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.
    Global environmental change effects on plant community composition trajectories depend upon management legacies
    Perring, Michael P. ; Bernhardt-Römermann, Markus ; Baeten, Lander ; Midolo, Gabriele ; Blondeel, Haben ; Depauw, Leen ; Landuyt, Dries ; Maes, Sybryn L. ; Lombaerde, Emiel De; Carón, Maria Mercedes ; Vellend, Mark ; Brunet, Jörg ; Chudomelová, Markéta ; Decocq, Guillaume ; Diekmann, Martin ; Dirnböck, Thomas ; Dörfler, Inken ; Durak, Tomasz ; Frenne, Pieter De; Gilliam, Frank S. ; Hédl, Radim ; Heinken, Thilo ; Hommel, Patrick ; Jaroszewicz, Bogdan ; Kirby, Keith J. ; Kopecký, Martin ; Lenoir, Jonathan ; Li, Daijiang ; Máliš, František ; Mitchell, Fraser J.G. ; Naaf, Tobias ; Newman, Miles ; Petřík, Petr ; Reczyńska, Kamila ; Schmidt, Wolfgang ; Standovár, Tibor ; Świerkosz, Krzysztof ; Calster, Hans Van; Vild, Ondřej ; Wagner, Eva Rosa ; Wulf, Monika ; Verheyen, Kris - \ 2018
    Global Change Biology 24 (2018)4. - ISSN 1354-1013 - p. 1722 - 1740.
    Biodiversity change - Climate change - Disturbance regime - ForestREplot - Herbaceous layer - Management intensity - Nitrogen deposition - Plant functional traits - Time lag - Vegetation resurvey
    The contemporary state of functional traits and species richness in plant communities depends on legacy effects of past disturbances. Whether temporal responses of community properties to current environmental changes are altered by such legacies is, however, unknown. We expect global environmental changes to interact with land-use legacies given different community trajectories initiated by prior management, and subsequent responses to altered resources and conditions. We tested this expectation for species richness and functional traits using 1814 survey-resurvey plot pairs of understorey communities from 40 European temperate forest datasets, syntheses of management transitions since the year 1800, and a trait database. We also examined how plant community indicators of resources and conditions changed in response to management legacies and environmental change. Community trajectories were clearly influenced by interactions between management legacies from over 200 years ago and environmental change. Importantly, higher rates of nitrogen deposition led to increased species richness and plant height in forests managed less intensively in 1800 (i.e., high forests), and to decreases in forests with a more intensive historical management in 1800 (i.e., coppiced forests). There was evidence that these declines in community variables in formerly coppiced forests were ameliorated by increased rates of temperature change between surveys. Responses were generally apparent regardless of sites' contemporary management classifications, although sometimes the management transition itself, rather than historic or contemporary management types, better explained understorey responses. Main effects of environmental change were rare, although higher rates of precipitation change increased plant height, accompanied by increases in fertility indicator values. Analysis of indicator values suggested the importance of directly characterising resources and conditions to better understand legacy and environmental change effects. Accounting for legacies of past disturbance can reconcile contradictory literature results and appears crucial to anticipating future responses to global environmental change.
    Seagrass ecosystem trajectory depends on the relative timescales of resistance, recovery and disturbance
    O'Brien, Katherine R. ; Waycott, Michelle ; Maxwell, Paul ; Kendrick, Gary A. ; Udy, James W. ; Ferguson, Angus J.P. ; Kilminster, Kieryn ; Scanes, Peter ; McKenzie, Len J. ; McMahon, Kathryn ; Adams, Matthew P. ; Samper-Villarreal, Jimena ; Collier, Catherine ; Lyons, Mitchell ; Mumby, Peter J. ; Radke, Lynda ; Christianen, Marjolijn J.A. ; Dennison, William C. - \ 2018
    Marine Pollution Bulletin 134 (2018). - ISSN 0025-326X - p. 166 - 176.
    Colonizing - Opportunistic - Persistent - Recovery - Resilience - Resistance - Seagrass - Trajectory
    Seagrass ecosystems are inherently dynamic, responding to environmental change across a range of scales. Habitat requirements of seagrass are well defined, but less is known about their ability to resist disturbance. Specific means of recovery after loss are particularly difficult to quantify. Here we assess the resistance and recovery capacity of 12 seagrass genera. We document four classic trajectories of degradation and recovery for seagrass ecosystems, illustrated with examples from around the world. Recovery can be rapid once conditions improve, but seagrass absence at landscape scales may persist for many decades, perpetuated by feedbacks and/or lack of seed or plant propagules to initiate recovery. It can be difficult to distinguish between slow recovery, recalcitrant degradation, and the need for a window of opportunity to trigger recovery. We propose a framework synthesizing how the spatial and temporal scales of both disturbance and seagrass response affect ecosystem trajectory and hence resilience.
    Erratum: Large meta-analysis of genome-wide association studies identifies five loci for lean body mass
    Zillikens, M.C. ; Demissie, Serkalem ; Hsu, Yi Hsiang ; Yerges-Armstrong, Laura M. ; Chou, Wen Chi ; Stolk, Lisette ; Livshits, Gregory ; Broer, Linda ; Johnson, Toby ; Koller, Daniel L. ; Kutalik, Zoltán ; Luan, J. ; Malkin, Ida ; Ried, Janina S. ; Smith, Albert V. ; Thorleifsson, Gudmar ; Vandenput, Liesbeth ; Hua Zhao, Jing ; Zhang, Weihua ; Aghdassi, Ali ; Åkesson, Kristina ; Amin, Najaf ; Baier, Leslie J. ; Barroso, Inês ; Bennett, David A. ; Bertram, Lars ; Biffar, Rainer ; Bochud, Murielle ; Boehnke, Michael ; Borecki, Ingrid B. ; Buchman, Aron S. ; Byberg, Liisa ; Campbell, Harry ; Campos Obanda, Natalia ; Cauley, Jane A. ; Cawthon, Peggy M. ; Cederberg, Henna ; Chen, Zhao ; Cho, Nam H. ; Jin Choi, Hyung ; Claussnitzer, Melina ; Collins, Francis ; Cummings, Steven R. ; Jager, Philip L. De; Demuth, Ilja ; Dhonukshe-Rutten, Rosalie A.M. ; Diatchenko, Luda ; Eiriksdottir, Gudny ; Enneman, Anke W. ; Erdos, Mike ; Eriksson, Johan G. ; Eriksson, Joel ; Estrada, Karol ; Evans, Daniel S. ; Feitosa, Mary F. ; Fu, Mao ; Garcia, Melissa ; Gieger, Christian ; Girke, Thomas ; Glazer, Nicole L. ; Grallert, Harald ; Grewal, Jagvir ; Han, Bok Ghee ; Hanson, Robert L. ; Hayward, Caroline ; Hofman, Albert ; Hoffman, Eric P. ; Homuth, Georg ; Hsueh, Wen Chi ; Hubal, Monica J. ; Hubbard, Alan ; Huffman, Kim M. ; Husted, Lise B. ; Illig, Thomas ; Ingelsson, Erik ; Ittermann, Till ; Jansson, John Olov ; Jordan, Joanne M. ; Jula, Antti ; Karlsson, Magnus ; Khaw, Kay Tee ; Kilpeläinen, Tuomas O. ; Klopp, Norman ; Kloth, Jacqueline S.L. ; Koistinen, Heikki A. ; Kraus, William E. ; Kritchevsky, Stephen ; Kuulasmaa, Teemu ; Kuusisto, Johanna ; Laakso, Markku ; Lahti, Jari ; Lang, Thomas ; Langdahl, Bente L. ; Launer, Lenore J. ; Lee, Jong Young ; Lerch, Markus M. ; Lewis, Joshua R. ; Lind, Lars ; Lindgren, Cecilia ; Liu, Yongmei ; Liu, Tian ; Liu, Youfang ; Ljunggren, Östen ; Lorentzon, Mattias ; Luben, Robert N. ; Maixner, William ; McGuigan, Fiona E. ; Medina-Gomez, Carolina ; Meitinger, Thomas ; Melhus, Håkan ; Mellström, Dan ; Melov, Simon ; Michaëlsson, Karl ; Mitchell, Braxton D. ; Morris, Andrew P. ; Mosekilde, Leif ; Newman, Anne ; Nielson, Carrie M. ; O'Connell, Jeffrey R. ; Oostra, Ben A. ; Orwoll, Eric S. ; Palotie, Aarno ; Parker, Stephen C.J. ; Peacock, Munro ; Perola, Markus ; Peters, Annette ; Polasek, Ozren ; Prince, Richard L. ; Räikkönen, Katri ; Ralston, Stuart H. ; Ripatti, Samuli ; Robbins, John A. ; Rotter, Jerome I. ; Rudan, Igor ; Salomaa, Veikko ; Satterfield, Suzanne ; Schadt, Eric E. ; Schipf, Sabine ; Scott, Laura ; Sehmi, Joban ; Shen, Jian ; Soo Shin, Chan ; Sigurdsson, Gunnar ; Smith, Shad ; Soranzo, Nicole ; Stančáková, Alena ; Steinhagen-Thiessen, Elisabeth ; Streeten, Elizabeth A. ; Styrkarsdottir, Unnur ; Swart, Karin M.A. ; Tan, Sian Tsung ; Tarnopolsky, Mark A. ; Thompson, Patricia ; Thomson, Cynthia A. ; Thorsteinsdottir, Unnur ; Tikkanen, Emmi ; Tranah, Gregory J. ; Tuomilehto, Jaakko ; Schoor, Natasja M. van; Verma, Arjun ; Vollenweider, Peter ; Völzke, Henry ; Wactawski-Wende, Jean ; Walker, Mark ; Weedon, Michael N. ; Welch, Ryan ; Wichmann, H.E. ; Widen, Elisabeth ; Williams, Frances M.K. ; Wilson, James F. ; Wright, Nicole C. ; Xie, Weijia ; Yu, Lei ; Zhou, Yanhua ; Chambers, John C. ; Döring, Angela ; Duijn, Cornelia M. van; Econs, Michael J. ; Gudnason, Vilmundur ; Kooner, Jaspal S. ; Psaty, Bruce M. ; Spector, Timothy D. ; Stefansson, Kari ; Rivadeneira, Fernando ; Uitterlinden, André G. ; Wareham, Nicholas J. ; Ossowski, Vicky ; Waterworth, Dawn ; Loos, Ruth J.F. ; Karasik, David ; Harris, Tamara B. ; Ohlsson, Claes ; Kiel, Douglas P. - \ 2017
    Nature Communications 8 (2017)1. - ISSN 2041-1723 - 1 p.

    A correction to this article has been published and is linked from the HTML version of this article.

