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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Mass spectrometric characterisation of avenanthramides and enhancing their production by germination of oat (Avena sativa)
Bruijn, Wouter J.C. de; Dinteren, Sarah van; Gruppen, Harry ; Vincken, Jean Paul - \ 2019
Food Chemistry 277 (2019). - ISSN 0308-8146 - p. 682 - 690.
Avena sativa - Avenanthramides - Cereal grain - Germination - LC-MS - Phytoalexin - Plant defence - Poaceae

Avenanthramides are amides, with a phenylalkenoic acid (PA) and an anthranilic acid (AA) subunit, which are secondary metabolites of oat. Oat seeds were germinated, extracted, and the avenanthramides analysed by a combination of UHPLC with ion trap and high resolution ESI-MS. Typical fragmentation pathways with corresponding diagnostic fragments belonging to the PA and AA subunits were identified and summarised in a decision guideline. Based on these findings 28 unique avenanthramides were annotated in the oat seed(ling) extracts, including the new avenanthramide 6f (with a 4/5-methoxy AA subunit). Avenanthramide content increased by 25 times from seed to seedling. Avenanthramides 2p, 2c, and 2f, which are commonly described as the major avenanthramides, represented less than 20% of the total content in the seedlings. Future quantitative analyses should, therefore, include a wider range of avenanthramides to avoid underestimation of the total avenanthramide content.

PISTILLATA paralogs in Tarenaya hassleriana have diverged in interaction specificity
Bruijn, Suzanne de; Zhao, Tao ; Muiño, Jose M. ; Schranz, Eric M. ; Angenent, Gerco C. ; Kaufmann, Kerstin - \ 2018
BMC Plant Biology 18 (2018)1. - ISSN 1471-2229
Cleomaceae - Flower development - Gene duplications - MADS - Paralogs - PISTILLATA - Tarenaya

Background: Floral organs are specified by MADS-domain transcription factors that act in a combinatorial manner, as summarized in the (A)BCE model. However, this evolutionarily conserved model is in contrast to a remarkable amount of morphological diversity in flowers. One of the mechanisms suggested to contribute to this diversity is duplication of floral MADS-domain transcription factors. Although gene duplication is often followed by loss of one of the copies, sometimes both copies are retained. If both copies are retained they will initially be redundant, providing freedom for one of the paralogs to change function. Here, we examine the evolutionary fate and functional consequences of a transposition event at the base of the Brassicales that resulted in the duplication of the floral regulator PISTILLATA (PI), using Tarenaya hassleriana (Cleomaceae) as a model system. Results: The transposition of a genomic region containing a PI gene led to two paralogs which are located at different positions in the genome. The original PI copy is syntenic in position with most angiosperms, whereas the transposed copy is syntenic with the PI genes in Brassicaceae. The two PI paralogs of T. hassleriana have very similar expression patterns. However, they may have diverged in function, as only one of these PI proteins was able to act heterologously in the first whorl of A. thaliana flowers. We also observed differences in protein complex formation between the two paralogs, and the two paralogs exhibit subtle differences in DNA-binding specificity. Sequence analysis indicates that most of the protein sequence divergence between the two T. hassleriana paralogs emerged in a common ancestor of the Cleomaceae and the Brassicaceae. Conclusions: We found that the PI paralogs in T. hassleriana have similar expression patterns, but may have diverged at the level of protein function. Data suggest that most protein sequence divergence occurred rapidly, prior to the origin of the Brassicaceae and Cleomaceae. It is tempting to speculate that the interaction specificities of the Brassicaceae-specific PI proteins are different compared to the PI found in other angiosperms. This could lead to PI regulating partly different genes in the Brassicaceae, and ultimately might result in change floral in morphology.

