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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    Symplasmic isolation marks cell fate changes during somatic embryogenesis
    Godel-Jedrychowska, Kamila ; Kulinska-Lukaszek, Katarzyna ; Horstman, A. ; Soriano Castan, Merche ; Li, M. ; Malota, Karol ; Boutilier, K.A. ; Kurczynska, Ewa U. - \ 2020
    Journal of Experimental Botany 71 (2020)9. - ISSN 0022-0957 - p. 2612 - 2628.
    Cell-to-cell signalling is a major mechanism controlling plant morphogenesis. Transport of signalling molecules through plasmodesmata is one way in which plants promote or restrict intercellular signalling over short distances. Plasmodesmata are membrane-lined pores between cells that regulate the intercellular flow of signalling molecules through changes in their size, creating symplasmic fields of connected cells. Here we examine the role of plasmodesmata and symplasmic communication in the establishment of plant cell totipotency, using somatic embryo induction from Arabidopsis explants as a model system. Cell-to-cell communication was evaluated using fluorescent tracers, supplemented with histological and ultrastructural analysis, and correlated with expression of a WOX2 embryo reporter. We showed that embryogenic cells are isolated symplasmically from non-embryogenic cells regardless of the explant type (immature zygotic embryos or seedlings) and inducer system (2,4-dichlorophenoxyacetic acid or the BABY BOOM (BBM) transcription factor), but that the symplasmic domains in different explants differ with respect to the maximum size of molecule capable of moving through the plasmodesmata. Callose deposition in plasmodesmata preceded WOX2 expression in future sites of somatic embryo development, but later was greatly reduced in WOX2-expressing domains. Callose deposition was also associated with a decrease DR5 auxin response in embryogenic tissue. Treatment of explants with the callose biosynthesis inhibitor 2-deoxy-D-glucose supressed somatic embryo formation in all three systems studied, and also blocked the observed decrease in DR5 expression. Together these data suggest that callose deposition at plasmodesmata is required for symplasmic isolation and establishment of cell totipotency in Arabidopsis.
    Pre-Columbian soil fertilization and current management maintain food resource availability in old-growth Amazonian forests
    Levis, Carolina ; Peña-Claros, Marielos ; Clement, Charles R. ; Costa, Flavia R.C. ; Alves, Rubana Palhares ; Ferreira, Maria Julia ; Figueiredo, Camila Guarim ; Bongers, Frans - \ 2020
    Plant and Soil (2020). - ISSN 0032-079X
    Anthropogenic soils - Domesticated plants - Forest resources - Historical ecology - Landscape domestication - Protected areas

    Aims: The extent and persistence of pre-Columbian human legacies in old-growth Amazonian forests are still controversial, partly because modern societies re-occupied old settlements, challenging the distinction between pre- and post-Columbian legacies. Here, we compared the effects of pre-Columbian vs. recent landscape domestication processes on soils and vegetation in two Amazonian regions. Methods: We studied forest landscapes at varying distances from pre-Columbian and current settlements inside protected areas occupied by traditional and indigenous peoples in the lower Tapajós and the upper-middle Madeira river basins. By conducting 69 free-listing interviews, participatory mappings, guided-tours, 27 forest inventories, and soil analysis, we assessed the influences of pre-Columbian and current activities in soils and plant resources surrounding the settlements. Results: In both regions, we found that pre-Columbian villages were more densely distributed across the landscape than current villages. Soil nutrients (mainly Ca and P) were higher closer to pre-Columbian villages but were generally not related to current villages, suggesting past soil fertilization. Soil charcoal was frequent in all forests, suggesting frequent fire events. The density of domesticated plants used for food increased in phosphorus enriched soils. In contrast, the density of plants used for construction decreased near current villages. Conclusions: We detected a significant effect of past soil fertilization on food resources over extensive areas, supporting the hypothesis that pre-Columbian landscape domestication left persistent marks on Amazonian landscapes. Our results suggest that a combination of pre-Columbian phosphorus fertilization with past and current management drives plant resource availability in old-growth forests.

