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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    Task 2: Analysis of the MS replies to the EEA request for inventorying existing LU information in the countries : D2 - Report containing an assessment of the LU inventory by MS, including an assessment on the impact of existing / missing LU parameters for the creation of CLC+ LULUCF and Legacy instances
    Hazeu, G.W. ; Vittek, Marian ; Kosztra, B. ; Bock, M. ; Kleeschulte, S. ; Costa, H. ; Caetano, M. ; Marcelino, F. ; Smith, G.M. - \ 2020
    EEA - 78 p.
    Implementation of CLC+ based on the EAGLE concept –
    additional support for further development of CLC+ databases (CLC+ and CLC+ instances, namely CLC+ LULUCF instance and CLC+ Legacy instance)
    Genomic Breeding Programs Realize Larger Benefits by Cooperation in the Presence of Genotype × Environment Interaction Than Conventional Breeding Programs
    Cao, Lu ; Liu, Huiming ; Mulder, Han A. ; Henryon, Mark ; Thomasen, Jørn Rind ; Kargo, Morten ; Sørensen, Anders Christian - \ 2020
    Frontiers in Genetics Livestock Genomics 11 (2020). - ISSN 1664-8021
    across-environment selection of sires - genetic gain - joint genetic evaluation - long-term cooperation - rate of inbreeding - stochastic simulation

    Genotype × environment interaction (G × E) is of increasing importance for dairy cattle breeders due to international multiple-environment selection of animals as well as the differentiation of production environments within countries. This theoretical simulation study tested the hypothesis that genomic selection (GS) breeding programs realize larger genetic benefits by cooperation in the presence of G × E than conventional pedigree-based selection (PS) breeding programs. We simulated two breeding programs each with their own cattle population and environment. Two populations had either equal or unequal population sizes. Selection of sires was done either across environments (cooperative) or within their own environment (independent). Four scenarios, (GS/PS) × (cooperative/independent), were performed. The genetic correlation (rg) between the single breeding goal trait expressed in two environments was varied between 0.5 and 0.9. We compared scenarios for genetic gain, rate of inbreeding, proportion of selected external sires, and the split-point rg that is the lowest value of rg for long-term cooperation. Between two equal-sized populations, cooperative GS breeding programs achieved a maximum increase of 19.3% in genetic gain and a maximum reduction of 24.4% in rate of inbreeding compared to independent GS breeding programs. The increase in genetic gain and the reduction in rate of inbreeding realized by GS breeding programs with cooperation were respectively at maximum 9.7% and 24.7% higher than those realized by PS breeding programs with cooperation. Secondly, cooperative GS breeding programs allowed a slightly lower split-point rg than cooperative PS breeding programs (0.85∼0.875 vs ≥ 0.9). Between two unequal-sized populations, cooperative GS breeding programs realized higher increase in genetic gain and showed greater probability for long-term cooperation than cooperative PS breeding programs. Secondly, cooperation using GS were more beneficial to the small population while also beneficial but much less to the large population. In summary, by cooperation in the presence of G × E, GS breeding programs realize larger improvements in terms of the genetic gain and rate of inbreeding, and have greater possibility of long-term cooperation than conventional PS breeding programs. Therefore, we recommend cooperative GS breeding programs in situations with mild to moderate G × E, depending on the sizes of two populations.

    Better pens mean better pigs
    Luo, Lu - \ 2020
    Optimum strip width increases dry matter, nutrient accumulation, and seed yield of intercrops under the relay intercropping system
    Raza, Muhammad Ali ; Feng, Ling Yang ; Werf, Wopke van der; Iqbal, Nasir ; Khan, Imran ; Khan, Ahsin ; Din, Atta Mohi Ud ; Naeem, Muhammd ; Meraj, Tehseen Ahmad ; Hassan, Muhammad Jawad ; Khan, Aaqil ; Lu, Feng Zhi ; Liu, Xin ; Ahmed, Mukhtar ; Yang, Feng ; Yang, Wenyu - \ 2020
    Food and Energy Security 9 (2020)2. - ISSN 2048-3694
    competition ratio - growing space - maize - relay intercropping - soybean

    Strip width management is a critical factor for producing higher crop yields in relay intercropping systems. A 2-year field experiment was carried out during 2012 and 2013 to evaluate the effects of different strip width treatments on dry-matter production, major-nutrient (nitrogen, phosphorus, and potassium) uptake, and competition parameters of soybean and maize in relay intercropping system. The strip width (SW) treatments were 0.40, 0.40, and 0.40 m (SW1); 0.40, 0.40, and 0.50 m (SW2); 0.40, 0.40, and 0.60 m (SW3); and 0.40, 0.40, and 0.70 m (SW4) for soybean row spacing, maize row spacing, and spacing between soybean and maize rows, respectively. As compared to sole maize (SM) and sole soybean (SS), relay-intercropped maize and soybean accumulated lower quantities of nitrogen, phosphorus, and potassium in all treatments. However, maize in SW1 accumulated higher nitrogen, phosphorus, and potassium than SW4 (9%, 9%, and 8% for nitrogen, phosphorus, and potassium, respectively). Soybean in SW3 accumulated 25% higher nitrogen, 33% higher phosphorus, and 24% higher potassium than in SW1. The improved nutrient accumulation in SW3 significantly increased the soybean dry matter by 19%, but slightly decreased the maize dry matter by 6% compared to SW1. Similarly, SW3 increased the competition ratio value of soybean (by 151%), but it reduced the competition ratio value of maize (by 171%) compared to SW1. On average, in SW3, relay-cropped soybean produced 84% of SS seed yield and maize produced 98% of SM seed yield and achieved the land equivalent ratio of 1.8, demonstrating the highest level in the world. Overall, these results suggested that by selecting the appropriate strip width (SW3; 0.40 m for soybean row spacing, 0.40 m maize row spacing, and 0.60 m spacing between soybean and maize rows), we can increase the nutrient uptake (especially nitrogen, phosphorus, and potassium), dry-matter accumulation, and seed yields of relay-intercrop species under relay intercropping systems.

