Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Epigenome-wide meta-analysis of blood DNA methylation in newborns and children identifies numerous loci related to gestational age
    Merid, Simon Kebede ; Novoloaca, Alexei ; Sharp, Gemma C. ; Küpers, Leanne K. ; Kho, Alvin T. ; Roy, Ritu ; Gao, Lu ; Annesi-Maesano, Isabella ; Jain, Pooja ; Plusquin, Michelle ; Kogevinas, Manolis ; Allard, Catherine ; Vehmeijer, Florianne O. ; Kazmi, Nabila ; Salas, Lucas A. ; Rezwan, Faisal I. ; Zhang, Hongmei ; Sebert, Sylvain ; Czamara, Darina ; Rifas-Shiman, Sheryl L. ; Melton, Phillip E. ; Lawlor, Debbie A. ; Pershagen, Göran ; Breton, Carrie V. ; Huen, Karen ; Baiz, Nour ; Gagliardi, Luigi ; Nawrot, Tim S. ; Corpeleijn, Eva ; Perron, Patrice ; Duijts, Liesbeth ; Nohr, Ellen Aagaard ; Bustamante, Mariona ; Ewart, Susan L. ; Karmaus, Wilfried ; Zhao, Shanshan ; Page, Christian M. ; Herceg, Zdenko ; Jarvelin, Marjo Riitta ; Lahti, Jari ; Baccarelli, Andrea A. ; Anderson, Denise ; Kachroo, Priyadarshini ; Relton, Caroline L. ; Bergström, Anna ; Eskenazi, Brenda ; Soomro, Munawar Hussain ; Vineis, Paolo ; Snieder, Harold ; Bouchard, Luigi ; Jaddoe, Vincent W. ; Sørensen, Thorkild I.A. ; Vrijheid, Martine ; Arshad, S.H. ; Holloway, John W. ; Håberg, Siri E. ; Magnus, Per ; Dwyer, Terence ; Binder, Elisabeth B. ; Demeo, Dawn L. ; Vonk, Judith M. ; Newnham, John ; Tantisira, Kelan G. ; Kull, Inger ; Wiemels, Joseph L. ; Heude, Barbara ; Sunyer, Jordi ; Nystad, Wenche ; Munthe-Kaas, Monica C. ; Raïkkönen, Katri ; Oken, Emily ; Huang, Rae Chi ; Weiss, Scott T. ; Antó, Josep Maria ; Bousquet, Jean ; Kumar, Ashish ; Söderhäll, Cilla ; Almqvist, Catarina ; Cardenas, Andres ; Gruzieva, Olena ; Xu, Cheng Jian ; Reese, Sarah E. ; Kere, Juha ; Brodin, Petter ; Solomon, Olivia ; Wielscher, Matthias ; Holland, Nina ; Ghantous, Akram ; Hivert, Marie France ; Felix, Janine F. ; Koppelman, Gerard H. ; London, Stephanie J. ; Melén, Erik - \ 2020
    Genome Medicine 12 (2020)1. - ISSN 1756-994X
    Development - Epigenetics - Gestational age - Preterm birth - Transcriptomics

    Background: Preterm birth and shorter duration of pregnancy are associated with increased morbidity in neonatal and later life. As the epigenome is known to have an important role during fetal development, we investigated associations between gestational age and blood DNA methylation in children. Methods: We performed meta-analysis of Illumina's HumanMethylation450-array associations between gestational age and cord blood DNA methylation in 3648 newborns from 17 cohorts without common pregnancy complications, induced delivery or caesarean section. We also explored associations of gestational age with DNA methylation measured at 4-18 years in additional pediatric cohorts. Follow-up analyses of DNA methylation and gene expression correlations were performed in cord blood. DNA methylation profiles were also explored in tissues relevant for gestational age health effects: Fetal brain and lung. Results: We identified 8899 CpGs in cord blood that were associated with gestational age (range 27-42 weeks), at Bonferroni significance, P < 1.06 × 10-7, of which 3343 were novel. These were annotated to 4966 genes. After restricting findings to at least three significant adjacent CpGs, we identified 1276 CpGs annotated to 325 genes. Results were generally consistent when analyses were restricted to term births. Cord blood findings tended not to persist into childhood and adolescence. Pathway analyses identified enrichment for biological processes critical to embryonic development. Follow-up of identified genes showed correlations between gestational age and DNA methylation levels in fetal brain and lung tissue, as well as correlation with expression levels. Conclusions: We identified numerous CpGs differentially methylated in relation to gestational age at birth that appear to reflect fetal developmental processes across tissues. These findings may contribute to understanding mechanisms linking gestational age to health effects.

    Benthic effects of offshore renewables: identification of knowledge gaps and urgently needed research
    Dannheim, Jennifer ; Bergström, Lena ; Birchenough, Silvana N.R. ; Brzana, Radosław ; Boon, Arjen R. ; Coolen, Joop W.P. ; Dauvin, Jean-Claude ; Mesel, Ilse De; Derweduwen, Jozefien ; Gill, Andrew B. ; Hutchison, Zoë L. ; Jackson, Angus C. ; Janas, Urszula ; Martin, Georg ; Raoux, Aurore ; Reubens, Jan ; Rostin, Liis ; Vanaverbeke, Jan ; Wilding, Thomas A. ; Wilhelmsson, Dan ; Degraer, Steven ; Norkko, Joanna - \ 2020
    ICES Journal of Marine Science 77 (2020)3. - ISSN 1054-3139 - p. 1092 - 1108.
    benthos - environmental impact - knowlegde gaps - marine ecology - offshore wind farms - renewable energy
    As the EU's commitment to renewable energy is projected to grow to 20% of energy generation by 2020, the use of marine renewable energy from wind, wave and tidal resources is increasing. This literature review (233 studies) (i) summarizes knowledge on how marine renewable energy devices affect benthic environments, (ii) explains how these effects could alter ecosystem processes that support major ecosystem services and (iii) provides an approach to determine urgent research needs. Conceptual diagrams were set up to structure hypothesized cause-effect relationships (i.e. paths). Paths were scored for (i) temporal and spatial scale of the effect, (ii) benthic sensitivity to these effects, (iii) the effect consistency and iv) scoring confidence, and consecutively ranked. This approach identified prominent knowledge gaps and research needs about (a) hydrodynamic changes possibly resulting in altered primary production with potential consequences for filter feeders, (b) the introduction and range expansion of non-native species (through stepping stone effects) and, (c) noise and vibration effects on benthic organisms. Our results further provide evidence that benthic sensitivity to offshore renewable effects is higher than previously indicated. Knowledge on changes of ecological functioning through cascading effects is limited and requires distinct hypothesis-driven research combined with integrative ecological modelling.
