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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    Machine Learning Crash Course : Classification
    Dijk, A.D.J. van - \ 2020
    Wageningen : Wageningen University & Research
    This one-day course includes various aspects of machine learning. Examples are decision trees, linear regression, neural networks, Brix prediction and casus regression.

    You will find the following information:
    1) A reader where you will find the content of the course
    2) Several presentations
    3) Several use cases
    4) Links to video recordings
    Unfortunately some parts of the lecture are missing in the recordings.
    Machine Learning for Beginners : Crash Course Machine Learning
    Kootstra, G.W. ; Dijk, A.D.J. van; Rapado Rincon, David ; Durairaj, J. - \ 2020
    Wageningen : Wageningen University & Research
    This one-day course includes various aspects of machine learning. Examples are decision trees, linear regression, neural networks, Brix prediction and casus regression.

    You will find the following information:
    1) A reader where you will find the content of the course
    2) Several presentations
    3) Several use cases
    4) Links to video recordings
    Unfortunately some parts of the lecture are missing in the recordings.
    Caretta – A multiple protein structure alignment and feature extraction suite
    Akdel, Mehmet ; Durairaj, Janani ; Ridder, Dick de; Dijk, Aalt D.J. van - \ 2020
    Computational and Structural Biotechnology Journal 18 (2020). - ISSN 2001-0370 - p. 981 - 992.
    Dynamic programming - Machine learning - Protein structure - Structure alignment

    The vast number of protein structures currently available opens exciting opportunities for machine learning on proteins, aimed at predicting and understanding functional properties. In particular, in combination with homology modelling, it is now possible to not only use sequence features as input for machine learning, but also structure features. However, in order to do so, robust multiple structure alignments are imperative. Here we present Caretta, a multiple structure alignment suite meant for homologous but sequentially divergent protein families which consistently returns accurate alignments with a higher coverage than current state-of-the-art tools. Caretta is available as a GUI and command-line application and additionally outputs an aligned structure feature matrix for a given set of input structures, which can readily be used in downstream steps for supervised or unsupervised machine learning. We show Caretta's performance on two benchmark datasets, and present an example application of Caretta in predicting the conformational state of cyclin-dependent kinases.

    Supplementary Information and R code from: Black soldier fly larvae show a stronger preference for manure than for a mass-rearing diet
    Parodi, Alejandro ; Dijk, Kim van; Loon, Joop van; Boer, Imke de; Schelt, Jeroen van; Zanten, Hannah van - \ 2020
    Wageningen University & Research
    Behaviour - Black soldier fly - Choice test - Hermetia illucens - Manure - Rearing
    Black soldier fly larvae (BSFL) was reared on two different feeds: a mass rearing diet made of food by-products and pig manure. Preference tests were performed to determine if at different larval ages, BSFL showed a preference for any of the two diets.
    Carbon-nitrogen interactions in European forests and semi-natural vegetation - Part 1 : Fluxes and budgets of carbon, nitrogen and greenhouse gases from ecosystem monitoring and modelling
    Sutton, Mark A. ; Flechard, Chris R. ; Ibrom, Andreas ; Skiba, Ute M. ; Vries, Wim De; Oijen, Marcel Van; Cameron, David R. ; DIse, Nancy B. ; Korhonen, Janne F.J. ; Buchmann, Nina ; Legout, Arnaud ; Simpson, David ; Sanz, Maria J. ; Aubinet, Marc ; Loustau, Denis ; Montagnani, Leonardo ; Neirynck, Johan ; Janssens, Ivan A. ; Pihlatie, Mari ; Kiese, Ralf ; Siemens, Jan ; Francez, Andre Jean ; Augustin, Jurgen ; Varlagin, Andrej ; Olejnik, Janusz ; Juszczak, Radoslaw ; Aurela, Mika ; Berveiller, Daniel ; Chojnicki, Bogdan H. ; Dämmgen, Ulrich ; Delpierre, Nicolas ; Djuricic, Vesna ; Drewer, Julia ; Dufrêne, Eric ; Eugster, Werner ; Fauvel, Yannick ; Fowler, David ; Frumau, Arnoud ; Granier, André ; Gross, Patrick ; Hamon, Yannick ; Helfter, Carole ; Hensen, Arjan ; Horvath, Laszlo ; Kitzler, Barbara ; Kruijt, Bart ; Kutsch, Werner L. ; Lobo-Do-Vale, Raquel ; Lohila, Annalea ; Longdoz, Bernard ; Marek, Michal V. ; Matteucci, Giorgio ; Mitosinkova, Marta ; Moreaux, Virginie ; Neftel, Albrecht ; Ourcival, Jean Marc ; Pilegaard, Kim ; Pita, Gabriel ; Sanz, Francisco ; Schjoerring, Jan K. ; Sebastià, Maria Teresa ; Sim Tang, Y. ; Uggerud, Hilde ; Urbaniak, Marek ; DIjk, Netty Van; Vesala, Timo ; Vidic, Sonja ; Vincke, Caroline ; Weidinger, Tamas ; Zechmeister-Boltenstern, Sophie ; Butterbach-Bahl, Klaus ; Nemitz, Eiko - \ 2020
    Biogeosciences 17 (2020)6. - ISSN 1726-4170 - p. 1583 - 1620.