    Neighbourhood fast food exposure and consumption: the mediating role of neighbourhood social norms
    Rongen, Sofie Van; Poelman, Maartje P. ; Thornton, Lukar ; Abbott, Gavin ; Lu, Meng ; Kamphuis, Carlijn B.M. ; Verkooijen, Kirsten ; Vet, Emely De - \ 2020
    International journal of behavioral nutrition and physical activity 17 (2020)1. - ISSN 1479-5868
    Background: The association between the residential fast food environment and diet has gained growing attention. However, why the food environment affects food consumption is under-examined. This study aimed to investigate neighbourhood social norms with respect to fast food consumption as a potential mediating pathway between residential fast food outlet exposure and residents’ fast food consumption.

    Methods: A correlational study was conducted in which a nationwide sample of 1038 respondents living across The Netherlands completed a survey. Respondents reported their fast food consumption (amount/week) as well as perceived descriptive and injunctive norms regarding fast food consumption in their neighbourhood. Fast food outlet exposure was measured by the average count of fast food outlets within a 400 m walking distance buffer around the zip-codes of the respondents, using a retail outlet database. Regression models were used to assess associations between residential fast food outlet exposure, fast food consumption, and social norm perceptions, and a bootstrapping procedure was used to test the indirect -mediation- effect. Separate analyses were performed for descriptive norms and injunctive norms.

    Results: There was no overall or direct association between residential fast food outlet exposure and residents’ fast food consumption. However, fast food outlet exposure was positively associated with neighbourhood social norms (descriptive and injunctive) regarding fast food consumption, which in turn were positively associated with the odds of consuming fast food. Moreover, results of the bootstrapped analysis provided evidence of indirect effects of fast food outlet exposure on fast food consumption, via descriptive norms and injunctive norms.

    Conclusions: In neighbourhoods with more fast food outlets, residents were more likely to perceive fast food consumption in the neighbourhood as more common and appropriate. In turn, stronger neighbourhood social norms were associated with higher fast food consumption. Acknowledging the correlational design, this study is the first that implies that neighbourhood social norms may be a mediating pathway in the relation between the residential fast food environment and fast food consumption. Future research may examine the role of neighbourhood social norms in other contexts and explore how the changing food environment may shift our consumption norms.
    Metagenomic-and cultivation-based exploration of anaerobic chloroform biotransformation in hypersaline sediments as natural source of chloromethanes
    Peng, Peng ; Lu, Yue ; Bosma, Tom N.P. ; Nijenhuis, Ivonne ; Nijsse, Bart ; Shetty, Sudarshan A. ; Ruecker, Alexander ; Umanets, Alexander ; Ramiro-Garcia, Javier ; Kappler, Andreas ; Sipkema, Detmer ; Smidt, Hauke ; Atashgahi, Siavash - \ 2020
    Microorganisms 8 (2020)5. - ISSN 2076-2607
    Biotransformation - Chloroform - Hypersaline lakes - Metagenome

    Chloroform (CF) is an environmental contaminant that can be naturally formed in various environments ranging from forest soils to salt lakes. Here we investigated CF removal potential in sediments obtained from hypersaline lakes in Western Australia. Reductive dechlorination of CF to dichloromethane (DCM) was observed in enrichment cultures derived from sediments of Lake Strawbridge, which has been reported as a natural source of CF. No CF removal was observed in abiotic control cultures without artificial electron donors, indicating biotic CF dechlorination in the enrichment cultures. Increasing vitamin B12 concentration from 0.04 to 4 µM in enrichment cultures enhanced CF removal and reduced DCM formation. In cultures amended with 4 µM vitamin B12 and13C labelled CF, formation of13CO2 was detected. Known organohalide-respiring bacteria and reductive dehalogenase genes were neither detected using quantitative PCR nor metagenomic analysis of the enrichment cultures. Rather, members of the order Clostridiales, known to co-metabolically transform CF to DCM and CO2, were detected. Accordingly, metagenome-assembled genomes of Clostridiales encoded enzymatic repertoires for the Wood-Ljungdahl pathway and cobalamin biosynthesis, which are known to be involved in fortuitous and nonspecific CF transformation. This study indicates that hypersaline lake microbiomes may act as a filter to reduce CF emission to the atmosphere.