    Impact of maternal body mass index and gestational weight gain on pregnancy complications: an individual participant data meta-analysis of European, North American and Australian cohorts
    Santos, S. ; Voerman, E. ; Amiano, P. ; Barros, H. ; Beilin, L.J. ; Bergström, A. ; Charles, M.A. ; Chatzi, L. ; Chevrier, C. ; Chrousos, G.P. ; Corpeleijn, E. ; Costa, O. ; Costet, N. ; Crozier, S. ; Devereux, G. ; Doyon, M. ; Eggesbø, M. ; Fantini, M.P. ; Farchi, S. ; Forastiere, F. ; Georgiu, V. ; Godfrey, K.M. ; Gori, D. ; Grote, V. ; Hanke, W. ; Hertz-Picciotto, I. ; Heude, B. ; Hivert, M.F. ; Hryhorczuk, D. ; Huang, R.C. ; Inskip, H. ; Karvonen, A.M. ; Kenny, L.C. ; Koletzko, B. ; Küpers, L.K. ; Lagström, H. ; Lehmann, I. ; Magnus, P. ; Majewska, R. ; Mäkelä, J. ; Manios, Y. ; McAuliffe, F.M. ; McDonald, S.W. ; Mehegan, J. ; Melén, E. ; Mommers, M. ; Morgen, C.S. ; Moschonis, G. ; Murray, D. ; Ní Chaoimh, C. ; Nohr, E.A. ; Nybo Andersen, A.M. ; Oken, E. ; Oostvogels, A.J.J.M. ; Pac, A. ; Papadopoulou, E. ; Pekkanen, J. ; Pizzi, C. ; Polanska, K. ; Porta, D. ; Richiardi, L. ; Rifas-Shiman, S.L. ; Roeleveld, N. ; Ronfani, L. ; Santos, A.C. ; Standl, M. ; Stigum, H. ; Stoltenberg, C. ; Thiering, E. ; Thijs, C. ; Torrent, M. ; Tough, S.C. ; Trnovec, T. ; Turner, S. ; Gelder, M.M.H.J. van; Rossem, L. van; Berg, A. von; Vrijheid, M. ; Vrijkotte, T.G.M. ; West, J. ; Wijga, A.H. ; Wright, J. ; Zvinchuk, O. ; Sørensen, T.I.A. ; Lawlor, D.A. ; Gaillard, R. ; Jaddoe, V.W.V. - \ 2019
    BJOG : an international journal of obstetrics and gynaecology 126 (2019)8. - ISSN 1470-0328 - p. 984 - 995.
    Birthweight - body mass index - pregnancy complications - preterm birth - weight gain

    Objective: To assess the separate and combined associations of maternal pre-pregnancy body mass index (BMI) and gestational weight gain with the risks of pregnancy complications and their population impact. Design: Individual participant data meta-analysis of 39 cohorts. Setting: Europe, North America, and Oceania. Population: 265 270 births. Methods: Information on maternal pre-pregnancy BMI, gestational weight gain, and pregnancy complications was obtained. Multilevel binary logistic regression models were used. Main outcome measures: Gestational hypertension, pre-eclampsia, gestational diabetes, preterm birth, small and large for gestational age at birth. Results: Higher maternal pre-pregnancy BMI and gestational weight gain were, across their full ranges, associated with higher risks of gestational hypertensive disorders, gestational diabetes, and large for gestational age at birth. Preterm birth risk was higher at lower and higher BMI and weight gain. Compared with normal weight mothers with medium gestational weight gain, obese mothers with high gestational weight gain had the highest risk of any pregnancy complication (odds ratio 2.51, 95% CI 2.31– 2.74). We estimated that 23.9% of any pregnancy complication was attributable to maternal overweight/obesity and 31.6% of large for gestational age infants was attributable to excessive gestational weight gain. Conclusions: Maternal pre-pregnancy BMI and gestational weight gain are, across their full ranges, associated with risks of pregnancy complications. Obese mothers with high gestational weight gain are at the highest risk of pregnancy complications. Promoting a healthy pre-pregnancy BMI and gestational weight gain may reduce the burden of pregnancy complications and ultimately the risk of maternal and neonatal morbidity. Tweetable abstract: Promoting a healthy body mass index and gestational weight gain might reduce the population burden of pregnancy complications.

