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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Nutrimetabolomics: An Integrative Action for Metabolomic Analyses in Human Nutritional Studies
Ulaszewska, Marynka M. ; Weinert, Christoph H. ; Trimigno, Alessia ; Portmann, Reto ; Andres Lacueva, Cristina ; Badertscher, René ; Brennan, Lorraine ; Brunius, Carl ; Bub, Achim ; Capozzi, Francesco ; Cialiè Rosso, Marta ; Cordero, Chiara E. ; Daniel, Hannelore ; Durand, Stéphanie ; Egert, Bjoern ; Ferrario, Paola G. ; Feskens, Edith J.M. ; Franceschi, Pietro ; Garcia-Aloy, Mar ; Giacomoni, Franck ; Giesbertz, Pieter ; González-Domínguez, Raúl ; Hanhineva, Kati ; Hemeryck, Lieselot Y. ; Kopka, Joachim ; Kulling, Sabine E. ; Llorach, Rafael ; Manach, Claudine ; Mattivi, Fulvio ; Migné, Carole ; Münger, Linda H. ; Ott, Beate ; Picone, Gianfranco ; Pimentel, Grégory ; Pujos-Guillot, Estelle ; Riccadonna, Samantha ; Rist, Manuela J. ; Rombouts, Caroline ; Rubert, Josep ; Skurk, Thomas ; Sri Harsha, Pedapati S.C. ; Meulebroek, Lieven Van; Vanhaecke, Lynn ; Vázquez-Fresno, Rosa ; Wishart, David ; Vergères, Guy - \ 2018
Molecular Nutrition & Food Research 63 (2018)1. - ISSN 1613-4125
GC–MS - LC–MS - metabolomics - NMR - nutrition
The life sciences are currently being transformed by an unprecedented wave of developments in molecular analysis, which include important advances in instrumental analysis as well as biocomputing. In light of the central role played by metabolism in nutrition, metabolomics is rapidly being established as a key analytical tool in human nutritional studies. Consequently, an increasing number of nutritionists integrate metabolomics into their study designs. Within this dynamic landscape, the potential of nutritional metabolomics (nutrimetabolomics) to be translated into a science, which can impact on health policies, still needs to be realized. A key element to reach this goal is the ability of the research community to join, to collectively make the best use of the potential offered by nutritional metabolomics. This article, therefore, provides a methodological description of nutritional metabolomics that reflects on the state-of-the-art techniques used in the laboratories of the Food Biomarker Alliance (funded by the European Joint Programming Initiative “A Healthy Diet for a Healthy Life” (JPI HDHL)) as well as points of reflections to harmonize this field. It is not intended to be exhaustive but rather to present a pragmatic guidance on metabolomic methodologies, providing readers with useful “tips and tricks” along the analytical workflow.
Green light for quantitative live-cell imaging in plants
Grossmann, Guido ; Krebs, Melanie ; Maizel, Alexis ; Stahl, Yvonne ; Vermeer, Joop E.M. ; Ott, Thomas - \ 2018
Journal of Cell Science 131 (2018)2. - ISSN 0021-9533
Imaging - Plant cell biology - Plant growth
Plants exhibit an intriguing morphological and physiological plasticity that enables them to thrive in a wide range of environments. To understand the cell biological basis of this unparalleled competence, a number ofmethodologies have been adapted or developed over the last decades that allow minimal or non-invasive live-cell imaging in the context of tissues. Combined with the ease to generate transgenic reporter lines in specific genetic backgrounds or accessions, we are witnessing a blooming in plant cell biology. However, the imaging of plant cells entails a number of specific challenges, such as high levels of autofluorescence, light scattering that is caused by cell walls and their sensitivity to environmental conditions. Quantitative live-cell imaging in plants therefore requires adapting or developing imaging techniques, as well as mounting and incubation systems, such as micro-fluidics. Here, we discuss some of these obstacles, and review a number of selected state-of-the-art techniques, such as two-photon imaging, light sheet microscopy and variable angle epifluorescence microscopy that allow high performance and minimal invasive live-cell imaging in plants.
