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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    Long-term thermal sensitivity of Earth's tropical forests
    Sullivan, Martin J.P. ; Lewis, Simon L. ; Affum-Baffoe, Kofi ; Castilho, Carolina ; Costa, Flávia ; Sanchez, Aida Cuni ; Ewango, Corneille E.N. ; Hubau, Wannes ; Marimon, Beatriz ; Monteagudo-Mendoza, Abel ; Qie, Lan ; Sonké, Bonaventure ; Martinez, Rodolfo Vasquez ; Baker, Timothy R. ; Brienen, Roel J.W. ; Feldpausch, Ted R. ; Galbraith, David ; Gloor, Manuel ; Malhi, Yadvinder ; Aiba, Shin Ichiro ; Alexiades, Miguel N. ; Almeida, Everton C. ; Oliveira, Edmar Almeida de; Dávila, Esteban Álvarez ; Loayza, Patricia Alvarez ; Andrade, Ana ; Vieira, Simone Aparecida ; Aragão, Luiz E.O.C. ; Araujo-Murakami, Alejandro ; Arets, Eric J.M.M. ; Arroyo, Luzmila ; Ashton, Peter ; Aymard C, Gerardo ; Baccaro, Fabrício B. ; Banin, Lindsay F. ; Baraloto, Christopher ; Camargo, Plínio Barbosa ; Barlow, Jos ; Barroso, Jorcely ; Bastin, Jean François ; Batterman, Sarah A. ; Beeckman, Hans ; Begne, Serge K. ; Bennett, Amy C. ; Berenguer, Erika ; Berry, Nicholas ; Blanc, Lilian ; Boeckx, Pascal ; Bogaert, Jan ; Bonal, Damien ; Bongers, Frans ; Bradford, Matt ; Brearley, Francis Q. ; Brncic, Terry ; Brown, Foster ; Burban, Benoit ; Camargo, José Luís ; Castro, Wendeson ; Céron, Carlos ; Ribeiro, Sabina Cerruto ; Moscoso, Victor Chama ; Chave, Jerôme ; Chezeaux, Eric ; Clark, Connie J. ; Souza, Fernanda Coelho de; Collins, Murray ; Comiskey, James A. ; Valverde, Fernando Cornejo ; Medina, Massiel Corrales ; Costa, Lola da; Dančák, Martin ; Dargie, Greta C. ; Davies, Stuart ; Cardozo, Nallaret Davila ; Haulleville, Thales de; Medeiros, Marcelo Brilhante de; Aguila Pasquel, Jhon Del; Derroire, Géraldine ; Fiore, Anthony Di; Doucet, Jean Louis ; Dourdain, Aurélie ; Droissant, Vincent ; Duque, Luisa Fernanda ; Ekoungoulou, Romeo ; Elias, Fernando ; Erwin, Terry ; Esquivel-Muelbert, Adriane ; Fauset, Sophie ; Ferreira, Joice ; Llampazo, Gerardo Flores ; Foli, Ernest ; Ford, Andrew ; Gilpin, Martin ; Hall, Jefferson S. ; Hamer, Keith C. ; Hamilton, Alan C. ; Harris, David J. ; Hart, Terese B. ; Hédl, Radim ; Herault, Bruno ; Herrera, Rafael ; Higuchi, Niro ; Hladik, Annette ; Coronado, Eurídice Honorio ; Huamantupa-Chuquimaco, Isau ; Huasco, Walter Huaraca ; Jeffery, Kathryn J. ; Jimenez-Rojas, Eliana ; Kalamandeen, Michelle ; Djuikouo, Marie Noël Kamdem ; Kearsley, Elizabeth ; Umetsu, Ricardo Keichi ; Kho, Lip Khoon ; Killeen, Timothy ; Kitayama, Kanehiro ; Klitgaard, Bente ; Koch, Alexander ; Labrière, Nicolas ; Laurance, William ; Laurance, Susan ; Leal, Miguel E. ; Levesley, Aurora ; Lima, Adriano J.N. ; Lisingo, Janvier ; Lopes, Aline P. ; Lopez-Gonzalez, Gabriela ; Lovejoy, Tom ; Lovett, Jon C. ; Lowe, Richard ; Magnusson, William E. ; Malumbres-Olarte, Jagoba ; Manzatto, Ângelo Gilberto ; Marimon, Ben Hur ; Marshall, Andrew R. ; Marthews, Toby ; Almeida Reis, Simone Matias de; Maycock, Colin ; Melgaço, Karina ; Mendoza, Casimiro ; Metali, Faizah ; Mihindou, Vianet ; Milliken, William ; Mitchard, Edward T.A. ; Morandi, Paulo S. ; Mossman, Hannah L. ; Nagy, Laszlo ; Nascimento, Henrique ; Neill, David ; Nilus, Reuben ; Vargas, Percy Núñez ; Palacios, Walter ; Camacho, Nadir Pallqui ; Peacock, Julie ; Pendry, Colin ; Peñuela Mora, Maria Cristina ; Pickavance, Georgia C. ; Pipoly, John ; Pitman, Nigel ; Playfair, Maureen ; Poorter, Lourens ; Poulsen, John R. ; Poulsen, Axel Dalberg ; Preziosi, Richard ; Prieto, Adriana ; Primack, Richard B. ; Ramírez-Angulo, Hirma ; Reitsma, Jan ; Réjou-Méchain, Maxime ; Correa, Zorayda Restrepo ; Sousa, Thaiane Rodrigues de; Bayona, Lily Rodriguez ; Roopsind, Anand ; Rudas, Agustín ; Rutishauser, Ervan ; Abu Salim, Kamariah ; Salomão, Rafael P. ; Schietti, Juliana ; Sheil, Douglas ; Silva, Richarlly C. ; Espejo, Javier Silva ; Valeria, Camila Silva ; Silveira, Marcos ; Simo-Droissart, Murielle ; Simon, Marcelo Fragomeni ; Singh, James ; Soto Shareva, Yahn Carlos ; Stahl, Clement ; Stropp, Juliana ; Sukri, Rahayu ; Sunderland, Terry ; Svátek, Martin ; Swaine, Michael D. ; Swamy, Varun ; Taedoumg, Hermann ; Talbot, Joey ; Taplin, James ; Taylor, David ; Steege, Hans Ter; Terborgh, John ; Thomas, Raquel ; Thomas, Sean C. ; Torres-Lezama, Armando ; Umunay, Peter ; Gamarra, Luis Valenzuela ; Heijden, Geertje van der; Hout, Peter van der; Meer, Peter van der; Nieuwstadt, Mark van; Verbeeck, Hans ; Vernimmen, Ronald ; Vicentini, Alberto ; Vieira, Ima Célia Guimarães ; Torre, Emilio Vilanova ; Vleminckx, Jason ; Vos, Vincent ; Wang, Ophelia ; White, Lee J.T. ; Willcock, Simon ; Woods, John T. ; Wortel, Verginia ; Young, Kenneth ; Zagt, Roderick ; Zemagho, Lise ; Zuidema, Pieter A. ; Zwerts, Joeri A. ; Phillips, Oliver L. - \ 2020
    Science 368 (2020)6493. - ISSN 0036-8075 - p. 869 - 874.

