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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    Working Group on Marine Mammal Ecology (WGMME)
    Galatius, Anders ; Gilles, Anita ; Ahola, M. ; Authier, Matthieu ; Brasseur, S.M.J.M. ; Geelhoed, S.C.V. - \ 2020
    ICES (ICES Scientific Reports 39) - 85 p.
    The Working Group on Marine Mammal Ecology (WGMME) meeting 2020 was chaired remotely by Anita Gilles (Germany) and Anders Galatius (Denmark) and on-site chairs Matthieu Authier (France) and Ross Culloch (Scotland, UK).
    Two terms of references were standing ToRs; under the first of these, ToR A, new and updated information on seal and cetacean population abundance, population/stock structure, manage-ment frameworks as well as anthropogenic threats to individual health and population status were reviewed. The latest abundance data on harbour, grey and ringed seals are also reviewed under this ToR along with findings on threats to marine mammals such as bycatch, pollution, marine debris and noise.
    ToR B arose to facilitate the work of WGBIOIV’s ToR A; “Investigate mechanisms linking trophic guilds under contrasting levels of pressure and/or primary production in case study areas”. The initial focus of work should be on harbour porpoise, grey seal and harbour seal in the North Sea as a case study and, therefore, a number of recent studies addressing diet, foraging distribution and trophic interactions were reviewed. Additionally, an overview of published and un-published data on diet and distribution of marine mammals in the North Sea was synthesized.
    ToR C was implemented to review aspects of marine mammal-fishery interactions not covered by ICES WGBYC. In 2020, WGMME focused its efforts on i) reviewing conservation objectives with respect to maximum mortality since the lack of conservation targets was identified as hin-dering the ability to address marine mammal-fisheries interactions, ii) assessing the use of stranding records as a source of information to identify abnormal mortality and possible rela-tions to fisheries. A country-by-country review of current stranding network activities was in-cluded.
    ToR D, updating the database for seals, is the second standing term of reference. The database format generated in 2019 was updated with the most recent data on seal abundance.
    Effects of eggshell temperature pattern during incubation on tibia characteristics of broiler chickens at slaughter age
    Güz, B.C. ; Molenaar, R. ; Jong, I.C. de; Kemp, B. ; Krimpen, M. van; Brand, H. van den - \ 2020
    Poultry Science 99 (2020)6. - ISSN 0032-5791 - p. 3020 - 3029.
    broiler chickens - eggshell temperature - incubation - leg health - tibia

    This study was designed to determine effects of eggshell temperature (EST) pattern in week 2 and week 3 of incubation on tibia development of broiler chickens at slaughter age. A total of 468 Ross 308 eggs were incubated at an EST of 37.8°C from incubation day (E) 0 to E7. Thereafter, a 2 × 2 factorial arrangement with 2 EST (37.8°C and 38.9°C) from E8 to E14 and 2 EST (36.7°C and 37.8°C) from E15 till hatch was applied. After hatching, chickens were reared until slaughter age with the 4 EST treatments and 8 replicates per treatment. At day 41 and 42, one male chicken per replicate per day was selected, and hock burn and food pad dermatitis were scored. Rotated tibia, tibia dyschondroplasia, epiphyseal plate abnormalities, bacterial chondronecrosis with osteomyelitis, and epiphysiolysis were assessed. Tibia weight, length, thickness, head thickness, and robusticity index were determined. X-ray analyses (osseous volume, pore volume, total volume, volume fraction, mineral content, and mineral density) and a 3-point bending test (ultimate strength, yield strength, stiffness, energy to fracture, and elastic modulus) were performed. A high EST (38.9°C) in week 2 of incubation, followed by a normal EST (37.8°C) in week 3 resulted in higher mineral content (P = 0.001), mineral density (P = 0.002), ultimate strength (P = 0.04), yield strength (P = 0.03), and stiffness (P = 0.05) compared with the other 3 EST groups (week 2 × week 3 interaction). A high EST (38.9°C) in week 2 of incubation, regardless of the EST in week 3, resulted in a higher tibia weight (P < 0.001), thickness (P = 0.05), osseous volume (P < 0.001), and total volume (P < 0.001) than a normal EST (37.8°C). It can be concluded that 1.1°C higher EST than normal in week 2 of incubation appears to stimulate tibia morphological, biophysical, and mechanical characteristics of broiler chickens at slaughter age. Additionally, a 1.1°C lower EST in week 3 of incubation appears to have negative effects on tibia characteristics, particularly in interaction with the EST in week 2 of incubation.

    Agroecosystem patterns and land management co-develop through environment, management, and land-use interactions
    Caulfield, Mark E. ; Fonte, Steven J. ; Groot, Jeroen C.J. ; Vanek, Steven J. ; Sherwood, Stephen ; Oyarzun, Pedro ; Borja, Ross Mary ; Dumble, Sam ; Tittonell, Pablo - \ 2020
    Ecosphere 11 (2020)4. - ISSN 2150-8925
    co-development - Ecuador - elevation - environmental gradients - farm management - socio-ecological systems - soil organic carbon

