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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    Legacy effects of nitrogen and phosphorus additions on vegetation and carbon stocks of upland heaths
    Paassen, José G. van; Britton, Andrea J. ; Mitchell, Ruth J. ; Street, Lorna E. ; Johnson, David ; Coupar, Andrew ; Woodin, Sarah J. - \ 2020
    New Phytologist (2020). - ISSN 0028-646X
    long term - nitrogen deposition - nutrient cycling - soil - upland heath - vegetation

    Soil carbon (C) pools and plant community composition are regulated by nitrogen (N) and phosphorus (P) availability. Atmospheric N deposition impacts ecosystem C storage, but the direction of response varies between systems. Phosphorus limitation may constrain C storage response to N, hence P application to increase plant productivity and thus C sequestration has been suggested. We revisited a 23-yr-old field experiment where N and P had been applied to upland heath, a widespread habitat supporting large soil C stocks. At 10 yr after the last nutrient application we quantified long-term changes in vegetation composition and in soil and vegetation C and P stocks. Nitrogen addition, particularly when combined with P, strongly influenced vegetation composition, favouring grasses over Calluna vulgaris, and led to a reduction in vegetation C stocks. However, soil C stocks did not respond to nutrient treatments. We found 40% of the added P had accumulated in the soil. This study showed persistent effects of N and N + P on vegetation composition, whereas effects of P alone were small and showed recovery. We found no indication that P application could mitigate the effects of N on vegetation or increase C sequestration in this system.

    Colonies of the fungus Aspergillus niger are highly differentiated to adapt to local carbon source variation
    Daly, Paul ; Peng, Mao ; Mitchell, Hugh D. ; Kim, Young Mo ; Ansong, Charles ; Brewer, Heather ; Gijsel, Peter de; Lipton, Mary S. ; Markillie, Lye Meng ; Nicora, Carrie D. ; Orr, Galya ; Wiebenga, Ad ; Hildén, Kristiina S. ; Kabel, Mirjam A. ; Baker, Scott E. ; Mäkelä, Miia R. ; Vries, Ronald P. de - \ 2020
    Environmental Microbiology 22 (2020)3. - ISSN 1462-2912 - p. 1154 - 1166.

    Saprobic fungi, such as Aspergillus niger, grow as colonies consisting of a network of branching and fusing hyphae that are often considered to be relatively uniform entities in which nutrients can freely move through the hyphae. In nature, different parts of a colony are often exposed to different nutrients. We have investigated, using a multi-omics approach, adaptation of A. niger colonies to spatially separated and compositionally different plant biomass substrates. This demonstrated a high level of intra-colony differentiation, which closely matched the locally available substrate. The part of the colony exposed to pectin-rich sugar beet pulp and to xylan-rich wheat bran showed high pectinolytic and high xylanolytic transcript and protein levels respectively. This study therefore exemplifies the high ability of fungal colonies to differentiate and adapt to local conditions, ensuring efficient use of the available nutrients, rather than maintaining a uniform physiology throughout the colony.

    A review on yolk sac utilization in poultry
    Wagt, Ilonka van der; Jong, I.C. de; Mitchell, M.A. ; Molenaar, R. ; Brand, H. van den - \ 2020
    Poultry Science 99 (2020)4. - ISSN 0032-5791 - p. 2162 - 2175.
    During incubation, embryonic growth and development are dependent on nutrients deposited in the egg. The content of the yolk can be transferred to the embryo in 2 ways: directly into the intestine via the yolk stalk or through the highly vascularized yolk sac membrane. It has been suggested that, as a result of genetic selection and improved management, the increase in posthatch growth rate and concurrently the increase in metabolic rate of broiler chickens during the last 50 yr has also increased embryonic metabolism. A higher metabolic rate during incubation would imply a lower residual yolk weight and possibly lower energy reserve for the hatchling. This might affect posthatch development and performance. This review examined scientific publications published between 1930 and 2018 to compare residual yolk weight at hatch, metabolic heat production, and yolk utilization throughout incubation. This review aimed to investigate 1) whether or not residual yolk weight and composition has been changed during the 88-yr period considered and 2) which abiotic and biotic factors affect yolk utilization in poultry during incubation and the early posthatch period. It can be concluded that 1) residual yolk weight and the total solid amount of the residual yolk at hatch seem to be decreased in the recent decades. It cannot be concluded whether the (lack of) differences between old and modern strains are due to genetic selection, changed management and incubation conditions, or moment of sampling (immediately after hatch or at pulling). It is remarkable that with the genetic progress and improved management and incubation conditions over the last 88 yr, effects on yolk utilization efficiency and embryonic metabolic heat production are limited; 2) factors specially affecting residual yolk weight at hatch include egg size and incubation temperature, whereas breeder age has more influence on nutrient composition of the residual yolk.
    Experimental translocations to low predation lead to non-parallel increases in relative brain size
    Mitchell, David J. ; Vega-Trejo, Regina ; Kotrschal, Alexander - \ 2020
    Biology Letters 16 (2020)1. - ISSN 1744-9561 - 1 p.
    cognition - convergent evolution - predator–prey interactions - telencephalon

    Predation is a near ubiquitous factor of nature and a powerful selective force on prey. Moreover, it has recently emerged as an important driver in the evolution of brain anatomy, though population comparisons show ambiguous results with considerable unexplained variation. Here, we test the reproducibility of reduced predation on evolutionary trajectories of brain evolution. We make use of an introduction experiment, whereby guppies (Poecilia reticulata) from a single high predation stream were introduced to four low predation streams. After 8-9 years of natural selection in the wild and two generations of common garden conditions in the laboratory, we quantified brain anatomy. Relative brain region sizes did not differ between populations. However, we found a general increase and striking variation in relative brain size of introduced populations, which varied from no change to a 12.5% increase in relative brain weight, relative to the ancestral high predation population. We interpret this as evidence for non-parallel evolution, which implies a weak or inconsistent association of relative brain size with fitness in low predation sites. The evolution of brain anatomy appears sensitive to unknown environmental factors, or contingent on either chance events or historical legacies of environmental change.