The significance of meaning. Why IPBES needs the social sciences and humanities
Jetzkowitz, Jens ; Koppen, C.S.A. van; Lidskog, Rolf ; Ott, Konrad ; Voget-Kleschin, Lieske ; Wong, Catherine Mei Ling - \ 2018
Innovation: The European Journal of Social Science Research 31 (2018)sup1. - ISSN 1351-1610 - p. S38 - S60.
biodiversity - ethics - foundations of biodiversity research - IPBES - methodology - science–policy interface - social sciences

The term “biodiversity” is often used to describe phenomena of nature, which can be studied without a reference to the socially constructed, evaluative, or indeed normative contexts. In our paper, we challenge this conception by focusing particularly on methodological aspects of biodiversity research. We thereby engage with the idea of interdisciplinary biodiversity research as a scientific approach directed at the recognition and management of contemporary society in its ecological embedding. By doing this, we explore how research on and assessments of biodiversity can be enhanced if meaning, aspiration, desires, and related aspects of agency are methodically taken into account. In six sections, we substantiate our claim that the discourse on biodiversity (including the IPBES (Intergovernmental science-policy Platform on Biodiversity and Ecosystem Services) debate) is incomplete without contributions from the social sciences and humanities. In the introduction, a brief overview of biodiversity’s conceptual history is provided showing that “biodiversity” is a lexical invention intended to create a strong political momentum. However, that does not impede its usability as a research concept. Section 2 examines the origins of the Convention on Biological Diversity (CBD) by way of sociological discourse analysis. Subsequently, it proposes a matrix as a means to structure the ambiguities and tensions inherent in the CBD. The matrix reemphasizes our main thesis regarding the need to bring social and ethical expertise to the biodiversity discourse. In Section 3, we offer a brief sketch of the different methods of the natural and social sciences as well as ethics. This lays the groundwork for our Section 4, which explains and illustrates what social sciences and ethics can contribute to biodiversity research. Section 5 turns from research to politics and argues that biodiversity governance necessitates deliberative discourses in which participation of lay people plays an important role. Section 6 provides our conclusions.

The borderline range of toxicological methods : Quantification and implications for evaluating precision
Leontaridou, Maria ; Urbisch, Daniel ; Kolle, Susanne N. ; Ott, Katharina ; Mulliner, Denis S. ; Gabbert, Silke ; Landsiedel, Robert - \ 2017
Altex 34 (2017)4. - ISSN 1868-596X - p. 525 - 538.
Borderline range - Non-animal methods - Skin sensitization - Variability
Test methods to assess the skin sensitization potential of a substance usually use threshold criteria to dichotomize continuous experimental read-outs into yes/no conclusions. The threshold criteria are prescribed in the respective OECD test guidelines and the conclusion is used for regulatory hazard assessment, i.e., classification and labelling of the substance. We can identify a borderline range (BR) around the classification threshold within which test results are inconclusive due to a test method's biological and technical variability. We quantified BRs in the prediction models of the non-animal test methods DPRA, LuSens and h-CLAT, and of the animal test LLNA, respectively. Depending on the size of the BR, we found that between 6% and 28% of the substances in the sets tested with these methods were considered borderline. When the results of individual non-animal test methods were combined into integrated testing strategies (ITS), borderline test results of individual tests also affected the overall assessment of the skin sensitization potential of the testing strategy. This was analyzed for the 2-out-of-3 ITS: Four out of 40 substances (10%) were considered borderline. Based on our findings we propose expanding the standard binary classification of substances into "positive"/"negative" or "hazardous"/"non-hazardous" by adding a "borderline" or "inconclusive" alert for cases where test results fall within the borderline range.