    A poor understanding of the interactions between biophysical and social elements within rural mountainous landscapes can lead to suboptimal management and recommendations. The objective of this study was to contribute to more contextualized natural resource management in a rural landscape in the Ecuadorian Andes by (1) identifying biophysical patterns in soil properties, biodiversity, and C stocks that emerge from natural landscape pedogenic processes, resulting from elevation-induced climate gradients, erosion and soil textural patterns, and (2) assessing farm management and land-use effects on and their interactions with these biophysical patterns. Our findings revealed that the climate and soil texture gradients within the landscape led to an exponential increase in SOC with elevation moderated by slope gradient, indicating significant erosion processes. Farmers adapted their farm management according to the observed environmental patterns creating three distinct management zones. Differentiated agricultural management in these zones and asymmetrical distribution of land-uses in turn were observed to significantly influence soil and agroecosystem properties. For example, available P was found to be significantly higher in the upper and middle agricultural management zones (24.0 and 28.7 mg/kg, respectively), where agricultural inputs were higher compared to the lower agricultural management zone (8.9 mg/kg, P < 0.001). Mixed hedgerows, on the other hand, displayed significantly higher Shannon index scores for ground vegetation (1.8) and soil macrofauna (2.0) compared to agricultural land-uses (1.0 and 1.7). Our results provide important insights into how agroecosystem patterns and land management co-developed through complex environment, management, and land-use interactions.

    Live barriers and associated organic amendments mitigate land degradation and improve crop productivity in hillside agricultural systems of the Ecuadorian Andes
    Caulfield, Mark ; Groot, Jeroen C.J. ; Fonte, Steven J. ; Sherwood, Stephen ; Oyarzun, Pedro ; Borja, Ross Mary ; Dumble, Sam ; Tittonell, Pablo - \ 2020
    Land Degradation and Development (2020). - ISSN 1085-3278
    Andean alder - Andes - canary grass - Ecuador - erosion - nutrient depletion

    Land degradation caused by erosion and nutrient depletion in the Andes poses serious existential threats to small-scale farming. Although the potential of hedgerows to decrease water erosion is well recognised, their potential dual-use as a source of organic amendments to supplement farmer inputs is much less studied. The objective of this investigation was therefore to explore locally developed options for hedgerows that address these twin challenges. Experimental plots were installed to assess water erosion control by hedgerows and the effect of organic amendments harvested from the hedgerows on soil productivity, soil moisture, and soil fertility over the course of 2 years and three crop cycles (two of barley and one of rye). The experiment was conducted in two sites within the community at distinct elevations and associated biophysical contexts. At each site, four treatments were established, comparing a control treatment versus three types of hedgerows: (a) Andean alder, (b) canary grass strips, and (c) mixed canary grass and Andean alder. Results demonstrated that hedgerows and associated organic inputs comprised canary grass, and mixed canary grass and Andean alder reduced water erosion by 50–60% and increased biomass production by up to 1.1 Mg ha−1 and grain yield by up to 0.5 Mg ha−1. We conclude that although hedgerows are unlikely to produce sufficient quantities of organic resources to satisfy all nutrient input requirements, their potential to decrease erosion and supplement existing organic matter inputs indicates that they should be strongly considered as an option for improved agricultural management within this and similar resource constrained contexts.

    Genomic Regions Associated With Skeletal Type Traits in Beef and Dairy Cattle Are Common to Regions Associated With Carcass Traits, Feed Intake and Calving Difficulty
    Doyle, Jennifer L. ; Berry, Donagh P. ; Veerkamp, Roel F. ; Carthy, Tara R. ; Walsh, Siobhan W. ; Evans, Ross D. ; Purfield, Deirdre C. - \ 2020
    Frontiers in Genetics Livestock Genomics 11 (2020). - ISSN 1664-8021
    cattle - genome-wide association study - linear type traits - sequence - single nucleotide polymorphism - skeletal

    Linear type traits describing the skeletal characteristics of an animal are moderately to strongly genetically correlated with a range of other performance traits in cattle including feed intake, reproduction traits and carcass merit; thus, type traits could also provide useful insights into the morphological differences among animals underpinning phenotypic differences in these complex traits. The objective of the present study was to identify genomic regions associated with five subjectively scored skeletal linear traits, to determine if these associated regions are common in multiple beef and dairy breeds, and also to determine if these regions overlap with those proposed elsewhere to be associated with correlated performance traits. Analyses were carried out using linear mixed models on imputed whole genome sequence data separately in 1,444 Angus, 1,129 Hereford, 6,433 Charolais, 8,745 Limousin, 1,698 Simmental, and 4,494 Holstein-Friesian cattle, all scored for the linear type traits. There was, on average, 18 months difference in age at assessment of the beef versus the dairy animals. While the majority of the identified quantitative trait loci (QTL), and thus genes, were both trait-specific and breed-specific, a large-effect pleiotropic QTL on BTA6 containing the NCAPG and LCORL genes was associated with all skeletal traits in the Limousin population and with wither height in the Angus. Other than that, little overlap existed in detected QTLs for the skeletal type traits in the other breeds. Only two QTLs overlapped the beef and dairy breeds; both QTLs were located on BTA5 and were associated with height in both the Angus and the Holstein-Friesian, despite the difference in age at assessment. Several detected QTLs in the present study overlapped with QTLs documented elsewhere that are associated with carcass traits, feed intake, and calving difficulty. While most breeding programs select for the macro-traits like carcass weight, carcass conformation, and feed intake, the higher degree of granularity with selection on the individual linear type traits in a multi-trait index underpinning the macro-level goal traits, presents an opportunity to help resolve genetic antagonisms among morphological traits in the pursuit of the animal with optimum performance metrics.

