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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    Variation in Verticillium wilts in woody hosts
    Hiemstra, Jelle - \ 2019
    variation - verticllium - woody hosts
    introductory presentation during Molecular en Evolutionary Ecology (MEE) course
    Data from: Remarkably divergent regions punctuate the genome assembly of the Caenorhabditis elegans Hawaiian strain CB4856
    Thompson, O.A. ; Snoek, Basten ; Nijveen, Harm ; Sterken, Mark ; Volkers, Rita ; Brenchley, R. ; Hof, A. van 't; Bevers, Roel ; Cossins, A.R. ; Yanai, I. ; Hajnal, A. ; Schmid, T. ; Perkins, J.D. ; Spencer, D. ; Kruglyak, L. ; Andersen, E.C. ; Moerman, D.G. ; Hillier, L.W. ; Kammenga, Jan ; Waterston, R.H. - \ 2016
    University of Washington
    Caenorhabditis elegans - evolution - genome assembly - variation
    The Hawaiian strain (CB4856) of Caenorhabditis elegans is one of the most divergent from the canonical laboratory strain N2 and has been widely used in developmental, population and evolutionary studies. To enhance the utility of the strain, we have generated a draft sequence of the CB4856 genome, exploiting a variety of resources and strategies. The CB4856 genome when compared against the N2 reference has 327,050 single nucleotide variants (SNVs) and 79,529 insertion-deletion events (indels) that result in a total of 3.3 megabasepairs (Mb) of N2 sequence missing from CB4856 and 1.4 Mb of sequence present in CB4856 not present in N2. As previously reported, the density of SNVs varies along the chromosomes, with the arms of chromosomes showing greater average variation than the centers. In addition, we find 61 regions totaling 2.8 Mb, distributed across all six chromosomes, that have a greatly elevated SNV density, ranging from 2% to 16% SNVs. A survey of other wild isolates show that the two alternative haplotypes for each region are widely distributed, suggesting they have been maintained by balancing selection over long evolutionary times. These divergent regions contain an abundance of genes from large rapidly evolving families encoding F-box, MATH, BATH, seven-transmembrane G-coupled receptors, and nuclear hormone receptors suggesting that they provide selective advantages in natural environments. The draft sequence makes available a comprehensive catalog of sequence differences between the CB4856 and N2 strains that will facilitate the molecular dissection of their phenotypic differences. Our work also emphasizes the importance of going beyond simple alignment of reads to a reference genome when assessing differences between genomes.
    Milk Oligosaccharide Variation in Sow Milk and Milk Oligosaccharide Fermentation in Piglet Intestine
    Difilippo, Elisabetta ; Pan, Feipeng ; Logtenberg, Madelon ; Willems, Rianne ; Braber, Saskia ; Fink-Gremmels, Johanna ; Schols, Henk Arie ; Gruppen, Harry - \ 2016
    Journal of Agricultural and Food Chemistry 64 (2016)10. - ISSN 0021-8561 - p. 2087 - 2093.
    abundance - chromatography - cow - mass analysis - pigs - sugars - variation

    Porcine milk oligosaccharides (PMOs) were analyzed in six colostrum and two mature milk samples from Dutch Landrace sows. In total, 35 PMOs were recognized of which 13 were new for the PMO literature: Neutral HexNAc-Hex, β4′-galactosyllactose, putative GalNAc(α/β1-3)Gal(β1-4)Glc, lacto-N-fucopentaose-II, lacto-N-tetraose, galactose substituted lacto-N-neohexaose, lacto-N-hexaose and difucosyl-lacto-N-hexaose, and acidic Neu5Ac(α2-6)GlcNAc(β1-3)Gal(β1-4)Glc, sialyllacto-N-tetraose-a and -b, Neu5Ac2-Hex3, and sialyllacto-N-fucopentaose-II. PMOs were analyzed using capillary electrophoresis with laser-induced florescence detection or mass spectrometry and using liquid chromatography with mass spectrometry. Interindividual variation regarding PMO presence and concentration was observed between porcine milks. Within a limited sample set, a 43% decrease of the major PMOs was found during a 1 w lactation period. Interestingly, while some PMOs decreased, some other PMOs increased in concentration. PMOs were also monitored in fecal samples of suckling piglets. In feces of 1-2 d old piglets, few intact PMOs were found, indicating considerable PMO fermentation at early stage of life.

    Study of natural variation for Zn deficiency tolerance in Arabidopsis thaliana
    Campos, A.C.A.L. - \ 2015
    Wageningen University. Promotor(en): Maarten Koornneef, co-promotor(en): Mark Aarts. - Wageningen : Wageningen University - ISBN 9789462572515 - 232
    arabidopsis thaliana - voedingsstoffentekorten - sporenelementtekorten - zink - genetische variatie - tolerantie - variatie - genetica - arabidopsis thaliana - nutrient deficiencies - trace element deficiencies - zinc - genetic variation - tolerance - variation - genetics

    English summary

    Zinc is an important structural component and co-factor of proteins in all living organisms. The model plant species for genetic and molecular studies, Arabidopsis thaliana, expresses more than 2,000 proteins with one or more Zn binding domains. Low Zn availability in arable soils is a widespread problem around the world which results in agricultural losses and the production of grains with low Zn content. The long-term consumption of low-Zn-content food items leads to severe health problems in humans as a result of severe or mild dietary Zn deficiency. Hence the importance of studying Zn homeostasis in plants and mechanisms involved in Zn deficiency tolerance aiming to enhance Zn concentration in plants edible parts and to develop varieties with a higher tolerance to Zn deficiency.