Characterization of SOC1’s central role in flowering by the identification of its upstream and downstream regulators
Immink, G.H. ; Posé, D. ; Ferrario, S.I.T. ; Ott, F. ; Kaufmann, K. ; Valentim, F.L. ; Folter, S. de; Wal, F. van der; Dijk, A.D.J. van; Schmid, M. ; Angenent, G.C. - \ 2016
Arabidopsis thaliana - GSE45846 - PRJNA196500
The transition from vegetative to reproductive development is one of the most important phase changes in the plant life cycle. This step is controlled by various environmental signals that are integrated at the molecular level by so-called floral integrators. One such floral integrator in Arabidopsis (Arabidopsis thaliana) is the MADS domain transcription factor SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1). Despite extensive genetic studies, little is known about the transcriptional control of SOC1, and we are just starting to explore the network of genes under the direct control of SOC1 transcription factor complexes. Here, we show that several MADS domain proteins, including SOC1 heterodimers, are able to bind SOC1 regulatory sequences. Genome-wide target gene analysis by ChIP-seq confirmed the binding of SOC1 to its own locus and shows that it also binds to a plethora of flowering-time regulatory and floral homeotic genes. In turn, the encoded floral homeotic MADS domain proteins appear to bind SOC1 regulatory sequences. Subsequent in planta analyses revealed SOC1 repression by several floral homeotic MADS domain proteins, and we show that, mechanistically, this depends on the presence of the SOC1 protein. Together, our data show that SOC1 constitutes a major hub in the regulatory networks underlying floral timing and flower development and that these networks are composed of many positive and negative autoregulatory and feedback loops. The latter seems to be crucial for the generation of a robust flower-inducing signal, followed shortly after by repression of the SOC1 floral integrator.
Scalable and Environmentally Benign Process for Smart Textile Nanofinishing
Feng, Jicheng ; Hontañón, Esther ; Blanes, Maria ; Meyer, Jörg ; Guo, Xiaoai ; Santos, Laura ; Paltrinieri, Laura ; Ramlawi, Nabil ; Smet, Louis C.P.M. de; Nirschl, Hermann ; Kruis, Frank Einar ; Schmidt-Ott, Andreas ; Biskos, George - \ 2016
ACS Applied Materials and Interfaces 8 (2016)23. - ISSN 1944-8244 - p. 14756 - 14765.
aerosol deposition - antibacterial - leaching test - nanoparticles - textile nanofinishing

A major challenge in nanotechnology is that of determining how to introduce green and sustainable principles when assembling individual nanoscale elements to create working devices. For instance, textile nanofinishing is restricted by the many constraints of traditional pad-dry-cure processes, such as the use of costly chemical precursors to produce nanoparticles (NPs), the high liquid and energy consumption, the production of harmful liquid wastes, and multistep batch operations. By integrating low-cost, scalable, and environmentally benign aerosol processes of the type proposed here into textile nanofinishing, these constraints can be circumvented while leading to a new class of fabrics. The proposed one-step textile nanofinishing process relies on the diffusional deposition of aerosol NPs onto textile fibers. As proof of this concept, we deposit Ag NPs onto a range of textiles and assess their antimicrobial properties for two strains of bacteria (i.e., Staphylococcus aureus and Klebsiella pneumoniae). The measurements show that the logarithmic reduction in bacterial count can get as high as ca. 5.5 (corresponding to a reduction efficiency of 99.96%) when the Ag loading is 1 order of magnitude less (10 ppm; i.e., 10 mg Ag NPs per kg of textile) than that of textiles treated by traditional wet-routes. The antimicrobial activity does not increase in proportion to the Ag content above 10 ppm as a consequence of a "saturation" effect. Such low NP loadings on antimicrobial textiles minimizes the risk to human health (during textile use) and to the ecosystem (after textile disposal), as well as it reduces potential changes in color and texture of the resulting textile products. After three washes, the release of Ag is in the order of 1 wt %, which is comparable to textiles nanofinished with wet routes using binders. Interestingly, the washed textiles exhibit almost no reduction in antimicrobial activity, much as those of as-deposited samples. Considering that a realm of functional textiles can be nanofinished by aerosol NP deposition, our results demonstrate that the proposed approach, which is universal and sustainable, can potentially lead to a wide number of applications.

Gut microbiota disturbance during antibiotic therapy: a multi-omic approach
Ferrer, M. ; Martins dos Santos, V.A.P. ; Ott, S.J. ; Moya, A. - \ 2014
Gut Microbes 5 (2014)1. - ISSN 1949-0976 - p. 64 - 70.