QSAR of 1,4-benzoxazin-3-one antimicrobials and their drug design perspectives
Bruijn, Wouter J.C. de; Hageman, Jos A. ; Araya-Cloutier, Carla ; Gruppen, Harry ; Vincken, Jean Paul - \ 2018
Bioorganic and Medicinal Chemistry 26 (2018)23-24. - ISSN 0968-0896 - p. 6105 - 6114.
2H-1,4-benzoxazin-3(4H)-one - Antibacterial - Antifungal - Benzoxazinoid - Benzoxazinone - Drug design - QSAR - SAR

Synthetic derivatives of 1,4-benzoxazin-3-ones have been shown to possess promising antimicrobial activity, whereas their natural counterparts were found lacking in this respect. In this work, quantitative structure-activity relationships (QSAR) of natural and synthetic 1,4-benzoxazin-3-ones as antimicrobials were established. Data published in literature were curated into an extensive dataset of 111 compounds. Descriptor selection was performed by a genetic algorithm. QSAR models revealed differences in requirements for activity against fungi, gram-positive and gram-negative bacteria. Shape, VolSurf, and H-bonding property descriptors were frequently picked in all models. The models obtained for gram-positive and gram-negative bacteria showed good predictive power (Q2 Ext 0.88 and 0.85, respectively). Based on the models generated, an additional set of 1,4-benzoxazin-3-ones, for which no antimicrobial activity had been determined in literature, were evaluated in silico. Additionally, newly designed lead compounds with a 1,4-benzoxazin-3-one scaffold were generated in silico by varying the positions and combinations of substituents. Two of these were predicted to be up to 5 times more active than any of the compounds in the current dataset. The 1,4-benzoxazin-3-one scaffold was concluded to possess potential for the design of new antimicrobial compounds with potent antibacterial activity, a multitarget mode of action, and possibly reduced susceptibility to gram negatives’ efflux pumps.

INNOVA Ezine 2 – Valencia Region, Droughts and Agricultural Interests in a Metropolitan Area in Spain
Timmermans, W. ; Jong, F. de; Martín, Adrià Rubio ; Bruijn, Daphne de; Harsema, H. - \ 2018
Wageningen : Blauwdruk
In the metropolitan area of Valencia the water use is intense and the region suffers from frequent droughts due to climate conditions. Valencia is surrounded by an agricultural landscape with deep cultural significance and with a multi-sectoral structure in which irrigated agriculture plays an important role in the consumption of water. The Albufera Natural Park, less than 10 km south of Valencia, is a freshwater lagoon and its surroundings rice plots. Given the predicted adverse effects of climate change, it is important for the City of Valencia to develop adaptation strategies for the future climate. The mandate for the INNOVA project is to develop a climate service that satisfies the water use needs to support the distribution of potable water to its users.

The second INNOVA e-zine shows the climate and adaptation challenges the Valencia region is facing. The first issue showed the Mirror Waal project in the Nijmegen area (NL).

From awareness of upcoming flooding risks, via complex planning and design efforts into the final result. Whereas Nijmegen is far in the Adaptation Cycle; the Valencia metropolitan area is between the steps of identifying adaptation options (Step 3) and assessing these options (Step 4).
INNOVA Ezine 1 – Nijmegen, the EU Green Capital 2018 and Room for the River Waal
Timmermans, W. ; Jong, F. de; Ginkel, M. van; Martinez, G. ; Bruijn, D. de; Harsema, H. - \ 2018
Wageningen : Blauwdruk
The Dutch city of Nijmegen is becoming well-known because of its planning approach that combines large scale climate adaptation measures with a strong emphasis on spatial quality. Nijmegen is situated along the Waal river, one of Europe’s largest transport and ecological corridors. More than 250M euro has been spent on a new bypass of the Waal, called the Mirror Waal, one of the major urban examples of the Dutch Room for the River project. This e-zine shows the Mirror Waal project. From awareness of upcoming flooding risks, via complex planning and design efforts into the final result, including innovative ecological engineering, new sport activities and spontaneous festivals. The e-zine is presented by the INNOVA project. It is the first e-zine out of ten. INNOVA is a research project aiming to facilitate the use of climate data and projections, scientifically known as climate services, in adaptation efforts by urban governments. The project focuses on three European cities, and a small island state. These are: Kiel Bay in Germany, Nijmegen in The Netherlands, Valencia in Spain, and finally, the French West-Indies Islands of Guadeloupe & Martinique.
Costs of persisting unreliable memory : Reduced foraging efficiency for free-flying parasitic wasps in a wind tunnel
Bruijn, Jessica A.C. de; Vet, Louise E.M. ; Smid, Hans M. - \ 2018
Frontiers in Ecology and Evolution 6 (2018)OCT. - ISSN 2296-701X
Cotesia glomerata - Foraging efficiency - Learning - Memory - Non-host - Oviposition - Prediction error - Unreliable information