    A data-driven methodology reveals novel myofiber clusters in older human muscles
    Raz, Yotam ; Akker, Erik B. van den; Roest, Tijmen ; Riaz, Muhammad ; Rest, Ondine van de; Suchiman, Eka D. ; Lakenberg, Nico ; Stassen, Stefanie A. ; Putten, Maaike van; Feskens, Edith J.M. ; Reinders, Marcel J.T. ; Goeman, Jelle ; Beekman, Marian ; Raz, Vered ; Slagboom, Pieternella Eline - \ 2020
    FASEB Journal 34 (2020)4. - ISSN 0892-6638 - p. 5525 - 5537.
    bioinformatics - clustering - fibertyping - human - muscle - muscle health - myofiber - myosin heavy chain - RNA-sequencing - sarcomere

    Skeletal muscles control posture, mobility and strength, and influence whole-body metabolism. Muscles are built of different types of myofibers, each having specific metabolic, molecular, and contractile properties. Fiber classification is, therefore, regarded the key for understanding muscle biology, (patho-) physiology. The expression of three myosin heavy chain (MyHC) isoforms, MyHC-1, MyHC-2A, and MyHC-2X, marks myofibers in humans. Typically, myofiber classification is performed by an eye-based histological analysis. This classical approach is insufficient to capture complex fiber classes, expressing more than one MyHC-isoform. We, therefore, developed a methodological procedure for high-throughput characterization of myofibers on the basis of multiple isoforms. The mean fluorescence intensity of the three most abundant MyHC isoforms was measured per myofiber in muscle biopsies of 56 healthy elderly adults, and myofiber classes were identified using computational biology tools. Unsupervised clustering revealed the existence of six distinct myofiber clusters. A comparison with the visual assessment of myofibers using the same images showed that some of these myofiber clusters could not be detected or were frequently misclassified. The presence of these six clusters was reinforced by RNA expressions levels of sarcomeric genes. In addition, one of the clusters, expressing all three MyHC isoforms, correlated with histological measures of muscle health. To conclude, this methodological procedure enables deep characterization of the complex muscle heterogeneity. This study opens opportunities to further investigate myofiber composition in comparative studies.

    Accelerated discovery of functional variation in pigs
    Derks, M.F.L. ; Megens, H.J.W.C. ; Bosse, M. ; Lopes, Marcos S. ; Harlizius, Barbara ; Groenen, M. - \ 2020
    In: Wias Annual Conference 2020. - WIAS - p. 38 - 38.
    The genotype-phenotype link is a major research topic in the life sciences, but remains highly complex to disentangle. Part of the complexity arises from the polygenicity of phenotypes,in which many (interacting) genes contribute to the observed phenotype. Genome wide association studies have been instrumental to associate genomic markers to important phenotypes. However, despite the vast increase of molecular data (e.g. whole genome sequences), pinpointing the causal variant underlying a phenotype of interest is still a major challenge, especially due to high levels of linkage disequilibrium in livestock. In this study we present a method to prioritize genomic variation underlying traits of interest from genome wide association studies in pigs. First, we select all sequence variants associated with the trait. Subsequently, we prioritize variation by utilizing and integrating predicted variant impact scores, gene expression data, epigenetic marks for promotor and enhancer identification, and associated phenotypes in other (well-studied) mammalian species. The power of the approach heavily relies on variant impact scores, for which we used pCADD, a tool which can assign scores to any variant in the genome including those in non-coding regions. Using our methodology, we are able to either pinpoint the likely causal mutation or substantially narrow down the list of potentially causal candidates from any association result. We demonstrate the efficacy of the tool by reporting known and novel causal variants, of which many affect (non-coding) regulatory sequences associated with important phenotypes in pigs. This study provides an approach to pinpoint likely causal variation and genes underlying important phenotypes in pigs, accelerating the discovery of new causal variants that could be directly implemented to improve selection.
    From GWAS Peak to Causal Mutation; Utilizing p(ig)CADD Scores to Prioritize Sequence Variation
    Derks, Martijn ; Gross, Christian ; Lopes, M.S. ; Reinders, M.J.T. ; Bosse, Mirte ; Gjuvsland, Arne B. ; Megens, Hendrik-Jan ; Ridder, Dick de; Groenen, Martien - \ 2020
    The genotype-phenotype link is a major research topic in life sciences, but remains highly complex to disentangle. Part of the complexity arises from the polygenicity of phenotypes, in which many (interacting) genes contribute to the observed phenotype. Genome wide association studies have been instrumental to associate genomic markers to important phenotypes. However, despite the vast increase of molecular data (e.g. whole genome sequences), pinpointing the causal variant underlying a phenotype of interest is still a major challenge, especially due to high levels of linkage disequilibrium.

    In this study we present a method to prioritize genomic variation underlying traits of interest from genome wide association studies in pigs. First, we select all sequence variants associated with the trait. Subsequently, we prioritize variation by utilizing and integrating predicted variant impact scores, gene expression data, epigenetic marks for promotor and enhancer identification, and associated phenotypes in other (well-studied) mammalian species. The power of the method heavily relies on variant impact scores, for which we used pCADD, a tool which can assign scores to any
    variant in the genome including those in non-coding regions. Using our methodology, we are able to either pinpoint the likely causal mutation or substantially narrow down the list of potential causal candidates from any association result. We demonstrate the efficacy of the tool by reporting known and novel causal variants, of which many affect (non-coding) regulatory sequences associated with important phenotypes in pigs.

