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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Weighted single-step GWAS and gene network analysis reveal new candidate genes for semen traits in pigs
Marques, Daniele B.D. ; Bastiaansen, John W.M. ; Broekhuijse, Marleen L.W.J. ; Lopes, Marcos S. ; Knol, Egbert F. ; Harlizius, Barbara ; Guimarães, Simone E.F. ; Silva, Fabyano F. ; Lopes, Paulo S. - \ 2018
Genetics, Selection, Evolution 50 (2018)1. - ISSN 0999-193X

Background: In recent years, there has been increased interest in the study of the molecular processes that affect semen traits. In this study, our aim was to identify quantitative trait loci (QTL) regions associated with four semen traits (motility, progressive motility, number of sperm cells per ejaculate and total morphological defects) in two commercial pig lines (L1: Large White type and L2: Landrace type). Since the number of animals with both phenotypes and genotypes was relatively small in our dataset, we conducted a weighted single-step genome-wide association study, which also allows unequal variances for single nucleotide polymorphisms. In addition, our aim was also to identify candidate genes within QTL regions that explained the highest proportions of genetic variance. Subsequently, we performed gene network analyses to investigate the biological processes shared by genes that were identified for the same semen traits across lines. Results: We identified QTL regions that explained up to 10.8% of the genetic variance of the semen traits on 12 chromosomes in L1 and 11 chromosomes in L2. Sixteen QTL regions in L1 and six QTL regions in L2 were associated with two or more traits within the population. Candidate genes SCN8A, PTGS2, PLA2G4A, DNAI2, IQCG and LOC102167830 were identified in L1 and NME5, AZIN2, SPATA7, METTL3 and HPGDS in L2. No regions overlapped between these two lines. However, the gene network analysis for progressive motility revealed two genes in L1 (PLA2G4A and PTGS2) and one gene in L2 (HPGDS) that were involved in two biological processes i.e. eicosanoid biosynthesis and arachidonic acid metabolism. PTGS2 and HPGDS were also involved in the cyclooxygenase pathway. Conclusions: We identified several QTL regions associated with semen traits in two pig lines, which confirms the assumption of a complex genetic determinism for these traits. A large part of the genetic variance of the semen traits under study was explained by different genes in the two evaluated lines. Nevertheless, the gene network analysis revealed candidate genes that are involved in shared biological pathways that occur in mammalian testes, in both lines.

Copy number variations in Friesian horses and genetic risk factors for insect bite hypersensitivity
Schurink, Anouk ; Silva, Vinicius H. da; Velie, Brandon D. ; Dibbits, Bert W. ; Crooijmans, Richard P.M.A. ; François, Liesbeth ; Janssens, Steven ; Stinckens, Anneleen ; Blott, Sarah ; Buys, Nadine ; Lindgren, Gabriella ; Ducro, Bart J. - \ 2018
BMC Genetics 19 (2018)1. - ISSN 1471-2156
Copy number variations - Friesian horse - Genome-wide association study - Insect bite hypersensitivity

Background: Many common and relevant diseases affecting equine welfare have yet to be tested regarding structural variants such as copy number variations (CNVs). CNVs make up a substantial proportion of total genetic variability in populations of many species, resulting in more sequence differences between individuals than SNPs. Associations between CNVs and disease phenotypes have been established in several species, but equine CNV studies have been limited. Aim of this study was to identify CNVs and to perform a genome-wide association (GWA) study in Friesian horses to identify genomic loci associated with insect bite hypersensitivity (IBH), a common seasonal allergic dermatitis observed in many horse breeds worldwide. Results: Genotypes were obtained using the Axiom® Equine Genotyping Array containing 670,796 SNPs. After quality control of genotypes, 15,041 CNVs and 5350 CNV regions (CNVRs) were identified in 222 Friesian horses. Coverage of the total genome by CNVRs was 11.2% with 49.2% of CNVRs containing genes. 58.0% of CNVRs were novel (i.e. so far only identified in Friesian horses). A SNP- and CNV-based GWA analysis was performed, where about half of the horses were affected by IBH. The SNP-based analysis showed a highly significant association between the MHC region on ECA20 and IBH in Friesian horses. Associations between the MHC region on ECA20 and IBH were also detected based on the CNV-based analysis. However, CNVs associated with IBH in Friesian horses were not often in close proximity to SNPs identified to be associated with IBH. Conclusions: CNVs were identified in a large sample of the Friesian horse population, thereby contributing to our knowledge on CNVs in horses and facilitating our understanding of the equine genome and its phenotypic expression. A clear association was identified between the MHC region on ECA20 and IBH in Friesian horses based on both SNP- and CNV-based GWA studies. These results imply that MHC contributes to IBH sensitivity in Friesian horses. Although subsequent analyses are needed for verification, nucleotide differences, as well as more complex structural variations like CNVs, seem to contribute to IBH sensitivity. IBH should be considered as a common disease with a complex genomic architecture.