    Meta-analysis of epigenome-wide association studies in neonates reveals widespread differential DNA methylation associated with birthweight
    Küpers, Leanne K. ; Monnereau, Claire ; Sharp, Gemma C. ; Yousefi, Paul ; Salas, Lucas A. ; Ghantous, Akram ; Page, Christian M. ; Reese, Sarah E. ; Wilcox, Allen J. ; Czamara, Darina ; Starling, Anne P. ; Novoloaca, Alexei ; Lent, Samantha ; Roy, Ritu ; Hoyo, Cathrine ; Breton, Carrie V. ; Allard, Catherine ; Just, Allan C. ; Bakulski, Kelly M. ; Holloway, John W. ; Everson, Todd M. ; Xu, Cheng Jian ; Huang, Rae Chi ; Plaat, Diana A. van der; Wielscher, Matthias ; Merid, Simon Kebede ; Ullemar, Vilhelmina ; Rezwan, Faisal I. ; Lahti, Jari ; Dongen, Jenny van; Langie, Sabine A.S. ; Richardson, Tom G. ; Magnus, Maria C. ; Nohr, Ellen A. ; Xu, Zongli ; Duijts, Liesbeth ; Zhao, Shanshan ; Zhang, Weiming ; Plusquin, Michelle ; DeMeo, Dawn L. ; Solomon, Olivia ; Heimovaara, Joosje H. ; Jima, Dereje D. ; Gao, Lu ; Bustamante, Mariona ; Perron, Patrice ; Wright, Robert O. ; Hertz-Picciotto, Irva ; Zhang, Hongmei ; Karagas, Margaret R. ; Gehring, Ulrike ; Marsit, Carmen J. ; Beilin, Lawrence J. ; Vonk, Judith M. ; Jarvelin, Marjo Riitta ; Bergström, Anna ; Örtqvist, Anne K. ; Ewart, Susan ; Villa, Pia M. ; Moore, Sophie E. ; Willemsen, Gonneke ; Standaert, Arnout R.L. ; Håberg, Siri E. ; Sørensen, Thorkild I.A. ; Taylor, Jack A. ; Räikkönen, Katri ; Yang, Ivana V. ; Kechris, Katerina ; Nawrot, Tim S. ; Silver, Matt J. ; Gong, Yun Yun ; Richiardi, Lorenzo ; Kogevinas, Manolis ; Litonjua, Augusto A. ; Eskenazi, Brenda ; Huen, Karen ; Mbarek, Hamdi ; Maguire, Rachel L. ; Dwyer, Terence ; Vrijheid, Martine ; Bouchard, Luigi ; Baccarelli, Andrea A. ; Croen, Lisa A. ; Karmaus, Wilfried ; Anderson, Denise ; Vries, Maaike de; Sebert, Sylvain ; Kere, Juha ; Karlsson, Robert ; Arshad, Syed Hasan ; Hämäläinen, Esa ; Routledge, Michael N. ; Boomsma, Dorret I. ; Feinberg, Andrew P. ; Newschaffer, Craig J. ; Govarts, Eva ; Moisse, Matthieu ; Fallin, M.D. ; Melén, Erik ; Prentice, Andrew M. ; Kajantie, Eero ; Almqvist, Catarina ; Oken, Emily ; Dabelea, Dana ; Boezen, H.M. ; Melton, Phillip E. ; Wright, Rosalind J. ; Koppelman, Gerard H. ; Trevisi, Letizia ; Hivert, Marie France ; Sunyer, Jordi ; Munthe-Kaas, Monica C. ; Murphy, Susan K. ; Corpeleijn, Eva ; Wiemels, Joseph ; Holland, Nina ; Herceg, Zdenko ; Binder, Elisabeth B. ; Davey Smith, George ; Jaddoe, Vincent W.V. ; Lie, Rolv T. ; Nystad, Wenche ; London, Stephanie J. ; Lawlor, Debbie A. ; Relton, Caroline L. ; Snieder, Harold ; Felix, Janine F. - \ 2019
    Nature Communications 10 (2019)1. - ISSN 2041-1723

    Birthweight is associated with health outcomes across the life course, DNA methylation may be an underlying mechanism. In this meta-analysis of epigenome-wide association studies of 8,825 neonates from 24 birth cohorts in the Pregnancy And Childhood Epigenetics Consortium, we find that DNA methylation in neonatal blood is associated with birthweight at 914 sites, with a difference in birthweight ranging from −183 to 178 grams per 10% increase in methylation (P Bonferroni < 1.06 x 10 −7 ). In additional analyses in 7,278 participants, <1.3% of birthweight-associated differential methylation is also observed in childhood and adolescence, but not adulthood. Birthweight-related CpGs overlap with some Bonferroni-significant CpGs that were previously reported to be related to maternal smoking (55/914, p = 6.12 x 10 −74 ) and BMI in pregnancy (3/914, p = 1.13x10 −3 ), but not with those related to folate levels in pregnancy. Whether the associations that we observe are causal or explained by confounding or fetal growth influencing DNA methylation (i.e. reverse causality) requires further research.

    Maternal body mass index, gestational weight gain, and the risk of overweight and obesity across childhood : An individual participant data meta-analysis
    Voerman, Ellis ; Santos, Susana ; Patro Golab, Bernadeta ; Amiano, Pilar ; Ballester, Ferran ; Barros, Henrique ; Bergström, Anna ; Charles, Marie Aline ; Chatzi, Leda ; Chevrier, Cécile ; Chrousos, George P. ; Corpeleijn, Eva ; Costet, Nathalie ; Crozier, Sarah ; Devereux, Graham ; Eggesbø, Merete ; Ekström, Sandra ; Fantini, Maria Pia ; Farchi, Sara ; Forastiere, Francesco ; Georgiu, Vagelis ; Godfrey, Keith M. ; Gori, Davide ; Grote, Veit ; Hanke, Wojciech ; Hertz-Picciotto, Irva ; Heude, Barbara ; Hryhorczuk, Daniel ; Huang, Rae Chi ; Inskip, Hazel ; Iszatt, Nina ; Karvonen, Anne M. ; Kenny, Louise C. ; Koletzko, Berthold ; Küpers, Leanne K. ; Lagström, Hanna ; Lehmann, Irina ; Magnus, Per ; Majewska, Renata ; Mäkelä, Johanna ; Manios, Yannis ; McAuliffe, Fionnuala M. ; McDonald, Sheila W. ; Mehegan, John ; Mommers, Monique ; Morgen, Camilla S. ; Mori, Trevor A. ; Moschonis, George ; Murray, Deirdre ; Chaoimh, Carol Ní ; Nohr, Ellen A. ; Nybo Andersen, Anne Marie ; Oken, Emily ; Oostvogels, Adriëtte J.J.M. ; Pac, Agnieszka ; Papadopoulou, Eleni ; Pekkanen, Juha ; Pizzi, Costanza ; Polanska, Kinga ; Porta, Daniela ; Richiardi, Lorenzo ; Rifas-Shiman, Sheryl L. ; Ronfani, Luca ; Santos, Ana C. ; Standl, Marie ; Stoltenberg, Camilla ; Thiering, Elisabeth ; Thijs, Carel ; Torrent, Maties ; Tough, Suzanne C. ; Trnovec, Tomas ; Turner, Steve ; Rossem, Lenie van; Berg, Andrea von; Vrijheid, Martine ; Vrijkotte, Tanja G.M. ; West, Jane ; Wijga, Alet ; Wright, John ; Zvinchuk, Oleksandr ; Sørensen, Thorkild I.A. ; Lawlor, Debbie A. ; Gaillard, Romy ; Jaddoe, Vincent W.V. - \ 2019
    PLOS Medicine 16 (2019)2. - ISSN 1549-1676 - p. e1002744 - e1002744.

