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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Harnessing longitudinal information to identify genetic variation in tolerance of pigs to Porcine Reproductive and Respiratory Syndrome virus infection
Lough, Graham ; Hess, Andrew ; Hess, Melanie ; Rashidi, Hamed ; Matika, Oswald ; Lunney, Joan K. ; Rowland, Raymond R.R. ; Kyriazakis, Ilias ; Mulder, Han A. ; Dekkers, Jack C.M. ; Doeschl-Wilson, Andrea - \ 2018
Genetics, Selection, Evolution 50 (2018). - ISSN 0999-193X

Background: High resistance (the ability of the host to reduce pathogen load) and tolerance (the ability to maintain high performance at a given pathogen load) are two desirable host traits for producing animals that are resilient to infections. For Porcine Reproductive and Respiratory Syndrome (PRRS), one of the most devastating swine diseases worldwide, studies have identified substantial genetic variation in resistance of pigs, but evidence for genetic variation in tolerance has so far been inconclusive. Resistance and tolerance are usually considered as static traits. In this study, we used longitudinal viremia measurements of PRRS virus infected pigs to define discrete stages of infection based on viremia profile characteristics. These were used to investigate host genetic effects on viral load (VL) and growth at different stages of infection, to quantify genetic variation in tolerance at these stages and throughout the entire 42-day observation period, and to assess whether the single nucleotide polymorphism (SNP) WUR10000125 (WUR) with known large effects on resistance confers significant differences in tolerance. Results: Genetic correlations between resistance and growth changed considerably over time. Individuals that expressed high genetic resistance early in infection tended to grow slower during that time-period, but were more likely to experience lower VL and recovery in growth by the later stage. The WUR genotype was most strongly associated with VL at early- to mid-stages of infection, and with growth at mid- to late-stages of infection. Both, single-stage and repeated measurements random regression models identified significant genetic variation in tolerance. The WUR SNP was significantly associated only with the overall tolerance slope fitted through all stages of infection, with the genetically more resistant AB pigs for the WUR SNP being also more tolerant to PRRS. Conclusions: The results suggest that genetic selection for improved tolerance of pigs to PRRS is possible in principle, but may be feasible only with genomic selection, requiring intense recording schemes that involve repeated measurements to reliably estimate genetic effects. In the absence of such records, consideration of the WUR genotype in current selection schemes appears to be a promising strategy to improve simultaneously resistance and tolerance of growing pigs to PRRS.

Fatty acid biomarkers of dairy fat consumption and incidence of type 2 diabetes : A pooled analysis of prospective cohort studies
Imamura, Fumiaki ; Fretts, Amanda ; Marklund, Matti ; Ardisson Korat, Andres V. ; Yang, Wei Sin ; Lankinen, Maria ; Qureshi, Waqas ; Helmer, Catherine ; Chen, Tzu An ; Wong, Kerry ; Bassett, Julie K. ; Murphy, Rachel ; Tintle, Nathan ; Yu, Chaoyu Ian ; Brouwer, Ingeborg A. ; Chien, Kuo Liong ; Frazier-Wood, Alexis C. ; Gobbo, Liana C. Del; Djoussé, Luc ; Geleijnse, Johanna M. ; Giles, Graham G. ; Goede, Janette de; Gudnason, Vilmundur ; Harris, William S. ; Hodge, Allison ; Hu, Frank ; Koulman, Albert ; Laakso, Markku ; Lind, Lars ; Lin, Hung Ju ; McKnight, Barbara ; Rajaobelina, Kalina ; Risérus, Ulf ; Robinson, Jennifer G. ; Samieri, Cécilia ; Siscovick, David S. ; Soedamah-Muthu, Sabita S. ; Sotoodehnia, Nona ; Sun, Qi ; Tsai, Michael Y. ; Uusitupa, Matti ; Wagenknecht, Lynne E. ; Wareham, Nick J. ; Wu, Jason Hy ; Micha, Renata ; Forouhi, Nita G. ; Lemaitre, Rozenn N. ; Mozaffarian, Dariush - \ 2018
PLOS Medicine 15 (2018)10. - ISSN 1549-1676 - p. e1002670 - e1002670.

BACKGROUND: We aimed to investigate prospective associations of circulating or adipose tissue odd-chain fatty acids 15:0 and 17:0 and trans-palmitoleic acid, t16:1n-7, as potential biomarkers of dairy fat intake, with incident type 2 diabetes (T2D).

METHODS AND FINDINGS: Sixteen prospective cohorts from 12 countries (7 from the United States, 7 from Europe, 1 from Australia, 1 from Taiwan) performed new harmonised individual-level analysis for the prospective associations according to a standardised plan. In total, 63,682 participants with a broad range of baseline ages and BMIs and 15,180 incident cases of T2D over the average of 9 years of follow-up were evaluated. Study-specific results were pooled using inverse-variance-weighted meta-analysis. Prespecified interactions by age, sex, BMI, and race/ethnicity were explored in each cohort and were meta-analysed. Potential heterogeneity by cohort-specific characteristics (regions, lipid compartments used for fatty acid assays) was assessed with metaregression. After adjustment for potential confounders, including measures of adiposity (BMI, waist circumference) and lipogenesis (levels of palmitate, triglycerides), higher levels of 15:0, 17:0, and t16:1n-7 were associated with lower incidence of T2D. In the most adjusted model, the hazard ratio (95% CI) for incident T2D per cohort-specific 10th to 90th percentile range of 15:0 was 0.80 (0.73-0.87); of 17:0, 0.65 (0.59-0.72); of t16:1n7, 0.82 (0.70-0.96); and of their sum, 0.71 (0.63-0.79). In exploratory analyses, similar associations for 15:0, 17:0, and the sum of all three fatty acids were present in both genders but stronger in women than in men (pinteraction < 0.001). Whereas studying associations with biomarkers has several advantages, as limitations, the biomarkers do not distinguish between different food sources of dairy fat (e.g., cheese, yogurt, milk), and residual confounding by unmeasured or imprecisely measured confounders may exist.