Corrigendum : Factors affecting quality and health promoting compounds during growth and postharvest life of sweet cherry (Prunus avium L.) (Front. Plant Sci (2017) 8, (2166), 10.3389/fpls.2017.02166)
Correia, Sofia ; Schouten, Rob ; Silva, Ana P. ; Gonçalves, Berta - \ 2018
Frontiers in Plant Science 9 (2018). - ISSN 1664-462X

There is an error in the Funding statement. The correct Name for the Funder is INTERACT project—Integrative Research in Environment, Agro-Chains and Technology, no. NORTE-01-0145-FEDER-000017, in its line of research entitled ISAC-P2, co-financed by the European Regional Development Fund (ERDF) through NORTE 2020 (North Regional Operational Program 2014/2020). The authors apologize for this error and state that this does not change the scientific conclusions of the article in any way. Authors acknowledge the support provided by European Investment Funds by FEDER/COMPETE/POCI-Operational Competitiveness and Internationalization Programme, under the Project POCI-01-0145-FEDER-006958 and National Funds by FCT-Portuguese Foundation for Science and Technology, under the project UID/AGR/04033/2013. SC acknowledge the support provided by the FCT-Portuguese Foundation for Science and Technology (SFRH/BD/52541/2014), under the Doctoral Programme Agricultural Production Chains—from fork to farm (PD/00122/2012).

Breed-specific genome-wide association study for purebred and crossbred performance
Sevillano Del Aguila, C.A. ; Guimaraes, S.E.F. ; Silva, F. ; Calus, M.P.L. - \ 2018
In: Proceedings 11th World Congress of Genetics Applied to Livestock Production. -
Insight into the Role of Facultative Bacteria Stimulated by Microaeration in Continuous Bioreactors Converting LCFA to Methane
Duarte, M.S. ; Silva, Sérgio A. ; Salvador, Andreia F. ; Cavaleiro, Ana J. ; Stams, Alfons J.M. ; Alves, M.M. ; Pereira, M.A. - \ 2018
Environmental Science and Technology 52 (2018)11. - ISSN 0013-936X - p. 6497 - 6507.

Conversion of unsaturated long chain fatty acids (LCFA) to methane in continuous bioreactors is not fully understood. Palmitate (C16:0) often accumulates during oleate (C18:1) biodegradation in methanogenic bioreactors, and the reason why this happens and which microorganisms catalyze this reaction remains unknown. Facultative anaerobic bacteria are frequently found in continuous reactors operated at high LCFA loads, but their function is unclear. To get more insight on the role of these bacteria, LCFA conversion was studied under microaerophilic conditions. For that, we compared bioreactors treating oleate-based wastewater (organic loading rates of 1 and 3 kg COD m-3 d-1), operated under different redox conditions (strictly anaerobic-AnR, -350 mV; microaerophilic-MaR, -250 mV). At the higher load, palmitate accumulated 7 times more in the MaR, where facultative anaerobes were more abundant, and only the biomass from this reactor could recover the methanogenic activity after a transient inhibition. In a second experiment, the abundance of facultative anaerobic bacteria, particularly Pseudomonas spp. (from which two strains were isolated), was strongly correlated (p < 0.05) with palmitate-to-total LCFA percentage in the biofilm formed in a continuous plug flow reactor fed with very high loads of oleate. This work strongly suggests that microaeration stimulates the development of facultative bacteria that are critical for achieving LCFA conversion to methane in continuous bioreactors. Microbial networks and interactions of facultative and strict anaerobes in microbial communities should be considered in future studies.