    Global, regional, and national burden of neurological disorders, 1990–2016: a systematic analysis for the Global Burden of Disease Study 2016
    Feigin, Valery L. ; Nichols, Emma ; Alam, Tahiya ; Bannick, Marlena S. ; Beghi, Ettore ; Blake, Natacha ; Culpepper, William J. ; Dorsey, E.R. ; Elbaz, Alexis ; Ellenbogen, Richard G. ; Fisher, James L. ; Fitzmaurice, Christina ; Giussani, Giorgia ; Glennie, Linda ; James, Spencer L. ; Johnson, Catherine Owens ; Kassebaum, Nicholas J. ; Logroscino, Giancarlo ; Marin, Benoît ; Mountjoy-Venning, W.C. ; Nguyen, Minh ; Ofori-Asenso, Richard ; Patel, Anoop P. ; Piccininni, Marco ; Roth, Gregory A. ; Steiner, Timothy J. ; Stovner, Lars Jacob ; Szoeke, Cassandra E.I. ; Theadom, Alice ; Vollset, Stein Emil ; Wallin, Mitchell Taylor ; Wright, Claire ; Zunt, Joseph Raymond ; Abbasi, Nooshin ; Abd-Allah, Foad ; Abdelalim, Ahmed ; Abdollahpour, Ibrahim ; Aboyans, Victor ; Abraha, Haftom Niguse ; Acharya, Dilaram ; Adamu, Abdu A. ; Adebayo, Oladimeji M. ; Adeoye, Abiodun Moshood ; Adsuar, Jose C. ; Afarideh, Mohsen ; Agrawal, Sutapa ; Ahmadi, Alireza ; Ahmed, Muktar Beshir ; Aichour, Amani Nidhal ; Geleijnse, Johanna M. - \ 2019
    The Lancet Neurology 18 (2019)5. - ISSN 1474-4422 - p. 459 - 480.

    Background: Neurological disorders are increasingly recognised as major causes of death and disability worldwide. The aim of this analysis from the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2016 is to provide the most comprehensive and up-to-date estimates of the global, regional, and national burden from neurological disorders. Methods: We estimated prevalence, incidence, deaths, and disability-adjusted life-years (DALYs; the sum of years of life lost [YLLs] and years lived with disability [YLDs]) by age and sex for 15 neurological disorder categories (tetanus, meningitis, encephalitis, stroke, brain and other CNS cancers, traumatic brain injury, spinal cord injury, Alzheimer's disease and other dementias, Parkinson's disease, multiple sclerosis, motor neuron diseases, idiopathic epilepsy, migraine, tension-type headache, and a residual category for other less common neurological disorders) in 195 countries from 1990 to 2016. DisMod-MR 2.1, a Bayesian meta-regression tool, was the main method of estimation of prevalence and incidence, and the Cause of Death Ensemble model (CODEm) was used for mortality estimation. We quantified the contribution of 84 risks and combinations of risk to the disease estimates for the 15 neurological disorder categories using the GBD comparative risk assessment approach. Findings: Globally, in 2016, neurological disorders were the leading cause of DALYs (276 million [95% UI 247–308]) and second leading cause of deaths (9·0 million [8·8–9·4]). The absolute number of deaths and DALYs from all neurological disorders combined increased (deaths by 39% [34–44] and DALYs by 15% [9–21]) whereas their age-standardised rates decreased (deaths by 28% [26–30] and DALYs by 27% [24–31]) between 1990 and 2016. The only neurological disorders that had a decrease in rates and absolute numbers of deaths and DALYs were tetanus, meningitis, and encephalitis. The four largest contributors of neurological DALYs were stroke (42·2% [38·6–46·1]), migraine (16·3% [11·7–20·8]), Alzheimer's and other dementias (10·4% [9·0–12·1]), and meningitis (7·9% [6·6–10·4]). For the combined neurological disorders, age-standardised DALY rates were significantly higher in males than in females (male-to-female ratio 1·12 [1·05–1·20]), but migraine, multiple sclerosis, and tension-type headache were more common and caused more burden in females, with male-to-female ratios of less than 0·7. The 84 risks quantified in GBD explain less than 10% of neurological disorder DALY burdens, except stroke, for which 88·8% (86·5–90·9) of DALYs are attributable to risk factors, and to a lesser extent Alzheimer's disease and other dementias (22·3% [11·8–35·1] of DALYs are risk attributable) and idiopathic epilepsy (14·1% [10·8–17·5] of DALYs are risk attributable). Interpretation: Globally, the burden of neurological disorders, as measured by the absolute number of DALYs, continues to increase. As populations are growing and ageing, and the prevalence of major disabling neurological disorders steeply increases with age, governments will face increasing demand for treatment, rehabilitation, and support services for neurological disorders. The scarcity of established modifiable risks for most of the neurological burden demonstrates that new knowledge is required to develop effective prevention and treatment strategies. Funding: Bill & Melinda Gates Foundation.

