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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Integrated Analys of High-Fat Challenge-Induced Changes in Blood Cell Whole-Genome Gene Expression
Matualatupauw, Juri C. ; O'Grada, Colm ; Hughes, Maria F. ; Roche, Helen M. ; Afman, Lydia A. ; Bouwman, Jildau - \ 2019
Molecular Nutrition & Food Research 63 (2019)20. - ISSN 1613-4125
bioinformatics - high-fat challenge - microarrays - nutrigenomics - phenotypic flexibility - saturated fatty acids

Scope: Several studies have examined the whole-genome gene expression response in blood cells to high-fat challenges with differing results. The study aims to identify consistently up- or downregulated genes and pathways in response to a high-fat challenge using several integration methods. Methods and results: Three studies measuring the gene expression response to a high-fat challenge in white blood cells are evaluated for common trends using several integration methods. Overlap in differentially expressed genes between separate studies is examined, p-values of each separate study are combined, and data are analyzed as one merged dataset. Differentially expressed genes and pathways are compared between these methods. Selecting genes differentially expressed in the three separate studies result in 67 differentially expressed genes, primarily involved in circadian pathways. Using the Fishers p-value method and a merged dataset analysis, changes in 1097 and 1182 genes, respectively, are observed. The upregulated genes upon a high-fat challenge are related to inflammation, whereas downregulated genes are related to unfolded protein response, protein processing, cholesterol biosynthesis, and translation. Conclusion: A general gene expression response to a high-fat challenge is identified. Compared to separate analyses, integrated analysis provides added value for the discovery of a consistent gene expression response.

Vitamin D-related genes, blood vitamin D levels and colorectal cancer risk in western european populations
Fedirko, Veronika ; Mandle, Hannah B. ; Zhu, Wanzhe ; Hughes, David J. ; Siddiq, Afshan ; Ferrari, Pietro ; Romieu, Isabelle ; Riboli, Elio ; Bueno-de-Mesquita, Bas ; Duijnhoven, Fränzel J.B. Van; Siersema, Peter D. ; Tjønneland, Anne ; Olsen, Anja ; Perduca, Vittorio ; Carbonnel, Franck ; Boutron-Ruault, Marie Christine ; Kühn, Tilman ; Johnson, Theron ; Krasimira, Aleksandrova ; Trichopoulou, Antonia ; Makrythanasis, Periklis ; Thanos, Dimitris ; Panico, Salvatore ; Krogh, Vittorio ; Sacerdote, Carlotta ; Skeie, Guri ; Weiderpass, Elisabete ; Colorado-Yohar, Sandra ; Sala, Núria ; Barricarte, Aurelio ; Sanchez, Maria Jose ; Quirós, Ramón ; Amiano, Pilar ; Gylling, Björn ; Harlid, Sophia ; Perez-Cornago, Aurora ; Heath, Alicia K. ; Tsilidis, Konstantinos K. ; Aune, Dagfinn ; Freisling, Heinz ; Murphy, Neil ; Gunter, Marc J. ; Jenab, Mazda - \ 2019
Nutrients 11 (2019)8. - ISSN 2072-6643
Colorectal neoplasms - Incidence - Single nucleotide polymorphism (SNP) - Vitamin D

Higher circulating 25-hydroxyvitamin D levels (25(OH)D) have been found to be associated with lower risk for colorectal cancer (CRC) in prospective studies. Whether this association is modified by genetic variation in genes related to vitamin D metabolism and action has not been well studied in humans. We investigated 1307 functional and tagging single-nucleotide polymorphisms (SNPs; individually, and by gene/pathway) in 86 vitamin D-related genes in 1420 incident CRC cases matched to controls from the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort. We also evaluated the association between these SNPs and circulating 25(OH)D in a subset of controls. We confirmed previously reported CRC risk associations between SNPs in the VDR, GC, and CYP27B1 genes. We also identified additional associations with 25(OH)D, as well as CRC risk, and several potentially novel SNPs in genes related to vitamin D transport and action (LRP2, CUBN, NCOA7, and HDAC9). However, none of these SNPs were statistically significant after Benjamini-Hochberg (BH) multiple testing correction. When assessed by a priori defined functional pathways, tumor growth factor β(TGFβ) signaling was associated with CRC risk (P ≤ 0.001), with most statistically significant genes being SMAD7 (PBH = 0.008) and SMAD3 (PBH = 0.008), and 18 SNPs in the vitamin D receptor (VDR) binding sites (P = 0.036). The 25(OH)D-gene pathway analysis suggested that genetic variants in the genes related to VDR complex formation and transcriptional activity are associated with CRC depending on 25(OH)D levels (interaction P = 0.041). Additional studies in large populations and consortia, especially with measured circulating 25(OH)D, are needed to confirm our findings.

