2020)
    The release of captive-bred animals into the wild is commonly practised to restore or supplement wild populations but comes with a suite of ecological and genetic consequences. Vast numbers of hatchery-reared fish are released annually, ostensibly to restore/enhance wild populations or provide greater angling returns. While previous studies have shown that captive-bred fish perform poorly in the wild relative to wild-bred conspecifics, few have measured individual lifetime reproductive success (LRS) and how this affects population productivity. Here, we analyse data on Atlantic salmon from an intensely studied catchment into which varying numbers of captive-bred fish have escaped/been released and potentially bred over several decades. Using a molecular pedigree, we demonstrate that, on average, the LRS of captive-bred individuals was only 36% that of wild-bred individuals. A significant LRS difference remained after excluding individuals that left no surviving offspring, some of which might have simply failed to spawn, consistent with transgenerational effects on offspring survival. The annual productivity of the mixed population (wild-bred plus captive-bred) was lower in years where captive-bred fish comprised a greater fraction of potential spawners. These results bolster previous empirical and theoretical findings that intentional stocking, or non-intentional escapees, threaten, rather than enhance, recipient natural populations.
  • Roberts, Sean G.; Killin, Anton; Deb, Angarika; Sheard, Catherine; Greenhill, Simon J.; Sinnemäki, Kaius; Segovia Martín, José; Nölle, Jonas; Berdicevskis, Aleksandrs; Humphreys-Balkwill, Archie; Little, Hannah; Opie, Kit; Jacques, Guillaume; Bromham, Lindell; Tinits, Peeter; Ross, Robert M.; Lee, Sean; Gasser, Emily; Calladine, Jasmine; Spike, Matthew; Mann, Stephen; Shcherbakova, Olena; Singer, Ruth; Zhang, Shuya; Benítez-Burraco, Antonio; Kliesch, Christian; Thomas-Colquhoun, Ewan; Skirgård, Hedvig; Tamariz, Monica; Passmore, Sam; Pellard, Thomas; Jordan, Fiona (2020)
    Language is one of the most complex of human traits. There are many hypotheses about how it originated, what factors shaped its diversity, and what ongoing processes drive how it changes. We present the Causal Hypotheses in Evolutionary Linguistics Database (CHIELD, https://chield.excd.org/), a tool for expressing, exploring, and evaluating hypotheses. It allows researchers to integrate multiple theories into a coherent narrative, helping to design future research. We present design goals, a formal specification, and an implementation for this database. Source code is freely available for other fields to take advantage of this tool. Some initial results are presented, including identifying conflicts in theories about gossip and ritual, comparing hypotheses relating population size and morphological complexity, and an author relation network.
  • Vazquez-Garcia, Ignacio; Salinas, Francisco; Li, Jing; Fischer, Andrej; Barre, Benjamin; Hallin, Johan; Bergstrom, Anders; Alonso-Perez, Elisa; Warringer, Jonas; Mustonen, Ville; Liti, Gianni (2017)
    The joint contribution of pre-existing and de novo genetic variation to clonal adaptation is poorly understood but essential to designing successful antimicrobial or cancer therapies. To address this, we evolve genetically diverse populations of budding yeast, S. cerevisiae, consisting of diploid cells with unique haplotype combinations. We study the asexual evolution of these populations under selective inhibition with chemotherapeutic drugs by time-resolved whole-genome sequencing and phenotyping. All populations undergo clonal expansions driven by de novo mutations but remain genetically and phenotypically diverse. The clones exhibit widespread genomic instability, rendering recessive de novo mutations homozygous and refining pre-existing variation. Finally, we decompose the fitness contributions of pre-existing and de novo mutations by creating a large recombinant library of adaptive mutations in an ensemble of genetic backgrounds. Both pre-existing and de novo mutations substantially contribute to fitness, and the relative fitness of preexisting variants sets a selective threshold for new adaptive mutations.