CONCLUSIONS: In a large meta-analysis that pooled the findings from 16 prospective cohort studies, higher levels of 15:0, 17:0, and t16:1n-7 were associated with a lower risk of T2D.

Embracing 3D Complexity in Leaf Carbon–Water Exchange
Earles, J.M. ; Buckley, Thomas N. ; Brodersen, Craig R. ; Busch, Florian A. ; Cano, F.J. ; Choat, Brendan ; Evans, John R. ; Farquhar, Graham D. ; Harwood, Richard ; Huynh, Minh ; John, Grace P. ; Miller, Megan L. ; Rockwell, Fulton E. ; Sack, Lawren ; Scoffoni, Christine ; Struik, Paul C. ; Wu, Alex ; Yin, Xinyou ; Barbour, Margaret M. - \ 2018
Trends in Plant Science (2018). - ISSN 1360-1385 - 10 p.
3D - leaf anatomy - leaf hydraulic conductance - mesophyll conductance - photosynthesis

Leaves are a nexus for the exchange of water, carbon, and energy between terrestrial plants and the atmosphere. Research in recent decades has highlighted the critical importance of the underlying biophysical and anatomical determinants of CO2 and H2O transport, but a quantitative understanding of how detailed 3D leaf anatomy mediates within-leaf transport has been hindered by the lack of a consensus framework for analyzing or simulating transport and its spatial and temporal dynamics realistically, and by the difficulty of measuring within-leaf transport at the appropriate scales. We discuss how recent technological advancements now make a spatially explicit 3D leaf analysis possible, through new imaging and modeling tools that will allow us to address long-standing questions related to plant carbon–water exchange.

Sorting of Molecular Building Blocks from Solution to Surface
Keisar, Hodaya ; Ruiter, Graham de; Velders, Aldrik H. ; Milko, Petr ; Gulino, Antonino ; Evmenenko, Guennadi ; Shimon, Linda J.W. ; Diskin-Posner, Yael ; Lahav, Michal ; Boom, Milko E. van der - \ 2018
Journal of the American Chemical Society 140 (2018)26. - ISSN 0002-7863 - p. 8162 - 8171.

We demonstrate that molecular gradients on an organic monolayer is formed by preferential binding of ruthenium complexes from solutions also containing equimolar amounts of isostructural osmium complexes. The monolayer consists of a nanometer-thick assembly of 1,3,5-tris(4-pyridylethenyl)benzene (TPEB) covalently attached to a silicon or metal-oxide surface. The molecular gradient of ruthenium and osmium complexes is orthogonal to the surface plane. This gradient propagates throughout the molecular assembly with thicknesses over 30 nm. Using other monolayers consisting of closely related organic molecules or metal complexes results in the formation of molecular assemblies having an homogeneous and equimolar distribution of ruthenium and osmium complexes. Spectroscopic and computational studies revealed that the geometry of the complexes and the electronic properties of their ligands are nearly identical. These subtle differences cause the isostructural osmium and ruthenium complexes to pack differently on modified surfaces as also demonstrated in crystals grown from solution. The different packing behavior, combined with the organic monolayer significantly contributes to the observed differences in chemical composition on the surface.

Spatial and risk factor analysis of bovine viral diarrhoea (BVD) virus after the first-year compulsory phase of BVD eradication programme in Northern Ireland
Charoenlarp, W. ; Frankena, K. ; Strain, S.A.J. ; Guelbenzu-Gonzalo, M. ; Graham, J. ; Byrne, A.W. - \ 2018
Preventive Veterinary Medicine 157 (2018). - ISSN 0167-5877 - p. 34 - 43.
Bovine viral diarrhoea virus - Northern Ireland - Risk factors - Spatial analysis - Spatial autocorrelation - Spatial risk factors

Bovine viral diarrhoea virus (BVDV) causes bovine viral diarrhoea (BVD), which is a contagious pathogen that can have a significant economic impact on cattle industries. In Northern Ireland (NI), the compulsory phase of a BVD eradication programme was implemented in 2016. The aim of this retrospective population based study was to utilize herd-level data after the first year of the compulsory phase (March 2016–March 2017) to determine the spatial distribution and variation of BVDV, to identify clusters of infection, and to quantify some risk factors associated with BVD in NI. Global spatial clustering (autocorrelation) and local spatial hot-spot analyses were used to specify the clustering areas (hot- and cold-spot). A suite of multivariable logistic analyses was performed to estimate the associations of spatial and non-spatial factors (relating to herd characteristics) with the risk of being a BVDV positive herd. Final models were compared by evaluating the model fit and the ability to account for spatial autocorrelation in the study area. There were 17,186 herds included in the analysis. The herd-level prevalence of BVDV was 11.31%. Significant spatial clustering of BVDV positive herds was presented in the central region of NI. A mixed effects logistic model, with a spatial random effect term, was considered the best model. The final model showed that a positive BVDV status during the voluntary phase prior to the compulsory phase started (OR = 2.25; CI 95% = 1.85–2.73), larger herd size (OR = 6.19; CI 95% = 5.22–7.34 for herd size > 100 animals) and a larger number of positive nearest neighbours within 4 km radius (OR = 1.24; CI 95% = 1.05–1.47 for 8–9 neighbours and OR = 1.41; CI 95% = 1.20–1.65 for 10–12 neighbours) were significantly related to the risk of a herd being tested positive for BVDV. The clear spatial pattern from the local spatial clustering analyses could be used for targeted surveillance and control measures by focusing on the central region of NI.