    Genomic regions associated with muscularity in beef cattle differ in five contrasting cattle breeds
    Doyle, Jennifer L. ; Berry, Donagh P. ; Veerkamp, Roel F. ; Carthy, Tara R. ; Evans, Ross D. ; Walsh, Siobhán W. ; Purfield, Deirdre C. - \ 2020
    Genetics, Selection, Evolution 52 (2020)1. - ISSN 0999-193X - 1 p.

    BACKGROUND: Linear type traits, which reflect the muscular characteristics of an animal, could provide insight into how, in some cases, morphologically very different animals can yield the same carcass weight. Such variability may contribute to differences in the overall value of the carcass since primal cuts vary greatly in price; such variability may also hinder successful genome-based association studies. Therefore, the objective of our study was to identify genomic regions that are associated with five muscularity linear type traits and to determine if these significant regions are common across five different breeds. Analyses were carried out using linear mixed models on imputed whole-genome sequence data in each of the five breeds, separately. Then, the results of the within-breed analyses were used to conduct an across-breed meta-analysis per trait. RESULTS: We identified many quantitative trait loci (QTL) that are located across the whole genome and associated with each trait in each breed. The only commonality among the breeds and traits was a large-effect pleiotropic QTL on BTA2 that contained the MSTN gene, which was associated with all traits in the Charolais and Limousin breeds. Other plausible candidate genes were identified for muscularity traits including PDE1A, PPP1R1C and multiple collagen and HOXD genes. In addition, associated (gene ontology) GO terms and KEGG pathways tended to differ between breeds and between traits especially in the numerically smaller populations of Angus, Hereford, and Simmental breeds. Most of the SNPs that were associated with any of the traits were intergenic or intronic SNPs located within regulatory regions of the genome. CONCLUSIONS: The commonality between the Charolais and Limousin breeds indicates that the genetic architecture of the muscularity traits may be similar in these breeds due to their similar origins. Conversely, there were vast differences in the QTL associated with muscularity in Angus, Hereford, and Simmental. Knowledge of these differences in genetic architecture between breeds is useful to develop accurate genomic prediction equations that can operate effectively across breeds. Overall, the associated QTL differed according to trait, which suggests that breeding for a morphologically different (e.g. longer and wider versus shorter and smaller) more efficient animal may become possible in the future.

    Effects of three major protein sources on performance, gut morphology and fermentation characteristics in broilers
    Qaisrani, S.N. ; Krimpen, M.M. Van; Verstegen, M.W.A. ; Hendriks, W.H. ; Kwakkel, R.P. - \ 2020
    British Poultry Science 61 (2020)1. - ISSN 0007-1668
    (in-)digestible protein - broilers - caecal fermentation - gut morphology - performance

    1. This study determined the effects of three protein sources (PS), each at two digestibility crude protein (DCP) levels, on performance, gut morphology and fermentation characteristics in the hindgut of broilers. 2. It was hypothesised that broilers fed ingredients high in indigestible CP, i.e. rapeseed meal (RSM) or maize gluten (MG), could potentially cause reduced growth, impaired gut health, and more protein fermentation products in caecal digesta. Increasing the DCP level in each of the indigestible CP diets may compensate for these detrimental effects. 3. In total, 288 one-d-old male Ross 308 broilers were used in a completely randomised 3 × 2 factorial design, with six replicate pens per treatment. Three PS: soybean meal (SBM), rapeseed meal (RSM) or maize gluten (MG), and two DCP levels: 15.8 and 17.2% were used. 4. Broilers fed SBM had increased feed intake and BWG and improved FCR compared with those fed RSM and MG diets. Broilers fed high DCP had better performance compared with those on low DCP. No significant effects of PS or DCP level were found on gastrointestinal tract development, caecal ammonia or volatile fatty acid concentrations. 5. Broilers fed SBM had longer villi, smaller crypts and increased villus height to crypt depth ratio compared with those fed RSM and MG diets. Broilers fed RSM diet had a lower caecal pH, and had 16.5% and 14.9% more branched chain fatty acid contents in caecal digesta compared with those fed SBM and MG diets, respectively, indicating more proteolytic fermentation. 6. Replacing SBM by RSM and MG negatively affected growth performance and gut morphology. Hindgut protein fermentation was substantially increased in RSM fed birds. 7. To a certain extent, retarded growth performance in RSM and MG fed birds could be counterbalanced by increasing the dietary level of digestible CP.

    Overview of consumer analytical devices for gluten and allergen detection
    Ross, Georgina - \ 2019
    Going with the flow: the development of smartphone-based lateral/flow-through immunoassays for the high-speed detection of food allergens
    Ross, Georgina - \ 2019
    Working Group on Marine Mammal Ecology (WGMME)
    Gilles, Anita ; Galatius, Anders ; Aloha, Markus ; Authier, Matthieu ; Brasseur, S.M.J.M. ; Carlsson, A. ; Carlström, Julia ; Chaudry, Farah ; Culloch, Ross ; Evans, P. ; Geelhoed, S.C.V. ; Lehnert, Kristina ; Lundstrom, Karl ; Pierce, Graham J. ; Rogan, Emer ; Santos, Begona ; Neer, Abbo van - \ 2019
    Copenhagen : ICES (ICES Scientific Reports 22) - 133 p.
    Effect of Feeding Zero- or High-Tannin Faba Bean Cultivars and Dehulling on Growth Performance, Carcass Traits and Yield of Saleable Cuts of Broiler Chickens
    Cho, M. ; Smit, M.N. ; He, L. ; Kopmels, F.C. ; Beltranena, E. - \ 2019
    Journal of Applied Poultry Research 28 (2019)4. - ISSN 1056-6171 - p. 1305 - 1323.
    broiler chicken - carcass trait - convicine - dehulling - faba bean cultivars - growth performance - vicine