  • Aykanat, Tutku; Ozerov, Mikhail; Vähä, Juha-Pekka; Orell, Panu; Niemelä, Eero; Erkinaro, Jaakko; Primmer, Craig R. (2019)
    Co-inheritance in life-history traits may result in unpredictable evolutionary trajectories if not accounted for in life-history models. Iteroparity (the reproductive strategy of reproducing more than once) in Atlantic salmon (Salmo salar) is a fitness trait with substantial variation within and among populations. In the Teno River in northern Europe, iteroparous individuals constitute an important component of many populations and have experienced a sharp increase in abundance in the last 20 years, partly overlapping with a general decrease in age structure. The physiological basis of iteroparity bears similarities to that of age at first maturity, another life-history trait with substantial fitness effects in salmon. Sea age at maturity in Atlantic salmon is controlled by a major locus around the vgll3 gene, and we used this opportunity demonstrate that these two traits are co-inherited around this genome region. The odds ratio of survival until second reproduction was up to 2.4 (1.8-3.5 90% CI) times higher for fish with the early-maturing vgll3 genotype (EE) compared to fish with the late-maturing genotype (LL). The L allele was dominant in individuals remaining only one year at sea before maturation, but the dominance was reversed, with the E allele being dominant in individuals maturing after two or more years at sea. Post hoc analysis indicated that iteroparous fish with the EE genotype had accelerated growth prior to first reproduction compared to first-time spawners, across all age groups, whereas this effect was not detected in fish with the LL genotype. These results broaden the functional link around the vgll3 genome region and help us understand constraints in the evolution of life-history variation in salmon. Our results further highlight the need to account for genetic correlations between fitness traits when predicting demographic changes in changing environments.
  • Berardo, Cecilia; Geritz, Stefanus (2021)
    The war of attrition in game theory is a model of a stand-off situation between two opponents where the winner is determined by its persistence. We model a stand-off between a predator and a prey when the prey is hiding and the predator is waiting for the prey to come out from its refuge, or when the two are locked in a situation of mutual threat of injury or even death. The stand-off is resolved when the predator gives up or when the prey tries to escape. Instead of using the asymmetric war of attrition, we embed the stand-off as an integral part of the predator-prey model of Rosenzweig and MacArthur derived from first principles. We apply this model to study the coevolution of the giving-up rates of the prey and the predator, using the adaptive dynamics approach. We find that the long term evolutionary process leads to three qualitatively different scenarios: the predator gives up immediately, while the prey never gives up; the predator never gives up, while the prey adopts any giving-up rate greater than or equal to a given positive threshold value; the predator goes extinct. We observe that some results are the same as for the asymmetric war of attrition, but others are quite different. (C) 2021 The Author(s). Published by Elsevier Ltd.
  • Mehmood, Furrukh; Abdullah,; Ubaid, Zartasha; Bao, Yiming; Poczai, Péter; Mirza, Bushra (2020)
    Within the family Solanaceae, Withania is a small genus belonging to the Solanoideae subfamily. Here, we report the de novo assembled chloroplast genome sequences of W. coagulans, W. adpressa, and W. riebeckii. The length of these genomes ranged from 154,162 to 154,364 base pairs (bp). These genomes contained a pair of inverted repeats (IRa and IRb) ranging from 25,029 to 25,071 bp that were separated by a large single-copy (LSC) region of 85,635-85,765 bp and a small single-copy (SSC) region of 18,457-18,469 bp. We analyzed the structural organization, gene content and order, guanine-cytosine content, codon usage, RNA-editing sites, microsatellites, oligonucleotide and tandem repeats, and substitutions of Withania plastomes, which revealed high similarities among the species. Comparative analysis among the Withania species also highlighted 10 divergent hotspots that could potentially be used for molecular marker development, phylogenetic analysis, and species identification. Furthermore, our analyses showed that even three mutational hotspots (rps4-trnT, trnM-atpE, and rps15) were sufficient to discriminate the Withania species included in current study.