It is known that the gastrointestinal tract (GIT) microbiota responds to different antibiotics in different ways and that while some antibiotics do not induce disturbances of the community, others drastically influence the richness, diversity, and prevalence of bacterial taxa. However, the metabolic consequences thereof, independent of the degree of the community shifts, are not clearly understood. In a recent article, we used an integrative OMICS approach to provide new insights into the metabolic shifts caused by antibiotic disturbance. The study presented here further suggests that specific bacterial lineage blooms occurring at defined stages of antibiotic intervention are mostly associated with organisms that possess improved survival and colonization mechanisms, such as those of the Enterococcus, Blautia, Faecalibacterium, and Akkermansia genera. The study also provides an overview of the most variable metabolic functions affected as a consequence of a β-lactam antibiotic intervention. Thus, we observed that anabolic sugar metabolism, the production of acetyl donors and the synthesis and degradation of intestinal/colonic epithelium components were among the most variable functions during the intervention. We are aware that these results have been established with a single patient and will require further confirmation with a larger group of individuals and with other antibiotics. Future directions for exploration of the effects of antibiotic interventions are discussed
Effects of ß-Lactam Antibiotics and Fluoroquinolones on Human Gut Microbiota in Relation to Clostridium difficile Associated Diarrhea
Knecht, H. ; Neulinger, S.C. ; Heinsen, F.A. ; Knecht, C. ; Schilhabel, A. ; Schmitz, R.A. ; Zimmermann, A. ; Martins dos Santos, V.A.P. ; Ferrer, R. ; Rosenstiel, P.C. ; Schreiber, S. ; Friedrichs, A.K. ; Ott, S.J. - \ 2014
PLoS ONE 9 (2014)2. - ISSN 1932-6203
irritable-bowel-syndrome - ribosomal-rna - colonization resistance - intestinal microbiota - fecal microbiota - fatty-acids - disease - diversity - differs - risk
Clostridium difficile infections are an emerging health problem in the modern hospital environment. Severe alterations of the gut microbiome with loss of resistance to colonization against C. difficile are thought to be the major trigger, but there is no clear concept of how C. difficile infection evolves and which microbiological factors are involved. We sequenced 16S rRNA amplicons generated from DNA and RNA/cDNA of fecal samples from three groups of individuals by FLX technology: (i) healthy controls (no antibiotic therapy); (ii) individuals receiving antibiotic therapy (Ampicillin/Sulbactam, cephalosporins, and fluoroquinolones with subsequent development of C. difficile infection or (iii) individuals receiving antibiotic therapy without C. difficile infection. We compared the effects of the three different antibiotic classes on the intestinal microbiome and the effects of alterations of the gut microbiome on C. difficile infection at the DNA (total microbiota) and rRNA (potentially active) levels. A comparison of antibiotic classes showed significant differences at DNA level, but not at RNA level. Among individuals that developed or did not develop a C. difficile infection under antibiotics we found no significant differences. We identified single species that were up- or down regulated in individuals receiving antibiotics who developed the infection compared to non-infected individuals. We found no significant differences in the global composition of the transcriptionally active gut microbiome associated with C. difficile infections. We suggest that up- and down regulation of specific bacterial species may be involved in colonization resistance against C. difficile providing a potential therapeutic approach through specific manipulation of the intestinal microbiome.
Ecosystem services and ethics
Jax, K. ; Barton, D.N. ; Chan, K.M.A. ; Groot, R.S. de; Doyle, U. ; Eser, U. ; Goerg, C. ; Gomez-Baggethun, E. ; Griewald, Y. ; Haber, W. ; Haines-Young, R. ; Heink, U. ; Jahn, T. ; Joosten, H. ; Kerschbaumer, L. ; Korn, H. ; Luck, G.W. ; Matzdorf, B. ; Muraca, B. ; Nesshover, C. ; Norton, B. ; Ott, K. ; Potschin, M. ; Rauschmayer, F. ; Haaren, C. von; Wichmann, S. - \ 2013
Ecological Economics 93 (2013). - ISSN 0921-8009 - p. 260 - 268.
environmental ethics - conservation - biodiversity - valuation - values - economics - ecology - science
A major strength of the ecosystem services (ESS) concept is that it allows a succinct description of how human well-being depends on nature, showing that the neglect of such dependencies has negative consequences on human well-being and the economy. As ESS refer to human needs and interests, values are to be considered when dealing with the concept in practice. As a result we argue that in using the concept there is a need to be clear about what different dimensions of value are involved, and be aware of ethical issues that might be associated with the concept. A systematic analysis of the ethical implications associated to the ESS concept is still lacking. We address this deficiency by scrutinising value dimensions associated with the concept, and use this to explore the associated ethical implications. We then highlight how improved transparency in the use of the ESS concept can contribute to using its strengths without succumbing to possible drawbacks arising from ethical problems. These problems concern the dangers that some uses of the concept have in obscuring certain types of value, and in masking unevenness in the distribution of costs and benefits that can arise in the management of ESS.
