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.

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Data from: Endure and call for help: strategies of black mustard plants to deal with a specialised caterpillar
Lucas Gomes Marques Barbosa, D. ; Dicke, M. ; Kranenburg, Twan ; Aartsma, Y.S.Y. ; Beek, T.A. van; Huigens, Martinus E. ; Loon, J.J.A. van - \ 2016
carbon - flowering plants - indirect defence - nitrogen - plant fitness - tolerance
raw data on: 1) pollinator visitation rates to Brassica nigra plants during day and night; 2) Plant Chemistry including volatile emission and carbon and nitrogen contents; 3) Plant fitness including biomass and seed production
Resistentieveredeling - Verdedigingsmechanisme : Kennisclip Bogo-project e-learning
Hop, M.E.C.M. - \ 2016
Groen Kennisnet
resistance breeding - susceptibility - resistance - tolerance - host pathogen interactions - plant protection - teaching materials - disease resistance - resistentieveredeling - vatbaarheid - weerstand - tolerantie - gastheer-pathogeen interacties - gewasbescherming - lesmaterialen - ziekteresistentie
Deze kennisclip maakt onderdeel uit van de lesmodule Resistentie Veredeling van het CIV T&U.
Breeding against infectious diseases in animals
Rashidi, H. - \ 2016
Wageningen University. Promotor(en): Johan van Arendonk, co-promotor(en): Herman Mulder; P.K. Mathur. - Wageningen University - ISBN 9789462576452 - 179 p.
livestock - infectious diseases - animal breeding - selective breeding - disease resistance - tolerance - genetic variation - breeding value - genetic correlation - traits - genomics - animal genetics - vee - infectieziekten - dierveredeling - selectief fokken - ziekteresistentie - tolerantie - genetische variatie - fokwaarde - genetische correlatie - kenmerken - genomica - diergenetica

Infectious diseases in farm animals are of major concern because of animal welfare, production costs, and public health. Farms undergo huge economic losses due to infectious disease. The costs of infections in farm animals are mainly due to production losses, treatment of infected animals, and disease control strategies. Control strategies, however, are not always successful. Selective breeding for the animals that can mount a defence against infection could therefore be a promising approach. Defensive ability of an animal has two main mechanisms: resistance (ability to control the pathogen burden) and tolerance (ability to maintain performance when pathogen burden increases). When it is difficult to distinguish between resistance and tolerance, defensive ability is measured as resilience that is the ability to maintain performance during a disease outbreak regardless of pathogen burden. Studies have focused on the genetics of resistance and resilience with little known about the genetics of tolerance and its relationship with resistance and resilience. The objectives of this thesis were to: 1) estimate the genetic variation in resistance, tolerance, and resilience to infection in order to assess the amenability of these traits for selective breeding in farm animals, 2) estimate the genetic correlation between resistance, tolerance and resilience and 3) detect genomic regions associated with resistance, tolerance, and resilience.

In chapter 2, we studied the variation among sows in response to porcine reproductive and respiratory syndrome (PRRS). First a statistical method was developed to detect PRRS outbreaks based on reproduction records of sows. The method showed a high sensitivity (78%) for disease phases. Then the variation of sows in response to PRRS was quantified using 2 models on the traits number of piglets born alive (NBA) and number of piglets born dead (LOSS): 1) bivariate model considering the trait in healthy and disease phases as different traits, and 2) reaction norm model modelling the response of sows as a linear regression of the trait on herd-year-week estimates of NBA. Trait correlations between healthy and disease phases deviated from unity (0.57±0.13 – 0.87±0.18). The repeatabilities ranged from 0.07±0.027 to 0.16±0.005. The reaction norm model had higher predictive ability in disease phase compared to the bivariate model.

In chapter 3 we studied 1) the genetic variation in resistance and tolerance of sheep to gastrointestinal nematode infection and 2) the genetic correlation between resistance and tolerance. Sire models on faecal nematode egg count (FEC), IgA, and pepsinogen were used to study the genetic variation in resistance. Heritability for resistance traits ranged from 0.19±0.10 to 0.59±0.20. A random regression model was used to study the reaction norm of sheep body weight on FEC as an estimate of tolerance to nematode infection. We observed a significant genetic variance in tolerance (P<0.05). Finally a bivariate model was used to study the genetic correlation between resistance and tolerance. We observed a negative genetic correlation (-0.63±0.25) between resistance and tolerance.

In chapter 4, we studied the response to selection in resistance and tolerance when using estimated breeding values for resilience. We used Monte Carlo simulation to generate 100 half-sib families with known breeding values for resistance (pathogen burden) and tolerance. We used selection index theory to predict response to selection for resistance and tolerance: 1) when pathogen burden is known and selection is based on true breeding values for resistance and tolerance and 2) when pathogen burden is unknown and selection is based on estimated breeding values for resilience. Using EBV for resilience in absence of records for pathogen burden resulted in favourable responses in resistance and tolerance to infections, with more emphasis on tolerance than on resistance. However, more genetic gain in resistance and tolerance could be achieved when pathogen burden was known.

In chapter 5 we studied genomics regions associated with resistance, resilience, and tolerance to PRRS. Resistance was modelled as sire effect on area under the PRRS viremia curve up to 14 days post infection (AUC14). Resilience was modelled as sire effects on daily growth of pigs up to 28 days post infection (ADG28). Tolerance was modelled as the sire effect on the regression of ADG28 on AUC14. We identified a major genomics region on chromosome 4 associated with resistance and resilience to PRRS. We also identified genomics regions on chromosome 1 associated with tolerance to PRRS.

In the general discussion (chapter 6) I discussed: 1) response to infection as a special case of genotype by environment interaction, 2) random regression model as a statistical tool for studying response to disease, 3) advantages and requirements of random regression models, and 4) selective breeding of farm animals for resistance, tolerance, and resilience to infections. I concluded that random regression is a powerful approach to estimate response to infection in animals. If the adequate amount of data is available random regression model could estimate breeding values of animals more accurately compared to other models. I also concluded that before including resistance and tolerance into breeding programs, breeders should make sure about the added values of including these traits on genetic progress. Selective breeding for resilience could be a pragmatic approach to simultaneously improve resistance and tolerance.