  • Suomalainen, Olli P.; Abou Elseoud, Ahmed; Martinez-Majander, Nicolas; Tiainen, Marjaana; Forss, Nina; Curtze, Sami (2021)
    Introduction: Patients with small core infarction and salvageable penumbra are likely to benefit from endovascular treatment (EVT). As computed tomography perfusion imaging (CTP) is not always available 24/7 for patient selection, many patients are transferred to stroke centers for CTP. We compared automatically measured infarct core volume (NCCTcore) from the non-contrast computed tomography (NCCT) with ischemic core volume (CTPcore) from CTP and the outcome of EVT to clarify if NCCTcore measurement alone is sufficient to identify patients that benefit from transfer to stroke centers for EVT. Patients and methods: We included all consecutive stroke-code patients imaged with both NCCT and CTP at Helsinki University Hospital during 9/2016-01/2018. NCCTcore and CTPcore volumes were automatically calculated from the acute NCCT images. Follow-up infarct volume (FIV) was measured from 24 h follow-up NCCT to evaluate efficacy of EVT. To study whether NCCTcore could be used to identify patients eligible to EVT, we subgrouped patients based on NCCTcore volumes (>50 mL and > 70 mL). Results: Out of 1743 patients, baseline NCCTcore, CTPcore and follow-up NCCT was available for 288 patients. Median time from symptom onset to baseline imaging was 74 min (IQR 52-118), and time to follow-up imaging 24.15 h (22.25-26.33). Baseline NCCTcore was 20 mL (10-42), CTPcore 4 mL (0-16), and FIV 5 mL (1-49). Out of 288 patients, 23 had NCCTcore > 70 mL and 26 had CTPcore > 70 mL. NCCTcore and CTPcore performed similarly well in predicting large FIV (>70 ml). Conclusion: NCCTcore is a promising tool to identify patients that are not eligible to EVT due to large ischemic cores at baseline imaging.
  • Puumalainen, Emmi; Airaksinen, Marja; Jalava, Sanni E.; Chen, Timothy F.; Dimitrow, Maarit (2020)
    Purpose This study aims to systematically review studies describing screening tools that assess the risk for drug-related problems (DRPs) in older adults (>= 60 years). The focus of the review is to compare DRP risks listed in different tools and describe their development methods and validation. Methods The systematic search was conducted using evidence-based medicine, Medline Ovid, Scopus, and Web of Science databases from January 1, 1985, to April 7, 2016. Publications describing general DRP risk assessment tools for older adults written in English were included. Disease, therapy, and drug-specific tools were excluded. Outcome measures included an assessment tool's content, development methods, and validation assessment. Results The search produced 15 publications describing 11 DRP risk assessment tools. Three major categories of risks for DRPs included (1) patient or caregiver related risks; (2) pharmacotherapy-related risks; and (3) medication use process-related risks. Of all the risks included in the tools only 8 criteria appeared in at least 4 of the tools, problems remembering to take the medication being the most common (n=7). Validation assessments varied and content validation was the most commonly conducted (n = 9). Reliability assessment was conducted for 6 tools, most commonly by calculating internal consistency (n = 3) and inter-rater reliability (n = 2). Conclusions The considerable variety between the contents of the tools indicates that there is no consensus on the risk factors for DRPs that should be screened in older adults taking multiple medicines. Further research is needed to improve the accuracy and timeliness of the DRP risk assessment tools.
  • Abdullah,; Henriquez, Claudia L.; Mehmood, Furrukh; Carlsen, Monica M.; Islam, Madiha; Waheed, Mohammad Tahir; Poczai, Peter; Croat, Thomas B.; Ahmed, Ibrar (2020)
    The subfamily Pothoideae belongs to the ecologically important plant family Araceae. Here, we report the chloroplast genomes of two species of the subfamily Pothoideae:Anthurium huixtlense(size: 163,116 bp) andPothos scandens(size: 164,719 bp). The chloroplast genome ofP. scandensshowed unique contraction and expansion of inverted repeats (IRs), thereby increasing the size of the large single-copy region (LSC: 102,956 bp) and decreasing the size of the small single-copy region (SSC: 6779 bp). This led to duplication of many single-copy genes due to transfer to IR regions from the small single-copy (SSC) region, whereas some duplicate genes became single copy due to transfer to large single-copy regions. The rate of evolution of protein-coding genes was affected by the contraction and expansion of IRs; we found higher mutation rates for genes that exist in single-copy regions as compared to those in IRs. We found a 2.3-fold increase of oligonucleotide repeats inP. scandenswhen compared withA. huixtlense, whereas amino acid frequency and codon usage revealed similarities. The ratio of transition to transversion mutations was 2.26 inP. scandensand 2.12 inA. huixtlense. Transversion mutations mostly translated in non-synonymous substitutions. The phylogenetic inference of the limited species showed the monophyly of the Araceae subfamilies. Our study provides insight into the molecular evolution of chloroplast genomes in the subfamily Pothoideae and family Araceae.