    The Cultural and Spiritual Significance of Nature in the Management and Governance of Protected Areas and World Heritage Sites
    Bernbaum, E. ; Verschuuren, B. - \ 2019
    In: Proceedings of the 2018 US/ICOMOS Symposium. - San Francisco : US/ICOMOS - 18 p.
    This paper chronicles the evolution of the IUCN Specialist Group on the Cultural and Spiritual Values of Protected Areas (CSVPA) with a focus on the development of its current Cultural and Spiritual Nature Program, which includes IUCN Best Practices Guidelines, a peer-reviewed book, training modules, case studies, and a network -- all dedicated to promoting and integrating the cultural and spiritual significance of nature in the management and governance of protected and conserved areas. The program is being developed in conjunction with the IUCN ICOMOS Nature Culture and Culture Nature Journeys and seeks to create a comprehensive approach to the conservation of natural and cultural heritage. Six principles distilled from the input of 200 international experts and reviewers through editorial work and workshops at the World Parks Congress in Australia, the World Conservation Congress in Hawai’i, and the Isle of Vilm in Germany provide key insights and lessons learned. The paper concludes with next steps for implementing the Best Practice Guidelines through the development of training modules and workshops and a network for providing support and sharing experiences.
    The Role of Visualization in Controversies over Technological Developments
    Gommeh, E. ; Metze, T.A.P. ; Dijstelbloem, Huub - \ 2019
    Societal controversies over technological development, among them food technologies, often have a visual dimension. For example, an image of flammable tap water (originally from the documentary Gasland) strengthened the association of a contested technology – hydraulic fracturing – with risk and influenced the evolution of the controversy in some countries (Mazur 2016; Metze 2017). Yet, visualizations in controversies over technological developments are often overlooked. To better understand the role of visualization in these controversies we develop the Visual Discourse Coalitions approach by drawing on work on discourse coalitions (Bulkeley, 2000; Dodge & Lee, 2017; Hajer, 1995), the Dynamic Discourse Coalitions approach (Metze & Dodge, 2016) and visual political theory (Bleiker 2018; Mitchell 1994). In this paper we conceptualize ‘Visual Discourse Coalition’ (VDC), a network of actors who share a similar storyline and similar visual representations of the issue at hand, and develop the ‘VDC theoretical framework’ which approaches visualization as a practice that contributes to the evolution of discourse coalitions. We explore a method to identify VDC’s in controversies over technological developments and to reveal manners in which visualization contributes to discourse coalitions evolution. The goal of our research is to reveal how actors use visualization and influence the dynamics of the controversy. Drawing on empirical examples from the shale gas case we reveal four ways in which visualization influences discourse coalitions: (1) visualization repeats and strengthens storylines of discourse coalitions, (2) visualization connects storyline of different discourse coalitions, (3) visualization contributes to breaking apart of a discourse coalition into different ways of interpreting a policy issue, and (4) visualization emphasizes and increases the tension between storylines of different discourse coalitions. We suggest that the VDC theoretical and methodological frameworks can be applied to controversies over food technologies. They can highlight special features of visualizations and a unique way in which they influence the controversy. Moreover, the visual dimension of a controversy can expose new aspects of the controversy, and in some cases can result in an emergence of new actors in it. Thus, it is important for decision makers to acknowledge the visual dimension of a controversy and to study it.
    A global synthesis reveals biodiversity-mediated benefits for crop production
    Dainese, Matteo ; Martin, Emily A. ; Aizen, Marcelo A. ; Albrecht, Matthias ; Bartomeus, Ignasi ; Bommarco, Riccardo ; Carvalheiro, Luisa G. ; Chaplin-Kramer, Rebecca ; Gagic, Vesna ; Garibaldi, Lucas A. ; Ghazoul, Jaboury ; Grab, Heather ; Jonsson, Mattias ; Karp, Daniel S. ; Kennedy, Christina M. ; Kleijn, David ; Kremen, Claire ; Landis, Douglas A. ; Letourneau, Deborah K. ; Marini, Lorenzo ; Poveda, Katja ; Rader, Romina ; Smith, Henrik G. ; Tscharntke, Teja ; Andersson, Georg K.S. ; Badenhausser, Isabelle ; Baensch, Svenja ; Bezerra, Antonio D.M. ; Bianchi, Felix J.J.A. ; Boreux, Virginie ; Bretagnolle, Vincent ; Caballero-Lopez, Berta ; Cavigliasso, Pablo ; Ćetković, Aleksandar ; Chacoff, Natacha P. ; Classen, Alice ; Cusser, Sarah ; Silva E Silva, Felipe D. Da; Groot, G.A. de; Dudenhöffer, Jan H. ; Ekroos, Johan ; Fijen, Thijs ; Franck, Pierre ; Freitas, Breno M. ; Garratt, Michael P.D. ; Gratton, Claudio ; Hipólito, Juliana ; Holzschuh, Andrea ; Hunt, Lauren ; Iverson, Aaron L. ; Jha, Shalene ; Keasar, Tamar ; Kim, Tania N. ; Kishinevsky, Miriam ; Klatt, Björn K. ; Klein, Alexandra Maria ; Krewenka, Kristin M. ; Krishnan, Smitha ; Larsen, Ashley E. ; Lavigne, Claire ; Liere, Heidi ; Maas, Bea ; Mallinger, Rachel E. ; Pachon, Eliana Martinez ; Martínez-Salinas, Alejandra ; Meehan, Timothy D. ; Mitchell, Matthew G.E. ; Molina, Gonzalo A.R. ; Nesper, Maike ; Nilsson, Lovisa ; O'Rourke, Megan E. ; Peters, Marcell K. ; Plećaš, Milan ; Potts, Simon G. ; L. Ramos, Davi de; Rosenheim, Jay A. ; Rundlöf, Maj ; Rusch, Adrien ; Sáez, Agustín ; Scheper, Jeroen ; Schleuning, Matthias ; Schmack, Julia M. ; Sciligo, Amber R. ; Seymour, Colleen ; Stanley, Dara A. ; Stewart, Rebecca ; Stout, Jane C. ; Sutter, Louis ; Takada, Mayura B. ; Taki, Hisatomo ; Tamburini, Giovanni ; Tschumi, Matthias ; Viana, Blandina F. ; Westphal, Catrin ; Willcox, Bryony K. ; Wratten, Stephen D. ; Yoshioka, Akira ; Zaragoza-Trello, Carlos ; Zhang, Wei ; Zou, Yi ; Steffan-Dewenter, Ingolf - \ 2019
    Science Advances 5 (2019)10. - ISSN 2375-2548

    Human land use threatens global biodiversity and compromises multiple ecosystem functions critical to food production. Whether crop yield-related ecosystem services can be maintained by a few dominant species or rely on high richness remains unclear. Using a global database from 89 studies (with 1475 locations), we partition the relative importance of species richness, abundance, and dominance for pollination; biological pest control; and final yields in the context of ongoing land-use change. Pollinator and enemy richness directly supported ecosystem services in addition to and independent of abundance and dominance. Up to 50% of the negative effects of landscape simplification on ecosystem services was due to richness losses of service-providing organisms, with negative consequences for crop yields. Maintaining the biodiversity of ecosystem service providers is therefore vital to sustain the flow of key agroecosystem benefits to society.