Desiccation tolerance in seeds and plants
Dias Costa, M.C. - \ 2016
Wageningen University. Promotor(en): Harro Bouwmeester; Henk Hilhorst; Wilco Ligterink. - Wageningen : Wageningen University - ISBN 9789462576278 - 183 p.
desiccation tolerance - tolerance - plants - seeds - plant physiology - stress tolerance - drought resistance - abscisic acid - uitdrogingstolerantie - tolerantie - planten - zaden - plantenfysiologie - stresstolerantie - droogteresistentie - abscisinezuur

The interest of research groups in desiccation tolerance (DT) has increased substantially over the last decades. The emergence of germinated orthodox seeds and resurrection plants as main research models has pushed the limits of our knowledge beyond boundaries. At the same time, new questions and new challenges were posed. The work presented in this thesis aims at shedding light on some of these questions, deepening our understanding of DT and providing relevant information to improve stress resistance in crops.

Chapter 2 is a survey of the literature and discusses the ecological and evolutionary significance for seeds to be able to re-acquire DT after germination. This chapter also discusses recent progress in DT studies using developing and germinated seeds of the model plants Arabidopsis thaliana and Medicago truncatula.

In Chapter 3 I used microarray data from a time series of DT re-acquisition, together with network analysis of gene expression, to gain temporal resolution and identify relevant genes involved in the re-acquisition of DT in germinated A. thaliana seeds by incubation in abscisic acid (ABA). Overall, genes related to protection, response to stresses, seed development and seed dormancy were up-regulated, whereas genes related to cell growth and photosynthesis were down-regulated with time. Genes that respond early to exogenous ABA were related to wax biosynthetic processes, lipid storage, seed development and response to ABA stimulus. Genes that respond late to exogenous ABA were related to syncytium formation and response to abiotic stimulus (mainly light stimulus). The robustness of the network was confirmed by the projection of sets of genes – related to the acquisition of DT, seed dormancy, drought responses of adult plants and re-induction of DT by polyethylene glycol – on this network.

In Chapter 4 the relation between DT in germinated seeds and drought resistance in adult plants is analysed, using rice (Oryza sativa) as experimental model. Considering the predictions of a future with lower availability of fresh water, efforts to increase rice drought tolerance without reducing yield are increasingly important. The results presented in this chapter suggest that the intrinsic mechanisms of drought tolerance in adult plants are part of the mechanisms used by seeds to tolerate desiccation, but the molecular nature of these mechanisms remains elusive.

Chapter 5 explores the relation between DT and longevity in germinated seeds of the Brazilian tree species Sesbania virgata as experimental model. DT and longevity are acquired by orthodox seeds during the maturation phase of development and lost upon germination. DT can be re-induced in germinated seeds by an osmotic and/or ABA treatment, but there is no information on how these treatments affect seed longevity. S. virgata seeds lose DT slowly upon radicle growth. The radicle appeared to be the most sensitive organ and the cotyledons the most resistant. The ability to produce lateral roots was key for whole seedling survival. An osmotic treatment improved DT in germinated S. virgata seeds, but not longevity. This implies that DT and seed longevity can be uncoupled.

Xerophyta viscosa is one of the best studied resurrection species. Despite the fact that adult plants and mature seeds display DT, young X. viscosa seedlings are sensitive to fast drying. A treatment with ABA can induce DT early in shoots of these seedlings, but not in roots. Chapter 6 addresses the changes in the transcriptome and proteome of X. viscosa seedlings during induction of DT. A draft genome sequence of X. viscosa was used to improve transcript and protein identification and annotation. Differences in ABA signalling and the cross talk between ABA and ethylene were presented as determinant for shoot and root responses. Moreover, differences in the accumulation of late embryogenesis abundant proteins were also shown as being key for DT in shoots and roots.

In Chapter 7, DT-transcriptomes of distantly related organisms are compared and surveyed for a core set of genes representing the signatures of critical adaptive DT mechanisms. A shortlist of 260 genes emerged, with a significant number of genes under the control of ABI3 and related to dormancy. The results reinforced the idea that core mechanisms and key regulators involved in DT developed early in the history of life and were carried forward by diverse species and life forms in a conserved manner and in conjunction with dormancy.

In Chapter 8, the findings of this thesis are integrated, showing how they can contribute to future improvement of stress tolerance in crops. The ability of germinated seeds to re-acquire DT is discussed in combination with dormancy and longevity and related to seed survival under unfavourable environmental conditions. The relationship between drought- and desiccation tolerance and the role of ABA are presented briefly. Possible approaches to mine for new genes for crop improvement, such as searching for conserved genes and analysing new genome sequences, are addressed. Finally, a new perspective of the way to consider the evolution of DT is proposed.

