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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    Aerobic swimming in intensive finfish aquaculture : applications for production, mitigation and selection
    McKenzie, David J. ; Palstra, Arjan P. ; Planas, Josep ; MacKenzie, Simon ; Bégout, Marie Laure ; Thorarensen, Helgi ; Vandeputte, Marc ; Mes, Daan ; Rey, Sonia ; Boeck, Gudrun De; Domenici, Paolo ; Skov, Peter V. - \ 2020
    Reviews in Aquaculture (2020). - ISSN 1753-5123
    aerobic exercise - growth - maturation - selection - stress - welfare

    We review knowledge on applications of sustained aerobic swimming as a tool to promote productivity and welfare of farmed fish species. There has been extensive interest in whether providing active species with a current to swim against can promote growth. The results are not conclusive but the studies have varied in species, life stage, swimming speed applied, feeding regime, stocking density and other factors. Therefore, much remains to be understood about mechanisms underlying findings of ‘swimming-enhanced growth’, in particular to demonstrate that swimming can improve feed conversion ratio and dietary protein retention under true aquaculture conditions. There has also been research into whether swimming can alleviate chronic stress, once again on a range of species and life stages. The evidence is mixed but swimming does improve recovery from acute stresses such as handling or confinement. Research into issues such as whether swimming can improve immune function and promote cognitive function is still at an early stage and should be encouraged. There is promising evidence that swimming can inhibit precocious sexual maturation in some species, so studies should be broadened to other species where precocious maturation is a problem. Swimming performance is a heritable trait and may prove a useful selection tool, especially if it is related to overall robustness. More research is required to better understand the advantages that swimming may provide to the fish farmer, in terms of production, mitigation and selection.

    Response of maize (Zea mays L.) to potassium nano-silica application under drought stress
    Aqaei, Pegah ; Weisany, Weria ; Diyanat, Marjan ; Razmi, Javad ; Struik, Paul C. - \ 2020
    Journal of Plant Nutrition 43 (2020)9. - ISSN 0190-4167 - p. 1205 - 1216.
    Drought - nutrients uptake - potassium nano-silica - stress

    To investigate the influence of potassium nano-silica (PNS) on maize plant under drought stress including non-stress (NS), moderate drought stress (MDS) and severe drought stress (SDS), a factorial experiment was conducted with completely randomized blocks with three replications. Drought stress decreased the concentrations in the shoot of phosphor (P), calcium (Ca), iron (Fe), zinc (Zn), manganese (Mn) and silica (Si) and nitrogen (N), P, Ca, Fe, Zn, copper (Cu), Mn and Si concentrations of seed. There was an increase in the concentration in the N seed and shoot potassium (K) concentration under drought stress. It was observed that applying PNS increased nutrient absorption. The highest concentration of N in the seed was obtained at 100 ppm PNS. The highest concentrations of seed K and N, Cu, Mn and Si in the shoot were found when 200 ppm of PNS was applied. Applying PNS had no significant effect on the concentrations of P, Ca, sodium (Na) and Cu in the seed, and of Ca and Na in the shoot. These findings demonstrate that the application of PNS can limit the negative effects of drought stress and improve plant’s resistance against drought stress.