Nutritional and management strategies to mitigate animal greenhouse gas emissions
Hristov, A.N. ; Oh, J. ; Lee, C. ; Meinen, R. ; Montes, F. ; Ott, T. ; Firkins, J.L. ; Rotz, A. ; Dell, C. ; Adesogan, A.T. ; Yang, W.Z. ; Tricarico, J.M. ; Kebreab, E. ; Waghorn, G. ; Dijkstra, J. ; Oosting, S.J. ; Gerber, P.J. ; Henderson, B.L. ; Makkar, H.P.S. - \ 2013
In: Proceedings 2013 24th Annual Florida Ruminant Nutrition Symposium, 5-6 February 2013, Gainesville, Florida, USA. - Gainesville : University of Florida - p. 90 - 98.
Mitigation of methane and nitrous oxide emissions from animal operations: III. A review of animal management mitigation options
Hristov, A.N. ; Ott, T. ; Tricarico, J. ; Rotz, A. ; Waghorn, G. ; Adesogan, A.T. ; Dijkstra, J. ; Montes, F. ; Oh, J. ; Kebreab, E. ; Oosting, S.J. ; Gerber, P.J. ; Henderson, B.L. ; Makkar, H.P.S. ; Firkins, J.L. - \ 2013
Journal of Animal Science 91 (2013)11. - ISSN 0021-8812 - p. 5095 - 5113.
greenhouse-gas emissions - crop-livestock systems - recombinant bovine somatotropin - residual feed-intake - different roughage contents - holstein-friesian cows - dry period management - pastoral dairy farms - 2 complete diets - reproductive-performance
The goal of this review was to analyze published data on animal management practices that mitigate enteric methane (CH4) and nitrous oxide (N2O) emissions from animal operations. Increasing animal productivity can be a very effective strategy for reducing greenhouse gas (GHG) emissions per unit of livestock product. Improving the genetic potential of animals through planned cross-breeding or selection within breeds and achieving this genetic potential through proper nutrition and improvements in reproductive efficiency, animal health, and reproductive lifespan are effective approaches for improving animal productivity and reducing GHG emission intensity. In subsistence production systems, reduction of herd size would increase feed availability and productivity of individual animals and the total herd, thus lowering CH4 emission intensity. In these systems, improving the nutritive value of low-quality feeds for ruminant diets can have a considerable benefit on herd productivity while keeping the herd CH4 output constant or even decreasing it. Residual feed intake may be a tool for screening animals that are low CH4 emitters, but there is currently insufficient evidence that low residual feed intake animals have a lower CH4 yield per unit of feed intake or animal product. Reducing age at slaughter of finished cattle and the number of days that animals are on feed in the feedlot can significantly reduce GHG emissions in beef and other meat animal production systems. Improved animal health and reduced mortality and morbidity are expected to increase herd productivity and reduce GHG emission intensity in all livestock production systems. Pursuing a suite of intensive and extensive reproductive management technologies provides a significant opportunity to reduce GHG emissions. Recommended approaches will differ by region and species but should target increasing conception rates in dairy, beef, and buffalo, increasing fecundity in swine and small ruminants, and reducing embryo wastage in all species. Interactions among individual components of livestock production systems are complex but must be considered when recommending GHG mitigation practices.