    The sensitivity of tropical forest carbon to climate is a key uncertainty in predicting global climate change. Although short-term drying and warming are known to affect forests, it is unknown if such effects translate into long-term responses. Here, we analyze 590 permanent plots measured across the tropics to derive the equilibrium climate controls on forest carbon. Maximum temperature is the most important predictor of aboveground biomass (-9.1 megagrams of carbon per hectare per degree Celsius), primarily by reducing woody productivity, and has a greater impact per °C in the hottest forests (>32.2°C). Our results nevertheless reveal greater thermal resilience than observations of short-term variation imply. To realize the long-term climate adaptation potential of tropical forests requires both protecting them and stabilizing Earth's climate.

    Greenhouse gas emissions in the Netherlands 1990-2018 : National Inventory Report 2020
    Ruyssenaars, P.G. ; Coenen, P.W.H.G. ; Rienstra, J.D. ; Zijlema, P.J. ; Arets, E.J.M.M. ; Baas, K. ; Dröge, R. ; Geilenkirchen, G. ; Hoen, M. 't; Honig, E. ; Huet, B. van; Huis, E.P. van; Koch, W.W.R. ; Lagerwerf, L.L. ; Molder, R.A. te; Montfoort, J.A. ; Vonk, J. ; Zanten, M.C. van - \ 2020
    Bilthoen : National Institute for Public Health and the Environment (RIVM) - 528 p.
    Total greenhouse gas (GHG) emissions in the Netherlands in 2018 decreased by approximately 2.7 percent, in comparison with 2017 emissions. This decrease was mainly the result of decreased coal combustion for energy and heat production.In 2018, total GHG emissions (including indirect CO2 emissions and excluding emissions from Land use, land use change and forestry (LULUCF)) in the Netherlands amounted to 188.2 Tg CO2 eq. This is approximately 15.1 percent below the emissions in the base year 1990 (221.7 Tg CO2 eq.).CO2 emissions in 2018 were 1.6 percent below the level in the base year. The total of the emissions of methane, nitrous oxide and fluorinated gases (CH4, N2O and F-gases) was reduced by more than 50% over this period.This report documents the Netherlands’ annual submission for 2020 of its GHG emissions inventory in accordance with the 2006 IPCC Guidelines for National Greenhouse Gas Inventories (IPCC, 2006) prescribed by the United Nations Framework Convention on Climate Change (UNFCCC), the Kyoto Protocol (KP) and the European Union’s Greenhouse Gas Monitoring Mechanism.This report includes explanations of observed trends in emissions, an assessment of the sources with the highest contribution to total national emissions (key sources) and a description of the uncertainty in the emissions es timates. Estimation methods, data sources and emission factors (EFs) are described for each source category, and there is also a description of the quality assurance system and the verification activities performed on the data. The report also describes changes in methodologies since the previous submission (NIR 2019), the results of recalculations and planned improvements.
    Emergence and Selection of a Highly Pathogenic Avian Influenza H7N3 Virus
    Beerens, Nancy ; Heutink, Rene ; Harders, Frank ; Bossers, Alex ; Koch, Guus ; Peeters, Ben - \ 2020
    Journal of Virology 94 (2020)8. - ISSN 0022-538X
    adaptive mutations - avian influenza virus - pathotypes - virulence determinants