Understanding root, tuber, and banana seed systems and coordination breakdown : a multi-stakeholder framework
Bentley, Jeffery W. ; Andrade-Piedra, Jorge ; Demo, Paul ; Dzomeku, Beloved ; Jacobsen, Kim ; Kikulwe, Enoch ; Kromann, Peter ; Kumar, P.L. ; McEwan, Margaret ; Mudege, Netsayi ; Ogero, Kwame ; Okechukwu, Richardson ; Orrego, Ricardo ; Ospina, Bernardo ; Sperling, Louise ; Walsh, Stephen ; Thiele, Graham - \ 2018
Journal of Crop Improvement 32 (2018)5. - ISSN 1542-7528 - p. 599 - 621.
Bananas and plantains - root crops - seed security - seed systems - tuber crops - vegetatively propagated crops (VPC)

Vegetatively propagated crop (VPC) seed tends to remain true to varietal type but is bulky, often carries disease, and is slow to produce. So VPC seed needs to be handled differently than that of other crops, e.g., it tends to be sourced locally, often must be fresh, and it is less often sold on the market. Hence, a framework was adapted to describe and support interventions in such seed systems. The framework was used with 13 case studies to understand VPC seed systems for roots, tubers, and bananas, including differing roles and sometimes conflicting goals of stakeholders, and to identify potential coordination breakdowns when actors fail to develop a shared understanding and vision. In this article, we review those case studies. The framework is a critical tool to (a) document VPC seed systems and build evidence; (b) diagnose and treat coordination breakdown and (c) guide decision-makers and donors on the design of more sustainable seed system interventions for VPCs. The framework can be used to analyze past interventions and will be useful for planning future VPC seed programs.

