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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    Optimal transformation of species cover for vegetation classification
    Tichý, Lubomír ; Hennekens, Stephan M. ; Novák, Pavel ; Rodwell, John S. ; Schaminée, Joop H.J. ; Chytrý, Milan - \ 2020
    Applied Vegetation Science (2020). - ISSN 1402-2001
    agglomerative clustering - Braun-Blanquet scale - cluster analysis - cover scale - cover value - phytosociology - pseudo-species - transformation - vegetation classification - vegetation type

    Aims: Vegetation-plot sampling usually involves estimating species cover. For classifying plots to vegetation types, covers are often transformed to decrease the effect of dominant species. However, it remains unclear which transformation is optimal. We suggest that for vegetation classification, optimal is such transformation that contributes to creating clusters of plots in an unsupervised classification that are most similar to the widely accepted vegetation types, e.g., phytosociological associations. Here our aim is to find and recommend such optimal transformation by testing a range of transformation options against the national vegetation classifications of three European countries. Location: Czech Republic, The Netherlands, Great Britain. Methods: Three national datasets of vegetation plots with species cover information, classified to associations or community types of the respective national vegetation classification systems, were analysed. From each dataset, multiple subsets of plots were selected randomly, each subset representing a vegetation-plot table containing several similar associations/community types. Species cover values in these subsets were subjected to various transformations (power transformation, logarithmic transformation and pseudo-species cut levels). Then each subset was classified by an agglomerative classification method (beta-flexible clustering with different beta values), and the classification was compared with the units of the national vegetation classification using the adjusted Rand index. Results: Power transformations of percentage covers with an exponent between 0.3 and 0.6 produced the best match between the unsupervised classifications and the national vegetation classifications. This result did not depend on the classification method used. A similar degree of matching was achieved with some cut levels of pseudo-species and with logarithmic transformation of percentage cover. Conclusions: If an unsupervised classification of vegetation plots aims at defining vegetation types that are close to the phytosociological associations accepted in national vegetation classifications, the best transformation is close to the square-root of percentage cover (i.e., power transformation with exponent 0.5).

    Complement active human and porcine serum induces natural competence for genetic transformation in the emerging zoonotic pathogen Streptococcus suis
    Ferrando, Laura ; Gussak, Alex ; Mentink, Saskia ; Baarlen, Peter van; Wells, Jerry - \ 2020
    Wageningen University & Research
    bacterial competence - genetic manipulation - infectious disease - transformation - zoonotic agent
    The acquisition of novel genetic traits by natural competence is a strategy used by bacteria in microbe-rich environments including animal or human hosts where microbial competition, antibiotics and host immune defences threaten their survival. We show here that several virulent strains of Streptococcus suis, an important porcine pathogen and zoonotic agent, become naturally competent for genetic transformation with plasmid or genomic DNA when cultured in active porcine and human serum, but not when it is pre-heated for 30 minutes at 56øC to inactivate complement. Competence is also not induced in active fetal bovine serum, which contains less complement factors and immunoglobulins than adult serum. Late competence genes, encoding the uptake machinery for environmental DNA, were highly upregulated in active serum. Competence development was independent of the early competence regulatory switch suggesting presence of an alternative stress-induced pathway for regulation of the transformasome, a type 4-like pilus DNA binding and transport apparatus.
    Multi-stakeholder participation for sustainable delta management: a challenge of the socio-technical transformation in the management practices in Bangladesh
    Mutahara, M. ; Warner, J.F. ; Khan, M.S.A. - \ 2020
    International Journal of Sustainable Development and World Ecology (2020). - ISSN 1350-4509
    community - delta - multi-stakeholder processes - participation - sustainability - Tidal River Management - transformation - water-logging

    In Bangladesh, participation discourse has officially become part of the objectives of the government and international agencies for water management projects since the mid-1990s. At the same historical timeframe, originating from indigenous knowledges Tidal River Management (TRM) has been formalized as a less structural and more natural management intervention to prevent the severe water-logging in the South-west region in the Bangladesh delta. It theoretically constituted a form of participation in the delta management system involving local community groups with government and management authorities. However, multi-stakeholder participation is still very challenging in practices. Even community management approaches are not sustained in delta management practices in Bangladesh. In this research, a socio-technical transformation is defined through a participatory research in the south-west coastal area having both qualitative and quantitative evaluation of changes in the delta management system brought about by TRM practices. This article also analyses the current problems besetting organized community participation in existing management practices and suggests the ways of developing effective multi-stakeholder processes (MSPs) with respect to sustainable management goal in deltas.