Theorizing Slum Politics in Recife, Brazil : Community leaders symbolize the inconsistency of the urban situation
Silva, Sven da; Vries, P.A. de - \ 2018
In: Cities and Citizenship in Latin America & the Carribean. - Delft : TU Delft - ISBN 9789463660501 - p. 64 - 71.
Cities and Citizenship in Contemporary Latin America and the Caribbean : conference proceedings NALACS Conference 16-17 June 2016, TU Delft
Rocco, Roberto ; Silva, Sven da - \ 2018
Delft : TU Delft - ISBN 9789463660501 - 184 p.
Whose gap counts? The role of yield gap analysis within a development-oriented agronomy
Silva, João Vasco ; Ramisch, Joshua J. - \ 2018
Experimental Agriculture (2018). - ISSN 0014-4797 - 28 p.
Yield gaps have become a useful tool for guiding development-related agronomy, especially in the global South. While critics have challenged some aspects of the yield gap methodology, and the relevance of food security advocacy based on yield gaps, very few studies question the actual relevance, application and scalability of yield gaps for smallholder farmers (and researchers) in the tropics. We assess these limitations using two contrasting case studies: maize-based farming systems in Western Kenya and ricebased
farming systems in Central Luzon, the Philippines. From these two cases, we propose improvements in the use of yield gaps that would acknowledge both the riskiness of crop improvement options and the role that yield increases might play within local livelihoods. Participatory research conducted in Western
Kenya calls into question the actual use and up-scaling of yield measurements from on-station agronomic trials to derive estimates of actual and water-limited yields in the region. Looking at maize yield gaps as cumulative probabilities demonstrates the challenges of assessing the real magnitude of yield gaps in
farmers’ fields and of deciding whose yield gaps count for agricultural development in Kenya. In the case of rice-based farming systems, we use a historical dataset (1966–2012) to assess changes in rice yields, labour productivity, gross margin and rice self-sufficiency in Central Luzon, the Philippines. While large rice yield gaps persist here, there appear to be few incentives to close that gap once we consider the position of crop production within local livelihoods. In this context, economic returns to labour for farm work were marginal: labour productivity increased over time in both wet and dry seasons, but gross margins decreased in the wet season while no trend was observed for the dry season. Since most households were rice selfsufficient
and further increases in crop production would offer minimal returns while relying increasingly on hired labour, we question who should close which yield gap. Our case studies show the importance of contextualising yield gaps within the broader livelihood context in which farmers operate. We propose that this should be done at farm and/or farming systems level while considering the risks associated with narrowing yield gaps and looking into multiple performance indicators.
Intensification of rice-based farming systems in Central Luzon, Philippines : Constraints at field, farm and regional levels
Silva, João Vasco ; Reidsma, Pytrik ; Lourdes Velasco, Ma ; Laborte, Alice G. ; Ittersum, Martin K. van - \ 2018
Agricultural Systems 165 (2018). - ISSN 0308-521X - p. 55 - 70.
Crop management - Farm structural change - Farmers’ objectives - Integrated assessment - Sustainable intensification - Yield gap

Understanding the opportunities for sustainable intensification requires an integrated assessment at field, farm and regional levels of past developments. Two hypotheses regarding current rice production in Central Luzon (Philippines) were developed for this purpose. First, we hypothesize that there are trade-offs between rice yields, labour productivity, gross margin and N use efficiency and, second, that farm(er) characteristics and socio-economic conditions at farm and regional level affect the management practices used by farmers. These hypotheses were tested using two household surveys characterizing rice-based farming systems in Central Luzon in terms of changes over time (1966–2012) and spatial variability. Over the past half-century there was an increase in the proportion of irrigated fields and adoption of improved varieties, which allowed the cultivation of a dry season rice crop in Central Luzon. Moreover, transplanting has been replaced by direct-seeding and herbicides substituted hand-weeding. These resulted in greater rice yields and labour productivity, and contributed to gradual transition from subsistence to commercial farming systems, as observed in the increasing proportion of hired labour and rice sold. Our results indicate the existence of a trade-off between rice yields, labour productivity and N use efficiency as yield levels maximising labour productivity and N use efficiency were ca. 25% and 35% lower than climatic potential yield in the wet and dry season, respectively. At field level, this can be explained by 1) the use of transplanting as crop establishment method, which resulted into higher yields but lower labour productivity as compared to direct-seeding, and 2) the high N application levels, which led to higher yields but lower N use efficiency. In contrast, yield levels which maximised gross margin were ca. 80% of the climatic potential in both wet and dry seasons, so there was little trade-off between rice yields and economic performance. Regarding the second hypothesis results were not always conclusive. As an example, N application per ha was negatively associated with farm size and the timing of the first fertiliser application positively associated with household size and with the number of parcels. More intensive practices, and better farm performance, were recorded in the province at the heart of the irrigation system. We thus conclude that closing rice yield gaps in the production systems of Central Luzon incurs trade-offs with environmental and social objectives at field and farm levels but less with economic objectives. However, we could not clearly show whether, and to what extent, management practices used by farmers are influenced by farm or regional level constraints.