    The impact of atmospheric reactive nitrogen (Nr) deposition on carbon (C) sequestration in soils and biomass of unfertilized, natural, semi-natural and forest ecosystems has been much debated. Many previous results of this dC=dN response were based on changes in carbon stocks from periodical soil and ecosystem inventories, associated with estimates of Nr deposition obtained from large-scale chemical transport models. This study and a companion paper (Flechard et al., 2020) strive to reduce uncertainties of N effects on C sequestration by linking multi-annual gross and net ecosystem productivity estimates from 40 eddy covariance flux towers across Europe to local measurement-based estimates of dry and wet Nr deposition from a dedicated collocated monitoring network. To identify possible ecological drivers and processes affecting the interplay between C and Nr inputs and losses, these data were also combined with in situ flux measurements of NO, N2O and CH4 fluxes; soil NO3 leaching sampling; and results of soil incubation experiments for N and greenhouse gas (GHG) emissions, as well as surveys of available data from online databases and from the literature, together with forest ecosystem (BASFOR) modelling. Multi-year averages of net ecosystem productivity (NEP) in forests ranged from 70 to 826 gCm2 yr1 at total wetCdry inorganic Nr deposition rates (Ndep) of 0.3 to 4.3 gNm2 yr1 and from 4 to 361 g Cm2 yr1 at Ndep rates of 0.1 to 3.1 gNm2 yr1 in short semi-natural vegetation (moorlands, wetlands and unfertilized extensively managed grasslands). The GHG budgets of the forests were strongly dominated by CO2 exchange, while CH4 and N2O exchange comprised a larger proportion of the GHG balance in short semi-natural vegetation. Uncertainties in elemental budgets were much larger for nitrogen than carbon, especially at sites with elevated Ndep where Nr leaching losses were also very large, and compounded by the lack of reliable data on organic nitrogen and N2 losses by denitrification. Nitrogen losses in the form of NO, N2O and especially NO3 were on average 27%(range 6 % 54 %) of Ndep at sites with Ndep < 1 gNm2 yr1 versus 65% (range 35 % 85 %) for Ndep > 3 gNm2 yr1. Such large levels of Nr loss likely indicate that different stages of N saturation occurred at a number of sites. The joint analysis of the C and N budgets provided further hints that N saturation could be detected in altered patterns of forest growth. Net ecosystem productivity increased with Nr deposition up to 2 2.5 gNm2 yr1, with large scatter associated with a wide range in carbon sequestration efficiency (CSE, defined as the NEP = GPP ratio). At elevated Ndep levels (> 2.5 gNm2 yr1), where inorganic Nr losses were also increasingly large, NEP levelled off and then decreased. The apparent increase in NEP at low to intermediate Ndep levels was partly the result of geographical cross-correlations between Ndep and climate, indicating that the actual mean dC=dN response at individual sites was significantly lower than would be suggested by a simple, straightforward regression of NEP vs. Ndep.