    Elucidating transmission patterns of endemic Mycobacterium avium subsp. paratuberculosis using molecular epidemiology
    Mitchell, Rebecca M. ; Beaver, Annabelle ; Knupfer, Elena ; Pradhan, Abani K. ; Fyock, Terry ; Whitlock, Robert H. ; Schukken, Ynte H. - \ 2019
    Veterinary Sciences 6 (2019)1. - ISSN 2306-7381
    MLSSR typing - Mutation rate - Mycobacterial co-infections - Mycobacterium avium subsp. paratuberculosis (MAP) - Vertical transmission - Within-host evolution

    Mycobacterial diseases are persistent and characterized by lengthy latent periods. Thus, epidemiological models require careful delineation of transmission routes. Understanding transmission routes will improve the quality and success of control programs. We aimed to study the infection dynamics of Mycobacterium avium subsp. paratuberculosis (MAP), the causal agent of ruminant Johne's disease, and to distinguish within-host mutation from individual transmission events in a longitudinally MAP-defined dairy herd in upstate New York. To this end, semi-annual fecal samples were obtained from a single dairy herd over the course of seven years, in addition to tissue samples from a selection of culled animals. All samples were cultured for MAP, and multi-locus short-sequence repeat (MLSSR) typing was used to determine MAP SSR types. We concluded from these precise MAP infection data that, when the tissue burden remains low, the majority of MAP infections are not detectable by routine fecal culture but will be identified when tissue culture is performed after slaughter. Additionally, we determined that in this herd vertical infection played only a minor role in MAP transmission. By means of extensive and precise longitudinal data from a single dairy herd, we have come to new insights regarding MAP co-infections and within-host evolution.

    Nature and mental health: An ecosystem service perspective
    Bratman, Gregory N. ; Anderson, Christopher B. ; Berman, Marc G. ; Cochran, Bobby ; Vries, Sjerp De; Flanders, Jon ; Folke, Carl ; Frumkin, Howard ; Gross, James J. ; Hartig, Terry ; Kahn, Peter H. ; Kuo, Ming ; Lawler, Joshua J. ; Levin, Phillip S. ; Lindahl, Therese ; Meyer-lindenberg, Andreas ; Mitchell, Richard ; Ouyang, Zhiyun ; Roe, Jenny ; Scarlett, Lynn ; Smith, Jeffrey R. ; Bosch, Matilda Van Den; Wheeler, Benedict W. ; White, Mathew P. ; Zheng, Hua ; Daily, Gretchen C. - \ 2019
    Science Advances 5 (2019)7. - ISSN 2375-2548 - 15 p.
    A growing body of empirical evidence is revealing the value of nature experience for mental health. With rapid urbanization and declines in human contact with nature globally, crucial decisions must be made about how to preserve and enhance opportunities for nature experience. Here, we first provide points of consensus across the natural, social, and health sciences on the impacts of nature experience on cognitive functioning, emotional well-being, and other dimensions of mental health. We then show how ecosystem service assessments can be expanded to include mental health, and provide a heuristic, conceptual model for doing so.
    Improving scientific advice for the conservation and management of oceanic sharks and rays : Final report - Study
    Coelho, R. ; Apostolaki, P. ; Bach, P. ; Brunel, T.P.A. ; Davies, T. ; Diez, G. ; Ellis, J. ; Escalle, L. ; Lopez, J. ; Merino, Gorka ; Mitchell, R. ; Macias, D. ; Murua, H. ; Overzee, H.M.J. van; Poos, J.J. ; Richardson, H. ; Rosa, D. ; Sanchez, S. ; Santos, C. ; Seret, B. ; Urbina, J.O. ; Walker, N. - \ 2019
    Brussels : European Commission - ISBN 9789292024550 - 658 p.
    The purpose of this specific study is to provide the Directorate-General for Maritime Affairs and Fisheries (DG MARE) with: Updated information regarding the association or occurrence of pelagic sharks and rays in different fisheries; Updated information regarding data collection and methodological approaches for the assessment of conservation status of sharks; A critical review of existing Conservation and Management Measures (CMMs) for sharks and of the current conservation status of the species concerned; and Proposals to improve and/or provide alternative options for conservation and management of sharks taking into account any recent methodological advances and new data or information. The species of interest are the main pelagic sharks caught by pelagic fisheries, including under Sustainable Fisheries Partnership Agreements (longline and purse seine fisheries). The study also considers some pelagic elasmobranchs included in Article 13 (species prohibitions) of the Council Regulation 2016/72 fixing for 2016 the fishing opportunities for certain fish stocks. The main regions focused are the oceanic regions covered by tuna-RFMOs where those species of elasmobranch are represented in the catches, specifically the Atlantic (ICCAT region), the Indian Ocean (IOTC region) and the Pacific (WCPFC and IATTC regions)
    Disentangling the genetics of lean mass
    Karasik, David ; Zillikens, M.C. ; Hsu, Yi Hsiang ; Aghdassi, Ali ; Akesson, Kristina ; Amin, Najaf ; Barroso, Inês ; Bennett, David A. ; Bertram, Lars ; Bochud, Murielle ; Borecki, Ingrid B. ; Broer, Linda ; Buchman, Aron S. ; Byberg, Liisa ; Campbell, Harry ; Campos-Obando, Natalia ; Cauley, Jane A. ; Cawthon, Peggy M. ; Chambers, John C. ; Chen, Zhao ; Cho, Nam H. ; Choi, Hyung Jin ; Chou, Wen Chi ; Cummings, Steven R. ; Groot, Lisette C.P.G.M. De; Jager, Phillip L. De; Demuth, Ilja ; Diatchenko, Luda ; Econs, Michael J. ; Eiriksdottir, Gudny ; Enneman, Anke W. ; Eriksson, Joel ; Eriksson, Johan G. ; Estrada, Karol ; Evans, Daniel S. ; Feitosa, Mary F. ; Fu, Mao ; Gieger, Christian ; Grallert, Harald ; Gudnason, Vilmundur ; Lenore, Launer J. ; Hayward, Caroline ; Hofman, Albert ; Homuth, Georg ; Huffman, Kim M. ; Husted, Lise B. ; Illig, Thomas ; Ingelsson, Erik ; Ittermann, Till ; Jansson, John Olov ; Johnson, Toby ; Biffar, Reiner ; Jordan, Joanne M. ; Jula, Antti ; Karlsson, Magnus ; Khaw, Kay Tee ; Kilpeläinen, Tuomas O. ; Klopp, Norman ; Kloth, Jacqueline S.L. ; Koller, Daniel L. ; Kooner, Jaspal S. ; Kraus, William E. ; Kritchevsky, Stephen ; Kutalik, Zoltán ; Kuulasmaa, Teemu ; Kuusisto, Johanna ; Laakso, Markku ; Lahti, Jari ; Lang, Thomas ; Langdahl, Bente L. ; Lerch, Markus M. ; Lewis, Joshua R. ; Lill, Christina ; Lind, Lars ; Lindgren, Cecilia ; Liu, Yongmei ; Livshits, Gregory ; Ljunggren, Östen ; Loos, Ruth J.F. ; Lorentzon, Mattias ; Luan, Jian An ; Luben, Robert N. ; Malkin, Ida ; McGuigan, Fiona E. ; Medina-Gomez, Carolina ; Meitinger, Thomas ; Melhus, Håkan ; Mellström, Dan ; Michaëlsson, Karl ; Mitchell, Braxton D. ; Morris, Andrew P. ; Mosekilde, Leif ; Nethander, Maria ; Newman, Anne B. ; Oconnell, Jeffery R. ; Oostra, Ben A. ; Orwoll, Eric S. ; Palotie, Aarno ; Peacock, Munro ; Perola, Markus ; Peters, Annette ; Prince, Richard L. ; Psaty, Bruce M. ; Räikkönen, Katri ; Ralston, Stuart H. ; Ripatti, Samuli ; Rivadeneira, Fernando ; Robbins, John A. ; Rotter, Jerome I. ; Rudan, Igor ; Salomaa, Veikko ; Satterfield, Suzanne ; Schipf, Sabine ; Shin, Chan Soo ; Smith, Albert V. ; Smith, Shad B. ; Soranzo, Nicole ; Spector, Timothy D. ; StanÄ Áková, Alena ; Stefansson, Kari ; Steinhagen-Thiessen, Elisabeth ; Stolk, Lisette ; Streeten, Elizabeth A. ; Styrkarsdottir, Unnur ; Swart, Karin M.A. ; Thompson, Patricia ; Thomson, Cynthia A. ; Thorleifsson, Gudmar ; Thorsteinsdottir, Unnur ; Tikkanen, Emmi ; Tranah, Gregory J. ; Uitterlinden, André G. ; Duijn, Cornelia M. Van; Schoor, Natasja M. Van; Vandenput, Liesbeth ; Vollenweider, Peter ; Völzke, Henry ; Wactawski-Wende, Jean ; Walker, Mark ; J Wareham, Nicholas ; Waterworth, Dawn ; Weedon, Michael N. ; Wichmann, H.E. ; Widen, Elisabeth ; Williams, Frances M.K. ; Wilson, James F. ; Wright, Nicole C. ; Yerges-Armstrong, Laura M. ; Yu, Lei ; Zhang, Weihua ; Zhao, Jing Hua ; Zhou, Yanhua ; Nielson, Carrie M. ; Harris, Tamara B. ; Demissie, Serkalem ; Kiel, Douglas P. ; Ohlsson, Claes - \ 2019
    American Journal of Clinical Nutrition 109 (2019)2. - ISSN 0002-9165 - p. 276 - 278.
    body composition - body fat - meta-Analysis of genome-wide association studies - metabolic profile - skeletal muscle