Human Milk Short-Chain Fatty Acid Composition is Associated with Adiposity Outcomes in Infants
Prentice, Philippa M. ; Schoemaker, Marieke H. ; Vervoort, Jacques ; Hettinga, Kasper ; Lambers, Tim T. ; Tol, Eric A.F. van; Acerini, Carlo L. ; Olga, Laurentya ; Petry, Clive J. ; Hughes, Ieuan A. ; Koulman, Albert ; Ong, Ken K. ; Dunger, David B. - \ 2019
The Journal of Nutrition 149 (2019)5. - ISSN 0022-3166 - p. 716 - 722.
breast milk - growth - lipids - nutrition - short chain fatty acids - weight

BACKGROUND: Presumed benefits of human milk (HM) in avoiding rapid infancy weight gain and later obesity could relate to its nutrient composition. However, data on breast milk composition and its relation with growth are sparse. OBJECTIVE: We investigated whether short-chain fatty acids (SCFAs), known to be present in HM and linked to energy metabolism, are associated with infancy anthropometrics. METHODS: In a prospective birth cohort, HM hindmilk samples were collected from 619 lactating mothers at 4-8 wk postnatally [median (IQR) age: 33.9 (31.3-36.5) y, body mass index (BMI) (kg/m2): 22.8 (20.9-25.2)]. Their offspring, born at 40.1 (39.1-41.0) wk gestation with weight 3.56 (3.22-3.87) kg and 51% male, were assessed with measurement of weight, length, and skinfold thickness at ages 3, 12, and 24 mo, and transformed to age- and sex-adjusted z scores. HM SCFAs were measured by 1H-nuclear magnetic resonance spectroscopy (NMR) and GC-MS. Multivariable linear regression models were conducted to analyze the relations between NMR HM SCFAs and infancy growth parameters with adjustment for potential confounders. RESULTS: NMR peaks for HM butyrate, acetate, and formic acid, but not propionate, were detected. Butyrate peaks were 17.8% higher in HM from exclusively breastfeeding mothers than mixed-feeding mothers (P = 0.003). HM butyrate peak values were negatively associated with changes in infant weight (standardized B = -0.10, P = 0.019) and BMI (B = -0.10, P = 0.018) between 3 and 12 mo, and negatively associated with BMI (B = -0.10, P = 0.018) and mean skinfold thickness (B = -0.10, P = 0.049) at age 12 mo. HM formic acid peak values showed a consistent negative association with infant BMI at all time points (B < = -0.10, P < = 0.014), whereas HM acetate was negatively associated with skinfold thickness at 3 mo (B = -0.10, P = 0.028) and 24 mo (B = -0.10, P = 0.036). CONCLUSIONS: These results suggest that HM SCFAs play a beneficial role in weight gain and adiposity during infancy. Further knowledge of HM SCFA function may inform future strategies to support healthy growth.

Nurturing Children's Healthy Eating : Position statement
Haines, Jess ; Haycraft, Emma ; Lytle, Leslie ; Nicklaus, Sophie ; Kok, Frans J. ; Merdji, Mohamed ; Fisberg, Mauro ; Moreno, Luis A. ; Goulet, Olivier ; Hughes, Sheryl O. - \ 2019
Appetite 137 (2019). - ISSN 0195-6663 - p. 124 - 133.
Adolescents - Children - Eating habits - Feeding practices - Feeding style - Pleasure of eating

The relationship between eating a healthy diet and positive health outcomes is well known; nurturing healthy eating among children therefore has the potential to improve public health. A healthy diet occurs when one's usual eating patterns include adequate nutrient intake and sufficient, but not excessive, energy intake to meet the energy needs of the individual. However, many parents struggle to establish healthy eating patterns in their children due to the pressures of modern life. Moreover, healthcare providers often do not have the time or the guidance they need to empower parents to establish healthy eating practices in their children. Based on existing evidence from epidemiologic and intervention research, the Nurturing Children's Healthy Eating collaboration, established by Danone Institute International, has identified four key themes that encourage and support healthy eating practices among children in the modern Western world. The first — positive parental feeding — explores how parenting practices and styles, such as avoiding food restriction, allowing children to make their own food choices, and encouraging children to self-limit their portion sizes, can influence children's dietary intake. The second — eating together — highlights the link between eating socialization through regular family meals and healthful diet among children. The third — a healthy home food environment — explores the impact on eating practices of family resources, food availability/accessibility, parental modeling, and cues for eating. The fourth — the pleasure of eating — associates children's healthy eating with pleasure through repeated exposure to healthful foods, enjoyable social meals, and enhancement of the cognitive qualities (e.g. thoughts or ideas) of healthful foods. This paper reviews the evidence leading to the characterization of these nurturing themes, and ways in which recommendations might be implemented in the home.