Allergen-specific cytokine polarization protects shetland ponies against culicoides obsoletus-induced insect bite hypersensitivity
Meulenbroeks, C. ; Lugt, J.J. van der; Meide, N.M.A. van der; Willemse, T. ; Rutten, V.P.M.G. ; Zaiss, D.M.W. - \ 2015
PLoS ONE 10 (2015)4. - ISSN 1932-6203 - 12 p.
e-bearing cells - mast-cells - british-columbia - friesian horses - skin biopsies - sweet itch - ige - antibodies - tolerance - immunotherapy
The immunological mechanisms explaining development of an allergy in some individuals and not in others remain incompletely understood. Insect bite hypersensitivity (IBH) is a common, seasonal, IgE-mediated, pruritic skin disorder that affects considerable proportions of horses of different breeds, which is caused by bites of the insect Culicoides obsoletus (C. obsoletus). We investigated the allergen-specific immune status of individual horses that had either been diagnosed to be healthy or to suffer of IBH. Following intradermal allergen injection, skin biopsies were taken of IBH-affected and healthy ponies and cytokine expression was determined by RT-PCR. In addition, allergen-specific antibody titers were measured and cytokine expression of in vitro stimulated, allergen-specific CD4 T-cells was determined. 24 hrs after allergen injection, a significant increase in mRNA expression of the type-2 cytokine IL-4 was observed in the skin of IBH-affected Shetland ponies. In the skin of healthy ponies, however, an increase in IFN¿ mRNA expression was found. Analysis of allergen-specific antibody titers revealed that all animals produced allergen-specific antibodies, and allergen-specific stimulation of CD4 T-cells revealed a significant higher percentage of IFN¿-expressing CD4 T-cells in healthy ponies compared to IBH-affected ponies. These data indicate that horses not affected by IBH, in contrast to the so far established dogma, are not immunologically ignorant but have a Th1-skewed allergen-specific immune response that appears to protect against IBH-associated symptoms. To our knowledge this is the first demonstration of a natural situation, in which an allergen-specific immune skewing is protective in an allergic disorder.
Effects of salinity on growth of plant species from terrestrializing fens
Stofberg, S.F. ; Klimkovska, A. ; Paulissen, M.P.C.P. ; Witte, J.Ph.M. ; Zee, S.E.A.T.M. van der - \ 2015
Aquatic Botany 121 (2015). - ISSN 0304-3770 - p. 83 - 90.
climate-change - water - tolerance - salt - nutrient - netherlands - macrophytes - competition - vegetation - diversity
Terrestrializing lowland fens may be temporarily exposed to elevated surface water salinity, which may have serious consequences for nature conservation. We investigated the response of five fresh water fen plant species to elevated salinity. In a controlled greenhouse experiment, these species were exposed to salt concentrations up to 3000 mg Cl- l-1. Total biomass of the five species together was significantly reduced for salinity levels from 200 mg Cl- l-1. Four individual species showed leaf death and relative growth rate reduction, with effects at 1000 mg Cl- l-1 for Succisa pratensis, Thelypteris palustris and Viola palustris, and 3000 mg Cl- l-1 for Myosotis scorpioides. Comarum palustre showed no significant (.05 level) sensitivity. Biomass distribution was investigated as well. Root-shoot ratio of four species was affected by salinity, which in at least two cases seemed to be related to leaf death. Differences in specific leaf area as a result of salinity were only observed for C. palustre. Dry matter content increased in four species as a result of salinity. Salinity tolerance did not correspond to the environmental distributions of the species, nor could species traits be related to tolerance. Surface water salinity may affect vegetation development in terrestrializing fens at low concentrations. A reduction of plant growth would cause reduced fitness of some species and may lead to reduced root mat growth. Exposure to higher concentrations could eventually lead to a decrease of species richness.
Fitness consequences of indirect plant defence in the annual weed, Sinapis arvensis
Gols, R. ; Wagenaar, R. ; Poelman, E.H. ; Kruidhof, H.M. ; Loon, J.J.A. van; Harvey, J.A. - \ 2015
Functional Ecology 29 (2015)8. - ISSN 0269-8463 - p. 1019 - 1025.
pieris-brassicae - herbivory - tolerance - evolution - volatiles - insects - parasitoids - strategies - selection - ecology
Plant traits that enhance the attraction of the natural enemies of their herbivores have been postulated to function as an 'indirect defence'. An important underlying assumption is that this enhanced attraction results in increased plant fitness due to reduced herbivory. This assumption has been rarely tested. We investigated whether there are fitness consequences for the charlock mustard Sinapis arvensis, a short-lived outcrossing annual weedy plant, when exposed to groups of large cabbage white (Pieris brassicae) caterpillars parasitized by either one of two wasp species, Hyposoter ebeninus and Cotesia glomerata, that allow the host to grow during parasitism. Hyposoter ebeninus is solitary and greatly reduces host growth compared with healthy caterpillars, whereas C. glomerata is gregarious and allows the host to grow approximately as large as unparasitized caterpillars. Both healthy and parasitized P. brassicae caterpillars initially feed on the foliage, but later stages preferentially consume the flowers. In a garden experiment, plants damaged by parasitized caterpillars produced more seeds than conspecific plants damaged by unparasitized caterpillars. Reproductive potential (germination success multiplied by total seed number) was similar for plants that were not exposed to herbivory and those that were damaged by parasitized caterpillars and lower for plants that were damaged by healthy unparasitized caterpillars. However, these quantitative seed traits negatively correlated with the qualitative seed traits, individual seed size and germination success, suggesting a trade-off between these two types of traits. We show that parasitism of insect herbivores that feed on reproductive plant tissues may have positive fitness consequences for S. arvensis. The extent to which plant fitness may benefit depends on parasitoid lifestyle (solitary or gregarious), which is correlated with the amount of damage inflicted on these tissues by the parasitized host
Distributions, ex situ conservation priorities, and genetic resource potential of crop wild relatives of sweetpotato [Ipomoea batatas (L.) Lam., I. series Batatas]
Khoury, C.K. ; Heider, B. ; Castaneda-Alvarez, N.P. ; Achicanoy, H.A. ; Sosa, C.C. ; Miller, R.E. ; Scotland, R.W. ; Wood, J.R.I. ; Rossel, G. ; Eserman, L.A. ; Jarret, R.L. ; Yencho, G.C. ; Bernau, V. ; Juarez, H. ; Sotelo, S. ; Haan, S. de; Struik, P.C. - \ 2015
Frontiers in Plant Science 6 (2015). - ISSN 1664-462X - 14 p.
species distribution models - phylogenetic-relationships - beta-carotene - convolvulaceae - sequences - diversity - evolution - bias - challenges - tolerance
Crop wild relatives of sweetpotato [Ipomoea batatas (L.) Lam., I. series Batatas] have the potential to contribute to breeding objectives for this important root crop. Uncertainty in regard to species boundaries and their phylogenetic relationships, the limited availability of germplasm with which to perform crosses, and the difficulty of introgression of genes from wild species has constrained their utilization. Here, we compile geographic occurrence data on relevant sweetpotato wild relatives and produce potential distribution models for the species. We then assess the comprehensiveness of ex situ germplasm collections, contextualize these results with research and breeding priorities, and use ecogeographic information to identify species with the potential to contribute desirable agronomic traits. The fourteen species that are considered the closest wild relatives of sweetpotato generally occur from the central United States to Argentina, with richness concentrated in Mesoamerica and in the extreme Southeastern United States. Currently designated species differ among themselves and in comparison to the crop in their adaptations to temperature, precipitation, and edaphic characteristics and most species also show considerable intraspecific variation. With 79% of species identified as high priority for further collecting, we find that these crop genetic resources are highly under-represented in ex situ conservation systems and thus their availability to breeders and researchers is inadequate. We prioritize taxa and specific geographic locations for further collecting in order to improve the completeness of germplasm collections. In concert with enhanced conservation of sweetpotato wild relatives, further taxonomic research, characterization and evaluation of germplasm, and improving the techniques to overcome barriers to introgression with wild species are needed in order to mobilize these genetic resources for crop breeding.
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 - 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.