    Color-flowered, high-tannin faba bean (FB; Vicia faba) cultivars are more tolerant to frost around harvest time than white-flowered, zero-tannin cultivars. Tannins concentrated on the seed hull reduce both starch and protein digestibility. We therefore evaluated feeding 2 zero-tannin (Snowbird, Snowdrop) or 2 high-tannin (Fabelle, Malik) FB cultivars and the effect of dehulling to reduce tannin content on broiler growth performance, carcass traits, and yield of saleable cuts. Male Ross 708 chicks (n = 585) were fed 1 of 4 FB cultivars either non-dehulled or dehulled in starter (12%, 0–12 d), grower (24%, 13–25 d), and finisher (36%, 26–41 d) mash diets replacing soybean meal (SBM) and wheat grain (control diet). Overall, daily feed intake was greatest for Snowbird and Fabelle, and lowest for Malik; Snowdrop was intermediate. Daily weight gain was greater for Fabelle than other cultivars, and greater for control than FB cultivars. Gain-to-feed ratio (G:F) was greatest for Fabelle but lowest for Snowbird; Snowdrop was not different from Fabelle or Malik, and Malik was not different from Snowbird. Broiler G:F and chilled carcass weight were greater for controls than FB cultivars. Breast meat yield (BMY) was greater for Snowbird, and lower for Fabelle; Malik was not different from Snowbird or Snowdrop; Snowdrop was not different from Fabelle. Dehulling FB lowered BMY. Feeding broilers low-vicine/convicine high-tannin Fabelle resulted in slightly better growth performance but lower BMY than feeding zero-tannin cultivars or high-tannin Malik. Dehulling FB did not improve broiler growth performance or carcass dressing to the level of controls fed SBM-wheat only.

    A critical comparison between flow-through and lateral flow immunoassay formats for visual and smartphone-based multiplex allergen detection
    Ross, G.M. ; Salentijn, Gert ; Nielen, M.W.F. - \ 2019
    Biosensors 9 (2019)4. - ISSN 2079-6374 - 21 p.
    (1) Background: The lack of globally standardized allergen labeling legislation necessitates consumer-focused multiplexed testing devices. These should be easy to operate, fast, sensitive and robust. (2) Methods: Herein, we describe the development of three different formats for multiplexed food allergen detection, namely active and passive flow-through assays, and lateral flow immunoassays with different test line configurations. (3) Results: The fastest assay time was 1 min, whereas even the slowest assay was within 10 min. With the passive flow approach, the limits of detection (LOD) of 0.1 and 0.5 ppm for total hazelnut protein (THP) and total peanut protein (TPP) in spiked buffer were reached, or 1 and 5 ppm of THP and TPP spiked into matrix. In comparison, the active flow approach reached LODs of 0.05 ppm for both analytes in buffer and 0.5 and 1 ppm of THP and TPP spiked into matrix. The optimized LFIA configuration reached LODs of 0.1 and 0.5 ppm of THP and TPP spiked into buffer or 0.5 ppm for both analytes spiked into matrix. The optimized LFIA was validated by testing in 20 different blank and spiked matrices. Using device-independent color space for smartphone analysis, two different smartphone models were used for the analysis of optimized assays.
    Effects of dietary crude protein levels on ammonia emission, litter and manure composition, N losses, and water intake in broiler breeders
    Emous, R.A. van; Winkel, A. ; Aarnink, A.J.A. - \ 2019
    Poultry Science 98 (2019)12. - ISSN 0032-5791 - p. 6618 - 6625.
    ammonia emission - broiler breeder - dietary crude protein - litter and manure composition - N losses

    This study determined the effects of different dietary crude protein (CP) levels on ammonia emission (NH3), litter and manure composition, nitrogen (N) losses, and water intake in broiler breeders. A total of 480 females and 64 males (Ross 308) 20 wk of age were randomly allotted to 2 dietary treatments with 8 replicates of 30 females and 4 males per replicate. Birds were fed either high CP (CPh) or low CP diets (CPl) supplemented with free amino acids (AA). Both diets consisted of 3 sub-diets; 1 for each phase of the laying period. Diets were formulated to be iso-caloric and calculated CP content of the CPl diets was 15 g/kg lower than the CPh diets (Breeder 1 (23 to 34 wk): 135 vs. 150, Breeder 2 (35 to 46 wk): 125 vs. 140 and Breeder 3 (47 to 60 wk of age): 115 vs. 130 g/kg, respectively). Pens consisted of an elevated slatted floor (25% of the floor surface) and a litter floor. Water and feed intake were recorded daily. Litter (floor) and manure (below slatted floor) composition and ammonia concentration were measured at 34, 44, and 54 wk of age. Ammonia concentration was measured using a flux chamber on top of the litter or manure. Estimated N losses were calculated. Dietary protein level did not affect water intake and dry matter (DM) content of the litter or manure. Compared to birds fed the CPh diets, the litter and manure samples of broiler breeders fed the CPl had 8% lower total-N and 13% lower ammonia-N content resulting in a 9% lower ammonia concentration, 9% lower ammonia emission, and 11% lower total-N losses. In conclusion, this study shows that reducing CP level in the diet of broiler breeders reduces ammonia emission and total N-losses from litter and manure.