Taxonomy of the order Bunyavirales : second update 2018
Maes, Piet ; Adkins, Scott ; Alkhovsky, Sergey V. ; Avšič-Županc, Tatjana ; Ballinger, Matthew J. ; Bente, Dennis A. ; Beer, Martin ; Bergeron, Éric ; Blair, Carol D. ; Briese, Thomas ; Buchmeier, Michael J. ; Burt, Felicity J. ; Calisher, Charles H. ; Charrel, Rémi N. ; Choi, Il Ryong ; Clegg, J.C.S. ; Torre, Juan Carlos de la; Lamballerie, Xavier de; DeRisi, Joseph L. ; Digiaro, Michele ; Drebot, Mike ; Ebihara, Hideki ; Elbeaino, Toufic ; Ergünay, Koray ; Fulhorst, Charles F. ; Garrison, Aura R. ; Gāo, George Fú ; Gonzalez, Jean Paul J. ; Groschup, Martin H. ; Günther, Stephan ; Haenni, Anne Lise ; Hall, Roy A. ; Hewson, Roger ; Hughes, Holly R. ; Jain, Rakesh K. ; Jonson, Miranda Gilda ; Junglen, Sandra ; Klempa, Boris ; Klingström, Jonas ; Kormelink, Richard ; Lambert, Amy J. ; Langevin, Stanley A. ; Lukashevich, Igor S. ; Marklewitz, Marco ; Martelli, Giovanni P. ; Mielke-Ehret, Nicole ; Mirazimi, Ali ; Mühlbach, Hans Peter ; Naidu, Rayapati ; Zhang, Yong Zhen - \ 2019
Archives of Virology 164 (2019)3. - ISSN 0304-8608 - p. 927 - 941.

In October 2018, the order Bunyavirales was amended by inclusion of the family Arenaviridae, abolishment of three families, creation of three new families, 19 new genera, and 14 new species, and renaming of three genera and 22 species. This article presents the updated taxonomy of the order Bunyavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).

CowPI: A Rumen Microbiome Focussed Version of the PICRUSt Functional Inference Software
Wilkinson, Toby J. ; Huws, Sharon A. ; Edwards, J.E. ; Kingston-Smith, Alison H. ; Siu-Ting, Karen ; Hughes, Martin ; Rubino, Francesco ; Friedersdorff, Maximillian ; Creevey, Christopher J. - \ 2018
rumen - microbiome - metataxonomics - metagenomics
Metataxonomic 16S rDNA based studies are a commonplace and useful tool in the research of the microbiome, but they do not provide the full investigative power of metagenomics and metatranscriptomics for revealing the functional potential of microbial communities. However, the use of metagenomic and metatranscriptomic technologies is hindered by high costs and skills barrier necessary to generate and interpret the data. To address this, a tool for Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) was developed for inferring the functional potential of an observed microbiome profile, based on 16S data. This allows functional inferences to be made from metataxonomic 16S rDNA studies with little extra work or cost, but its accuracy relies on the availability of completely sequenced genomes of representative organisms from the community being investigated. The rumen microbiome is an example of a community traditionally underrepresented in genome and sequence databases, but recent efforts by projects such as the Global Rumen Census and Hungate 1000 have resulted in a wide sampling of 16S rDNA profiles and almost 500 fully sequenced microbial genomes from this environment. Using this information, we have developed “CowPI,” a focused version of the PICRUSt tool provided for use by the wider scientific community in the study of the rumen microbiome. We evaluated the accuracy of CowPI and PICRUSt using two 16S datasets from the rumen microbiome: one generated from rDNA and the other from rRNA where corresponding metagenomic and metatranscriptomic data was also available. We show that the functional profiles predicted by CowPI better match estimates for both the meta-genomic and transcriptomic datasets than PICRUSt, and capture the higher degree of genetic variation and larger pangenomes of rumen organisms. Nonetheless, whilst being closer in terms of predictive power for the rumen microbiome, there were differences when compared to both the metagenomic and metatranscriptome data and so we recommend, where possible, functional inferences from 16S data should not replace metagenomic and metatranscriptomic approaches. The tool can be accessed at http://www.cowpi.org and is provided to the wider scientific community for use in the study of the rumen microbiome
DeepGlobe 2018: A Challenge to Parse the Earth through Satellite Images
Demir, I. ; Koperski, K. ; Lindenbaum, D. ; Pang, G. ; Huang, J. ; Basu, S. ; Hughes, F. ; Tuia, D. ; Raska, R. - \ 2018
In: Proceedings 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition Workshops CVPRW 2018. - IEEE - ISBN 9781538661017 - p. 17200 - 17209.
We present the DeepGlobe 2018 Satellite Image Understanding Challenge, which includes three public competitions for segmentation, detection, and classification tasks on satellite images (Figure 1). Similar to other challenges in computer vision domain such as DAVIS[21] and COCO[33], DeepGlobe proposes three datasets and corresponding evaluation methodologies, coherently bundled in three competitions with a dedicated workshop co-located with CVPR 2018. We observed that satellite imagery is a rich and structured source of information, yet it is less investigated than everyday images by computer vision researchers. However, bridging modern computer vision with remote sensing data analysis could have critical impact to the way we understand our environment and lead to major breakthroughs in global urban planning or climate change research. Keeping such bridging objective in mind, DeepGlobe aims to bring together researchers from different domains to raise awareness of remote sensing in the computer vision community and vice-versa. We aim to improve and evaluate state-of-the-art satellite image understanding approaches, which can hopefully serve as reference benchmarks for future research in the same topic. In this paper, we analyze characteristics of each dataset, define the evaluation criteria of the competitions, and provide baselines for each task.
Bottom trawl fishing footprints on the world’s continental shelves
Amoroso, Ricardo O. ; Pitcher, C.R. ; Rijnsdorp, Adriaan D. ; Mcconnaughey, Robert A. ; Parma, Ana M. ; Suuronen, Petri ; Eigaard, Ole R. ; Bastardie, Francois ; Hintzen, Niels T. ; Althaus, Franziska ; Baird, Susan Jane ; Black, Jenny ; Buhl-Mortensen, Lene ; Campbell, Alexander B. ; Catarino, Rui ; Collie, Jeremy ; Cowan, James H. ; Durholtz, Deon ; Engstrom, Nadia ; Fairweather, Tracey P. ; Fock, Heino O. ; Ford, Richard ; Gálvez, Patricio A. ; Gerritsen, Hans ; Góngora, María Eva ; González, Jessica A. ; Hiddink, Jan G. ; Hughes, Kathryn M. ; Intelmann, Steven S. ; Jenkins, Chris ; Jonsson, Patrik ; Kainge, Paulus ; Kangas, Mervi ; Kathena, Johannes N. ; Kavadas, Stefanos ; Leslie, Rob W. ; Lewis, Steve G. ; Lundy, Mathieu ; Makin, David ; Martin, Julie ; Mazor, Tessa ; Gonzalez-Mirelis, Genoveva ; Newman, Stephen J. ; Papadopoulou, Nadia ; Posen, Paulette E. ; Rochester, Wayne ; Russo, Tommaso ; Sala, Antonello ; Semmens, Jayson M. ; Silva, Cristina - \ 2018
Proceedings of the National Academy of Sciences of the United States of America 115 (2018)43. - ISSN 0027-8424 - p. E10275 - E10282.
Bottom trawlers land around 19 million tons of fish and invertebrates annually, almost one-quarter of wild marine landings. The extent of bottom trawling footprint (seabed area trawled at least once in a specified region and time period) is often contested but poorly described. We quantify footprints using high-resolution satellite vessel monitoring system (VMS) and logbook data on 24 continental shelves and slopes to 1,000-m depth over at least 2 years. Trawling footprint varied markedly among regions: from <10% of seabed area in Australian and New Zealand waters, the Aleutian Islands, East Bering Sea, South Overall, 14% of the 7.8 million-km2 study area was trawled, and 86% was not trawled. Trawling activity was aggregated; the most intensively trawled areas accounting for 90% of activity comprised 77% of footprint on average. Regional swept area ratio (SAR; ratio of total swept area trawled annually to total area of region, a metric of trawling intensity) and footprint area were related, providing an approach to estimate regional trawling footprints when highresolution spatial data are unavailable. If SAR was ≤0.1, as in 8 of 24 regions, therewas >95% probability that >90%of seabed was not trawled. If SAR was 7.9, equal to the highest SAR recorded, there was >95% probability that >70% of seabed was trawled. Footprints were smaller and SAR was ≤0.25 in regions where fishing rates consistently met international sustainability benchmarks for fish stocks, implying collateral environmental benefits from sustainable fishing.
CowPI: A rumen microbiome focussed version of the PICRUSt functional inference software
Wilkinson, Toby J. ; Huws, Sharon A. ; Edwards, Joan E. ; Kingston-Smith, Alison H. ; Siu-Ting, Karen ; Hughes, Martin ; Rubino, Francesco ; Friedersdorff, Maximillian ; Creevey, Christopher J. - \ 2018
Frontiers in Microbiology 9 (2018). - ISSN 1664-302X
16S amplicon - CowPI - Function - PICRUSt - Rumen

