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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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.

Food reward from a behavioural and (neuro)physiological perspective
Bruijn, Suzanne E.M. - \ 2017
University. Promotor(en): Kees de Graaf; Renger Witkamp, co-promotor(en): Gerry Jager. - Wageningen : Wageningen University - ISBN 9789463436748 - 154
food - physiological functions - feeding behaviour - food preferences - perception - hormones - responses - neurohormonal control - stomach bypass - gastric bypass - satiety - voedsel - fysiologische functies - voedingsgedrag - voedselvoorkeuren - perceptie - hormonen - reacties - neurohormonale controle - maag bypass - buik bypass - verzadigdheid

Food reward is an important driver of food intake and triggers consumption of foods for pleasure, so-called hedonic eating, even in the absence of any energy deficits. Hedonic eating can trigger overeating and may therefore lead to obesity. Given the rise in obesity rates and the health risks associated with being obese, hedonic eating and food reward are important phenomena to study. This thesis aimed to add on to the existing knowledge on food reward. The phenomenon was approached from a behavioural, sensory and (neuro)physiological perspective in healthy, lean and in obese gastric bypass populations.

For the behavioural perspective, the main outcome measure used in this thesis was food preferences. To be able to study food preferences for four macronutrient and two taste categories, a new food preference task was developed. In chapter 2, the development and validation of the Macronutrient and Taste Preference Ranking Task (MTPRT) were described. The MTPRT uses a ranking method to determine preferences for four macronutrient (high-carbohydrate, high-fat, high-protein, low-energy) and two taste (sweet and savoury) categories.

For the sensory and physiological perspective, focus was put on the endocannabinoid system (ECS): a neuromodulatory system that plays a role in food reward. To gain more insight into this role, the effect of ECS modulation with pharmacological challenges on sensory perception of sweet taste and on food preferences were studied, as well as endocannabinoid responses to food intake. In chapter 3 it was shown that inhaling Cannabis with low doses of Δ9-tetrahydrocannabinol (THC) and cannabidiol (CBD) does not alter sweet taste intensity perception and liking in humans, nor does it affect food preferences. Vice versa, in chapter 4 it was found that liking of a food taste does not affect endocannabinoid responses to food intake, after controlling for expectations. When palatability of the food is unknown until the first bite, response of endocannabinoids, ghrelin and pancreatic polypeptide did not differ between a palatable and a neutral food across anticipatory, consummatory and post-ingestive phases of food intake. Endocannabinoid and ghrelin plasma concentrations decreased after food intake, which suggests an orexigenic function for endocannabinoids.

In chapters 5, 6 and 7, studies with patients who underwent Roux-en-Y gastric bypass surgery were described. These studies were intended to gain more insight into alterations in food reward in relation to (morbid) obesity and in response to surgical treatment by RYGB surgery.

First, in chapter 5 food preferences were assessed before, and at two months and one year after RYGB. It was shown that patients have decreased preference for high-carbohydrate and high-fat foods, and increased preference for low-energy foods after compared with before surgery. In addition, liking ratings for the high-carbohydrate and high-fat foods were decreased after RYGB surgery, whereas liking of low-energy products changed minimally. Potential mechanisms behind these alterations in food preferences include changes in neural processing of food cues and changes in appetite-related gut hormones.

In chapter 6, it was shown that alterations in food preferences after RYGB surgery are indeed related to changes in neural activation in response to food cues. With regards to the appetite-related hormones it was shown that plasma concentrations of the endocannabinoid anandamide were increased after compared with before surgery. Plasma concentrations of other endocannabinoids and ghrelin did not change. Moreover, changes in endocannabinoid or ghrelin concentrations did not correlate with changes in food preferences or neural response to food cues. Together, these results suggest that changes in neural processing of food cues contribute to changes in food preferences towards low-energy foods, and provide a first indication that the endocannabinoid system does not seem to play a role in this process.

To gain more insight into behavioural responses to food cues, a response-inhibition paradigm was used in chapter 7, in which response-inhibition to high-energy and low-energy food cues was assessed during brain imaging. The behavioural data did not show differences in performance when comparing before and two months after RYGB surgery. The brain imaging data showed that activation in reward-related brain areas was decreased in response to both high- and low-energy food pictures after RYGB surgery. Also, prefrontal brain areas were more activated in response to the high-energy pictures, which suggests improved response inhibition.