Human buccal epithelium acquires microbial hyporesponsiveness at birth, a role for secretory leukocyte protease inhibitor
Menckeberg, C.L. ; Hol, J. ; Simons-Oosterhuis, Y. ; Raatgeep, H.R. ; Ruiter, L.F. de; Lindenbergh-Kortleve, D.J. ; Korteland-van Male, A.M. ; Aidy, S.F. El; Lierop, P.P.E. van; Kleerebezem, M. ; Groeneweg, M. ; Kraal, G. ; Elink-Schuurman, B.E. ; Jongste, J.C. de; Nieuwenhuis, E.E.S. ; Samsom, J.N. - \ 2015
Gut 64 (2015). - ISSN 0017-5749 - p. 884 - 893.
toll-like receptors - negative regulation - intestinal-mucosa - crohn-disease - responses - cells - tolerance - lipopolysaccharide - inflammation - mechanisms
Objective Repetitive interaction with microbial stimuli renders epithelial cells (ECs) hyporesponsive to microbial stimulation. Previously, we have reported that buccal ECs from a subset of paediatric patients with Crohn's disease are not hyporesponsive and spontaneously released chemokines. We now aimed to identify kinetics and mechanisms of acquisition of hyporesponsiveness to microbial stimulation using primary human buccal epithelium. Design Buccal ECs collected directly after birth and in later stages of life were investigated. Chemokine release and regulatory signalling pathways were studied using primary buccal ECs and the buccal EC line TR146. Findings were extended to the intestinal mucosa using murine model systems. Results Directly after birth, primary human buccal ECs spontaneously produced the chemokine CXCL-8 and were responsive to microbial stimuli. Within the first weeks of life, these ECs attained hyporesponsiveness, associated with inactivation of the NF-¿B pathway and upregulation of the novel NF-¿B inhibitor SLPI but no other known NF-¿B inhibitors. SLPI protein was abundant in the cytoplasm and the nucleus of hyporesponsive buccal ECs. Knock-down of SLPI in TR146-buccal ECs induced loss of hyporesponsiveness with increased NF-¿B activation and subsequent chemokine release. This regulatory mechanism extended to the intestine, as colonisation of germfree mice elicited SLPI expression in small intestine and colon. Moreover, SLPI-deficient mice had increased chemokine expression in small intestinal and colonic ECs. Conclusions We identify SLPI as a new player in acquisition of microbial hyporesponsiveness by buccal and intestinal epithelium in the first weeks after microbial colonisation.
Comparative transcriptome analysis of the metal hyperaccumulator Noccaea caerulescens
Halimaa, P. ; Blande, D. ; Aarts, M.G.M. ; Tuomainen, M. ; Tervahauta, A. ; Karenlampi, S. - \ 2014
Frontiers in Plant Science 5 (2014). - ISSN 1664-462X
gene copy number - thlaspi-caerulescens - arabidopsis-thaliana - expression differences - zinc accumulation - topology prediction - tobacco plants - cadmium - tolerance - populations
The metal hyperaccumulator Noccaea caerulescens is an established model to study the adaptation of plants to metalliferous soils. Various comparators have been used in these studies. The choice of suitable comparators is important and depends on the hypothesis to be tested and methods to be used. In high-throughput analyses such as microarray, N. caerulescens has been compared to non-tolerant, non-accumulator plants like Arabidopsis thaliana or Thlaspi arvense rather than to the related hypertolerant or hyperaccumulator plants. An underutilized source is N. caerulescens populations with considerable variation in their capacity to accumulate and tolerate metals. Whole transcriptome sequencing (RNA-Seq) is revealing interesting variation in their gene expression profiles. Combining physiological characteristics of N. caerulescens accessions with their RNA-Seq has a great potential to provide detailed insight into the underlying molecular mechanisms, including entirely new gene products. In this review we will critically consider comparative transcriptome analyses carried out to explore metal hyperaccumulation and hypertolerance of N. caerulescens, and demonstrate the potential of RNA-Seq analysis as a tool in evolutionary genomics
Expression profiling reveals functionally redundant multiple-copy genes related to zinc, iron and cadmium responses in Brassica rapa
Li, J. ; Liu, B. ; Cheng, F. ; Wang, X. ; Aarts, M.G.M. ; Wu, J. - \ 2014
New Phytologist 203 (2014)1. - ISSN 0028-646X - p. 182 - 194.
hyperaccumulator thlaspi-caerulescens - ferric-chelate reductase - arabidopsis-thaliana - metal homeostasis - human-nutrition - deficiency - tolerance - plants - toxicity - protein
Genes underlying environmental adaptability tend to be over-retained in polyploid plant species. Zinc deficiency (ZnD) and iron deficiency (FeD), excess Zn (ZnE) and cadmium exposure (CdE) are major environmental problems for crop cultivation, but little is known about the differential expression of duplicated genes upon these stress conditions. Applying Tag-Seq technology to leaves of Brassica rapa grown under FeD, ZnD, ZnE or CdE conditions, with normal conditions as a control, we examined global gene expression changes and compared the expression patterns of multiple paralogs. We identified 812, 543, 331 and 447 differentially expressed genes under FeD, ZnD, ZnE and CdE conditions, respectively, in B. rapa leaves. Genes involved in regulatory networks centered on the transcription factors bHLH038 or bHLH100 were differentially expressed under (ZnE-induced) FeD. Further analysis revealed that genes associated with Zn, Fe and Cd responses tended to be over-retained in the B. rapa genome. Most of these multiple-copy genes showed the same direction of expression change under stress conditions. We conclude that the duplicated genes involved in trace element responses in B. rapa are functionally redundant, making the regulatory network more complex in B. rapa than in Arabidopsis thaliana
Earthworms increase plant production: a meta- analysis
Groenigen, J.W. van; Lubbers, I.M. ; Vos, H.M.J. ; Brown, G.G. ; Deyn, G.B. de; Groenigen, K.J. van - \ 2014
Scientific Reports 4 (2014). - ISSN 2045-2322
ecosystem services - soil carbon - n pools - management - nitrogen - growth - agroecosystems - agriculture - communities - tolerance
To meet the challenge of feeding a growing world population with minimal environmental impact, we need comprehensive and quantitative knowledge of ecological factors affecting crop production. Earthworms are among the most important soil dwelling invertebrates. Their activity affects both biotic and abiotic soil properties, in turn affecting plant growth. Yet, studies on the effect of earthworm presence on crop yields have not been quantitatively synthesized. Here we show, using meta-analysis, that on average earthworm presence in agroecosystems leads to a 25% increase in crop yield and a 23% increase in aboveground biomass. The magnitude of these effects depends on presence of crop residue, earthworm density and type and rate of fertilization. The positive effects of earthworms become larger when more residue is returned to the soil, but disappear when soil nitrogen availability is high. This suggests that earthworms stimulate plant growth predominantly through releasing nitrogen locked away in residue and soil organic matter. Our results therefore imply that earthworms are of crucial importance to decrease the yield gap of farmers who can't -or won't- use nitrogen fertilizer.
Continuous light on tomato : from gene to yield
Velez Ramirez, A.I. - \ 2014
Wageningen University. Promotor(en): Harro Bouwmeester, co-promotor(en): Wim van Ieperen; Dick Vreugdenhil. - Wageningen : Wageningen University - ISBN 9789462570788 - 214
solanum lycopersicum - tomaten - licht - gewasproductie - gewasopbrengst - genen - tolerantie - lichtregiem - beschadigingen - plantenfysiologie - tomatoes - light - crop production - crop yield - genes - tolerance - light regime - injuries - plant physiology