Metataxonomic 16S rDNA based studies are a commonplace and useful tool in the research of the microbiome, but they do not provide the full investigative power of metagenomics and metatranscriptomics for revealing the functional potential of microbial communities. However, the use of metagenomic and metatranscriptomic technologies is hindered by high costs and skills barrier necessary to generate and interpret the data. To address this, a tool for Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) was developed for inferring the functional potential of an observed microbiome profile, based on 16S data. This allows functional inferences to be made from metataxonomic 16S rDNA studies with little extra work or cost, but its accuracy relies on the availability of completely sequenced genomes of representative organisms from the community being investigated. The rumen microbiome is an example of a community traditionally underrepresented in genome and sequence databases, but recent efforts by projects such as the Global Rumen Census and Hungate 1000 have resulted in a wide sampling of 16S rDNA profiles and almost 500 fully sequenced microbial genomes from this environment. Using this information, we have developed "CowPI," a focused version of the PICRUSt tool provided for use by the wider scientific community in the study of the rumen microbiome. We evaluated the accuracy of CowPI and PICRUSt using two 16S datasets from the rumen microbiome: one generated from rDNA and the other from rRNA where corresponding metagenomic and metatranscriptomic data was also available. We show that the functional profiles predicted by CowPI better match estimates for both the meta-genomic and transcriptomic datasets than PICRUSt, and capture the higher degree of genetic variation and larger pangenomes of rumen organisms. Nonetheless, whilst being closer in terms of predictive power for the rumen microbiome, there were differences when compared to both the metagenomic and metatranscriptome data and so we recommend, where possible, functional inferences from 16S data should not replace metagenomic and metatranscriptomic approaches. The tool can be accessed at http://www.cowpi.org and is provided to the wider scientific community for use in the study of the rumen microbiome.