    Nature Based Solutions
    Spijker, J.H. - \ 2019
    urban planning - urban areas - ecosystem services - greening - health - water - heat resistance - trees - climatic change - water holding capacity - biodiversity - stress - population education - mobility
    Voor de uitdagingen van de stad 21e eeuw: 25 jaar VBG, Wageningen 22 maart 2019
    Greenery and Healthcare : The positive effects of greenery in urban environments
    Hiemstra, J.A. ; Vries, S. de; Spijker, J.H. - \ 2019
    Wageningen : Wageningen University & Research - 6 p.
    health - hospitals - patient care - patients - well-being - public green areas - botanical gardens - plantations - social welfare - health indicators - stress - rehabilitation - gezondheid - ziekenhuizen - patiëntenzorg - patiënten - welzijn - openbaar groen - botanische tuinen - beplantingen - sociaal welzijn - gezondheidsindicatoren - stress - herstel
    Greenery in and around nursing homes, hospitals and other clinics is good for the climate inside and outside the building, and has a positive effect on patient’s state of mind and ability to recover, as well as the general well-being of patients, staff and visitors. This document provides information on the benefits of greenery for recovery and well-being, including references to scientific literature. It concludes with some tips on how to ensure the successful and beneficial inclusion of greenery
    Greenery and Work : The positive effects of greenery in urban environments
    Hiemstra, J.A. ; Vries, S. de; Spijker, J.H. - \ 2019
    Wageningen : Wageningen University & Research - 6 p.
    offices - work - climate - health - well-being - stress - stress tolerance - labour - kantoren - werk - klimaat - gezondheid - welzijn - stress - stresstolerantie - arbeid (werk)
    Greenery in and around offices and other working environments is good for both the indoor and outdoor climate, and has a positive effect on the health and general well-being of employees and visitors. It aids concentration, helps reduce stress and increases staff productivity. This document provides information on the benefits of greenery in relation to work and well-being, including references to scientific literature. It concludes with some tips on how to ensure the successful and beneficial inclusion of greenery.
    Methodologies for Assessing Disease Tolerance in Pigs
    Nakov, Dimitar ; Hristov, Slavcha ; Stankovic, Branislav ; Pol, Françoise ; Ivan Dimitrov, Ivan ; Dixhoorn, I.D.E. van - \ 2019
    - p. 12 - 12.
    behavior - disease tolerance - environment - performance - stress
    Features of intensive farming can seriously threaten pig homeostasis, well-being and productivity. Disease tolerance of an organism is the adaptive ability in preserving homeostasis and at the same time limiting the detrimental impact that infection can inflict on its health and performance without affecting pathogen burden per se. While disease resistance (DRs) can be assessed measuring appropriately the pathogen burden within the host, the tolerance cannot be quantified easily. Indeed, it requires the assessment of the changes in performance as well as the changes in pathogen burden. In this paper, special attention is given to criteria required to standardize methodologies for assessing disease tolerance (DT) in respect of infectious diseases in pigs. The concept is applied to different areas of expertise and specific examples are given. The basic physiological mechanisms of DT are reviewed. Disease tolerance pathways, genetics of the tolerance-related traits, stress and disease tolerance, and role of metabolic stress in DT are described. In addition, methodologies based on monitoring of growth and reproductive performance, welfare, emotional affective states, sickness behavior for assessment of disease tolerance, and methodologies based on the relationship between environmental challenges and disease tolerance are considered. Automated Precision Livestock Farming technologies available for monitoring performance, health and welfare-related measures in pig farms, and their limitations regarding DT in pigs are also presented. Since defining standardized methodologies for assessing DT is a serious challenge for biologists, animal scientists and veterinarians, this work should contribute to improvement of health, welfare and production in pigs.
    Uitdagingen van de stad 21e eeuw
    Spijker, J.H. - \ 2018
    urban planning - urban areas - mobility - greening - health - water - heat resistance - trees - climatic change - water holding capacity - biodiversity - stress - population education
    Green and Healthcare : A summary of the positive effects of greenery on well-being in recovery environments
    Hiemstra, J.A. ; Vries, S. de; Spijker, J.H. - \ 2017
    Wageningen : Wageningen University & Research - 6
    health - hospitals - patient care - patients - well-being - public green areas - botanical gardens - plantations - social welfare - health indicators - stress - rehabilitation - gezondheid - ziekenhuizen - patiëntenzorg - patiënten - welzijn - openbaar groen - botanische tuinen - beplantingen - sociaal welzijn - gezondheidsindicatoren - stress - herstel
    Greenery in and around nursing homes, hospitals and clinics is beneficial for the climate inside and outside the organisation, and has a positive effect on the patients’ state of mind and ability to recover, as well as the general well-being of patients, staff and visitors. This document provides information on the benefits of greenery in relation to recovery and well-being, including references to scientific literature. It concludes with some tips on how to ensure the successful and beneficial inclusion of greenery.
    Greenery and Work : A summary of the positive effects of greenery on well-being in working environments
    Hiemstra, J.A. ; Vries, S. de; Spijker, J.H. - \ 2017
    Wageningen : Wageningen University & Research - 6
    offices - work - climate - health - well-being - stress - stress tolerance - labour - kantoren - werk - klimaat - gezondheid - welzijn - stress - stresstolerantie - arbeid (werk)
    Greenery in and around offices and other working environments is good for both the indoor and outdoor climate, and has a positive effect on the health and general well-being of employees and visitors. It aids concentration, helps reduce stress and increases staff productivity. This document provides information on the benefits of greenery in relation to work and well-being, including references to scientific literature. It concludes with some tips on how to ensure the successful and beneficial inclusion of greenery.
    Behavioural and physiological characterisation of laying hen lines divergently selected on feather pecking
    Eijk, J.A.J. van der; Lammers, A. ; Rodenburg, T.B. - \ 2017
    In: Xth European Symposium on Poultry Welfare, 19-22 June 2017, Ploufragan - France. - World's Poultry Science Association (WPSA) - p. 60 - 60.
    broiler breeders - nesting behaviour - genetics - nest design - housing - climate - laying hens - feather pecking - fearfulness - coping style - stress - imune system
    Broilers have been selected for growth related characteristics, which are negatively correlated to reproductive traits. This genetic background creates challenges in broiler breeders, as the hens do not make optimal use of the nests provided. This project aims to investigate what factors determine nesting behaviour, i.e. where a broiler breeder hen prefers to lay her eggs. Factors such as genetic background, social interactions, physical characteristics of the nest and climate might interfere with the natural nesting behaviour of the hen. Also fundamental trade-offs between different motivations, such as hunger, comfort and safety, might influence nesting behaviour. Behaviour and use of space will be measured in experimental set-ups in order to gain insight in the importance of different system components. This knowledge will be used to optimise housing conditions and develop strategies that stimulate the hen to lay her egg in the nest. The performance of this improved system will be tested in field experiments to investigate the transferability of results from experimental to field conditions.
    In vivo 1H NMR methods to study dynamics of chloroplast water and thylakoid membrane lipids in leaves and in photosynthetic microorganisms
    Pagadala, Shanthi - \ 2017
    Wageningen University. Promotor(en): H. van Amerongen, co-promotor(en): H. van As. - Wageningen : Wageningen University - ISBN 9789463431569 - 130
    cell membranes - membranes - chloroplasts - thylakoids - photosynthesis - in vivo experimentation - stress conditions - stress - proteins - lipids - mobility - dynamics - celmembranen - membranen - chloroplasten - thylakoïden - fotosynthese - in vivo experimenten - stress omstandigheden - stress - eiwitten - lipiden - mobiliteit - dynamica