    This study provides a framework to pinpoint likely causal variation and genes underlying important phenotypes in pigs. Hence, the tool accelerates the discovery of new causal variants that could be directly implemented to improve selection. Finally, we report several common pathways and molecular mechanisms involved in analogous phenotypes between human and pig, proving the suitability of pig as a model to study human (metabolic) disease.
    Inhibition of methyltransferase activity of enhancer of zeste 2 leads to enhanced lipid accumulation and altered chromatin status in zebrafish
    Broeder, Marjo J. den; Ballangby, Jarle ; Kamminga, Leonie M. ; Aleström, Peter ; Legler, Juliette ; Lindeman, Leif C. ; Kamstra, Jorke H. - \ 2020
    Epigenetics and Chromatin 13 (2020)1. - ISSN 1756-8935 - 1 p.
    ATAC-seq - Epigenetics - Histone methyl transferases - Metabolism - Zebrafish

    BACKGROUND: Recent studies indicate that exposure to environmental chemicals may increase susceptibility to developing metabolic diseases. This susceptibility may in part be caused by changes to the epigenetic landscape which consequently affect gene expression and lead to changes in lipid metabolism. The epigenetic modifier enhancer of zeste 2 (Ezh2) is a histone H3K27 methyltransferase implicated to play a role in lipid metabolism and adipogenesis. In this study, we used the zebrafish (Danio rerio) to investigate the role of Ezh2 on lipid metabolism and chromatin status following developmental exposure to the Ezh1/2 inhibitor PF-06726304 acetate. We used the environmental chemical tributyltin (TBT) as a positive control, as this chemical is known to act on lipid metabolism via EZH-mediated pathways in mammals. RESULTS: Zebrafish embryos (0-5 days post-fertilization, dpf) exposed to non-toxic concentrations of PF-06726304 acetate (5 μM) and TBT (1 nM) exhibited increased lipid accumulation. Changes in chromatin were analyzed by the assay for transposase-accessible chromatin sequencing (ATAC-seq) at 50% epiboly (5.5 hpf). We observed 349 altered chromatin regions, predominantly located at H3K27me3 loci and mostly more open chromatin in the exposed samples. Genes associated to these loci were linked to metabolic pathways. In addition, a selection of genes involved in lipid homeostasis, adipogenesis and genes specifically targeted by PF-06726304 acetate via altered chromatin accessibility were differentially expressed after TBT and PF-06726304 acetate exposure at 5 dpf, but not at 50% epiboly stage. One gene, cebpa, did not show a change in chromatin, but did show a change in gene expression at 5 dpf. Interestingly, underlying H3K27me3 marks were significantly decreased at this locus at 50% epiboly. CONCLUSIONS: Here, we show for the first time the applicability of ATAC-seq as a tool to investigate toxicological responses in zebrafish. Our analysis indicates that Ezh2 inhibition leads to a partial primed state of chromatin linked to metabolic pathways which results in gene expression changes later in development, leading to enhanced lipid accumulation. Although ATAC-seq seems promising, our in-depth assessment of the cebpa locus indicates that we need to consider underlying epigenetic marks as well.

    A PXY-Mediated Transcriptional Network Integrates Signaling Mechanisms to Control Vascular Development in Arabidopsis
    Smit, Margot ; Mcgregor, Shauni ; Sun, Heng ; Gough, Catherine ; Bågman, Anne-Maarit ; Soyars, Cara L. ; Kroon, Johan T.M. ; Gaudinier, Allison ; Williams, Clara J. ; Yang, Xiyan ; Nimchuk, Zachary L. ; Weijers, Dolf ; Turner, Simon R. ; Brady, Siobhan M. ; Etchells, Peter - \ 2020
    The Plant Cell 32 (2020)2. - ISSN 1040-4651
    Vascular meristems generate the majority of biomass in higher plants. They constitute a bifacial stem cell population from which xylem and phloem are specified on opposing sides by positional signals. The PHLOEM INTERCALATED WITH XYLEM (PXY) receptor kinase promotes vascular cell division and organisation. However, how these functions are specified and integrated is unknown. Here, a putative PXY-mediated transcriptional regulatory network comprised of 690 transcription factor-promoter interactions was mapped. Among these interactions was a feed-forward loop containing transcription factors WUSCHEL HOMEOBOX RELATED 14 (WOX14) and TARGET OF MONOPTEROS 6 (TMO6), which each regulate the expression of a third transcription factor, LATERAL ORGAN BOUNDARIES DOMAIN 4 (LBD4). PXY signalling in turn regulates the WOX14, TMO6, LBD4 loop to control vascular proliferation. Genetic interaction between LBD4 and PXY suggests that LBD4 marks the phloem-procambium boundary, thus defining the shape of the vascular bundle. These data collectively support a novel mechanism that influences recruitment of cells into the phloem lineage, and defines the role of PXY signalling in this context to the arrangement of vascular tissue.
    Miniaturised interaction proteomics on a microfluidic platform with ultra-low input requirements
    Furlan, Cristina ; Dirks, René A.M. ; Thomas, Peter C. ; Jones, Robert C. ; Wang, Jing ; Lynch, Mark ; Marks, Hendrik ; Vermeulen, Michiel - \ 2019
    Nature Communications 10 (2019)1. - ISSN 2041-1723