    BACKGROUND: Maternal obesity and excessive gestational weight gain may have persistent effects on offspring fat development. However, it remains unclear whether these effects differ by severity of obesity, and whether these effects are restricted to the extremes of maternal body mass index (BMI) and gestational weight gain. We aimed to assess the separate and combined associations of maternal BMI and gestational weight gain with the risk of overweight/obesity throughout childhood, and their population impact. METHODS AND FINDINGS: We conducted an individual participant data meta-analysis of data from 162,129 mothers and their children from 37 pregnancy and birth cohort studies from Europe, North America, and Australia. We assessed the individual and combined associations of maternal pre-pregnancy BMI and gestational weight gain, both in clinical categories and across their full ranges, with the risks of overweight/obesity in early (2.0-5.0 years), mid (5.0-10.0 years) and late childhood (10.0-18.0 years), using multilevel binary logistic regression models with a random intercept at cohort level adjusted for maternal sociodemographic and lifestyle-related characteristics. We observed that higher maternal pre-pregnancy BMI and gestational weight gain both in clinical categories and across their full ranges were associated with higher risks of childhood overweight/obesity, with the strongest effects in late childhood (odds ratios [ORs] for overweight/obesity in early, mid, and late childhood, respectively: OR 1.66 [95% CI: 1.56, 1.78], OR 1.91 [95% CI: 1.85, 1.98], and OR 2.28 [95% CI: 2.08, 2.50] for maternal overweight; OR 2.43 [95% CI: 2.24, 2.64], OR 3.12 [95% CI: 2.98, 3.27], and OR 4.47 [95% CI: 3.99, 5.23] for maternal obesity; and OR 1.39 [95% CI: 1.30, 1.49], OR 1.55 [95% CI: 1.49, 1.60], and OR 1.72 [95% CI: 1.56, 1.91] for excessive gestational weight gain). The proportions of childhood overweight/obesity prevalence attributable to maternal overweight, maternal obesity, and excessive gestational weight gain ranged from 10.2% to 21.6%. Relative to the effect of maternal BMI, excessive gestational weight gain only slightly increased the risk of childhood overweight/obesity within each clinical BMI category (p-values for interactions of maternal BMI with gestational weight gain: p = 0.038, p < 0.001, and p = 0.637 in early, mid, and late childhood, respectively). Limitations of this study include the self-report of maternal BMI and gestational weight gain for some of the cohorts, and the potential of residual confounding. Also, as this study only included participants from Europe, North America, and Australia, results need to be interpreted with caution with respect to other populations. CONCLUSIONS: In this study, higher maternal pre-pregnancy BMI and gestational weight gain were associated with an increased risk of childhood overweight/obesity, with the strongest effects at later ages. The additional effect of gestational weight gain in women who are overweight or obese before pregnancy is small. Given the large population impact, future intervention trials aiming to reduce the prevalence of childhood overweight and obesity should focus on maternal weight status before pregnancy, in addition to weight gain during pregnancy.

    Conflicts in the coastal zone : Human impacts on commercially important fish species utilizing coastal habitat
    Brown, Elliot J. ; Vasconcelos, Rita P. ; Wennhage, Håkan ; Bergström, Ulf ; Stottrup, Josianne G. ; Wolfshaar, Karen van de; Millisenda, Giacomo ; Colloca, Francesco ; Pape, Olivier Le - \ 2018
    ICES Journal of Marine Science 75 (2018)4. - ISSN 1054-3139 - p. 1203 - 1213.
    Anthropogenic pressure - coastal - ecosystem-based management - fisheries - habitat degradation - habitat loss - human activity

    Coastal ecosystems are ecologically, culturally, and economically important, and hence are under pressure from diverse human activities. We reviewed the literature for existing evidence of effects of human-induced habitat changes on exploited fish utilizing coastal habitats. We focused on fish species of the Northeast Atlantic for which fisheries advice is provided by International Council for the Exploration of the Sea (ICES) and which utilize coastal habitats for at least one life-history stage (LHS). We found that 92% of these species are impacted by human activity in at least one LHS while utilizing coastal habitat and 38% in multiple stages. Anthropogenic pressures most commonly shown to impact these fish species were toxicants and pollutants (75% of species). Eutrophication and anoxia, invasive species, and physical coastal development affected about half of the species (58, 54, and 42% of species, respectively), while indirect fishing impacts affected a minority (17% of species). Moreover, 71% of the ICES advice species that utilize coastal habitats face impacts from more than one pressure, implying cumulative effects. Given that three-fourths of the commercial landings come from fish species utilizing coastal habitats, there is an obvious need for a better understanding of the impacts that human activities cause in these habitats for the development of ecosystem-based fisheries management.

    Data from: Intestinal Ralstonia pickettii augments glucose intolerance in obesity
    Udayappan, Shanthadevi D. ; Kovatcheva-Datchary, Petia ; Bakker, Guido J. ; Havik, Stefan R. ; Herrema, Hilde ; Cani, Patrice D. ; Bouter, Kristien E. ; Belzer, C. ; Witjes, Julia J. ; Vrieze, Anne ; Sonnaville, Noor De; Chaplin, Alice ; Raalte, Daniël H. van; Aalvink, S. ; Dallinga-Thie, Geesje M. ; Heilig, G.H.J. ; Bergström, Göran ; Meij, Suzan Van Der; Wagensveld, Bart A. Van; Hoekstra, Joost B.L. ; Holleman, Frits ; Stroes, Erik S.G. ; Groen, Albert K. ; Bäckhed, Fredrik ; Vos, W.M. de; Nieuwdorp, Max - \ 2017
    University of Amsterdam
    microbiome - obesity - glucose intolerance - inflammation - Ralstonia pickettii
    An altered intestinal microbiota composition has been implicated in the pathogenesis of metabolic disease including obesity and type 2 diabetes mellitus (T2DM). Low grade inflammation, potentially initiated by the intestinal microbiota, has been suggested to be a driving force in the development of insulin resistance in obesity. Here, we report that bacterial DNA is present in mesenteric adipose tissue of obese but otherwise healthy human subjects. Pyrosequencing of bacterial 16S rRNA genes revealed that DNA from the Gram-negative species Ralstonia was most prevalent. Interestingly, fecal abundance of Ralstonia pickettii was increased in obese subjects with pre-diabetes and T2DM. To assess if R. pickettii was causally involved in development of obesity and T2DM, we performed a proof-of-concept study in diet-induced obese (DIO) mice. Compared to vehicle-treated control mice, R. pickettii-treated DIO mice had reduced glucose tolerance. In addition, circulating levels of endotoxin were increased in R. pickettii-treated mice. In conclusion, this study suggests that intestinal Ralstonia is increased in obese human subjects with T2DM and reciprocally worsens glucose tolerance in DIO mice.