Atmosphere-vegetation-soil interactions in a climate change context; Impact of changing conditions on engineered transport infrastructure slopes in Europe
Tang, A.M. ; Hughes, P.N. ; Dijkstra, T.A. ; Askarinejad, A. ; Brenčič, M. ; Cui, Y.J. ; Diez, J.J. ; Firgi, T. ; Gajewska, B. ; Gentile, F. ; Grossi, G. ; Jommi, C. ; Kehagia, F. ; Koda, E. ; Maat, H.W. Ter; Lenart, S. ; Lourenco, S. ; Oliveira, M. ; Osinski, P. ; Springman, S.M. ; Stirling, R. ; Toll, D.G. ; Beek, V. Van - \ 2018
Quarterly Journal of Engineering Geology and Hydrogeology 51 (2018)2. - ISSN 1470-9236 - p. 156 - 168.

In assessing the impact of climate change on infrastructure, it is essential to consider the interactions between the atmosphere, vegetation and the near-surface soil. This paper presents an overview of these processes, focusing on recent advances from the literature and those made by members of COST Action TU1202 - Impacts of climate change on engineered slopes for infrastructure. Climate- and vegetation-driven processes (suction generation, erosion, desiccation cracking, freeze- thaw effects) are expected to change in incidence and severity, which will affect the stability of new and existing infrastructure slopes. This paper identifies the climate- and vegetation-driven processes that are of greatest concern, the suite of known unknowns that require further research, and lists key aspect that should be considered for the design of engineered transport infrastructure slopes in the context of climate change.