Sweet cherry fruit cracking mechanisms and prevention strategies : A review
Correia, Sofia ; Schouten, Rob ; Silva, Ana Paula ; Gonçalves, Berta - \ 2018
Scientia Horticulturae 240 (2018). - ISSN 0304-4238 - p. 369 - 377.
Biostimulants - Candidate compounds - Cracking markers - Cracking mechanisms - Prunus avium L. - Rainfall

Sweet cherry (Prunus avium L.) is highly perishable and is greatly affected by orchard management and environmental conditions, such as excess rainfall before harvest. Rain-induced cracking is the major cause of crop loss in sweet cherry in most production areas of the world. Advances in understanding the physiological and molecular mechanisms involved in cracking physiology in combination with orchard management strategies to limit cherry cracking are discussed. The current opinions to explain fruit cracking is that the process initiates with water uptake by the fruit surface that results in localised bursting of cells that release malic acid into the apoplast. This results in swelling of the epidermis and weakening of the epidermal and hypodermal cells until macroscopic fruit cracking. This review focusses on management strategies such as rain cover protection, mineral sprays, anti-transpirants and growth regulators. Tree responses to growth regulators and biostimulants vary with cultivar, application frequency, concentration and type, making it hard to generalize their effects. New approaches to limit cracking are presented, including the development of tolerant cultivars, candidate mineral sprays, biostimulants and technologies for rainwater removal such as orchard air-blast sprayers or creating downwash by helicopters.

Disturbance intensity is a stronger driver of biomass recovery than remaining tree-community attributes in a managed Amazonian forest
Avila, Angel L. de; Sande, M.T. van der; Dormann, C.F. ; Pena Claros, M. ; Poorter, L. ; Mazzei, Lucas ; Ruschel, Ademir Roberto ; Silva, José N.M. ; Carvalho, J.O.P. ; Bauhus, J. - \ 2018
Journal of Applied Ecology 55 (2018)4. - ISSN 0021-8901 - p. 1647 - 1657.
Forest recovery following management interventions is important to maintain ecosystem functioning and the provision of ecosystem services. It remains, however, largely unclear how above‐ground biomass (AGB) recovery of species‐rich tropical forests is affected by disturbance intensity and post‐disturbance (remaining) tree‐community attributes, following logging and thinning interventions. We investigated whether annual AGB increment (∆AGB) decreases with management‐related disturbance intensity (disturbance hypothesis), and increases with the diversity (niche‐complementarity hypothesis) and the community‐weighted mean (CWM) of acquisitive traits of dominant species (biomass‐ratio hypothesis) in the remaining tree community. We analysed data from a long‐term forest‐management experiment in the Brazilian Amazon over two recovery periods: post‐logging (1983–1989) and post‐thinning (1995–2012). We computed the ∆AGB of surviving trees, recruit trees and of the total tree community. Disturbance intensity was quantified as basal area reduction and basal area remaining. Remaining diversity (taxonomic, functional and structural) and CWM of five functional traits linked to biomass productivity (specific leaf area, leaf nitrogen and phosphorous concentration, leaf toughness and wood density) were calculated for the post‐intervention inventories. Predictors were related to response variables using multiple linear regressions and structural equation modelling.