    Background Lean body mass (LM) plays an important role in mobility and metabolic function. We previously identified five loci associated with LM adjusted for fat mass in kilograms. Such an adjustment may reduce the power to identify genetic signals having an association with both lean mass and fat mass. Objectives To determine the impact of different fat mass adjustments on genetic architecture of LM and identify additional LM loci. Methods We performed genome-wide association analyses for whole-body LM (20 cohorts of European ancestry with n = 38,292) measured using dual-energy X-ray absorptiometry) or bioelectrical impedance analysis, adjusted for sex, age, age 2, and height with or without fat mass adjustments (Model 1 no fat adjustment; Model 2 adjustment for fat mass as a percentage of body mass; Model 3 adjustment for fat mass in kilograms). Results Seven single-nucleotide polymorphisms (SNPs) in separate loci, including one novel LM locus (TNRC6B), were successfully replicated in an additional 47,227 individuals from 29 cohorts. Based on the strengths of the associations in Model 1 vs Model 3, we divided the LM loci into those with an effect on both lean mass and fat mass in the same direction and refer to those as "sumo wrestler" loci (FTO and MC4R). In contrast, loci with an impact specifically on LM were termed "body builder" loci (VCAN and ADAMTSL3). Using existing available genome-wide association study databases, LM increasing alleles of SNPs in sumo wrestler loci were associated with an adverse metabolic profile, whereas LM increasing alleles of SNPs in "body builder" loci were associated with metabolic protection. Conclusions In conclusion, we identified one novel LM locus (TNRC6B). Our results suggest that a genetically determined increase in lean mass might exert either harmful or protective effects on metabolic traits, depending on its relation to fat mass.