Response of benthic fauna to experimental bottom fishing : A global meta-analysis
Sciberras, Marija ; Hiddink, Jan Geert ; Jennings, Simon ; Szostek, Claire L. ; Hughes, Kathryn M. ; Kneafsey, Brian ; Clarke, Leo J. ; Ellis, Nick ; Rijnsdorp, Adriaan D. ; Mcconnaughey, Robert A. ; Hilborn, Ray ; Collie, Jeremy S. ; Pitcher, C.R. ; Amoroso, Ricardo O. ; Parma, Ana M. ; Suuronen, Petri ; Kaiser, Michel J. - \ 2018
Fish and Fisheries 19 (2018)4. - ISSN 1467-2960 - p. 698 - 715.
Dredging - Effects of trawling - Fishing impacts - Invertebrate communities - Systematic review - Taxonomic analysis
Bottom-contact fishing gears are globally the most widespread anthropogenic sources of direct disturbance to the seabed and associated biota. Managing these fishing disturbances requires quantification of gear impacts on biota and the rate of recovery following disturbance. We undertook a systematic review and meta-analysis of 122 experiments on the effects-of-bottom fishing to quantify the removal of benthos in the path of the fishing gear and to estimate rates of recovery following disturbance. A gear pass reduced benthic invertebrate abundance by 26% and species richness by 19%. The effect was strongly gear-specific, with gears that penetrate deeper into the sediment having a significantly larger impact than those that penetrate less. Sediment composition (% mud and presence of biogenic habitat) and the history of fishing disturbance prior to an experimental fishing event were also important predictors of depletion, with communities in areas that were not previously fished, predominantly muddy or biogenic habitats being more strongly affected by fishing. Sessile and low mobility biota with longer life-spans such as sponges, soft corals and bivalves took much longer to recover after fishing (>3 year) than mobile biota with shorter life-spans such as polychaetes and malacostracans (<1 year). This meta-analysis provides insights into the dynamics of recovery. Our estimates of depletion along with estimates of recovery rates and large-scale, high-resolution maps of fishing frequency and habitat will support more rigorous assessment of the environmental impacts of bottom-contact gears, thus supporting better informed choices in trade-offs between environmental impacts and fish production.
Ranavirus genotypes in Netherlands and their potential association with virulence in water frogs (Pelophylax spp.) article
Saucedo, Bernardo ; Hughes, Joseph ; Spitzen-Van Der Sluijs, Annemarieke ; Kruithof, Natasja ; Schills, Marc ; Rijks, Jolianne M. ; Jacinto-Maldonado, Mónica ; Suarez, Nicolás ; Haenen, Olga L.M. ; Voorbergen-Laarman, Michal ; Broek, Jan Van Den; Gilbert, Maarten ; Gröne, Andrea ; Beurden, Steven J. Van; Verheije, M.H. - \ 2018
Emerging Microbes and Infections 7 (2018)1. - ISSN 2222-1751
Ranaviruses are pathogenic viruses for poikilothermic vertebrates worldwide. The identification of a common midwife toad virus (CMTV) associated with massive die-offs in water frogs (Pelophylax spp.) in Netherlands has increased awareness for emerging viruses in amphibians in the country. Complete genome sequencing of 13 ranavirus isolates collected from ten different sites in the period 2011-2016 revealed three CMTV groups present in distinct geographical areas in Netherlands. Phylogenetic analysis showed that emerging viruses from the northern part of Netherlands belonged to CMTV-NL group I. Group II and III viruses were derived from the animals located in the center-east and south of the country, and shared a more recent common ancestor to CMTV-amphibian associated ranaviruses reported in China, Italy, Denmark, and Switzerland. Field monitoring revealed differences in water frog host abundance at sites where distinct ranavirus groups occur; with ranavirus-associated deaths, host counts decreasing progressively, and few juveniles found in the north where CMTV-NL group I occurs but not in the south with CMTV-NL group III. Investigation of tandem repeats of coding genes gave no conclusive information about phylo-geographical clustering, while genetic analysis of the genomes revealed truncations in 17 genes across CMTV-NL groups II and III compared to group I. Further studies are needed to elucidate the contribution of these genes as well as environmental variables to explain the observed differences in host abundance.
The intracellular immune receptor Rx1 regulates the DNA-binding activity of a Golden2-like transcription factor
Townsend, Philip D. ; Dixon, Christopher H. ; Slootweg, Erik J. ; Sukarta, Octavina C.A. ; Yang, Ally W.H. ; Hughes, Timothy R. ; Sharples, Gary J. ; Palsson, Lars-Olof ; Takken, Frank L.W. ; Goverse, Aska ; Cann, Martin J. - \ 2018
Journal of Biological Chemistry 293 (2018)9. - ISSN 0021-9258 - p. 3218 - 3233.
Plant NLR proteins enable the immune system to recognise and respond to pathogen attack. An early consequence of immune activation is transcriptional reprogramming and some NLRs have been shown to act in the nucleus and interact with transcription factors. The Rx1 NLR protein of potato is further able to bind and distort double-stranded DNA. However, Rx1 host targets that support a role for Rx1 in transcriptional reprogramming at DNA are unknown. Here we report a functional interaction between Rx1 and NbGlk1, a Golden2- like transcription factor. Rx1 binds to NbGlk1 in vitro and in planta. NbGlk1 binds to known Golden2-like consensus DNA sequences. Rx1 reduces the binding affinity of NbGlk1 for DNA in vitro. NbGlk1 activates cellular responses to potato virus X, whereas Rx1 associates with NbGlk1 and prevents its assembly on DNA in planta unless activated by PVX. This study provides new mechanistic insight into how an NLR can co-ordinate an immune signalling response at DNA following pathogen perception.
Complete genome sequence of a Frog Virus 3-like ranavirus from an Oophaga pumilio frog imported to the Netherlands
Saucedo, Bernardo ; Hughes, J. ; Suárez, Nicolás ; Haenen, O.L.M. ; Voorbergen-Laarman, H.A. ; Gröne, Andrea ; Kik, Marja J.L. ; Beurden, S.J. van - \ 2017
Complete genome sequence of frog virus 3, isolated from a strawberry poison frog (Oophaga pumilio) imported from nicaragua into the Netherlands
Saucedo, Bernardo ; Hughes, Joseph ; Beurden, Steven J. van; Suárez, Nicolás M. ; Haenen, Olga L.M. ; Voorbergen-Laarman, Michal ; Gröne, Andrea ; Kika, Marja J.L. - \ 2017
Genome Announcements 5 (2017)35. - ISSN 2169-8287
Frog virus 3 was isolated from a strawberry poison frog (Oophaga pumilio) imported from Nicaragua via Germany to the Netherlands, and its complete genome sequence was determined. Frog virus 3 isolate Op/2015/Netherlands/UU3150324001 is 107,183 bp long and has a nucleotide similarity of 98.26% to the reference Frog virus 3 isolate. ©
Global analysis of depletion and recovery of seabed biota after bottom trawling disturbance
Hiddink, Jan Geert ; Jennings, Simon ; Sciberras, Marija ; Szostek, Claire L. ; Hughes, Kathryn M. ; Ellis, Nick ; Rijnsdorp, Adriaan D. ; Mcconnaughey, Robert A. ; Mazor, Tessa ; Hilborn, Ray ; Collie, Jeremy S. ; Pitcher, C.R. ; Amoroso, Ricardo O. ; Parma, Ana M. ; Suuronen, Petri ; Kaiser, Michel J. - \ 2017
Proceedings of the National Academy of Sciences of the United States of America 114 (2017)31. - ISSN 0027-8424 - p. 8301 - 8306.
logistic recovery model - systematic review - metaanalysis - impacts - trawling
Bottom trawling is the most widespread human activity affecting seabed habitats. Here, we collate all available data for experimental and comparative studies of trawling impacts on whole communities of seabed macroinvertebrates on sedimentary habitats and develop widely applicable methods to estimate depletion and recovery rates of biota after trawling. Depletion of biota and trawl penetration into the seabed are highly correlated. Otter trawls caused the least depletion, removing 6% of biota per pass and penetrating the seabed on average down to 2.4 cm, whereas hydraulic dredges caused the most depletion, removing 41% of biota and penetrating the seabed on average 16.1 cm. Median recovery times posttrawling (from 50 to 95% of unimpacted biomass) ranged between 1.9 and 6.4 y. By accounting for the effects of penetration depth, environmental variation, and uncertainty, the models explained much of the variability of depletion and recovery estimates from single studies. Coupled with
large-scale, high-resolution maps of trawling frequency and habitat, our estimates of depletion and recovery rates enable the assessment of trawling impacts on unprecedented spatial scales.
Coral reefs in the Anthropocene
Hughes, Terry P. ; Barnes, Michele L. ; Bellwood, David R. ; Cinner, Joshua E. ; Cumming, Graeme S. ; Jackson, Jeremy B.C. ; Kleypas, Joanie ; De Leemput, Ingrid A. Van; Lough, Janice M. ; Morrison, Tiffany H. ; Palumbi, Stephen R. ; Nes, Egbert H. Van; Scheffer, Marten - \ 2017
Nature 546 (2017)7656. - ISSN 0028-0836 - p. 82 - 90.
Coral reefs support immense biodiversity and provide important ecosystem services to many millions of people. Yet reefs are degrading rapidly in response to numerous anthropogenic drivers. In the coming centuries, reefs will run the gauntlet of climate change, and rising temperatures will transform them into new configurations, unlike anything observed previously by humans. Returning reefs to past configurations is no longer an option. Instead, the global challenge is to steer reefs through the Anthropocene era in a way that maintains their biological functions. Successful navigation of this transition will require radical changes in the science, management and governance of coral reefs.
Estimating the sustainability of towed fishing-gear impacts on seabed habitats: a simple quantitative risk assessment method applicable to data-limited fisheries
Pitcher, C.R. ; Ellis, Nick ; Jennings, Simon ; Hiddink, Jan G. ; Mazor, Tessa ; Kaiser, Michel J. ; Kangas, Mervi I. ; Mcconnaughey, Robert A. ; Parma, Ana M. ; Rijnsdorp, Adriaan D. ; Suuronen, Petri ; Collie, Jeremy S. ; Amoroso, Ricardo ; Hughes, Kathryn M. ; Hilborn, Ray ; Freckleton, Robert - \ 2017
Methods in Ecology and Evolution 8 (2017). - ISSN 2041-210X - p. 472 - 480.
benthic fauna - depletion - ecological risk assessment - ecoystem-based fishery management - effects of trawling - recovery - resilience - sensivity - trawl footprints - vulnerability indicators
1. Impacts of bottom fishing, particularly trawling and dredging, on seabed (benthic) habitats are commonly perceived to pose serious environmental risks. Quantitative ecological risk assessment can be used to evaluate actual risks and to help guide the choice of management measures needed to meet sustainability objectives. 2. We develop and apply a quantitative method for assessing the risks to benthic habitats by towed bottom-fishing gears. The meth od is based on a simple eq uation for relative benthic status (RBS), derived by solving the logistic population growth equation for the equilibrium state. Estimating RBS requires only maps of fishing intensity and habitat type – and parameters for impact and recovery rates, which may be taken from meta-analyses of multiple experimental studies of towed-gear impacts. The aggregate status of habitats in an assessed region is indicated by the distribution of RBS values for the region. The application of RBS is illustrated for a tropical shrimp-trawl fishery. 3. The status of trawled habitats and their RBS value depend on impact rate (depletion per trawl), recovery rate and exposure to tra wling. In the shrimp-trawl fishery region, gravel habitat was most sensitive, and though less exposed than sand or mudd y-sand, was most affected overall (regional RBS = 91% relative to un-trawled RBS = 100%). Muddy-sand was less sensitive, and though relatively most exposed, was less affected overall (RBS = 95%). Sand was most heavily trawled but least sensitive and least affected overall (RBS = 98%). Region-wide , >94% of habitat area had >80% RBS because most tra wling and impacts were confined to small areas. RBS was also applied to the region’s benthic invertebrate communities with similar results. 4. Conclu sions. Unlike qualitative or categorical trait-based risk assessments, the RBS method provides a quantitative estimate of status relative to an unimpacted baseline, with minimal requireme nts for input data. It could be applied to bottom-contact fish erie s world-wide, including situations where detailed data on characteristics of seabed habitats, or the abundance of seabed fauna are not available. The approach supports assessment against sustainability criteria and evaluation of alternative management strategies (e.g. closed areas, effort management, gear modifications).
First report of Truncatella Angustata causing postharvest rot on ‘topaz’ apples in the Netherlands
Wenneker, M. ; Pham, K.T.K. ; Boekhoudt, L.C. ; Boer, F.A. de; Leeuwen, P.J. van; Hollinger, T.C. ; Thomma, B.P.H.J. - \ 2017
Plant Disease 101 (2017)3. - ISSN 0191-2917 - p. 508 - 508.