    Dynamics of thylakoid membranes and mobility of pigment-protein complexes therein are essential for survival of photosynthetic organisms under changing environmental conditions. The published approaches to probe mobility of the thylakoid membrane lipids and protein complexes are either dependent on the use of external labels or are used only for in vitro studies. Here, we present non-invasive 1H NMR methods (DOSY and DRCOSY) to study dynamics of water in chloroplasts, lipids in oil bodies and in thylakoid membranes and pigment-protein complexes under complete in vivo conditions in leaf disks of F. benjamina and A. platanoides and in suspensions of the green alga Chlamydomonas reinhardtii and blue-green alga Synechocystissp.PCC 6803.

    In leaf disks of Ficus benjamina and Acer platanoides, water in chloroplasts could be clearly discriminated from other pools. Both water in chloroplasts, and water in vacuoles of palisade and spongy cells showed resonances in the high field part of the spectra (with respect to pure water), in contrast to what has been reported in literature. Subepidermal cells (present only in F. benjamina but not in A. platanoides) may act as a water storage, buffer pool during drought. This pool prevented the fast loss of water from the chloroplasts. Nutrient stress and excess salt stress resulted in accumulated lipid bodies and in striking differences in the dynamics and spectra/composition of the different components. T2 values of the different components are compared with those observed in suspensions of Synechocystissp.PCC 6803. The differences in membrane composition (ratio of the different membrane lipids) were clearly observed in the DANS of the oil bodies and the (thylakoid) membranes, but the diffusion coefficients were quite comparable. Also the DANS of the component that is assigned to the pigment-protein complexes are quite different, reflecting the differed composition. The diffusion coefficients of this component in isolated spinach thylakoids and in C. reinhardtii are very comparable, but about a factor of 10 lower with respect to that of Synechocystis at short diffusion times. The dynamics of these complexes in these systems are thus quite different.