Parasitic wasps are known to improve their foraging efficiency after learning of herbivore-induced plant volatiles (HIPVs) upon encountering their hosts on these plants. However, due to spatial and temporal variation of herbivore communities, learned HIPV cues can become unreliable, no longer correctly predicting host presence. Little is known about the potential fitness costs when memories holding such unreliable information persist. Here we studied how persistent memory, containing unreliable information, affects the foraging efficiency for hosts in Cotesia glomerata. Wasps were conditioned to associate one of two types of HIPVs with either P. brassicae frass, 1 single oviposition in P. brassicae, 3 ovipositions in P. brassicae spaced in time or they were kept unconditioned. The following day, wasps were allowed to forage in a wind tunnel, in an environment that either conflicted or was congruent with their learned plant experience. The foraging environment consisted of host (P. brassicae) and non-host (Mamestra brassicae) infested plants. The conflicting environment had non-hosts on the conditioned plant species and hosts on the non-conditioned plant species, whereas the congruent environment had hosts on the conditioned plant species and non-hosts on the unconditioned plant species. Wasps had to navigate through five non-host infested plants to reach the host-infested plant. Since C. glomerata wasps do not distinguish between HIPVs induced by host and non-host caterpillars, the conflicting foraging situation caused a prediction error, by guiding wasps to non-host infested plants. Especially wasps given 3 spaced oviposition experiences, tested in a conflicting situation, spent significantly more time on non-host infested plants and showed a high tendency to oviposit in the non-hosts. As a result, they took significantly more time to find their hosts. Conditioned wasps, which were tested in a congruent situation, were more responsive than unconditioned wasps, but there was no difference in foraging efficiency between these two groups in the wasps that showed a response. We conclude that persistent memories, such as formed after 3 experiences spaced in time, can lead to maladaptive foraging behavior if the contained information becomes unreliable.

Structure and biosynthesis of benzoxazinoids : Plant defence metabolites with potential as antimicrobial scaffolds
Bruijn, Wouter J.C. de; Gruppen, Harry ; Vincken, Jean Paul - \ 2018
Phytochemistry 155 (2018). - ISSN 0031-9422 - p. 233 - 243.
Antibacterial - Antifungal - Benzoxazinone - Benzoxazolinone - Cereal - Classification - Modification - Plant defence - Poaceae - Synthetic

Benzoxazinoids, comprising the classes of benzoxazinones and benzoxazolinones, are a set of specialised metabolites produced by the plant family Poaceae (formerly Gramineae), and some dicots. The family Poaceae in particular contains several important crops like maize and wheat. Benzoxazinoids play a role in allelopathy and as defence compounds against (micro)biological threats. The effectivity of benzoxazinones in these functionalities is largely imposed by the subclasses (determined by N substituent). In this review, we provide an overview of all currently known natural benzoxazinoids and a summary of the current state of knowledge of their biosynthesis. We also evaluated their antimicrobial activity based on minimum inhibitory concentration (MIC) values reported in literature. Monomeric natural benzoxazinoids seem to lack potency as antimicrobial agents. The 1,4-benzoxazin-3-one backbone, however, has been shown to be a potential scaffold for designing new antimicrobial compounds. This has been demonstrated by a number of studies that report potent activity of synthetic derivatives of 1,4-benzoxazin-3-one, which possess MIC values down to 6.25 μg mL−1 against pathogenic fungi (e.g. C. albicans) and 16 μg mL−1 against bacteria (e.g. S. aureus and E. coli). Observations on the structural requirements for allelopathy, insecticidal, and antimicrobial activity suggest that they are not necessarily conferred by similar mechanisms.