    Essentially all cellular processes are orchestrated by protein-protein interactions (PPIs). In recent years, affinity purification coupled to mass spectrometry (AP-MS) has been the preferred method to identify cellular PPIs. Here we present a microfluidic-based AP-MS workflow, called on-chip AP-MS, to identify PPIs using minute amounts of input material. By using this automated platform we purify the human Cohesin, CCC and Mediator complexes from as little as 4 micrograms of input lysate, representing a 50─100-fold downscaling compared to regular microcentrifuge tube-based protocols. We show that our platform can be used to affinity purify tagged baits as well as native cellular proteins and their interaction partners. As such, our method holds great promise for future biological and clinical AP-MS applications in which sample amounts are limited.

    Allele-specific RNA-seq expression profiling of imprinted genes in mouse isogenic pluripotent states
    Dirks, René A.M. ; Mierlo, Guido Van; Kerstens, Hindrik H.D. ; Bernardo, Andreia S. ; Kobolák, Julianna ; Bock, István ; Maruotti, Julien ; Pedersen, Roger A. ; Dinnyés, András ; Huynen, Martijn A. ; Jouneau, Alice ; Marks, Hendrik - \ 2019
    Epigenetics and Chromatin 12 (2019)1. - ISSN 1756-8935
    Allele-specific RNA-seq - Embryonic stem cells - EpiSCs - ESCs - Genomic imprinting - Genotyping - Mouse embryo - Nuclear transfer (NT) - Parthenogenetic activation (PGA) - Pluripotency

    Background: Genomic imprinting, resulting in parent-of-origin specific gene expression, plays a critical role in mammalian development. Here, we apply allele-specific RNA-seq on isogenic B6D2F1 mice to assay imprinted genes in tissues from early embryonic tissues between E3.5 and E7.25 and in pluripotent cell lines to evaluate maintenance of imprinted gene expression. For the cell lines, we include embryonic stem cells (ESCs) and epiblast stem cells (EpiSCs) derived from fertilized embryos and from embryos obtained after nuclear transfer (NT) or parthenogenetic activation (PGA). Results: As homozygous genomic regions of PGA-derived cells are not compatible with allele-specific RNA-seq, we developed an RNA-seq-based genotyping strategy allowing identification of informative heterozygous regions. Global analysis shows that proper imprinted gene expression as observed in embryonic tissues is largely lost in the ESC lines included in this study, which mainly consisted of female ESCs. Differentiation of ESC lines to embryoid bodies or NPCs does not restore monoallelic expression of imprinted genes, neither did reprogramming of the serum-cultured ESCs to the pluripotent ground state by the use of 2 kinase inhibitors. Fertilized EpiSC and EpiSC-NT lines largely maintain imprinted gene expression, as did EpiSC-PGA lines that show known paternally expressed genes being silent and known maternally expressed genes consistently showing doubled expression. Notably, two EpiSC-NT lines show aberrant silencing of Rian and Meg3, two critically imprinted genes in mouse iPSCs. With respect to female EpiSC, most of the lines displayed completely skewed X inactivation suggesting a (near) clonal origin. Conclusions: Altogether, our analysis provides a comprehensive overview of imprinted gene expression in pluripotency and provides a benchmark to allow identification of cell lines that faithfully maintain imprinted gene expression and therefore retain full developmental potential.

    Integrative Proteomic Profiling Reveals PRC2-Dependent Epigenetic Crosstalk Maintains Ground-State Pluripotency
    Mierlo, Guido van; Dirks, René A.M. ; Clerck, Laura De; Brinkman, Arie B. ; Huth, Michelle ; Kloet, Susan L. ; Saksouk, Nehmé ; Kroeze, Leonie I. ; Willems, Sander ; Farlik, Matthias ; Bock, Christoph ; Jansen, Joop H. ; Deforce, Dieter ; Vermeulen, Michiel ; Déjardin, Jérôme ; Dhaenens, Maarten ; Marks, Hendrik - \ 2019
    Cell Stem Cell 24 (2019)1. - ISSN 1934-5909 - p. 123 - 137.e8.
    chromatin profiling - embryonic stem cells - epigenetics - ground-state pluripotency - H3K27me3 - histone modifications

    Marks and colleagues use integrative mass spectrometry to profile post-translational histone modifications and the chromatin-associated proteome in ground-state pluripotency. This reveals H3K27me3 and PRC2 as widespread hallmarks on euchromatin and heterochromatin. They show that ubiquitous chromatin-associated PRC2 protects the epigenome from priming, in particular from gaining DNA methylation.