    Intestinal Ralstonia pickettii augments glucose intolerance in obesity
    Udayappan, Shanthadevi D. ; Kovatcheva-Datchary, Petia ; Bakker, Guido J. ; Havik, Stefan R. ; Herrema, Hilde ; Cani, Patrice D. ; Bouter, Kristien E. ; Belzer, Clara ; Witjes, Julia J. ; Vrieze, Anne ; Sonnaville, Noor De; Chaplin, Alice ; Raalte, Daniël H. van; Aalvink, Steven ; Dallinga-Thie, Geesje M. ; Heilig, Hans G.H.J. ; Bergström, Göran ; Meij, Suzan Van Der; Wagensveld, Bart A. Van; Hoekstra, Joost B.L. ; Holleman, Frits ; Stroes, Erik S.G. ; Groen, Albert K. ; Bäckhed, Fredrik ; Vos, Willem M. de; Nieuwdorp, Max - \ 2017
    PLoS ONE 12 (2017)11. - ISSN 1932-6203
    An altered intestinal microbiota composition has been implicated in the pathogenesis of metabolic disease including obesity and type 2 diabetes mellitus (T2DM). Low grade inflammation, potentially initiated by the intestinal microbiota, has been suggested to be a driving force in the development of insulin resistance in obesity. Here, we report that bacterial DNA is present in mesenteric adipose tissue of obese but otherwise healthy human subjects. Pyrosequencing of bacterial 16S rRNA genes revealed that DNA from the Gram-negative species Ralstonia was most prevalent. Interestingly, fecal abundance of Ralstonia pickettii was increased in obese subjects with pre-diabetes and T2DM. To assess if R. pickettii was causally involved in development of obesity and T2DM, we performed a proof-of-concept study in diet-induced obese (DIO) mice. Compared to vehicle-treated control mice, R. pickettii-treated DIO mice had reduced glucose tolerance. In addition, circulating levels of endotoxin were increased in R. pickettii-treated mice. In conclusion, this study suggests that intestinal Ralstonia is increased in obese human subjects with T2DM and reciprocally worsens glucose tolerance in DIO mice.
    Genetic characterization of the horse breeds from the Netherlands using single nucleotide polymorphisms
    Shrestha, M. ; Eriksson, S. ; Schurink, A. ; Bergstrom, T. ; Ducro, B.J. ; Johansson, A. - \ 2016
    - p. P0560 - P0560.
    Genetic - nucleotide - Polymorphisms
    Interest on preservation and improvement of performance, fitness and aesthetic traits have created diverse populations in modern horses. This study aims to comprehend genetic diversity status within and across breeds or types of horses sampled in the Netherlands. The genetic diversity is important to maintain survival and adaptive potential of populations and avoid inbreeding in the long term. This study will also identify potential regions of selection. To our knowledge it is the first study to use single nucleotide polymorphism (SNP) information in a diversity study for the horses in the Netherlands. Principal component analysis (PCA) was performed using 203 randomly selected horses (about 20 per breed) and 43,721 autosomal SNPs that remained after pruning for call rate per SNP, per horse and minor allele frequency. The relationships among breeds were visualized by plotting the first two principal components. The Friesian breed seemed genetically distant from the other breeds in the dataset. The relationships among breeds will also be quantified based on FST values. Runs of homozygosity (ROH) using the software PliNK will be determined to identify the regions of selection. Also, diversity indices as heterozygosity (observed and expected) and fixation index (FIS) values will be investigated to understand within breed diversity.
    Future agriculture with minimized phosphorus losses to waters : Research needs and direction
    Sharpley, Andrew N. ; Bergström, Lars ; Aronsson, Helena ; Bechmann, Marianne ; Bolster, Carl H. ; Börling, Katarina ; Djodjic, Faruk ; Jarvie, Helen P. ; Schoumans, Oscar F. ; Stamm, Christian ; Tonderski, Karin S. ; Ulén, Barbro ; Uusitalo, Risto ; Withers, Paul J.A. - \ 2015
    Ambio 44 (2015)Supplement 2. - ISSN 0044-7447 - p. 163 - 179.
    Implementation - Manure - Mitigation measures - Monitoring - P management - Transport pathways
    The series of papers in this issue of AMBIO represent technical presentations made at the 7th International Phosphorus Workshop (IPW7), held in September, 2013 in Uppsala, Sweden. At that meeting, the 150 delegates were involved in round table discussions on major, predetermined themes facing the management of agricultural phosphorus (P) for optimum production goals with minimal water quality impairment. The six themes were (1) P management in a changing world; (2) transport pathways of P from soil to water; (3) monitoring, modeling, and communication; (4) importance of manure and agricultural production systems for P management; (5) identification of appropriate mitigation measures for reduction of P loss; and (6) implementation of mitigation strategies to reduce P loss. This paper details the major challenges and research needs that were identified for each theme and identifies a future roadmap for catchment management that cost-effectively minimizes P loss from agricultural activities.
    Genome-wide association study of insect bite hypersensitivity in swedish-born icelandic horses
    Shrestha, M. ; Eriksson, S. ; Schurink, A. ; Andersson, L.S. ; Sundquist, M. ; Frey, R. ; Brostrom, H. ; Bergstrom, T. ; Ducro, B.J. ; lindgren, G. - \ 2015
    Journal of Heredity 106 (2015)4. - ISSN 0022-1503 - p. 366 - 374.