In the Netherlands, about 30% of the organic apple (Malus domestica Borkh.) production consists of apple scab resistant cultivars, such as Topaz and Santana. However, organic ‘Topaz’ apples show a high incidence of fungal rot after storage. Hot-water treatment (HWT) of freshly harvested apple fruit prior to long-term storage is an important strategy for the control of postharvest diseases, especially in the organic production sector (Maxin et al. 2012). The recommended treatment temperatures and times vary according to the cultivar because of the risk of heat damage to the fruit peel. In January 2016, light peel damage caused by HWT was observed on ‘Topaz’ apples from an organic orchard. Also, up to 15% of the ‘Topaz’ apples showed typical rot lesions of an unknown causal agent. The lesions showed brown, irregular necrosis and were slightly sunken. To isolate the causal agent, fruits were rinsed with sterile water, lesions were sprayed with 70% ethanol until droplet runoff, the skin was removed aseptically with a scalpel, and tissue under the lesion was placed onto potato dextrose agar (PDA). The PDA plates were incubated at 20°C in the dark, and single spore isolates were transferred to fresh PDA plates. The colonies that appeared on PDA were cottony to woolly, dull white to brown in color, with black acervuli mainly in the center of the PDA plates. The isolates produced four-celled conidia, 16 to 19 × 7 to 9 µm, straight to slightly curved, with two brown to dark-brown median cells that had thick walls. More than one hyaline apical appendage, variable in size and branched dichotomically, were observed and a basal appendage was absent. The fungus was morphologically identical to Truncatella angustata (Pers.) S. Hughes (Sutton 1980). The identity of two representative isolates (PPO-45246 and PPO-45321) was confirmed by means of gene sequencing. To this end, DNA was extracted using the LGC Mag Plant Kit (Berlin, Germany) in combination with the Kingfisher method (Waltham, MA). Sequences of the ITS region were amplified using primers ITS1/ITS4, sequenced, and deposited in GenBank under accession numbers KX085227 and KX085228. MegaBLAST analysis revealed that both of our ITS sequences matched 99% with T. angustata isolates in GenBank (EU342216, JX390614, and KF646105). Koch’s postulates were fulfilled using 10 ‘Topaz’ apples. Surface sterilized fruits were inoculated with 20 μl of 105 conidiospores ml–1 in water, prepared from a 15-day-old PDA culture of the isolate PPO-45246, after wounding with a needle. Inoculated fruits were sealed in a plastic bag and incubated in darkness at 20°C. Symptoms appeared after 7 days on 100% of the fruits while mock-inoculated controls with water remained symptomless. Fungal colonies isolated from the lesions and cultured on PDA morphologically resembled the inoculated isolates. The identity of the reisolations was confirmed as T. angustata by sequencing. T. angustata has a worldwide distribution and has also been reported to cause leaf spot on Rosa canina (Eken et al. 2009), canker and twig dieback on blueberry (Vaccinium spp.) (Espinoza et al. 2008), and fruit rot of olive (Olea europaea) (Arzanlou et al. 2012). To the best of our knowledge, this is the first report of T. angustata causing fruit rot of apples. Importantly, we note that the occurrence of this fruit rot may be enhanced by wounding, in this case as a result of hot water treatment.