Light essentially sustains all life on planet earth surface. Plants transform light energy into chemical energy through photosynthesis. Hence, it can be anticipated that extending the daily photoperiod, using artificial light, results in increased plant productivity. Although this premise is true for many plant species, a limit exists. For instance, the seminal work of Arthur et al. (1930) showed that tomato plants develop leaf injuries if exposed to continuous light (CL). Many studies have investigated the physiological mechanism inducing such CL-induced injury. Although important and valuable discoveries were done over the decades, by the time the present project started, a detailed and proven physiological explanation of this disorder was still missing. Here, I present the results of a 5-year effort to better understand the physiological basis of the CL-induced injury in tomato and develop the tools (genetic and conceptual) to cultivate tomatoes under CL.

After an exhaustive literature search, it was found that Daskaloff and Ognjanova (1965) reported that wild tomato species are tolerant to CL. Unfortunately, this important finding was ignored by numerous studies done after its publication. Here, we used the CL-tolerance found in wild tomatoes as a fundamental resource. Hence, the specific objectives of this thesis were to (i) better understand the physiological basis of the CL-induced injuries in tomato, (ii) identify the gene(s) responsible for CL-tolerance in wild tomato species, (iii) breed a CL-tolerant tomato line and (iv) use it to cultivate a greenhouse tomato crop under CL.

Chapter 1 describes how innovation efforts encountered the unsolved scientific enigma of the injuries that tomato plants develop when exposed to CL. The term CL-induced injury is defined, and a detailed description of the symptoms observed in this disorder is shown. Additionally, an overview of the most important studies, influencing the hypotheses postulated and/or tested in this dissertation, is presented. Finally, a description and motivation of the main questions that this dissertation pursued to answer is presented alongside a short description of the strategy chosen to answer them.

Chapter 2 reviews the literature, published over the last 80 years, on CL-induced injury using modern knowledge of plant physiology. By doing so, new hypotheses aiming to explain this disorder are postulated in addition to the ones collected from literature. Additionally, we highlight that CL is an essential tool for understanding the plant circadian clock, but using CL in research has its challenges. For instance, most of the circadian-clock-oriented experiments are performed under CL; consequently, interactions between the circadian clock and the light signalling pathway are overlooked. This chapter is published here.

Chapter 3 explores the benefits and challenges of cultivating CL-tolerant tomato under CL. Considering that current commercial tomato varieties need six hours of darkness per day for optimal growth, photosynthesis does not take place during a quarter of the day. Hence, if tomatoes could be grown under CL, a substantial increase in production is anticipated. A simulation study is presented, which shows that if an ideal continuous-light-tolerant tomato genotype is used and no crop adaptations to CL are assumed, greenhouse tomato production could be 26% higher when supplementing light to 24 h day-1 in comparison with a photoperiod (including supplementary lighting) of only 18 h day-1. In addition, the expected changes in greenhouse energy budgets and alterations in crop physiological responses that might arise from cultivating tomatoes under continuous light are discussed. This chapter is published here.