In conclusion, the findings in this thesis show that modulating the ECS with low doses of THC and CBD does not influence sweet taste perception and liking and food preferences, and vice versa, food taste liking in the absence of expectations does not affect endocannabinoid responses to food intake. With regards to RYGB surgery it was uncovered that changes in food preferences after RYGB surgery are related to altered brain reward processing, but no relation with changes in endocannabinoid tone was found. The success of RYGB surgery and the changes in food choice might in part be caused by an improved inhibitory response to high-energy foods.

Phylogenomic Synteny Network Analysis of MADS-Box Transcription Factor Genes Reveals Lineage-Specific Transpositions, Ancient Tandem Duplications, and Deep Positional Conservation
Zhao, T. ; Holmer, R. ; Bruijn, S.A. de; Angenent, G.C. ; Burg, H.A. van den; Schranz, M.E. - \ 2017
The Plant Cell (2017). - ISSN 1040-4651
Conserved genomic context provides critical information for comparative evolutionary analysis. 29 With the increase in numbers of sequenced plant genomes, synteny analysis can provide new 30 insight into gene family evolution. Here, we exploit a network analysis approach to organize and
31 interpret massive pairwise syntenic relationships. Specifically, we analyzed synteny networks of 32 the MADS-box transcription factor gene family using fifty-one completed plant genomes. In 33 combination with phylogenetic profiling, several novel evolutionary patterns were inferred and 34 visualized from synteny network clusters. We found lineage-specific clusters that derive from 35 transposition events for the regulators of floral development (APETALA3 and PI) and flowering36 time (FLC) in the Brassicales and for the regulators of root-development (AGL17) in Poales. We 37 also identified two large gene clusters that jointly encompass many key phenotypic regulatory 38 Type II MADS-box gene clades (SEP1, SQUA, TM8, SEP3, FLC, AGL6 and TM3). Gene
39 clustering and gene trees support the idea that these genes are derived from an ancient tandem 40 gene duplication that likely predates the radiation of the seed plants and then expanded by 41 subsequent polyploidy events. We also identified angiosperm-wide conservation of synteny of 42 several other less studied clades. Combined, these findings provide new hypotheses for the
43 genomic origins, biological conservation and divergence of MADS-box gene family members.
Microbiome dynamics of disease suppresive soils
Gómez Expósito, Ruth - \ 2017
University. Promotor(en): Francine Govers; Jos Raaijmakers, co-promotor(en): Joeke Postma; Irene de Bruijn. - Wageningen : Wageningen University - ISBN 9789463431774 - 267
suppressive soils - soil suppressiveness - plant diseases - thanatephorus cucumeris - microbial ecology - soil microbiology - rhizosphere bacteria - soil bacteria - community ecology - soil fungi - transcriptomics - taxonomy - ziektewerende gronden - bodemweerbaarheid - plantenziekten - microbiële ecologie - bodemmicrobiologie - rizosfeerbacteriën - bodembacteriën - gemeenschapsecologie - bodemschimmels - transcriptomica - taxonomie

Disease suppressive soils are soils in which plants do not get diseased from plant pathogens due to the presence (and activities) of the microbes present in the soil. Understanding which microbes contribute to confer suppression and through which mechanisms they can protect plants is crucial for a sustainable control of plant diseases. In the research conducted in this thesis, I first examined the role of Lysobacter species, previously associated with disease suppressive soils, in suppressing damping-off disease caused by the soil-borne fungal pathogen Rhizoctonia solani on sugar beet. The majority of the Lysobacter strains tested revealed a broad metabolic potential in producing a variety of enzymes and secondary metabolites able to suppress R. solani in vitro. However, any of these strains could consistently suppress damping-off disease when applied in soil bioassays. Their ability to promote plant growth was also tested for sugar beet, cauliflower, onion or Arabidopsis thaliana. Results indicated that any of the Lysobacter strains could consistently promote plant growth, neither via direct contact nor via volatile production. Second, I investigated whether the antagonistic activity of Lysobacter species could be triggered when applied as bacterial consortia, together with Pseudomonas and Streptomyces species. Although several bacterial combinations showed an increased antagonistic effect towards R. solani in vitro, no consistent effects were observed when these bacterial consortia were applied in vivo. Third, I investigated the dynamical changes in the bacterial community composition and functions occurring during the process of disease suppressiveness induction by performing whole community analyses using next-generation sequencing techniques. Results indicated that suppressiveness induction was most associated with changes in certain bacterial traits rather than changes in the bacteria community composition itself. Among the functions found as more active in suppressive soils were several ‘classic’ mechanisms of disease suppression, including competition for nutrients, iron and space and production of extracellular enzymes, indol-acetic-acid and hydrogen cyanide. Among the enzymes found in higher abundance in suppressive soil were these ones involved in the degradation of oxalic acid, a pathogenicity factor produced by pathogenic fungi to help infecting the host plant. Hence, I finally studied the role of bacteria able to produce enzymes able to degrade oxalic acid in suppressing R. solani disease. Enrichment of native oxalotrophic bacteria existing in soil, their isolation and further application into soil revealed that they could effectively suppress Rhizoctonia disease. Characterization of these oxalotrophic bacteria revealed that members within the Caulobacter and Nocardioides species could suppress R. solani disease by their own. Furthermore, the research done in this thesis highlights the importance of combining different techniques to unravel the mechanisms underlying disease suppression and the importance of studying function-over-phylogeny. Additionally, it also highlights the importance of organic amendments (such as oxalic acid) directly into soils in order to “engineer” the bacterial functions towards the control of diseases caused by R. solani.