    Groen en herstellen : de meerwaarde van groen voor het welbevinden in de herstelomgeving samengevat
    Spijker, J.H. - \ 2017
    Wageningen : Wageningen Environmental Research - 6
    welzijn - gezondheid - gezondheidsindicatoren - tuinen - warmtestress - klimaat - temperatuur - luchtkwaliteit - stress - sociaal welzijn - participatie - beplantingen - herstellen - well-being - health - health indicators - gardens - heat stress - climate - temperature - air quality - stress - social welfare - participation - plantations - reconditioning
    Groen in en rondom verzorgingshuizen, ziekenhuizen en overige klinieken is goed voor het klimaat binnen en buiten de instelling en heeft een positief effect op het herstellend vermogen en de gemoedstoestand van patiënten, en het algehele welbevinden van patiënten, medewerkers en bezoekers. Dit document biedt meer inzicht in de voordelen van groen in relatie tot herstellen en welbevinden, inclusief verwijzingen naar de wetenschappelijke onderbouwing. Het document sluit af met tips die helpen om groen succesvol en volwaardig toe te passen.
    Effects of environmental enrichment and regrouping on natural autoantibodies-binding danger and neural antigens in healthy pigs with different individual characteristics
    Luo, L. ; Geers, R. ; Reimert, I. ; Kemp, B. ; Parmentier, H.K. ; Bolhuis, J.E. - \ 2017
    Animal 11 (2017)11. - ISSN 1751-7311 - p. 2019 - 2026.
    environmental enrichment - immunity - natural autoantibody - pig - stress
    Pigs living in commercial husbandry systems may experience both acute stress due to standard management procedures and chronic stress through limitations in their barren housing environment. This might influence their immune status, including antibody responses to neural and danger autoantigens. Levels of natural autoantibody (NAAb)-binding phosphorylcholine-conjugated bovine serum albumin (PC-BSA) and myelin basic protein (MBP) were measured over time in pigs that were kept in environmental enriched v. barren housing, and that underwent a regrouping test. In total, 480 pigs were housed in 80 pens in either barren or straw-enriched pens from 4 through 23 weeks of age. Blood samples were taken from pigs before (week 8), and 3 days after a 24 h regrouping test (week 9), and at 22 weeks of age. Phosphorylcholine-conjugated bovine serum albumin (PC-BSA) and MBP antibody titres in serum were measured using ELISA. Enriched-housed pigs had higher levels of IgM-binding MBP, and tended to have higher levels of IgG-binding MBP and IgA-binding PC-BSA than barren-housed pigs. Each NAAb measured in this study was affected by gender and litter. These results suggest that enriched housing conditions, as well as acute regrouping stress, have an influence on levels of serum NAAb-binding danger and neural antigens in pigs.
    De Groene Agenda, topsectoronderzoek
    Spijker, J.H. ; Hiemstra, J.A. - \ 2016
    Stadswerk 2016 (2016)7. - ISSN 0927-7641 - p. 56 - 57.
    klimaat - luchtkwaliteit - bedrijven - waterbergend vermogen - gezondheid - welzijn - openbaar groen - beplantingen - kantoren - stedelijke gebieden - toegepast onderzoek - innovaties - arbeid (werk) - stress - warmtestress - sociaal welzijn - participatie - regenwateropvang - climate - air quality - businesses - water holding capacity - health - well-being - public green areas - plantations - offices - urban areas - applied research - innovations - labour - stress - heat stress - social welfare - participation - water harvesting
    Steeds meer mensen wonen in de stad. Dit is niet altijd een gezonde leefomgeving. Veel mensen ervaren stress, het ontbreekt aan sociale samenhang, de lucht is vervuild en het veranderende klimaat leidt tot toenemende hittestress en wateroverlast. Slim gebruik van groen is deel van de oplossing voor al deze uitdagingen.
    A short-term extremely low frequency electromagnetic field exposure increases circulating leukocyte numbers and affects HPA-axis signaling in mice
    Kleijn, Stan de; Ferwerda, Gerben ; Wiese, Michelle ; Trentelman, Jos ; Cuppen, Jan ; Kozicz, Tamas ; Jager, Linda de; Hermans, Peter W.M. ; Kemenade, Lidy van - \ 2016
    Bioelectromagnetics 37 (2016)7. - ISSN 0197-8462 - p. 433 - 443.
    ELF-EMF - immune response - in vivo exposure - leukocytes - stress

    There is still uncertainty whether extremely low frequency electromagnetic fields (ELF-EMF) can induce health effects like immunomodulation. Despite evidence obtained in vitro, an unambiguous association has not yet been established in vivo. Here, mice were exposed to ELF-EMF for 1, 4, and 24 h/day in a short-term (1 week) and long-term (15 weeks) set-up to investigate whole body effects on the level of stress regulation and immune response. ELF-EMF signal contained multiple frequencies (20–5000 Hz) and a magnetic flux density of 10 μT. After exposure, blood was analyzed for leukocyte numbers (short-term and long-term) and adrenocorticotropic hormone concentration (short-term only). Furthermore, in the short-term experiment, stress-related parameters, corticotropin-releasing hormone, proopiomelanocortin (POMC) and CYP11A1 gene-expression, respectively, were determined in the hypothalamic paraventricular nucleus, pituitary, and adrenal glands. In the short-term but not long-term experiment, leukocyte counts were significantly higher in the 24 h-exposed group compared with controls, mainly represented by increased neutrophils and CD4 ± lymphocytes. POMC expression and plasma adrenocorticotropic hormone were significantly lower compared with unexposed control mice. In conclusion, short-term ELF-EMF exposure may affect hypothalamic-pituitary-adrenal axis activation in mice. Changes in stress hormone release may explain changes in circulating leukocyte numbers and composition. Bioelectromagnetics. 37:433–443, 2016.