    Formation and Morphology Evolution from Ferrihydrite to Hematite in the Presence of Tartaric Acid
    Wang, Mingxia ; Tao, Zhengxing ; Xiong, Juan ; Wang, Xiaoming ; Hou, Jingtao ; Koopal, Luuk K. ; Tan, Wenfeng - \ 2019
    ACS Earth and Space Chemistry 3 (2019)4. - ISSN 2472-3452 - p. 562 - 570.
    dissolution-crystallization - hematite - iron oxide - low molecular organic acids - morphology - transformation

    Hematite, with ferrihydrite as the common precursor, is the most stable iron oxide in soils and sediments and has many applications in environmental systems. As a common reducing agent in soils, tartaric acid (L-TA) can reduce Fe3+ to Fe2+ and template the formation of hematite from ferrihydrite. Here, the formation of hematite in the presence of L-TA was investigated under different L-TA concentrations, initial suspension pH, and aging time. The products were characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM), and high- resolution transmission electron microscopy (HRTEM). Both the transformation process and the particle morphology of hematite were affected by the initial suspension pHi at which the L-TA was added to the suspension. Optimal pHi values at a L-TA/Fe(III) molar ratio of 1.0% and an aging time of 10 h at 100 °C were pHi 7 and pHi 11. At pHi 7, the optimal L-TA/Fe(III) molar ratio for the transformation was 1.0% and aging at 100 °C was completed after about 20 h. The transformation occurred through a dissolution-crystallization process. Crystalline corn-like particles (84 m2/g) were obtained through an oriented attachment mechanism. At a L-TA/Fe(III) molar ratio of 3.0% the ferrihydrite surface was saturated with L-TA and the transformation was inhibited. At pHi 11, L-TA/Fe(III) of 1.0% and aging for 10 h (100 °C), subrounded crystalline particles (24 m2/g) were obtained by solid-phase transformation, oriented attachment, and Ostwald ripening mechanism.

    A Synthesis on Strategic Delta Planning in Action: Wishful Thinking, Vested Practices and Unexpected Changes
    Seijger, Chris ; Halsema, Gerardo E. Van; Korbee, Dorien - \ 2019
    Journal of Environmental Planning and Management 62 (2019)9. - ISSN 0964-0568 - p. 1654 - 1674.
    adaptive management - long-term planning - policy - strategic thinking - transformation

    In this review, we take stock of 10 research articles that cover strategic delta planning processes in Asia, Europe, and the US. We test working hypotheses about consent, innovations, actor coalitions, and planning tools in different phases. We posit that strategic delta planning is a deliberate effort to influence delta developments, wherein wishful thinking on how a delta could develop is repeatedly confronted with vested practices and interests. These confrontations produce expected (e.g., institutional embedment, changing people’s minds) and unexpected changes (e.g., actors suddenly consenting or stepping out). Strategic delta planning is therefore not only an ambitious planning process, it is also highly uncertain, as consent on strategic directions has to be renegotiated across phases and arenas. Recommendations for practice are therefore highlighted that cover vocabulary, persuasiveness and tools. Further research is proposed to study the vagaries of strategic delta plans in urbanising deltas.

    Achieving best-fit configurations through advisory subsystems in AKIS : case studies of advisory service provisioning for diverse types of farmers in Norway
    Klerkx, Laurens ; Petter Stræte, Egil ; Kvam, Gunn Turid ; Ystad, Eystein ; Butli Hårstad, Renate Marie - \ 2017
    The Journal of Agricultural Education and Extension 23 (2017)3. - ISSN 1389-224X - p. 213 - 229.
    Advisory services - AKIS - extension - farming styles - Norway - transformation
    Purpose: In light of the discussion on ‘best-fit’ in pluralistic advisory systems, this article aims to present and discuss challenges for advisory services in serving various types of farmers when they seek and acquire farm business advice. Design/methodology/approach: The empirical basis is data derived from four workshops, five interviews with staff from advisory organizations, and interviews with 11 farmers. Findings: Emerging configurations serve different types of farmers, that is, private advisors serve different clients in different ways; these could be considered subsystems within the overall advisory system. Practical implications: Best-fit configurations of advisory services exist within a country setting in response to farmers’ information demands and how they seek information, as well as public goals of the advisory system, and lead to advisory subsystems. Policy-makers should monitor the emergence of these subsystems and become active participants in some of them, in line with the concept of the public sector as regulator of private and commercial advisory systems. Theoretical implications: Best-fit has been mainly explored at country level, but this study shows that, within countries, different advisory service configurations are formed. So, best-fit should not be considered at national level only, in view of subsystems which can have wider or narrower boundaries. More broadly, the concept of Agricultural Knowledge and Innovation Systems (AKIS) should not be confined to the national level, for example, in view of farmer specializations within countries and the international dimensions of advisory systems. Originality/value: The originality lies in the further unraveling of heterogeneity within AKIS and what this implies for advisory service delivery configurations.
    Strain improvement of oleaginous microalgae
    Jaeger, L. de - \ 2015
    Wageningen University. Promotor(en): Gerrit Eggink; Rene Wijffels, co-promotor(en): Dirk Martens. - Wageningen : Wageningen University - ISBN 9789462574847 - 200
    algen - biomassa - oliën - productiviteit - opbrengsten - transcriptomica - triacylglycerol lipase - bioreactoren - transformatie - mutanten - algenteelt - biomassa productie - algae - biomass - oils - productivity - yields - transcriptomics - triacylglycerol lipase - bioreactors - transformation - mutants - algae culture - biomass production