    Insect bite hypersensitivity (IBH) is the most common allergic skin disease in horses and is caused by biting midges, mainly of the genus Culicoides. The disease predominantly comprises a type I hypersensitivity reaction, causing severe itching and discomfort that reduce the welfare and commercial value of the horse. It is a multifactorial disorder influenced by both genetic and environmental factors, with heritability ranging from 0.16 to 0.27 in various horse breeds. The worldwide prevalence in different horse breeds ranges from 3% to 60%; it is more than 50% in Icelandic horses exported to the European continent and approximately 8% in Swedish-born Icelandic horses. To minimize the influence of environmental effects, we analyzed Swedish-born Icelandic horses to identify genomic regions that regulate susceptibility to IBH. We performed a genomewide association (GWA) study on 104 affected and 105 unaffected Icelandic horses genotyped using Illumina® EquineSNP50 Genotyping BeadChip. Quality control and population stratification analyses were performed with the GenABEL package in R (¿ = 0.81). The association analysis was performed using the Bayesian variable selection method, Bayes C, implemented in GenSel software. The highest percentage of genetic variance was explained by the windows on X chromosomes (0.51% and 0.36% by 73 and 74 mb), 17 (0.34% by 77 mb), and 18 (0.34% by 26 mb). Overlapping regions with previous GWA studies were observed on chromosomes 7, 9, and 17. The windows identified in our study on chromosomes 7, 10, and 17 harbored immune system genes and are priorities for further investigation.
    Genomics and the challenging translation into conservation practice
    Shafer, A.B.A. ; Wolf, J.B.W. ; Alves, P.C. ; Bergstrom, L. ; Bruford, M.W. ; Brannstrom, I. ; Colling, G. ; Dalen, L. van; Meester, L. de; Ekblom, R. ; Vergeer, P. - \ 2015
    Trends in Ecology and Evolution 30 (2015)2. - ISSN 0169-5347 - p. 78 - 87.
    genetic diversity - background selection - population genomics - insular population - dna - divergence - speciation - evolution - sequence - markers
    The global loss of biodiversity continues at an alarming rate. Genomic approaches have been suggested as a promising tool for conservation practice as scaling up to genome-wide data can improve traditional conservation genetic inferences and provide qualitatively novel insights. However, the generation of genomic data and subsequent analyses and interpretations remain challenging and largely confined to academic research in ecology and evolution. This generates a gap between basic research and applicable solutions for conservation managers faced with multifaceted problems. Before the real-world conservation potential of genomic research can be realized, we suggest that current infrastructures need to be modified, methods must mature, analytical pipelines need to be developed, and successful case studies must be disseminated to practitioners.
    Targeting Membrane-Bound Viral RNA Synthesis Reveals Potent Inhibition of Diverse Coronaviruses Including the Middle East Respiratory Syndrome Virus
    Lundin, A. ; Dijkman, R. ; Bergstrom, T. ; Kann, N. ; Adamiak, B. ; Hannoun, C. ; Kindler, E. ; Jonsdottir, H.R. ; Muth, D. ; Kint, J. ; Forlenza, M. - \ 2014
    PLoS Pathogens 10 (2014)5. - ISSN 1553-7366 - 15 p.
    mouse hepatitis-virus - double-stranded-rna - sars coronavirus - replication complex - main proteinase - functional receptor - 3c-like proteinase - vaccinia virus - cell-cultures - in-vitro
    Coronaviruses raise serious concerns as emerging zoonotic viruses without specific antiviral drugs available. Here we screened a collection of 16671 diverse compounds for anti-human coronavirus 229E activity and identified an inhibitor, designated K22, that specifically targets membrane-bound coronaviral RNA synthesis. K22 exerts most potent antiviral activity after virus entry during an early step of the viral life cycle. Specifically, the formation of double membrane vesicles (DMVs), a hallmark of coronavirus replication, was greatly impaired upon K22 treatment accompanied by near-complete inhibition of viral RNA synthesis. K22-resistant viruses contained substitutions in non-structural protein 6 (nsp6), a membrane-spanning integral component of the viral replication complex implicated in DMV formation, corroborating that K22 targets membrane bound viral RNA synthesis. Besides K22 resistance, the nsp6 mutants induced a reduced number of DMVs, displayed decreased specific infectivity, while RNA synthesis was not affected. Importantly, K22 inhibits a broad range of coronaviruses, including Middle East respiratory syndrome coronavirus (MERS–CoV), and efficient inhibition was achieved in primary human epithelia cultures representing the entry port of human coronavirus infection. Collectively, this study proposes an evolutionary conserved step in the life cycle of positive-stranded RNA viruses, the recruitment of cellular membranes for viral replication, as vulnerable and, most importantly, druggable target for antiviral intervention. We expect this mode of action to serve as a paradigm for the development of potent antiviral drugs to combat many animal and human virus infections.
    Ecological value of coastal habitats for commercially and ecologically important species
    Seitz, R.D. ; Wennhage, H. ; Bergstrom, U. ; Lipcius, R.M. ; Ysebaert, T. - \ 2014
    ICES Journal of Marine Science 71 (2014)3. - ISSN 1054-3139 - p. 648 - 665.
    lobster homarus-gammarus - crab cancer-pagurus - bivalve macoma-balthica - shrimp crangon-crangon - mussel mytilus-edulis - southern north-sea - scallop placopecten-magellanicus - anchovy engraulis-encrasicolus - fish assemblage structure - sprat sprattus-sprattus
    Many exploited fish and macroinvertebrates that utilize the coastal zone have declined, and the causes of these declines, apart from overfishing, remain largely unresolved. Degradation of essential habitats has resulted in habitats that are no longer adequate to fulfil nursery, feeding, or reproductive functions, yet the degree to which coastal habitats are important for exploited species has not been quantified. Thus, we reviewed and synthesized literature on the ecological value of coastal habitats (i.e. seagrass beds, shallow subtidal and intertidal habitats, kelp beds, shallow open water habitats, saltmarshes, mussel beds, macroalgal beds, rocky bottom, and mariculture beds) as feeding grounds, nursery areas, spawning areas, and migration routes of 59 taxa, for which the International Council for the Exploration of the Sea (ICES) gives management advice, and another 12 commercially or ecologically important species. In addition, we provide detailed information on coastal habitat use for plaice (Pleuronectes platessa), cod (Gadus morhua), brown shrimp (Crangon crangon), and European lobster (Homarus gammarus). Collectively, 44% of all ICES species utilized coastal habitats, and these stocks contributed 77% of the commercial landings of ICES-advice species, indicating that coastal habitats are critical to population persistence and fishery yield of ICES species. These findings will aid in defining key habitats for protection and restoration and provide baseline information needed to define knowledge gaps for quantifying the habitat value for exploited fish and invertebrates.