    Characterization of Male-Produced Aggregation Pheromone of the Bean Flower Thrips Megalurothrips sjostedti (Thysanoptera: Thripidae)
    Niassy, Saliou ; Tamiru, Amanuel ; Hamilton, James G.C. ; Kirk, William D.J. ; Mumm, R. ; Sims, Cassie ; Kogel, W.J. de; Ekesi, Sunday ; Maniania, N.K. ; Bandi, Krishnakumari ; Mitchell, Fraser ; Subramanian, Sevgan - \ 2019
    Journal of Chemical Ecology 45 (2019). - ISSN 0098-0331 - p. 348 - 355.
    Aggregation of the bean flower thrips, Megalurothrips sjostedti (Trybom) (Thysanoptera: Thripidae), has been observed on cowpea, Vigna unguiculata (L.) Walp. To understand the mechanism underpinning this behavior, we studied
    the responses of M. sjostedti to headspace volatiles from conspecifics in a four-arm olfactometer. Both male and female M. sjostedti were attracted to male, but not to female odor. Gas chromatography/mass spectrometry (GC/
    MS) analyses revealed the presence of two distinct compounds in male M. sjostedti headspace, namely (R)-lavandulyl 3-methylbutanoate (major compound) and (R)-lavandulol (minor compound); by contrast, both compounds were only present in trace amounts in female headspace collections. A behavioral assay using synthetic compounds showed that male M. sjostedti was attracted to both (R)-lavandulyl 3-methylbutanoate and (R)-lavandulol, while females responded only to (R)-lavandulyl 3-methylbutanoate. This is the first report of a male-produced aggregation pheromone in the genus Megalurothrips. The bean flower thrips is the primary pest of cowpea, which is widely grown in sub-Saharan Africa. The attraction of male and female M. sjostedti to these compounds offers an opportunity to develop ecologically sustainable management methods for M. sjostedti in Africa.
    Diacylglycerol acyltransferase 1 contributes to freezing tolerance
    Arisz, Steven A. ; Heo, Jae-Yun ; Koevoets, Iko Tamar ; Zhao, Tao ; Egmond, Pieter van; Meyer, Jessica ; Zeng, Weiqing ; Niu, Xiaomu ; Wang, Baosheng ; Mitchell-Olds, Thomas ; Schranz, M.E. ; Testerink, Christa - \ 2018
    Plant Physiology 177 (2018)4. - ISSN 0032-0889 - p. 1410 - 1424.
    Freezing limits plant growth and crop productivity, and plant species in temperate zones have the capacity to develop freezing tolerance through complex modulation of gene expression affecting various aspects of metabolism and physiology. While many components of freezing tolerance have been identified in model species under controlled laboratory conditions, little is known about the mechanisms that impart freezing tolerance in natural populations of wild species. Here, we performed a quantitative trait locus (QTL) study of acclimated freezing tolerance in seedlings of Boechera stricta, a highly adapted relative of Arabidopsis thaliana native to the Rocky Mountains. A single QTL was identified that contained the gene encoding ACYL-COA:DIACYLGLYCEROL ACYLTRANSFERASE 1 (BstDGAT1), whose expression is highly cold responsive. The primary metabolic enzyme DGAT1 catalyzes the final step in assembly of triacylglycerol (TAG) by acyl transfer from acyl-CoA to diacylglycerol. Freezing tolerant plants showed higher DGAT1 expression during cold acclimation than more sensitive plants and this resulted in increased accumulation of TAG in response to subsequent freezing. Levels of oligogalactolipids which are produced by SFR2 (SENSITIVE TO FREEZING 2), an indispensable element of freezing tolerance in Arabidopsis, were also higher in freezing tolerant plants. Furthermore, overexpression of AtDGAT1 led to increased freezing tolerance. We propose that DGAT1 confers freezing tolerance in plants by supporting SFR2-mediated remodeling of chloroplast membranes.
    Understanding meta-population trends of the Australian fur seal, with insights for adaptive monitoring
    McIntosh, Rebecca R. ; Kirkman, Steve P. ; Thalmann, Sam ; Sutherland, Duncan R. ; Mitchell, Anthony ; Arnould, John P.Y. ; Salton, Marcus ; Slip, David J. ; Dann, Peter ; Kirkwood, Roger - \ 2018
    PLoS ONE 13 (2018)9. - ISSN 1932-6203
    Effective ecosystem-based management requires estimates of abundance and population trends of species of interest. Trend analyses are often limited due to sparse or short-term abundance estimates for populations that can be logistically difficult to monitor over time. Therefore it is critical to assess regularly the quality of the metrics in long-term monitoring programs. For a monitoring program to provide meaningful data and remain relevant, it needs to incorporate technological improvements and the changing requirements of stakeholders, while maintaining the integrity of the data. In this paper we critically examine the monitoring program for the Australian fur seal (AFS) Arctocephalus pusillus doriferus as an example of an ad-hoc monitoring program that was co-ordinated across multiple stakeholders as a range-wide census of live pups in the Austral summers of 2002, 2007 and 2013. This 5-yearly census, combined with historic counts at individual sites, successfully tracked increasing population trends as signs of population recovery up to 2007. The 2013 census identified the first reduction in AFS pup numbers (14,248 live pups, -4.2% change per annum since 2007), however we have limited information to understand this change. We analyse the trends at breeding colonies and perform a power analysis to critically examine the reliability of those trends. We then assess the gaps in the monitoring program and discuss how we may transition this surveillance style program to an adaptive monitoring program than can evolve over time and achieve its goals. The census results are used for ecosystem-based modelling for fisheries management and emergency response planning. The ultimate goal for this program is to obtain the data we need with minimal cost, effort and impact on the fur seals. In conclusion we identify the importance of power analyses for interpreting trends, the value of regularly assessing long-term monitoring programs and proper design so that adaptive monitoring principles can be applied.
    The functional change and deletion of FLC homologs contribute to the evolution of rapid flowering in Boechera stricta
    Lee, Cheng-Ruei ; Hsieh, Jo-Wei ; Schranz, M.E. ; Mitchell-Olds, Thomas - \ 2018
    Frontiers in Plant Science 9 (2018). - ISSN 1664-462X