  • Gyllenberg, Mats; Hanski, Ilkka; Lindstrom, Torsten (2017)
    Within the framework of adaptive dynamics we consider the evolution by natural selection of reproductive strategies in which individuals may adjust their reproductive behaviour in response to changing environmental conditions. As a specific example we considered a discrete-time model in which possible fluctuations in the environmental conditions are caused by predator-prey interaction. Our main findings include: (1) Coexistence between two fixed strategies (i.e., strategies that do not adjust to changing environmental conditions) is impossible; there exists a best fixed strategy, which invades and ousts all other fixed strategies. (2) A necessary condition for conditional (adjustable) strategies to evolve is that there are fluctuations in the environmental conditions. Predator-prey interactions may cause such fluctuations and under natural assumptions there exists an optimal conditional strategy which is uninvadable and invades and ousts all other strategies.
  • Culina, Antica; Adriaensen, Frank; Bailey, Liam D.; Burgess, Malcolm D.; Charmantier, Anne; Cole, Ella F.; Eeva, Tapio; Matthysen, Erik; Nater, Chloe R.; Sheldon, Ben C.; Saether, Bernt-Erik; Vriend, Stefan J. G.; Zajkova, Zuzana; Adamik, Peter; Aplin, Lucy M.; Angulo, Elena; Artemyev, Alexandr; Barba, Emilio; Barisic, Sanja; Belda, Eduardo; Bilgin, Cemal Can; Bleu, Josefa; Both, Christiaan; Bouwhuis, Sandra; Branston, Claire J.; Broggi, Juli; Burke, Terry; Bushuev, Andrey; Camacho, Carlos; Campobello, Daniela; Canal, David; Cantarero, Alejandro; Caro, Samuel P.; Cauchoix, Maxime; Chaine, Alexis; Cichon, Mariusz; Cikovic, Davor; Cusimano, Camillo A.; Deimel, Caroline; Dhondt, Andre A.; Dingemanse, Niels J.; Doligez, Blandine; Dominoni, Davide M.; Doutrelant, Claire; Drobniak, Szymon M.; Dubiec, Anna; Eens, Marcel; Erikstad, Kjell Einar; Espin, Silvia; Farine, Damien R.; Figuerola, Jordi; Gulbeyaz, Pinar Kavak; Gregoire, Arnaud; Hartley, Ian R.; Hau, Michaela; Hegyi, Gergely; Hille, Sabine; Hinde, Camilla A.; Holtmann, Benedikt; Ilyina, Tatyana; Isaksson, Caroline; Iserbyt, Arne; Ivankina, Elena; Kania, Wojciech; Kempenaers, Bart; Kerimov, Anvar; Komdeur, Jan; Korsten, Peter; Kral, Miroslav; Krist, Milos; Lambrechts, Marcel; Lara, Carlos E.; Leivits, Agu; Liker, Andras; Lodjak, Jaanis; Magi, Marko; Mainwaring, Mark C.; Mand, Raivo; Massa, Bruno; Massemin, Sylvie; Martinez-Padilla, Jesus; Mazgajski, Tomasz D.; Mennerat, Adele; Moreno, Juan; Mouchet, Alexia; Nakagawa, Shinichi; Nilsson, Jan-Ake; Nilsson, Johan F.; Norte, Ana Claudia; van Oers, Kees; Orell, Markku; Potti, Jaime; Quinn, John L.; Reale, Denis; Reiertsen, Tone Kristin; Rosivall, Balazs; Russell, Andrew F.; Rytkonen, Seppo; Sanchez-Virosta, Pablo; Santos, Eduardo S. A.; Schroeder, Julia; Senar, Juan Carlos; Seress, Gabor; Slagsvold, Tore; Szulkin, Marta; Teplitsky, Celine; Tilgar, Vallo; Tolstoguzov, Andrey; Torok, Janos; Valcu, Mihai; Vatka, Emma; Verhulst, Simon; Watson, Hannah; Yuta, Teru; Zamora-Marin, Jose M.; Visser, Marcel E. (2021)
    The integration and synthesis of the data in different areas of science is drastically slowed and hindered by a lack of standards and networking programmes. Long-term studies of individually marked animals are not an exception. These studies are especially important as instrumental for understanding evolutionary and ecological processes in the wild. Furthermore, their number and global distribution provides a unique opportunity to assess the generality of patterns and to address broad-scale global issues (e.g. climate change). To solve data integration issues and enable a new scale of ecological and evolutionary