Technical options for the mitigation of direct methane and nitrous oxide emissions from livestock: a review
Gerber, P.J. ; Hristov, A.N. ; Henderson, B.L. ; Makkar, H.P.S. ; Oh, J. ; Lee, C. ; Meinen, R. ; Montes, F. ; Ott, T. ; Firkins, J. ; Rotz, A. ; Dell, C. ; Adesogan, A.T. ; Yang, W.Z. ; Tricarico, J.M. ; Kebreab, E. ; Waghorn, G. ; Dijkstra, J. ; Oosting, S.J. - \ 2013
Animal 7 (2013)s2. - ISSN 1751-7311 - p. 220 - 234.
greenhouse-gas emissions - dietary nitrate supplementation - phase compost biofilters - lactating dairy-cows - cereal grain diet - nitrification inhibitors - reduce methane - pig slurry - management options - rumen fermentation
Although livestock production accounts for a sizeable share of global greenhouse gas emissions, numerous technical options have been identified to mitigate these emissions. In this review, a subset of these options, which have proven to be effective, are discussed. These include measures to reduce CH4 emissions from enteric fermentation by ruminants, the largest single emission source from the global livestock sector, and for reducing CH4 and N2O emissions from manure. A unique feature of this review is the high level of attention given to interactions between mitigation options and productivity. Among the feed supplement options for lowering enteric emissions, dietary lipids, nitrates and ionophores are identified as the most effective. Forage quality, feed processing and precision feeding have the best prospects among the various available feed and feed management measures. With regard to manure, dietary measures that reduce the amount of N excreted (e.g. better matching of dietary protein to animal needs), shift N excretion from urine to faeces (e.g. tannin inclusion at low levels) and reduce the amount of fermentable organic matter excreted are recommended. Among the many ‘end-of-pipe’ measures available for manure management, approaches that capture and/or process CH4 emissions during storage (e.g. anaerobic digestion, biofiltration, composting), as well as subsurface injection of manure, are among the most encouraging options flagged in this section of the review. The importance of a multiple gas perspective is critical when assessing mitigation potentials, because most of the options reviewed show strong interactions among sources of greenhouse gas (GHG) emissions. The paper reviews current knowledge on potential pollution swapping, whereby the reduction of one GHG or emission source leads to unintended increases in another
Mitigation of greenhouse gas emissions in livestock production - A review of technical options for non-CO2 emissions
Hristov, A.N. ; Oh, J. ; Lee, C. ; Meinen, R. ; Montes, F. ; Ott, T. ; Firkins, J. ; Rotz, A. ; Dell, C. ; Adesogan, C. ; Yang, W. ; Tricarico, J. ; Kebreab, E. ; Waghorn, G. ; Dijkstra, J. ; Oosting, S.J. - \ 2013
Rome : FAO (FAO animal production and health paper 177) - ISBN 9789251076583 - 231
Temperature-dependent regulation of flowering by antagonistic FLM variants
Posé, D. ; Verhage, D.S.L. ; Ott, F. ; Yant, L. ; Mathieu, J. ; Angenent, G.C. ; Immink, G.H. ; Schmid, M. - \ 2013
Nature 503 (2013)7476. - ISSN 0028-0836 - p. 414 - 417.
mads-box gene - arabidopsis-thaliana - transcription factor - circadian clock - functional-analysis - floral transition - identification - repressor - time - vernalization
The appropriate timing of flowering is crucial for plant reproductive success. It is therefore not surprising that intricate genetic networks have evolved to perceive and integrate both endogenous and environmental signals, such as carbohydrate and hormonal status, photoperiod and temperature1,2. In contrast to our detailed understanding of the vernalization pathway, little is known about how flowering time is controlled in response to changes in the ambient growth temperature. In Arabidopsis thaliana, the MADSbox transcription factor genesFLOWERING LOCUSM (FLM) and SHORTVEGETATIVEPHASE (SVP)have key roles in this process3,4. FLM is subject to temperature-dependent alternative splicing3. Here we report that the two mainFLMprotein splice variants,FLM-b and FLM-d, compete for interaction with the floral repressor SVP. The SVP–FLM-b complex is predominately formed at low temperatures and prevents precocious flowering. By contrast, the competingSVP–FLM-d complex is impaired in DNA binding and acts as a dominant-negative activator of flowering at higher temperatures. Our results show a new mechanism that controls the timing of the floral transition in response to changes in ambient temperature. A better understanding of how temperature controls the molecular mechanismsof flowering will be important to cope with current changes in global climate5,6.