Stal van de Toekomst proeftuin voor duurzame varkenshouderij
Verdoes, Nico - \ 2018
Automated high-throughput individual tracking system for insect behavior : Applications on memory retention in parasitic wasps
Bruijn, Jessica A.C. de; Vet, Louise E.M. ; Jongsma, Maarten A. ; Smid, Hans M. - \ 2018
Journal of Neuroscience Methods 309 (2018). - ISSN 0165-0270 - p. 208 - 217.
Cotesia glomerata - Learning - Memory retention - Nasonia vitripennis - Parasitic wasps - Tracking system

Background: Insects are important models to study learning and memory formation in both an ecological and neuroscience context due to their small size, behavioral flexibility and ecological diversity. Measuring memory retention is often done through simple time-consuming set-ups, producing only a single parameter for conditioned behavior. We wished to obtain higher sample sizes with fewer individuals to measure olfactory memory retention more efficiently. New method: The high-throughput individual T-maze uses commercially available tracking software, Ethovision XT®, in combination with a Perspex stack of plates as small as 18 × 18 cm, which accommodates 36 olfactory T-mazes, where each individual wasp could choose between two artificial odors. Various behavioral parameters, relevant to memory retention, were acquired in this set-up; first choice, residence time, giving up time and zone entries. From these parameters a performance index was calculated as a measure of memory retention. Groups of 36 wasps were simultaneously tested within minutes, resulting in efficient acquisition of sufficiently high sample sizes. Results: This system was tested with two very different parasitic wasp species, the larval parasitoid Cotesia glomerata and the pupal parasitoid Nasonia vitripennis, and has proven to be highly suitable for testing memory retention in both these species. Comparison with existing methods: Unlike other bioassays, this system allows for both high-throughput and recording of detailed individual behavior. Conclusions: The high-throughput individual T-maze provides us with a standardized high-throughput, labor-efficient and cost-effective method to test various kinds of behavior, offering excellent opportunities for comparative studies of various aspects of insect behavior.

Antibacterial prenylated stilbenoids from peanut (Arachis hypogaea)
Bruijn, Wouter J.C. de; Araya-Cloutier, Carla ; Bijlsma, Judith ; Swart, Anne de; Sanders, Mark G. ; Waard, Pieter de; Gruppen, Harry ; Vincken, Jean Paul - \ 2018
Phytochemistry letters 28 (2018). - ISSN 1874-3900 - p. 13 - 18.
Antimicrobial - Leguminosae - Natural product - Prenylation - Secondary metabolite - Stilbene

Stilbenoids are a class of secondary metabolites with a stilbene backbone that can be produced by peanut (Arachis hypogaea) as defence metabolites. Six monomeric prenylated stilbenoids, including the compound arachidin-6 (4), were isolated from extracts of fungus-elicited peanuts (Arachis hypogaea) using preparative liquid chromatography. Their structures were confirmed by MSn, HRMS and NMR spectroscopy and their antibacterial activity was evaluated against methicillin-resistant Staphylococcus aureus (MRSA). Similarly to other phenolic compounds, prenylated derivatives of stilbenoids were more active than their non-prenylated precursors piceatannol, resveratrol, and pinosylvin. Chiricanine A (6), a chain-prenylated pinosylvin derivative, was the most potent compound tested, with a minimum inhibitory concentration (MIC) of 12.5 μg mL−1. Arachidin-6 (4), a ring-prenylated piceatannol derivative, had moderate potency (MIC 50–75 μg mL−1). In conclusion, prenylated stilbenoids represent a group of potential natural antibacterials which show promising activity against MRSA.

Altered neural responsivity to food cues in relation to food preferences, but not appetite-related hormone concentrations after RYGB-surgery
Zoon, Harriët F.A. ; Bruijn, Suzanne E.M. de; Smeets, Paul A.M. ; Graaf, Cees de; Janssen, Ignace M.C. ; Schijns, Wendy ; Aarts, Edo O. ; Jager, Gerry ; Boesveldt, Sanne - \ 2018
Behavioural Brain Research 353 (2018). - ISSN 0166-4328 - p. 194 - 202.
Endocannabinoid - Energy-density - fMRI - Food cues - Ghrelin - Obesity - Olfactory - Reward - Roux-en-Y gastric bypass surgery - Visual