    Plants are sessile organisms which trough evolution have developed specific traits in order to adapt to certain environmental conditions in their surroundings. As a result some plant genotypes are more tolerant to Zn deficiency and when exposed to low Zn conditions are able to perform better than others. To investigate the physiological mechanisms involved in Zn deficiency tolerance I examined natural variation present in a set of twenty diverse Arabidopsis thaliana accessions. In chapter 2, differences in shoot biomass production, Zn usage index (ZnUI), ionome (concentration of elements) and expression level of six key Zn deficiency responsive genes were studied. Accessions did not show large natural variation for shoot Zn concentration under Zn deficiency, while the decreases in shoot biomass and ZnUI were more variable. The conclusion from this is that accessions differ for the minimum Zn concentration required for growth which is associated with differences in Zn deficiency tolerance. We also found that the gene expression levels of three Zn transmembrane transporters (IRT3, ZIP3 and 4) in shoot were positively correlated with ZnUI and shoot biomass, but negatively correlated with shoot Zn concentration. This implies that a higher tolerance to Zn deficiency in A. thaliana is associated with an increased Zn translocation from root to shoot under low Zn. Furthermore, I used a logistic regression model to demonstrate that differences in the shoot ionome can be used as a biomarker to identify the plant Zn physiological state. Based on the changes in the concentrations of some elements in each of the Zn deficiency treatments it was possible to predict the Zn physiological state of the plants similarly to when Zn concentration is used alone.

    The adaptive response to Zn deficiency involves physiological changes in shoots, but also in roots which play a key role in the acquisition of nutrients. In chapter 3 I used the same twenty A. thaliana accessions as described in chapter 2 to identify root system architecture traits and changes in the root ionome involved in a higher tolerance to Zn deficiency in plants. Similar to shoots, all accessions showed a strong reduction in root Zn concentration under Zn deficiency, whereas changes in other root system architecture traits were more variable between the accessions. These analyses showed that differences between the accessions in root system architecture traits and minimum Zn concentration required for growth are important for Zn deficiency tolerance. The Zn deficiency treatment also affects the formation of lateral roots and thus root system architecture. It was therefore not surprising that the Zn deficiency treatment induced changes in the concentrations of other elements which were correlated with changes in root traits.

    Plants respond to different concentrations of Zn supply by changing the expression levels of genes involved in the Zn homeostasis network. This is important for the control of the Zn concentration and sequestration in plant cells, tissues and organs and involves the uptake, accumulation, transport and redistribution of Zn within the plant. Based on the work described in chapter 2, three A. thaliana accessions were selected with contrasting tolerance to Zn deficiency, and used for a whole genome transcription profiling analysis using RNA sequencing. Chapter 4 describes the identification of sets of general and core genes used by A. thaliana in its response to Zn deficiency. The purpose of using three accessions was to complement previous studies, which used only one accession, and identify new candidate genes involved in the general response to Zn deficiency in A. thaliana. General transcriptional changes were observed in the regulation of carbohydrate metabolism, glucosinolate biosynthesis and the circadian clock. As the transcriptional changes were recorded at two time points, it was also possible to distinguish early and late responses to Zn deficiency. The early response to Zn deficiency was stronger in roots with the induction of several Zn homeostasis genes and repression of Fe uptake genes. The late response to Zn deficiency comprised of the strong induction of several Zn uptake, transport and remobilization genes in both roots and shoots. These analysis confirmed several genes previously identified in Col-0 to have a general role in the Zn deficiency response, but it also led to the identification of new candidate genes, such as defensins and defensin-like genes, as very promising new actors in the A. thaliana Zn deficiency homeostasis network.

    Chapter 5 describes the A. thaliana accession-specific Zn deficiency responsive transcript profiles, comparing Tsu-0, Pa-2 and Col-0, with the aim to identify biological processes involved in the observed differences in Zn deficiency tolerance between these three accessions. Tsu-0 displayed a high tolerance to Zn deficiency in shoot, Col-0 (reference accession) showed a high tolerance to Zn deficiency in both root and shoot, whereas Pa-2 root and shoot were more sensitive to Zn deficiency. Some of the accession-specific Zn deficiency responsive transcripts were involved in similar biological processes, such as defence response, programmed cell death and carbohydrates and glucosinolates metabolism. The differential regulation of these processes between the three accessions may reflect their differences in Zn deficiency tolerance. Among the Col-0 specific transcripts were several genes encoding proteins kinases which may play a role in a more specific separation of the abiotic and biotic stress responses in this accession and possibly involved in its higher tolerance to Zn deficiency in both shoots and roots. Tsu-0 specifically changes the expression of a set of shoot transcripts encoding ethylene responsive transcription factors which are involved in the regulation of shoot growth and plant tolerance to abiotic and biotic stresses, corresponding well with the observed shoot Zn deficiency tolerance. Accession Pa-2 down-regulated transcripts involved in cell wall organization in roots which correlates with its high sensitivity to Zn deficiency in this organ. Finally, the accessions specific response to Zn deficiency also resulted in the differential regulation of transcripts encoding transposases which may reflect large scale chromatin reorganization or demethylation in response to the stress condition.