    Prevalence of coeliac disease in Northwest China: heterogeneity across Northern Silk road ethnic populations
    Zhou, Chunyan ; Gao, Feng ; Gao, Jinyan ; Yuan, Juanli ; Lu, Jiajie ; Sun, Zhenzhu ; Xu, Mengyu ; Engel, J. ; Hui, Wenjia ; Gilissen, L.J.W.J. ; Chen, Hongbing - \ 2020
    Alimentary Pharmacology and Therapeutics 51 (2020)11. - ISSN 0269-2813 - p. 1116 - 1129.
    Background: Epidemiological data of coeliac disease are lacking from the central Asian region. Aims: To verify the occurrence of coeliac disease amongst four major ethnic groups of Xinjiang Uyghur Autonomus Region, China. Methods: 2277 in-patients with gastrointestinal symptoms (1391 Han, 608 Uyghur, 146 Kazakh and 132 Hui; mean age: 54 ± 12.8 years) were included. Total IgA, anti-deamidated gliadin peptide (DGP)-IgG, and anti-tissue transglutaminase (anti-tTG)-IgA were analysed. All antibody-positive subjects were further tested for endomysial (EMA) antibodies and were HLA genotyped. All subjects with antibody positivity were asked to undergo intestinal biopsy. In addition, a subset of antibody-negative subjects were tested for HLA-DQA1and DQB1. Results: Among the 2277 subjects, 29 subjects were defined as coeliac disease au-toimmune (positive results for anti-tTG IgA and EMA-IgA) (1.27%; 95% confidence interval, 0.81%-1.73%), eight of them underwent biopsy and all showed coeliac dis-ease histology (0.35%; 95% Cl, 0.11%-0.59%). The frequency of coeliac disease au-toimmunity was lowest among the Han (0.79%), followed by the Uyghur (1.81%), the Kazakh (2.05%) and the Hui (3.03%). The frequency of the HLA-DQ2 and/or DQ8 haplotype was highest in the Uyghur (52.1%), followed by the Hui (44.4%), the Kazakh (40.0%) and the Han (39.4%). Besides, a three times higher frequency of coeliac dis-ease autoimmunity was found among rural living subjects with significantly higher wheat consumption compared to urban living subjects (3.16% vs 0.97%, P < 0.01). Conclusions: In Xinjiang, coeliac disease does occur, especially in the rural area. The HLA haplotype and environment play key roles in the development of coeliac disease.
    Valuation of Wetland Ecosystem Services in National Nature Reserves in China’s Coastal Zones
    Li, Xiaowei ; Yu, Xiubo ; Hou, Xiyong ; Liu, Yubin ; Li, Hui ; Zhou, Yangming ; Xia, Shaoxia ; Liu, Yu ; Duan, Houlang ; Wang, Yuyu ; Dou, Yuehan ; Yang, Meng ; Zhang, Li - \ 2020
    Sustainability 12 (2020)8. - ISSN 2071-1050
    Wetlands provide ecosystem services for regional development, and, thus, have considerable economic value. In this study, a combination of evaluation methods was carried out to evaluate the wetland ecosystem services provided by national nature reserves in 11 coastal provinces/municipalities in China. We constructed a literature database containing 808observations (over 170 papers) on field-scale research for wetlands in China’s coastal zones. Using this literature database, as well as land use (LU) data, net primary productivity (NPP), and statistical data, and digital elevation model (DEM) data, we established a valuation framework and database for nine important ecosystem services of the 13 wetland types in the study area. After the large-scale academic literature review, the ordinary kriging offered by Geostatistical Analyst tools was used to interpolate the physical dimensions of the unmeasured locations. The results showed that: 1) the wetland ecosystem services in 35 national nature reserves have a total value of 33.168billion USD/year; 2) the values of wetland ecosystem services revealed considerable spatial variability along China’s coastal zones; and 3) assessments provide additional insights into the trade-offs between different ecosystem services and wetland types. The valuation framework and database established in this study can contribute to the mapping of wetland ecosystem services in coastal zones.
    Effects of early life and current environmental enrichment on behaviour, affective state and immunity in pigs
    Luo, Lu - \ 2020
    Wageningen University. Promotor(en): B. Kemp, co-promotor(en): J.E. Bolhuis; H.K. Parmentier. - Wageningen : Wageningen University - ISBN 9789463953290 - 356

    The main aim of this thesis was to investigate whether and how early life and current environmental enrichment affect behaviour, affective state, and immunity (which may influence health) in pigs.

    First of all, the effects of environmental enrichment on natural (auto)antibodies (NA(A)b) in relative healthy pigs and in pigs co-infected with PRRSV and A. pleuropneumoniae were studied.  We found that environmental enrichment per se has an impact on immunity in pigs, by affecting NA(A)b levels and their changes in response to challenges and infection.

    Thereafter we aimed to further investigate the effects of early life environmental enrichment and a (mis)match in early life and current housing on behaviour, affective state, and immunity in pigs. To this aim, 30 litters of pigs were housed in either barren or enriched pens from birth. The coping style of the pigs was assessed by the backtest, and pigs were classified as reactive (LR) or proactive (HR). At 28 days of age, pigs were weaned, and in total 192 pigs were selected and regrouped in 32 new pens containing 6 non-littermate pigs each. All pigs were equally regrouped by taking sex, coping style and body weight into account. Housing treatment (barren vs. enriched) for each pig was kept the same as before weaning. At 47 days of age, half of the groups of pigs experienced a switch in housing type, and the other half did not. Thus, after the switch, there were four housing treatment groups: barren-barren (B1B2), barren-enriched (B1E2), enriched-enriched (E1E2) and enriched-barren (E1B2), n=8 pens per group.