    The increasing world population and living standards have enlarged the demand for food, feed, and for chemicals. Traditional fossil fuel based commodities need to be replaced, not only because these resources are finite, but also to relieve the impact of carbon emission and pollution, resulting from fossil fuel derived processes. Much attention is on using plants to produce sustainable, renewable alternatives to petrochemical based processes. Palm oil is the crop with the highest lipid yield known today, but the production of palm oil causes deforestation on a large scale. Microalgae are a promising platform for the production of sustainable commodity products. A commodity product that can be produced in microalgae is triacylglycerol (TAG). The TAG molecules that are accumulated in microalgae are comparable to the TAG profiles of commonly used vegetable oils, and can directly be applied for edible oil as well as for biodiesel production. Currently, microalgae derived products have proven to be functional and a potential replacement for conventional crops. However, microalgae derived products, especially TAGs, are not economically feasible yet. In order to make microalgal derived products a reality we need to decrease the production costs by smart technological solutions, biological understanding and metabolic engineering.

    To get more insight in the lipid accumulation mechanism of microalgae, and to define targets for future strain improvement strategies, transcriptome sequencing of the oleaginous microalgae Neochloris oleoabundans was done. This oleaginous microalga can be cultivated in fresh water as well as salt water. The possibility to use salt water gives opportunities for reducing production costs and fresh water footprint for large scale cultivation.

    In chapter 2 the lipid accumulation pathway was studied to gain insight in the gene regulation 24 hours after nitrogen was depleted. Oil accumulation is increased under nitrogen depleted conditions in a comparable way in both fresh and salt water. The transcriptome sequencing revealed a number of genes, such as glycerol-3-phosphate acyltransferase and via glycerol-3-phosphate dehydrogenase, that are of special interest and can be targeted to increase TAG accumulation in microalgae. NMR spectroscopy revealed an increase in proline content in saline adapted cells, which was supported by up regulation of the genes involved in proline biosynthesis. In addition to proline, the ascorbate-glutathione cycle seems to be of importance for successful osmoregulation by removal of reactive oxygen species in N. oleoabundans, because multiple genes in this pathway were upregulated under salt conditions. The mechanism behind the biosynthesis of compatible osmolytes in N. oleoabundans can be used to improve salt resistance in other industrially relevant microalgal strains.

    Another very promising candidate for TAG production is the oleaginous green microalga Scenedesmus obliquus.

    In chapter 3, UV mutagenesis was used to create starchless mutants, since no transformation approach was available for this species, due to its rigid and robust cell wall. All five starchless mutants that were isolated from over 3500 screened mutants, showed an increased triacylglycerol productivity. All five starchless mutants showed a decreased or completely absent starch content. In parallel, an increased TAG accumulation rate was observed for the starchless mutants and no substantial decrease in biomass productivity was perceived. The most promising mutant (Slm1) showed an increase in TFA productivity of 41% at 4 days after nitrogen depletion and reached a TAG content of 49.4% (%CDW).

    In chapter 4 the Slm1 strain was compared to the wild type strain using photobioreactors. In the wild type, TAG and starch accumulated simultaneously during initial nitrogen starvation, and starch was subsequently degraded and likely converted into TAG. The Slm1 did not produce starch and the carbon and energy acquired from photosynthesis was partitioned towards TAG synthesis. This resulted in an increase of the maximum TAG content in Slm1 to 57% (%CDW) compared to 45% (%CDW) in the wild type. Furthermore, it increased the maximum yield of TAG on light by 51%, from 0.144 in the wild type to 0.217 g TAG mol-1 photon-1 in the Slm1 mutant. No differences in photosynthetic efficiency between the Slm1 mutant and the wild type were observed, indicating that the mutation specifically improved carbon partitioning towards TAG and the photosynthetic capacity was not affected.