Characterization of SOC1’s Central Role in Flowering by the Identification of Its Upstream and Downstream Regulators1[C][W]
Immink, R.G.H. ; Posé, D. ; Ferrario, S.I.T. ; Ott, F. ; Kaufmann, K. ; Valentim, F.L. ; Folter, S. de; Wal, F. van der; Dijk, A.D.J. van; Schmid, M. ; Angenent, G.C. - \ 2012
Plant Physiology 160 (2012)1. - ISSN 0032-0889 - p. 433 - 449.
floral organ identity - mads domain proteins - time gene soc1 - arabidopsis-thaliana - transcription factor - homeotic gene - target genes - negative regulator - ectopic expression - meristem identity
The transition from vegetative to reproductive development is one of the most important phase changes in the plant life cycle. This step is controlled by various environmental signals that are integrated at the molecular level by so-called floral integrators. One such floral integrator in Arabidopsis (Arabidopsis thaliana) is the MADS domain transcription factor SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1). Despite extensive genetic studies, little is known about the transcriptional control of SOC1, and we are just starting to explore the network of genes under the direct control of SOC1 transcription factor complexes. Here, we show that several MADS domain proteins, including SOC1 heterodimers, are able to bind SOC1 regulatory sequences. Genome-wide target gene analysis by ChIP-seq confirmed the binding of SOC1 to its own locus and shows that it also binds to a plethora of flowering-time regulatory and floral homeotic genes. In turn, the encoded floral homeotic MADS domain proteins appear to bind SOC1 regulatory sequences. Subsequent in planta analyses revealed SOC1 repression by several floral homeotic MADS domain proteins, and we show that, mechanistically, this depends on the presence of the SOC1 protein. Together, our data show that SOC1 constitutes a major hub in the regulatory networks underlying floral timing and flower development and that these networks are composed of many positive and negative autoregulatory and feedback loops. The latter seems to be crucial for the generation of a robust flower-inducing signal, followed shortly after by repression of the SOC1 floral integrator.
The effects of housing system and feeding level on the joint-specific prevalence of osteochondrosis in fattening pigs
Grevenhof, E.M. van; Ott, S. ; Hazeleger, W. ; Weeren, P.R. van; Bijma, P. ; Kemp, B. - \ 2011
Livestock Science 135 (2011)1. - ISSN 1871-1413 - p. 53 - 61.
leg weakness - finishing pigs - growth-rate - genetic-parameters - production traits - space allowance - slaughter pigs - protein-levels - arthrosis - swine
Osteochondrosis (OC) is seen as the main cause of leg weakness in pigs, leading to welfare problems and economic losses. Environmental factors in pig husbandry, such as the housing system and feeding strategy are expected to influence the prevalence of OC. Therefore, this study investigated the effects of housing system and feeding strategy on the prevalence and severity of OC. In the experiment 345 pigs were used. At an age of 69 days intact boars and gilts were separated and assigned to groups of five or six individuals. A two by two factorial design of housing system and feeding strategy was applied. The housing system was either a conventional concrete floor partial slatted, or a deep litter floor with extra space allowance. The feeding strategy was either ad libitum or restricted to 80% of ad libitum. Pigs were slaughtered at the age of 161–176 days. In total, five joints of the left front and hind limbs were macroscopically assessed for OC on a five-point scale, ranged from no OC through (semi-)loose cartilage fragments. The prevalence of OC in the experimental population was 41.4%, and 12.4% of the individuals had severe lesions. The tarsocrural joint was most affected (30.2%) by OC. OC scores between the different joints were not correlated. Medial sections of joints were most affected (63–100%). Boars were more affected than gilts in the elbow joint. Conventionally housed pigs were more affected than deep litter housed pigs. Ad libitum fed pigs had more OC than restrictedly fed pigs. OC was most prevalent with 57.5% in the pigs on the conventional floor with ad libitum feeding. OC was least prevalent with 33.7% in pigs kept in deep litter housing with restricted feeding. The sex, housing system and feeding strategy did not affect OC in the femoropatellar, metacarpophalangeal, and metatarsophalangeal joints. Our results demonstrate that the OC prevalence can be reduced by applying deep litter floors with extra space allowance and/or restricted feeding in fattening pigs
Laboratory populations as a resource for understanding the relationship between genotypes and phenotypes: A global case study in locusts
Berthier, K. ; Chapuis, M.P. ; Simpson, S.J. ; Ferenz, H.J. ; Habib Kane, C.M. ; Kang, L. ; Lange, A. ; Ott, S.R. ; Babah Ebbe, M.A. ; Rodenburg, K.W. ; Rogers, S.M. ; Torto, B. ; Vanden Broeck, J. ; Loon, J.J.A. van; Sword, G.A. - \ 2010
Advances in Insect Physiology 39 (2010). - ISSN 0065-2806 - p. 1 - 37.