    In the home pen observations, environmental enrichment increased time spent on exploring, chewing and play, and decreased damaging behaviours directed at pen mates, such as tail biting and ear biting, and pen-directed exploring and chewing. Behaviour of pigs that switched from barren to enriched pens or vice versa reflected not only their current environment, but also their early life housing conditions. Effects of early life and current enrichment on most behaviours were in opposite direction. The effects of (lack of) enrichment after the switch were therefore more pronounced in pigs that had experienced a different early life condition.   This might reflect frustration in pigs that switched from enriched to barren pens, and a ‘catching up’ effect in pigs that went from barren to enriched pens. For some behaviours this effect of the switch was affected by the coping style of the pigs.  For instance, the LR pigs that switched from enriched to barren pens showed more damaging behaviours directed at their pen mates than all other pigs. Enriched pigs gained more weight and had a higher feed intake in the first weeks post-weaning, suggesting that they were better able to cope with the weaning transition. Barren housed pigs had a lower body weight than enriched pigs just before the switch, after which growth was mainly determined by actual housing, with enriched kept pigs having a higher feed intake and final body weight.

    Barren housed pigs were expected to have a more negative affective state than enriched pigs, and even more so if they originated from an enriched early life environment. To investigate whether housing experiences in early life, and a (mis)match with current housing conditions, would have long-term effects on affective state, pigs were exposed to an attention bias test (ABT) and successive negative contrast test (SNC). In the ABT, current housing, but not early life housing, affected behaviour in a coping-style-dependent manner, as E2-HR pigs paid attention towards the threat more frequently, were more likely to utter high-pitched vocalisations and walked more compared to (part of) the other groups. This unexpected effect could be related to the larger contrast between the pigs’ home pen and the test environment for enriched housed pigs. The behaviour in the ABT may therefore have reflected a short-term effect of the test, rather than the long-term effect of housing, on affective state.  In the SNC, B1B2 pigs generally had a lower probability and higher latency to get the reward than other pigs. HR pigs ran overall slower than LR pigs. Reward downshift increased the latency and reduced the probability to get to the reward, but only in pigs exposed to barren conditions in early life, which thus were more sensitive to reward loss than pigs from enriched early life housing.

    To assess the effects of early life and current housing conditions on innate and adaptive immune competence, 64 pigs were primary  and secondary immunized with the same dose of KLH-TNP. Blood samples were collected, and IgM and IgG antibody responses and leukocyte subpopulations were measured. We found that both early life and later life enrichment, and, notably, a switch in housing conditions influenced specific antibodies and leukocyte subpopulations in pigs. Regarding the relative frequencies of leukocyte subsets, the immune system seemed to respond to a change in housing condition, in either direction, rather than to the long-term effects of housing per se.

    Lastly, the relationships between immunity and behaviour and/or affective states were explored, indicating that play behaviour in the home pen and growth were found to relate to immunity to some extent.

    To conclude, this thesis confirms that environmental enrichment has positive effects on the behaviour of pigs. It also indicates that switching from enriched to barren conditions is more detrimental for pigs’ behaviour than housing in barren pens throughout. Effects of environmental enrichment on behaviour in tests of affective state were equivocal. Both early life and current housing, and a switch in housing conditions influenced specific antibody levels and the frequencies of leukocyte subpopulations in pigs, and the immune system seems to be alerted by changes in the environment.  The results of this thesis underline the importance of enrichment for pigs, as well as a fit between their early and later life housing conditions.

    Genome-wide association study for genotype by lactation stage interaction of milk production traits in dairy cattle
    Lu, Haibo ; Wang, Yachun ; Bovenhuis, Henk - \ 2020
    Journal of Dairy Science (2020). - ISSN 0022-0302
    genetic background - genome-wide association study (GWAS) - lactose - negative energy balance - pregnancy

    Substantial evidence demonstrates that the genetic background of milk production traits changes during lactation. However, most GWAS for milk production traits assume that genetic effects are constant during lactation and therefore might miss those quantitative trait loci (QTL) whose effects change during lactation. The GWAS for genotype by lactation stage interaction are aimed at explicitly detecting the QTL whose effects change during lactation. The purpose of this study was to perform GWAS for genotype by lactation stage interaction for milk yield, lactose yield, lactose content, fat yield, fat content, protein yield, and somatic cell score to detect QTL with changing effects during lactation. For this study, 19,286 test-day records of 1,800 first-parity Dutch Holstein cows were available and cows were genotyped using a 50K SNP panel. A total of 7 genomic regions with effects that change during lactation were detected in the GWAS for genotype by lactation stage interaction. Two regions on Bos taurus autosome (BTA)14 and BTA19 were also significant based on a GWAS that assumed constant genetic effects during lactation. Five regions on BTA4, BTA10, BTA11, BTA16, and BTA23 were only significant in the GWAS for genotype by lactation stage interaction. The biological mechanisms that cause these changes in genetic effects are still unknown, but negative energy balance and effects of pregnancy may play a role. These findings increase our understanding of the genetic background of lactation and may contribute to the development of better management indicators based on milk composition.