    To identify the mutation that caused the starchless phenotype of Slm1 the transcriptome of both the wild type and the Slm1 mutant was sequenced as described in chapter 5. A single nucleotide polymorphism (SNP) was discovered in the small subunit of the starch biosynthesis rate-controlling enzyme ADP-glucose pyrophosphorylase, which resulted in the introduction of a STOP codon in the messenger RNA of the enzyme. The characterization of the mutation increases the understanding of carbon partitioning in oleaginous microalgae, leading to a promising target for future genetic engineering approaches to increase TAG accumulation in microalgae.

    To use the insight that is gained in chapters 2-5 for metabolic engineering of TAG accumulation and carbon partitioning, a metabolic engineering toolbox is required. However, the development of transformation protocols for new and less well studied industrially relevant microalgae is challenging. In chapter 6, a simple and effective tool for the optimization of transformation protocols is proposed. Optimal voltage settings were determined for five microalgae: C. reinhardtii, Chlorella vulgaris, N. oleoabundans, S. obliquus, and Nannochloropsis sp. This method can be used to speed up the screening process for species that are susceptible for transformation and to successfully develop transformation strategies for industrially relevant microalgae, which lack an efficient transformation protocol.

    In addition to the increase in productivity, improving the quality in terms of fatty acid composition of TAG molecules would be desired as well. For example, the accumulation of stearic acid rich TAG molecules is of special interest, because of the improved structural properties. The lipid accumulating starchless mutant of the model species C. reinhardtii BAFJ5 was used as model species in chapter 7, since genetic toolbox is well established for this species. In this chapter, stearoyl-ACP desaturase (SAD), is silenced by artificial microRNA. The mRNA levels for SAD were reduced after the silencing construct was induced. In one of the strains, the reduction in SAD mRNA resulted in a doubling of the stearic acid content in triacylglycerol molecules, which shows that increasing the fraction of stearic acid in TAG is possible. Furthermore, we hypothesize that in addition to direct conversion in the chloroplast, C. reinhardtii is able to redirect stearic acid from the chloroplast to the cytosol and convert it to oleic acid in the endoplasmic reticulum by stearoyl-CoA desaturase.

    In chapter 8, an outlook is given on microalgal strain improvement strategies for the future, reflecting on the results obtained in this thesis. Also a roadmap is suggested to get genetically modified microalgal derived products on the market. The results presented in this thesis, provide a significant improvement in the understanding of TAG accumulation and carbon partitioning in oleaginous microalgae. Furthermore, improved microalgal strains with increased TAG accumulation or improved TAG fatty acid composition under nitrogen depleted conditions were generated. In addition, an outlook is presented in which the major bottlenecks are presented in future industrial applications of microalgae.

    Shape Evolution Synthesis of Monodisperse Spherical, Ellipsoidal, and Elongated Hematite (alpha-Fe2O3) Nanoparticles Using Ascorbic Acid
    Tan, W.F. ; Yu, Y.T. ; Wang, M.X. ; Liu, F. ; Koopal, L.K. - \ 2014
    Crystal Growth and Design 14 (2014)1. - ISSN 1528-7483 - p. 157 - 164.
    iron-oxide nanoparticles - iron(iii) oxides - water-treatment - ferrihydrite - particles - transformation - size - degradation - dissolution - systems
    Spherical, ellipsoidal, and elongated hematite particles have been obtained via a simple chemical precipitation reaction of FeCl3 and NaOH in the presence of ascorbic acid,(AA). The effects of pH, molar ratio of AA/Fe(III), and time on the formation and shape of the hematite particles were investigated. The optimal conditions to well obtain crystalline hematite are 0.1 mol/L FeCl3, 6 mol/L NaOH, pH 7, and AA/Fe(III) ratios of 0.5-2.0%. The presence of AA catalyzed the formation of hematite by reductive dissolution of ferrihydrite and the molar ratio of AA/Fe(III) determined the crystal structure and morphology of hematite. As the ratio of AA increased from 0.5 to 2%, the morphology changed from spherical to ellipsoidal particles and then to elongated particles. The dissolution of Fe(II) from the ferrihydrite precursor is enhanced by AA, and this leads to the formation of hematite by precipitation and crystallization. The effect of AA on the particle shape can be explained by the difference in AA adsorption on the various crystal planes. The hematite samples with different morphologies enhanced the photodegradation of methylene blue in an acid solution with peroxide; the elongated particles that had the highest specific surface area were most effective with the methylene blue degradation.
    Rural development and the entwining of dependencies: Transition as evolving governance in Khorezm, Uzbekistan
    Assche, K.A.M. van; Djanibekov, N. ; Hornidge, A.K. ; Shtaltovna, A. ; Verschraegen, G. - \ 2014
    Futures 63 (2014). - ISSN 0016-3287 - p. 75 - 85.
    planning systems - transformation - resilience - management - economies - networks - politics - delta - water
    We develop an analytical framework that allows to grasp the evolving patterns of rules and roles in rural transitions, and the concomitant changes in the functions of expertise. Institutional change is understood as governed by a combination of path dependence, interdependence and goal dependence. We illustrate and develop the framework by means of an in-depth analysis of rural transition in the Khorezm province, Uzbekistan. In Khorezm, the Soviet actors were tightly coupled in order to contribute to shared goals first of all cotton and grain production. After independence, dissolution of collective farms, a diminished interest in planning and policy coordination, and locally different styles of political steering, led to a much less coordinated rural governance, to a scattering of expertise and to opacity regarding its supply and demand. We reflect on the implications of our findings for the analysis of rural transitions more broadly, and especially the impact of policies and plans aiming at a rural transition in a specific direction. (C) 2014 Elsevier Ltd. All rights reserved.
    Development of the recombinase-based in vivo expression technology in Streptococcus thermophilus and validation using the lactose operon promoter
    Junjua, M. ; Galia, W. ; Gaci, N. ; Uriot, O. ; Genay, M. ; Bachmann, H. ; Kleerebezem, M. ; Dary, A. ; Roussel, Y. - \ 2014
    Journal of Applied Microbiology 116 (2014)3. - ISSN 1364-5072 - p. 620 - 631.
    lactic-acid bacteria - gene-expression - lactococcus-lactis - human gut - yogurt - system - mice - identification - transformation - proteinase