    The main findings of the research described in this thesis and their implications are described in the General Discussion (chapter 6). By investigating the response to Zn deficiency in a diverse set of A. thaliana accessions both at the physiological and transcriptional level important mechanisms involved in Zn deficiency tolerance were identified. Furthermore, several key candidate genes among the accessions general and accession-specific Zn deficiency responsive transcripts were identified. The further functional characterization of these genes is expected to reveal important new steps in the regulation of Zn homeostasis and Zn deficiency tolerance in A. thaliana.

    Cooperative and uniform fish? : social interactions and variability in live body weight in the GIFT strain (Nile tilapia, Oreochromic niloticus) in Malaysia
    Khaw, H.L. - \ 2015
    Wageningen University. Promotor(en): Johan van Arendonk, co-promotor(en): Piter Bijma; R.W. Ponzoni. - Wageningen : Wageningen University - ISBN 9789462572157 - 161
    oreochromis niloticus - sociaal gedrag - lichaamsgewicht - variatie - genetische effecten - inteelt - kenmerken - heritability - genotype-milieu interactie - genotypische variatie - genetische verbetering - veredelingsprogramma's - visteelt - maleisië - oreochromis niloticus - social behaviour - body weight - variation - genetic effects - inbreeding - traits - heritability - genotype environment interaction - genetic variance - genetic improvement - breeding programmes - fish culture - malaysia

    Abstract

    Khaw, HL. (2014). Cooperative and uniform fish? Social interactions and variability in live body weight in the GIFT strain (Nile tilapia, Oreochromic niloticus) in Malaysia. PhD thesis, Wageningen University, the Netherlands.

    Social interactions are present everywhere in the living world. Such social interactions may lead to indirect genetic effects (IGE), which are heritable effects of an individual on trait values of the other individuals its interacts with. IGEs may affect the direction and magnitude of response to selection in breeding programs. Moreover, social interactions may affect variability of traits. In aquaculture, competition for resources inflates size variation within populations. In this thesis, we used the Genetically Improved Farmed Tilapia (GIFT; Oreochromis niloticus) strain to investigate the genetic basis for social interactions and variability in harvest weight for tropical finfish. Social interaction experiments were established for quantifying the genetic and non-genetic indirect effects on harvest weight in the GIFT strain. We found evidence for IGEs on harvest weight, and a negative direct-indirect genetic correlation, which suggesting heritable competitive interactions for harvest weight in GIFT. Hence, breeding schemes may need to be adapted to avoid an increase in competition. A stochastic simulation study was conducted to examine the effect of BLUP selection on the rate of inbreeding for socially affected traits. The rates of inbreeding for scenarios with IGEs were greater than for scenarios without IGE. Therefore, with IGEs there is a greater need for a selection algorithm that restricts the increase of mean kinship. In aquaculture industry, there is a wide range of commercial production environments, which may leads to genotype by environment (GxE) interaction, for example due to differential social interactions. The GIFT fish were tested in ponds and cages to study the GxE interaction. The genetic correlations between environments (0.73 to 0.85, for harvest weight and body measurements) indicate little GxE-interaction. The data collected from the social interaction experiments were also used to investigate the presence of genetic variation in uniformity for harvest weight. The genetic coefficient of variation for standard deviation of harvest weight (0.17) shows that uniformity of harvest weight is heritable and can be increased by selective breeding. In the General Discussion of this thesis, the uniformity study was extended to incorporate IGE. The result indicates that more cooperative fish are not necessary more uniform for harvest weight. Overall, our results suggest that genetic improvement in fish breeding programs can be increased by accounting for social interactions.

    Natural variation in casein composition of milk
    Bijl, E. - \ 2014
    Wageningen University. Promotor(en): Toon van Hooijdonk, co-promotor(en): T. Huppertz; Hein van Valenberg. - Wageningen : Wageningen University - ISBN 9789461739445 - 145
    melk - caseïne - melksamenstelling - variatie - milk - casein - milk composition - variation

    Bovine milk contains 3-4 % protein and almost 80% of the milk protein fraction consist of four caseins; αs1-casein, β-casein, αs2-casein and κ-casein. Most of the caseins in milk are assembled in casein micelles, which consist of several thousands of individual casein molecules and salts. The unique structure of casein micelles allows the delivery of large amounts of calcium and phosphate to the neonate. Considerable natural variation in casein content and composition exists between milk samples from individual cows, however the impact of these variations on casein micelle structure and technological properties of dairy products are largely unknown. This study showed that the expression of caseins and their post-translational modification as well as inclusion of calcium in casein micelles are well-balanced processes. Analysis of the genetic background of phosphorylation of αs1-casein with eight or nine phosphate groupsshowed that αs1-casein phosphorylation was regulated by a different set of genes. Also, variation in αs1-casein phosphorylation resulted in changes in the core of casein micelles and was associated with a difference in degradation efficiency by chymosin in milk gels. Another post-translational modification, glycosylation of κ-casein, resulted in changes in the surface of casein micelles. Natural variation in αs1-CN phosphorylationand glycosylation of κ-casein are both relevant factors to consider for optimization of dairy products and the design of future breeding strategies.