Sequence diversity of CV777 PEDV strains
Rasmussen, Thomas Bruun ; Boniotti, Maria Beatrice ; Papetti, Alice ; Grasland, Béatrice ; Frossard, Jean Pierre ; Dastjerdi, Akbar ; Hulst, M.M. ; Hanke, Dennis ; Pohlmann, Anne ; Blome, Sandra ; Poel, W.H.M. van der; Steinbach, Falko ; Blanchard, Yannick ; Lavazza, Antonio ; Bøtner, Anette ; Belsham, Graham J. - \ 2018
PRJEB20818 - ERP023004
Reviewing research priorities in weed ecology, evolution and management: a horizon scan
Neve, P. ; Barney, J.N. ; Buckley, Y. ; Cousens, R.D. ; Graham, S. ; Jordan, N.R. ; Lawton-Rauh, A. ; Liebman, M. ; Mesgaran, M.B. ; Shaw, J. ; Storkey, J. ; Baraibar, B. ; Baucom, R.S. ; Chalak, M. ; Childs, D.Z. ; Christensen, S. ; Eizenberg, H. ; Fernández-Quintanilla, C. ; French, K. ; Harsch, M. ; Heijting, S. ; Harrison, L. ; Loddo, D. ; Macel, M. ; Maczey, N. ; Merotto, A. ; Mortensen, D. ; Necajeva, J. ; Peltzer, D.A. ; Recasens, J. ; Renton, M. ; Riemens, M. ; Sønderskov, M. ; Williams, M. ; Rew, Lisa - \ 2018
Weed Research 58 (2018)4. - ISSN 0043-1737 - p. 250 - 258.
Weedy plants pose a major threat to food security, biodiversity, ecosystem services and consequently to human health and wellbeing. However, many currently used weed management approaches are increasingly unsustainable. To address this knowledge and practice gap, in June 2014, 35 weed and invasion ecologists, weed scientists, evolutionary biologists and social scientists convened a workshop to explore current and future perspectives and approaches in weed ecology and management. A horizon scanning exercise ranked a list of 124 pre‐submitted questions to identify a priority list of 30 questions. These questions are discussed under seven themed headings that represent areas for renewed and emerging focus for the disciplines of weed research and practice. The themed areas considered the need for transdisciplinarity, increased adoption of integrated weed management and agroecological approaches, better understanding of weed evolution, climate change, weed invasiveness and finally, disciplinary challenges for weed science. Almost all the challenges identified rested on the need for continued efforts to diversify and integrate agroecological, socio‐economic and technological approaches in weed management. These challenges are not newly conceived, though their continued prominence as research priorities highlights an ongoing intransigence that must be addressed through a more system‐oriented and transdisciplinary research agenda that seeks an embedded integration of public and private research approaches. This horizon scanning exercise thus set out the building blocks needed for future weed management research and practice; however, the challenge ahead is to identify effective ways in which sufficient research and implementation efforts can be directed towards these needs.
A regional benthic fauna assessment method for the Southern North Sea using Margalef diversity and reference value modelling
Loon, Willem M.G.M. van; Walvoort, Dennis J.J. ; Hoey, Gert van; Vina-Herbon, Christina ; Blandon, Abigayil ; Pesch, Roland ; Schmitt, Petra ; Scholle, Jörg ; Heyer, Karin ; Lavaleye, Marc ; Phillips, Graham ; Duineveld, Gerard C.A. ; Blomqvist, Mats - \ 2018
Ecological Indicators 89 (2018). - ISSN 1470-160X - p. 667 - 679.
AMBI - Benthic assessment method - Fishing pressure - Index - ITI - Margalef diversity - Marine benthos - MMI - Model - MSFD - Multi-metric index - Organic enrichment - OSPAR - PIE - Reference value estimation - Sedimentation - Shannon index - SN - SNA - Species richness
The aims of this study are to develop an optimized method for regional benthic fauna assessment of the Southern North Sea which (a) is sensitive and precise (quantified as the slope and the R2 value of the pressure-impact relationships, respectively) for the anthropogenic pressures bottom fishing and organic enrichment, (b) is suitable for estimating and modelling reference values, (c) is transparent, (d) can be efficiently applied using dedicated software; and to apply this method to benthic data from the Southern North Sea. Margalef diversity appeared to be the best performing benthic index regarding these criteria, even better than several Multi-Metric Indices (MMIs) containing e.g. AMBI (AZTI Marine Biotic Index) and ITI (Infaunal Trophic Index). Therefore, this relatively simple and very practical index, including a new reference value estimation and modelling method, and BENMMI software were selected as a common OSPAR (Oslo Paris convention) method for the benthic fauna assessment of the Southern North Sea. This method was applied to benthic fauna data from the Southern North Sea collected during the period 2010–2015. The results in general show lower normalized Margalef values in coastal areas, and higher normalized Margalef values in deeper offshore areas. The following benthic indices were compared in this study: species richness, Margalef diversity, SNA index, Shannon index, PIE index, AMBI, ITI. For each assessment area, the least disturbed benthic dataset was selected as an adjacent 6 year period with, on average, the highest Margalef diversity values. For these datasets, the reference values were primarily set as the 99th percentile values of the respective indices. This procedure results in the highest stable reference values that are not outliers. In addition, a variable percentile method was developed, in which the percentile value is adjusted to the average bottom fishing pressure (according to data from the International Council for the Exploration of the Sea, ICES) in the period 2009–2013. The adjusted percentile values were set by expert judgement, at 75th (low fishing pressure), 95th (medium fishing pressure) and 99th (high fishing pressure) percentile. The estimated reference values for Margalef diversity correlate quite well with the median depth of the assessment areas using a sigmoid model (pseudo-R2 = 0.86). This relationship between depth and Margalef diversity was used to estimate reference values in case an assessment area had insufficient benthic data For testing the effects of bottom fishing pressure, normalized index values (NIV; index value divided by reference value) were used. The rationale for using NIVs is the assumption that, although a certain level of bottom fishing pressure will have a larger absolute effect on more biodiverse benthic communities in deeper waters than on more robust and less biodiverse coastal benthic communities, the relative effects (tested using NIVs) are comparable. A clear exponentially decreasing relationship (R2 = 0.26–0.27, p < 0.00001) was found between both bottom surface and subsurface fishing activity (penetration depth <2 cm and >2 cm, respectively) and normalized Margalef diversity values, with an asymptotic normalized Margalef value of 0.45 at a subsurface fishing activity >2.3 sweeps/year. This asymptotic value is predominantly found in coastal waters, and probably shows that the naturally more robust coastal benthic communities have been transformed into resilient benthic communities, which rapidly recover from increasing fishing pressure.
Full-length genome sequences of porcine epidemic diarrhoea virus strain CV777; use of NGS to analyse genomic and sub-genomic RNAs
Rasmussen, Thomas Bruun ; Boniotti, Maria Beatrice ; Papetti, Alice ; Grasland, Béatrice ; Frossard, Jean Pierre ; Dastjerdi, Akbar ; Hulst, Marcel ; Hanke, Dennis ; Pohlmann, Anne ; Blome, Sandra ; Poel, Wim H.M. Van Der; Steinbach, Falko ; Blanchard, Yannick ; Lavazza, Antonio ; Bøtner, Anette ; Belsham, Graham J. - \ 2018
PLoS One 13 (2018)3. - ISSN 1932-6203
Porcine epidemic diarrhoea virus, strain CV777, was initially characterized in 1978 as the causative agent of a disease first identified in the UK in 1971. This coronavirus has been widely distributed among laboratories and has been passaged both within pigs and in cell culture. To determine the variability between different stocks of the PEDV strain CV777, sequencing of the full-length genome (ca. 28kb) has been performed in 6 different laboratories, using different protocols. Not surprisingly, each of the different full genome sequences were distinct from each other and from the reference sequence (Accession number AF353511) but they are >99% identical. Unique and shared differences between sequences were identified. The coding region for the surface-exposed spike protein showed the highest proportion of variability including both point mutations and small deletions. The predicted expression of the ORF3 gene product was more dramatically affected in three different variants of this virus through either loss of the initiation codon or gain of a premature termination codon. The genome of one isolate had a substantially rearranged 5´-terminal sequence. This rearrangement was validated through the analysis of sub-genomic mRNAs from infected cells. It is clearly important to know the features of the specific sample of CV777 being used for experimental studies.