Chapter 4 maps the locus conferring CL-tolerance in wild tomatoes to chromosome seven, and shows that its introgression into modern tomato cultivars enhances yield by 20%, when grown under CL. In addition, genetic evidence, RNAseq data, silencing experiments and sequence analysis all point to the type III Light-Harvesting Chlorophyll a/b Binding protein 13 (CAB-13) gene as a major factor responsible for the tolerance. In Arabidopsis thaliana this protein is thought to have a regulatory role in balancing light harvesting by photosystems I and II. The likely mechanisms that link CAB-13 with CL-tolerance are discussed. This chapter is published here.

Chapter 5 investigates from which part of the plant CL-tolerance originates and whether this trait acts systemically. By exposing grafted plants bearing both tolerant and sensitive shoots to CL, the trait was functionally located to the shoot rather than the roots. Additionally, an increase in continuous-light tolerance was observed in sensitive plants when a continuous-light-tolerant shoot was grafted on it. Our results show that in order to increase yield in greenhouse tomato production by using CL, the trait should be bred into scion rather than rootstock lines.

Chapter 6 discusses the factors that differ between injurious and non-injurious light regimes. Each of these factors may potentially be responsible for triggering the injury in CL-grown tomato and was experimentally tested here. In short, these factors include (i) differences in the light spectral distribution between sunlight and artificial light, (ii) continuous signalling to the photoreceptors, (iii) constant supply of light for photosynthesis, (iv) constant photo-oxidative pressure, and (v) circadian asynchrony — a mismatch between the internal circadian clock frequency and the external light/dark cycles. The evidence presented here suggests that the continuous-light-induced injury does not result from the unnatural spectral distribution of artificial light or the continuity of the light per se. Instead, circadian asynchrony seems to be the factor inducing the injury. As the discovered diurnal fluctuations in photoinhibition sensitivity of tomato seedlings are not under circadian control, it seems that circadian asynchrony does not directly induce injury via photoinhibition as it has been proposed.

Chapter 7 investigates a possible role for phytochromes (PHY) in CL-induced injury in tomato. Mutant and transgenic tomato plants lacking or over-expressing phytochromes were exposed to CL, with and without far-red light enrichment, to test the role of individual phytochromes on the induction and/or prevention of injury. PHYA over-expression confers complete tolerance to CL regardless the light spectrum. Under CL with low far-red content, PHYB1 and PHYB2 diminished and enhanced the injury, respectively, yet the effects were small. These results confirm that phytochrome signaling networks are involved in the injury induction under CL. The link between CAB-13 and PHYA is discussed.

Chapter 8 investigates the role of carbohydrate accumulation in the induction of CL-induced injury in tomato by using untargeted metabolomics and transcriptomics data. These data reveal a clear effect of CL on sugar metabolism and photosynthesis. A strong negative correlation between sucrose and starch with the maximum quantum efficiency of photosystem II (Fv /Fm) was found across several abnormal light/dark cycles, supporting the hypothesis that carbohydrates play an important role in CL-induced injury. I suggest that CL-induced injury in tomato is caused by a photosynthetic down-regulation showing characteristics of both cytokinin-regulated senescence and light-modulated retrograde signaling. Molecular mechanisms linking carbohydrate accumulation with photosynthetic down-regulation are discussed.

Chapter 9 provides a synthesis of the most important findings and proposes a generic model of CL-induced injury in tomato. I propose that CL-induced injury in tomato arises from retrograde signals that counteract signals derived from the cellular developmental program that promote chloroplast development, such that chloroplast development cannot be completed, resulting in the chlorotic phenotype. Finally, perspectives on what future directions to take to further elucidate the physiological basis of this trait and successfully implement it in greenhouses are presented.

Abiotic stress QTLs in lettuce crop–wild hybrids: comparing greenhouse and field experiments
Hartman, Y. ; Hooftman, D.A.P. ; Uwimana, B. ; Schranz, M.E. ; Wiel, C.C.M. van de; Smulders, M.J.M. ; Visser, R.G.F. ; Michelmore, R.W. ; Tienderen, P.H. van - \ 2014
Ecology and Evolution 4 (2014)12. - ISSN 2045-7758 - p. 2395 - 2409.
quantitative trait loci - genetically-modified crops - lactuca-sativa l. - domestication traits - root architecture - weedy populations - linkage maps - selection - introgression - tolerance
The development of stress-tolerant crops is an increasingly important goal of current crop breeding. A higher abiotic stress tolerance could increase the probability of introgression of genes from crops to wild relatives. This is particularly relevant to the discussion on the risks of new GM crops that may be engineered to increase abiotic stress resistance. We investigated abiotic stress QTL in greenhouse and field experiments in which we subjected recombinant inbred lines from a cross between cultivated Lactuca sativa cv. Salinas and its wild relative L. serriola to drought, low nutrients, salt stress, and aboveground competition. Aboveground biomass at the end of the rosette stage was used as a proxy for the performance of plants under a particular stress. We detected a mosaic of abiotic stress QTL over the entire genome with little overlap between QTL from different stresses. The two QTL clusters that were identified reflected general growth rather than specific stress responses and colocated with clusters found in earlier studies for leaf shape and flowering time. Genetic correlations across treatments were often higher among different stress treatments within the same experiment (greenhouse or field), than among the same type of stress applied in different experiments. Moreover, the effects of the field stress treatments were more correlated with those of the greenhouse competition treatments than to those of the other greenhouse stress experiments, suggesting that competition rather than abiotic stress is a major factor in the field. In conclusion, the introgression risk of stress tolerance (trans-)genes under field conditions cannot easily be predicted based on genomic background selection patterns from controlled QTL experiments in greenhouses, especially field data will be needed to assess potential (negative) ecological effects of introgression of these transgenes into wild relatives.
An evolutionary perspective on differential regulation of zinc and cadmium homeostatis genes in Arabidopsis thaliana and Noccaea caerulescens
Lin, Y.F. - \ 2014
Wageningen University. Promotor(en): Maarten Koornneef, co-promotor(en): Mark Aarts. - Wageningen : Wageningen University - ISBN 9789461738950 - 220
arabidopsis thaliana - zink - cadmium - homeostase - genen - evolutie - nucleotidenvolgordes - tolerantie - zinc - homeostasis - genes - evolution - nucleotide sequences - tolerance