    Differences in the timing of vegetative-to-reproductive phase transition have evolved independently and repeatedly in different plant species. Due to their specific biological functions and positions in pathways, some genes are important targets of repeated evolution – independent mutations on these genes caused the evolution of similar phenotypes in distantly related organisms. While many studies have investigated these genes, it remains unclear how gene duplications influence repeated phenotypic evolution. Here we characterized the genetic architecture underlying a novel rapid-flowering phenotype in Boechera stricta and investigated the candidate genes BsFLC1 and BsFLC2. The expression patterns of BsFLC1 suggested its function in flowering time suppression, and the deletion of BsFLC1 is associated with rapid flowering and loss of vernalization requirement. In contrast, BsFLC2 did not appear to be associated with flowering and had accumulated multiple amino acid substitutions in the relatively short evolutionary timeframe after gene duplication. These non-synonymous substitutions greatly changed the physicochemical properties of the original amino acids, concentrated non-randomly near a protein-interacting domain, and had greater substitution rate than synonymous changes. Here we suggested that, after recent gene duplication of the FLC gene, the evolution of rapid phenology was made possible by the change of BsFLC2 expression pattern or protein sequences and the deletion of BsFLC1.
    Crop pests and predators exhibit inconsistent responses to surrounding landscape composition
    Karp, Daniel S. ; Chaplin-Kramer, Rebecca ; Meehan, Timothy D. ; Martin, Emily A. ; Declerck, Fabrice ; Grab, Heather ; Gratton, Claudio ; Hunt, Lauren ; Larsen, Ashley E. ; Martínez-Salinas, Alejandra ; O’Rourke, Megan E. ; Rusch, Adrien ; Poveda, Katja ; Jonsson, Mattias ; Rosenheim, Jay A. ; Schellhorn, Nancy A. ; Tscharntke, Teja ; Wratten, Stephen D. ; Zhang, Wei ; Iverson, Aaron L. ; Adler, Lynn S. ; Albrecht, Matthias ; Alignier, Audrey ; Angelella, Gina M. ; Zubair Anjum, Muhammad ; Avelino, Jacques ; Batáry, Péter ; Baveco, Johannes M. ; Bianchi, Felix J.J.A. ; Birkhofer, Klaus ; Bohnenblust, Eric W. ; Bommarco, Riccardo ; Brewer, Michael J. ; Caballero-López, Berta ; Carrière, Yves ; Carvalheiro, Luísa G. ; Cayuela, Luis ; Centrella, Mary ; Ćetković, Aleksandar ; Henri, Dominic Charles ; Chabert, Ariane ; Costamagna, Alejandro C. ; La Mora, Aldo De; Kraker, Joop De; Desneux, Nicolas ; Diehl, Eva ; Diekötter, Tim ; Dormann, Carsten F. ; Eckberg, James O. ; Entling, Martin H. ; Fiedler, Daniela ; Franck, Pierre ; Veen, F.J.F. van; Frank, Thomas ; Gagic, Vesna ; Garratt, Michael P.D. ; Getachew, Awraris ; Gonthier, David J. ; Goodell, Peter B. ; Graziosi, Ignazio ; Groves, Russell L. ; Gurr, Geoff M. ; Hajian-Forooshani, Zachary ; Heimpel, George E. ; Herrmann, John D. ; Huseth, Anders S. ; Inclán, Diego J. ; Ingrao, Adam J. ; Iv, Phirun ; Jacot, Katja ; Johnson, Gregg A. ; Jones, Laura ; Kaiser, Marina ; Kaser, Joe M. ; Keasar, Tamar ; Kim, Tania N. ; Kishinevsky, Miriam ; Landis, Douglas A. ; Lavandero, Blas ; Lavigne, Claire ; Ralec, Anne Le; Lemessa, Debissa ; Letourneau, Deborah K. ; Liere, Heidi ; Lu, Yanhui ; Lubin, Yael ; Luttermoser, Tim ; Maas, Bea ; Mace, Kevi ; Madeira, Filipe ; Mader, Viktoria ; Cortesero, Anne Marie ; Marini, Lorenzo ; Martinez, Eliana ; Martinson, Holly M. ; Menozzi, Philippe ; Mitchell, Matthew G.E. ; Miyashita, Tadashi ; Molina, Gonzalo A.R. ; Molina-Montenegro, Marco A. ; O’Neal, Matthew E. ; Opatovsky, Itai ; Ortiz-Martinez, Sebaastian ; Nash, Michael ; Östman, Örjan ; Ouin, Annie ; Pak, Damie ; Paredes, Daniel ; Parsa, Soroush ; Parry, Hazel ; Perez-Alvarez, Ricardo ; Perović, David J. ; Peterson, Julie A. ; Petit, Sandrine ; Philpott, Stacy M. ; Plantegenest, Manuel ; Plećaš, Milan ; Pluess, Therese ; Pons, Xavier ; Potts, Simon G. ; Pywell, Richard F. ; Ragsdale, David W. ; Rand, Tatyana A. ; Raymond, Lucie ; Ricci, Benoît ; Sargent, Chris ; Sarthou, Jean-Pierre ; Saulais, Julia ; Schäckermann, Jessica ; Schmidt, Nick P. ; Schneider, Gudrun ; Schüepp, Christof ; Sivakoff, Frances S. ; Smith, Henrik G. ; Stack Whitney, Kaitlin ; Stutz, Sonja ; Szendrei, Zsofia ; Takada, Mayura B. ; Taki, Hisatomo ; Tamburini, Giovanni ; Thomson, Linda J. ; Tricault, Yann ; Tsafack, Noelline ; Tschumi, Matthias ; Valantin-Morison, Muriel ; Trinh, Mai Van; Werf, Wopke Van Der; Vierling, Kerri T. ; Werling, Ben P. ; Wickens, Jennifer B. ; Wickens, Victoria J. ; Woodcock, Ben A. ; Wyckhuys, Kris ; Xiao, Haijun ; Yasuda, Mika ; Yoshioka, Akira - \ 2018
    Proceedings of the National Academy of Sciences of the United States of America 115 (2018)33. - ISSN 0027-8424 - p. E7863 - E7870.
    IPM
    The idea that noncrop habitat enhances pest control and represents a win–win opportunity to conserve biodiversity and bolster yields has emerged as an agroecological paradigm. However, while noncrop habitat in landscapes surrounding farms sometimes benefits pest predators, natural enemy responses remain heterogeneous across studies and effects on pests are inconclusive. The observed heterogeneity in species responses to noncrop habitat may be biological in origin or could result from variation in how habitat and biocontrol are measured. Here, we use a pest-control database encompassing 132 studies and 6,759 sites worldwide to model natural enemy and pest abundances, predation rates, and crop damage as a function of landscape composition. Our results showed that although landscape composition explained significant variation within studies, pest and enemy abundances, predation rates, crop damage, and yields each exhibited different responses across studies, sometimes increasing and sometimes decreasing in landscapes with more noncrop habitat but overall showing no consistent trend. Thus, models that used landscape-composition variables to predict pest-control dynamics demonstrated little potential to explain variation across studies, though prediction did improve when comparing studies with similar crop and landscape features. Overall, our work shows that surrounding noncrop habitat does not consistently improve pest management, meaning habitat conservation may bolster production in some systems and depress yields in others. Future efforts to develop tools that inform farmers when habitat conservation truly represents a win–win would benefit from increased understanding of how landscape effects are modulated by local farm management and the biology of pests and their enemies.
    Soil protists: A fertile frontier in soil biology research
    Geisen, Stefan ; Mitchell, Edward A.D. ; Adl, Sina ; Bonkowski, Michael ; Dunthorn, Micah ; Ekelund, Flemming ; Fernández, Leonardo D. ; Jousset, Alexandre ; Krashevska, Valentyna ; Singer, David ; Spiegel, Frederick W. ; Walochnik, Julia ; Lara, Enrique - \ 2018
    FEMS Microbiology Reviews 42 (2018)3. - ISSN 0168-6445 - p. 293 - 323.
    Biogeography - Functional diversity - Plant performance - Soil food web - Soil microbiome - Taxonomic diversity