    Low-pathogenicity avian influenza (LPAI) viruses of subtypes H5 and H7 have the ability to spontaneously mutate to highly pathogenic (HPAI) virus variants, causing high mortality in poultry. The highly pathogenic phenotype is caused by mutation of the hemagglutinin (HA) cleavage site, but additional mutations may play a role. Evidence from the field for the switch to high pathogenicity remains scarce. This study provides direct evidence for LPAI-to-HPAI virus mutation during H7N3 infection of a turkey farm in the Netherlands. No severe clinical symptoms were reported at the farm, but deep sequencing of isolates from the infected turkeys revealed a minority of HPAI virus sequences (0.06%) in the virus population. The HPAI virus contained a 12-nucleotide insertion in the HA cleavage site that was likely introduced by a single event as no intermediates with shorter inserts were identified. This suggests nonhomologous recombination as the mechanism of insertion. Analysis of different organs of the infected turkeys showed the largest amount of HPAI virus in the lung (4.4%). The HPAI virus was rapidly selected in experimentally infected chickens after both intravenous and intranasal/intratracheal inoculation with a mixed virus preparation. Full-genome sequencing revealed that both pathotypes contained a deletion in the stalk region of the neuraminidase protein. We identified additional mutations in HA and polymerase basic protein 1 (PB1) in the HPAI virus, which were already present as minority variants in the LPAI virus population. Our findings provide more insight into the molecular changes and mechanisms involved in the emergence and selection of HPAI viruses.IMPORTANCE Low-pathogenicity avian influenza (LPAI) viruses circulate in wild birds and can be transmitted to poultry. LPAI viruses can mutate to become highly pathogenic avian influenza (HPAI) viruses causing severe disease and death in poultry. Little is known about this switch to high pathogenicity. We isolated an LPAI H7N3 virus from an infected turkey farm and showed that this contains small amounts of HPAI virus. The HPAI virus rapidly outcompeted the LPAI virus in chickens that were experimentally infected with this mixture of viruses. We analyzed the genome sequences of the LPAI and HPAI viruses and identified several changes that may be important for a virus to become highly pathogenic. This knowledge may be used for timely identification of LPAI viruses that pose a risk of becoming highly pathogenic in the field.

    Novel toscana virus reverse genetics system establishes NSS as an antagonist of type I interferon responses
    Woelfl, Franziska ; Léger, Psylvia ; Oreshkova, Nadia ; Pahmeier, Felix ; Windhaber, Stefan ; Koch, Jana ; Stanifer, Megan ; Sosa, Gleyder Roman ; Uckeley, Zina M. ; Rey, Felix A. ; Boulant, Steeve ; Kortekaas, Jeroen ; Wichgers Schreur, Paul J. ; Lozach, Pierre Yves - \ 2020
    Viruses 12 (2020)4. - ISSN 1999-4915
    Arbovirus - Bunyavirales - Interferon - Neglected diseases - Phenuiviridae - Phlebovirus - Reverse genetics - Sand fly fever - Toscana virus

    The sand fly-borne Toscana virus (TOSV) is the major cause of human meningoencephalitis in the Mediterranean basin during the summer season. In this work, we have developed a T7 RNA polymerase-driven reverse genetics system to recover infectious particles of a lineage B strain of TOSV. The viral protein pattern and growth properties of the rescued virus (rTOSV) were found to be similar to those of the corresponding wild-type (wt) virus. Using this system, we genetically engineered a TOSV mutant lacking expression of the non-structural protein NSs (rTOSVϕNSs). Unlike rTOSV and the wt virus, rTOSVϕNSs was unable to (i) suppress interferon (IFN)-b messenger RNA induction; and (ii) grow efficiently in cells producing IFN-b. Together, our results highlight the importance of NSs for TOSV in evading the IFN response and provide a comprehensive toolbox to investigate the TOSV life cycle in mammalian and insect host cells, including several novel polyclonal antibodies.