    Large-scale GWAS identifies multiple loci for hand grip strength providing biological insights into muscular fitness
    Willems, Sara M. ; Wright, D.J. ; Day, Felix R. ; Trajanoska, Katerina ; Joshi, P.K. ; Morris, John A. ; Matteini, Amy M. ; Garton, Fleur C. ; Grarup, Niels ; Oskolkov, Nikolay ; Thalamuthu, Anbupalam ; Mangino, Massimo ; Liu, Jun ; Demirkan, Ayse ; Lek, Monkol ; Xu, Liwen ; Wang, Guan ; Oldmeadow, Christopher ; Gaulton, Kyle J. ; Lotta, Luca A. ; Miyamoto-Mikami, Eri ; Rivas, Manuel A. ; White, Tom ; Loh, Po Ru ; Aadahl, Mette ; Amin, Najaf ; Attia, John R. ; Austin, Krista ; Benyamin, Beben ; Brage, Søren ; Cheng, Yu Ching ; Ciȩszczyk, Paweł ; Derave, Wim ; Eriksson, Karl Fredrik ; Eynon, Nir ; Linneberg, Allan ; Lucia, Alejandro ; Massidda, Myosotis ; Mitchell, Braxton D. ; Miyachi, Motohiko ; Murakami, Haruka ; Padmanabhan, Sandosh ; Pandey, Ashutosh ; Papadimitriou, Ioannis ; Rajpal, Deepak K. ; Sale, Craig ; Schnurr, Theresia M. ; Sessa, Francesco ; Shrine, Nick ; Groot, Lisette C.P.G.M. De - \ 2017
    Nature Communications 8 (2017). - ISSN 2041-1723
    Hand grip strength is a widely used proxy of muscular fitness, a marker of frailty, and predictor of a range of morbidities and all-cause mortality. To investigate the genetic determinants of variation in grip strength, we perform a large-scale genetic discovery analysis in a combined sample of 195,180 individuals and identify 16 loci associated with grip strength (P<5 × 10-8) in combined analyses. A number of these loci contain genes implicated in structure and function of skeletal muscle fibres (ACTG1), neuronal maintenance and signal transduction (PEX14, TGFA, SYT1), or monogenic syndromes with involvement of psychomotor impairment (PEX14, LRPPRC and KANSL1). Mendelian randomization analyses are consistent with a causal effect of higher genetically predicted grip strength on lower fracture risk. In conclusion, our findings provide new biological insight into the mechanistic underpinnings of grip strength and the causal role of muscular strength in age-related morbidities and mortality.
    Large meta-analysis of genome-wide association studies identifies five loci for lean body mass
    Zillikens, M.C. ; Demissie, Serkalem ; Hsu, Yi Hsiang ; Yerges-Armstrong, Laura M. ; Chou, Wen Chi ; Stolk, Lisette ; Livshits, Gregory ; Broer, Linda ; Johnson, Toby ; Koller, Daniel L. ; Kutalik, Zoltán ; Luan, J.A. ; Malkin, Ida ; Ried, Janina S. ; Smith, Albert V. ; Thorleifsson, Gudmar ; Vandenput, Liesbeth ; Hua Zhao, Jing ; Zhang, Weihua ; Aghdassi, Ali ; Åkesson, Kristina ; Amin, Najaf ; Baier, Leslie J. ; Barroso, Inês ; Bennett, David A. ; Bertram, Lars ; Biffar, Rainer ; Bochud, Murielle ; Boehnke, Michael ; Borecki, Ingrid B. ; Buchman, Aron S. ; Byberg, Liisa ; Campbell, Harry ; Campos Obanda, Natalia ; Cauley, Jane A. ; Cawthon, Peggy M. ; Cederberg, Henna ; Chen, Zhao ; Cho, Nam H. ; Jin Choi, Hyung ; Claussnitzer, Melina ; Collins, Francis ; Cummings, Steven R. ; Jager, Philip L. De; Demuth, Ilja ; Dhonukshe-Rutten, Rosalie A.M. ; DIatchenko, Luda ; Eiriksdottir, Gudny ; Enneman, Anke W. ; Erdos, Mike ; Eriksson, Johan G. ; Eriksson, Joel ; Estrada, Karol ; Evans, Daniel S. ; Feitosa, Mary F. ; Fu, Mao ; Garcia, Melissa ; Gieger, Christian ; Girke, Thomas ; Glazer, Nicole L. ; Grallert, Harald ; Grewal, Jagvir ; Han, Bok Ghee ; Hanson, Robert L. ; Hayward, Caroline ; Hofman, Albert ; Hoffman, Eric P. ; Homuth, Georg ; Hsueh, Wen Chi ; Hubal, Monica J. ; Hubbard, Alan ; Huffman, Kim M. ; Husted, Lise B. ; Illig, Thomas ; Ingelsson, Erik ; Ittermann, Till ; Jansson, John Olov ; Jordan, Joanne M. ; Jula, Antti ; Karlsson, Magnus ; Khaw, Kay Tee ; Kilpelaïnen, Tuomas O. ; Klopp, Norman ; Kloth, Jacqueline S.L. ; Koistinen, Heikki A. ; Kraus, William E. ; Kritchevsky, Stephen ; Kuulasmaa, Teemu ; Kuusisto, Johanna ; Laakso, Markku ; Lahti, Jari ; Lang, Thomas ; Langdahl, Bente L. ; Launer, Lenore J. ; Lee, Jong Young ; Lerch, Markus M. ; Lewis, Joshua R. ; Lind, Lars ; Lindgren, Cecilia M. ; Liu, Yongmei ; Liu, Tian ; Liu, Youfang ; Ljunggren, Östen ; Lorentzon, Mattias ; Luben, Robert N. ; Maixner, William ; McGuigan, Fiona E. ; Medina-Gomez, Carolina ; Meitinger, Thomas ; Melhus, Håkan ; Mellström, Dan ; Melov, Simon ; Michaëlsson, Karl ; Mitchell, Braxton D. ; Morris, Andrew P. ; Mosekilde, Leif ; Newman, Anne ; Nielson, Carrie M. ; O'Connell, Jeffrey R. ; Oostra, Ben A. ; Orwoll, Eric S. ; Palotie, Aarno ; Parker, Stephan ; Peacock, Munro ; Perola, Markus ; Peters, Annette ; Polasek, Ozren ; Prince, Richard L. ; Raïkkönen, Katri ; Ralston, Stuart H. ; Ripatti, Samuli ; Robbins, John A. ; Rotter, Jerome I. ; Rudan, Igor ; Salomaa, Veikko ; Satterfield, Suzanne ; Schadt, Eric E. ; Schipf, Sabine ; Scott, Laura ; Sehmi, Joban ; Shen, Jian ; Soo Shin, Chan ; Sigurdsson, Gunnar ; Smith, Shad ; Soranzo, Nicole ; Stančáková, Alena ; Steinhagen-Thiessen, Elisabeth ; Streeten, Elizabeth A. ; Styrkarsdottir, Unnur ; Swart, Karin M.A. ; Tan, Sian Tsung ; Tarnopolsky, Mark A. ; Thompson, Patricia ; Thomson, Cynthia A. ; Thorsteinsdottir, Unnur ; Tikkanen, Emmi ; Tranah, Gregory J. ; Tuomilehto, Jaakko ; Schoor, Natasja M. van; Verma, Arjun ; Vollenweider, Peter ; Völzke, Henry ; Wactawski-Wende, Jean ; Walker, Mark ; Weedon, Michael N. ; Welch, Ryan ; Wichman, H.E. ; Widen, Elisabeth ; Williams, Frances M.K. ; Wilson, James F. ; Wright, Nicole C. ; Xie, Weijia ; Yu, Lei ; Zhou, Yanhua ; Chambers, John C. ; Döring, Angela ; Duijn, Cornelia M. Van; Econs, Michael J. ; Gudnason, Vilmundur ; Kooner, Jaspal S. ; Psaty, Bruce M. ; Spector, Timothy D. ; Stefansson, Kari ; Rivadeneira, Fernando ; Uitterlinden, André G. ; Wareham, Nicholas J. ; Ossowski, Vicky ; Waterworth, Dawn M. ; Loos, Ruth J.F. ; Karasik, David ; Harris, Tamara B. ; Ohlsson, Claes ; Kiel, Douglas P. - \ 2017
    Nature Communications 8 (2017)1. - ISSN 2041-1723
    Lean body mass, consisting mostly of skeletal muscle, is important for healthy aging. We performed a genome-wide association study for whole body (20 cohorts of European ancestry with n = 38,292) and appendicular (arms and legs) lean body mass (n = 28,330) measured using dual energy X-ray absorptiometry or bioelectrical impedance analysis, adjusted for sex, age, height, and fat mass. Twenty-one single-nucleotide polymorphisms were significantly associated with lean body mass either genome wide (p < 5 × 10-8) or suggestively genome wide (p < 2.3 × 10-6). Replication in 63,475 (47,227 of European ancestry) individuals from 33 cohorts for whole body lean body mass and in 45,090 (42,360 of European ancestry) subjects from 25 cohorts for appendicular lean body mass was successful for five single-nucleotide polymorphisms in/near HSD17B11, VCAN, ADAMTSL3, IRS1, and FTO for total lean body mass and for three single-nucleotide polymorphisms in/near VCAN, ADAMTSL3, and IRS1 for appendicular lean body mass. Our findings provide new insight into the genetics of lean body mass.
    Low-Frequency Synonymous Coding Variation in CYP2R1 Has Large Effects on Vitamin D Levels and Risk of Multiple Sclerosis
    Manousaki, Despoina ; Dudding, Tom ; Haworth, Simon ; Hsu, Yi Hsiang ; Liu, Ching Ti ; Medina-Gómez, Carolina ; Voortman, Trudy ; Velde, Nathalie Van Der; Melhus, Håkan ; Vandenput, Liesbeth ; Noordam, Raymond ; Forgetta, Vincenzo ; Greenwood, Celia M.T. ; Biggs, Mary L. ; Psaty, Bruce M. ; Rotter, Jerome I. ; Zemel, Babette S. ; Mitchell, Jonathan A. ; Taylor, Bruce ; Lorentzon, Mattias ; Karlsson, Magnus ; Jaddoe, Vincent W.V. ; Tiemeier, Henning ; Campos-Obando, Natalia ; Franco, Oscar H. ; Utterlinden, Andre G. ; Broer, Linda ; Schoor, Natasja M. van; Ham, Annelies C. ; Ikram, Arfan M.A. ; Karasik, David ; Mutsert, Renée De; Rosendaal, Frits R. ; Heijer, Martin den; Wang, Thomas J. ; Lind, Lars ; Orwoll, Eric S. ; Mook-Kanamori, Dennis O. ; Michaëlsson, Karl ; Kestenbaum, Bryan ; Ohlsson, Claes ; Mellström, Dan ; Groot, Lisette C.P.G.M. de; Grant, Struan F.A. ; Kiel, Douglas P. ; Zillikens, M.C. ; Rivadeneira, Fernando ; Sawcer, Stephen ; Timpson, Nicholas J. ; Richards, J.B. - \ 2017
    American Journal of Human Genetics 101 (2017)2. - ISSN 0002-9297 - p. 227 - 238.
    GWAS - Low-frequency genetic variants - Multiple sclerosis - Vitamin D
    Vitamin D insufficiency is common, correctable, and influenced by genetic factors, and it has been associated with risk of several diseases. We sought to identify low-frequency genetic variants that strongly increase the risk of vitamin D insufficiency and tested their effect on risk of multiple sclerosis, a disease influenced by low vitamin D concentrations. We used whole-genome sequencing data from 2,619 individuals through the UK10K program and deep-imputation data from 39,655 individuals genotyped genome-wide. Meta-analysis of the summary statistics from 19 cohorts identified in CYP2R1 the low-frequency (minor allele frequency = 2.5%) synonymous coding variant g.14900931G>A (p.Asp120Asp) (rs117913124[A]), which conferred a large effect on 25-hydroxyvitamin D (25OHD) levels (-0.43 SD of standardized natural log-transformed 25OHD per A allele; p value = 1.5 × 10-88). The effect on 25OHD was four times larger and independent of the effect of a previously described common variant near CYP2R1. By analyzing 8,711 individuals, we showed that heterozygote carriers of this low-frequency variant have an increased risk of vitamin D insufficiency (odds ratio [OR] = 2.2, 95% confidence interval [CI] = 1.78-2.78, p = 1.26 × 10-12). Individuals carrying one copy of this variant also had increased odds of multiple sclerosis (OR = 1.4, 95% CI = 1.19-1.64, p = 2.63 × 10-5) in a sample of 5,927 case and 5,599 control subjects. In conclusion, we describe a low-frequency CYP2R1 coding variant that exerts the largest effect upon 25OHD levels identified to date in the general European population and implicates vitamin D in the etiology of multiple sclerosis.
    AntiSMASH 4.0 - improvements in chemistry prediction and gene cluster boundary identification
    Blin, Kai ; Wolf, Thomas ; Chevrette, Marc G. ; Lu, Xiaowen ; Schwalen, Christopher J. ; Kautsar, Satria A. ; Suarez Duran, Hernando G. ; Los Santos, Emmanuel L.C. De; Kim, Hyun Uk ; Nave, Mariana ; Dickschat, Jeroen S. ; Mitchell, Douglas A. ; Shelest, Ekaterina ; Breitling, Rainer ; Takano, Eriko ; Lee, Sang Yup ; Weber, Tilmann ; Medema, Marnix H. - \ 2017
    Nucleic acids research 45 (2017)W1. - ISSN 0305-1048 - p. W36 - W41.
    Many antibiotics, chemotherapeutics, crop protection agents and food preservatives originate from molecules produced by bacteria, fungi or plants. In recent years, genome mining methodologies have been widely adopted to identify and characterize the biosynthetic gene clusters encoding the production of such compounds. Since 2011, the â € antibiotics and secondary metabolite analysis shell - antiSMASH' has assisted researchers in efficiently performing this, both as a web server and a standalone tool. Here, we present the thoroughly updated antiSMASH version 4, which adds several novel features, including prediction of gene cluster boundaries using the ClusterFinder method or the newly integrated CASSIS algorithm, improved substrate specificity prediction for non-ribosomal peptide synthetase adenylation domains based on the new SANDPUMA algorithm, improved predictions for terpene and ribosomally synthesized and post-translationally modified peptides cluster products, reporting of sequence similarity to proteins encoded in experimentally characterized gene clusters on a per-protein basis and a domain-level alignment tool for comparative analysis of trans-AT polyketide synthase assembly line architectures. Additionally, several usability features have been updated and improved. Together, these improvements make antiSMASH up-to-date with the latest developments in natural product research and will further facilitate computational genome mining for the discovery of novel bioactive molecules.
    Stadium Coltan : artisanal mining, reforms and social change in eastern Democratic Republic of Congo
    Wakenge, Claude Iguma - \ 2017
    Wageningen University. Promotor(en): D.J.M. Hilhorst, co-promotor(en): K. Vlassenroot; J.G.R. Cuvelier. - Wageningen : Wageningen University - ISBN 9789463434560 - 210
    mining - conflict - economic sociology - cooperatives - reconstruction - poverty - rural sociology - workers - feedstocks - minerals - congo democratic republic - central africa - mijnbouw - conflict - economische sociologie - coöperaties - reconstructie - armoede - rurale sociologie - werkers - industriële grondstoffen - mineralen - democratische republiek kongo - centraal-afrika