Microbioom-analyses zorgen voor nieuwe inzichten in de microbiële populaties van Rhizoctonia-ziektewerende gronden
Gomez Exposito, R. ; Postma, J. ; Bruijn, I. de; Raaijmakers, J.M. - \ 2017
Gewasbescherming 48 (2017)1. - ISSN 0166-6495 - p. 24 - 24.
Assessment in Dutch vocational education: Overview and tensions of the past 15 years
Baartman, L. ; Gulikers, J.T.M. - \ 2017
In: Enhancing Teaching and Learning in the Dutch Vocational Education System / de Bruijn, Elly, Billett, Stephen, Onstenk, Jeroen, Dordrecht : Springer International Publishing - ISBN 9783319507323 - p. 245 - 266.
This chapter describes the developments in assessment practices in Dutch Vocational Education and Training (VET) in the past 15 years. Two developments have been particularly influential: (i) continuous changes in the national qualification structure describing the end goals of VET trajectories, and (ii) changes in the system of quality assurance of VET assessments. The goal of this chapter is to describe how VET institutions (re)developed their assessment practices to address these changes, through a combination of addressing changing policy and scientific research. Five tensions were identified that characterise the struggle around VET assessments: (1) new goals require new assessment methods, (2) assessment as a one-shot measurement versus a coherent programme appraisal, (3) the increased involvement of the labour market in VET, (4) securing a balance between governmental control and VET institutions’ responsibility in developing and quality assuring assessments, and (5) realising the balance between the formative and summative functions of assessment. The chapter concludes with the presentation of the Process Architecture Assessment, which is advanced as representing the state-of-the art in VET assessments. In the Process Architecture, the entire assessment process is described including the responsibilities of the different stakeholders.
Monitoring training response in young Friesian dressage horses using two different standardised exercise tests (SETs)
Bruijn, Cornelis Marinus de; Houterman, Willem ; Ploeg, Margreet ; Ducro, Bart ; Boshuizen, Berit ; Goethals, Klaartje ; Verdegaal, Elisabeth Lidwien ; Delesalle, Catherine - \ 2017
BMC Veterinary Research 13 (2017). - ISSN 1746-6148
Friesian - Heart rate - Lactic acid - Longitudinal - Standardized exercise test - Trot

Background: Most Friesian horses reach their anaerobic threshold during a standardized exercise test (SET) which requires lower intensity exercise than daily routine training. Aim: to study strengths and weaknesses of an alternative SET-protocol. Two different SETs (SETA and SETB) were applied during a 2 month training period of 9 young Friesian dressage horses. SETB alternated short episodes of canter with trot and walk, lacking long episodes of cantering, as applied in SETA. Following parameters were monitored: blood lactic acid (BLA) after cantering, average heart rate (HR) in trot and maximum HR in canter. HR and BLA of SETA and SETB were analyzed using a paired two-sided T-test and Spearman Correlation-coefficient (p* <0.05). Results: BLA after cantering was significantly higher in SETA compared to SETB and maximum HR in canter was significantly higher in SETA compared to SETB. The majority of horses showed a significant training response based upon longitudinal follow-up of BLA. Horses with the lowest fitness at start, displayed the largest training response. BLA was significantly lower in week 8 compared to week 0, in both SETA and SETB. A significantly decreased BLA level after cantering was noticeable in week 6 in SETA, whereas in SETB only as of week 8. In SETA a very strong correlation for BLA and average HR at trot was found throughout the entire training period, not for canter. Conclusions: Young Friesian horses do reach their anaerobic threshold during a SET which requires lower intensity than daily routine training. Therefore close monitoring throughout training is warranted. Longitudinal follow up of BLA and not of HR is suitable to assess training response. In the current study, horses that started with the lowest fitness level, showed the largest training response. During training monitoring HR in trot rather than in canter is advised. SETB is best suited as a template for daily training in the aerobic window.