Some plants can tolerate and accumulate unusually high levels of toxic metals, and the analysis of such plants can provide insights into the ecology of environments that are polluted with heavy metals due to human industrial activities. The study of heavy metal hyperaccumulators such as Noccaea caerulescens can show how plants cope with excess metals and increase their fitness when growing in metalliferous environments. In this thesis, I compared the molecular mechanisms of zinc (Zn) homeostasis and cadmium (Cd) response in the hyperaccumulator species N. caerulescens and its non-accumulator relative Arabidopsis thalianaby investigating the regulation of the ZNT1/ZIP4gene that promotes Zn uptake and Zn/Cd tolerance.I also studied the ecological advantages of metal hyperaccumulators in nature and determined the DNA sequences of the N. caerulescens transcriptometo find candidate genes that control metal hyperaccumulation and provide an evolutionary perspective on the emergence of this trait.

The functional characterization of the N. caerulescens and A. thaliana Zn-transporter genes NcZNT1 and AtZIP4 (and their promoters) showed how their differential expression pattern contributed to their role in metal tolerance and accumulation. The NcZNT1 gene is induced by Zn deficiency and the NcZNT1 protein is localized in the plasma membrane. Transgenic N. caerulescens roots containing a transgene for the green fluorescent protein (GFP) driven by the NcZNT1promoter revealed GFP fluorescence localized to pericycle and vascular tissues. This suggests that NcZNT1 contributes to metal loading into the xylem and long-distance metal transport. The overexpression of NcZNT1 in A. thaliana increased Zn and Cd tolerance and the capacity to accumulate these metals compared to wild-type plants. These results suggest that NcZNT1 plays an important role in Zn and Cd hypertolerance and hyperaccumulation in N. caerulescens, where it is expressed in both Zn-sufficient and Zn-excess conditions. The differential activity of the NcZNT1 and AtZIP4 promoters in N. caerulescens and A. thaliana implies that different cis-regulatory elements and trans-regulatory factors are present in both species.

The ecological advantage of hyperaccumulators in metal-contaminated soils was investigated by studying a natural nas1mutant, in which the Nicotianamine Synthase1 gene is disrupted by a transposon insertion. This mutant allele was found in three natural N. caerulescens populations, which were compared to wild-type plants in terms of phenotype and adaptive advantage. Although the transposon disrupted the gene, the loss of NAS1 gene activity was compensated by enhanced expression of NAS3 and NAS4, resulting in increased nicotianamine (NA) production, which enhanced the Zn and Cd accumulation in the nas1 mutants. This increased their metal sensitivity compared to wild-type plants, but also made them more toxic towards Pieris rapae caterpillars, which developed more slowly and gained less weight when fed on mutant plants exposed to excess Zn or Cd. Therefore, the possible selective advantage of the nas1 mutant in nature is high metal accumulation and the protection of plants from herbivores. Differences in nas1 allele frequency among the three natural populations suggests that nas1 alleles experience different degrees of natural selection or may be at different stages on the route to fixation.

Molecular evolutionary studies involve the identification of candidate genes that play a role in adaptation. Therefore, a comprehensive set of transcript sequences was obtained from N. caerulescens accession Ganges (GA) by 454 pyrosequencing. In total, the collected 23,836 isotigs (putative transcripts) were grouped into 20,378 isogroups and 93.2% of them could be matched to Brassicaceae protein sequences, which allowedtheir functional annotation. A total of 87 isogroups was annotated as metal homeostasis related genes, including metal transporter families, metal chelator biosynthesis families, and metal tolerance gene families, which are candidate genes for the molecular analysis of heavy metal homeostasis mechanisms. A group of genes required for the synthesis of glucosinolates, which are important secondary metabolites that protect plants against herbivores, were also shown to be expressed in N. caerulescens. The METALLOTHIONEIN3 (MT3) gene was found to have been duplicated in the N. caerulescens genome, when compared to related Brassicaceae. These transcript sequences will provide an important tool to annotate the genome sequence of the N. caerulescensGanges accession, which is in progress. This genome sequence will also be the basis of genome comparisons between the different N. caerulescens accessions that have different levels of metal accumulation and metal tolerance and which may therefore differ in terms of gene expression levels or modes of actions that affect metal homeostasis.