    Critical assessment of recent trends related to screening and confirmatory analytical methods for selected food contaminants and allergens
    Tsagkaris, A.S. ; Nelis, J.L.D. ; Ross, G.M.S. ; Jafari, S. ; Guercetti, J. ; Kopper, K. ; Zhao, Y. ; Rafferty, K. ; Salvador, J.P. ; Migliorelli, D. ; Salentijn, G. ; Campbell, K. ; Marco, M.P. ; Elliot, C.T. ; Nielen, M.W.F. ; Pulkrabova, J. ; Hajslova, J. - \ 2019
    TrAC : Trends in Analytical Chemistry 121 (2019). - ISSN 0165-9936
    Confirmatory methods - EU legal framework - Food contaminants - Inventory - Screening methods - Smartphones

    Food contaminants monitoring is conducted in an intensive manner yet, there are still food safety scandals related to various chemical compounds. This fact highlights the need to review the requirements posed by the current legal framework on analytical methods performance and evaluate its application in published studies. Herein, we present an inventory including more than 470 publications on screening and confirmatory methods, which were used to control hazardous compounds such as pesticides, antibiotics, mycotoxins, aquatic toxins and allergens. Analytical performance characteristics, trends and state of the art, both merits and shortcomings, are critically discussed and summarized in excel tabulations. This repository highlights the ever-increasing use of screening methods and the necessity to confirm their performance by applying confirmatory methods. In conclusion, more effort is needed on validation and benchmarking, especially of newly developed technology such as smartphone-based methods, to avoid false-negative results and ensure that methods fit for purpose.

    Effect of challenge dose of plasmid-mediated extended-spectrum β-lactamase and AmpC β-lactamase producing Escherichia coli on time-until-colonization and level of excretion in young broilers
    Dame-Korevaar, Anita ; Fischer, Egil A.J. ; Goot, Jeanet van der; Velkers, Francisca ; Broek, Jan van den; Veldman, Kees ; Ceccarelli, Daniela ; Mevius, Dik ; Stegeman, Arjan - \ 2019
    Veterinary Microbiology 239 (2019). - ISSN 0378-1135
    Animal model - Antibiotic resistance - Dose-response - Inoculation - Poultry - Transmission

    Plasmid-mediated extended-spectrum β-lactamase and AmpC β-lactamase (ESBL/pAmpC) producing bacteria are present at all levels of the broiler production pyramid. Young birds can be found positive for ESBL/pAmpC-producing Escherichia coli shortly after arrival at farm. The aim of this study was to determine the effect of different challenge doses of ESBL/pAmpC-producing E. coli on time-until-colonization and the level of excretion in young broilers. One-day-old broilers (specific-pathogen free (SPF) and conventional Ross 308) were housed in isolators and challenged with 0.5 ml ESBL/pAmpC-producing E. coli strains of varying doses (101–105 CFU/ml). Presence and concentration (CFU/gram feces) of ESBL/pAmpC-producing E. coli and total E. coli were determined longitudinally from cloacal swabs, and in cecal content 72 h after challenge. Higher challenge doses resulted in shorter time-until-colonization. However, even the lowest dose (101 CFU/ml) resulted in colonization of the broilers which excreted >106 CFU/gram feces 72 h after inoculation. Conventional broilers were colonized later than SPF broilers, although within 72 h after challenge all broilers were excreting ESBL/pAmpC-producing E. coli. A probabilistic model was used to estimate the probability of colonization by initial inoculation or transmission. The higher the dose the higher the probability of excreting ESBL/pAmpC-producing E. coli as a result of inoculation. In conclusion, low initial doses of ESBL/pAmpC-producing E. coli can result in rapid colonization of a flock. Interventions should thus be aimed to eliminate ESBL/pAmpC-producing bacteria in the environment of the hatchlings and measures focusing at reducing colonization and transmission of ESBL/pAmpC-producing E. coli should be applied shortly after hatching.

    Associations between carcass weight uniformity and production measures on farm and at slaughter in commercial broiler flocks
    Vasdal, Guro ; Granquist, Erik Georg ; Skjerve, Eystein ; Jong, Ingrid C. de; Berg, Charlotte ; Michel, Virginie ; Moe, Randi Oppermann - \ 2019
    Poultry Science 98 (2019)10. - ISSN 0032-5791 - p. 4261 - 4268.
    chicken - health - indicator - poultry - welfare

    In poultry flocks, flock weight uniformity is often defined as the percent individuals within 10% of the mean body weight (BW) and the variability of this uniformity can be expressed as the CV of BW. Flock weight uniformity is a standardized and objective measured, and could potentially be used as a welfare indicator; however, little is known about the relationship between flock uniformity and other production measures on-farm or at slaughter. The aim of this study was to investigate the associations between carcass weight uniformity (CV of BW) and production measures on-farm and at slaughter in Norwegian commercial broiler flocks. A total of 45 randomly selected mixed-sex Ross 308 broiler flocks were visited prior to slaughter at 28 to 30 D of age (average slaughter age 30.6 D). All flocks were raised under similar farm management systems. The Welfare Quality protocol for broilers was used to assess different animal welfare indicators in each flock. All production data from the slaughterhouse were collected for each flock, including carcass weight uniformity (%), mortality (%), growth rate (g), feed conversion ratio (FCR), and rejected birds (%) in different rejection categories. Univariable and multivariable linear regression models were used to investigate the associations between flock weight uniformity and production and welfare measures. The results showed that flock uniformity varied from 11% to 18% between flocks within the same hybrid, similar management standards, and similar slaughter age (day 29 to 32). Poorer uniformity (i.e., high CV) was associated with increased first week mortality (P < 0.004, r = 1.48, increased total mortality (P < 0.013, r = 0.01), increased FCR (i.e., less efficient growth) (P < 0.024, r = 0.06), reduced growth rate (P < 0.0012, r = -0.01), and a reduced rejection rate at slaughter (P < 0.006, r = -0.01). The results show that flock uniformity varies across broiler flocks, and is associated with several production measures.

    Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe
    Frantz, Laurent A.F. ; Haile, James ; Lin, Audrey T. ; Scheu, Amelie ; Geörg, Christina ; Benecke, Norbert ; Alexander, Michelle ; Linderholm, Anna ; Mullin, Victoria E. ; Daly, Kevin G. ; Battista, Vincent M. ; Price, Max ; Gron, Kurt J. ; Alexandri, Panoraia ; Arbogast, Rose Marie ; Arbuckle, Benjamin ; Bǎlǎşescu, Adrian ; Barnett, Ross ; Bartosiewicz, László ; Baryshnikov, Gennady ; Bonsall, Clive ; Borić, Dušan ; Boroneanţ, Adina ; Bulatović, Jelena ; Çakirlar, Canan ; Carretero, José Miguel ; Chapman, John ; Church, Mike ; Crooijmans, Richard ; Cupere, Bea De; Detry, Cleia ; Dimitrijevic, Vesna ; Dumitraşcu, Valentin ; Plessis, Louis Du; Edwards, Ceiridwen J. ; Erek, Cevdet Merih ; Erim-Özdoǧan, Asli ; Ervynck, Anton ; Fulgione, Domenico ; Gligor, Mihai ; Götherström, Anders ; Gourichon, Lionel ; Groenen, Martien A.M. ; Helmer, Daniel ; Hongo, Hitomi ; Horwitz, Liora K. ; Irving-Pease, Evan K. ; Lebrasseur, Ophélie ; Lesur, Joséphine ; Malone, Caroline ; Manaseryan, Ninna ; Marciniak, Arkadiusz ; Martlew, Holley ; Mashkour, Marjan ; Matthews, Roger ; Matuzeviciute, Giedre Motuzaite ; Maziar, Sepideh ; Meijaard, Erik ; McGovern, Tom ; Megens, Hendrik Jan ; Miller, Rebecca ; Mohaseb, Azadeh Fatemeh ; Orschiedt, Jörg ; Orton, David ; Papathanasiou, Anastasia ; Pearson, Mike Parker ; Pinhasi, Ron ; Radmanović, Darko ; Ricaut, François Xavier ; Richards, Mike ; Sabin, Richard ; Sarti, Lucia ; Schier, Wolfram ; Sheikhi, Shiva ; Stephan, Elisabeth ; Stewart, John R. ; Stoddart, Simon ; Tagliacozzo, Antonio ; Tasić, Nenad ; Trantalidou, Katerina ; Tresset, Anne ; Valdiosera, Cristina ; Hurk, Youri Van Den; Poucke, Sophie Van; Vigne, Jean Denis ; Yanevich, Alexander ; Zeeb-Lanz, Andrea ; Triantafyllidis, Alexandros ; Gilbert, M.T.P. ; Schibler, Jörg ; Rowley-Conwy, Peter ; Zeder, Melinda ; Peters, Joris ; Cucchi, Thomas ; Bradley, Daniel G. ; Dobney, Keith ; Burger, Joachim ; Evin, Allowen ; Girdland-Flink, Linus ; Larson, Greger - \ 2019
    Proceedings of the National Academy of Sciences of the United States of America 116 (2019)35. - ISSN 0027-8424 - p. 17231 - 17238.
    Domestication - Evolution - Gene flow - Neolithic

    Archaeological evidence indicates that pig domestication had begun by ∼10,500 y before the present (BP) in the Near East, and mitochondrial DNA (mtDNA) suggests that pigs arrived in Europe alongside farmers ∼8,500 y BP. A few thousand years after the introduction of Near Eastern pigs into Europe, however, their characteristic mtDNA signature disappeared and was replaced by haplotypes associated with European wild boars. This turnover could be accounted for by substantial gene flow from local European wild boars, although it is also possible that European wild boars were domesticated independently without any genetic contribution from the Near East. To test these hypotheses, we obtained mtDNA sequences from 2,099 modern and ancient pig samples and 63 nuclear ancient genomes from Near Eastern and European pigs. Our analyses revealed that European domestic pigs dating from 7,100 to 6,000 y BP possessed both Near Eastern and European nuclear ancestry, while later pigs possessed no more than 4% Near Eastern ancestry, indicating that gene flow from European wild boars resulted in a near-complete disappearance of Near East ancestry. In addition, we demonstrate that a variant at a locus encoding black coat color likely originated in the Near East and persisted in European pigs. Altogether, our results indicate that while pigs were not independently domesticated in Europe, the vast majority of human-mediated selection over the past 5,000 y focused on the genomic fraction derived from the European wild boars, and not on the fraction that was selected by early Neolithic farmers over the first 2,500 y of the domestication process.