    Genome-wide association study for genotype by lactation stage interaction of milk production traits in dairy cattle
    Lu, Haibo ; Wang, Yachun ; Bovenhuis, Henk - \ 2020
    Journal of Dairy Science 103 (2020)6. - ISSN 0022-0302 - p. 5234 - 5245.
    genetic background - genome-wide association study (GWAS) - lactose - negative energy balance - pregnancy

    Substantial evidence demonstrates that the genetic background of milk production traits changes during lactation. However, most GWAS for milk production traits assume that genetic effects are constant during lactation and therefore might miss those quantitative trait loci (QTL) whose effects change during lactation. The GWAS for genotype by lactation stage interaction are aimed at explicitly detecting the QTL whose effects change during lactation. The purpose of this study was to perform GWAS for genotype by lactation stage interaction for milk yield, lactose yield, lactose content, fat yield, fat content, protein yield, and somatic cell score to detect QTL with changing effects during lactation. For this study, 19,286 test-day records of 1,800 first-parity Dutch Holstein cows were available and cows were genotyped using a 50K SNP panel. A total of 7 genomic regions with effects that change during lactation were detected in the GWAS for genotype by lactation stage interaction. Two regions on Bos taurus autosome (BTA)14 and BTA19 were also significant based on a GWAS that assumed constant genetic effects during lactation. Five regions on BTA4, BTA10, BTA11, BTA16, and BTA23 were only significant in the GWAS for genotype by lactation stage interaction. The biological mechanisms that cause these changes in genetic effects are still unknown, but negative energy balance and effects of pregnancy may play a role. These findings increase our understanding of the genetic background of lactation and may contribute to the development of better management indicators based on milk composition.

    Critical transitions in Chinese dunes during the past 12,000 years
    Xu, Zhiwei ; Mason, Joseph A. ; Xu, Chi ; Yi, Shuangwen ; Bathiany, Sebastian ; Yizhaq, Hezi ; Zhou, Yali ; Cheng, Jun ; Holmgren, Milena ; Lu, Huayu - \ 2020
    Science Advances 6 (2020)9. - ISSN 2375-2548 - p. eaay8020 - eaay8020.

    Dune systems can have alternative stable states that coexist under certain environmental conditions: a vegetated, stabilized state and a bare active state. This behavior implies the possibility of abrupt transitions from one state to another in response to gradual environmental change. Here, we synthesize stratigraphic records covering 12,000 years of dynamics of this system at 144 localities across three dune fields in northern China. We find side-by-side coexistence of active and stabilized states, and occasional sharp shifts in time between those contrasting states. Those shifts occur asynchronously despite the fact that the entire landscape has been subject to the same gradual changes in monsoon rainfall and other conditions. At larger scale, the spatial heterogeneity in dune dynamics averages out to produce relatively smooth change. However, our results do show different paths of recovery and collapse of vegetation at system-wide scales, implying that hysteretic behavior occurs in spatially extended systems.

    Impact of conjugation with maltodextrin on rheological properties of sodium caseinate
    Zhang, Lu ; Versteege, Sabine ; Alting, Arno C. ; Schutyser, Maarten A.I. - \ 2020
    International Dairy Journal 105 (2020). - ISSN 0958-6946

    Aqueous dispersions of sodium caseinate-maltodextrin (NaCas-MD) conjugates were prepared by heating to study the impact of Maillard reaction on protein functionality. Conjugation with MD affected rheological properties, colour and microstructure of NaCas-MD dispersions. Gelation temperature of NaCas-MD dispersions increased by 7 °C after conjugation, whereas the gelation time was not significantly affected. Shear thickening of the dispersions occurred at high shear rates, and temperature-viscosity relationship was described by the Arrhenius equation. Gels formed at 25 °C had a lower gel strength after conjugation, associated with changes in microstructure. Strain hardening appeared at large amplitude oscillatory shear, which was more profound after conjugation. Moreover, a higher dextrose-equivalent-value of maltodextrin resulted in conjugates with higher degree of conjugation, darker colour, and larger particulates on a microscale. The study indicates that rheological properties of NaCas can be modified by conjugation with maltodextrin, which is in principle applicable for other protein-polysaccharide combinations.

    Epigenome-wide meta-analysis of blood DNA methylation in newborns and children identifies numerous loci related to gestational age
    Merid, Simon Kebede ; Novoloaca, Alexei ; Sharp, Gemma C. ; Küpers, Leanne K. ; Kho, Alvin T. ; Roy, Ritu ; Gao, Lu ; Annesi-Maesano, Isabella ; Jain, Pooja ; Plusquin, Michelle ; Kogevinas, Manolis ; Allard, Catherine ; Vehmeijer, Florianne O. ; Kazmi, Nabila ; Salas, Lucas A. ; Rezwan, Faisal I. ; Zhang, Hongmei ; Sebert, Sylvain ; Czamara, Darina ; Rifas-Shiman, Sheryl L. ; Melton, Phillip E. ; Lawlor, Debbie A. ; Pershagen, Göran ; Breton, Carrie V. ; Huen, Karen ; Baiz, Nour ; Gagliardi, Luigi ; Nawrot, Tim S. ; Corpeleijn, Eva ; Perron, Patrice ; Duijts, Liesbeth ; Nohr, Ellen Aagaard ; Bustamante, Mariona ; Ewart, Susan L. ; Karmaus, Wilfried ; Zhao, Shanshan ; Page, Christian M. ; Herceg, Zdenko ; Jarvelin, Marjo Riitta ; Lahti, Jari ; Baccarelli, Andrea A. ; Anderson, Denise ; Kachroo, Priyadarshini ; Relton, Caroline L. ; Bergström, Anna ; Eskenazi, Brenda ; Soomro, Munawar Hussain ; Vineis, Paolo ; Snieder, Harold ; Bouchard, Luigi ; Jaddoe, Vincent W. ; Sørensen, Thorkild I.A. ; Vrijheid, Martine ; Arshad, S.H. ; Holloway, John W. ; Håberg, Siri E. ; Magnus, Per ; Dwyer, Terence ; Binder, Elisabeth B. ; Demeo, Dawn L. ; Vonk, Judith M. ; Newnham, John ; Tantisira, Kelan G. ; Kull, Inger ; Wiemels, Joseph L. ; Heude, Barbara ; Sunyer, Jordi ; Nystad, Wenche ; Munthe-Kaas, Monica C. ; Raïkkönen, Katri ; Oken, Emily ; Huang, Rae Chi ; Weiss, Scott T. ; Antó, Josep Maria ; Bousquet, Jean ; Kumar, Ashish ; Söderhäll, Cilla ; Almqvist, Catarina ; Cardenas, Andres ; Gruzieva, Olena ; Xu, Cheng Jian ; Reese, Sarah E. ; Kere, Juha ; Brodin, Petter ; Solomon, Olivia ; Wielscher, Matthias ; Holland, Nina ; Ghantous, Akram ; Hivert, Marie France ; Felix, Janine F. ; Koppelman, Gerard H. ; London, Stephanie J. ; Melén, Erik - \ 2020
    Genome Medicine 12 (2020)1. - ISSN 1756-994X
    Development - Epigenetics - Gestational age - Preterm birth - Transcriptomics