polymorphic microsatellite loci - genetic differentiation measure - australian plague locust - schistocerca-gregaria - desert locust - drosophila-melanogaster - migratory locust - chortoicetes-terminifera - phase polyphenism - inbred strains
Publisher Summary The expression of phenotypic plasticity is widespread in insects. One of the most extraordinary and economically devastating examples of phenotypic plasticity is found in locusts. In contrast to typical grasshoppers, locust species express an extreme form of density-dependent phenotypic plasticity known as “phase polyphenism.” Environmental factors such as temperature, photoperiod, resource availability and population density, are known to affect the development of a myriad of phenotypic traits that have consequences for individual performance, ecology, life-history, fitness and subsequent evolution. Given their diversity of responses and amenability to experimental manipulation and rearing in the lab, insects continue to play an important role as model organisms in empirical analyses of the fundamental relationships between genotypes and phenotypes in animals. Critical conclusions and recommendations from the analysis of recent laboratory stocks, findings that are broadly applicable across taxa to any research program rearing organisms in the lab, are also given in the chapter.
Factsheet: SCHMIDT-OTT & ERICA SEAMOUNT
Bos, O.G. - \ 2009
Morphological transitions and the genetic basis of the evolution of extraembryonic tissues in flies
Rafiqi, A.M. - \ 2008
Wageningen University. Promotor(en): Ton Bisseling, co-promotor(en): U. Schmidt-Ott. - [S.l.] : S.n. - ISBN 9789085852100 - 118
drosophila - moleculaire genetica - evolutie - genexpressie - episyrphus balteatus - genen - serosa - ontogenie - molecular genetics - evolution - gene expression - genes - ontogeny
Defensins from insects and plants interact with fungal glucosylceramides
Thevissen, K. ; Warnecke, D.C. ; François, I.E.J.A. ; Leipelt, M. ; Heinz, E. ; Ott, C. ; Zähringer, U. ; Thomma, B.P.H.J. ; Ferket, K.K.A. ; Cammue, B.P.A. - \ 2004
Journal of Biological Chemistry 279 (2004)6. - ISSN 0021-9258 - p. 3900 - 3905.
tandem mass-spectrometry - dahlia dahlia-merckii - saccharomyces-cerevisiae - antifungal activity - protein-synthesis - candida-albicans - barley endosperm - binding-sites - cerebrosides - cells
Growth of the yeast species Candida albicans and Pichia pastoris is inhibited by RsAFP2, a plant defensin isolated from radish seed (Raphanus sativus), at micromolar concentrations. In contrast, gcs-deletion mutants of both yeast species are resistant toward RsAFP2. GCS genes encode UDP-glucose:ceramide glucosyltransferases, which catalyze the final step in the biosynthesis of the membrane lipid glucosylceramide. In an enzyme-linked immunosorbent assay-based binding assay, RsAFP2 was found to interact with glucosylceramides isolated from P. pastoris but not with soybean nor human glucosylceramides. Furthermore, the P. pastoris parental strain is sensitive toward RsAFP2-induced membrane permeabilization, whereas the corresponding gcs-deletion mutant is highly resistant to RsAFP2-mediated membrane permeabilization. A model for the mode of action of RsAFP2 is presented in which all of these findings are linked. Similarly to RsAFP2, heliomicin, a defensin-like peptide from the insect Heliothis virescens, is active on C. albicans and P. pastoris parental strains but displays no activity on the gcs-deletion mutants of both yeast species. Furthermore, heliomicin interacts with glucosylceramides isolated from P. pastoris and soybean but not with human glucosylceramides. These data indicate that structurally homologous anti-fungal peptides present in species from different eukaryotic kingdoms interact with the same target in the fungal plasma membrane, namely glucosylceramides, and as such support the hypothesis that defensins from plants and insects have evolved from a single precursor.
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