    In the Democratic Republic of Congo (DRC), the mining sector has the potential to play a pivotal role in post-conflict reconstruction (World Bank, 2008), and artisanal mining sustains the livelihoods of millions people in the country (PACT, 2010). However, in the last 15 years, minerals from this artisanal mining have been ill-reputed. Eastern DRC has often been characterised by chronic instability and violent conflicts (Autesserre, 2010; Stearns, 2011) because it is widely believed that minerals in this region have attracted the greed of national and foreign armed groups, who benefit from the mining business.

    Although this ‘greed hypothesis’ has been criticised for its inconsistent performance in explaining resource-related conflicts (Le Billon, 2010; Ross, 2006), various national and international reform initiatives have gained momentum (Verbruggen et al., 2011). These initiatives aim to make the Congolese artisanal mining sector more transparent and to prevent ‘conflict minerals’ from entering the international market. In 2014, 13 reform initiatives—10 focusing on 3T (tantalum, tin and tungsten) and three on gold—were operational in eastern DRC (Cuvelier et al. 2014: 5). The implicit assumptions are that mining reforms will fully ‘clean’ artisanal mining of violence and corruption and that this will contribute to sustaining people’s livelihoods (Garrett and Mitchell, 2009: 12).

    This study investigated initiatives intended to ‘formalise’ artisanal mining in DRC—in other words, they aimed to bring mining under state control. The study especially focuses on the effects of one among these initiatives—the ITRI Tin Supply Chain Initiative (iTSCi)—on two groups of actors: miners (creuseurs) and middlemen (négociants). This thesis thus presents a fine-grained case study of the iTSCi. Designed by the International Tin Research Institute in 2009, iTSCi provides a means of determining the origin of 3T and documenting the trading chain for these minerals by ‘tagging and bagging’ the loads of 3T near miners’ shafts (at postes d’achat/selling points or buying stations), at counting offices (comptoirs) and in mineral depots, before the minerals are exported through the international market.

    This is a qualitative study undertaken at three coltan mining sites of northern Katanga: Kahendwa, Kisengo and Mai-Baridi. Coltan has been extracted at these sites since 2007. From March 2013 to September 2014, data were collected using participant observation of people’s practices (extraction/sale of coltan and various types of interactions between trading houses, cooperatives, mineworkers (creuseurs) and middlemen (négociants), as well as detailed in-depth interviews with creuseurs, négociants and their households. Data were also collected from the staff of mining cooperatives, trading houses, state authorities and civil servants—predominantly of the Service d’Assistance et d’Encadrement du Small-Scale Mining (SAESSCAM) and the Division des Mines. The last group of informants were a group of clandestine coltan négociants (known as hiboux—literally, ‘owls’), who were followed in the study.

    The purpose of this research is to study the micro-dynamics of changes after the reforms following the implementation of iTSCi. The study thus provides insights into how iTSCi is concretely implemented and how it has altered the organisation of mining and the trade of coltan. The study also aims to examine how this organisation affected creuseurs and négociants. The main research question of this study is as follows:

    How have initiatives to reform artisanal mining (iTSCi in particular) affected institutional change, how does this relate to changes in patterns of coltan production and trade, how were creuseurs and négociants affected by these changes, and how did these groups respond in the coltan mining areas of Kahendwa, Kisengo and Mai Baridi (northern Katanga) from 2009 to 2014?

    Analytically, the study adopted three main theoretical perspectives. First, an actor-oriented approach was taken, building on the premise that individual actors have the agency, knowledge and experience to reflect upon their situation and to respond to changes in their surrounding context (Giddens, 1984). Although the examined mining reforms consist predominantly of ‘ready-made’ techniques such as iTSCi’s ‘tagging and bagging’, analysing reforms with an actor orientation helps to highlight people’s reactions and responses. This includes how reform policies are applied in institutions (e.g. mining cooperatives), how they interact, how they are assigned meaning and how they are negotiated by social actors (Christoplos and Hilhorst, 2009).

    Second, the study builds on the sociology of economic life, which holds that economic action is a form of social action that is socially ‘embedded’, meaning that it is linked with or dependent on actions and institutions (such as social networks) that are noneconomic in content, goals and processes (Granovetter, 2005). This perspective facilitates the analysis of the livelihoods of négociants, including mechanisms of smuggling minerals into and beyond the mining areas where iTSCi is in force.

    Third, this thesis introduced the original concept of ‘enclaves of regulations’. These enclaves refer to the mining areas where iTSCi or other reforms are in force. This thesis has shown that, although these ‘enclaves’ appear to be ‘closed’ and insulated from the environment in terms of the locally applied rules for the mining and trading of minerals (e.g. ‘tagging and bagging’), in reality, such closure is not complete. This thesis has demonstrated that it would therefore be more appropriate to consider these ‘enclaves’ as semi-autonomous fields with porous boundaries.

    Apart from the introduction and the concluding chapters, this thesis is composed of five chapters. Chapter 2 explores the evolution of the mineral sector in the Katanga province. It analyses the history of mining, the initiation of artisanal mining and how the ongoing reforms have been informed by this history. In this chapter, it is shown that there is a long history of the organisation of mining in the Katangese province. The reforms therefore did not enter into a stage of anarchy, or an institutional void, but they added a layer to already existing forms of organisation.

    Chapter 3 focuses on mining cooperatives as newly introduced institutions aimed at governing the artisanal mining sites. Through a single case study, the chapter analyses how these cooperatives —especially the Coopérative des Artisanaux Miniers du Congo, CDMC—were introduced into the mining areas and how they interacted and blended with pre-existing miners’ organisations. This chapter demonstrates that cooperatives have been an emergent—rather than durable—solution in terms of representing the interests of artisanal miners.

    In Chapter 4, I provide a different perspective on ‘conflict minerals’. I thus introduce the notion of ‘reform conflicts’ to emphasise that, although ongoing reforms aim to sever the supposed linkages between the artisanal mining business and violent conflicts, these reforms have become a driving force behind the emergence of new conflicts over property rights and access to minerals.