    Uniformiteit uitgangsmateriaal bij aardbeien
    Dieleman, Anja - \ 2013
    fruit crops - small fruits - strawberries - propagation materials - planting stock - cuttings - crop yield - plant development - variation
    Variation in behaviour and growth of common sole : genetic and environmental influences
    Mas Muñoz, J. - \ 2013
    Wageningen University. Promotor(en): Johan Verreth, co-promotor(en): Johan Schrama; Hans Komen; Robbert Blonk. - [S.l.] : S.n. - ISBN 9789461735324 - 165
    tong (vis) - groei - voedingsgedrag - diergedrag - variatie - genetische factoren - milieufactoren - genotype-milieu interactie - visteelt - aquacultuur - dover soles - growth - feeding behaviour - animal behaviour - variation - genetic factors - environmental factors - genotype environment interaction - fish culture - aquaculture

    Common sole (Solea solea) has a high potential for commercial aquaculture because of its consumer popularity and high market values in Europe. However, a major economic constraint for the culture of sole is its slow and variable growth. The aim of this thesis was to investigate: 1) the importance of (non-) feeding behaviour of sole in relation to variation in growth; 2) the effect of (social and physical) environmental factors on behaviour, growth and the relation between them; 3) the existence of GE interaction regarding growth. Feeding consistency, swimming activity in the tank, and boldness during (novel environment and light avoidance) behavioural tests explained variation in feed intake and thereby growth of individually housed sole. For communally housed sole, behavioural factors derived from individual behavioural tests and sex also explained variation in growth. The motivation to bury was negatively related to growth, whereas the motivation to explore a novel environment was positively related. Social interactions, both in quality (i.e., size hierarchies) and in quantity (i.e.,stocking density), influenced (non-) feeding behaviour and growth of sole. High stocking density in sole reared without substrate results in more fish-fish interactions, which increases swimming activity, FCR and variation in growth. These conditions seem to induce social stress in sole, which is alleviated when sand is provided. Environmental factors which differ between nature and farming conditions, such as food type, sand and variability of environmental conditions, influenced individual behavioural responses of sole to a novel environment test but did not induce variation in growth. Results suggest that consistent relationships between behaviour and growth develop when fish are reared in stable barren environments but not when fish experience more variable, enriched/natural environments. The role of environmental factors in the relationship between (non)-feeding behaviour and growth was supported by strong genotype by environment interaction for growth of sole reared in a semi-natural or an intensive aquaculture environment. In conclusion, the effect of (non-) feeding behaviour on growth should be taken into account to foster progress in the farming of sole. Environmental factors (i.e., substrate, stocking density) that influence behaviour and growth should be used to optimize culture systems. Future genetic selection strategies should focus more on behavioural characteristics to select sole which will be able to cope and grow best in the different rearing conditions present in commercial aquaculture.

    Piglet birth weight and litter uniformity : importance of pre-mating nutritional and metabolic conditions
    Wientjes, J.G.M. - \ 2013
    Wageningen University. Promotor(en): Bas Kemp, co-promotor(en): Nicoline Nieuwenhuizen-Soede; Henry van den Brand. - S.l. : s.n. - ISBN 9789461735027 - 238
    biggen - zeugen - geboortegewicht - variatie - worpen - metabolisme - insuline - tijd tussen werpen van biggen - voer - samenstelling - varkensvoeding - voedingsfysiologie - diervoeding - dierfysiologie - piglets - sows - birth weight - variation - litters - metabolism - insulin - farrowing interval - feeds - composition - pig feeding - nutrition physiology - animal nutrition - animal physiology

    High piglet birth weights and litter uniformity are important for piglet survival and piglet performance. Within-litter variation in piglet birth weight is the consequence of within-litter variation in early embryo development, which in turn reflects variation in follicle and oocyte development. Insulin-stimulating diets before mating can influence litter development and uniformity, probably through beneficial effects of insulin on IGF-1 and follicle development. The first aim of this thesis, therefore, was to study effects of insulin-stimulating diets during the weaning-to-estrus interval (WEI) on plasma insulin and IGF-1 levels and follicle development, and consequences for embryo, fetal and placental development and uniformity at different stages of pregnancy in sows. Results of this thesis show that plasma insulin levels during WEI can be effectively enhanced by dietary sugars as dextrose and sucrose (high peaks directly after feeding) and starch (enhanced insulin levels at ~4h after feeding) in a dose-dependent manner. Follicle development and subsequent litter uniformity of embryos (at day 10 of pregnancy) or fetuses and placentas (at day 42 of pregnancy), however, were not affected by insulin-stimulating diets during WEI, nor related to plasma insulin and IGF-1 levels during WEI. Besides effects of pre-mating diets, plasma insulin and IGF-1 levels and follicle development are also influenced by the pre-mating metabolic state of the sow: in sows with severe body condition loss during lactation, plasma insulin and IGF-1 levels and follicle development at weaning are suppressed, and restoration of plasma insulin and IGF-1 levels and follicle development occurs in sows with a prolonged lactation or a prolonged weaning-to-pregnancy interval (WPI). The second aim of this thesis, therefore, was to study effects of these pre-mating conditions related to sow metabolic state on subsequent piglet birth weight and litter uniformity. In this thesis it is shown for the first time that pre-mating conditions related to sow metabolic state affect subsequent litter uniformity. Litter uniformity at birth was compromised by severe sow body condition loss during previous lactation and improved in sows with a prolonged WPI. Furthermore, it was shown that in (organic) sows with prolonged lactations (6 weeks) and large litters (17.4±0.3 piglets), insulin-stimulating diets before mating did not result in improved piglet birth weights or litter uniformity. This may be related to a restored follicle development at weaning in these sows. In these large organic litters, piglet birth weight and litter uniformity were strongly related to piglet survival during lactation. To conclude, results of this thesis confirm that litter uniformity at birth is already (partly) determined during the pre-mating period, likely related to (insufficient) restoration of follicle development. In contrast to previous studies, insulin-stimulating diets during WEI did not improve litter uniformity of embryos, fetuses or placentas and/or piglets in sows. The role of plasma IGF-1 levels and follicle development at weaning (both related to sow parity and sow body condition loss), and effects of insulin-stimulating diets during lactation, need further study. Finally, although effects of pre-mating nutritional and metabolic conditions on subsequent piglet birth weight and litter uniformity seem only marginal, these marginal effects can have substantial effects on pre-weaning piglet survival.