    Ontwerp Boerderij van de Toekomst
    Visser, Chris de; Sukkel, Wijnand ; Kempenaar, Corné ; Wal, Tamme van der; Wolf, Pieter de; Visser, Andries ; Smit, Bert ; Schoorlemmer, Herman ; Schoutsen, Maureen ; Klompe, Koen ; Veldhuisen, Bram ; Selin-Noren, Isabella ; Dijk, Chris van; Hol, Stefan ; Voort, Marcel van der; Janssens, Bas - \ 2020
    Wageningen : Stichting Wageningen Research, Wageningen Plant Research, Business unit Open Teelten (Rapport / Stichting Wageningen Research, Wageningen Plant Research, Business unit Open Teelten WPR-823) - 45
    "We zien de bodem in 'Puntje Dijk' jaar op jaar verbeteren"
    Tramper, Marcel - \ 2020
    Modelling alternative futures of global food security: Insights from FOODSECURE
    Meijl, Hans van; Shutes, Lindsay ; Valin, Hugo ; Stehfest, Elke ; Dijk, Michiel van; Kuiper, Marijke ; Tabeau, Andrzej ; Zeist, Willem Jan van; Hasegawa, Tomoko ; Havlik, Petr - \ 2020
    Global Food Security 25 (2020). - ISSN 2211-9124
    Environment - Food security - Integrated assessment - Long run - Scenario analysis

    Global economic models have been increasingly used to project food and agricultural developments for long term-time horizons, but food security aspects have often been limited to food availability projections. In this paper, we propose a broader framework to explore the future of food and nutrition security with a focus on food availability, food access, and a reasonable proxy for food utilisation. This framework is applied to a new set of stakeholder-designed scenarios of alternative future worlds that were developed for the FOODSECURE project and are structured around the two dimensions of inequality and sustainability. The framework is tested with two global models, MAGNET-IMAGE and GLOBIOM, and illustrated through an assessment of the possible trade-offs between food and nutrition security and sustainability in each of the worlds. Our results indicate that more equal worlds improve food security over a wider range of food security indicators and neglecting the sustainability dimension might revert food security gains over time. This paper concludes that there is a need for model-based scenario analysis to assess the complex and multi-dimensional characteristics of global food security.

    HILPDA Uncouples Lipid Droplet Accumulation in Adipose Tissue Macrophages from Inflammation and Metabolic Dysregulation
    Dierendonck, Xanthe A.M.H. van; Rosa Rodriguez, Montserrat A. de la; Georgiadi, Anastasia ; Mattijssen, Frits ; Dijk, Wieneke ; Weeghel, Michel van; Singh, Rajat ; Borst, Jan Willem ; Stienstra, Rinke ; Kersten, Sander - \ 2020
    Cell Reports 30 (2020)6. - ISSN 2211-1247 - p. 1811 - 1822.e6.
    ATGL - fatty acid metabolism - Hilpda - inflammation - lipid droplets - macrophages - obesity

    Obesity leads to a state of chronic, low-grade inflammation that features the accumulation of lipid-laden macrophages in adipose tissue. Here, we determined the role of macrophage lipid-droplet accumulation in the development of obesity-induced adipose-tissue inflammation, using mice with myeloid-specific deficiency of the lipid-inducible HILPDA protein. HILPDA deficiency markedly reduced intracellular lipid levels and accumulation of fluorescently labeled fatty acids. Decreased lipid storage in HILPDA-deficient macrophages can be rescued by inhibition of adipose triglyceride lipase (ATGL) and is associated with increased oxidative metabolism. In diet-induced obese mice, HILPDA deficiency does not alter inflammatory and metabolic parameters, despite markedly reducing lipid accumulation in macrophages. Overall, we find that HILPDA is a lipid-inducible, physiological inhibitor of ATGL-mediated lipolysis in macrophages and uncouples lipid storage in adipose tissue macrophages from inflammation and metabolic dysregulation. Our data question the contribution of lipid droplet accumulation in adipose tissue macrophages in obesity-induced inflammation and metabolic dysregulation.