    Background: Preterm birth and shorter duration of pregnancy are associated with increased morbidity in neonatal and later life. As the epigenome is known to have an important role during fetal development, we investigated associations between gestational age and blood DNA methylation in children. Methods: We performed meta-analysis of Illumina's HumanMethylation450-array associations between gestational age and cord blood DNA methylation in 3648 newborns from 17 cohorts without common pregnancy complications, induced delivery or caesarean section. We also explored associations of gestational age with DNA methylation measured at 4-18 years in additional pediatric cohorts. Follow-up analyses of DNA methylation and gene expression correlations were performed in cord blood. DNA methylation profiles were also explored in tissues relevant for gestational age health effects: Fetal brain and lung. Results: We identified 8899 CpGs in cord blood that were associated with gestational age (range 27-42 weeks), at Bonferroni significance, P < 1.06 × 10-7, of which 3343 were novel. These were annotated to 4966 genes. After restricting findings to at least three significant adjacent CpGs, we identified 1276 CpGs annotated to 325 genes. Results were generally consistent when analyses were restricted to term births. Cord blood findings tended not to persist into childhood and adolescence. Pathway analyses identified enrichment for biological processes critical to embryonic development. Follow-up of identified genes showed correlations between gestational age and DNA methylation levels in fetal brain and lung tissue, as well as correlation with expression levels. Conclusions: We identified numerous CpGs differentially methylated in relation to gestational age at birth that appear to reflect fetal developmental processes across tissues. These findings may contribute to understanding mechanisms linking gestational age to health effects.

    Denitrification performance and microbial communities of solid-phase denitrifying reactors using poly (butylene succinate)/bamboo powder composite
    Qi, Wanhe ; Taherzadeh, Mohammad J. ; Ruan, Yunjie ; Deng, Yale ; Chen, Ji Shuang ; Lu, Hui Feng ; Xu, Xiang Yang - \ 2020
    Bioresource Technology 305 (2020). - ISSN 0960-8524
    Bacterial community - Fungal community - PBS/Bamboo composite - RAS effluent treatment - Solid-phase denitrification

    This study explored the denitrification performance of solid-phase denitrification (SPD) systems packed with poly (butylene succinate)/bamboo powder composite to treat synthetic aquaculture wastewater under different salinity conditions (0‰ Vs. 25‰). The results showed composite could achieve the maximum denitrification rates of 0.22 kg (salinity, 0‰) and 0.34 kg NO3 -N m−3 d−1 (salinity, 25‰) over 200-day operation. No significant nitrite accumulation and less dissolved organic carbon (DOC) release (<15 mg/L) were found. The morphological and spectroscopic analyses demonstrated the mixture composites degradation. Microbial community analysis showed that Acidovorax, Simplicispira, Denitromonas, SM1A02, Marinicella and Formosa were the dominant genera for denitrifying bacteria, while Aspergillus was the major genus for denitrifying fungus. The co-network analysis also indicated the interactions between bacterial and fungal community played an important role in composite degradation and denitrification. The outcomes provided a potential strategy of DOC control and cost reduction for aquaculture nitrate removal by SPD.

    Controlled oleosome extraction to produce a plant-based mayonnaise-like emulsion using solely rapeseed seeds
    Romero-Guzmán, María Juliana ; Köllmann, Nienke ; Zhang, Lu ; Boom, Remko M. ; Nikiforidis, Constantinos V. - \ 2020
    Food Science and Technology = Lebensmittel-Wissenschaft und Technologie 123 (2020). - ISSN 0023-6438
    Emulsion - Mayonnaise - Novel-ingredients - Oil-bodies - Oleosomes - Plant-based

    Oleosomes are oil storage structures in seeds, consisting of triglycerides surrounded by a protein-phospholipid mixed monolayer. They can be extracted aqueously together with other seed components such as proteins and soluble fibers. The co-extracted biomolecules can affect the properties of the extracts. Nevertheless, it is possible to control the electrostatic and hydrophobic interactions between these biomolecules and oleosomes by adjusting the extraction conditions. Hence, our aim was to adjust the extraction conditions in order to recover a natural emulsion with a specific functionality: a plant-based mayonnaise-like product, derived solely from rapeseed seeds. By varying the pH of extraction, the droplet size was customized and by increasing the number of purification steps, the right amount of co-extracted material was removed. A combination of these conditions shifted the rheological properties of the obtained natural emulsion to a range similar to the benchmark mayonnaises. This work shows that it is feasible to produce a plant-based mayonnaise with an oil content ranging from 61.7 g/100g to 72.0 g/100g through a simple and continuous oleosome extraction process by controlling the interactions between oleosomes and co-extracted material.