    Genome wide association study of insect bite hypersensitivity in two populations of Icelandic horses
    Shrestha, M. ; Andersson, L.S. ; Fikse, F. ; Bergstrom, T. ; Schurink, A. ; Ducro, B.J. ; Eriksson, S. ; lindgren, G. - \ 2013
    - p. 146 - 146.
    insect bite hypersensitivity - icelandic horses
    Equine Insect Bite Hypersensitivity (IBH) is a chronic, intensely pruritic, recurrent seasonal dermatitis. lt is caused by an allergie reaction to protein in the saliva of biting midges of the genus Culicoides and sometimes also ~he genus Simulium. IBH in harses is mediated by lgE type 1 and type IV hypersensitivity reactions. Clinical symptoms such as hair loss, thickening of skin and formation of skin lesions leads to discomfort and disfigurement that impairs the quality of life of the horse and economical loss for the horse owner. Severely affected harses
    are sometimes euthanized. There are no cures or effective treatments for IBH till now, though preventive measures can ease the symptoms. IBH is a multifactorial disease that involves both environmental and genetic factors for development. The current worldwide prevalence ranges from 3% to 60%. Heritability for IBH has been estimated to be around 0.10 on the observable scale and 0.33 (sd=0.19) on the liability scale in Swedish born lcelandic harses, and to 0.24 (sd=0.06) for Dutch Sh etland breeding mares and 0.16 (sd=0.06) on the liability scale
    for Friesian broodmares. Reducing prevalence through breeding is therefore possible, but traditional breeding would req uire extensive progeny testing, which is less efficient and not feasible in small breeds. lf genetic tests could be used this would improve the possibility to reduce IBH. With an aim to identify and quantify genomic regions associated with IBH, a genome wide association study was performed using lllumina Equine SOK SNP chip data for 209 Swedish born lcelandic harses, collected on a matched c~se control (104 cases and 105
    controls) half sib design. The analysis was based on single marker effect using the GenABEL package in R. A genome-wide significant association was observed on chromosome 23. The odds ratio for IBH development of the unfavorable allele was 23.4 and had a frequency of 0.1 in cases compared to 0.004 in controls. However, this tentative association needs to be confirmed by re -genotyping the individuals included in GWAS as well as genotyping additional harses. Borderline associations were observed on chromosomes 3, 10, 17, 18 and 32. For
    further confirmation association analysis using multi marker association model, based on a Bayesian variable selection method, will be performed. In addition, a combined GWAS will be performed on data of 146 lcelandic harses from the Netherlands and 209 lcelandic harses from Sweden using Bayesian methodology
    Genome wide association study of insect bite hypersensitivity in two populations of Icelandic horses
    Shrestha, M. ; Andersson, L.S. ; Fikse, F. ; Bergstrom, T. ; Schurink, A. ; Ducro, B.J. ; Eriksson, S. ; lindgren, G. - \ 2013
    icelandic horses - insect bite hypersensitivity
    Equine Insect Bite Hypersensitivity (IBH) is a chronic, intensely pruritic, recurrent seasonal dermatitis. lt is caused by an allergie reaction to protein in the saliva of biting midges of the genus Culicoides and sometimes also ~he genus Simulium. IBH in harses is mediated by lgE type 1 and type IV hypersensitivity reactions. Clinical symptoms such as hair loss, thickening of skin and formation of skin lesions leads to discomfort and disfigurement that impairs the quality of life of the horse and economical loss for the horse owner. Severely affected harses
    are sometimes euthanized. There are no cures or effective treatments for IBH till now, though preventive measures can ease the symptoms. IBH is a multifactorial disease that involves both environmental and genetic factors for development. The current worldwide prevalence ranges from 3% to 60%. Heritability for IBH has been estimated to be around 0.10 on the observable scale and 0.33 (sd=0.19) on the liability scale in Swedish born lcelandic harses, and to 0.24 (sd=0.06) for Dutch Sh etland breeding mares and 0.16 (sd=0.06) on the liability scale
    for Friesian broodmares. Reducing prevalence through breeding is therefore possible, but traditional breeding would req uire extensive progeny testing, which is less efficient and not feasible in small breeds. lf genetic tests could be used this would improve the possibility to reduce IBH. With an aim to identify and quantify genomic regions associated with IBH, a genome wide association study was performed using lllumina Equine SOK SNP chip data for 209 Swedish born lcelandic harses, collected on a matched c~se control (104 cases and 105
    controls) half sib design. The analysis was based on single marker effect using the GenABEL package in R. A genome-wide significant association was observed on chromosome 23. The odds ratio for IBH development of the unfavorable allele was 23.4 and had a frequency of 0.1 in cases compared to 0.004 in controls. However, this tentative association needs to be confirmed by re -genotyping the individuals included in GWAS as well as genotyping additional harses. Borderline associations were observed on chromosomes 3, 10, 17, 18 and 32. For
    further confirmation association analysis using multi marker association model, based on a Bayesian variable selection method, will be performed. In addition, a combined GWAS will be performed on data of 146 lcelandic harses from the Netherlands and 209 lcelandic harses from Sweden using Bayesian methodology
    Challenges to the Future - Conservation of the Antarctic
    Chown, S.L. ; Lee, J.E. ; Hughes, K.A. ; Barnes, J. ; Bergstrom, D.M. ; Convey, P. ; Cowan, D.A. ; Crosbie, K. ; Dyer, G. ; Frenot, Y. ; Grant, S.M. ; Herr, D. ; Kennicutt, M.C. ; Lamers, M.A.J. ; Murray, A. ; Possingham, H.P. ; Reid, K. ; Riddle, M.J. ; Ryan, P.G. ; Sanson, L. ; Shaw, J.D. ; Sparrow, M.D. ; Summerhayes, C. ; Terauds, A. ; Wall, D.H. - \ 2012
    Science 337 (2012)6091. - ISSN 0036-8075 - p. 158 - 159.