    Are low humidity levels a limiting factor for spider mite control by phytoseiid predators under fluctuating climatic conditions?
    Messelink, G.J. ; Leman, A. - \ 2020
    In: Integrated Control of Plant-Feeding Mites In: WG "Integrated Control of Plant-Feeding Mites". - IOBC-WPRS (IOBC-WPRS Bulletin ) - p. 101 - 102.
    Low humidity levels are assumed to be an important limiting factor for biological control of spider mites by phytoseiid predatory mites, mainly because of the vulnerability of the egg stage for drought. In this study, we evaluated the efficacy of several species of phythoseiid predatory mites for control of the spider mite Tetranychus urticae Koch at low(55%) and high (80%) humidity levels on greenhouse cucumber in two greenhouse trials where predators were released either before or after spider mite introductions. In the preventive trial,the best control was achieved by Neoseiulus californicus McGregor at both humidity levels.Spider mites were completely eradicated. None of the other species of predatory mites was able to reduce spider mite densities, except Transeius montdorensis (Schicha) at the low humidity level. In the curative trial, N. californicus was again the best performing predatory mite,together with Phytoseiulus persimilis Athias-Henriot. Spider mites were completely controlled at both humidity levels by these species. This suggests that low humidity levels during daytime do not necessarily disrupt the control of spider mites by these predators, possibly because of the humidity fluctuations between day and night. Humidity did also directly affect spider mites;densities were up to 3 times higher on plants in the greenhouse with low humidity levels than on plants with a high humidity level. This increased growth rate of spider mites at low humidity levels may be another explanation for the failure of spider mite control in practice. Yet, in order to enhance the biological control of spider mites at low humidity levels, it might be better to focus on methods that support the establishment of effective spider mite predators, rather than selecting drought adapted strains of predatory mites.
    Quality assurance program in HBM4EU: first results and future challenges
    Esteban, M. ; Nuebler, Stephanie ; Goen, Thomas ; Mol, J.G.J. ; Koch, Holger M. ; Hajslova, Jana ; Lankova, Darina ; Antignac, J.P. ; Vaccher, Vincent ; Pedraza, Susana ; Ramos, J. ; Bartolome, Monica ; Haji Abbas, Karin ; Kasper-Sonnenberg, Monika ; Bury, Daniel ; Castano, Argelia - \ 2019
    Highly pathogenic avian influenza a(H5n1) outbreaks in West Java Indonesia 2015–2016: Clinical manifestation and associated risk factors
    Karo-Karo, Desniwaty ; Diyantoro, ; Pribadi, Eko Sugeng ; Sudirman, Fransiscus Xaverius ; Kurniasih, Sussi Widi ; Sukirman, ; Indasari, Iin ; Muljono, David Handojo ; Koch, Guus ; Stegeman, Jan Arend - \ 2019
    Microorganisms 7 (2019)9. - ISSN 2076-2607
    Case-control - HPAI (H5N1) - Outbreak investigation - Risk factors - West Java

    Knowledge of outbreaks and associated risk factors is helpful to improve control of the Highly Pathogenic Avian Influenza A(H5N1) virus (HPAI) in Indonesia. This study was conducted to detect outbreaks of HPAI H5N1 in endemically infected regions by enhanced passive surveillance, to describe the clinical manifestation of these outbreaks and identify associated risk factors. From November 2015 to November 2016, HPAI outbreak investigations were conducted in seven districts of West Java. In total 64 outbreaks were confirmed out of 75 reported suspicions and outbreak characteristics were recorded. The highest mortality was reported in backyard chickens (average 59%, CI95%: 49–69%). Dermal apoptosis and lesions (64%, CI95%: 52–76%) and respiratory signs (39%, CI95%: 27–51%) were the clinical signs observed overall most frequently, while neurological signs were most frequently observed in ducks (68%, CI95%: 47–90%). In comparison with 60 non-infected control farms, the rate of visitor contacts onto a farm was associated with the odds of HPAI infection. Moreover, duck farms had higher odds of being infected than backyard farms, and larger farms had lower odds than small farms. Results indicate that better external biosecurity is needed to reduce transmission of HPAI A(H5N1) in Indonesia.

    Colletotrichum species associated with anthracnose of Pyrus spp. in China
    Fu, M. ; Crous, P.W. ; Bai, Q. ; Zhang, P.F. ; Xiang, J. ; Guo, Y.S. ; Zhao, F.F. ; Yang, M.M. ; Hong, N. ; Xu, W.X. ; Wang, G.P. - \ 2019
    Persoonia 42 (2019). - ISSN 0031-5850 - p. 1 - 35.
    Colletotrichum - Multi-gene phylogeny - Pathogenicity - Pyrus