Recreational sea fishing in Europe in a global context-Participation rates, fishing effort, expenditure, and implications for monitoring and assessment
Hyder, Kieran ; Weltersbach, Marc Simon ; Armstrong, Mike ; Ferter, Keno ; Townhill, Bryony ; Ahvonen, Anssi ; Arlinghaus, Robert ; Baikov, Andrei ; Bellanger, Manuel ; Birzaks, Janis ; Borch, Trude ; Cambie, Giulia ; Graaf, Martin De; Diogo, Hugo M.C. ; Dziemian, Łukasz ; Gordoa, Ana ; Grzebielec, Ryszard ; Hartill, Bruce ; Kagervall, Anders ; Kapiris, Kostas ; Karlsson, Martin ; Kleiven, Alf Ring ; Lejk, Adam M. ; Levrel, Harold ; Lovell, Sabrina ; Lyle, Jeremy ; Moilanen, Pentti ; Monkman, Graham ; Morales-Nin, Beatriz ; Mugerza, Estanis ; Martinez, Roi ; O'Reilly, Paul ; Olesen, Hans Jakob ; Papadopoulos, Anastasios ; Pita, Pablo ; Radford, Zachary ; Radtke, Krzysztof ; Roche, William ; Rocklin, Delphine ; Ruiz, Jon ; Scougal, Callum ; Silvestri, Roberto ; Skov, Christian ; Steinback, Scott ; Sundelöf, Andreas ; Svagzdys, Arvydas ; Turnbull, David ; Hammen, Tessa Van Der; Voorhees, David Van; Winsen, Frankwin Van; Verleye, Thomas ; Veiga, Pedro ; Vølstad, Jon-Helge ; Zarauz, Lucia ; Zolubas, Tomas ; Strehlow, Harry V. - \ 2018
Fish and Fisheries 19 (2018)2. - ISSN 1467-2960 - p. 225 - 243.
European marine recreational fisheries - fisheries assessment and management - fishing effort and expenditure - participation - surveys and monitoring of marine recreational fisheries
Marine recreational fishing (MRF) is a high-participation activity with large economic value and social benefits globally, and it impacts on some fish stocks. Although reporting MRF catches is a European Union legislative requirement, estimates are only available for some countries. Here, data on numbers of fishers, participation rates, days fished, expenditures, and catches of two widely targeted species were synthesized to provide European estimates of MRF and placed in the global context. Uncertainty assessment was not possible due to incomplete knowledge of error distributions; instead, a semi-quantitative bias assessment was made. There were an estimated 8.7 million European recreational sea fishers corresponding to a participation rate of 1.6%. An estimated 77.6 million days were fished, and expenditure was €5.9 billion annually. There were higher participation, numbers of fishers, days fished and expenditure in the Atlantic than the Mediterranean, but the Mediterranean estimates were generally less robust. Comparisons with other regions showed that European MRF participation rates and expenditure were in the mid-range, with higher participation in Oceania and the United States, higher expenditure in the United States, and lower participation and expenditure in South America and Africa. For both northern European sea bass (Dicentrarchus labrax, Moronidae) and western Baltic cod (Gadus morhua, Gadidae) stocks, MRF represented 27% of the total removals. This study highlights the importance of MRF and the need for bespoke, regular and statistically sound data collection to underpin European fisheries management. Solutions are proposed for future MRF data collection in Europe and other regions to support sustainable fisheries management.
Entry into force and then? The Paris agreement and state accountability
Karlsson-Vinkhuyzen, Sylvia I. ; Groff, Maja ; Tamás, Peter A. ; Dahl, Arthur L. ; Harder, Marie K. ; Hassall, Graham - \ 2018
Climate Policy 18 (2018)5. - ISSN 1469-3062 - p. 593 - 599.
Accountability - climate change policy - global governance - states - transparency
The entry into force of the Paris Agreement on climate change brings expectations that states will be held to account for their commitments. The article elaborates on why this is not a realistic assumption unless a broader multilevel perspective is taken on the nature of accountability regimes for international (legal) agreements. The formal accountability mechanisms of such agreements tend to be weak, and there are no indications that they will be stronger for the recent global goals adopted in the Paris Agreement. Looking beyond only peer review among states, national institutions, direct civil society engagement and internal government processes – while each coming with their own strengths and weaknesses – provide additional accountability pathways that together may do a better job. Scientific enquiry is, however, required to better understand, support and find improved mixtures of, and perhaps to move beyond, these accountability pathways. Policy relevance This perspective provides something of a clarion call for a variety of different types of actors at both global and national levels to engage in ensuring that states keep the promises they made in the Paris Agreement. It particularly highlights the importance of national institutions and civil society to step up to the task in the present world order, where states are reluctant to build strong accountability regimes at the global level.
Modernizing Polish Agricultural economics teaching and research: An evaluation of academic cooperation
Dalton, Graham ; Heijman, W.J.M. ; Majewski, Edward - \ 2017
Acta Scientiarum Polonorum. Oeconomia 16 (2017)4. - ISSN 1644-0757 - p. 13 - 21.
Tempus - MBA - Human Capital - AGRIMBA - Cost Benefits of Education
Twenty-five years ago in response to the collapse of communism in Poland, an academic consortium was formed around two Polish Universities of Life Sciences (formerly Universities of Agriculture) for a Tempus project. The consortium has expanded from a project to revise curricula in agricultural economics within a market economy to much wider educational and research interests. The consortium’s main achievement has been in the organisation and accreditation of MBA programmes which has subsequently been augmented by a network for other educational and research programmes in a number of countries (AGRIMBA). This article explores the social net benefits of this example of investment in human capital relying on the concepts laid down by the Nobel Prize winners Theodore Schulz and Gary Becker.
A comparative analysis of nonhost resistance across the two Triticeae crop species wheat and barley
Delventhal, Rhoda ; Rajaraman, Jeyaraman ; Stefanato, Francesca L. ; Rehman, S. ; Aghnoum, R. ; McGrann, Graham R.D. ; Bolger, Marie ; Usadel, Björn ; Hedley, Pete E. ; Boyd, Lesley A. ; Niks, R.E. ; Schweizer, Patrick ; Schaffrath, Ulrich - \ 2017
wheat - barley - Blumeria - Magnaporthe - Puccinia - adapted isolate - non-adapted isolate - nonhost resistance - quantitative resistance - global transcriptome analysis
Background Nonhost resistance (NHR) protects plants against a vast number of non-adapted pathogens which implicates a potential exploitation as source for novel disease resistance strategies. Aiming at a fundamental understanding of NHR a global analysis of transcriptome reprogramming in the economically important Triticeae cereals wheat and barley, comparing host and nonhost interactions in three major fungal pathosystems responsible for powdery mildew (Blumeria graminis ff. ssp.), cereal blast (Magnaporthe sp.) and leaf rust (Puccinia sp.) diseases, was performed. Results In each pathosystem a significant transcriptome reprogramming by adapted- or non-adapted pathogen isolates was observed, with considerable overlap between Blumeria, Magnaporthe and Puccinia. Small subsets of these general pathogen-regulated genes were identified as differentially regulated between host and corresponding nonhost interactions, indicating a fine-tuning of the general pathogen response during the course of co-evolution. Additionally, the host- or nonhost-related responses were rather specific for each pair of adapted and non-adapted isolates, indicating that the nonhost resistance-related responses were to a great extent pathosystem-specific. This pathosystem-specific reprogramming may reflect different resistance mechanisms operating against non-adapted pathogens with different lifestyles, or equally, different co-option of the hosts by the adapted isolates to create an optimal environment for infection. To compare the transcriptional reprogramming between wheat and barley, putative orthologues were identified. Within the wheat and barley general pathogen-regulated genes, temporal expression profiles of orthologues looked similar, indicating conserved general responses in Triticeae against fungal attack. However, the comparison of orthologues differentially expressed between host and nonhost interactions revealed fewer commonalities between wheat and barley, but rather suggested different host or nonhost responses in the two cereal species. Conclusions Taken together, our results suggest independent co-evolutionary forces acting on host pathosystems mirrored by barley- or wheat-specific nonhost responses. As a result of evolutionary processes, at least for the pathosystems investigated, NHR appears to rely on rather specific plant responses.
A comparative analysis of nonhost resistance across the two Triticeae crop species wheat and barley