    Exploring the genetics underlying the responses to consecutive combinations of biotic stresses and drought in Arabidopsis thaliana
    Huang, Pingping - \ 2016
    Wageningen University. Promotor(en): Maarten Koornneef, co-promotor(en): Mark Aarts. - Wageningen : Wageningen University - ISBN 9789462578593 - 291
    arabidopsis thaliana - genetic models - stress - stress response - drought - botrytis - pieris (lepidoptera) - genetics - gene expression - arabidopsis thaliana - genetische modellen - stress - stressreactie - droogte - botrytis - pieris (lepidoptera) - genetica - genexpressie

    Plants growing in natural environments are exposed to a broad range of biotic (pathogen attack, insect herbivory, etc.) and abiotic factors (drought, extreme temperatures, UV radiation, salinity, etc.) that are known to cause stress symptoms in many species (Pareek et al., 2010; Robert-Seilaniantz et al., 2010). Biotic and abiotic stress-inducing determinants often adversely impact plant growth and development, frequently leading to severe annual yield losses in agricultural production (Pierik et al., 2013; Pieterse et al., 2012; Stam et al., 2014). In the research endeavors described in this thesis, Arabidopsis thaliana was used as a model organism to study plant responses to different sequential combinations of biotic factors (infection with Botrytis or herbivory by Pieris) and drought. The main objective was to identify genes that contribute to tolerance to the aforementioned sequential stress combinations. Genome-wide association (GWA) mapping and RNA sequencing (RNA-seq) approaches were used to identify combinatorial stress responsive genes. A number of candidate genes to combinatorial stress responses were identified by GWA analysis and RNA-seq. The physiological function of some candidate genes in different stress conditions were characterized using T-DNA insertion mutants and gene expression study. However, the physiological function of many allelic variants in stress conditions remain to be discovered. The study highlights the importance of an array of genes, crucial to the underlying defense processes, as targets for breeding by allele mining, ultimately aimed at improvement of crop tolerance to frequent combinations of stress factors.

    Epigenetic inheritance in apomictic dandelions : stress-induced and heritable modifications in DNA methylation and small RNA
    Preite, V. - \ 2016
    Wageningen University. Promotor(en): Wim van der Putten, co-promotor(en): K.J.F. Verhoeven. - Wageningen : Wageningen University - ISBN 9789462578715 - 152
    taraxacum officinale - epigenetics - inheritance - apomixis - dna methylation - rna - heritability - stress - taraxacum officinale - epigenetica - overerving - apomixis - dna-methylering - rna - heritability - stress

    Epigenetic variation, such as changes in DNA methylations, regulatory small RNAs (sRNAs) and chromatin modifications can be induced by environmental stress. There is increasing information that such induced epigenetic modifications can be transmitted to offspring, potentially mediating adaptive transgenerational responses to environmental changes. However, it is unclear if this phenomenon is common and relevant for adaptation under natural conditions. My thesis study aimed to examine epigenetic inheritance in common and widespread apomictic dandelions (Taraxacum officinale Wig.). Due to their asexual reproduction mode by producing clonal seeds offspring from seeds are genetically uniform and thus suitable to investigate epigenetic effects that are not confounded with genetic variation.

    I exposed apomictic dandelion lineages to drought and salicylic acid (SA) stress, which induces plant defense responses following pathogen attack, and found effects on patterns of DNA methylation up to two stress-free offspring generations after exposure. However, a heritable stress signal was not present in all tests and was stress- and lineage-dependent. Drought stress triggered a weak and lineage-dependent signal that was lost again in the second offspring generation. SA treatment revealed a stress-related increased rate of DNA methylation changes in the two offspring generations, but no stress signal was found in the stressed generation itself. I also observed changes in small RNA production due the drought and SA stress experienced two generations ago. These transgenerational sRNA effects showed association with gene functions related to grandparental drought and SA stress, which suggests functional relevance of the transgenerational effects.

    I used a reciprocal transplantation field experiment to investigate whether exposing dandelions to natural field stresses also triggers DNA methylation changes. The experiment revealed evidence of adaptive divergence between the populations, suggesting that non-native habitats are experienced as more stressful. However, under these field conditions no induction-based DNA methylation changes were found that persisted into offspring.