    Epigenetic contribution to phenotypic plasticity and biotic stress-induced memory in Populus nigra
    Peña Ponton, C.J. ; Verhoeven, Koen - \ 2019
    In long-lived sessile organisms such as trees, phenotypic plasticity is an important requirement for successful persistence in changing or variable environments. In this sense, epigenetic mechanisms have the potential to mediate long-term plastic responses to environmental change. Part of this adaptive plasticity occurs almost immediately after new stress exposure, through coordinated modulation of gene expression associated with the epigenetic machinery (DNA methylation, histone modifications and/or small RNA interference). More important, these epigenetic marks can be long-lasting and sometimes heritable without a change in the DNA sequence. Long-lasting mechanisms for environmental responses may be of particular relevance to long-lived species such as trees, however the specific epigenetic mechanisms of phenotypic plasticity are still far from completely understood. In this project, we will focus on a clonal tree species, Populus nigra Italica, which has been distributed via planted cuttings across Europe since the 18th century. The low genetic variation in a single and geographically widespread clonal lineage gives way to studying phenotypic plasticity being explained mostly by epigenetic related mechanisms. Moreover, many poplar plantations regularly suffer from severe infections by biotrophic rust fungi Melampsora larici-populina. However, until now, studies have focused only on the first infection cycle and posterior responses/interactions are still unknown. The main aims of the present research project are to (1) identify genomic regions
    associated with stress-induced epigenetic modifications and their functional consequences, (2) evaluate the temporal methylation stability of such loci, and (3) explore the interplay of epigenetic mechanisms involved in plant-pathogen interaction.
    Avian ecological epigenetics: pitfalls and promises
    Sepers, Bernice ; Heuvel, Krista van den; Lindner, Melanie ; Viitaniemi, Heidi ; Husby, Arild ; Oers, Kees van - \ 2019
    Journal of Ornithology 160 (2019)4. - ISSN 2193-7192 - p. 1183 - 1203.
    Ecology - Evolution - Genetics - Ornithology - Phenotypic plasticity

    Epigenetic mechanisms can alter gene expression without a change in the nucleotide sequence and are increasingly recognized as important mechanisms that can generate phenotypic diversity. Most of our current knowledge regarding the origin and role of epigenetic variation comes from research on plants or mammals, often in controlled rearing conditions. Epigenetic research on birds in their natural habitats is still in its infancy, but is needed to answer questions regarding the origin of epigenetic marks and their role in phenotypic variation and evolution. Here we review the potential for studying epigenetic variation in natural bird systems. We aim to provide insights into (1) the origin of epigenetic variation, (2) the relationship between epigenetic variation and trait variation, and (3) the possible role of epigenetic variation in adaptation to changing environments. As there is currently little research on epigenetics in wild birds, we examine how findings on other taxa such as plants and mammals relate to birds. We also examine some of the pros and cons of the most commonly used methods to study patterns of DNA methylation in birds, and suggest some topics we believe need to be addressed to develop the field of wild avian epigenetics further.