Background: After Roux-en-Y gastric bypass (RYGB) surgery, patients report a shift in food preferences away from high-energy foods. Objective: We aimed to elucidate the potential mechanisms underlying this shift in food preferences by assessing changes in neural responses to food pictures and odors before and after RYGB. Additionally, we investigated whether altered neural responsivity was associated with changes in plasma endocannabinoid and ghrelin concentrations. Design: 19 RYGB patients (4 men; age 41 ± 10 years; BMI 41 ± 1 kg/m2 before; BMI 36 ± 1 kg/m2 after) participated in this study. Before and two months after RYGB surgery, they rated their food preferences using the Macronutrient and Taste Preference Ranking Task and BOLD fMRI responses towards pictures and odors of high-, and low-energy foods and non-food items were measured. Blood samples were taken to determine plasma endocannabinoid and ghrelin concentrations pre- and post-surgery. Results: Patients demonstrated a shift in food preferences away from high-fat/sweet and towards low-energy/savory food products, which correlated with decreased superior parietal lobule responsivity to high-energy food odor and a reduced difference in precuneus responsivity to high-energy versus low-energy food pictures. In the anteroventral prefrontal cortex (superior frontal gyrus) the difference in deactivation towards high-energy versus non-food odors reduced. The precuneus was less deactivated in response to all cues. Plasma concentrations of anandamide were higher after surgery, while plasma concentrations of other endocannabinoids and ghrelin did not change. Alterations in appetite-related hormone concentrations did not correlate with changes in neural responsivity. Conclusions: RYGB leads to changed responsivity of the frontoparietal control network that orchestrates top-down control to high-energy food compared to low-energy food and non-food cues, rather than in reward related brain regions, in a satiated state. Together with correlations with the shift in food preference from high- to low-energy foods this indicates a possible role in new food preference formation.

Altered neural inhibition responses to food cues after Roux-en-Y Gastric Bypass
Zoon, H.F.A. ; Bruijn, S.E.M. de; Jager, G. ; Smeets, P.A.M. ; Graaf, C. de; Janssen, I.M.C. ; Schijns, W. ; Deden, L. ; Boesveldt, S. - \ 2018
Biological Psychology 137 (2018). - ISSN 0301-0511 - p. 34 - 41.
Bariatric surgery - fMRI - Food preferences - go/no-go - Impulsivity - Inhibitory control - Weight-Loss

Background: Roux-en-Y gastric bypass (RYGB) surgery is a highly effective weight-loss intervention that often reduces preference and intake of high-energy foods. Research into the neural mechanisms behind this shift has mainly focused on reward processing of food cues. However, the ability to successfully control food intake and thereby weight-loss also depends on inhibitory control capacity. We investigated whether RYGB leads to alterations in neural inhibitory control in response to food cues. Methods: A food-specific go/no-go task with pictures of high-energy (desserts) and low-energy foods (vegetables), was used to assess neural inhibition responses before and after RYGB with functional magnetic resonance imaging. Data from 18 morbidly obese patients (15 females; age 41 ± 11 years; BMI 42 ± 4 kg/m2 before; BMI 36 ± 4 kg/m2 after) were analysed. Pre- and post-RYGB BOLD fMRI responses were compared for response inhibition towards high- and low-energy foods. Participants were tested in a satiated state. Results: Response inhibition to high-energy foods was associated with increased activation of the right lateral prefrontal cortex (PFC), right medial PFC, dorsolateral PFC, right middle cingulate cortex and the right inferior frontal operculum (involved in inhibitory control), after compared to before surgery. Response inhibition to low-energy foods elicited diminished post- compared to pre-surgery responses in the left superior temporal pole, right parahippocampal gyrus and right hypothalamus (involved in metabolic control). Conclusion: Neural changes indicate improved response inhibition towards high-energy food cues, altered influence of metabolic control during response inhibition towards low-energy food cues and a more positive attitude to both high-energy and low-energy food after RYGB. Alterations in neural circuits involved in inhibitory control, satiety signalling and reward processing may contribute to effective weight-loss after RYGB.