    To construct and validate the recombinase-based in vivo expression technology (R-IVET) tool in Streptococcus thermophilus (ST).

    Methods and Results

    The R-IVET system we constructed in the LMD-9 strain includes the plasmid pULNcreB allowing transcriptional fusion with the gene of the site-specific recombinase Cre and the chromosomal cassette containing a spectinomycin resistance gene flanked by two loxP sites. When tested in M17 medium, promoters of the genes encoding the protease PrtS, the heat-shock protein Hsp16 and of the lactose operon triggered deletion of the cassette, indicating promoter activity in these conditions. The lactose operon promoter was also found to be activated during the transit in the murine gastrointestinal tract.


    The R-IVET system developed in ST is relatively stable, functional, very sensitive and can be used to assay activity of promoters, which are specifically active in in vivo conditions.

    Significance and Impact of the Study

    This first adaptation of R-IVET to ST provides a highly valuable tool allowing an exploration of the physiological state of ST in the GIT of mammals, fermentation processes or dairy products.
    Base-Free, One-Pot Chemocatalytic Conversion of Glycerol to Methyl Lactate using Supported Gold Catalysts
    Purushothaman, R.K.P. ; Haveren, J. van; Melian-Cabrera, I. ; Eck, E.R.H. van; Heeres, H.J. - \ 2014
    ChemSusChem 7 (2014)4. - ISSN 1864-5631 - p. 1140 - 1147.
    lactic-acid - selective oxidation - commodity chemicals - aqueous-solutions - d-glucose - hydrogenolysis - transformation - methanol - alcohol - insight
    We report an efficient one-pot conversion of glycerol (GLY) to methyl lactate (MLACT) in methanol in good yields (73% at 95% GLY conversion) by using Au nanoparticles on commercially available ultra-stable zeolite-Y (USY) as the catalyst (160 degrees C, air, 47bar pressure, 0.25M GLY, GLY-to-Au mol ratio of 1407, 10h). The best results were obtained with zeolite USY-600, a catalyst that has both Lewis and BrOnsted sites. This methodology provides a direct chemo-catalytic route for the synthesis of MLACT from GLY. MLACT is stable under the reaction conditions, and the Au/USY catalyst was recycled without a decrease in the activity and selectivity.
    A cost-effective approach for improving the quality of soil sealing change detection from Landsat imagery
    Smiraglia, D. ; Rinaldo, S. ; Ceccarelli, T. ; Bajocco, S. ; Salvati, L. ; Ricotta, C. ; Perini, L. - \ 2014
    European Journal of Remote Sensing 47 (2014). - ISSN 2279-7254 - p. 805 - 819.
    urban - modis - tm - transformation - segmentation - phenology - sprawl - region - ndvi - area
    The aim of this study is to develop a cost-effective approach for soil sealing change detection integrating radiometric analysis, multi-resolution segmentation and object-based classifiers in two study areas in Italy: Campania region and Veneto region. The integrated approach uses multi-temporal satellite images and CORINE Land Cover (CLC) maps. A good overall accuracy was obtained for the soil sealing maps produced. The results show an improvement in terms of size of the minimum mapping unit and of the changed object (1,44 ha in both cases) in respect to the CLC. The approach proves to be cost-effective given the data which are provided at low or no cost and as well as the level of automation achievable.
    Exploratory Catalyst Screening Studies on the Base Free Conversion of Glycerol to Lactic Acid and Glyceric Acid in Water Using Bimetallic Au–Pt Nanoparticles on Acidic Zeolites
    Purushothaman, R.K.P. ; Haveren, J. van; Mayoral, A. ; Melian-Cabrera, I. ; Heeres, H.J. - \ 2014
    Topics in Catalysis 57 (2014)17-20. - ISSN 1022-5528 - p. 1445 - 1453.
    supported gold catalysts - free aqueous-solution - selective oxidation - phase oxidation - commodity chemicals - aerobic oxidation - carbon-monoxide - transformation - temperature - insight
    The base free oxidation of glycerol with molecular oxygen in water using bimetallic Au-Pt catalysts on three different acidic zeolite supports (H-mordenite, H-beta and H-USY) was explored in a batch setup. At temperatures between 140 and 180 degrees C, lactic acid formation was significant and highest selectivity (60 % lactic acid at 80 % glycerol conversion) was obtained using Au-Pt/USY-600 (180 degrees C). A selectivity switch to glyceric acid (GLYA) was observed when the reactions were performed at 100 degrees C. Highest conversion and selectivity towards GLYA were obtained with Au-Pt/H-beta as the catalyst (68 % selectivity at 68 % conversion).