    Combining metabolomics and genomics to elucidate physiological processes related to tail damage score in pigs
    Dervishi, E. ; Zande, Lisette van der; Silva Valente, T. da; Reimert, I. ; Mathur, Pramod K. ; Lopes, M.S. ; Knol, E.F. ; Plastow, G.S. - \ 2019
    In: Proceedings of the 37th International Society for Animal Genetics Conference (ISAG). - - p. 147 - 147.
    The purpose of this study was to identify important metabolitesrelated to tail damage (TDAM) score and to identify genomic regionsassociated with variation in the metabolites. We used 181 Tempo ×Topigs-20 animals divided over 2 batches balanced for gender and selectedfor positive (n = 81) or negative (n = 100) indirect genetic effect(IGE) for growth. Half of the pigs were housed in a barren environment,and the other half in an enriched environment. The tail scores were recordedat weaning and thereafter once a week (score 1 no visible taildamage, score 2 hair removed from the tail, score 3 bite marks and score4 clearly visible wound). Blood samples collected at 8, 9 and 22 weeksof age were used to determine metabolic profiles at The MetabolomicsInnovation Centre (University of Alberta). A total of 53 compoundswere quantified. Statistical analyses were performed in R version 3.5using a generalized mixed model with repeated measurements. A singlestep genome-wide association study (ssGWAS) was performed toidentify genomic regions associated with significant metabolites for tailbiting score. Preliminary results show that serum levels of glycerol andisopropanol were significantly associated with tail damage score. Animalswith TDAM 2 had greater glycerol concentration in blood whencompared with animals with TDAM 3 and 4 (P < 0.05). In addition,animals with TDAM 1 had lower isopropanol concentration when comparedwith animals with TDAM 2 and 3 (P < 0.05). GWAS identified2 candidate regions located on chromosome 6 associated with glyceroland isopropanol (at 45Mb, and at 149Mb respectively). The candidategenes identified in these regions were ZFP14, DOCK7, ANGPTL3,USP1 and KANK4. Angiopoietin like 3 is a secreted protein encoded byANGPTL3 that is involved in the regulation of lipid and glucose metabolism.This protein is present at high levels in the liver where it can bindto adipocytes to activate lipolysis, releasing free fatty acids and glycerol.These results suggest that animals with tail damage (propensity tobeing bitten) might have impaired lipolysis processes.
    Combining metabolomics and genomics to elucidate physiological processes related to tail damage score in pigs
    Dervishi, E. ; Zande, Lisette van der; Silva Valente, T. da; Reimert, I. ; Mathur, Pramod K. ; Lopes, M.S. ; Knol, E.F. ; Plastow, G.S. - \ 2019
    The purpose of this study was to identify important metabolitesrelated to tail damage (TDAM) score and to identify genomic regionsassociated with variation in the metabolites. We used 181 Tempo ×Topigs-20 animals divided over 2 batches balanced for gender and selectedfor positive (n = 81) or negative (n = 100) indirect genetic effect(IGE) for growth. Half of the pigs were housed in a barren environment,and the other half in an enriched environment. The tail scores were recordedat weaning and thereafter once a week (score 1 no visible taildamage, score 2 hair removed from the tail, score 3 bite marks and score4 clearly visible wound). Blood samples collected at 8, 9 and 22 weeksof age were used to determine metabolic profiles at The MetabolomicsInnovation Centre (University of Alberta). A total of 53 compoundswere quantified. Statistical analyses were performed in R version 3.5using a generalized mixed model with repeated measurements. A singlestep genome-wide association study (ssGWAS) was performed toidentify genomic regions associated with significant metabolites for tailbiting score. Preliminary results show that serum levels of glycerol andisopropanol were significantly associated with tail damage score. Animalswith TDAM 2 had greater glycerol concentration in blood whencompared with animals with TDAM 3 and 4 (P < 0.05). In addition,animals with TDAM 1 had lower isopropanol concentration when comparedwith animals with TDAM 2 and 3 (P < 0.05). GWAS identified2 candidate regions located on chromosome 6 associated with glyceroland isopropanol (at 45Mb, and at 149Mb respectively). The candidategenes identified in these regions were ZFP14, DOCK7, ANGPTL3,USP1 and KANK4. Angiopoietin like 3 is a secreted protein encoded byANGPTL3 that is involved in the regulation of lipid and glucose metabolism.This protein is present at high levels in the liver where it can bindto adipocytes to activate lipolysis, releasing free fatty acids and glycerol.These results suggest that animals with tail damage (propensity tobeing bitten) might have impaired lipolysis processes.
    Loss of function mutations in essential genes cause embryonic lethality in pigs
    Derks, Martijn F.L. ; Gjuvsland, Arne B. ; Bosse, Mirte ; Lopes, Marcos S. ; Son, Maren van; Harlizius, Barbara ; Tan, Beatrice F. ; Hamland, Hanne ; Grindflek, Eli ; Groenen, Martien A.M. ; Megens, Hendrik Jan - \ 2019
    Plos Genetics 15 (2019)3. - ISSN 1553-7404 - p. e1008055 - e1008055.

    Lethal recessive alleles cause pre- or postnatal death in homozygous affected individuals, reducing fertility. Especially in small size domestic and wild populations, those alleles might be exposed by inbreeding, caused by matings between related parents that inherited the same recessive lethal allele from a common ancestor. In this study we report five relatively common (up to 13.4% carrier frequency) recessive lethal haplotypes in two commercial pig populations. The lethal haplotypes have a large effect on carrier-by-carrier matings, decreasing litter sizes by 15.1 to 21.6%. The causal mutations are of different type including two splice-site variants (affecting POLR1B and TADA2A genes), one frameshift (URB1), and one missense (PNKP) variant, resulting in a complete loss-of-function of these essential genes. The recessive lethal alleles affect up to 2.9% of the litters within a single population and are responsible for the death of 0.52% of the total population of embryos. Moreover, we provide compelling evidence that the identified embryonic lethal alleles contribute to the observed heterosis effect for fertility (i.e. larger litters in crossbred offspring). Together, this work marks specific recessive lethal variation describing its functional consequences at the molecular, phenotypic, and population level, providing a unique model to better understand fertility and heterosis in livestock.