We found support for the disturbance hypothesis in both recovery periods. AGB increment of survivors and of the total tree community increased with basal area remaining, indicating the importance of remaining growing stock for biomass recovery. Conversely, AGB increment of recruit trees increased with basal area reduction because changes in forest structure increased resource availability for young trees. We did not find consistent support for the niche‐complementarity and biomass‐ratio hypotheses, possibly because of a high redundancy in these extremely species‐rich forests. Synthesis and applications. The intensity of disturbance through management, expressed as basal area reduction and basal area remaining, was consistently more important for explaining forest biomass recovery following harvesting and thinning than remaining diversity or trait composition. This points to the importance of controlling logging and thinning intensity in forests of the eastern Amazon. Given the high intervention intensities applied in this experiment, it is likely that low to moderate harvesting intensities permitted by the current legislation for the Brazilian Amazon (30 m³/ha) will not impair biomass recovery in these forests.
Incorporating soil ecosystem services into urban planning : status, challenges and opportunities
Teixeira da Silva, Ricardo ; Fleskens, Luuk ; Delden, Hedwig van; Ploeg, Martine van der - \ 2018
Landscape Ecology 33 (2018)7. - ISSN 0921-2973 - p. 1087 - 1102.
Ecosystem services - Integrated planning - Soil - Sustainable development - Urban planning

Context: Traditionally soils have not received much attention in urban planning. For this, tools are needed that can both be understood both by soil scientists and urban planners. Purpose: The purpose of this paper is to enhance the role of soil knowledge in urban planning practice, through the following objectives: (1) identifying the role soil plays in recent urban plans; (2) analysing the ecosystem services and indicators used in soil science in an urban context; and (3) inferring the main challenges and opportunities to integrate soil into urban planning. Methods: Seven urban plans and reports of world cities that include sustainability goals were analysed using text-mining and qualitative analysis, with a critical view on the inclusion of soil-related concepts. Secondly, the contribution of soil science to urban planning was assessed with an overview of case studies in the past decade that focus on soil-related ecosystem services in urban context. Results: The results show an overall weak attention to soil and soil-related ecosystem services in the implementation and monitoring phases of urban plans. The majority of soil science case studies uses a haphazard approach to measure ecosystem service indicators which may not capture the ecosystem services appropriately and hence lack relevance for urban planning. Conclusions: Even though the most urban plans assessed recognize soil as a key resource, most of them fail to integrate indicators to measure or monitor soil-related functions. There is a need to develop soil-related ecosystem services that can be easily integrated and understood by other fields.

The influence of groundwater depth on coastal dune development at sand flats close to inlets
Silva, Filipe Galiforni ; Wijnberg, Kathelijne M. ; Groot, Alma V. de; Hulscher, Suzanne J.M.H. - \ 2018
Ocean Dynamics 68 (2018)7. - ISSN 1616-7341 - p. 885 - 897.
Cellular automata - Coastal dunes - Groundwater level - Sand flats

A cellular automata model is used to analyze the effects of groundwater levels and sediment supply on aeolian dune development occurring on sand flats close to inlets. The model considers, in a schematized and probabilistic way, aeolian transport processes, groundwater influence, vegetation development, and combined effects of waves and tides that can both erode and accrete the sand flat. Next to three idealized cases, a sand flat adjoining the barrier island of Texel, the Netherlands, was chosen as a case study. Elevation data from 18 annual LIDAR surveys was used to characterize sand flat and dune development. Additionally, a field survey was carried out to map the spatial variation in capillary fringe depth across the sand flat. Results show that for high groundwater situations, sediment supply became limited inducing formation of Coppice-like dunes, even though aeolian losses were regularly replenished by marine import during sand flat flooding. Long dune rows developed for high sediment supply scenarios which occurred for deep groundwater levels. Furthermore, a threshold depth appears to exist at which the groundwater level starts to affect dune development on the inlet sand flat. The threshold can vary spatially depending on external conditions such as topography. On sand flats close to inlets, groundwater is capable of introducing spatial variability in dune growth, which is consistent with dune development patterns found on the Texel sand flat.