    By using AFLP and MS-AFLP screening of natural apomictic dandelion populations across a north-south transect in Europe I examined if natural, heritable DNA methylation variation reflects underlying genetic variation, or if it shows patterns that are not predictable from underlying genetics. I found that a large part of heritable DNA methylation differentiation along the north-south transect was correlated with genetic differentiation. However, a fraction of differentiation in heritable DNA methylation was independent from genetic variation. This suggests a potential of epigenetics to play an evolutionary role independently, at least to some extent, from underlying genetics. Overall, I found indications of epigenetic inheritance in apomictic dandelions. Whether epigenetic variation would result in adaptive phenotypic variation in nature and whether it would persist long enough to play a relevant role in adaptation remains unclear and requires further study.

    Transcriptional regulation of receptor-like protein genes by environmental stresses and hormones and their overexpression activities in Arabidopsis thaliana
    Wu, Jinbin ; Liu, Zhijun ; Zhang, Zhao ; Lv, Yanting ; Yang, Nan ; Zhang, Guohua ; Wu, Menyao ; Lv, Shuo ; Pan, Lixia ; Joosten, Matthieu H.A.J. ; Wang, Guodong - \ 2016
    Journal of Experimental Botany 67 (2016)11. - ISSN 0022-0957 - p. 3339 - 3351.
    Arabidopsis - hormone - overexpression - receptor-like protein - stress - transcriptional regulation

    Receptor-like proteins (RLPs) have been implicated in multiple biological processes, including plant development and immunity to microbial infection. Fifty-seven AtRLP genes have been identified in Arabidopsis, whereas only a few have been functionally characterized. This is due to the lack of suitable physiological screening conditions and the high degree of functional redundancy among AtRLP genes. To overcome the functional redundancy and further understand the role of AtRLP genes, we studied the evolution of AtRLP genes and compiled a comprehensive profile of the transcriptional regulation of AtRLP genes upon exposure to a range of environmental stresses and different hormones. These results indicate that the majority of AtRLP genes are differentially expressed under various conditions that were tested, an observation that will help to select certain AtRLP genes involved in a specific biological process for further experimental studies to eventually dissect their function. A large number of AtRLP genes were found to respond to more than one treatment, suggesting that one single AtRLP gene may be involved in multiple physiological processes. In addition, we performed a genome-wide cloning of the AtRLP genes, and generated and characterized transgenic Arabidopsis plants overexpressing the individual AtRLP genes, presenting new insight into the roles of AtRLP genes, as exemplified by AtRLP3, AtRLP11 and AtRLP28. Our study provides an overview of biological processes in which AtRLP genes may be involved, and presents valuable resources for future investigations into the function of these genes.

    Aspects of bulblet growth of lily in vitro
    Askari Rabori, N. - \ 2016
    Wageningen University. Promotor(en): Richard Visser, co-promotor(en): Geert-Jan de Klerk. - Wageningen : Wageningen University - ISBN 9789462577602 - 130
    lilium - in vitro - growth - in vitro regeneration - abiotic conditions - stress - bulbs - lilium - in vitro - groei - in vitro regeneratie - abiotiek - stress - bollen

    Many geophytes have a high ornamental value. They are preferably propagated by micropropagation because in this way large quantities of uniform, disease-free starting material are produced in a short period of time. In comparison with shoots, bulblets have several clear advantages as starting material. Therefore, in vitro bulblet formation is an important target for improvement of tissue culture of geophytes. The research described in this thesis was carried out with the lily cultivars ‘Santander’ and ‘Stargazer’.

    Commercially, lily is the second geophyte in the global flower industry. The size of lily bulblets regenerated in vitro has a direct effect on the performance in the field. After planting, large bulblets sprout with a stem and gain twice as much weight compared with small bulblets that sprout with a rosette. In the present study we studied basic and applied aspects of the following topics: (1) new methods for sterilization during initiation, (2) the effect of scale-related factors on bulblet growth, (3) growth enhancement by moderate abiotic stresses, and (4) the effect of CO2 removal from headspace of tissue culture containers on lily bulblet growth and as a control Arabidopsis thaliana seedling growth.