Delventhal, Rhoda ; Rajaraman, Jeyaraman ; Stefanato, Francesca L. ; Rehman, Sajid ; Aghnoum, Reza ; McGrann, Graham R.D. ; Bolger, Marie ; Usadel, Björn ; Hedley, Pete E. ; Boyd, Lesley ; Niks, Rients E. ; Schweizer, Patrick ; Schaffrath, Ulrich - \ 2017
BMC Plant Biology 17 (2017)1. - ISSN 1471-2229
Adapted isolate - Barley - Blumeria - Global transcriptome analysis - Magnaporthe - Non-adapted isolate - Nonhost resistance - Puccinia - Quantitative resistance - Wheat
Background: Nonhost resistance (NHR) protects plants against a vast number of non-adapted pathogens which implicates a potential exploitation as source for novel disease resistance strategies. Aiming at a fundamental understanding of NHR a global analysis of transcriptome reprogramming in the economically important Triticeae cereals wheat and barley, comparing host and nonhost interactions in three major fungal pathosystems responsible for powdery mildew (Blumeria graminis ff. ssp.), cereal blast (Magnaporthe sp.) and leaf rust (Puccinia sp.) diseases, was performed. Results: In each pathosystem a significant transcriptome reprogramming by adapted- or non-adapted pathogen isolates was observed, with considerable overlap between Blumeria, Magnaporthe and Puccinia. Small subsets of these general pathogen-regulated genes were identified as differentially regulated between host and corresponding nonhost interactions, indicating a fine-tuning of the general pathogen response during the course of co-evolution. Additionally, the host- or nonhost-related responses were rather specific for each pair of adapted and non-adapted isolates, indicating that the nonhost resistance-related responses were to a great extent pathosystem-specific. This pathosystem-specific reprogramming may reflect different resistance mechanisms operating against non-adapted pathogens with different lifestyles, or equally, different co-option of the hosts by the adapted isolates to create an optimal environment for infection. To compare the transcriptional reprogramming between wheat and barley, putative orthologues were identified. Within the wheat and barley general pathogen-regulated genes, temporal expression profiles of orthologues looked similar, indicating conserved general responses in Triticeae against fungal attack. However, the comparison of orthologues differentially expressed between host and nonhost interactions revealed fewer commonalities between wheat and barley, but rather suggested different host or nonhost responses in the two cereal species. Conclusions: Taken together, our results suggest independent co-evolutionary forces acting on host pathosystems mirrored by barley- or wheat-specific nonhost responses. As a result of evolutionary processes, at least for the pathosystems investigated, NHR appears to rely on rather specific plant responses.
Novel Selectivity-Based Forensic Toxicological Validation of a Paper Spray Mass Spectrometry Method for the Quantitative Determination of Eight Amphetamines in Whole Blood
Teunissen, Sebastiaan F. ; Fedick, Patrick W. ; Berendsen, Bjorn J.A. ; Nielen, Michel W.F. ; Eberlin, Marcos N. ; Graham Cooks, R. ; Asten, Arian C. van - \ 2017
Journal of the American Society for Mass Spectrometry 28 (2017)12. - ISSN 1044-0305 - p. 2665 - 2676.
Amphetamines - Forensic toxicology - Paper spray mass spectrometry - Selectivity - Validation - Whole blood
Paper spray tandem mass spectrometry is used to identify and quantify eight individual amphetamines in whole blood in 1.3 min. The method has been optimized and fully validated according to forensic toxicology guidelines, for the quantification of amphetamine, methamphetamine, 3,4-methylenedioxyamphetamine (MDA), 3,4-methylenedioxy-N-methylamphetamine (MDMA), 3,4-methylenedioxy-N-ethylamphetamine (MDEA), para-methoxyamphetamine (PMA), para-methoxymethamphetamine (PMMA), and 4-fluoroamphetamine (4-FA). Additionally, a new concept of intrinsic and application-based selectivity is discussed, featuring increased confidence in the power to discriminate the amphetamines from other chemically similar compounds when applying an ambient mass spectrometric method without chromatographic separation. Accuracy was within ±15% and average precision was better than 15%, and better than 20% at the LLOQ. Detection limits between 15 and 50 ng/mL were obtained using only 12 μL of whole blood. [Figure not available: see fulltext.].
Omega-6 fatty acid biomarkers and incident type 2 diabetes : Pooled analysis of individual-level data for 39 740 adults from 20 prospective cohort studies
Wu, Jason H.Y. ; Marklund, Matti ; Imamura, Fumiaki ; Tintle, Nathan ; Ardisson Korat, Andres V. ; Goede, Janette de; Zhou, Xia ; Yang, Wei Sin ; Oliveira Otto, Marcia C. de; Kröger, Janine ; Qureshi, Waqas ; Virtanen, Jyrki K. ; Bassett, Julie K. ; Frazier-Wood, Alexis C. ; Lankinen, Maria ; Murphy, Rachel A. ; Rajaobelina, Kalina ; Gobbo, Liana C. Del; Forouhi, Nita G. ; Luben, Robert ; Khaw, Kay Tee ; Wareham, Nick ; Kalsbeek, Anya ; Veenstra, Jenna ; Luo, Juhua ; Hu, Frank B. ; Lin, Hung Ju ; Siscovick, David S. ; Boeing, Heiner ; Chen, Tzu An ; Steffen, Brian ; Steffen, Lyn M. ; Hodge, Allison ; Eriksdottir, Gudny ; Smith, Albert V. ; Gudnason, Vilmunder ; Harris, Tamara B. ; Brouwer, Ingeborg A. ; Berr, Claudine ; Helmer, Catherine ; Samieri, Cecilia ; Laakso, Markku ; Tsai, Michael Y. ; Giles, Graham G. ; Nurmi, Tarja ; Wagenknecht, Lynne ; Schulze, Matthias B. ; Lemaitre, Rozenn N. ; Chien, Kuo Liong ; Soedamah-Muthu, Sabita S. ; Geleijnse, Johanna M. ; Sun, Qi ; Harris, William S. ; Lind, Lars ; Ärnlöv, Johan ; Riserus, Ulf ; Micha, Renata ; Mozaffarian, Dariush - \ 2017
The Lancet Diabetes & Endocrinology 5 (2017)12. - ISSN 2213-8587 - p. 965 - 974.
Background: The metabolic effects of omega-6 polyunsaturated fatty acids (PUFAs) remain contentious, and little evidence is available regarding their potential role in primary prevention of type 2 diabetes. We aimed to assess the associations of linoleic acid and arachidonic acid biomarkers with incident type 2 diabetes. Methods: We did a pooled analysis of new, harmonised, individual-level analyses for the biomarkers linoleic acid and its metabolite arachidonic acid and incident type 2 diabetes. We analysed data from 20 prospective cohort studies from ten countries (Iceland, the Netherlands, the USA, Taiwan, the UK, Germany, Finland, Australia, Sweden, and France), with biomarkers sampled between 1970 and 2010. Participants included in the analyses were aged 18 years or older and had data available for linoleic acid and arachidonic acid biomarkers at baseline. We excluded participants with type 2 diabetes at baseline. The main outcome was the association between omega-6 PUFA biomarkers and incident type 2 diabetes. We assessed the relative risk of type 2 diabetes prospectively for each cohort and lipid compartment separately using a prespecified analytic plan for exposures, covariates, effect modifiers, and analysis, and the findings were then pooled using inverse-variance weighted meta-analysis. Findings: Participants were 39 740 adults, aged (range of cohort means) 49-76 years with a BMI (range of cohort means) of 23·3-28·4 kg/m2, who did not have type 2 diabetes at baseline. During a follow-up of 366 073 person-years, we identified 4347 cases of incident type 2 diabetes. In multivariable-adjusted pooled analyses, higher proportions of linoleic acid biomarkers as percentages of total fatty acid were associated with a lower risk of type 2 diabetes overall (risk ratio [RR] per interquintile range 0·65, 95% CI 0·60-0·72, p<0·0001; I 2=53·9%, pheterogeneity=0·002). The associations between linoleic acid biomarkers and type 2 diabetes were generally similar in different lipid compartments, including phospholipids, plasma, cholesterol esters, and adipose tissue. Levels of arachidonic acid biomarker were not significantly associated with type 2 diabetes risk overall (RR per interquintile range 0·96, 95% CI 0·88-1·05; p=0·38; I 2=63·0%, pheterogeneity<0·0001). The associations between linoleic acid and arachidonic acid biomarkers and the risk of type 2 diabetes were not significantly modified by any prespecified potential sources of heterogeneity (ie, age, BMI, sex, race, aspirin use, omega-3 PUFA levels, or variants of the FADS gene; all pheterogeneity≥0·13). Interpretation: Findings suggest that linoleic acid has long-term benefits for the prevention of type 2 diabetes and that arachidonic acid is not harmful. Funding: Funders are shown in the
Persistent Listeria monocytogenes strains isolated from mussel production facilities form more biofilm but are not linked to specific genetic markers
Nowak, Jessika ; Cruz, Cristina D. ; Tempelaars, Marcel ; Abee, Tjakko ; Vliet, Arnoud H.M. van; Fletcher, Graham C. ; Hedderley, Duncan ; Palmer, Jon ; Flint, Steve - \ 2017
International Journal of Food Microbiology 256 (2017). - ISSN 0168-1605 - p. 45 - 53.
Biofilm - Heat resistance - L. monocytogenes - Persistence