    A mechanistic model for studying the initiation of anguillid vitellogenesis by comparing the European eel (Anguilla anguilla) and the shortfinned eel (A. australis)
    Jéhannet, P. ; Kruijt, L. ; Damsteegt, E.L. ; Swinkels, W. ; Heinsbroek, L.T.N. ; Lokman, P.M. ; Palstra, A.P. - \ 2019
    General and Comparative Endocrinology 279 (2019). - ISSN 0016-6480 - p. 129 - 138.
    Brain-pituitary-gonad axis - Dopaminergic inhibition - Eel reproduction - Growth hormone - Sex steroids - Silvering

    An inverse relation exists between the maturation stage at the start of the oceanic reproductive migration and the migration distance to the spawning grounds for the various eel species. The European eel Anguilla anguilla migrates up to 5–6000 km and leaves in a previtellogenic state. The shortfinned eel A. australis migrates 2–4000 km and leaves in an early vitellogenic state. In this study, we compared the early pubertal events in European silver eels with those in silver shortfinned eels to gain insights into the initiation of vitellogenesis. Immediately after being caught, yellow and silver eels of both species were measured and sampled for blood and tissues. Eye index (EI), gonadosomatic index (GSI) and hepatosomatic index (HSI) were calculated. Plasma 11-ketotestosterone (11-KT) and 17β-estradiol (E2) levels were measured by radioimmunoassay. Pituitary, liver and ovaries were dissected for quantitative real-time PCR analyses (pituitary dopamine 2b receptor d2br, gonadotropin-releasing hormone receptors 1 and 2 gnrhr1 and gnrhr2, growth hormone gh and follicle-stimulating hormone-β fshb; liver estrogen receptor 1 esr1; gonad follicle-stimulating hormone receptor fshr, androgen receptors α and β ara and arb, vitellogenin receptor vtgr and P450 aromatase cyp19). Silver eels of both species showed a drop in pituitary gh expression, progressing gonadal development (GSI of ∼1.5 in European eels and ∼3.0 in shortfinned eels) and steroid level increases. In shortfinned eels, but not European eels, expression of fshb, gnrhr1 and gnrhr2, and d2br in the pituitary was up-regulated in the silver-stage as compared to yellow-stage females, as was expression of fshr, ara and arb in the ovaries. Expression of esr1 in European eels remained low while esr1 expression was up-regulated over 100-fold in silver shortfinned eels. The mechanistic model for anguillid vitellogenesis that we present suggests a first step that involves a drop in Gh and a second step that involves Fsh increase when switching in the life history trade-off from growth to reproduction. The drop in Gh is associated with gonadal development and plasma steroid increase but precedes brain-pituitary-gonad axis (BPG) activation. The Fsh increase marks BPG activation and increased sensitivity of the liver to estrogenic stimulation, but also an increase in D2br-mediated dopaminergic signaling to the pituitary.

    Benefits of herbivorous fish outweigh costs of corallivory in coral nurseries placed close to a Kenyan patch reef
    Knoester, E.G. ; Murk, A.J. ; Osinga, R. - \ 2019
    Marine Ecology Progress Series 611 (2019). - ISSN 0171-8630 - p. 143 - 155.
    Coral gardening - Coral predation - Coral reef conservation - Coral–algae interactions - Herbivory

    Coral mariculture involves time-consuming removal of fouling. On natural reefs, this service is provided by grazers. As natural reefs also harbour corallivores, it is debated whether reef-bound fish have a positive or negative effect on coral maricultured near natural reefs. This study quantified the net impact of herbivorous and corallivorous fish on coral mariculture. Nursery trees either uncaged, caged or as cage-control (15 per treatment) were placed near a patch reef at Wasini, Kenya, each hosting 10 Acropora verweyi fragments. From April to July 2016, survival and growth of the corals and bite marks on the corals were monitored. Using remote underwater video, bites by herbivorous and corallivorous fish were quantified. Upon termination of the experiment, dry weight of fouling from the nursery trees was determined. Caging of nurseries strongly reduced herbivory and corallivory. Results of cage-controls were not significantly different from uncaged trees. In caged nurseries, coral survival and growth were significantly lower than in uncaged nurseries, respectively 9% and 40% lower. Fouling was nearly 800% higher in caged nurseries. Herbivory was dominated by the surgeonfish Ctenochaetus striatus, which was responsible for 77% of the grazing. Monthly assessments showed bite marks on 10% of the uncaged coral fragments. Our study reveals that fouling control by herbivorous fish outweighs the costs of incidental corallivory on the survival and growth of A. verweyi. The vigour of unrestricted fouling, its negative impact on coral performance and the scarcity of corallivory justify the recommendation to place coral nurseries in Wasini near the reef.