Functional traits predict drought performance and distribution of Mediterranean woody species
Lopez-Iglesias, B. ; Villar, R. ; Poorter, L. - \ 2014
Acta Oecologica-International Journal of Ecology 56 (2014). - ISSN 1146-609X - p. 10 - 18.
trade-offs - niche differentiation - seedling survival - rooting depth - plant traits - quercus-ilex - rain-forest - tolerance - water - growth
Water availability is one of the key environmental factors that affect plant establishment and distribution. In many regions water availability will decline with climate change, exposing small seedlings to a greater likelihood of drought. In this study, 17 leaves, stem, root, and whole-plant traits of ten woody Mediterranean species were measured under favourable growing conditions and seedling drought survival was evaluated during a simulated dry-down episode. The aims of this study were: i) to assess drought survival of different species, ii) to analyse which functional traits predict drought survival time, and iii) to explain species distribution in the field, based on species drought survival and drought strategies. Drought survival time varied ten-fold across species, from 19 to 192 days. Across species, drought survival was positively related to the rooting depth per leaf area, i.e., the ability to acquire water from deeper soil layers while reducing transpiring leaf area. Drought survival time was negatively related to species ability to grow quickly, as indicated by high relative growth and net assimilation rates. Drought survival also explained species distribution in the field. It was found that species were sorted along a continuum, ranging between two contrasting species functional extremes based on functional traits and drought performance. One extreme consisted of acquisitive fast-growing deciduous species, with thin, soft metabolically active leaves, with high resource use and vulnerability to drought. The opposite extreme consisted of conservative slow-growing evergreen species with sclerophyllous leaves, deep roots, a low transpiring area, and low water use, resulting in high drought survival and drought tolerance. The results show that these drought strategies shape species distribution in this Mediterranean area
Variation among sows in response to porcine reproductive and respiratory syndrome
Rashidi, H. ; Mulder, H.A. ; Mathur, P.K. ; Knol, E.F. ; Arendonk, J.A.M. van - \ 2014
Journal of Animal Science 92 (2014)1. - ISSN 0021-8812 - p. 95 - 105.
syndrome virus - syndrome prrs - dairy-cattle - tolerance - resistance - performance - infection - selection - genotype - models
Porcine reproductive and respiratory syndrome (PRRS) is a viral disease with negative impacts on reproduction of sows. Genetic selection to improve the response of sows to PRRS could be an approach to control the disease. Determining sow response to PRRS requires knowing pathogen burden and sow performance. In practice, though, records of pathogen burden are unavailable. We develop a statistical method to distinguish healthy and disease phases and to develop a method to quantify sows’ responses to PRRS without having individual pathogen burden. We analyzed 10,910 sows with 57,135 repeated records of reproduction performance. Disease phases were recognized as strong deviation of herd-year-week estimates for reproduction traits using two methods: Method 1 used raw weekly averages of the herd; Method 2 used a linear model with fixed effects for seasonality, parity, and year, and random effects for herd-year-week and sow. The variation of sows in response to PRRS was quantified using 2 models on the traits number of piglets born alive (NBA) and number of piglets born dead (LOSS): 1) bivariate model considering the trait in healthy and disease phases as different traits, and 2) reaction norm model modeling the response of sows as a linear regression of the trait on herd-year-week estimates of NBA. The linear model for NBA had the highest sensitivity (78%) for disease phases. Residual variances of both were more than doubled in the disease phase compared with the healthy phase. Trait correlations between healthy and disease phases deviated from unity (0.57 ± 0.13 – 0.87 ± 0.18). In the bivariate model, repeatabilities were lower in disease phase compared with healthy phase (0.07 ± 0.027 and 0.16 ± 0.005 for NBA; 0.07 ± 0.027 and 0.09 ± 0.004 for LOSS). The reaction norm model fitted the data better than the bivariate model based on Akaike’s information criterion, and had also higher predictive ability in disease phase based on cross validation. Our results show that the linear model is a practical method to distinguish between healthy and disease phases in farm data. We showed that there is variation among sows in response to PRRS, implying possibilities for selection, and the reaction norm model is a good model to study the response of animals toward diseases.
Unsaturated hydraulic properties of xerophilous mosses: towards implementation of moss covered soils in hydrological models
Voortman, B.R. ; Bartholomeus, R.P. ; Bodegom, P.M. van; Gooren, H.P.A. ; Zee, S.E.A.T.M. van der; Witte, J.P.M. - \ 2014
Hydrological Processes 28 (2014)26. - ISSN 0885-6087 - p. 6251 - 6264.
evaporatie - bryophyta - hydraulisch geleidingsvermogen - korstmossen - mossen - hydrologie - waterbalans - bodemwaterretentie - modelleren - evaporation - hydraulic conductivity - lichens - mosses - hydrology - water balance - soil water retention - modeling - sphagnum moss - water - conductivity - bryophytes - desiccation - ecosystems - tolerance
Evaporation from mosses and lichens can form a major component of the water balance, especially in ecosystems where mosses and lichens often grow abundantly, such as tundra, deserts and bogs. To facilitate moss representation in hydrological models, we parameterized the unsaturated hydraulic properties of mosses and lichens such that the capillary water flow through moss and lichen material during evaporation could be assessed. We derived the Mualem-van Genuchten parameters of the drying retention and the hydraulic conductivity functions of four xerophilous moss species and one lichen species. The shape parameters of the retention functions (2.17¿
In vitro selection and characterization of putative probiotics isolated from the gut of Acipenser baerii (Brandt, 1869)
Geraylou, Z. ; Vanhove, M.P.M. ; Souffreau, C. ; Rurangwa, E. ; Buyse, J. ; Ollevier, F. - \ 2014
Aquaculture Research 45 (2014)2. - ISSN 1355-557X - p. 341 - 352.
lactic-acid bacteria - gastrointestinal-tract - fish pathogens - intestinal microbiota - growth-performance - aquaculture - marine - lactobacillus - prevention - tolerance
To select and characterize potential probiotic bacteria from the gut microbiota of Siberian sturgeon (Acipenser baerii), 129 strains isolated from the hindgut were screened for antagonistic activity against five fish pathogens. Ten isolates showed antagonism towards three or more pathogens. Nine of these isolates were Gram-positive, belonging to Lactococcus (seven) and Bacillus (two), and a single strain belonging to the Gram-negative Citrobacter. These inhibitory isolates were identified using genetic, phentotypic and biochemical traits, and further characterized by in vitro tests assessing the adhesion and growth in mucus and resistance to gastric and intestinal fluids. The candidate probiotics were determined to be non-pathogenic through an in vivo study. Based on these assays, Lactococcus lactis ssp. lactis STG45 and STG81 showed the broadest inhibitory potential, a high viability in simulated gastrointestinal juice and the highest adhesion capacity to mucus. They were therefore selected as the most promising candidate probiotics. This is the first study screening probiotics among the gut microflora of Siberian sturgeon.
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