Contamination of mussels with the human pathogen Listeria monocytogenes occurs during processing in the factory, possibly from bacteria persisting in the factory's indoor and outdoor areas. In this study, a selection of persistent (n = 8) and sporadic (n = 8) L. monocytogenes isolates associated with mussel-processing premises in New Zealand were investigated for their phenotypic and genomic characteristics. To identify traits that favour or contribute to bacterial persistence, biofilm formation, heat resistance, motility and recovery from dry surfaces were compared between persistent and sporadic isolates. All isolates exhibited low biofilm formation at 20 °C, however, at 30 °C persistent isolates showed significantly higher biofilm formation after 48 h using cell enumeration and near significant difference using the crystal violet assay. All 16 isolates were motile at 20 °C and 30 °C and motility was fractionally higher for sporadic isolates, but no significant difference was observed. We found persistent isolates tend to exhibit greater recovery after incubation on dry surfaces compared to sporadic isolates. Two of the three most heat-resistant isolates were persistent, while four of five isolates lacking heat resistance were sporadic isolates. Comparison of genome sequences of persistent and sporadic isolates showed that there was no overall clustering of persistent or sporadic isolates, and that differences in prophages and plasmids were not associated with persistence. Our results suggest a link between persistence and biofilm formation, which is most likely multifactorial, combining subtle phenotypic and genotypic differences between isolates.