    The biology of milk synthesis from a proteomics perspective
    Lu, J. - \ 2013
    Wageningen University. Promotor(en): Toon van Hooijdonk, co-promotor(en): Kasper Hettinga; Jacques Vervoort. - S.l. : s.n. - ISBN 9789461734600 - 177
    melksynthese - melksecretie - melksamenstelling - oppervlakte-eiwitten - eiwitexpressieanalyse - variatie - milk synthesis - milk secretion - milk composition - surface proteins - proteomics - variation

    Large variation in bovine milk composition of Dutch Holstein cows has been observed. The factors influencing the milk synthesis and secretion process in the mammary gland and the variations in this process lead to variation in milk composition. The understanding of milk synthesis was improved during the last decades, however, much is still unknown, especially with regard to lipid synthesis and secretion. In this research, a proteomics technique (FASP-Dimethyl labeling-NanoLC-Orbitrap-MS/MS) was used to identify and quantify low abundant proteins in milk. By using this proteomics technique combined with a metabolomics technique (1H-NMR), the variation in milk synthesis and secretion processes were shown as affected by several factors influencing milk composition: DGAT1 polymorphism, fat globule size and energy balance of the cow. Stomatin, cholesterol and cholesterol synthesis enzymes were shown to be important for milk synthesis and secretion in lactating cows in all the different studies. Cytoplasmic vesicle and cytoskeleton proteins were shown to be involved in milk fat globule secretion. These results led to new insights in milk synthesis and secretion.