    Chapter 5 is about livelihoods. It analyses how the reforms have influenced the livelihoods and socioeconomic position of négociants. This chapter also explores what kind of opportunities the reforms have offered to this group of mineral brokers often considered powerful in the mineral supply chain and explains what kind of constraints the négociants have confronted and why they have opted to diversify their livelihood portfolios. The chapter has shown that the reforms have affected this group of mineral brokers in different ways. Some négociants were well off, whereas others have been excluded from the mineral commodity chain. These findings contradict the widespread opinion that négociants are always abusive brokers in the mineral production and commodity chain.

    Chapter 6 analyses the responses of creuseurs and négociants to iTSCi. Although the mining sites where iTSCi is in force appear to be ‘enclaves of regulations’, I explore the strategies of creuseurs and négociants to bypass iTSCi and the reforms, especially around the coltan trade. This chapter demonstrates that coltan smuggling is a deeply rooted practice. Despite the reforms, smuggling continues in different forms.

    All of the elements highlighted above suggest that mining reforms have undergone a major shift, from addressing the initial problems associated with ‘conflict minerals’ to creating or reinforcing various types of problems, such as the influence of ‘big men’ in the mining business, coltan smuggling and the emergence of new conflicts over accessing minerals. This means that reform initiatives such as iTSCi should be based on knowledge about the actual situation. Thus, understanding and addressing these new types of problems calls for a comprehensive approach at both local and broader levels.

    Current remote sensing approaches to monitoring forest degradation in support of countries measurement, reporting and verification (MRV) systems for REDD+
    Mitchell, Anthea L. ; Rosenqvist, Ake ; Mora, Brice - \ 2017
    Carbon Balance and Management 12 (2017)1. - ISSN 1750-0680
    Above-ground biomass - Carbon emissions - Degradation - Disturbance - Forests - Measurement reporting and verification - Monitoring - REDD+ - Time-series

    Forest degradation is a global phenomenon and while being an important indicator and precursor to further forest loss, carbon emissions due to degradation should also be accounted for in national reporting within the frame of UN REDD+. At regional to country scales, methods have been progressively developed to detect and map forest degradation, with these based on multi-resolution optical, synthetic aperture radar (SAR) and/or LiDAR data. However, there is no one single method that can be applied to monitor forest degradation, largely due to the specific nature of the degradation type or process and the timeframe over which it is observed. The review assesses two main approaches to monitoring forest degradation: first, where detection is indicated by a change in canopy cover or proxies, and second, the quantification of loss (or gain) in above ground biomass (AGB). The discussion only considers degradation that has a visible impact on the forest canopy and is thus detectable by remote sensing. The first approach encompasses methods that characterise the type of degradation and track disturbance, detect gaps in, and fragmentation of, the forest canopy, and proxies that provide evidence of forestry activity. Progress in these topics has seen the extension of methods to higher resolution (both spatial and temporal) data to better capture the disturbance signal, distinguish degraded and intact forest, and monitor regrowth. Improvements in the reliability of mapping methods are anticipated by SAR-optical data fusion and use of very high resolution data. The second approach exploits EO sensors with known sensitivity to forest structure and biomass and discusses monitoring efforts using repeat LiDAR and SAR data. There has been progress in the capacity to discriminate forest age and growth stage using data fusion methods and LiDAR height metrics. Interferometric SAR and LiDAR have found new application in linking forest structure change to degradation in tropical forests. Estimates of AGB change have been demonstrated at national level using SAR and LiDAR-assisted approaches. Future improvements are anticipated with the availability of next generation LiDAR sensors. Improved access to relevant satellite data and best available methods are key to operational forest degradation monitoring. Countries will need to prioritise their monitoring efforts depending on the significance of the degradation, balanced against available resources. A better understanding of the drivers and impacts of degradation will help guide monitoring and restoration efforts. Ultimately we want to restore ecosystem service and function in degraded forests before the change is irreversible.