    Rekenregels van de KringloopWijzer 2019 : Achtergronden van BEX, BEA, BEN, BEP en BEC: actualisatie van de 2018-versie
    Dijk, W. van; Schröder, J.J. ; Šebek, L.B. ; Oenema, J. ; Conijn, J.G. ; Vellinga, Th.V. ; Boer, J. de; Haan, M.H.A. de; Verloop, J. - \ 2020
    Wageningen : Stichting Wageningen Research, Wageningen Plant Research, Business Unit Agrosystems Research (Rapport / Stichting Wageningen Research, Wageningen Plant Research, Business unit Agrosystems Research WPR-956) - 129
    Meiotic recombination profiling of interspecific hybrid F1 tomato pollen by linked read sequencing
    Fuentes, Roven ; Hesselink, T. ; Nieuwenhuis, Ronald ; Bakker, L.V. ; Schijlen, E.G.W.M. ; Dooijeweert, W. van; Diaz Trivino, S. ; Haan, Jorn R. de; Sanchez Perez, G.F. ; Zhang, Xinyue ; Fransz, Paul ; Jong, J.H.S.G.M. de; Dijk, A.D.J. van; Ridder, D. de; Peters, S.A. - \ 2020
    The Plant Journal 102 (2020)3. - ISSN 0960-7412 - p. 480 - 492.
    Genome wide screening of pooled pollen samples from a single interspecific F1 hybrid obtained from a cross between tomato, Solanum lycopersicum and its wild relative, Solanum pimpinellifolium using linked read sequencing of the haploid nuclei, allowed profiling of the crossover (CO) and gene conversion (GC) landscape. We observed a striking overlap between cold regions of CO in the male gametes and our previously established F6 recombinant inbred lines (RILs) population. COs were overrepresented in non‐coding regions in the gene promoter and 5′UTR regions of genes. Poly‐A/T and AT rich motifs were found enriched in 1 kb promoter regions flanking the CO sites. Non‐crossover associated allelic and ectopic GCs were detected in most chromosomes, confirming that besides CO, GC represents also a source for genetic diversity and genome plasticity in tomato. Furthermore, we identified processed break junctions pointing at the involvement of both homology directed and non‐homology directed repair pathways, suggesting a recombination machinery in tomato that is more complex than currently anticipated.
    Integration of epidemiologic, pharmacologic, genetic and gut microbiome data in a drug–metabolite atlas
    Liu, Jun ; Lahousse, Lies ; Nivard, Michel G. ; Bot, Mariska ; Chen, Lianmin ; Klinken, Jan Bert van; Thesing, Carisha S. ; Beekman, Marian ; Akker, Erik Ben van den; Slieker, Roderick C. ; Waterham, Eveline ; Kallen, Carla J.H. van der; Boer, Irene de; Li-Gao, Ruifang ; Vojinovic, Dina ; Amin, Najaf ; Radjabzadeh, Djawad ; Kraaij, Robert ; Alferink, Louise J.M. ; Murad, Sarwa Darwish ; Uitterlinden, André G. ; Willemsen, Gonneke ; Pool, Rene ; Milaneschi, Yuri ; Heemst, Diana van; Suchiman, H.E. ; Rutters, Femke ; Elders, Petra J.M. ; Beulens, Joline W.J. ; Heijden, Amber A.W.A. van der; Greevenbroek, Marleen M.J. van; Arts, Ilja C.W. ; Onderwater, Gerrit L.J. ; Maagdenberg, Arn M.J.M. van den; Mook-Kanamori, Dennis O. ; Hankemeier, Thomas ; Terwindt, Gisela M. ; Stehouwer, Coen D.A. ; Geleijnse, Johanna M. ; ‘t Hart, Leen M. ; Slagboom, Eline P. ; Dijk, Ko Willems van; Zhernakova, Alexandra ; Fu, Jingyuan ; Penninx, Brenda W.J.H. ; Boomsma, Dorret I. ; Demirkan, Ayşe ; Stricker, Bruno H.C. ; Duijn, Cornelia M. van - \ 2020
    Nature Medicine 26 (2020)1. - ISSN 1078-8956 - p. 110 - 117.

    Progress in high-throughput metabolic profiling provides unprecedented opportunities to obtain insights into the effects of drugs on human metabolism. The Biobanking BioMolecular Research Infrastructure of the Netherlands has constructed an atlas of drug–metabolite associations for 87 commonly prescribed drugs and 150 clinically relevant plasma-based metabolites assessed by proton nuclear magnetic resonance. The atlas includes a meta-analysis of ten cohorts (18,873 persons) and uncovers 1,071 drug–metabolite associations after evaluation of confounders including co-treatment. We show that the effect estimates of statins on metabolites from the cross-sectional study are comparable to those from intervention and genetic observational studies. Further data integration links proton pump inhibitors to circulating metabolites, liver function, hepatic steatosis and the gut microbiome. Our atlas provides a tool for targeted experimental pharmaceutical research and clinical trials to improve drug efficacy, safety and repurposing. We provide a web-based resource for visualization of the atlas (http://bbmri.researchlumc.nl/atlas/).