Involvement of Burkholderiaceae and sulfurous volatiles in disease-suppressive soils
Carrión, Víctor J. ; Cordovez, Viviane ; Tyc, Olaf ; Etalo, Desalegn W. ; Bruijn, Irene de; Jager, Victor C.L. de; Medema, Marnix H. ; Eberl, Leo ; Raaijmakers, Jos M. - \ 2018
ISME Journal 12 (2018). - ISSN 1751-7362 - p. 2307 - 2321.

Disease-suppressive soils are ecosystems in which plants suffer less from root infections due to the activities of specific microbial consortia. The characteristics of soils suppressive to specific fungal root pathogens are comparable to those of adaptive immunity in animals, as reported by Raaijmakers and Mazzola (Science 352:1392–3, 2016), but the mechanisms and microbial species involved in the soil suppressiveness are largely unknown. Previous taxonomic and metatranscriptome analyses of a soil suppressive to the fungal root pathogen Rhizoctonia solani revealed that members of the Burkholderiaceae family were more abundant and more active in suppressive than in non-suppressive soils. Here, isolation, phylogeny, and soil bioassays revealed a significant disease-suppressive activity for representative isolates of Burkholderia pyrrocinia, Paraburkholderia caledonica, P. graminis, P. hospita, and P. terricola. In vitro antifungal activity was only observed for P. graminis. Comparative genomics and metabolite profiling further showed that the antifungal activity of P. graminis PHS1 was associated with the production of sulfurous volatile compounds encoded by genes not found in the other four genera. Site-directed mutagenesis of two of these genes, encoding a dimethyl sulfoxide reductase and a cysteine desulfurase, resulted in a loss of antifungal activity both in vitro and in situ. These results indicate that specific members of the Burkholderiaceae family contribute to soil suppressiveness via the production of sulfurous volatile compounds.

Comparative analysis of binding patterns of MADS-domain proteins in Arabidopsis thaliana
Aerts, Niels ; Bruijn, Suzanne de; Mourik, Hilda van; Angenent, Gerco C. ; Dijk, Aalt D.J. van - \ 2018
BMC Plant Biology 18 (2018)1. - ISSN 1471-2229
CArG-box - ChIP-seq - MADS-domain proteins - Sequence conservation - Transcription factor binding specificity

Background: Correct flower formation requires highly specific temporal and spatial regulation of gene expression. In Arabidopsis thaliana the majority of the master regulators that determine flower organ identity belong to the MADS-domain transcription factor family. The canonical DNA binding motif for this transcription factor family is the CArG-box, which has the consensus CC(A/T)6GG. However, so far, a comprehensive analysis of MADS-domain binding patterns has not yet been performed. Results: Eight publicly available ChIP-seq datasets of MADS-domain proteins that regulate the floral transition and flower formation were analyzed. Surprisingly, the preferred DNA binding motif of each protein was a CArG-box with an NAA extension. Furthermore, motifs of other transcription factors were found in the vicinity of binding sites of MADS-domain transcription factors, suggesting that interaction of MADS-domain proteins with other transcription factors is important for target gene regulation. Finally, conservation of CArG-boxes between Arabidopsis ecotypes was assessed to obtain information about their evolutionary importance. CArG-boxes that fully matched the consensus were more conserved than other CArG-boxes, suggesting that the perfect CArG-box is evolutionary more important than other CArG-box variants. Conclusion: Our analysis provides detailed insight into MADS-domain protein binding patterns. The results underline the importance of an extended version of the CArG-box and provide a first view on evolutionary conservation of MADS-domain protein binding sites in Arabidopsis ecotypes.