    Protists include all eukaryotes except plants, fungi and animals. They are an essential, yet often forgotten, component of the soil microbiome. Method developments have now furthered our understanding of the real taxonomic and functional diversity of soil protists. They occupy key roles in microbial foodwebs as consumers of bacteria, fungi and other small eukaryotes. As parasites of plants, animals and even of larger protists, they regulate populations and shape communities. Pathogenic forms play a major role in public health issues as human parasites, or act as agricultural pests. Predatory soil protists release nutrients enhancing plant growth. Soil protists are of key importance for our understanding of eukaryotic evolution and microbial biogeography. Soil protists are also useful in applied research as bioindicators of soil quality, as models in ecotoxicology and as potential biofertilizers and biocontrol agents. In this review, we provide an overview of the enormous morphological, taxonomical and functional diversity of soil protists, and discuss current challenges and opportunities in soil protistology. Research in soil biology would clearly benefit from incorporating more protistology alongside the study of bacteria, fungi and animals.

    Responses of competitive understorey species to spatial environmental gradients inaccurately explain temporal changes
    Lombaerde, Emiel De; Verheyen, Kris ; Perring, Michael P. ; Bernhardt-Römermann, Markus ; Calster, Hans Van; Brunet, Jörg ; Chudomelová, Markéta ; Decocq, Guillaume ; Diekmann, Martin ; Durak, Tomasz ; Hédl, Radim ; Heinken, Thilo ; Hommel, Patrick ; Jaroszewicz, Bogdan ; Kopecký, Martin ; Lenoir, Jonathan ; Macek, Martin ; Máliš, František ; Mitchell, Fraser J.G. ; Naaf, Tobias ; Newman, Miles ; Petřík, Petr ; Reczyńska, Kamila ; Schmidt, Wolfgang ; Świerkosz, Krzysztof ; Vild, Ondřej ; Wulf, Monika ; Baeten, Lander - \ 2018
    Basic and Applied Ecology 30 (2018). - ISSN 1439-1791 - p. 52 - 64.
    Canopy - Chronosequence - Cover abundance - forestREplot - Global change - Herb layer - Nitrogen deposition - Spatiotemporal resurvey data - Temperate forest - Tree regeneration

    Understorey plant communities play a key role in the functioning of forest ecosystems. Under favourable environmental conditions, competitive understorey species may develop high abundances and influence important ecosystem processes such as tree regeneration. Thus, understanding and predicting the response of competitive understorey species as a function of changing environmental conditions is important for forest managers. In the absence of sufficient temporal data to quantify actual vegetation changes, space-for-time (SFT) substitution is often used, i.e. studies that use environmental gradients across space to infer vegetation responses to environmental change over time. Here we assess the validity of such SFT approaches and analysed 36 resurvey studies from ancient forests with low levels of recent disturbances across temperate Europe to assess how six competitive understorey plant species respond to gradients of overstorey cover, soil conditions, atmospheric N deposition and climatic conditions over space and time. The combination of historical and contemporary surveys allows (i) to test if observed contemporary patterns across space are consistent at the time of the historical survey, and, crucially, (ii) to assess whether changes in abundance over time given recorded environmental change match expectations from patterns recorded along environmental gradients in space. We found consistent spatial relationships at the two periods: local variation in soil variables and overstorey cover were the best predictors of individual species’ cover while interregional variation in coarse-scale variables, i.e. N deposition and climate, was less important. However, we found that our SFT approach could not accurately explain the large variation in abundance changes over time. We thus recommend to be cautious when using SFT substitution to infer species responses to temporal changes.

    Effect of model root exudate on denitrifier community dynamics and activity at different water-filled pore space levels in a fertilised soil
    Langarica-Fuentes, Adrian ; Manrubia, Marta ; Giles, Madeline E. ; Mitchell, Susan ; Daniell, Tim J. - \ 2018
    Soil Biology and Biochemistry 120 (2018). - ISSN 0038-0717 - p. 70 - 79.
    Denitrification - Microbial community dynamics - nirK - nirS - Nitrous oxide emissions - nosZ - Root exudate addition
    Although a “rhizosphere effect” on denitrification rates has been established, a clear understanding of the effects of exudate addition on denitrifier community dynamics remains elusive. A microcosm experiment was designed to explore the interaction between exudate addition and soil moisture on community dynamics and denitrification rates. Artificial root exudate at 5 different carbon concentrations was added daily to soil microcosms at contrasting target WFPS (50, 70 and 90%). After a 7-day period, total denitrification and N2O emission rates were measured and community dynamics assessed using molecular methods. The response of denitrifier genes to exudate addition was different, with nirS and nosZ-I showing a stronger effect than nirK and nosZ-II. Distinct community structures were observed for nirS and nosZ-I at 90% target WFPS when compared to 50% and 70%. NirS denitrifier population size showed a ca. 5-Fold increase in gene copy number at 90% WFPS when exudate was added at the highest C input. Significant total denitrification and N2O emission rates were observed only at 90% WFPS, which increased with C input. Our study improves the understanding of the complex interaction between microbial communities, the abiotic environment and process rates which can inform management practices aimed at increasing complete denitrification and controlling greenhouse gas production from agriculture.
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