Legume abundance along successional and rainfall gradients in Neotropical forests
Gei, Maga ; Rozendaal, Danaë M.A. ; Poorter, Lourens ; Bongers, Frans ; Sprent, Janet I. ; Garner, Mira D. ; Aide, T.M. ; Andrade, José Luis ; Balvanera, Patricia ; Becknell, Justin M. ; Brancalion, Pedro H.S. ; Cabral, George A.L. ; César, Ricardo Gomes ; Chazdon, Robin L. ; Cole, Rebecca J. ; Colletta, Gabriel Dalla ; Jong, Ben De; Denslow, Julie S. ; Dent, Daisy H. ; Dewalt, Saara J. ; Dupuy, Juan Manuel ; Durán, Sandra M. ; Espírito Santo, Mário Marcos Do; Fernandes, G.W. ; Nunes, Yule Roberta Ferreira ; Finegan, Bryan ; Moser, Vanessa Granda ; Hall, Jefferson S. ; Hernández-Stefanoni, José Luis ; Junqueira, André B. ; Kennard, Deborah ; Lebrija-Trejos, Edwin ; Letcher, Susan G. ; Lohbeck, Madelon ; Marín-Spiotta, Erika ; Martínez-Ramos, Miguel ; Meave, Jorge A. ; Menge, Duncan N.L. ; Mora, Francisco ; Muñoz, Rodrigo ; Muscarella, Robert ; Ochoa-Gaona, Susana ; Orihuela-Belmonte, Edith ; Ostertag, Rebecca ; Peña-Claros, Marielos ; Pérez-García, Eduardo A. ; Piotto, Daniel ; Reich, Peter B. ; Reyes-García, Casandra ; Rodríguez-Velázquez, Jorge ; Romero-Pérez, I.E. ; Sanaphre-Villanueva, Lucía ; Sanchez-Azofeifa, Arturo ; Schwartz, Naomi B. ; Almeida, Arlete Silva De; Almeida-Cortez, Jarcilene S. ; Silver, Whendee ; Souza Moreno, Vanessa De; Sullivan, Benjamin W. ; Swenson, Nathan G. ; Uriarte, Maria ; Breugel, Michiel Van; Wal, Hans Van Der; Veloso, Maria Das Dores Magalhães ; Vester, Hans F.M. ; Vieira, Ima Célia Guimarães ; Zimmerman, Jess K. ; Powers, Jennifer S. - \ 2018
Nature Ecology & Evolution 2 (2018)7. - ISSN 2397-334X - p. 1104 - 1111.
The nutrient demands of regrowing tropical forests are partly satisfied by nitrogen-fixing legume trees, but our understanding of the abundance of those species is biased towards wet tropical regions. Here we show how the abundance of Leguminosae is affected by both recovery from disturbance and large-scale rainfall gradients through a synthesis of forest inventory plots from a network of 42 Neotropical forest chronosequences. During the first three decades of natural forest regeneration, legume basal area is twice as high in dry compared with wet secondary forests. The tremendous ecological success of legumes in recently disturbed, water-limited forests is likely to be related to both their reduced leaflet size and ability to fix N2, which together enhance legume drought tolerance and water-use efficiency. Earth system models should incorporate these large-scale successional and climatic patterns of legume dominance to provide more accurate estimates of the maximum potential for natural nitrogen fixation across tropical forests.
Desiccation sensitive seeds: understanding their evolution, genetics and physiology
Correia Silva de Santana Marques, Alexandre - \ 2018
University. Promotor(en): Richard Immink, co-promotor(en): Henk Hilhorst; Wilco Ligterink. - Wageningen : Wageningen University - ISBN 9789463438599 - 189
Adaptation to climate change at local level in Europe: An overview
Aguiar, F.C. ; Bentz, J. ; Silva, J.M.N. ; Fonseca, A.L. ; Swart, R.J. ; Santos, F.D. ; Penha-Lopes, Gil - \ 2018
Environmental Science & Policy 86 (2018). - ISSN 1462-9011 - p. 38 - 63.
Europe’s climate change vulnerability pushes for initiatives such as the European Adaptation Strategy and the associated Covenant of Mayors for Climate and Energy. What are the triggers and barriers, for which sectors and for which risks and how is adaptation funded? This paper examines 147 Local Adaptation Strategies in Europe. Key triggers were incentives via research projects, implementation of EU policies and the increasing frequency of extreme climate events. Insufficient resources, capacity, political commitment and uncertainty were the main barriers. Prioritized sectors reflected the main local vulnerabilities - flood protection and water management, built environment and urban planning. Differing patterns of adaptation planning and adaptive capacity were identified among different regions in Europe. Large municipalities generally fund adaptation locally, whereas international and national funding appears to be more important for adaptation in less urban or densely populated territories. The database of LAS described in the present study can be expanded and used to increase the understanding of and promotion of local adaptation action in Europe and beyond.
Propagating annotations of molecular networks using in silico fragmentation
Silva, Ricardo R. da; Wang, Mingxun ; Nothias, Louis Félix ; Hooft, Justin J.J. van der; Caraballo-Rodríguez, Andrés Mauricio ; Fox, Evan ; Balunas, Marcy J. ; Klassen, Jonathan L. ; Lopes, Norberto Peporine ; Dorrestein, Pieter C. - \ 2018
PLoS Computational Biology 14 (2018)4. - ISSN 1553-734X