    Colletotrichum species are plant pathogens, saprobes, and endophytes on a range of economically important hosts. However, the species occurring on pear remain largely unresolved. To determine the morphology, phylogeny and biology of Colletotrichum species associated with Pyrus plants, a total of 295 samples were collected from cultivated pear species (including P. pyrifolia, P. bretschneideri, and P. communis) from seven major pear-cultivation provinces in China. The pear leaves and fruits affected by anthracnose were sampled and subjected to fungus isolation, resulting in a total of 488 Colletotrichum isolates. Phylogenetic analyses based on six loci (ACT, TUB2, CAL, CHS-1, GAPDH, and ITS) coupled with morphology of 90 representative isolates revealed that they belong to 10 known Colletotrichum species, including C. aenigma, C. citricola, C. conoides, C. fioriniae, C. fructicola, C. gloeosporioides, C. karstii, C. plurivorum, C. siamense, C. wuxiense, and two novel species, described here as C. jinshuiense and C. pyrifoliae. Of these, C. fructicola was the most dominant, occurring on P. pyrifolia and P. bretschneideri in all surveyed provinces except in Shandong, where C. siamense was dominant. In contrast, only C. siamense and C. fioriniae were isolated from P. communis, with the former being dominant. In order to prove Koch’s postulates, pathogenicity tests on pear leaves and fruits revealed a broad diversity in pathogenicity and aggressiveness among the species and isolates, of which C. citricola, C. jinshuiense, C. pyrifoliae, and C. conoides appeared to be organ-specific on either leaves or fruits. This study also represents the first reports of C. citricola, C. conoides, C. karstii, C. plurivorum, C. siamense, and C. wuxiense causing anthracnose on pear.

    Greenhouse gas emissions in the Netherlands 1990-2017 : National inventory report 2019
    Ruyssenaars, P.G. ; Coenen, P.W.H.G. ; Zijlema, P.J. ; Arets, E.J.M.M. ; Baas, K. ; Dröge, R. ; Geilenkirchen, G. ; Hoen, M. 't; Honig, E. ; Huet, B. van; Huis, E.P. van; Koch, W.W.R. ; Lagerwerf, L.L. ; Molder, R.A. te; Montfoort, J.A. ; Peek, C.J. ; Vonk, J. ; Zanten, M.C. van - \ 2019
    RIVM - 420 p.
    An early β-glucan bath during embryo development increases larval size of Nile tilapia
    Jesus, Raphael B. de; Petit, Jules ; Pilarski, Fabiana ; Wiegertjes, Geert F. ; Koch, João Fernando A. ; Oliveira, Carlos A.F. de; Zanuzzo, Fábio S. - \ 2019
    Aquaculture Research 50 (2019)7. - ISSN 1355-557X - p. 2012 - 2014.
    fish larvae - growth performance - hatching - immunostimulant - prebiotics
    Genetic relationship between poultry and wild bird viruses during the highly pathogenic avian influenza H5N6 epidemic in the Netherlands, 2017–2018
    Beerens, N. ; Heutink, R. ; Pritz-Verschuren, S. ; Germeraad, E.A. ; Bergervoet, S.A. ; Harders, F. ; Bossers, A. ; Koch, G. - \ 2019
    Transboundary and Emerging Diseases 66 (2019)3. - ISSN 1865-1674 - p. 1370 - 1378.
    Avian influenza - full genome sequencing - genetic analysis - H5N6

    In the Netherlands, three commercial poultry farms and two hobby holdings were infected with highly pathogenic avian influenza (HPAI) H5N6 virus in the winter of 2017–2018. This H5N6 virus is a reassortant of HPAI H5N8 clade 2.3.4.4 group B viruses detected in Eurasia in 2016. H5N6 viruses were also detected in several dead wild birds during the winter. However, wild bird mortality was limited compared to the caused by the H5N8 group B virus in 2016–2017. H5N6 virus was not detected in wild birds after March, but in late summer infected wild birds were found again. In this study, the complete genome sequences of poultry and wild bird viruses were determined to study their genetic relationship. Genetic analysis showed that the outbreaks in poultry were not the result of farm-to-farm transmissions, but rather resulted from separate introductions from wild birds. Wild birds infected with viruses related to the first outbreak in poultry were found at short distances from the farm, within a short time frame. However, no wild bird viruses related to outbreaks 2 and 3 were detected. The H5N6 virus isolated in summer shares a common ancestor with the virus detected in outbreak 1. This suggests long-term circulation of H5N6 virus in the local wild bird population. In addition, the pathogenicity of H5N6 virus in ducks was determined, and compared to that of H5N8 viruses detected in 2014 and 2016. A similar high pathogenicity was measured for H5N6 and H5N8 group B viruses, suggesting that biological or ecological factors in the wild bird population may have affected the mortality rates during the H5N6 epidemic. These observations suggest different infection dynamics for the H5N6 and H5N8 group B viruses in the wild bird population.

    Reassortments among avian influenza A(H5N1) viruses circulating in Indonesia, 2015-2016
    Karo-Karo, Desniwaty ; Bodewes, Rogier ; Wibawa, Hendra ; Artika, I.M. ; Pribadi, Eko Sugeng ; Diyantoro, D. ; Pratomo, Widya ; Sugama, Agus ; Hendrayani, Nani ; Indasari, Iin ; Wibowo, Michael Haryadi ; Muljono, David Handojo ; Stegeman, Jan Arend ; Koch, Guus - \ 2019
    Emerging Infectious Diseases 25 (2019)3. - ISSN 1080-6040 - p. 465 - 472.