    Contamination is an everlasting problem in tissue culture laboratories. Lily bulbs are underground organs and contain therefore more contaminants as compared with aerial organs. During initiation, operators cause additional contamination in two ways that have as yet not been recognized adequately. (1) Rinsing explants with sterile water after surface-sterilization is the generally advised method to remove the residues of decontaminants. However, when scales are heavily contaminated, the surface-sterilization does not kill microorganisms in all scales. Surface-sterilization is usually done with batches of 10 to 30 scales and the contaminated scales may cross-contaminate uninfected scales during rinsing in water. We have tested the rinsing water and found heavy bacterial contamination in the 2th and especially the 3rd rinse. The contaminated rinsing water resulted in a high incidence of cross-contamination. Cross contamination was reduced almost fully by rinsing in diluted NaClO solution (0.03%) instead of sterile water. There was no negative effect of diluted NaClO on growth. (2) A second way of introducing contamination by the operator is the entering of microorganisms during detachment from mother bulbs via the vascular bundles caused by negative hydrostatic pressure within the bulb tissue. By detaching scales from bulbs submerged in 0.03% NaClO, hydrostatic-pressure related contamination was strongly reduced. The growth of bulblets increased by 22% and 17% when cross contamination and negative-hydrostatic pressure related contamination were prevented.

    Storage organ formation is controlled by interacting environmental, biochemical and genetic factors. We studied various aspects of the effect of the scale explant. We found that large explants produced larger bulblets than small explants. When bulblets were excised and cultured in vitro, growth was improved by 33% when a small piece of the original scale explant was left attached to the bulblet. The position in the scale from where the explant was excised affected the growth of the regenerating bulblets. Basal-scale explants improved bulblet growth by 40-50 % compared with apical-scale explants. This might be related to the physiological state of the tissues: there was more starch and there were more vascular bundles present in basal scale explants. Furthermore, excision of an explant from the middle of the scale improved bulblet growth by 40-50 % compared with explants excised from the edge of the scale. In general, the middle scale explants were heavier and contained wider vascular bundles.

    Plants in stressful conditions tend to allocate a higher proportion of biomass to below-ground biomass (roots and storage organs) as compared to above ground biomass. We investigated the effect of moderate abiotic stresses on lily bulblets grown in vitro. In general, lily bulblets showed an increased growth after moderate stresses. Hot air increased growth by 30%, hot water by 40%. We also examined the effect of drought and anaerobiosis. Drought stress increased growth of bulblets by 40% in the cultivar ‘Stargazer’, but significantly decreased bulblet growth in cv ‘Santander’. Anaerobiosis increased growth in ‘Stargazer’ and ‘Santander’ by 32% and 65%, respectively. We also showed that a moderate stresses treatment protects lily bulblets against future severe abiotic stresses.

    In general, the in vitro situation is not favorable for plants. Composition of the headspace (high humidity, strongly fluctuating CO2- and O2-levels and accumulation of gases like ethylene), low light, and wounding are unfavorable conditions that plants have to deal with. We examined the effect of CO2 starvation on growth in vitro with and without addition of 3% sucrose to the medium. A CO2-poor headspace reduced the growth of bulblets, leaves, roots and scale explants strongly, also in the presence of 3% sucrose. CO2 removal from the headspace decreased growth of Arabidopsis seedlings by 50 % on medium with 3% sucrose. It seems unlikely that the growth reduction on medium with 3% sucrose is caused solely by the lack of sucrose production in photosynthesis when CO2 is removed. Indeed, we found evidence that the low CO2 resulted in heavy stress that in turn may reduce growth. Fv/Fm in lily and Arabidopsis dropped when CO2 was removed. Occurrence of reactive oxygen radicals (ROS) was examined in Arabidopsis seedlings by staining with nitroblue tetrazolium (NBT). ROS was virtually absent in ex vitro growing seedlings and very abundant in seedlings grown under CO2 starvation. Seedlings grown under normal tissue culture conditions showed an intermediate presence of ROS. We hypothesize that low levels of CO2 may results in ROS in in vitro seedlings which reduces growth.

    Quantitative and ecological aspects of Listeria monocytogenes population heterogeneity
    Metselaar, K.I. - \ 2016
    Wageningen University. Promotor(en): Marcel Zwietering; Tjakko Abee, co-promotor(en): Heidy den Besten. - Wageningen : Wageningen University - ISBN 9789462577664 - 173
    listeria - listeria monocytogenes - stress - stress tolerance - ribosomes - proteins - lactobacillus plantarum - behaviour - ecological assessment - genome analysis - dna sequencing - resistance - heterogeneity - listeria - listeria monocytogenes - stress - stresstolerantie - ribosomen - eiwitten - lactobacillus plantarum - gedrag - ecologische beoordeling - genoomanalyse - dna-sequencing - weerstand - heterogeniteit