    Identification of Novel Loci and New Risk Variant in Known Loci for Colorectal Cancer Risk in East Asians
    Lu, Yingchang ; Kweon, Sun Seog ; Cai, Qiuyin ; Tanikawa, Chizu ; Shu, Xiao Ou ; Jia, Wei Hua ; Xiang, Yong Bing ; Huyghe, Jeroen R. ; Harrison, Tabitha A. ; Kim, Jeongseon ; Shin, Aesun ; Kim, Dong Hyun ; Matsuo, Keitaro ; Jee, Sun Ha ; Guo, Xingyi ; Wen, Wanqing ; Shi, Jiajun ; Li, Bingshan ; Wang, Nan ; Shin, Min Ho ; Li, Hong Lan ; Ren, Zefang ; Oh, Jae Hwan ; Oze, Isao ; Ahn, Yoon Ok ; Jung, Keum Ji ; Gao, Jing ; Gao, Yu Tang ; Pan, Zhi Zhong ; Kamatani, Yoichiro ; Chan, Andrew T. ; Gsur, Andrea ; Hampe, Jochen ; Marchand, Loic Le; Li, Li ; Lindblom, Annika ; Moreno, Victor ; Newcomb, Polly A. ; Offit, Kenneth ; Pharoah, Paul D.P. ; Duijnhoven, Franzel J.B. van; Guelpen, Bethany Van; Vodicka, Pavel ; Weinstein, Stephanie J. ; Wolk, Alicja ; Wu, Anna H. ; Hsu, Li ; Zeng, Yi Xin ; Long, Jirong ; Peters, Ulrike ; Matsuda, Koichi ; Zheng, Wei - \ 2020
    Cancer Epidemiology Biomarkers & Prevention 29 (2020)2. - ISSN 1055-9965 - p. 477 - 486.

    BACKGROUND: Risk variants identified so far for colorectal cancer explain only a small proportion of familial risk of this cancer, particularly in Asians. METHODS: We performed a genome-wide association study (GWAS) of colorectal cancer in East Asians, including 23,572 colorectal cancer cases and 48,700 controls. To identify novel risk loci, we selected 60 promising risk variants for replication using data from 58,131 colorectal cancer cases and 67,347 controls of European descent. To identify additional risk variants in known colorectal cancer loci, we performed conditional analyses in East Asians. RESULTS: An indel variant, rs67052019 at 1p13.3, was found to be associated with colorectal cancer risk at P = 3.9 × 10-8 in Asians (OR per allele deletion = 1.13, 95% confidence interval = 1.08-1.18). This association was replicated in European descendants using a variant (rs2938616) in complete linkage disequilibrium with rs67052019 (P = 7.7 × 10-3). Of the remaining 59 variants, 12 showed an association at P < 0.05 in the European-ancestry study, including rs11108175 and rs9634162 at P < 5 × 10-8 and two variants with an association near the genome-wide significance level (rs60911071, P = 5.8 × 10-8; rs62558833, P = 7.5 × 10-8) in the combined analyses of Asian- and European-ancestry data. In addition, using data from East Asians, we identified 13 new risk variants at 11 loci reported from previous GWAS. CONCLUSIONS: In this large GWAS, we identified three novel risk loci and two highly suggestive loci for colorectal cancer risk and provided evidence for potential roles of multiple genes and pathways in the etiology of colorectal cancer. In addition, we showed that additional risk variants exist in many colorectal cancer risk loci identified previously. IMPACT: Our study provides novel data to improve the understanding of the genetic basis for colorectal cancer risk.

    Assessing land-based mitigation implications for biodiversity
    Nunez, Sarahi ; Verboom, Jana ; Alkemade, Rob - \ 2020
    Environmental Science & Policy 106 (2020). - ISSN 1462-9011 - p. 68 - 76.
    Biodiversity change - Carbon sequestration - Climate change - Land-based mitigation

    The Paris Agreement to keep global temperature increase to well-below 2 °C and to pursue efforts to limit it to 1.5 °C requires to formulate ambitious climate-change mitigation scenarios to reduce CO2 emissions and to enhance carbon sequestration. These scenarios likely require significant land-use change. Failing to mitigate climate change will result in an unprecedented warming with significant biodiversity loss. The mitigation potential on land is high. However, how land-based mitigation options potentially affect biodiversity is poorly understood. Some land-based mitigation options could also counter the biodiversity loss. Here we reviewed the recently scientific literature to assess twenty land-based mitigation options that are implemented in different mitigation pathways to comply with the Paris Agreement for their biodiversity impacts by using the Mean Species Abundance (MSALU) indicator for land use. We showed the likely land-use transition and potential MSALU changes for each option, compared their carbon sequestration opportunities (tC per ha) and assessed the resulting biodiversity change in two case scenarios. Our results showed that most options benefit biodiversity. Reforestation of cultivated and managed areas together with restoration of wetlands deliver the largest MSALU increases, if land is allowed to reach a mature state over time. A quarter of the assessed options, including intensification of agricultural areas and bioenergy with carbon capture and storage, decreased MSALU. Options, such as afforestation and reduced deforestation, either positively or negatively affected MSALU. This depends on their local implementation and adopted forest-conservation schemes. Comparing the different options showed that avoiding deforestation by implementing agroforestry at the expense of pastures delivered both the largest MSALU increases and the highest carbon sequestration opportunities. However, agroforestry that leads to deforestation, enhanced carbon sequestration slightly but with a marginal MSALU increase. This stresses the importance of avoiding forest conversion. Our study advances the understanding on current and future benefits and adverse effects of land-based mitigation options on biodiversity. This certainly helps biodiversity conservation and determines the regions with large land-based mitigation potential.