    Effects of dietary organic minerals, fish oil, and hydrolyzed collagen on growth performance and tibia characteristics of broiler chickens
    Guz, Bahadir ; Molenaar, R. ; Jong, I.C. de; Kemp, B. ; Brand, H. van den; Krimpen, M.M. van - \ 2019
    Poultry Science 98 (2019)12. - ISSN 0032-5791 - p. 6552 - 6563.
    Nutrition is a crucial factor for growth and bone development in broiler chickens. Adjustments in dietary ingredients might affect bone development and consequently locomotion related problems. This study was designed to evaluate effects of dietary organic minerals (ORM), fish oil (FISH), and hydrolyzed collagen (COL) on growth performance and tibia characteristics of broiler chickens. A total of three hundred eighty four 1-day-old Ross 308 male broiler chickens were used in a complete randomized block design with 4 diet groups and 8 replicates per diet group. In the ORM diet, the inorganic macro and trace minerals were replaced by their organic varieties. In the FISH diet, palm oil and soybean oil were partly replaced by FISH. In the COL diet, soybean meal was partly replaced by COL. Results showed that the ORM and COL diet groups reached a higher body weight (BW) at 42 D of age than the FISH diet group, whereas the control group was in between. The feed conversion ratio between day 1 and 42 was lower in the ORM and COL diet groups than in both other diet groups. On day 28, 35, and 42, gait score (GS), Varus Valgus deformity, tibia length (TL), thickness, femoral and metatarsal head thickness (THT), mineral content (TMC), mineral density (TMD), breaking strength (TBS), stiffness (TSF), and energy to fracture (TEF) were measured (n = 3/replicate). The ORM diet group had higher TL at day 42, higher THT at day 28, higher TMC at day 42, higher TMD at day 28, 35, and 42, higher TBS at day 42, higher TSF at day 35 and 42, and higher TEF at day 42 compared to the FISH diet group, with the COL and control diet groups in between. It can be concluded that replacing dietary inorganic macro and trace minerals by their organic varieties seems to stimulate tibia dimensions, strength, and mineral content of broiler chickens. On the contrary, FISH appears to negatively affect tibia characteristics.

    Twenty-three unsolved problems in hydrology (UPH)–a community perspective
    Blöschl, Günter ; Bierkens, Marc F.P. ; Chambel, Antonio ; Cudennec, Christophe ; Destouni, Georgia ; Fiori, Aldo ; Kirchner, James W. ; McDonnell, Jeffrey J. ; Savenije, Hubert H.G. ; Sivapalan, Murugesu ; Stumpp, Christine ; Toth, Elena ; Volpi, Elena ; Carr, Gemma ; Lupton, Claire ; Salinas, Josè ; Széles, Borbála ; Viglione, Alberto ; Aksoy, Hafzullah ; Allen, Scott T. ; Amin, Anam ; Andréassian, Vazken ; Arheimer, Berit ; Aryal, Santosh K. ; Baker, Victor ; Bardsley, Earl ; Barendrecht, Marlies H. ; Bartosova, Alena ; Batelaan, Okke ; Berghuijs, Wouter R. ; Beven, Keith ; Blume, Theresa ; Bogaard, Thom ; Borges de Amorim, Pablo ; Böttcher, Michael E. ; Boulet, Gilles ; Breinl, Korbinian ; Brilly, Mitja ; Brocca, Luca ; Buytaert, Wouter ; Castellarin, Attilio ; Castelletti, Andrea ; Chen, Xiaohong ; Chen, Yangbo ; Chen, Yuanfang ; Chifflard, Peter ; Claps, Pierluigi ; Clark, Martyn P. ; Collins, Adrian L. ; Croke, Barry ; Dathe, Annette ; David, Paula C. ; Barros, Felipe P.J. de; Rooij, Gerrit de; Baldassarre, Giuliano Di; Driscoll, Jessica M. ; Duethmann, Doris ; Dwivedi, Ravindra ; Eris, Ebru ; Farmer, William H. ; Feiccabrino, James ; Ferguson, Grant ; Ferrari, Ennio ; Ferraris, Stefano ; Fersch, Benjamin ; Finger, David ; Foglia, Laura ; Fowler, Keirnan ; Gartsman, Boris ; Gascoin, Simon ; Gaume, Eric ; Gelfan, Alexander ; Geris, Josie ; Gharari, Shervan ; Gleeson, Tom ; Glendell, Miriam ; Gonzalez Bevacqua, Alena ; González-Dugo, María P. ; Grimaldi, Salvatore ; Gupta, A.B. ; Guse, Björn ; Han, Dawei ; Hannah, David ; Harpold, Adrian ; Haun, Stefan ; Heal, Kate ; Helfricht, Kay ; Herrnegger, Mathew ; Hipsey, Matthew ; Hlaváčiková, Hana ; Hohmann, Clara ; Holko, Ladislav ; Hopkinson, Christopher ; Hrachowitz, Markus ; Illangasekare, Tissa H. ; Inam, Azhar ; Innocente, Camyla ; Istanbulluoglu, Erkan ; Jarihani, Ben ; Kalantari, Zahra ; Kalvans, Andis ; Khanal, Sonu ; Khatami, Sina ; Kiesel, Jens ; Kirkby, Mike ; Knoben, Wouter ; Kochanek, Krzysztof ; Kohnová, Silvia ; Kolechkina, Alla ; Krause, Stefan ; Kreamer, David ; Kreibich, Heidi ; Kunstmann, Harald ; Lange, Holger ; Liberato, Margarida L.R. ; Lindquist, Eric ; Link, Timothy ; Liu, Junguo ; Loucks, Daniel Peter ; Luce, Charles ; Mahé, Gil ; Makarieva, Olga ; Malard, Julien ; Mashtayeva, Shamshagul ; Maskey, Shreedhar ; Mas-Pla, Josep ; Mavrova-Guirguinova, Maria ; Mazzoleni, Maurizio ; Mernild, Sebastian ; Misstear, Bruce Dudley ; Montanari, Alberto ; Müller-Thomy, Hannes ; Nabizadeh, Alireza ; Nardi, Fernando ; Neale, Christopher ; Nesterova, Nataliia ; Nurtaev, Bakhram ; Odongo, Vincent O. ; Panda, Subhabrata ; Pande, Saket ; Pang, Zhonghe ; Papacharalampous, Georgia ; Perrin, Charles ; Pfister, Laurent ; Pimentel, Rafael ; Polo, María J. ; Post, David ; Prieto Sierra, Cristina ; Ramos, Maria Helena ; Renner, Maik ; Reynolds, José Eduardo ; Ridolfi, Elena ; Rigon, Riccardo ; Riva, Monica ; Robertson, David E. ; Rosso, Renzo ; Roy, Tirthankar ; Sá, João H.M. ; Salvadori, Gianfausto ; Sandells, Mel ; Schaefli, Bettina ; Schumann, Andreas ; Scolobig, Anna ; Seibert, Jan ; Servat, Eric ; Shafiei, Mojtaba ; Sharma, Ashish ; Sidibe, Moussa ; Sidle, Roy C. ; Skaugen, Thomas ; Smith, Hugh ; Spiessl, Sabine M. ; Stein, Lina ; Steinsland, Ingelin ; Strasser, Ulrich ; Su, Bob ; Szolgay, Jan ; Tarboton, David ; Tauro, Flavia ; Thirel, Guillaume ; Tian, Fuqiang ; Tong, Rui ; Tussupova, Kamshat ; Tyralis, Hristos ; Uijlenhoet, Remko ; Beek, Rens van; Ent, Ruud J. van der; Ploeg, Martine van der; Loon, Anne F. Van; Meerveld, Ilja van; Nooijen, Ronald van; Oel, Pieter R. van; Vidal, Jean Philippe ; Freyberg, Jana von; Vorogushyn, Sergiy ; Wachniew, Przemyslaw ; Wade, Andrew J. ; Ward, Philip ; Westerberg, Ida K. ; White, Christopher ; Wood, Eric F. ; Woods, Ross ; Xu, Zongxue ; Yilmaz, Koray K. ; Zhang, Yongqiang - \ 2019
    Hydrological Sciences Journal 64 (2019)10. - ISSN 0262-6667 - p. 1141 - 1158.
    hydrology - interdisciplinary - knowledge gaps - research agenda - science questions