    Polycistronic expression of a ß-carotene biosynthetic pathway in Saccharomyces cerevisiae coupled to ß-ionone production
    Beekwilder, J. ; Rossum, H.M. ; Koopman, F. ; Sonntag, F. ; Buchhaupt, M. ; Schrader, J. ; Hall, R.D. ; Bosch, H.J. ; Pronk, J.T. ; Maris, A.J.A. van; Daran, J.M. - \ 2014
    Journal of Biotechnology 192 (2014)partB. - ISSN 0168-1656 - p. 383 - 392.
    cleavage dioxygenase - yeast - genes - sequences - transformation - translation - polyprotein - versatile - genome - strain
    The flavour and fragrance compound ß-ionone, which naturally occurs in raspberry and many other fruits and flowers, is currently produced by synthetic chemistry. This study describes a synthetic biology approach for ß-ionone production from glucose by Saccharomyces cerevisiae that is partially based on polycistronic expression. Experiments with model proteins showed that the T2A sequence of the Thosea asigna virus mediated efficient production of individual proteins from a single transcript in S. cerevisiae. Subsequently, three ß-carotene biosynthesis genes from the carotenoid-producing ascomycete Xanthophyllomyces dendrorhous (crtI, crtE and crtYB) were expressed in S. cerevisiae from a single polycistronic construct. In this construct, the individual crt proteins were separated by T2A sequences. Production of the individual proteins from the polycistronic construct was confirmed by Western blot analysis and by measuring the production of ß-carotene. To enable ß-ionone production, a carotenoid-cleavage dioxygenase from raspberry (RiCCD1) was co-expressed in the ß-carotene producing strain. In glucose-grown cultures with a second phase of dodecane, ß-ionone and geranylacetone accumulated in the organic phase. Thus, by introducing a polycistronic construct encoding a fungal carotenoid pathway and an expression cassette encoding a plant dioxygenase, a novel microbial production system has been established for a fruit flavour compound.
    Irreversible fate commitment in the Arabidopsis stomatal lineage requires a Fama and Retinoblastoma-related module
    Matos, J.L. ; Lau, O.S. ; Hachez, C. ; Cruz-Ramirez, A. ; Scheres, B. ; Bergmann, D.C. - \ 2014
    eLife 3 (2014). - ISSN 2050-084X
    asymmetric cell divisions - gateway binary vectors - transcription factor - secretory peptide - guard-cells - differentiation - expression - genes - transformation - termination
    The presumed totipotency of plant cells leads to questions about how specific stem cell lineages and terminal fates could be established. In the Arabidopsis stomatal lineage, a transient self-renewing phase creates precursors that differentiate into one of two epidermal cell types, guard cells or pavement cells. We found that irreversible differentiation of guard cells involves RETINOBLASTOMA-RELATED (RBR) recruitment to regulatory regions of master regulators of stomatal initiation, facilitated through interaction with a terminal stomatal lineage transcription factor, FAMA. Disrupting physical interactions between FAMA and RBR preferentially reveals the role of RBR in enforcing fate commitment over its role in cell-cycle control in this developmental context. Analysis of the phenotypes linked to the modulation of FAMA and RBR sheds new light on the way iterative divisions and terminal differentiation are coordinately regulated in a plant stem-cell lineage. - See more at:
    Grass allometry and estimation of above-ground biomass in tropical alpine tussock grasslands
    Oliveras Menor, I. ; Eynden, M. van der; Malhi, Y. ; Cahuana, N. ; Menor, C. ; Zamora, F. ; Haugaasen, T. - \ 2014
    Austral Ecology: a journal of ecology in the Southern Hemisphere 39 (2014)4. - ISSN 1442-9985 - p. 408 - 415.
    net primary productivity - carbon stocks - forests - transformation - vegetation - equations - dynamics - ecuador - balance - paramo
    The puna/páramo grasslands span across the highest altitudes of the tropical Andes, and their ecosystem dynamics are still poorly understood. In this study we examined the above-ground biomass and developed species specific and multispecies power-law allometric equations for four tussock grass species in Peruvian high altitude grasslands, considering maximum height (hmax), elliptical crown area and elliptical basal area. Although these predictors are commonly used among allometric literature, they have not previously been used for estimating puna grassland biomass. Total above-ground biomass was estimated to be of 6.7¿±¿0.2 Mg ha-1 (3.35¿±¿0.1 Mg C ha-1). All allometric relationships