    Early and later life environmental enrichment affect specific antibody responses and blood leukocyte subpopulations in pigs
    Luo, Lu ; Jansen, Christine A. ; Bolhuis, Elizabeth ; Arts, Joop ; Kemp, Bas ; Parmentier, Henk - \ 2020
    Physiology and Behavior 217 (2020). - ISSN 0031-9384
    Antibody response - Coping style - Early life history - Enrichment - Immunity - Pigs

    This study addressed the impact of early and later life environmental enrichment, and their combination, on specific antibody responses and peripheral blood leukocyte subpopulations in pigs. Pigs were kept in either barren (B1) or enriched (E1) housing from birth, and half of the pigs switched to barren or enriched housing on day 47, resulting in four treatment combinations: B1B2, B1E2, E1B2, E1E2). Pigs were immunized with keyhole limpet hemocyanin-conjugated trinitrophenyl (KLH-TNP) on day 74 and 109 to induce primary and secondary antibody responses. Blood samples were taken weekly until day 130, and IgM and IgG antibody responses were measured. Leukocyte subpopulations were measured on day 74 and 130. Time course of the antibody responses was not affected by housing. Early life enrichment increased the IgG response to KLH, particularly the primary one. At day 74 the relative frequency of lymphocytes, DC and SLA-II expression on monocytes were higher in E1 pigs, whereas the percentage of granulocytes tended to be lower in E1 pigs at day 74. Early life enrichment increased the SLA-II expression on monocytes, the granulocyte to lymphocyte ratio, and tended to increase the percentage of granulocytes, but tended to decrease the percentage of monocytes at day 130. Later life enrichment reduced percentages of CD4+CD8α+ T cells before and after immunization and the SLA-II expression on monocytes at day 74, the percentage of granulocytes and the granulocyte to lymphocyte ratio at day 130. Notably, early and later life housing interacted in their effects on several immune parameters. KLH-IgM responses (both primary and secondary) were affected by the interaction between early and later life housing. IgM titers were higher for B1B2 than for E1E2, with the switched animals (B1E2 and E1B2) moving towards the titers of the animals kept in their later life environment from birth onwards. At day 130 the percentage of gamma delta T cells, CD8α+ cytotoxic T cells and DC were not different between pigs kept in B1B2 and E1E2, but there was a clear impact of the switch in housing conditions, particularly for the pigs that changed from barren to enriched housing. We also found effects of coping style (personality) and sex on some immune parameters. In conclusion, both early life and later life enrichment, and, notably a switch in housing conditions influenced specific antibodies and leukocyte subpopulations in pigs. The current study implies that the early life history of animals and the (mis)match with their current environment could thus be of major importance for their immune system. Further research is needed to investigate potential consequences for the pigs’ health.

    Organohalide-respiring Desulfoluna species isolated from marine environments
    Peng, Peng ; Goris, Tobias ; Lu, Yue ; Nijsse, Bart ; Burrichter, Anna ; Schleheck, David ; Koehorst, Jasper J. ; Liu, Jie ; Sipkema, Detmer ; Sinninghe Damste, Jaap S. ; Stams, Alfons J.M. ; Häggblom, Max M. ; Smidt, Hauke ; Atashgahi, Siavash - \ 2020
    ISME Journal 14 (2020). - ISSN 1751-7362 - p. 815 - 827.

    The genus Desulfoluna comprises two anaerobic sulfate-reducing strains, D. spongiiphila AA1T and D. butyratoxydans MSL71T, of which only the former was shown to perform organohalide respiration (OHR). Here we isolated a third strain, designated D. spongiiphila strain DBB, from marine intertidal sediment using 1,4-dibromobenzene and sulfate as the electron acceptors and lactate as the electron donor. Each strain harbors three reductive dehalogenase gene clusters (rdhABC) and corrinoid biosynthesis genes in their genomes, and dehalogenated brominated but not chlorinated organohalogens. The Desulfoluna strains maintained OHR in the presence of 20 mM sulfate or 20 mM sulfide, which often negatively affect other organohalide-respiring bacteria. Strain DBB sustained OHR with 2% oxygen in the gas phase, in line with its genetic potential for reactive oxygen species detoxification. Reverse transcription-quantitative PCR revealed differential induction of rdhA genes in strain DBB in response to 1,4-dibromobenzene or 2,6-dibromophenol. Proteomic analysis confirmed expression of rdhA1 with 1,4-dibromobenzene, and revealed a partially shared electron transport chain from lactate to 1,4-dibromobenzene and sulfate, which may explain accelerated OHR during concurrent sulfate reduction. Versatility in using electron donors, de novo corrinoid biosynthesis, resistance to sulfate, sulfide and oxygen, and concurrent sulfate reduction and OHR may confer an advantage to marine Desulfoluna strains.

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