    This paper is the outcome of a community initiative to identify major unsolved scientific problems in hydrology motivated by a need for stronger harmonisation of research efforts. The procedure involved a public consultation through online media, followed by two workshops through which a large number of potential science questions were collated, prioritised, and synthesised. In spite of the diversity of the participants (230 scientists in total), the process revealed much about community priorities and the state of our science: a preference for continuity in research questions rather than radical departures or redirections from past and current work. Questions remain focused on the process-based understanding of hydrological variability and causality at all space and time scales. Increased attention to environmental change drives a new emphasis on understanding how change propagates across interfaces within the hydrological system and across disciplinary boundaries. In particular, the expansion of the human footprint raises a new set of questions related to human interactions with nature and water cycle feedbacks in the context of complex water management problems. We hope that this reflection and synthesis of the 23 unsolved problems in hydrology will help guide research efforts for some years to come.

    Effect of low protein diets supplemented with free amino acids on growth performance, slaughter yield, litter quality, and footpad lesions of male broilers
    Harn, J. van; Dijkslag, M.A. ; Krimpen, M.M. van - \ 2019
    Poultry Science 98 (2019)10. - ISSN 0032-5791 - p. 4868 - 4877.
    A study with 884 Ross 308 male broilers, housed in 68 floor pens (0.75 m2) from 0 to 35 days of age was conducted to evaluate the effects of low crude protein (CP) diets, with partial replacement of soybean meal by free amino acids (AA), on performance, slaughter yields, litter quality and footpad lesions. During the first 11 d, all broilers received the same control starter diet (216 g/kg CP, 11.5 g/kg apparent fecal digestible (AFD) lysine, and 2900 kcal/kg AMEn). Thereafter, four experimental feeding programs with different levels of dietary CP (control and control with 1% (CP-1%), 2% (CP-2%) and 3% (CP-3%) less CP units) were provided in both the grower and finisher phase. In the control grower and finisher diet, the CP content was 208 and 198 g/kg, respectively. All diets were formulated to meet or exceed the recommendations concerning AFD AA, and to be iso-caloric within each feeding phase. Feed and water were provided for ad libitum intake during the entire experimental period.

    None of the low CP feeding programs affected body weight gain, feed intake or mortality from 0 to 35 d. However, CP conversion was improved with the reduction of CP content of the diet. Broilers fed the CP-2% or CP-3% feeding program had an improved feed conversion ratio. Broilers fed the low CP protein feeding programs had a better litter quality and less footpad lesions, compared to broilers fed the control feeding program. Broilers fed the CP-3% feeding program had a lower breast meat yield than broilers fed the control feeding program. Slaughter yields of broilers fed CP-1% or CP-2% feeding program did not differ from the control feeding program. This study demonstrated that the CP content of grower and finisher diets can be reduced by 2.2–2.3% units without adverse effects on growth performance of broilers, while CP reduction seems promising to reduce nitrogen excretion from broiler houses, improve bird welfare, and reduces dependence on vegetable protein sources.
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