Colonization and diversification of aquatic insects on three Macaronesian archipelagos using 59 nuclear loci derived from a draft genome
Rutschmann, Sereina ; Detering, Harald ; Simon, Sabrina ; Funk, David H. ; Gattolliat, Jean Luc ; Hughes, Samantha J. ; Raposeiro, Pedro M. ; DeSalle, Rob ; Sartori, Michel ; Monaghan, Michael T. - \ 2017
Molecular Phylogenetics and Evolution 107 (2017). - ISSN 1055-7903 - p. 27 - 38.
Baetidae - Island radiation - Multispecies coalescent - Phylogeny - Phylogeography

The study of processes driving diversification requires a fully sampled and well resolved phylogeny, although a lack of phylogenetic markers remains a limitation for many non-model groups. Multilocus approaches to the study of recent diversification provide a powerful means to study the evolutionary process, but their application remains restricted because multiple unlinked loci with suitable variation for phylogenetic or coalescent analysis are not available for most non-model taxa. Here we identify novel, putative single-copy nuclear DNA (nDNA) phylogenetic markers to study the colonization and diversification of an aquatic insect species complex, Cloeon dipterum L. 1761 (Ephemeroptera: Baetidae), in Macaronesia. Whole-genome sequencing data from one member of the species complex were used to identify 59 nDNA loci (32,213 base pairs), followed by Sanger sequencing of 29 individuals sampled from 13 islands of three Macaronesian archipelagos. Multispecies coalescent analyses established six putative species. Three island species formed a monophyletic clade, with one species occurring on the Azores, Europe and North America. Ancestral state reconstruction indicated at least two colonization events from the mainland (to the Canaries, respectively Azores) and one within the archipelago (between Madeira and the Canaries). Random subsets of the 59 loci showed a positive linear relationship between number of loci and node support. In contrast, node support in the multispecies coalescent tree was negatively correlated with mean number of phylogenetically informative sites per locus, suggesting a complex relationship between tree resolution and marker variability. Our approach highlights the value of combining genomics, coalescent-based phylogeography, species delimitation, and phylogenetic reconstruction to resolve recent diversification events in an archipelago species complex.

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