    Highly pathogenic avian influenza (HPAI) A(H5N1) viruses have been circulating since 2003 in Indonesia, with major impacts on poultry health, severe economic losses, and 168 fatal laboratory-confirmed human cases. We performed phylogenetic analysis on 39 full-genome H5N1 virus samples collected during outbreaks among poultry in 2015-2016 in West Java and compared them with recently published sequences from Indonesia. Phylogenetic analysis revealed that the hemagglutinin gene of all samples belonged to 2 genetic groups in clade 2.3.2.1c. We also observed these groups for the neuraminidase, nucleoprotein, polymerase, and polymerase basic 1 genes. Matrix, nonstructural protein, and polymerase basic 2 genes of some HPAI were most closely related to clade 2.1.3 instead of clade 2.3.2.1c, and a polymerase basic 2 gene was most closely related to Eurasian low pathogenicity avian influenza. Our results detected a total of 13 reassortment types among HPAI in Indonesia, mostly in backyard chickens in Indramayu.

    The development of a multiplex serological assay for avian influenza based on Luminex technology
    Germeraad, Evelien ; Achterberg, René ; Venema, Sandra ; Post, Jacob ; Leeuw, Olav de; Koch, Guus ; Wal, Fimme Jan van der; Beerens, Nancy - \ 2019
    Methods : a companion to Methods in enzymology 158 (2019). - ISSN 1046-2023 - p. 54 - 60.
    Avian influenza - Luminex - Multiplex - Poultry - Serology - Subtyping

    Avian influenza (AI) is an infectious disease in birds with enormous impact on the poultry sector. AI viruses are divided into different subtypes based on the antigenicity of their surface proteins haemagglutinin (HA) and neuraminidases (NA). In birds, 16 HA subtypes and 9 NA subtypes are detected in different combinations. Traditional serological methods for the subtyping of AI antibodies are labour-intensive and have to be performed for each HA and NA subtype separately. This study describes the development of a multiplex serological assay for subtyping AI antibodies in poultry sera using Luminex xMAP technology. This multiplex assay allows the detection of all AI serotypes in one single assay. For all HA and NA subtypes, recombinant proteins were purified and coupled to colour-coded magnetic bead sets. Using the Luminex MAGPIX device, binding of serum antibodies to the antigens on the bead sets is detected by fluorescent secondary antibodies, and the different bead sets are identified. The results of the multiplex assay were compared with that of the traditional singleplex assays. We show that serotyping using the novel multiplex serological assay is consistent with the results of the traditional assays in 97.8% of the reference sera and in 90.8% of the field sera. The assay has a higher sensitivity than the traditional assays, and requires a smaller sample volume. Therefore, the assay will allow complete AI-serotyping in small volumes of field sera, which will improve the monitoring of AI subtypes circulating in poultry significantly.