    The Antarctic Treaty System, acknowledged as a successful model of cooperative regulation of one of the globe's largest commons (1), is under substantial pressure. Concerns have been raised about increased stress on Antarctic systems from global environmental change and growing interest in the region's resources (2, 3). Although policy-makers may recognize these challenges, failure to respond in a timely way can have substantial negative consequences. We provide a horizon scan, a systematic means for identifying emerging trends and assisting decision-makers in identifying policies that address future challenges (2, 3). Previous analyses of conservation threats in the Antarctic have been restricted to matters for which available evidence is compelling (4). We reconsider these concerns because they might escalate quickly, judging from recent rapid environmental change in parts of Antarctica and increasing human interest in the region (see the map). We then focus on a more distant time horizon.
    Skill and uncertainty of a regional air quality model ensemble
    Vautard, R. ; Schaap, M. ; Bergström, R. ; Bessagnet, B. ; Brandt, J. ; Builtjes, P.J.H. ; Krol, M.C. - \ 2009
    Atmospheric Environment 43 (2009)31. - ISSN 1352-2310 - p. 4822 - 4832.
    2003 heat-wave - climate-change - pollution model - western-europe - surface ozone - aerosol - simulations - summer - validation - transport
    Recently several regional air quality projects were carried out to support the negotiation under the Clean Air For Europe (CAFE) programme by predicting the impact of emission control policies with an ensemble of models. Within these projects, CITYDELTA and EURODELTA, the fate of air quality at the scale of European cities or that of the European continent was studied using several models. In this article we focus on the results of EURODELTA. The predictive skill of the ensemble of models is described for ozone, nitrogen dioxide and secondary inorganic compounds, and the uncertainty in air quality modelling is examined through the model ensemble spread of concentrations. For ozone daily maxima the ensemble spread origin differs from one region to another. In the neighbourhood of cities or in mountainous areas the spread of predicted values does not span the range of observed data, due to poorly resolved emissions or complex-terrain meteorology. By contrast in Atlantic and North Sea coastal areas the spread of predicted values is found to be larger than the observations. This is attributed to large differences in the boundary conditions used in the different models. For NO2 daily averages the ensemble spread is generally too small compared with observations. This is because models miss highest values occurring in stagnant meteorology in stable boundary layers near cities. For secondary particulate matter compounds the simulated concentration spread is more balanced, observations falling nearly equiprobably within the ensemble, and the spread originates both from meteorology and aerosol chemistry and thermodynamics
    Evaluation of long-term ozone simulations from seven regional air quality models and their ensemble
    Loon, M. van; Vautard, R. ; Schaap, M. ; Bergström, R. ; Bessagnet, B. ; Brandt, J. ; Krol, M.C. - \ 2007
    Atmospheric Environment 41 (2007)10. - ISSN 1352-2310 - p. 2083 - 2097.
    tropospheric ozone - pollution model - european cities - western-europe - impact - variability - citydelta - summer
    Long-term ozone simulations from seven regional air quality models, the Unified EMEP model, LOTOS-EUROS, CHIMERE, RCG, MATCH, DEHM and TM5, are intercompared and compared to ozone measurements within the framework of the EuroDelta experiment, designed to assess air quality improvement at the European scale in response to emission reduction scenarios for 2020. Modelled ozone concentrations for the year 2001 are evaluated. The models reproduce the main features of the ozone diurnal cycle, but generally overestimate daytime ozone. LOTOS-EUROS and RCG have a more pronounced diurnal cycle variation than observations, while the reverse occurs for TM5. CHIMERE has a large positive bias, which can be explained by a systematic bias in boundary conditions. The other models and the ¿ensemble model¿, whose concentrations are by definition averaged over all models, represent accurately the diurnal cycle. The ability of the models to simulate day-to-day daily ozone average or maxima variability is examined by means of percentiles, root mean square errors and correlations. In general, daily maxima are better simulated than daily averages, and summertime concentrations are better simulated than wintertime concentrations. Summertime correlations range between 0.5 and 0.7 for daily averages and 0.6 and 0.8 for daily maxima. Two health-related indicators are used, the number of days of exceedance of the threshold for the daily maximal 8-h ozone concentration and the SOMO35. Both are well reproduced in terms of frequency, but the simultaneity of occurrence of exceedance days between observations and simulations is not well captured. The advantage of using an ensemble of models instead of a single model for the assessment of air quality is demonstrated. The ensemble average concentrations almost always exhibit a closer proximity to observations than any of the models. We also show that the spread of the model ensemble is fairly representative of the uncertainty in the simulations.
    Is regional air quality model diversity representative of uncertainty for ozone simulation?
    Vautard, R. ; Loon, M. van; Schaap, M. ; Bergstrom, R. ; Bessagnet, B. ; Brandt, J. ; Builtjes, P.J.H. ; Christensen, J.H. ; Cuvelier, C. ; Graff, A. ; Jonson, J.E. ; Krol, M.C. ; Langner, J. ; Roberts, P. ; Rouil, L. ; Stern, R. ; Tarrason, L. ; Thunis, P. ; Vignati, E. ; White, L. ; Wind, P. - \ 2006
    Geophysical Research Letters 33 (2006). - ISSN 0094-8276 - 5 p.
    pollution model - western-europe - ensemble
    We examine whether seven state-of-the-art European regional air quality models provide daily ensembles of predicted ozone maxima that encompass observations. Using tools borrowed from the evaluation of ensemble weather forecasting, we analyze statistics of simulated ensembles of ozone daily maxima over an entire summer season. Although the model ensemble overestimates ozone, the distribution of simulated concentrations is representative of the uncertainty. The spread of simulations is due to random fluctuations resulting from differences in model formulations and input data, but also to the spread between individual model systematic biases. The ensemble average skill increases as the spread decreases. The skill of the ensemble in giving probabilistic predictions of threshold exceedances is also demonstrated. These results allow for optimism about the ability of this ensemble to simulate the uncertainty of the impact of emission control scenarios.
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