    Soil protistology rebooted: 30 fundamental questions to start with
    Geisen, Stefan ; Mitchell, Edward A.D. ; Wilkinson, David M. ; Adl, Sina ; Bonkowski, Michael ; Brown, Matthew W. ; Fiore-Donno, Anna Maria ; Heger, Thierry J. ; Jassey, Vincent E.J. ; Krashevska, Valentyna ; Lahr, Daniel J.G. ; Marcisz, Katarzyna ; Mulot, Matthieu ; Payne, Richard ; Singer, David ; Anderson, O.R. ; Charman, Dan J. ; Ekelund, Flemming ; Griffiths, Bryan S. ; Rønn, Regin ; Smirnov, Alexey ; Bass, David ; Belbahri, Lassaâd ; Berney, Cédric ; Blandenier, Quentin ; Chatzinotas, Antonis ; Clarholm, Marianne ; Dunthorn, Micah ; Feest, Alan ; Fernández, Leonardo D. ; Foissner, Wilhelm ; Fournier, Bertrand ; Gentekaki, Eleni ; Hájek, Michal ; Helder, Hans ; Jousset, Alexandre ; Koller, Robert ; Kumar, Santosh ; Terza, Antonietta La; Lamentowicz, Mariusz ; Mazei, Yuri ; Santos, Susana S. ; Seppey, Christophe V.W. ; Spiegel, Frederick W. ; Walochnik, Julia ; Winding, Anne ; Lara, Enrique - \ 2017
    Soil Biology and Biochemistry 111 (2017). - ISSN 0038-0717 - p. 94 - 103.
    Protists are the most diverse eukaryotes. These microbes are keystone organisms of soil ecosystems and
    regulate essential processes of soil fertility such as nutrient cycling and plant growth. Despite this,
    protists have received little scientific attention, especially compared to bacteria, fungi and nematodes in
    soil studies. Recent methodological advances, particularly in molecular biology techniques, have made
    the study of soil protists more accessible, and have created a resurgence of interest in soil protistology.
    This ongoing revolution now enables comprehensive investigations of the structure and functioning of
    soil protist communities, paving the way to a new era in soil biology. Instead of providing an exhaustive
    review, we provide a synthesis of research gaps that should be prioritized in future studies of soil
    protistology to guide this rapidly developing research area. Based on a synthesis of expert opinion we
    propose 30 key questions covering a broad range of topics including evolution, phylogenetics, functional
    ecology, macroecology, paleoecology, and methodologies. These questions highlight a diversity of topics
    that will establish soil protistology as a hub discipline connecting different fundamental and applied
    fields such as ecology, biogeography, evolution, plant-microbe interactions, agronomy, and conservation
    biology. We are convinced that soil protistology has the potential to be one of the most exciting frontiers
    in biology.
    The genome of Chenopodium quinoa
    Jarvis, D.E. ; Shwen Ho, Yung ; Lightfoot, Damien J. ; Schmöckel, Sandra M. ; Li, Bo ; Borm, T.J.A. ; Ohyanagi, Hajime ; Mineta, Katsuhiko ; Mitchell, Craig T. ; Saber, Noha ; Kharbatia, Najeh M. ; Rupper, Ryan R. ; Sharp, Aaron R. ; Dally, Nadine ; Boughton, Berin A. ; Woo, Yong H. ; Gao, Ge ; Schijlen, E.G.W.M. ; Guo, Xiujie ; Momin, Afaque A. ; Negräo, Sónia ; Al-Babili, Salim ; Gehring, Christoph ; Roessner, Ute ; Jung, Christian ; Murphy, Kevin ; Arold, Stefan T. ; Gojobori, Takashi ; Linden, C.G. van der; Loo, E.N. van; Jellen, Eric N. ; Maughan, Peter J. ; Tester, Mark - \ 2017
    Nature 542 (2017)7641. - ISSN 0028-0836 - p. 307 - 312.
    Chenopodium quinoa (quinoa) is a highly nutritious grain identified as an important crop to improve world food security. Unfortunately, few resources are available to facilitate its genetic improvement. Here we report the assembly of a high-quality, chromosome-scale reference genome sequence for quinoa, which was produced using single-molecule real-time sequencing in combination with optical, chromosome-contact and genetic maps. We also report the sequencing of two diploids from the ancestral gene pools of quinoa, which enables the identification of sub-genomes in quinoa, and reduced-coverage genome sequences for 22 other samples of the allotetraploid goosefoot complex. The genome sequence facilitated the identification of the transcription factor likely to control the production of anti-nutritional triterpenoid saponins found in quinoa seeds, including a mutation that appears to cause alternative splicing and a premature stop codon in sweet quinoa strains. These genomic resources are an important first step towards the genetic improvement of quinoa.
    Nutrition for the ageing brain: Towards evidence for an optimal diet
    Vauzour, David ; Camprubi-Robles, Maria ; Miquel-Kergoat, Sophie ; Andres-Lacueva, Cristina ; Bánáti, Diána ; Barberger-Gateau, Pascale ; Bowman, Gene L. ; Caberlotto, Laura ; Clarke, Robert ; Hogervorst, Eef ; Kiliaan, Amanda J. ; Lucca, Ugo ; Manach, Claudine ; Minihane, Anne-Marie ; Mitchell, Ellen Siobhan ; Perneczky, Robert ; Perry, Hugh ; Roussel, Anne-Marie ; Schuermans, Jeroen ; Sijben, John ; Spencer, Jeremy P.E. ; Thuret, Sandrine ; De Rest, Ondine Van; Vandewoude, Maurits ; Wesnes, Keith ; Williams, Robert J. ; Williams, Robin S.B. ; Ramirez, Maria - \ 2017
    Ageing Research Reviews 35 (2017). - ISSN 1568-1637 - p. 222 - 240.
    As people age they become increasingly susceptible to chronic and extremely debilitating brain diseases. The precise cause of the neuronal degeneration underlying these disorders, and indeed normal brain ageing remains however elusive. Considering the limits of existing preventive methods, there is a desire to develop effective and safe strategies. Growing preclinical and clinical research in healthy individuals or at the early stage of cognitive decline has demonstrated the beneficial impact of nutrition on cognitive functions. The present review is the most recent in a series produced by the Nutrition and Mental Performance Task Force under the auspice of the International Life Sciences Institute Europe (ILSI Europe). The latest scientific advances specific to how dietary nutrients and non-nutrient may affect cognitive ageing are presented. Furthermore, several key points related to mechanisms contributing to brain ageing, pathological conditions affecting brain function, and brain biomarkers are also discussed. Overall, findings are inconsistent and fragmented and more research is warranted to determine the underlying mechanisms and to establish dose-response relationships for optimal brain maintenance in different population subgroups. Such approaches are likely to provide the necessary evidence to develop research portfolios that will inform about new dietary recommendations on how to prevent cognitive decline.
    Genome-wide analysis identifies 12 loci influencing human reproductive behavior
    Barban, Nicola ; Jansen, Rick ; Vlaming, Ronald de; Vaez, Ahmad ; Mandemakers, Jornt J. ; Tropf, Felix C. ; Shen, Xia ; Wilson, James F. ; Chasman, Daniel I. ; Nolte, Ilja M. ; Tragante, Vinicius ; Laan, Sander W. van der; Perry, John R.B. ; Kong, Augustine ; Ahluwalia, Tarunveer S. ; Albrecht, Eva ; Yerges-Armstrong, Laura ; Atzmon, Gil ; Auro, Kirsi ; Ayers, Kristin ; Bakshi, Andrew ; Ben-Avraham, Danny ; Berger, Klaus ; Bergman, Aviv ; Bertram, Lars ; Bielak, Lawrence F. ; Bjornsdottir, Gyda ; Bonder, Marc Jan ; Broer, Linda ; Bui, Minh ; Barbieri, Caterina ; Cavadino, Alana ; Chavarro, Jorge E. ; Turman, Constance ; Concas, Maria Pina ; Cordell, Heather J. ; Davies, Gail ; Eibich, Peter ; Eriksson, Nicholas ; Esko, Tõnu ; Eriksson, Joel ; Falahi, Fahimeh ; Felix, Janine F. ; Fontana, Mark Alan ; Franke, Lude ; Gandin, Ilaria ; Gaskins, Audrey J. ; Gieger, Christian ; Gunderson, Erica P. ; Guo, Xiuqing ; Hayward, Caroline ; He, Chunyan ; Hofer, Edith ; Huang, Hongyan ; Joshi, Peter K. ; Kanoni, Stavroula ; Karlsson, Robert ; Kiechl, Stefan ; Kifley, Annette ; Kluttig, Alexander ; Kraft, Peter ; Lagou, Vasiliki ; Lecoeur, Cecile ; Lahti, Jari ; Li-Gao, Ruifang ; Lind, Penelope A. ; Liu, Tian ; Makalic, Enes ; Mamasoula, Crysovalanto ; Matteson, Lindsay ; Mbarek, Hamdi ; McArdle, Patrick F. ; McMahon, George ; Meddens, S.F.W. ; Mihailov, Evelin ; Miller, Mike ; Missmer, Stacey A. ; Monnereau, Claire ; Most, Peter J. van der; Myhre, Ronny ; Nalls, Mike A. ; Nutile, Teresa ; Kalafati, Ioanna Panagiota ; Porcu, Eleonora ; Prokopenko, Inga ; Rajan, Kumar B. ; Rich-Edwards, Janet ; Rietveld, Cornelius A. ; Robino, Antonietta ; Rose, Lynda M. ; Rueedi, Rico ; Ryan, Kathleen A. ; Saba, Yasaman ; Schmidt, Daniel ; Smith, Jennifer A. ; Stolk, Lisette ; Streeten, Elizabeth ; Tönjes, Anke ; Thorleifsson, Gudmar ; Ulivi, Sheila ; Wedenoja, Juho ; Wellmann, Juergen ; Willeit, Peter ; Yao, Jie ; Yengo, Loic ; Zhao, Jing Hua ; Zhao, Wei ; Zhernakova, Daria V. ; Amin, Najaf ; Andrews, Howard ; Balkau, Beverley ; Barzilai, Nir ; Bergmann, Sven ; Biino, Ginevra ; Bisgaard, Hans ; Bønnelykke, Klaus ; Boomsma, Dorret I. ; Buring, Julie E. ; Campbell, Harry ; Cappellani, Stefania ; Ciullo, Marina ; Cox, Simon R. ; Cucca, Francesco ; Toniolo, Daniela ; Davey-Smith, George ; Deary, Ian J. ; Dedoussis, George ; Deloukas, Panos ; Duijn, Cornelia M. van; Geus, Eco J.C. de; Eriksson, Johan G. ; Evans, Denis A. ; Faul, Jessica D. ; Sala, Cinzia Felicita ; Froguel, Philippe ; Gasparini, Paolo ; Girotto, Giorgia ; Grabe, Hans-Jörgen ; Greiser, Karin Halina ; Groenen, Patrick J.F. ; Haan, Hugoline G. de; Haerting, Johannes ; Harris, Tamara B. ; Heath, Andrew C. ; Heikkilä, Kauko ; Hofman, Albert ; Homuth, Georg ; Holliday, Elizabeth G. ; Hopper, John ; Hyppönen, Elina ; Jacobsson, Bo ; Jaddoe, Vincent W.V. ; Johannesson, Magnus ; Jugessur, Astanand ; Kähönen, Mika ; Kajantie, Eero ; Kardia, Sharon L.R. ; Keavney, Bernard ; Kolcic, Ivana ; Koponen, Päivikki ; Kovacs, Peter ; Kronenberg, Florian ; Kutalik, Zoltan ; Bianca, Martina la; Lachance, Genevieve ; Iacono, William G. ; Lai, Sandra ; Lehtimäki, Terho ; Liewald, David C. ; Lindgren, Cecilia M. ; Liu, Yongmei ; Luben, Robert ; Lucht, Michael ; Luoto, Riitta ; Magnus, Per ; Magnusson, Patrik K.E. ; Martin, Nicholas G. ; McGue, Matt ; McQuillan, Ruth ; Medland, Sarah E. ; Meisinger, Christa ; Mellström, Dan ; Metspalu, Andres ; Traglia, Michela ; Milani, Lili ; Mitchell, Paul ; Montgomery, Grant W. ; Mook-Kanamori, Dennis ; Mutsert, Renée de; Nohr, Ellen A. ; Ohlsson, Claes ; Olsen, Jørn ; Ong, Ken K. ; Paternoster, Lavinia ; Pattie, Alison ; Penninx, Brenda W.J.H. ; Perola, Markus ; Peyser, Patricia A. ; Pirastu, Mario ; Polasek, Ozren ; Power, Chris ; Kaprio, Jaakko ; Raffel, Leslie J. ; Räikkönen, Katri ; Raitakari, Olli ; Ridker, Paul M. ; Ring, Susan M. ; Roll, Kathryn ; Rudan, Igor ; Ruggiero, Daniela ; Rujescu, Dan ; Salomaa, Veikko ; Schlessinger, David ; Schmidt, Helena ; Schmidt, Reinhold ; Schupf, Nicole ; Smit, Johannes ; Sorice, Rossella ; Spector, Tim D. ; Starr, John M. ; Stöckl, Doris ; Strauch, Konstantin ; Stumvoll, Michael ; Swertz, Morris A. ; Thorsteinsdottir, Unnur ; Thurik, A.R. ; Timpson, Nicholas J. ; Tung, Joyce Y. ; Uitterlinden, André G. ; Vaccargiu, Simona ; Viikari, Jorma ; Vitart, Veronique ; Völzke, Henry ; Vollenweider, Peter ; Vuckovic, Dragana ; Waage, Johannes ; Wagner, Gert G. ; Wang, Jie Jin ; Wareham, Nicholas J. ; Weir, David R. ; Willemsen, Gonneke ; Willeit, Johann ; Wright, Alan F. ; Zondervan, Krina T. ; Stefansson, Kari ; Krueger, Robert F. ; Lee, James J. ; Benjamin, Daniel J. ; Cesarini, David ; Koellinger, Philipp D. ; Hoed, Marcel den; Snieder, Harold ; Mills, Melinda C. - \ 2016
    Nature Genetics 48 (2016)12. - ISSN 1061-4036 - p. 1462 - 1472.
    The genetic architecture of human reproductive behavior—age at first birth (AFB) and number of children ever born (NEB)—has a strong relationship with fitness, human development, infertility and risk of neuropsychiatric disorders. However, very few genetic loci have been identified, and the underlying mechanisms of AFB and NEB are poorly understood. We report a large genome-wide association study of both sexes including 251,151 individuals for AFB and 343,072 individuals for NEB. We identified 12 independent loci that are significantly associated with AFB and/or NEB in a SNP-based genome-wide association study and 4 additional loci associated in a gene-based effort. These loci harbor genes that are likely to have a role, either directly or by affecting non-local gene expression, in human reproduction and infertility, thereby increasing understanding of these complex traits.
    Results of a desk study on best practices for animal transport
    Mitchell, M.A. ; Spoolder, H.A.M. - \ 2016
    In: Book of Abstracts of the 67th Annual Meeting of the European Association for Animal Production. - EAAP scientific committee - ISBN 9789086868308 - p. 531 - 531.
    The EU has provides a harmonised legal framework for animal transport. Part of that framework is the EU adopted Regulation (EC) 1/2005. The content and impact of the Regulation has been the subject of a Scientific Opinion by EFSA in 2011 followed in 2012 by an impact report from the Commission to the European
    Parliament and the Council. Three key recommendations were formulated the latter of which stated ‘As regards the gap between the requirements of the legislation and available scientific evidence the Commission sees that this is best addressed by the adoption of guides to good practice’. It is expected that the development of Guides to Good and Best Practice can improve the welfare of animals during transportation, particularly by reducing national and regional differences in interpretation of the requirements of the Regulation. The
    Transport Guides project was commissioned by DG SANTE to produce Guides to Good Practice for cattle, sheep, pigs, horses and poultry in the European Union (http://www.animaltransportguides.eu). The project has been undertaken by a research consortium comprised of 16 representative organisations from 9 Member States and a stakeholder platform with 10 member organisations. The first phase of this project involved the examination of a wide range of information sources and literature to identify and evaluate available recommendations for good and best practices during all stages of transport. Good practices are those that reflect the requirements in the legislation. Best Practices are defined as providing additional guidance on how to exceed legally defined minimum welfare requirements. The first results of this project include analyses of the collected information for each of the species: each species section includes analyses of the practices identified, followed by an overview of all available practices presented in tabulated form. These findings are
    the basis for the development of Guides to Good and Best Practices in the next steps of the project, and will be presented at the meeting.
    Impact of the shedding level on transmission of persistent infections in Mycobacterium avium subspecies paratuberculosis (MAP)
    Slater, Noa ; Mitchell, Rebecca Mans ; Whitlock, Robert H. ; Fyock, Terry ; Pradhan, Abani Kumar ; Knupfer, Elena ; Schukken, Ynte Hein ; Louzoun, Yoram - \ 2016
    Veterinary Research 47 (2016)1. - ISSN 0928-4249

    Super-shedders are infectious individuals that contribute a disproportionate amount of infectious pathogen load to the environment. A super-shedder host may produce up to 10 000 times more pathogens than other infectious hosts. Super-shedders have been reported for multiple human and animal diseases. If their contribution to infection dynamics was linear to the pathogen load, they would dominate infection dynamics. We here focus on quantifying the effect of super-shedders on the spread of infection in natural environments to test if such an effect actually occurs in Mycobacterium avium subspecies paratuberculosis (MAP). We study a case where the infection dynamics and the bacterial load shed by each host at every point in time are known. Using a maximum likelihood approach, we estimate the parameters of a model with multiple transmission routes, including direct contact, indirect contact and a background infection risk. We use longitudinal data from persistent infections (MAP), where infectious individuals have a wide distribution of infectious loads, ranging upward of three orders of magnitude. We show based on these parameters that the effect of super-shedders for MAP is limited and that the effect of the individual bacterial load is limited and the relationship between bacterial load and the infectiousness is highly concave. A 1000-fold increase in the bacterial contribution is equivalent to up to a 2-3 fold increase in infectiousness.