    Detecting signatures of pathogen-mediated selection using population genomics
    Buckley, James ; Holub, Eric B. ; Koch, Marcus A. ; Vergeer, P. ; Mable, Barbara K. - \ 2018
    University of Glasgow
    SRP148549 - PRJNA472246 - Arabidopsis lyrata
    This study used RAD-sequencing of Arabidopsis lyrata individuals sampled from across the range of two subspecies, A.l. lyrata (N.American) and A.l .petraea (European), to determine genome-wide patterns of polymorphism and genetic structure in this species. Using these data we also investigated whether genomic smoothing approaches across RAD loci could detect genomic regions showing signatures of balancing selection, specifically significantly elevated diversity and either elevated differentiation among geographic regions or shifts towards intermediate allele frequencies within regions. We then identified annotated disease resistance loci within these genomic regions of interest. Together this project shows that genome scans based on a small number of individuals sampled from a wide range of populations confirmed the relative scarcity of signatures of balancing selection across the genome, but also identified new potential disease resistance candidates within genomic regions showing signatures of balancing selection that would be strong candidates for further sequencing efforts.
    Data from: Brassicales phylogeny inferred from 72 plastid genes: a reanalysis of the phylogenetic localization of two paleopolyploid events and origin of novel chemical defenses
    Edger, Patrick P. ; Hall, Jocelyn C. ; Harkess, Alex ; Tang, Michelle ; Mohammadin, S. ; Schranz, M.E. ; Xiong, Zhiyong ; Leebens-Mack, James ; Meyers, Blake C. ; Sytsma, Kenneth J. ; Koch, Marcus A. ; Al-Shehbaz, Ihsan A. ; Pires, J.C. - \ 2018
    Michigan State University
    Glucosinolates - Phylogenetics - Plastomes - polyploidy - Whole Genome Duplications
    PREMISE OF THE STUDY - Previous phylogenetic studies employing molecular markers have yielded various insights into the evolutionary history across Brassicales, but many relationships between families remain poorly supported or unresolved. A recent phylotranscriptomic approach utilizing 1155 nuclear markers obtained robust estimates for relationships among 14 of 17 families. Here we report a complete family‐level phylogeny estimated using the plastid genome. METHODS - We conducted phylogenetic analyses on a concatenated data set comprising 44,926 bp from 72 plastid genes for species distributed across all 17 families. Our analysis includes three additional families, Tovariaceae, Salvadoraceae, and Setchellanthaceae, that were omitted in the previous phylotranscriptomic study. KEY RESULTS - Our phylogenetic analyses obtained fully resolved and strongly supported estimates for all nodes across Brassicales. Importantly, these findings are congruent with the topology reported in the phylotranscriptomic study. This consistency suggests that future studies could utilize plastid genomes as markers for resolving relationships within some notoriously difficult clades across Brassicales. We used this new phylogenetic framework to verify the placement of the At‐α event near the origin of Brassicaceae, with median date estimates of 31.8 to 42.8 million years ago and restrict the At‐β event to one of two nodes with median date estimates between 85 to 92.2 million years ago. These events ultimately gave rise to novel chemical defenses and are associated with subsequent shifts in net diversification rates. CONCLUSIONS - We anticipate that these findings will aid future comparative evolutionary studies across Brassicales, including selecting candidates for whole‐genome sequencing projects.
    SerpinA3N is a novel hypothalamic gene upregulated by a high-fat diet and leptin in mice
    Sergi, Domenico ; Campbell, Fiona M. ; Grant, Christine ; Morris, Amanda C. ; Bachmair, Eva Maria ; Koch, Christiane ; McLean, Fiona H. ; Muller, Aifric ; Hoggard, Nigel ; Roos, Baukje de; Porteiro, Begona ; Boekschoten, Mark V. ; McGillicuddy, Fiona C. ; Kahn, Darcy ; Nicol, Phyllis ; Benzler, Jonas ; Mayer, Claus Dieter ; Drew, Janice E. ; Roche, Helen M. ; Muller, Michael ; Nogueiras, Ruben ; Dieguez, Carlos ; Tups, Alexander ; Williams, Lynda M. - \ 2018
    Genes & Nutrition 13 (2018). - ISSN 1555-8932
    High-fat diet - Hypothalamus - Leptin - SerpinA3N

    Background: Energy homeostasis is regulated by the hypothalamus but fails when animals are fed a high-fat diet (HFD), and leptin insensitivity and obesity develops. To elucidate the possible mechanisms underlying these effects, a microarray-based transcriptomics approach was used to identify novel genes regulated by HFD and leptin in the mouse hypothalamus. Results: Mouse global array data identified serpinA3N as a novel gene highly upregulated by both a HFD and leptin challenge. In situ hybridisation showed serpinA3N expression upregulation by HFD and leptin in all major hypothalamic nuclei in agreement with transcriptomic gene expression data. Immunohistochemistry and studies in the hypothalamic clonal neuronal cell line, mHypoE-N42 (N42), confirmed that alpha 1-antichymotrypsin (α1AC), the protein encoded by serpinA3, is localised to neurons and revealed that it is secreted into the media. SerpinA3N expression in N42 neurons is upregulated by palmitic acid and by leptin, together with IL-6 and TNFα, and all three genes are downregulated by the anti-inflammatory monounsaturated fat, oleic acid. Additionally, palmitate upregulation of serpinA3 in N42 neurons is blocked by the NFκB inhibitor, BAY11, and the upregulation of serpinA3N expression in the hypothalamus by HFD is blunted in IL-1 receptor 1 knockout (IL-1R1 -/- ) mice. Conclusions: These data demonstrate that serpinA3 expression is implicated in nutritionally mediated hypothalamic inflammation.

    Biocontrol of plant diseases is not an unsafe technology!
    Koch, Eckhard ; Becker, J.O. ; Berg, Gabriele ; Hauschild, R. ; Jehle, J. ; Köhl, J. ; Smalle, Kornelia - \ 2018
    Journal of Plant Diseases and Protection 125 (2018)2. - ISSN 1861-3829 - p. 121 - 125.
    Biocontrol - Safety - Registration - Metabolites
    In their opinion paper "The unpredictable risk imposed by microbial secondary metabolites: how safe is biological control of plant diseases?" (J. Plant Dis. Prot. 124, 413-419; https://doi.org/10.1007/s41348-017-0109-5), H.B. Deising, I. Gase and Y. Kubo criticize the use of microbial pesticides in plant protection. They point to the ability of microorganisms to form toxic metabolites and fear severe health problems when antagonistic microorganisms are increasingly released into agro-ecosystems. In our opinion, this view fails to reflect the reality because it largely ignores the ecology of microorganisms. In this contribution, we state reasons why biocontrol of plant diseases is a safe technology.
    Restriction associated DNA-genotyping at multiple spatial scales in Arabidopsis lyrata reveals signatures of pathogen-mediated selection
    Buckley, James ; Holub, Eric B. ; Koch, Marcus A. ; Vergeer, Philippine ; Mable, Barbara K. - \ 2018
    BMC Genomics 19 (2018)1. - ISSN 1471-2164
    Arabidopsis lyrata - Balancing selection - Disease resistance - Genome scan - Mating system - Pathogens - Polymorphism - R-genes - RAD-seq