What if the trucks stop coming? : exploring the framing of local food by cooperative food retailers in New Mexico
Constance, Cheron Z. - \ 2017
University. Promotor(en): Han Wiskerke, co-promotor(en): Lummina Horlings; L. Shaw. - Wageningen : Wageningen University - ISBN 9789463431941 - 261
food - agricultural products - cooperatives - cooperative farm enterprises - food products - new mexico - voedsel - landbouwproducten - coöperaties - coöperatieve landbouwbedrijven - voedselproducten

Proponents of local food cite a variety of economic and environmental advantages of short food supply chains. Consumer interest in local food has also offered a point of differentiation for many players in the food industry, including restaurants and grocery stores. Engaging with local food has significant challenges, however, and many production and distribution systems engender and support more diffuse food provisioning, not less. Though food can travel thousands of miles from its point of origin to consumption, many cooperative (co-op) grocery stores have long sold locally-produced food and have deep ties to their supplier communities. This thesis offers case studies of two co-ops in the natural and organic food sector and examines how they think about and work with local food. The theories of embeddedness (after Polanyi) and diverse economies (from Gibson-Graham) undergird the analyses of these co-ops’ involvement with local food and how the cooperative business model relates to it.

Use of multi-trait and random regression models to identify genetic variation in tolerance to porcine reproductive and respiratory syndrome virus
Lough, Graham ; Rashidi, Hamed ; Kyriazakis, Ilias ; Dekkers, Jack C.M. ; Hess, Andrew ; Hess, Melanie ; Deeb, Nader ; Kause, Antti ; Lunney, Joan K. ; Rowland, Raymond R.R. ; Mulder, Herman ; Doeschl-Wilson, Andrea - \ 2017
Genetics, Selection, Evolution 49 (2017)1. - ISSN 0999-193X - p. 1 - 15.

Background: A host can adopt two response strategies to infection: resistance (reduce pathogen load) and tolerance (minimize impact of infection on performance). Both strategies may be under genetic control and could thus be targeted for genetic improvement. Although there is evidence that supports a genetic basis for resistance to porcine reproductive and respiratory syndrome (PRRS), it is not known whether pigs also differ genetically in tolerance. We determined to what extent pigs that have been shown to vary genetically in resistance to PRRS also exhibit genetic variation in tolerance. Multi-trait linear mixed models and random regression sire models were fitted to PRRS Host Genetics Consortium data from 1320 weaned pigs (offspring of 54 sires) that were experimentally infected with a virulent strain of PRRS virus to obtain genetic parameter estimates for resistance and tolerance. Resistance was defined as the inverse of within-host viral load (VL) from 0 to 21 (VL21) or 0 to 42 (VL42) days post-infection and tolerance as the slope of the reaction-norm of average daily gain (ADG21, ADG42) on VL21 or VL42. Results: Multi-trait analysis of ADG associated with either low or high VL was not indicative of genetic variation in tolerance. Similarly, random regression models for ADG21 and ADG42 with a tolerance slope fitted for each sire did not result in a better fit to the data than a model without genetic variation in tolerance. However, the distribution of data around average VL suggested possible confounding between level and slope estimates of the regression lines. Augmenting the data with simulated growth rates of non-infected half-sibs (ADG0) helped resolve this statistical confounding and indicated that genetic variation in tolerance to PRRS may exist if genetic correlations between ADG0 and ADG21 or ADG42 are low to moderate. Conclusions: Evidence for genetic variation in tolerance of pigs to PRRS was weak when based on data from infected piglets only. However, simulations indicated that genetic variance in tolerance may exist and could be detected if comparable data on uninfected relatives were available. In conclusion, of the two defense strategies, genetics of tolerance is more difficult to elucidate than genetics of resistance.

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