    Mesttool: Zinvol? En wat moet er in?
    Dijk, Wim van; Klompe, Koen ; Galama, Paul - \ 2020
    Validity of absolute intake and nutrient density of protein, potassium, and sodium assessed by various dietary assessment methods: An exploratory study
    Trijsburg, Laura ; Geelen, Anouk ; Hulshof, Paul J.M. ; Van’T Veer, Pieter ; Boshuizen, Hendriek C. ; Hollman, Peter C.H. ; Dijk, Gertjan van; Feskens, Edith J.M. ; Vries, Jeanne H.M. de - \ 2020
    Nutrients 12 (2020)1. - ISSN 2072-6643
    Dietary assessment - Doubly labeled water - Measurement errors - Multivariate models - Nutrient density - Validation

    It is suggested that nutrient densities are less affected by measurement errors than absolute intake estimates of dietary exposure. We compared the validity of absolute intakes and densities of protein (kJ from protein/total energy (kJ)), potassium, and sodium (potassium or sodium (in mg)/total energy (kJ)) assessed by different dietary assessment methods. For 69 Dutch subjects, two duplicate portions (DPs), five to fifteen 24-h dietary recalls (24 hRs, telephone-based and web-based) and two food frequency questionnaires (FFQs) were collected and compared to duplicate urinary biomarkers and one or two doubly labelled water measurements. Multivariate measurement error models were used to estimate validity coefficients (VCs) and attenuation factors (AFs). This research showed that group bias diminished for protein and sodium densities assessed by all methods as compared to the respective absolute intakes, but not for those of potassium. However, the VCs and AFs for the nutrient densities did not improve compared to absolute intakes for all four methods; except for the AF of sodium density (0.71) or the FFQ which was better than that of the absolute sodium intake (0.51). Thus, using nutrient densities rather than absolute intakes does not necessarily improve the performance of the DP, FFQ, or 24 hR.

    Heritability estimates for 361 blood metabolites across 40 genome-wide association studies
    Hagenbeek, Fiona A. ; Pool, René ; Dongen, Jenny van; Draisma, Harmen H.M. ; Hottenga, Jouke Jan ; Willemsen, Gonneke ; Abdellaoui, Abdel ; Fedko, Iryna O. ; Braber, Anouk den; Visser, Pieter Jelle ; Geus, Eco J.C.N. de; Willems van Dijk, Ko ; Verhoeven, Aswin ; Suchiman, H.E. ; Beekman, Marian ; Slagboom, Eline P. ; Duijn, Cornelia M. van; Barkey Wolf, J.J.H. ; Cats, D. ; Amin, N. ; Beulens, J.W. ; Bom, J.A. van der; Bomer, N. ; Demirkan, A. ; Hilten, J.A. van; Meessen, J.M.T.A. ; Moed, M.H. ; Fu, J. ; Onderwater, G.L.J. ; Rutters, F. ; So-Osman, C. ; Flier, W.M. van der; Heijden, A.A.W.A. van der; Spek, A. van der; Asselbergs, F.W. ; Boersma, E. ; Elders, P.M. ; Geleijnse, J.M. ; Ikram, M.A. ; Kloppenburg, M. ; Meulenbelt, I. ; Mooijaart, S.P. ; Nelissen, R.G.H.H. ; Netea, M.G. ; Penninx, B.W.J.H. ; Stehouwer, C.D.A. ; Teunissen, C.E. ; Terwindt, G.M. ; Jukema, J.W. ; Reinders, M.J.T. - \ 2020
    Nature Communications 11 (2020)1. - ISSN 2041-1723

    Metabolomics examines the small molecules involved in cellular metabolism. Approximately 50% of total phenotypic differences in metabolite levels is due to genetic variance, but heritability estimates differ across metabolite classes. We perform a review of all genome-wide association and (exome-) sequencing studies published between November 2008 and October 2018, and identify >800 class-specific metabolite loci associated with metabolite levels. In a twin-family cohort (N = 5117), these metabolite loci are leveraged to simultaneously estimate total heritability (h2 total), and the proportion of heritability captured by known metabolite loci (h2 Metabolite-hits) for 309 lipids and 52 organic acids. Our study reveals significant differences in h2 Metabolite-hits among different classes of lipids and organic acids. Furthermore, phosphatidylcholines with a high degree of unsaturation have higher h2 Metabolite-hits estimates than phosphatidylcholines with low degrees of unsaturation. This study highlights the importance of common genetic variants for metabolite levels, and elucidates the genetic architecture of metabolite classes.