    Bacterial stress response and heterogeneity therein is one of the biggest challenges posed by minimal processing. Heterogeneity and resulting tailing representing a more resistant fraction of the population, can have several causes and can be transient or stably in nature. Stable increased stress resistance is caused by alterations in the genome and therefore inheritable and is referred to as stable stress resistant variants. Also L. monocytogenes exhibits a heterogeneous response upon stress exposure which can be partially attributed to the presence of stable stress resistant variants. Adverse environments were shown to select for stable stress resistant variants. The objective of the research described in this thesis was to evaluate if L. monocytogenes population diversity and the presence of stable resistant variants is a general phenomenon that is observed upon different types of stress exposure, to get more insight in the mechanisms leading to increased resistance and to evaluate the ecological behaviour and potential impact on food safety of these stable resistant variants. Acid stress was chosen as it is an important hurdle both in food preservation, as well as in stomach survival.

    First, the non-linear inactivation kinetics of L. monocytogenes upon acid exposure were quantitatively described. A commonly used biphasic inactivation model was reparameterized, which improved the statistical performance of the model and resulted in more accurate estimation of the resistant fraction within L. monocytogenes WT populations. The observed tailing suggested that stable stress resistant variants might also be found upon acid exposure. Indeed, 23 stable acid resistant variants of L. monocytogenes LO28 were isolated from the tail after exposure of late-exponential phase cells to pH 3.5 for 90 min, with different degrees of acid resistance amongst them. Increased acid resistance showed to be significantly correlated to reduced growth rate. Studying the growth boundaries of the WT and a representative set of variants indicated that the increased resistance of the variants was only related to survival of severe pH stress but did not allow for better growth or survival at mild pH stress.
    A set of variants were further characterized phenotypically and cluster analysis was performed. This resulted in three clusters and four individual variants and revealed multiple-stress resistance, with both unique and overlapping features related to stress resistance, growth, motility, biofilm formation and virulence indicators. A higher glutamate decarboxylase (GAD) activity correlated with increased acid resistance. Whole genome sequencing of a set of variants was performed and revealed mutations in rpsU, encoding ribosomal protein S21. This rpsU mutation was found in all 11 variants comprising the largest phenotypic cluster, indicating a potential role of this ribosomal protein in stress resistance. Mutations in ctsR, which were previously shown to be responsible for increased resistance of heat and HHP resistant variants, were not found in the acid resistant variants. This underlined that large population diversity exists within one L. monocytogenes strain and that different adverse conditions drive selection for different variants.

    Next, the performance in mixed species biofilms with Lactobacillus plantarum was evaluated, as well as their benzalkonium chloride (BAC) resistance in these biofilms. It was hypothesized that the acid resistant variants might also show better survival in biofilms with L. plantarum, which provide an acidic environment by lactose fermentation with pH values below the growth boundary of L. monocytogenes when biofilms mature. L. monocytogenes LO28 WT and eight acid resistant variants were capable of forming mixed biofilms with L. plantarum at 20°C and 30°C in BHI supplemented with manganese and glucose. Some of the variants were able to withstand the low pH in the mixed biofilms for a longer time than the WT and there were clear differences in survival between the variants which could not be correlated to (lactic) acid resistance alone. Adaptation to mild pH of liquid cultures during growth to stationary phase increased the acid resistance of some variants to a greater extent than of others, which could be correlated to increased survival in the mixed biofilms. There were no clear differences in BAC resistance between the wild type and variants in mixed biofilms.

    Lastly, a set of robustness and fitness parameters of WT and variants was obtained and used to model their growth behaviour under combined mild stress conditions and to model their performance in a simulated food chain. This gave more insight in the trade-off between increased stress resistance and growth capacity. Predictions of performance were validated in single and mixed cultures by plate counts and by qPCR in which WT and an rpsU deletion variant were distinguished by specific primers. Growth predictions for WT and rpsU deletion variant were matching the experimental data generally well. Globally, the variants are more robust than the WT but the WT grows faster than most variants. Validation of performance in a simulated food chain consisting of subsequent growth and inactivation steps, confirmed the trend of higher growth fitness and lower stress robustness for the WT compared to the rpsU variant. This quantitative data set provides insights into the conditions which can select for stress resistant variants in industrial settings and their potential persistence in food processing environments.

    In conclusion, the work presented in this thesis highlights the population diversity of L. monocytogenes and the impact of environmental conditions on the population composition, which is of great importance for minimal processing. The work of this thesis resulted in more insight in the mechanisms underlying increased resistance of stress resistant variants and quantitative data on the behaviour of stress resistant variants which can be implemented in predictive microbiology and quantitative risk assessments aiming at finding the balance between food safety and food quality.

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