    Background: Genome scans based on outlier analyses have revolutionized detection of genes involved in adaptive processes, but reports of some forms of selection, such as balancing selection, are still limited. It is unclear whether high throughput genotyping approaches for identification of single nucleotide polymorphisms have sufficient power to detect modes of selection expected to result in reduced genetic differentiation among populations. In this study, we used Arabidopsis lyrata to investigate whether signatures of balancing selection can be detected based on genomic smoothing of Restriction Associated DNA sequencing (RAD-seq) data. We compared how different sampling approaches (both within and between subspecies) and different background levels of polymorphism (inbreeding or outcrossing populations) affected the ability to detect genomic regions showing key signatures of balancing selection, specifically elevated polymorphism, reduced differentiation and shifts towards intermediate allele frequencies. We then tested whether candidate genes associated with disease resistance (R-gene analogs) were detected more frequently in these regions compared to other regions of the genome. Results: We found that genomic regions showing elevated polymorphism contained a significantly higher density of R-gene analogs predicted to be under pathogen-mediated selection than regions of non-elevated polymorphism, and that many of these also showed evidence for an intermediate site-frequency spectrum based on Tajima's D. However, we found few genomic regions that showed both elevated polymorphism and reduced FST among populations, despite strong background levels of genetic differentiation among populations. This suggests either insufficient power to detect the reduced population structure predicted for genes under balancing selection using sparsely distributed RAD markers, or that other forms of diversifying selection are more common for the R-gene analogs tested. Conclusions: Genome scans based on a small number of individuals sampled from a wide range of populations were sufficient to confirm the relative scarcity of signatures of balancing selection across the genome, but also identified new potential disease resistance candidates within genomic regions showing signatures of balancing selection that would be strong candidates for further sequencing efforts.

    Evaluation of ELISA and haemagglutination inhibition as screening tests in serosurveillance for H5/H7 avian influenza in commercial chicken flocks
    Arnold, M.E. ; Slomka, M.J. ; Breed, A.C. ; Hjulsager, C.K. ; Pritz-Verschuren, S. ; Venema-Kemper, S. ; Bouwstra, R.J. ; Trebbien, R. ; Zohari, S. ; Ceeraz, V. ; Larsen, L.E. ; Manvell, R.J. ; Koch, G. ; Brown, I.H. - \ 2018
    Epidemiology and Infection 146 (2018)3. - ISSN 0950-2688 - p. 306 - 313.
    AIV (avian influenza virus) - Bayesian - ELISA (enzyme-linked immunosorbent assay) - H5/H7 AIV surveillance - HI (haemagglutination inhibition)

    Avian influenza virus (AIV) subtypes H5 and H7 can infect poultry causing low pathogenicity (LP) AI, but these LPAIVs may mutate to highly pathogenic AIV in chickens or turkeys causing high mortality, hence H5/H7 subtypes demand statutory intervention. Serological surveillance in the European Union provides evidence of H5/H7 AIV exposure in apparently healthy poultry. To identify the most sensitive screening method as the first step in an algorithm to provide evidence of H5/H7 AIV infection, the standard approach of H5/H7 antibody testing by haemagglutination inhibition (HI) was compared with an ELISA, which detects antibodies to all subtypes. Sera (n = 1055) from 74 commercial chicken flocks were tested by both methods. A Bayesian approach served to estimate diagnostic test sensitivities and specificities, without assuming any ‘gold standard’. Sensitivity and specificity of the ELISA was 97% and 99.8%, and for H5/H7 HI 43% and 99.8%, respectively, although H5/H7 HI sensitivity varied considerably between infected flocks. ELISA therefore provides superior sensitivity for the screening of chicken flocks as part of an algorithm, which subsequently utilises H5/H7 HI to identify infection by these two subtypes. With the calculated sensitivity and specificity, testing nine sera per flock is sufficient to detect a flock seroprevalence of 30% with 95% probability.

    Greenhouse gas emissions in the Netherlands 1990-2016 : National Inventory Report 2018
    Coenen, P.W.H.G. ; Zanten, M.C. van; Zijlema, P.J. ; Arets, E.J.M.M. ; Baas, K. ; Berghe, A.C.W.M. van den; Huis, E.P. van; Geilenkirchen, G. ; Hoen, M. 't; Hoogsteen, M. ; Molder, R. te; Dröge, R. ; Montfoort, J.A. ; Peek, C.J. ; Vonk, J. ; Dellaert, S. ; Koch, W.W.R. - \ 2018
    Bilthoven : National Institute for Public Health and the Environment (RIVM report 2018-0006) - 406
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