    Improvisation and harm avoidance: An ethnographic study of adherence to postnatal care protocols in two hospitals in Southern Ghana
    Yevoo, Linda L. ; Agyepong, Irene A. ; Gerrits, Trudie ; Dijk, Han van - \ 2020
    Midwifery 82 (2020). - ISSN 0266-6138
    Ethnography - Harm avoidance - Improvisation - Postnatal care - Protocols

    Providers’ adherence to case management protocols can affect quality of care. However, how and why protocols are adhered to by frontline health workers in low- and middle-income countries is not always clear. This study explored midwives’ adherence to national postnatal care protocols in two public hospitals in Southern Ghana using an ethnographic study design. Ninety participant observations and 88 conversations were conducted over a 20-months period, and two group interviews held with the midwives in the two hospitals. Data was analysed using a grounded theory approach. Findings: Midwives collectively decided when to adhere, modify or totally ignore postnatal care protocols. Adherence often occurred if required resources (equipment, tools, supplies) were available. Modification occurred when midwives felt that strict adherence could have negative implications for patients and they could be seen as acting ‘unprofessionally’. Ignoring or modifying protocols also occurred when midwives were uncertain of the patient's health condition; basic supplies, logistics and infrastructure needed for adherence were unavailable or inappropriate; or midwives felt they might expose themselves or their clients to physical, psychological, emotional, financial or social harm. Regardless of the reasons that midwives felt justified to ignore or modify postnatal care protocols, it appeared in many instances to lead to the provision of care of suboptimal quality. Conclusion and recommendations: Providing clinical decision-making protocols is not enough to improve mother and new born care quality and outcomes. Faced with constraining conditions of work, providers are likely to modify guidelines as part of coping behaviour. Addressing constraining conditions of work must accompany guidelines. This includes adequate risks protection for health workers and clients; and resolution of deficits in essential equipment, infrastructure, supplies and staffing.

    Transfer of natural auto-antibodies via egg yolk in chickens divergently selected for natural antibodies binding keyhole limpet hemocyanin
    Dijk, Kaylee S.E. van; Parmentier, Henk K. - \ 2020
    Developmental and Comparative Immunology 102 (2020). - ISSN 0145-305X
    Chicken - Maternal transfer - Natural (auto-) antibodies - Selection lines - Western blot

    Barcodes of natural auto-antibody (NAAb) profiles based on staining intensity of isotypes binding numbers of self-(tissue) antigen fragments were suggested as parameters for immune diversity, and related to genetic background and health status in man, rodents and poultry. Here, hens, eggs and hatchlings from chicken lines divergently selected and bred for high (H line) or low (L line) total natural antibodies (NAb) levels in plasma binding keyhole limpet hemocyanin (KLH) at 16 weeks of age were tested for their NAAb repertoire binding chicken liver homogenate (CLH) fragments using quantitative Western immunoblotting. The aims of this study were 1. to detect line differences between the H and L line adult hens, eggs and hatchlings for the IgM and IgG isotypes binding CLH fragments, 2. study the presence of NAAb of both isotypes in yolk and albumen, as well as in hatchlings to detect a maternal NAAb transfer route via the egg to the hatchling, and 3. study whether new self-antigen binding isotypes and idiotypes are present in the hatchling. NAAb binding CLH fragments were found in plasma of adult hens (both IgM and IgG), in yolk (IgG only), and hatchlings (mostly IgG, but low levels of IgM). Auto-profiles of IgM showed homogeneity, while IgG profiles were heterogenic between individual hens and individual hatchlings. Significant higher levels as indicated by staining intensity and number of stained CLH fragments were found in plasma of hens genetically selected for high levels of NAb binding KLH. Lines could be clustered based on their auto-profiles indicating that profiles of self-binding IgM and IgG antibodies are genetically based. Visual comparison, clustering and correlation of hens and their hatchlings showed similarities for the IgG, but not the IgM isotype, indicating maternal transfer of IgG NAAb via the yolk. The IgM profile in the hatchlings on the other hand might represent neonatal self-binding antibody formation. As a consequence, hatchlings initially depend for self-binding antibodies on maternal IgG provision during early life.