Uitroeier gezocht voor hardnekkige Japanse plant
Dijk, Chris van - \ 2018
Exploring fish microbial communities to mitigate emerging diseases in aquaculture
Bruijn, Irene de; Liu, Yiying ; Wiegertjes, Geert F. ; Raaijmakers, Jos M. - \ 2018
FEMS Microbiology Ecology 94 (2018)1. - ISSN 0168-6496
Aquaculture - Beneficial microbes - Emerging diseases - Fish - Microbiomes
Aquaculture is the fastest growing animal food sector worldwide and expected to further increase to feed the growing human population. However, existing and (re-)emerging diseases are hampering fish and shellfish cultivation and yield. For many diseases, vaccination protocols are not in place and the excessive use of antibiotics and other chemicals is of substantial concern. A more sustainable disease control strategy to protect fish and shellfish from (re-)emerging diseases could be achieved by introduction or augmentation of beneficial microbes. To establish and maintain a 'healthy' fish microbiome, a fundamental understanding of the diversity and temporal-spatial dynamics of fish-associated microbial communities and their impact on growth and health of their aquatic hosts is required. This review describes insights in the diversity and functions of the fish bacterial communities elucidated with next-generation sequencing and discusses the potential of the microbes to mitigate (re-)emerging diseases in aquaculture.
The shadow price of fossil groundwater
Bierkens, M.F.P. ; Reinhard, A.J. ; Bruijn, J.A. de; Wada, Yoshihide - \ 2017
Veren, wat vertellen ze ons?
Janssen, T. ; Rooij, J.M.S.F. de; Niekerk, T.G.C.M. van; Bruijn, N. de - \ 2017
De Pluimveehouderij (2017). - ISSN 0166-8250 - p. 22 - 23.
Current insights into the role of rhizosphere bacteria in disease suppressive soils
Gomez Exposito, R. ; Bruijn, I. de; Postma, J. ; Raaijmakers, J.M. - \ 2017
Frontiers in Microbiology 8 (2017). - ISSN 1664-302X
Disease suppressive soils offer effective protection to plants against infection by soilborne pathogens, including fungi, oomycetes, bacteria, and nematodes. The specific disease suppression that operates in these soils is, in most cases, microbial in origin. Therefore, suppressive soils are considered as a rich resource for the discovery of beneficial microorganisms with novel antimicrobial and other plant protective traits. To date, several microbial genera have been proposed as key players in disease suppressiveness of soils, but the complexity of the microbial interactions as well as the underlying mechanisms and microbial traits remain elusive for most disease suppressive soils. Recent developments in next generation sequencing and other ‘omics’ technologies have provided new insights into the microbial ecology of disease suppressive soils and the identification of microbial consortia and traits involved in disease suppressiveness. Here, we review the results of recent ‘omics’-based studies
on the microbial basis of disease suppressive soils, with specific emphasis on the role of rhizosphere bacteria in this intriguing microbiological phenomenon.
MADS evolution : insights into evolutionary changes in transcription factors and their binding sites
Bruijn, Suze-Annigje de - \ 2017
University. Promotor(en): Gerco Angenent. - Wageningen : Wageningen University - ISBN 9789463436700 - 195
plants - evolution - mads-box proteins - transcription factors - flowers - molecular biology - planten - evolutie - mads-box eiwitten - transcriptiefactoren - bloemen - moleculaire biologie

Although most flowers follow a conserved 'bauplan' consisting of sepals, petals, stamens and carpels, there is a remarkable amount of morphological diversity. Interestingly, all flowers are specified by the conserved (A)BCE-model. Most of the transcription factors in this model belong to the MADS-domain family. We examined how these transcription factors and their binding sites in the genome evolved, as a first step to elucidate how diversity in flower morphology has been created.

We analyzed the evolution of transcription factor binding sites by comparing binding sites of the major floral regulator SEPALLATA3 between two closely related Arabidopsis species, as well as between A. thaliana ecotypes. We found substantial overlap in transcription factor binding profiles between ecotypes, but limited overlap between the related species.

We also assessed how transcription factors themselves can change in their properties by analyzing the divergence between paralogs. We examined how the PISTILLATA paralogs in Tarenaya hassleriana diverged, as this species occupies an interesting position in the eudicot phylogeny. We also studied whether divergence of the APETALA3 paralogs in Aquilegia could explain the specification of an additional floral organ in this genus. In both cases, we conclude that the paralogs diverged from each other in their biochemical properties.

In the future, it would be interesting to assess how these changes in transcription factors and their binding sites affect floral regulatory networks and ultimately floral shape.

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