research based on long-term studies of birds, we have created the SPI-Birds Network and Database ()-a large-scale initiative that connects data from, and researchers working on, studies of wild populations of individually recognizable (usually ringed) birds. Within year and a half since the establishment, SPI-Birds has recruited over 120 members, and currently hosts data on almost 1.5 million individual birds collected in 80 populations over 2,000 cumulative years, and counting. SPI-Birds acts as a data hub and a catalogue of studied populations. It prevents data loss, secures easy data finding, use and integration and thus facilitates collaboration and synthesis. We provide community-derived data and meta-data standards and improve data integrity guided by the principles of Findable, Accessible, Interoperable and Reusable (FAIR), and aligned with the existing metadata languages (e.g. ecological meta-data language). The encouraging community involvement stems from SPI-Bird's decentralized approach: research groups retain full control over data use and their way of data management, while SPI-Birds creates tailored pipelines to convert each unique data format into a standard format. We outline the lessons learned, so that other communities (e.g. those working on other taxa) can adapt our successful model. Creating community-specific hubs (such as ours, COMADRE for animal demography, etc.) will aid much-needed large-scale ecological data integration.
  • Miyauchi, Shingo; Hage, Hayat; Drula, Elodie; Lesage-Meessen, Laurence; Berrin, Jean-Guy; Navarro, David; Favel, Anne; Chaduli, Delphine; Grisel, Sacha; Haon, Mireille; Piumi, Francois; Levasseur, Anthony; Lomascolo, Anne; Ahrendt, Steven; Barry, Kerrie; LaButti, Kurt M.; Chevret, Didier; Daum, Chris; Mariette, Jerome; Klopp, Christophe; Cullen, Daniel; de Vries, Ronald P.; Gathman, Allen C.; Hainaut, Matthieu; Henrissat, Bernard; Hilden, Kristiina S.; Kuees, Ursula; Lilly, Walt; Lipzen, Anna; Maekelae, Miia R.; Martinez, Angel T.; Morel-Rouhier, Melanie; Morin, Emmanuelle; Pangilinan, Jasmyn; Ram, Arthur F. J.; Woesten, Han A. B.; Ruiz-Duenas, Francisco J.; Riley, Robert; Record, Eric; Grigoriev, Igor; Rosso, Marie-Noelle (2020)
    White-rot (WR) fungi are pivotal decomposers of dead organic matter in forest ecosystems and typically use a large array of hydrolytic and oxidative enzymes to deconstruct lignocellulose. However, the extent of lignin and cellulose degradation may vary between species and wood type. Here, we combined comparative genomics, transcriptomics and secretome proteomics to identify conserved enzymatic signatures at the onset of wood-decaying activity within the Basidiomycota genus Pycnoporus. We observed a strong conservation in the genome structures and the repertoires of protein-coding genes across the four Pycnoporus species described to date, despite the species having distinct geographic distributions. We further analysed the early response of P. cinnabarinus, P. coccineus and P. sanguineus to diverse (ligno)-cellulosic substrates. We identified a conserved set of enzymes mobilized by the three species for breaking down cellulose, hemicellulose and pectin. The co-occurrence in the exo-proteomes of H2O2-producing enzymes with H2O2-consuming enzymes was a common feature of the three species, although each enzymatic partner displayed independent transcriptional regulation. Finally, cellobiose dehydrogenase-coding genes were systematically co-regulated with at least one AA9 lytic polysaccharide monooxygenase gene, indicative of enzymatic synergy in vivo. This study highlights a conserved core white-rot fungal enzymatic mechanism behind the wood-decaying process.