The annotation of small molecules is one of the most challenging and important steps in untargeted mass spectrometry analysis, as most of our biological interpretations rely on structural annotations. Molecular networking has emerged as a structured way to organize and mine data from untargeted tandem mass spectrometry (MS/MS) experiments and has been widely applied to propagate annotations. However, propagation is done through manual inspection of MS/MS spectra connected in the spectral networks and is only possible when a reference library spectrum is available. One of the alternative approaches used to annotate an unknown fragmentation mass spectrum is through the use of in silico predictions. One of the challenges of in silico annotation is the uncertainty around the correct structure among the predicted candidate lists. Here we show how molecular networking can be used to improve the accuracy of in silico predictions through propagation of structural annotations, even when there is no match to a MS/MS spectrum in spectral libraries. This is accomplished through creating a network consensus of re-ranked structural candidates using the molecular network topology and structural similarity to improve in silico annotations. The Network Annotation Propagation (NAP) tool is accessible through the GNPS web-platform https://gnps.ucsd.edu/ProteoSAFe/static/gnps-theoretical.jsp.

Erratum to “Investigation of Clostridium botulinum group III's mobilome content” [Anaerobe 49 (2018) 71–77]
Woudstra, Cédric ; Maréchal, Caroline Le; Souillard, Rozenn ; Anniballi, Fabrizio ; Auricchio, Bruna ; Bano, Luca ; Bayon-Auboyer, Marie Hélène ; Koene, Miriam ; Mermoud, Isabelle ; Brito, Roseane B. ; Lobato, Francisco C.F. ; Silva, Rodrigo O.S. ; Dorner, Martin B. ; Fach, Patrick - \ 2018
Anaerobe (2018). - ISSN 1075-9964
Genetic correlations between feed efficiency traits, and growth performance and carcass traits in purebred and crossbred pigs
Godinho, R.M. ; Bergsma, R. ; Silva, F.F. ; Sevillano, C.A. ; Knol, E.F. ; Lopes, M.S. ; Lopes, P.S. ; Bastiaansen, J.W.M. ; Guimarães, S.E.F. - \ 2018
Journal of Animal Science 96 (2018)3. - ISSN 0021-8812 - p. 817 - 829.
Breeding program - Carcass traits - Feed efficiency - Genetic correlations - Growing-Finishing pigs - Growth
Selection for feed efficiency (FE) is a strategy to reduce the production costs per unit of animal product, which is one of the major objectives of current animal breeding programs. In pig breeding, selection for FE and other traits traditionally takes place based on purebred pig (PB) performance at the nucleus level, while pork production typically makes use of crossbred animals (CB). The success of this selection, therefore, depends on the genetic correlation between the performance of PB and CB (rpc) and on the genetic correlation (rg) between FE and the other traits that are currently under selection. Different traits are being used to account for FE, but the rpc has been reported only for feed conversion rate. Therefore, this study aimed 1) to estimate the rpc for growth performance, carcass, and FE traits; 2) to estimate rg between traits within PB and CB populations; and 3) to compare three different traits representing FE: feed conversion rate, residual energy intake (REI), and residual feed intake (RFI). Phenotypes of 194,445 PB animals from 23 nucleus farms, and 46,328 CB animals from three farms where research is conducted under near commercial production conditions were available for this study. From these, 22,984 PB and 8,657 CB presented records for feed intake. The PB population consisted of five sire and four dam lines, and the CB population consisted of terminal cross-progeny generated by crossing sires from one of the five PB sire lines with commercially available two-way maternal sow crosses. Estimates of rpc ranged from 0.61 to 0.71 for growth performance traits, from 0.75 to 