    Minimaliseren van klimaatvariatie - “Uitkomsten van het onderzoek naar toepassing van mini-sensoren voor RV-T”
    Balendonck, Jos - \ 2011
    greenhouse horticulture - greenhouse technology - air conditioning - greenhouses - variation - sensors - cropping systems
    Met flora meer fauna de stad in trekken
    Hoffman, M.H.A. - \ 2010
    Tuin en Landschap 32 (2010)26. - ISSN 0165-3350 - p. 25 - 29.
    ecologie - flora - fauna - vegetatie - variatie - stedelijke ecologie - ecology - flora - fauna - vegetation - variation - urban ecology
    Meer flora en fauna in de stedelijke omgeving begint met de aanplant van gevarieerd groen. Plant Publicity Holland geeft in een overzicht aan welke bomen, heesters en vaste planten daarvoor geschikt zijn.
    Variability in carbon exchange of European croplands
    Moors, E.J. ; Jacobs, C.M.J. ; Jans, W.W.P. ; Supit, I. ; Werners, S.E. ; Kutsch, W.L. ; Elbers, J.A. ; Kruijt, B. - \ 2010
    Agriculture, Ecosystems and Environment 139 (2010)3. - ISSN 0167-8809 - p. 325 - 335.
    netto ecosysteem uitwisseling - kooldioxide - emissie - landbouwgrond - gewasproductie - variatie - europa - net ecosystem exchange - carbon dioxide - emission - agricultural land - crop production - variation - europe - agricultural soils - net carbon - sequestration - forests - respiration - ecosystems - fluxes - model
    The estimated net ecosystem exchange (NEE) of CO2 based on measurements at 17 flux sites in Europe for 45 cropping periods showed an average loss of -38 gC m-2 per cropping period. The cropping period is defined as the period after sowing or planting until harvest. The variability taken as the standard deviation of these cropping periods was 251 gC m-2. These numbers do not include lateral inputs such as the carbon content of applied manure, nor the carbon exchange out of the cropping period. Both are expected to have a major effect on the C budget of high energy summer crops such as maize. NEE and gross primary production (GPP) can be estimated by crop net primary production based on inventories of biomass at these sites, independent of species and regions. NEE can also be estimated by the product of photosynthetic capacity and the number of days with the average air temperature >5 °C. Yield measured at these sites or reported at the NUTS2 level dataset of EUROSTAT is a relatively poor predictor of NEE. To investigate the difference in the variability in CO2 emissions of different crops at the same location and to compare this variation with the variation of the same crop at different locations and with the inter-annual variation the measured dataset at the flux sites was extended with simulated data. These simulations show that the variability in carbon exchange is determined by: firstly the choice of crop and the location and to a lesser extent by the yearly differences in climate.
    The Benefish consortium reports on deviation from expected feed intake in relation to farm management at turbot, sole, trout, salmon, seabass farms
    Schneider, O. ; Schram, E. ; Noble, C. - \ 2009
    IJmuiden : IMARES (Report / Wageningen IMARES no. C036.09) - 39
    visteelt - viskwekerijen - teeltsystemen - dierenwelzijn - dierfysiologie - voeropname - variatie - fish culture - fish farms - cropping systems - animal welfare - animal physiology - feed intake - variation
    The objective of the present study is therefore to relate deviations in expected feed intake to farm management practices for various species and culture systems.
    Resultaten precisieketen zomergerst
    Jukema, J.N. ; Vogelzang, K. - \ 2008
    Kennisakker.nl 2008 (2008)11 sept.
    gerst - graansoorten - rassen (planten) - gewasopbrengst - variatie - gewasteelt - precisielandbouw - landbouwkundig onderzoek - akkerbouw - barley - cereals - varieties - crop yield - variation - crop management - precision agriculture - agricultural research - arable farming
    Dit rapport beschrijft een deel van de resultaten vanuit het project “De precisieketen”. “De precisieketen” is een project welke een looptijd had van 2003 – 2006. Het project speelde zich af op de Veenkoloniën, op bedrijven van ongeveer 18 telers. Het betreft hier in alle gevallen bedrijven op de zand- en dalgronden. De doelstelling van het project was het verbeteren van het ketenrendement van de brouwgerst teelt. Daarnaast werd het ketenrendement van brouwgerst gebruikt als toets voor opbrengstverbeteringen van de volgteelten.
    Resultaten Perceel Centraal 2006 : verslag van de proeven op proefbedrijf 't Kompas te Valthermond
    Wijnholds, K.H. ; Berg, W. van den; Jukema, J.N. - \ 2008
    Lelystad : PPO AGV (PPO rapport ) - 15
    variatie - gewasopbrengst - gewaskwaliteit - optimalisatiemethoden - bodemonderzoek - satellietbeelden - proefbedrijven - precisielandbouw - veenkolonien - variation - crop yield - crop quality - optimization methods - soil testing - satellite imagery - pilot farms - precision agriculture - veenkolonien
    Binnen het project “Perceel Centraal” vormt een biomassakaart met behulp van LORIS ® de basis van de zoektocht naar een optimaal teeltrendement. Een perceel wordt vroeg in het teeltseizoen gescand waarna een biomassakaart ontstaat. Ieder gebrek of overschot waaraan een plant wordt blootgesteld uit zij in dit stadium van haar ontwikkeling in de groei en kleur van het blad. Met een biomassakaart worden de verschillen binnen een perceel meetbaar, stuurbaar en waardeerbaar. De oorzaken van deze verschillen kunnen uiteenlopen door bijvoorbeeld een te hoge of juist een te lage pH, structuurproblemen, aaltjeshaarden of nutriëntentekort. Perceel Centraal is gestart in 2006 en in dat eerste jaar is geïnventariseerd wat de variatie binnen percelen nu werkelijk is. Er is in beeld gebracht wat de variatie is in biomassa, opbrengst en kwaliteit. Die data is geanalyseerd op mogelijke verbanden. De resultaten van dat onderzoek zijn in dit verslag opgenomen
    Horizontale variatie
    Campen, J.B. ; Gelder, A. de - \ 2007
    Wageningen : Plant Research International (Rapport / Plant Research International 131) - 16
    kassen - luchttemperatuur - variatie - thermische schermen - nederland - binnenklimaat - greenhouses - air temperature - variation - thermal screens - netherlands - indoor climate
    Het klimaat in een kas is nooit helemaal gelijk. Het is onvermijdelijk dat er lokaal koudere of warmere plekken aanwezig zijn, dat de CO2-concentratie varieert, dat de luchtvochtigheidsverdeling niet uniform is, etc. In de praktijk wordt het klimaat geregeld op de koudste, natste of een gemiddelde plek. Het gevolg hiervan is dat het energieverbruik en de gewasontwikkeling niet optimaal zijn. In dit project is onderzocht: -wat de oorzaken en oplossingen zijn voor het bestaan van horizontale variatie - of er gebruik kan worden gemaakt van horizontale variatie - wat in termen van energie en productie de potentie is van mogelijke oplossingen
    Pleidooi voor uniforme regels en kosten bij waterwinning voor beregening
    Stoof, C.R. ; Ritsema, C.J. - \ 2006
    H2O : tijdschrift voor watervoorziening en afvalwaterbehandeling 39 (2006)25/26. - ISSN 0166-8439 - p. 24 - 26.
    grondwaterwinning - wetgeving - variatie - kosten - irrigatie - watervoorziening - waterwinning - waterschappen - provincies - harmonisatie - sportterreinen - beregening - irrigation - groundwater extraction - water supply - legislation - variation - costs - water catchment - polder boards - provinces - harmonization - sports grounds - overhead irrigation
    Zowel de regels als de kosten voor grondwateronttrekkingen variëren binnen Nederland zo sterk dat er navrante verschillen bestaan voor de gebruikers van water. Doordat provincies en waterschappen hun eigen regels en prijzen mogen bepalen, kan het voorkomen dat de ene gebruiker veel meer betaalt voor precies hetzelfde water als zijn buurman of aan geheel andere regels moet voldoen. Harmonisatie van regels en kosten is noodzakelijk voor een eerlijk beleid, waarbij niet de provincie of waterschapsgrenzen leidend moeten zijn, maar het hydrologische systeem waaruit onttrokken wordt.
    Whole-farm risk management in arable farming: portfolio methods for farm-specific business analysis and planning
    Kobzar, O. - \ 2006
    Wageningen University. Promotor(en): Ruud Huirne, co-promotor(en): Marcel van Asseldonk. - [S.l. ] : S.n. - ISBN 9789085044789 - 156
    agrarische bedrijfsvoering - akkerbouw - risico - risicogedrag - inkomsten uit het landbouwbedrijf - lineair programmeren - variatie - verandering - economische analyse - oogstverzekering - nederland - farm management - arable farming - risk - risk behaviour - farm income - linear programming - variation - change - economic analysis - crop insurance - netherlands
    Keywords:Economics, panel data, arable farming, revenue variability, farm business and financial characteristics, portfolio analysis, quadratic risk programming, utility-efficient programming, crop insurance