fitted to similar power-law models, with basal area and crown area as the most influential predictors, although the fit improved when tussock maximum height was included in the model. Multispecies allometries gave better fits than the other species-specific equations, but the best equation should be used depending on the species composition of the target grassland. These allometric equations provide an useful approach for measuring above-ground biomass and productivity in high-altitude Andean grasslands, where destructive sampling can be challenging and difficult because of the remoteness of the area. These equations can be also applicable for establishing above-ground reference levels before the adoption of carbon compensation mechanisms or grassland management policies, as well as for measuring the impact of land use changes in Andean ecosystems.
    Development of late blight resistant potatoes by cisgenic stacking
    Jo, K.R. ; Kim, C.J. ; Kim, S.J. ; Kim, T.J. ; Bergervoet-van Deelen, J.E.M. ; Jongsma, M.A. ; Visser, R.G.F. ; Jacobsen, E. ; Vossen, J.H. - \ 2014
    BMC Biotechnology 14 (2014). - ISSN 1472-6750
    broad-spectrum resistance - cultivar sarpo mira - phytophthora-infestans - solanum-bulbocastanum - r-gene - plants - transformation - genomics - tomato - biotechnology
    Background Phytophthora infestans, causing late blight in potato, remains one of the most devastating pathogens in potato production and late blight resistance is a top priority in potato breeding. The introduction of multiple resistance (R) genes with different spectra from crossable species into potato varieties is required. Cisgenesis is a promising approach that introduces native genes from the crops own gene pool using GM technology, thereby retaining favourable characteristics of established varieties. Results We pursued a cisgenesis approach to introduce two broad spectrum potato late blight R genes, Rpi-sto1 and Rpi-vnt1.1 from the crossable species Solanum stoloniferum and Solanum venturii, respectively, into three different potato varieties. First, single R gene-containing transgenic plants were produced for all varieties to be used as references for the resistance levels and spectra to be expected in the respective genetic backgrounds. Next, a construct containing both cisgenic late blight R genes (Rpi-vnt1.1 and Rpi-sto1), but lacking the bacterial kanamycin resistance selection marker (NPTII) was transformed to the three selected potato varieties using Agrobacterium-mediated transformation. Gene transfer events were selected by PCR among regenerated shoots. Through further analyses involving morphological evaluations in the greenhouse, responsiveness to Avr genes and late blight resistance in detached leaf assays, the selection was narrowed down to eight independent events. These cisgenic events were selected because they showed broad spectrum late blight resistance due to the activity of both introduced R genes. The marker-free transformation was compared to kanamycin resistance assisted transformation in terms of T-DNA and vector backbone integration frequency. Also, differences in regeneration time and genotype dependency were evaluated. Conclusions We developed a marker-free transformation pipeline to select potato plants functionally expressing a stack of late blight R genes. Marker-free transformation is less genotype dependent and less prone to vector backbone integration as compared to marker-assisted transformation. Thereby, this study provides an important tool for the successful deployment of R genes in agriculture and contributes to the production of potentially durable late blight resistant potatoes.
    Prediction of heterosis using genome-wide SNP-marker data: application to egg production traits in white Leghorn crosses
    Amuzu-Aweh, E.N. ; Bijma, P. ; Kinghorn, B.P. ; verreijken, A. ; Arendonk, J.A.M. van; Bovenhuis, H. - \ 2013
    Heredity 111 (2013)6. - ISSN 0018-067X - p. 530 - 538.
    normal probability integrals - hybrid performance - genetic-distance - dna fingerprints - chickens - identification - transformation - information - populations - models