0.82 for carcass traits, and from 0.62 to 0.67 for FE traits. Estimates of rg between growth performance, carcass, and FE traits differed within PB and CB. REI and RFI showed substantial positive rg estimates in PB (0.84) and CB (0.90) populations. The magnitudes of rpc estimates indicate that genetic progress is being realized in CB at the production level from selection on PB performance at nucleus level. However, including CB phenotypes recorded on production farms, when predicting breeding values, has the potential to increase genetic progress for these traits in CB. Given the genetic correlations with growth performance traits and the genetic correlation between the performance of PB and CB, REI is an attractive FE parameter for a breeding program.
Effects of rumen-undegradable protein on intake, performance, and mammary gland development in prepubertal and pubertal dairy heifers
Silva, A.L. ; Detmann, E. ; Dijkstra, J. ; Pedroso, A.M. ; Silva, L.H.P. ; Machado, A.F. ; Sousa, F.C. ; Santos, G.B. dos; Marcondes, M.I. - \ 2018
Journal of Dairy Science 101 (2018)7. - ISSN 0022-0302 - p. 5991 - 6001.
growth - mammary gland ultrasound - nitrogen retention
The objective of this study was to evaluate the influence of different amounts of rumen-undegradable protein (RUP) on intake, N balance, performance, mammary gland development, carcass traits, and hormonal status of Holstein heifers at different physiological stages (PS). Sixteen prepubertal (PRE) heifers (initial BW = 106 ± 7.6 kg; age = 4.3 ± 0.46 mo) and 16 pubertal (PUB) heifers (initial BW = 224 ± 7.9 kg; age = 12.6 ± 0.45 mo) were used in an experiment over a period of 84 d. Four diets with increasing RUP contents (38, 44, 51, and 57% of dietary crude protein) and heifers at 2 PS (PRE or PUB) were used in a 4 × 2 factorial arrangement of treatments in a completely randomized design. Throughout the experiment, 2 digestibility trials were performed over 5 consecutive days (starting at d 36 and 78) involving feed and ort sampling and spot collections of feces and urine. At d 0 and 83, body ultrasound images were obtained for real-time carcass trait evaluation. The mammary gland was ultrasonically scanned at d 0 and every 3 wk during the experiment. Blood samples were taken at d 0 and 84 to determine serum concentrations of progesterone, estrogen, insulin-like growth factor I (IGF-I), and insulin. No interaction between PS and the level of RUP was found for any trait. Apparent digestibility of dry matter, organic matter, and neutral detergent fiber corrected for ash and protein was not affected by RUP level but was lower for PRE compared with PUB heifers. Sorting against neutral detergent fiber corrected for ash and protein (tendency only) and for crude protein was greater for PUB than PRE heifers. Pubertal heifers had greater average daily gain (905 vs. 505 g/d) and N retention (25.9 vs. 12.5 g/d) than PRE heifers. In addition, average daily gain and N retention were greatest at 51% RUP of dietary protein. Mammary ultrasonography indicated no effects of RUP amounts on mammary gland composition, whereas PRE heifers had greater pixel values than PUB, indicating higher contents of fat rather than protein in the mammary glands of PRE heifers. Serum progesterone and IGF-I concentration was affected only by PS, and PRE heifers had greater values of progesterone and IGF-I concentrations than PUB heifers. Serum insulin concentration was unaffected by PS but tended to be higher at 51% of RUP. In conclusion, an RUP level of 51% increases body weight, average daily gain, feed efficiency, and N retention in heifers regardless of the PS. In addition, PRE heifers have a lower sorting ability and reduced intake, total-tract digestibility, and N retention. They also have higher amounts of fat in their mammary glands, even at moderate growth rates.
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