    Assessing convergence processes at the intersection of the food and pharmaceutical industries in functional food innovation using different perspectives
    Bornkessel, S. - \ 2016
    Wageningen University. Promotor(en): Onno Omta; Stefanie Broring. - Wageningen : Wageningen University - ISBN 9789462576599 - 129
    functional foods - innovations - food industry - non-food industries - pharmacology - functionele voedingsmiddelen - innovaties - voedselindustrie - non-food industrieën - farmacologie

    Assessing convergence processes at the intersection of the food and pharmaceutical industries in functional food innovation using different perspectives

    Sabine Bornkessel

    The worldwide growing functional food market (e.g. Menrad, 2003, Ding et al., 2015) is based on the convergence of the food and pharmaceutical sectors (Omta, 2004, Bröring, 2005), since functional foods incorporate a nutritional as well as a health benefit (Spence, 2006, Hasler, 2002). Several studies provide a comprehensive overview of convergence definitions and their different emphases (Bröring, 2005, Curran, 2010, Hacklin, 2008, Preschitschek, 2014), mainly following the common idea summarised by the Organisation for Economic Co‐operation and Development as follows: ‘the blurring of technical and regulatory boundaries between sectors of the economy’ (OECD, 1992). On the one hand, this emerging segment offers a plethora of innovation opportunities. On the other hand, companies focusing on this emerging segment have to employ knowledge and technologies outside of their traditional expertise. The importance of innovation increases, since the emergence of the functional food market implies an intensification of competitive pressure. Due to high failure rates, there is an urgent need to improve the food innovation process (Stewart-Knox and Mitchell, 2003).

    The convergence process is considered to follow the consecutive steps of science, technology and market convergence, leading to a complete industry convergence in which companies or whole industry segments fuse (Curran et al., 2010, Hacklin, 2008). Linking these steps to the simplified innovation process, the comparative perspective on the innovation and convergence processes delivers a framework with which to analyse innovation processes in converging industries using different perspectives. Therefore, the present thesis aims

    Ø to evaluate convergence processes using different perspectives in order to derive an assessment framework of the innovation process in converging industries.

    This study deals with the functional food sector emerging between the food and pharmaceutical industries while using certain functional ingredients as units of analysis.

    The present thesis comprises two parts. It first focuses on the procedural perspective of convergence processes in order to deliver a comprehensive analysis of the complete convergence process. This is then complemented in the second part by a focus on the later steps of market and industry convergence.

    In the first part, this study delivers quantitative (Chapter 2 – life cycle approach) and qualitative (Chapter 3 – perspective of innovation value chain) measures for the comprehensive analysis of the complete convergence process. While the life cycle approach focuses on the development showing the movement of complete industry sectors, the innovation value chain perspective delivers insights into the underlying strategic cross-industry activities on a company level. Next to the comprehensive analysis of the convergence process, this study delivers two levels with which to analyse the later phases in converging industries: first, the analysis of cross-industry collaborations on a company level (Chapter 4), and second, the analysis of ingredient awareness on a consumer level (Chapter 5). While the analysis on a company level delivers an approach to analyse cross-industry innovation using the resource-based view, the consumer perspective sheds light upon the consumers’ perception of the products delivered in the convergence areas.

    In summary, convergence implies a changing competitive environment. The evaluation of this phenomenon is therefore of high importance for researchers and practitioners alike. This thesis enhances the research field of convergence by delivering an overall assessment framework that integrates different perspectives to screen convergence processes and to analyse converging competences. The scope and the unit of analysis, along with the adaptation of theoretical concepts, extend already existing convergence assessment approaches. Besides the analysis of the early phases of convergence processes used to anticipate industrial developments (e.g. Curran et al., 2010), the elaboration of the complete convergence process delivers an approach to face the multifaceted challenges during the innovation process in converging industries. The practical implications of this study is that it provides companies in convergence areas different measures to evaluate convergence processes in order to identify relevant convergence areas. Depending on the phase of the convergence process, the appropriate method or mixture of methods can be used to substantiate strategic corporate decisions such as for instance product positioning.

    CCoAOMT down-regulation activates anthocyanin biosynthesis in petunia
    Shaipulah, N.F.M. ; Muhlemann, Joëlle K. ; Woodworth, Benjamin D. ; Moerkercke, Alex Van; Verdonk, J.C. ; Ramirez, A.A. ; Haring, Michel A. ; Dudareva, Natalia ; Schuurink, Robert C. - \ 2016
    Plant Physiology 170 (2016)2. - ISSN 0032-0889 - p. 717 - 731.

    Anthocyanins and volatile phenylpropenes (isoeugenol and eugenol) in petunia (Petunia hybrida) flowers have the precursor 4-coumaryl coenzyme A (CoA) in common. These phenolics are produced at different stages during flower development. Anthocyanins are synthesized during early stages of flower development and sequestered in vacuoles during the lifespan of the flowers. The production of isoeugenol and eugenol starts when flowers open and peaks after anthesis. To elucidate additional biochemical steps toward (iso)eugenol production, we cloned and characterized a caffeoyl-coenzyme A O-methyltransferase (PhCCoAOMT1) from the petals of the fragrant petunia ‘Mitchell’. Recombinant PhCCoAOMT1 indeed catalyzed the methylation of caffeoyl-CoA to produce feruloyl CoA. Silencing of PhCCoAOMT1 resulted in a reduction of eugenol production but not of isoeugenol. Unexpectedly, the transgenic plants had purple-colored leaves and pink flowers, despite the fact that cv Mitchell lacks the functional R2R3-MYB master regulator ANTHOCYANIN2 and has normally white flowers. Our results indicate that down-regulation of PhCCoAOMT1 activated the anthocyanin pathway through the R2R3-MYBs PURPLE HAZE (PHZ) and DEEP PURPLE, with predominantly petunidin accumulating. Feeding cv Mitchell flowers with caffeic acid induced PHZ expression, suggesting that the metabolic perturbation of the phenylpropanoid pathway underlies the activation of the anthocyanin pathway. Our results demonstrate a role for PhCCoAOMT1 in phenylpropene production and reveal a link between PhCCoAOMT1 and anthocyanin production.

    Combining satellite data for better tropical forest monitoring
    Reiche, Johannes ; Lucas, Richard ; Mitchell, A.L. ; Verbesselt, Jan ; Hoekman, D.H. ; Haarpaintner, Jörg ; Kellndorfer, J.M. ; Rosenqvist, Ake ; Lehmann, E.A. ; Woodcock, C.E. ; Seifert, Frank Martin ; Herold, Martin - \ 2016
    Nature Climate Change 6 (2016)2. - ISSN 1758-678X - p. 120 - 122.
    Implementation of policies to reduce forest loss challenges the Earth observation community to improve forest monitoring. An important avenue for progress is the use of new satellite missions and the combining of optical and synthetic aperture radar sensor data.
    Minimum Information about a Biosynthetic Gene cluster
    Medema, M.H. ; Kottmann, Renzo ; Yilmaz, Pelin ; Cummings, Matthew ; Biggins, J.B. ; Blin, Kai ; Bruijn, Irene De; Chooi, Yit Heng ; Claesen, Jan ; Coates, R.C. ; Cruz-Morales, Pablo ; Duddela, Srikanth ; Düsterhus, Stephanie ; Edwards, Daniel J. ; Fewer, David P. ; Garg, Neha ; Geiger, Christoph ; Gomez-Escribano, Juan Pablo ; Greule, Anja ; Hadjithomas, Michalis ; Haines, Anthony S. ; Helfrich, Eric J.N. ; Hillwig, Matthew L. ; Ishida, Keishi ; Jones, Adam C. ; Jones, Carla S. ; Jungmann, Katrin ; Kegler, Carsten ; Kim, Hyun Uk ; Kötter, Peter ; Krug, Daniel ; Masschelein, Joleen ; Melnik, Alexey V. ; Mantovani, Simone M. ; Monroe, Emily A. ; Moore, Marcus ; Moss, Nathan ; Nützmann, Hans Wilhelm ; Pan, Guohui ; Pati, Amrita ; Petras, Daniel ; Reen, F.J. ; Rosconi, Federico ; Rui, Zhe ; Tian, Zhenhua ; Tobias, Nicholas J. ; Tsunematsu, Yuta ; Wiemann, Philipp ; Wyckoff, Elizabeth ; Yan, Xiaohui ; Yim, Grace ; Yu, Fengan ; Xie, Yunchang ; Aigle, Bertrand ; Apel, Alexander K. ; Balibar, Carl J. ; Balskus, Emily P. ; Barona-Gómez, Francisco ; Bechthold, Andreas ; Bode, Helge B. ; Borriss, Rainer ; Brady, Sean F. ; Brakhage, Axel A. ; Caffrey, Patrick ; Cheng, Yi Qiang ; Clardy, Jon ; Cox, Russell J. ; Mot, René De; Donadio, Stefano ; Donia, Mohamed S. ; Donk, Wilfred A. Van Der; Dorrestein, Pieter C. ; Doyle, Sean ; Driessen, Arnold J.M. ; Ehling-Schulz, Monika ; Entian, Karl Dieter ; Fischbach, Michael A. ; Gerwick, Lena ; Gerwick, William H. ; Gross, Harald ; Gust, Bertolt ; Hertweck, Christian ; Höfte, Monica ; Jensen, Susan E. ; Ju, Jianhua ; Katz, Leonard ; Kaysser, Leonard ; Klassen, Jonathan L. ; Keller, Nancy P. ; Kormanec, Jan ; Kuipers, Oscar P. ; Kuzuyama, Tomohisa ; Kyrpides, Nikos C. ; Kwon, Hyung Jin ; Lautru, Sylvie ; Lavigne, Rob ; Lee, Chia Y. ; Linquan, Bai ; Liu, Xinyu ; Liu, Wen ; Luzhetskyy, Andriy ; Mahmud, Taifo ; Mast, Yvonne ; Méndez, Carmen ; Metsä-Ketelä, Mikko ; Micklefield, Jason ; Mitchell, Douglas A. ; Moore, Bradley S. ; Moreira, Leonilde M. ; Müller, Rolf ; Neilan, Brett A. ; Nett, Markus ; Nielsen, Jens ; O'Gara, Fergal ; Oikawa, Hideaki ; Osbourn, Anne ; Osburne, Marcia S. ; Ostash, Bohdan ; Payne, Shelley M. ; Pernodet, Jean Luc ; Petricek, Miroslav ; Piel, Jörn ; Ploux, Olivier ; Raaijmakers, Jos M. ; Salas, José A. ; Schmitt, Esther K. ; Scott, Barry ; Seipke, Ryan F. ; Shen, Ben ; Sherman, David H. ; Sivonen, Kaarina ; Smanski, Michael J. ; Sosio, Margherita ; Stegmann, Evi ; Süssmuth, Roderich D. ; Tahlan, Kapil ; Thomas, Christopher M. ; Tang, Yi ; Truman, Andrew W. ; Viaud, Muriel ; Walton, Jonathan D. ; Walsh, Christopher T. ; Weber, Tilmann ; Wezel, Gilles P. Van; Wilkinson, Barrie ; Willey, Joanne M. ; Wohlleben, Wolfgang ; Wright, Gerard D. ; Ziemert, Nadine ; Zhang, Changsheng ; Zotchev, Sergey B. ; Breitling, Rainer ; Takano, Eriko ; Glöckner, Frank Oliver - \ 2015
    Nature Chemical Biology 11 (2015)9. - ISSN 1552-4450 - p. 625 - 631.