    Prediction of heterosis has a long history with mixed success, partly due to low numbers of genetic markers and/or small data sets. We investigated the prediction of heterosis for egg number, egg weight and survival days in domestic white Leghorns, using ~400¿000 individuals from 47 crosses and allele frequencies on ~53¿000 genome-wide single nucleotide polymorphisms (SNPs). When heterosis is due to dominance, and dominance effects are independent of allele frequencies, heterosis is proportional to the squared difference in allele frequency (SDAF) between parental pure lines (not necessarily homozygous). Under these assumptions, a linear model including regression on SDAF partitions crossbred phenotypes into pure-line values and heterosis, even without pure-line phenotypes. We therefore used models where phenotypes of crossbreds were regressed on the SDAF between parental lines. Accuracy of prediction was determined using leave-one-out cross-validation. SDAF predicted heterosis for egg number and weight with an accuracy of ~0.5, but did not predict heterosis for survival days. Heterosis predictions allowed preselection of pure lines before field-testing, saving ~50% of field-testing cost with only 4% loss in heterosis. Accuracies from cross-validation were lower than from the model-fit, suggesting that accuracies previously reported in literature are overestimated. Cross-validation also indicated that dominance cannot fully explain heterosis. Nevertheless, the dominance model had considerable accuracy, clearly greater than that of a general/specific combining ability model. This work also showed that heterosis can be modelled even when pure-line phenotypes are unavailable. We concluded that SDAF is a useful predictor of heterosis in commercial layer breeding.
    Functional analysis of the ComK protein of Bacillus coagulans
    Kovács, Á.T. ; Eckhardt, T.H. ; Hartskamp, M. van; Kranenburg, R. van; Kuipers, O.P. - \ 2013
    PLoS ONE 8 (2013)1. - ISSN 1932-6203
    competence transcription factor - gram-positive bacteria - subtilis k-state - gene-expression - natural competence - biofilm formation - genome sequence - lactic-acid - dna uptake - transformation
    The genes for DNA uptake and recombination in Bacilli are commonly regulated by the transcriptional factor ComK. We have identified a ComK homologue in Bacillus coagulans, an industrial relevant organism that is recalcitrant for transformation. Introduction of B. coagulans comK gene under its own promoter region into Bacillus subtilis comK strain results in low transcriptional induction of the late competence gene comGA, but lacking bistable expression. The promoter regions of B. coagulans comK and the comGA genes are recognized in B. subtilis and expression from these promoters is activated by B. subtilis ComK. Purified ComK protein of B. coagulans showed DNA-binding ability in gel retardation assays with B. subtilis- and B. coagulans-derived probes. These experiments suggest that the function of B. coagulans ComK is similar to that of ComK of B. subtilis. When its own comK is overexpressed in B. coagulans the comGA gene expression increases 40-fold, while the expression of another late competence gene, comC is not elevated and no reproducible DNA-uptake could be observed under these conditions. Our results demonstrate that B. coagulans ComK can recognize several B.subtilis comK-responsive elements, and vice versa, but indicate that the activation of the transcription of complete sets of genes coding for a putative DNA uptake apparatus in B. coagulans might differ from that of B. subtilis
    Evidence for regulation of columnar habit in apple encodes a putative 2og-fe(ii) oxygenase
    Wolters, P.J. ; Schouten, H.J. ; Riccardo, V. ; Si-Ammour, A. ; Baldi, P. - \ 2013
    New Phytologist 200 (2013)4. - ISSN 0028-646X - p. 993 - 999.
    malus-x-domestica - growth habit - arabidopsis - gene - transformation - activation - expression - abscission - genome - spur
    Understanding the genetic mechanisms controlling columnar-type growth in the apple mutant Wijcik will provide insights on how tree architecture and growth are regulated in fruit trees. In apple, columnar-type growth is controlled by a single major gene at the Columnar (Co) locus. By comparing the genomic sequence of the Co region of Wijcik with its wild-type McIntosh, a novel non-coding DNA element of 1956 bp specific to Pyreae was found to be inserted in an intergenic region of Wijcik. Expression analysis of selected genes located in the vicinity of the insertion revealed the upregulation of the MdCo31 gene encoding a putative 2OG-Fe(II) oxygenase in axillary buds of Wijcik. Constitutive expression of MdCo31 in Arabidopsis thaliana resulted in compact plants with shortened floral internodes, a phenotype reminiscent of the one observed in columnar apple trees. We conclude that MdCo31 is a strong candidate gene for the control of columnar growth in Wijcik.
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