  • Gurarie, Eliezer; Fleming, Christen H.; Fagan, William F.; Laidre, Kristin L.; Hernandez-Pliego, Jesus; Ovaskainen, Otso (2017)
    Background: Continuous time movement models resolve many of the problems with scaling, sampling, and interpretation that affect discrete movement models. They can, however, be challenging to estimate, have been presented in inconsistent ways, and are not widely used. Methods: We review the literature on integrated Ornstein-Uhlenbeck velocity models and propose four fundamental correlated velocity movement models (CVM's): random, advective, rotational, and rotational-advective. The models are defined in terms of biologically meaningful speeds and time scales of autocorrelation. We summarize several approaches to estimating the models, and apply these tools for the higher order task of behavioral partitioning via change point analysis. Results: An array of simulation illustrate the precision and accuracy of the estimation tools. An analysis of a swimming track of a bowhead whale (Balaena mysticetus) illustrates their robustness to irregular and sparse sampling and identifies switches between slower and faster, and directed vs. random movements. An analysis of a short flight of a lesser kestrel (Falco naumanni) identifies exact moments when switches occur between loopy, thermal soaring and directed flapping or gliding flights. Conclusions: We provide tools to estimate parameters and perform change point analyses in continuous time movement models as an R package (smoove). These resources, together with the synthesis, should facilitate the wider application and development of correlated velocity models among movement ecologists.
  • Annila, Arto; Salthe, Stanley (2010)
  • Karinen, Sirkku; Heikkinen, Tuomas; Nevanlinna, Heli; Hautaniemi, Sampsa (2011)
  • Garzon, Marta Benito; Robson, T. Matthew; Hampe, Arndt (2019)
    Improving our understanding of species ranges under rapid climate change requires application of our knowledge of the tolerance and adaptive capacity of populations to changing environmental conditions. Here, we describe an emerging modelling approach, Delta TraitSDM, which attempts to achieve this by explaining species distribution ranges based on phenotypic plasticity and local adaptation of fitness-related traits measured across large geographical gradients. The collection of intraspecific trait data measured in common gardens spanning broad environmental clines has promoted the development of these new models - first in trees but now rapidly expanding to other organisms. We review, explain and harmonize the main findings from this new generation of models that, by including trait variation over geographical scales, are able to provide new insights into future species ranges. Overall, Delta TraitSDM predictions generally deliver a less alarming message than previous models of species distribution under new climates, indicating that phenotypic plasticity should help, to a considerable degree, some plant populations to persist under climate change. The development of Delta TraitSDMs offers a new perspective to analyse intraspecific variation in single and multiple traits, with the rationale that trait (co)variation and consequently fitness can significantly change across geographical gradients and new climates.
  • O'Toole, John M.; Boylan, Geraldine B.; Lloyd, Rhodri O.; Goulding, Robert M.; Vanhatalo, Sampsa; Stevenson, Nathan J. (2017)
    Aim: To develop a method that segments preterm EEG into bursts and inter-bursts by extracting and combining multiple EEG features. Methods: Two EEG experts annotated bursts in individual EEG channels for 36 preterm infants with gestational age <30 weeks. The feature set included spectral, amplitude, and frequency-weighted energy features. Using a consensus annotation, feature selection removed redundant features and a support vector machine combined features. Area under the receiver operator characteristic (AUC) and Cohen's kappa (K) evaluated performance within a cross-validation procedure. Results: The proposed channel-independent method improves AUC by 4-5% over existing methods (p <0.001, n = 36), with median (95% confidence interval) AUC of 0.989 (0.973-0.997) and sensitivity -specificity of 95.8-94.4%. Agreement rates between the detector and experts' annotations, K = 0.72 (0.36-0.83) and K = 0.65 (0.32-0.81), are comparable to inter-rater agreement, K = 0.60 (0.21-0.74). Conclusions: Automating the visual identification of bursts in preterm EEG is achievable with a high level of accuracy. Multiple features, combined using a data-driven approach, improves on existing single-feature methods. (C) 2017 The Authors. Published by Elsevier Ltd on behalf of IPEM.