    The problem of farm income instability remains an important problem for agricultural decision-makers. Due to the difficulties in making an accurate prediction of the future, agricultural business is a risky business with unstable incomes. However, farmers have a number of tools to manage such risky situations (for instance, they use diversification possibilities on farm or price contracts). Portfolio optimisation is a useful tool to evaluate the consequences of alternative risk management strategies for a farmer, providing the protections and opportunities with respect to a wide range of risky prospects. The main advantage of portfolio optimisation is that it is able to capture much data covering whole-farm context, finding an optimum taken the interaction between the activities into account.

    The main aim of this research is to analyse an individual whole-farm portfolio structure and to evaluate the possibilities of risk-reduction in order to stabilise farm income in arable farming. In the analysis four main steps have been distinguished. First, farm revenue variability was analysed between farms and within a farm. Within-farm analysis overviews the variability and dependency of crop revenue components (i.e., yields and prices) over time and their effect on farm revenue. Between-farm analysis refers to farm revenue variability that is affected by differences in business and financial characteristics of farms. Second, an evaluation of the trade-off between expected gross margins and standard deviations was carried out using linear programming and quadratic risk programming. This analysis showed (considerable) differences between farms, which should be recognised in advising farms on portfolio selection. Then an analysis was carried out that clarifies the advantages and disadvantages of two portfolio optimisation approaches (parametric versus non-parametric). This analysis deals with the complex problem of specification and inclusion of the joint distribution of farm activities into the analysis. Finally an evaluation of farm income stabilisation by diversification and insurance within farm portfolio context was presented using the two portfolio optimisation approaches (parametric and non-parametric). Three hypothetical types of insurance products were considered: yield insurance, price insurance and revenue insurance. Insurance was found to be an efficient risk-management tool to stabilise farm income.

    Individual variation in growth of African catfish Clarias gariepinus: a search for explanatory factors
    Matos Martins, C.I. de - \ 2005
    Wageningen University. Promotor(en): Johan Verreth, co-promotor(en): Johan Schrama. - Wageningen : - ISBN 9789085043065 - 166
    clarias gariepinus - groei - variatie - lichaamsafmetingen - voedingsgedrag - dierenwelzijn - voeropname - stressreactie - genetische variatie - visteelt - clarias gariepinus - growth - variation - body measurements - feeding behaviour - animal welfare - feed intake - stress response - genetic variation - fish culture
    Among farmed animals, fish exhibit the largest individual variation in growth, yet most of the studies reporting data on growth do not take individual variation into account. Usually a mean value is considered and although the variation around the mean is also mentioned, it is generally viewed as a sort of "statistical noise". The importance of individual variation in growth should not be underestimated since it has important consequences for water quality, aggression, stress levels, farm management, selection programmes, etc. Among the factors responsible for growth variation, social hierarchy is often considered as the most important. Social hierarchies may induce behavioural inhibition and stress on subordinate fish, affecting their feed intake, feed efficiency and as a consequence reducing their growth. However, for most fish species there is no unambiguous proof that individual differences in feed intake, feed efficiency and growth result from social hierarchies. Some studies suggest that inherent (genetic) factors may also cause the variation in growth.

    The general aim of this study was to understand the underlying factors responsible for the individual variation in growth of African catfish Clarias gariepinus . The following factors were investigated: 1) if individual variation in growth is mainly a consequence of social hierarchies, 2) the contribution of individual differences in feed intake and feed efficiency to the individual differences in growth and 3) the contribution of feeding behaviour and stress response in explaining individual differences in feed efficiency.

    Chapters 2 and 3 investigated the importance of social hierarchy as an explanatory factor for the individual variation in growth of African catfish. The growth performance, behaviour (feeding behaviour, aggression levels) and stress response between groups of low-, medium- and heavy- weight fish were compared. Chapter 2 showed that low-weight fish do not exhibit increased growth rates in the absence of heavier fish. Apparently, the growth differences were not induced by social hierarchies where the larger fish suppress the growth of smaller fish. Instead, this study suggests that feeding behaviour is a crucial factor. Heavier fish exhibit feeding behaviours that may give advantage when feed is limited, such as being more active swimmers, spending more time at the feeding areas and eating their meal faster than low-weight fish. These differences in behaviour may result in growth variation, as found in this study.