    Designing Eukaryotic Gene Expression Regulation Using Machine Learning
    Jongh, Ronald P.H. de; Dijk, Aalt D.J. van; Julsing, Mattijs K. ; Schaap, Peter J. ; Ridder, Dick de - \ 2020
    Trends in Biotechnology 38 (2020)2. - ISSN 0167-7799 - p. 191 - 201.
    DNA design - eukaryotic gene expression - gene regulation - machine learning - synthetic biology

    Controlling the expression of genes is one of the key challenges of synthetic biology. Until recently fine-tuned control has been out of reach, particularly in eukaryotes owing to their complexity of gene regulation. With advances in machine learning (ML) and in particular with increasing dataset sizes, models predicting gene expression levels from regulatory sequences can now be successfully constructed. Such models form the cornerstone of algorithms that allow users to design regulatory regions to achieve a specific gene expression level. In this review we discuss strategies for data collection, data encoding, ML practices, design algorithm choices, and finally model interpretation. Ultimately, these developments will provide synthetic biologists with highly specific genetic building blocks to rationally engineer complex pathways and circuits.

    B-vitamins and body composition: integrating observational and experimental evidence from the B-PROOF study
    Oliai Araghi, Sadaf ; Braun, Kim V.E. ; Velde, Nathalie van der; Dijk, Suzanne C. van; Schoor, Natasja M. van; Zillikens, M.C. ; Groot, Lisette C.P.G.M. de; Uitterlinden, Andre G. ; Stricker, Bruno H. ; Voortman, Trudy ; Kiefte-de Jong, Jessica C. - \ 2020
    European Journal of Nutrition 59 (2020). - ISSN 1436-6207 - p. 1253 - 1262.
    BMI - Body composition - Effect of vitamin B12 and folic acid on obesity - Fat (Free) mass - Vitamin B12 and folic acid

    Purpose: Higher folate and vitamin-B12 have been linked to lower risk of overweight. However, whether this is a causal effect of these B-vitamins on obesity risk remains unclear and evidence in older individuals is scarce. This study aimed to assess the role of B-vitamin supplementation and levels on body composition in older individuals. Methods: A double-blind, randomized controlled trial in 2919 participants aged ≥ 65 years with elevated homocysteine levels. The intervention comprised a 2-year supplementation with a combination of folic acid (400 µg) and vitamin B12 (500 µg), or with placebo. Serum folate, vitamin-B12, active vitamin-B12 (HoloTC), methylmalonic acid (MMA), and anthropometrics were measured at baseline and after 2 years of follow-up. Dietary intake of folate and vitamin-B12 was measured at baseline in a subsample (n = 603) using a validated food-frequency questionnaire. Fat mass index (FMI) and fat-free mass index (FFMI) were assessed with Dual Energy X-ray absorptiometry (DXA). Results: Cross-sectional analyses showed that a 1 nmol/L higher serum folate was associated with a 0.021 kg/m 2 lower BMI (95% CI − 0.039; − 0.004). Higher HoloTC (per pmol/L log-transformed) was associated with a 0.955 kg/m 2 higher FMI (95% CI 0.262; 1.647), and higher MMA (per μgmol/L) was associated with a 1.108 kg/m 2 lower FMI (95% CI − 1.899; − 0.316). However, random allocation of B-vitamins did not have a significant effect on changes in BMI, FMI or FFMI during 2 years of intervention. Conclusions: Although observational data suggested that folate and vitamin B12 status are associated with body composition, random allocation of a supplement with both B-vitamins combined versus placebo did not confirm an effect on BMI or body composition.

    Towards a Theory of Claim Making: Bridging Access and Property Theory
    Kronenburg García, Angela ; Dijk, Han van - \ 2020
    Society & Natural Resources 33 (2020)2. - ISSN 0894-1920 - p. 167 - 183.
    access - Claim making - land - natural resources - property - theory

    This article proposes a framework for studying and understanding how people make claims to land and other natural resources. We argue that a focus on claim-making practices of actors (individuals, groups, institutions, companies, the state), and the processes of appropriation, accessing and contestation that come along with it, best responds to Sikor and Lund’s call to examine “the grey zone” between access and property. We identify and discuss three practices of claim making: “grounding claims” is the practice of inscribing or altering the landscape with visible markers connoting ownership; “talking claims” is when speech is used strategically to make, justify and contest claims; and “representing claims” is when claims are represented on material objects (maps, title deeds) that are detached from the resource. We contribute to debates on enclosure, large-scale land acquisitions and resource grabbing by providing a lens of claim making through which these processes can be conceptualized.

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