    A wide variety of enzymatic pathways that produce specialized metabolites in bacteria, fungi and plants are known to be encoded in biosynthetic gene clusters. Information about these clusters, pathways and metabolites is currently dispersed throughout the literature, making it difficult to exploit. To facilitate consistent and systematic deposition and retrieval of data on biosynthetic gene clusters, we propose the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard.

    Differences in intermittent and continuous fecal shedding patterns between natural and experimental Mycobacterium avium subspecies paratuberculosis infections in cattle
    Mitchell, R.M. ; Schukken, Ynte ; Koets, A.P. ; Weber, Maarten ; Bakker, D. ; Stabel, Judy ; Whitlock, R.H. ; Louzoun, Yoram - \ 2015
    Veterinary Research 46 (2015). - ISSN 0928-4249 - 10 p.
    The objective of this paper is to study shedding patterns of cows infected with Mycobacterium avium subsp. paratuberculosis (MAP). While multiple single farm studies of MAP dynamics were reported, there is not large scale meta-analysis of both natural and experimental infections. Large difference in shedding patterns between experimentally and naturally infected cows were observed. Experimental infections are thus probably driven by different pathological mechanisms. For further evaluations of shedding patterns only natural infections were used. Within such infections, the transition to high shedding was studied as a proxy to the development of a clinical disease. The majority of studied cows never developed high shedding levels. Those that do, typically never reduced their shedding level to low or no shedding. Cows that eventually became high shedders showed a pattern of continuous shedding. In contrast, cows with an intermittent shedding pattern had a low probability to ever become high shedders. In addition, cows that start shedding at a younger age (less than three years of age) have a lower hazard of becoming high shedders compared to cows starting to shed at an older age. These data suggest the presence of three categories of immune control. Cows that are intermittent shedders have the infection process under control (no progressive infection). Cows that start shedding persistently at a young age partially control the infection, but eventually will be high shedders (slow progressive infection), while cows that start shedding persistently at an older age cannot effectively control the infection and become high shedders rapidly.
    Root exudates can control soil N dynamics
    Langarica Fuentes, A. ; Mitchell, S. ; Manrubia Freixa, M. ; Daniell, T. - \ 2015
    In: Proceedings of Rhizosphere 4 Conference Stretching the Interface of Life. - - p. 168 - 168.
    Agriculture represents the dominant source of the potent greenhouse gas nitrous oxide (N2O). This is largely due to the conversion of added nitrogen-based fertiliser through the action of the microbial nitrogen cycle in soil. Denitrification represents the main source of nitrous oxide emission and is a carbon driven process, as it maintains respiration under low oxygen conditions with nitrogen oxides acting as alternative electron acceptors. Initial experiments using barley plants (Hordeum vulgare) indicated that different cultivars support significant variation in N2O emission from denitrification from associated soil and that these effects are connected to root exudation difference rather than direct interaction or litter effects. In this study, a controlled microcosm experiment was designed to explore the interaction between root exudation and denitrification in terms of N2O production and community dynamics. Different quantities of artificial root exudates were added daily to soil at three different water regimes. N2O emissions were measured and community dynamics were assessed using T-RFLP and real time PCR. Results suggest that N2O emissions are driven by nitrous oxide reductase activity (consumption) rather than nitrite reductase activity (production). Soil condition, through differential aerobic status and variability, also appeared to have a marked effect both on flux through denitrification and community dynamics. Further work is underway to dissect the role of exudation quality in driving the alteration in nitrogen cycle flux and the end product of denitrification.
    Review of Priority Research & Development Topics: R&D related to the use of Remote Sensing in National Forest Monitoring
    Mitchell, A. ; Hoekman, D.H. - \ 2014
    Geneva, Switzerland : GEO-GFOI (GEO-GFOI R&D-document, version 1 GEO-GFOI R&D-document, version 1) - ISBN 9789299004753 - 163 p.
    This document reviews the potential of the various remote sensing-derived forest map products that can be used in implementing and improving national forest monitoring systems8 and help meet the requirements of the IPCC Guidelines. It identifies any research and development topics that need to be addressed to ensure that these products can be widely used by forest countries around the world. The Global Forest Observations Initiative (GFOI) aims to facilitate the supply and use of earth observation information, so that all countries can better manage their forest resources. Initially GFOI aims to support countries’ national forest monitoring systems in accordance with the IPCC Guidelines such as the systems needed to implement the United National Framework Convention on Climate Change (UNFCCC) programme on REDD+ (reducing emissions from deforestation; forest degradation; conservation of forest carbon stocks; sustainable management of forests; and enhancement of forest carbon stocks). GFOI was set up by the Group on Earth Observations (GEO) and has the active support and involvement of 13 space agencies (and data providers). It has been explicitly endorsed by 90 countries plus the EU and 67 international organisations. GFOI engages and coordinates with key organisations and institutions such as the UNFCCC, FAO, World Bank and IPCC as well as developing country participants. GFOI developed from the GEO Forest Carbon Tracking project which successfully demonstrated its approach through selected national demonstrator countries and which started in 2008.GFOI has identified a list of thematic forest map product specifications (see next section) that can be derived from a combination of Earth Observation and ground measurement data, and that are needed for countries to measure and report their changes in carbon stocks in forests and the subsequent greenhouse emissions. A country may not need to use all of these products: their choice will depend on their national circumstances and the additional objectives they have. This review considers these products and for each determines what, if any, additional research and development may be needed before the products can be widely used and recommended for use in long term systematic forest monitoring. These R&D topics are then prioritised by both needs expressed by countries and by the IPCC ´s Greenhouse Gas (GHG) inventory good practice requirements of transparency, completeness, consistency, comparability and accuracy, as endorsed by the UNFCCC. The need for forest information may extend beyond NFMS, MRV, and GHGI objectives. Indeed, the nine societal benefit areas of GEO need some type of information about the forests. Information about the status of forest resources is used in forestry operations, natural resource assessment, conservation and reserve planning and illegal logging detection systems. Similar forest map products may be useful for biodiversity initiatives such as GEOBON. The GEO Initiative provides a unique opportunity for coordination of data and information between different sectors. Global Initiatives such as GEO and GEOBON should consult on cross-cutting information needs and the possibility of generating a suite of forest map products that serve different purposes across sectors. The current report is the first step in the development of a comprehensive R&D Plan. This Plan will be further developed by the GFOI Office, based on inputs from demonstrator countries, interested organisations and relevant research expertise. Priority Research Topics will be presented to donors for funding.
    Inter-organizational network analysis in synergy parks
    Nuhoff-Isakhanyan, G. ; Wubben, E.F.M. ; Omta, S.W.F. - \ 2014
    Organizational collaborations are important means for organizations to access new resources and enhance the sustainable performance. Recent examples of inter-organizational collaborations towards more sustainable production are synergy parks, such as eco-industrial parks and agroparks. Synergy parks are collaborations among organizations across different sectors, mainly from agriculture and industry, aiming at enhanced economic and environmental performance, sustainable agri-food and bio-energy production through exchanging waste and by-products, creating production synergies. Because synergy parks connect organizations in their non-core business activities, these organizations are not always keen in the realization of synergy parks. A synergy park consists of multiple organizations from various sectors linked through multiple ties, its coordination can be explained by means of organizational network theory (Van de Ven & Fery, 1980). Consequently, a synergy park can be seen as a network where companies are the nodes and their collaborations the ties. Companies with direct ties, can affect the behavior of one another (Rowley, 1997). Recently more and more scholars use network analysis in understanding firms, stakeholders, and their social and behavioral phenomena (Ahuja, 2000; Ahuja, et al., 2009; Corsaro, et al., 2012; Gulati, 2007; Gulati, et al., 2000). Theories that discuss organizational networks, however, pay more attention to relations at dyadic level. Network analysis use in understanding firms, stakeholders, and their social and behavioral phenomena beyond dyadic level is slowly increasing (Ackermann & Eden, 2011; Frooman, 1999; Rowley, 1997). It provides scholars new insights to develop the inter-organizational network theory, to further it from dyadic relationship and examine systems of dyadic interactions capturing the influence of multiple and interdependent relations on network development. The purpose of the study is to understand how the structure of inter-organizational networks impact the realization of synergy parks by analyzing network attributes. In this study we answer the following questions: What is the impact of the network structure attributes (size, type of relation, centrality, and density) on realization of inter-organizational collaborations, such as a synergy park? What alternative network structures are effective in different inter-organizational collaborations? We suggest the following propositions: 1) The relation between the size of the network and the potential of a synergy park realization has an inverse convex shape (n shape) 2) Companies connected with both formal and informal ties have stronger and enduring relationships than the ones connected with formal ties only. 3) Decentralized and dense network structures are more suited for the realization of a synergy park if the set of involved companies are more heterogeneous. We conducted cross-case analysis in three synergy parks through using mixed qualitative and quantitative methods. The unit of analysis is the exchange relationship among the organizations within the networks. We focus on formal, informal, and trust related relations. We identified the boundary spanners in each organization, and asked managers who are the most knowledgeable about the relation of other organizations in the parks. These persons are formally or informally responsible for managing the collaborative relationships with other organizations. The main method of data collection was semi-structured interviews. The network survey has complex design comparing to standard surveys, therefore, we decided to interview each respondent personally by using ONA online survey tools. Concerning to