    Chapter 3 showed that the aggression and stress levels did not increase in heterogeneous (weight) groups as compared with homogeneous (weight) groups. Furthermore, low-weight fish did not exhibit a higher number of skin lesions and higher stress levels when reared in heterogeneous groups as compared with low-weight fish reared in homogeneous groups. These results suggested that low-weight fish were not behaving as subordinates and heavy fish as dominants.

    To further investigate the importance of inherent differences in growth variation, a set of experiments were designed using individually housed fish. Housing fish individually enabled the study of individual differences in the absence of social interactions and to measure individual feed intake accurately. This raised the question whether the results obtained from housing fish individually could be representative of a group housing situation. Chapter 4 compared the growth performance, feeding behaviour and stress response of isolated and non-isolated fish. This study suggested that in African catfish feed intake is stimulated by the presence of conspecifics resulting in higher feed intake and growth rates. However, isolation per se seems not to act as a stressor in the short term or to affect the stress response, probably because periods of isolation are part of the African catfish lifestyle. In addition, Chapter 5 compared the growth of fish housed individually and afterwards in a group. The average growth of individually housed fish was lower than fish in group housing. However, slow and fast growing fish under individual housing remained slow and fast growing fish, respectively, under group housing. This suggests that the different growth rates observed when fish are housed individually are a characteristic of the individual and not simply a consequence of isolation.

    Chapters 5 to 7 used individually housed fish to supply experimental data on inherent factors responsible for individual variation in growth. Chapter 5 quantified individual differences in performance traits and feeding behaviour and focused on the repeatability of such individual differences when fish were fed ad libitum. Fish exhibited pronounced individual variation in growth (CV = 52.8 %), in feed intake (34.3 %) and in total feeding time (>100 %). The repeatability estimates were 0.55 for growth, 0.70 for feed intake, 0.49 for feed efficiency and 0.81 for total feeding time. These high repeatability estimates suggested that individual differences in growth, feed intake/efficiency and feeding behaviour are consistent over time and therefore probably inherent. Individual differences in growth were explained mainly by individual differences in feed intake (~85 %). Individual differences in feeding behaviour were shown to be related to feed efficiency, measured as residual feed intake (i.e., the difference between actual feed intake and that predicted from mean observed requirements for growth and maintenance). With increasing total feeding time, the maintenance requirements also increased suggesting that slow eaters have higher maintenance costs. Chapter 6 tested whether individual differences in feeding behaviour explained the differences in growth rate by affecting feed efficiency, using restrictively fed fish. This study showed that despite the low variation in initial body weight (6.5 %) and in cumulative feed consumption (7.5 %) over the experimental period, catfish exhibited high variation in final body weight (18.1 %), specific growth rate (17.2 %) and feed conversion ratio (27.9 %), suggesting that individual variation in growth/feed efficiency is important in determining growth. This individual variation may be related to individual differences in protein/fat deposition since faster growing fish deposited more protein and less fat than slower growing fish. Pronounced individual differences in feeding behaviour (reaction towards feed and time spent eating) were also observed and correlated to individual differences in growth/feed efficiency. Fast eaters were the fast growers.

    Chapter 7 presented two experiments to investigate individual differences in basal and post-stress levels of glucose, lactate and cortisol and their relation to individual differences in feed efficiency. There was a pronounced individual variation in both basal and post-stress levels of plasma glucose, lactate and cortisol. Basal levels of glucose, lactate and cortisol did not contribute significantly to explain differences in feed efficiency. However, glucose levels obtained after a stress test (netting) could explain differences in feed efficiency by 1.3 % in experiment 1 and 5.9 % in experiment 2. In experiment 2, the cortisol levels obtained after the stress test also explained part of the differences in feed efficiency (8.7 %). Apparently, high stress responders are less efficient fish. The stress response probably adds to differences in maintenance costs, thereby affecting the feed efficiency.

    The findings of this thesis are discussed and the main conclusions are presented in Chapter 8 . The importance of social hierarchy in explaining individual growth variation should be considered species-dependent. In addition, social hierarchy should not be accepted a priori as the major cause of individual growth variation without previous investigation. The results of this thesis suggested that in African catfish the individual variation in growth is not the result of marked dominance-subordinance relationships. Instead, genetic-based differences in feed intake, feed efficiency, feeding behaviour and stress response seem to play a role in explaining growth variation in African catfish. In practical terms, one may question the use of grading in this species as grading is done under the assumption that it disrupts an existing social hierarchy. Furthermore, the results of this thesis called for the development of selection programmes in African catfish. Selecting for feed efficiency (residual feed intake) is a promising direction to pursue. The most efficient fish (low residual feed intake) were shown to be fast eaters and low stress responders which may be advantageous under aquaculture conditions.

    It was also concluded that individual differences in feed intake and feed efficiency (residual feed intake) contributed ~85 and ~15 %, respectively, to the individual differences in the growth of African catfish. Individual differences in feeding behaviour (total feeding time) and stress response (plasma glucose and cortisol after an acute stress) contributed to explain variation in residual feed intake (maintenance requirements) up to 8.7 %.

    Despite the results obtained in this thesis, our understanding of the causes of growth variation in African catfish is far from being complete. The challenge is to find the mechanisms responsible for this variation and how they are related to the individual differences in behaviour and stress response found in this thesis
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