    Assessment of browsed plants in a sub-tropical forest frontier by means of fuzzy inference
    Dechnik-Vázquez, Yanus A. ; García-Barrios, Luis ; Ramírez-Marcial, Neptalí ; Noordwijk, Meine van; Alayón-Gamboa, Armando - \ 2019
    Journal of Environmental Management 236 (2019). - ISSN 0301-4797 - p. 163 - 181.
    Agroforestry - Browsing - Cattle - Fuzzy inference - Silvopastoral systems

    Browsing of forest frontiers by cattle in sub-tropical landscapes is detrimental to ecosystem health, but essential to smallholder livelihoods. We described a silvopastoral landscape, searching for browsed plants to assess how much of the forest is actually used for this end, and also searching for potential new useful species for silvopastoral purposes. The first objective was accomplished through a floristic description, making observations of individuals with browsing marks. Information from interviews, bromatological analyses and vegetative propagation tests further complemented this information to achieve the second objective. We classified the results using Fuzzy Inference Systems (FISs). A great variety of nutritious browsed plants was found, distributed across various types of vegetation, growth habits and taxonomic groups: forest frontiers already are like silvopastoral systems. Various plants like Acalypha leptopoda, Montanoa tomentosa and Verbesina perymenioides are interesting prospects for further intensification of silvopastoral systems.

    Combined antioxidant-biofuel production from coffee silverskin
    Procentese, Alessandra ; Raganati, Francesca ; Olivieri, Giuseppe ; Russo, Maria Elena ; Marzocchella, Antonio - \ 2019
    Applied Microbiology and Biotechnology 103 (2019)2. - ISSN 0175-7598 - p. 1021 - 1029.
    Agro-industrial waste - Antioxidant - Biorefinery - Butanol - Coffee silverskin

    Biorefinery concept asks for an integrated processing approach to exploit all biomass components. The self-sustainability target may be approached if molecules characterized by high added value and fermentable sugars are produced simultaneously. In the present study, sequential (i) mild hydrothermal pretreatment to produce antioxidants and (ii) NaOH pretreatment to produce a fermentable sugar solution were carried out on coffee silverskin. Twenty-minute treatment and biomass to liquid ratio 1:30 (g mL−1) were identified as optimal operating conditions to extract bioactive compounds characterized by antioxidant activity (22.2 mgGAE/gCSS; 13.9 mgTE/gCSS). Twenty-minutes and biomass to liquid ratio of 1:20 (g mL−1) were identified as optimal operating conditions to maximize sugar recovery and ABE production (solvent yield YABE/Sugars and ABE productivity of 0.21 g g−1 and 0.12 g L−1 h−1 were obtained, respectively). The study marks the highly economic potential of the process aimed to exploit the CSS as feesdstock for antioxidant and biofuel production.

    Some personal reflections on the social production of multiple natures
    Macnaghten, Philip ; Jensen, Ole B. ; Kesselring, Sven ; Sheller, Mimi - \ 2018
    In: Mobilities and Complexities Routledge, Taylor & Francis Group - ISBN 9780429470097 - p. 64 - 69.
    The new ‘mobilities turn’ has become a powerful perspective in social theory. John Urry’s oeuvre has been very influential in the emergence of this new field and has had lasting impacts on many scholars. This collection presents originally commissioned essays from leading scholars in the field who reflect on how Urry’s writing influenced the course of their research and theorizing.

    This volume gathers contributions in relation to John Urry’s path-breaking work. The new ‘mobilities turn’ made a strong imprint in European social theory and is beginning to make an impact in the Americas and Asia as well. It challenges mainstream theoretical and empirical approaches that were grounded in a sedentary and bounded view of states. It propels innovative thinking about social and media ecologies, complex systems and social change. It bridges many disciplines and methodologies, leading to new approaches to existing problems while also resonating with questions about both history and the future. Mobilities research marks the rise of academic and intellectual cooperation and collaboration ‘beyond societies’, as nations around the world face the ecological limits of contemporary mobility and energy systems.

    The contributors represent several national contexts, including England, Germany, Denmark, Finland, Taiwan, Brazil, Canada, Australia and the USA. This book collects personal essays and gives insight into a vivid network of scientists who have connections of various degrees to the late John Urry as an academic figure, an author and a person.
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