  • Marttinen, Pekka; Hanage, William P.; Croucher, Nicholas J.; Connor, Thomas R.; Harris, Simon R.; Bentley, Stephen D.; Corander, Jukka (2012)
  • Leskinen, Tuija; Rinnankoski-Tuikka, Rita; Rintala, Mirva; Seppanen-Laakso, Tuulikki; Pollanen, Eija; Alen, Markku; Sipila, Sarianna; Kaprio, Jaakko; Kovanen, Vuokko; Rahkila, Paavo; Oresic, Matej; Kainulainen, Heikki; Kujala, Urho M. (2010)
    High physical activity/aerobic fitness predicts low morbidity and mortality. Our aim was to identify the most up-regulated gene sets related to long-term physical activity vs. inactivity in skeletal muscle and adipose tissues and to obtain further information about their link with cardio-metabolic risk factors. We studied ten same-sex twin pairs (age range 50-74 years) who had been discordant for leisure-time physical activity for 30 years. The examinations included biopsies from m. vastus lateralis and abdominal subcutaneous adipose tissue. RNA was analyzed with the genome-wide Illumina Human WG-6 v3.0 Expression BeadChip. For pathway analysis we used Gene Set Enrichment Analysis utilizing active vs. inactive co-twin gene expression ratios. Our findings showed that among the physically active members of twin pairs, as compared to their inactive co-twins, gene expression in the muscle tissue samples was chronically up-regulated for the central pathways related to energy metabolism, including oxidative phosphorylation, lipid metabolism and supportive metabolic pathways. Up-regulation of these pathways was associated in particular with aerobic fitness and high HDL cholesterol levels. In fat tissue we found physical activity-associated increases in the expression of polyunsaturated fatty acid metabolism and branched-chain amino acid degradation gene sets both of which associated with decreased 'high-risk' ectopic body fat and plasma glucose levels. Consistent with other findings, plasma lipidomics analysis showed up-regulation of the triacylglycerols containing the polyunsaturated fatty acids. Our findings identified skeletal muscle and fat tissue pathways which are associated with the long-term physical activity and reduced cardio-metabolic disease risk, including increased aerobic fitness. In particular, improved skeletal muscle oxidative energy and lipid metabolism as well as changes in adipocyte function and redistribution of body fat are associated with reduced cardio-metabolic risk.
  • de Groot, Pieter F.; Belzer, Clara; Aydin, Omrum; Levin, Evgeni; Levels, Johannes H.; Aalvink, Steven; Boot, Fransje; Holleman, Frits; van Raalte, Daniel H.; Scheithauer, Torsten P.; Simsek, Suat; Schaap, Frank G.; Damink, Steven W. M. Olde; Roep, Bart O.; Hoekstra, Joost B.; de Vos, Willem M.; Nieuwdorp, Max (2017)
    Objective Environmental factors driving the development of type 1 diabetes (T1D) are still largely unknown. Both animal and human studies have shown an association between altered fecal microbiota composition, impaired production of short-chain fatty acids (SCFA) and T1D onset. However, observational evidence on SCFA and fecal and oral microbiota in adults with longstanding T1D vs healthy controls (HC) is lacking. Research design and methods We included 53 T1D patients without complications or medication and 50 HC matched for age, sex and BMI. Oral and fecal microbiota, fecal and plasma SCFA levels, markers of intestinal inflammation (fecal IgA and calprotectin) and markers of low-grade systemic inflammation were measured. Results Oral microbiota were markedly different in T1D (eg abundance of Streptococci) compared to HC. Fecal analysis showed decreased butyrate producing species in T1D and less butyryl-CoA transferase genes. Also, plasma levels of acetate and propionate were lower in T1D, with similar fecal SCFA. Finally, fecal strains Christensenella and Subdoligranulum correlated with glycemic control, inflammatory parameters and SCFA. Conclusions We conclude that T1D patients harbor a different amount of intestinal SCFA (butyrate) producers and different plasma acetate and propionate levels. Future research should disentangle cause and effect and whether supplementation of SCFA-producing bacteria or SCFA alone can have disease-modifying effects in T1D.