network ties, we gather value and binary data. Each tie among the same companies have been measured and analyzed separately, and compared with one another. The data is coded and analyzed by using UCINET network analysis software (Borgatti, et al., 2002; Hanneman & Riddle, 2005). Networks are framed and analyzed per synergy park separate, which is followed by the analysis across networks. The discussion and the conclusion will be presented in the full paper. Reference Ackermann, F., & Eden, C., 2011. Strategic Management of Stakeholders: Theory and Practice. Long Range Planning, 44(3): 179-196. Ahuja, G., 2000. Collaboration Networks, Structural Holes, and Innovation: A Longitudinal Study. Administrative Science Quarterly, 45(3): 425-455. Ahuja, G., Polidoro, F., & Mitchell, W., 2009. Structural homophily or social asymmetry? The formation of alliances by poorly embedded firms. Strategic Management Journal, 30(9): 941-958. Borgatti, S. P., Everett, M. G., & Freeman, L. C., 2002. UCINET for Windows, Version 6.59: Software for Social Network Analysis. Harvard, MA Analytic Technologies. Corsaro, D., Cantu, C., & Tunisini, A., 2012. Actors' Heterogeneity in Innovation Networks. Industrial Marketing Management, 41(5): 780-789. Frooman, J., 1999. Stakeholder influence strategies. Academy of Management Review, 24(2): 191-205. Gulati, R., 2007. Managing network resources: alliances, affiliations and other relational assets. Oxford: Oxford University Press. Gulati, R., Nohria, N., & Zaheer, A., 2000. Strategic networks. Strategic Management Journal, 21(3): 203-215. Hanneman, R. A., & Riddle, M., 2005. Introduction to Social Network Methods. Riverside CA: University of California. Rowley, T. J., 1997. Moving beyond dyadic ties: A network theory of stakeholder influences. Academy of Management Review, 22(4): 887-910. Van de Ven, A. H., & Fery, D. L., 1980. Measuring and Assessing Organizations: John Wiley & Sons, Inc.
    Identification of quantitative trait loci and a candidate locus for freezing tolerance in controlled and outdoor environments in the overwintering crucifer Boechera stricta.
    Heo, J. ; Feng, D. ; Niu, X. ; Mitchell-Olds, T. ; Tienderen, P.H. van; Tomes, D. ; Schranz, M.E. - \ 2014
    Plant, Cell & Environment 37 (2014)11. - ISSN 0140-7791 - p. 2459 - 2469.
    cold-acclimation - arabidopsis-thaliana - chlorophyll fluorescence - transcription factor - natural variation - frost tolerance - genes - temperature - wheat - expression
    Development of chilling and freezing tolerance is complex and can be affected by photoperiod, temperature and photosynthetic performance; however, there has been limited research on the interaction of these three factors. We evaluated 108 recombinant inbred lines of Boechera stricta, derived from a cross between lines originating from Montana and Colorado, under controlled long day (LD), short-day (SD) and in an outdoor environment (OE). We measured maximum quantum yield of photosystem II, lethal temperature for 50% survival and electrolyte leakage of leaves. Our results revealed significant variation for chilling and freezing tolerance and photosynthetic performance in different environments. Using both single- and multi-trait analyses, three main-effect quantitative trait loci (QTL) were identified. QTL on linkage group (LG)3 were SD specific, whereas QTL on LG4 were found under both LD and SD. Under all conditions, QTL on LG7 were identified, but were particularly predictive for the outdoor experiment. The co-localization of photosynthetic performance and freezing tolerance effects supports these traits being co-regulated. Finally, the major QTL on LG7 is syntenic to the Arabidopsis C-repeat binding factor locus, known regulators of chilling and freezing responses in Arabidopsis thaliana and other species.
    Recovering? sea populations
    Kirkwood, R.J. ; Kirkman, S. ; Arnould, J. ; Carlyon, K. ; Alderman, R. ; Mitchell, T. ; Sutherland, D. ; Brasseur, S.M.J.M. ; Aarts, G.M. - \ 2014
    Nature and Health
    Hartig, T. ; Mitchell, R. ; Vries, S. de; Frumkin, H. - \ 2014
    Annual Review of Public Health 35 (2014). - ISSN 0163-7525 - p. 207 - 228.
    urban green space - public open space - quality-of-life - physical-activity - mental-health - inner-city - possible mechanism - nature experience - social cohesion - air-quality
    Urbanization, resource exploitation, and lifestyle changes have diminished possibilities for human contact with nature in urbanized societies. Concern about the loss has helped motivate research on the health benefits of contact with nature. Reviewing that research here, we focus on nature as represented by aspects of the physical environment relevant to planning, design, and policy measures that serve broad segments of urbanized societies.Wediscuss difficulties in defining “nature” and reasons for the current expansion of the research field, and we assess available reviews. We then consider research on pathways between nature and health involving air quality, physical activity, social cohesion, and stress reduction. Finally, we discuss methodological issues and priorities for future research. The extant research does describe an array of benefits of contact with nature, and evidence regarding some benefits is strong; however, some findings indicate caution is needed in applying beliefs about those benefits, and substantial gaps in knowledge remain.
    Global Forest Observations Initiative (GFOI) - Review of priority research & development Topics
    Mitchell, A. ; Hoekman, D.H. - \ 2013
    Geneva, Switserland : GEO-GFOI GEO Geneva (GEO-GFOI R&D document version 1.0 ) - 159 p.
    On the origin and evolution of apomixis in Boechera
    Lovell, J.T. ; Aliyu, O.M. ; Mau, M. ; Schranz, M.E. ; Koch, M. ; Kiefer, C. ; Song, B.H. ; Mitchell-Olds, T. ; Sharbel, T.F. - \ 2013
    Plant Reproduction 26 (2013)4. - ISSN 2194-7953 - p. 309 - 315.
    north-american boechera - genus boechera - holboellii brassicaceae - asexual reproduction - arabis-drummondii - hybridization - arabidopsis - angiosperms - expression - reappraisal
    The genetic mechanisms causing seed development by gametophytic apomixis in plants are predominantly unknown. As apomixis is consistently associated with hybridity and polyploidy, these confounding factors may either (a) be the underlying mechanism for the expression of apomixis, or (b) obscure the genetic factors which cause apomixis. To distinguish between these hypotheses, we analyzed the population genetic patterns of diploid and triploid apomictic lineages and their sexual progenitors in the genus Boechera (Brassicaceae). We find that while triploid apomixis is associated with hybridization, the majority of diploid apomictic lineages are likely the product of intra-specific crosses. We then show that these diploid apomicts are more likely to sire triploid apomictic lineages than conspecific sexuals. Combined with flow cytometric seed screen phenotyping for male and female components of apomixis, our analyses demonstrate that hybridization is an indirect correlate of apomixis in Boechera.
    Cytotoxicity of surface-functionalized silicon and germanium nanoparticles: the dominant role of surface charges
    Bhattacharjee, S. ; Rietjens, I.M.C.M. ; Singh, M.P. ; Atkins, T.M. ; Purkait, T.K. ; Xu, Z. ; Regli, S. ; Shukaliak, A. ; Clark, R.J. ; Mitchell, B.S. ; Alink, G.M. ; Marcelis, A.T.M. ; Fink, M.J. ; Veinot, J.G.C. ; Kauzlarich, S.M. ; Zuilhof, H. - \ 2013
    Nanoscale 5 (2013). - ISSN 2040-3364 - p. 4870 - 4883.
    block copolymer nanoparticles - cerium oxide nanoparticles - quantum dots - in-vitro - oxidative stress - gold nanoparticles - cellular toxicity - dependent endocytosis - hemolytic-activity - epithelial-cells
    Although it is frequently hypothesized that surface (like surface charge) and physical characteristics (like particle size) play important roles in cellular interactions of nanoparticles (NPs), a systematic study probing this issue is missing. Hence, a comparative cytotoxicity study, quantifying nine different cellular endpoints, was performed with a broad series of monodisperse, well characterized silicon (Si) and germanium (Ge) NPs with various surface functionalizations. Human colonic adenocarcinoma Caco-2 and rat alveolar macrophage NR8383 cells were used to clarify the toxicity of this series of NPs. The surface coatings on the NPs appeared to dominate the cytotoxicity: the cationic NPs exhibited cytotoxicity, whereas the carboxylic acid-terminated and hydrophilic PEG- or dextran-terminated NPs did not. Within the cationic Si NPs, smaller Si NPs were more toxic than bigger ones. Manganese-doped (1% Mn) Si NPs did not show any added toxicity, which favors their further development for bioimaging. Iron-doped (1% Fe) Si NPs showed some added toxicity, which may be due to the leaching of Fe3+ ions from the core. A silica coating seemed to impart toxicity, in line with the reported toxicity of silica. Intracellular mitochondria seem to be the target for the toxic NPs since a dose-, surface charge- and size-dependent imbalance of the mitochondrial membrane potential was observed. Such an imbalance led to a series of other cellular events for cationic NPs, like decreased mitochondrial membrane potential (¿¿m) and ATP production, induction of ROS generation, increased cytoplasmic Ca2+ content, production of TNF-a and enhanced caspase-3 activity. Taken together, the results explain the toxicity of Si NPs/Ge NPs largely by their surface characteristics, provide insight into the mode of action underlying the observed cytotoxicity, and give directions on synthesizing biocompatible Si and Ge NPs, as this is crucial for bioimaging and other applications in for example the field of medicine.
    New tools for studying osteoarthritis genetics in zebrafish
    Mitchell, R.E. ; Huitema, L.F. ; Skinner, R.E. ; Brunt, L.H. ; Severn, C. ; Schulte-Merker, S. ; Hammond, C.L. - \ 2013
    Osteoarthritis and Cartilage 21 (2013)2. - ISSN 1063-4584 - p. 269 - 278.
    nucleotide exchange factor - danio-rerio - osteogenesis-imperfecta - developing skeleton - signaling pathways - cell-migration - bone-formation - retinoic acid - expression - gdf5
    Objective: Increasing evidence points to a strong genetic component to osteoarthritis (OA) and that certain changes that occur in osteoarthritic cartilage recapitulate the developmental process of endochondral ossification. As zebrafish are a well validated model for genetic studies and developmental biology, our objective was to establish the spatiotemporal expression pattern of a number of OA susceptibility genes in the larval zebrafish providing a platform for functional studies into the role of these genes in OA. Design: We identified the zebrafish homologues for Mcf2l, Gdf5, PthrP/Pthlh, Co19a2, and Col10a1 from the Ensembl genome browser. Labelled probes were generated for these genes and in situ hybridisations were performed on wild type zebrafish larvae. In addition, we generated transgenic reporter lines by modification of bacterial artificial chromosomes (BACs) containing full length promoters for col2a1 and col10a1. Results: For the first time, we show the spatiotemporal expression pattern of Mcf2l. Furthermore, we show that all six putative OA genes are dynamically expressed during zebrafish larval development, and that all are expressed in the developing skeletal system. Furthermore, we demonstrate that the transgenic reporters we have generated for col2a1 and col10al can be used to visualise chondrocyte hypertrophy in vivo. Conclusion: In this study we describe the expression pattern of six OA susceptibility genes in zebrafish larvae and the generation of two new transgenic lines marking chondrocytes at different stages of maturation. Moreover, the tools used demonstrate the utility of the zebrafish model for functional studies on genes identified as playing a role in OA. (C) 2012 Osteoarthritis Research Society International. Published by Elsevier Ltd. All rights reserved.
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