The reliability and validity of the Macronutrient and Taste Preference Ranking Task : A new method to measure food preferences
Bruijn, Suzanne E.M. de; Vries, Yfke C. de; Graaf, Kees de; Boesveldt, Sanne ; Jager, Gerry - \ 2017
Food Quality and Preference 57 (2017). - ISSN 0950-3293 - p. 32 - 40.
Food preferences - Macronutrients - Savory - Sensory-specific satiety - Sweet

Food preferences are for a large part determined by the macronutrient content and taste of foods, but may change depending on internal and external factors. Here, we discuss a newly developed food preference task, the Macronutrient and Taste Preference Ranking Task (MTPRT), in which participants rank groups of four food products according to how much they desire to eat the products. The MTPRT includes pictures of sweet and savory food products from four categories: high-carbohydrate, high-fat, high-protein and low-energy. A within-subjects study on sensory-specific satiety was conducted to assess the task's reliability and validity. Sixty-nine healthy participants performed two test sessions that were at least one week apart. Participants ate either a sweet or a savory meal, which were similar in macronutrient content. Before and after eating the meal participants rated appetite and completed the MTPRT. In hungry state, preference scores for all food categories were significantly correlated between the two test sessions (all r > 0.68, all p <0.001). Preference for sweet decreased after the sweet meal and increased after the savory meal. In addition, preference for protein decreased more after consuming the savory meal than it did after consuming the sweet meal. Preference for carbohydrate and fat decreased after meal consumption, regardless of taste. Preference for low-energy increased after meal consumption. These results show the MTPRT is a reliable and valid task for measuring food preferences. The MTPRT can be used for both hypothesis-driven and exploratory studies to examine the influence of different factors on changes in food preferences.

LPS challenge in jonge biggen : VDI-12: effect voerinterventie op biggen
Greeff, Astrid de; Allaart, Janneke ; Bruijn, Carlijn de; Schokker, Dirkjan ; Roubos, Petra ; Winkelman-Goedhart, Hélène ; Vastenhouw, Stéphanie ; Ruuls, Lisette ; Rebel, Johanna ; Smits, Mari - \ 2016
Wageningen : Wageningen Livestock Research (Wageningen Livestock Research rapport 1009) - 21
biggen - maatregel op voedingsgebied - adequate immuniteit - diergezondheid - lipopolysacchariden - varkenshouderij - dierhouderij - immunologie - piglets - nutritional intervention - immune competence - animal health - lipopolysaccharides - pig farming - animal husbandry - immunology
The PLETHORA Gene Regulatory Network Guides Growth and Cell Differentiation in Arabidopsis Roots
Santuari, Luca ; Sanchez-Perez, Gabino F. ; Luijten, Marijn ; Rutjens, Bas ; Terpstra, Inez ; Berke, Lidija ; Gorte, Maartje ; Prasad, Kalika ; Bao, Dongping ; Timmermans-Hereijgers, Johanna L.P.M. ; Maeo, Kenichiro ; Nakamura, Kenzo ; Shimotohno, Akie ; Pencik, Ales ; Novak, Ondrej ; Ljung, Karin ; Heesch, Sebastiaan Van; Bruijn, Ewart De; Cuppen, Edwin ; Willemsen, Viola ; Mähönen, Ari Pekka ; Lukowitz, Wolfgang ; Snel, Berend ; Ridder, Dick De; Scheres, Ben ; Heidstra, Renze - \ 2016
The Plant Cell 28 (2016)12. - ISSN 1040-4651 - p. 2937 - 2951.
Organ formation in animals and plants relies on precise control of cell state transitions to turn stem cell daughters into fully differentiated cells. In plants, cells cannot rearrange due to shared cell walls. Thus, differentiation progression and the accompanying cell expansion must be tightly coordinated across tissues. PLETHORA (PLT) transcription factor gradients are unique in their ability to guide the progression of cell differentiation at different positions in the growing Arabidopsis thaliana root, which contrasts with well-described transcription factor gradients in animals specifying distinct cell fates within an essentially static context. To understand the output of the PLT gradient, we studied the gene set transcriptionally controlled by PLTs. Our work reveals how the PLT gradient can regulate cell state by region-specific induction of cell proliferation genes and repression of differentiation. Moreover, PLT targets include major patterning genes and autoregulatory feedback components, enforcing their role as master regulators of organ development.
. XIV Meeting of the IOBC-WPRS Working Group Biological Control of Fungal and Bacterial Plant Pathogens
Postma, Joeke - \ 2016
R. Gomez Exposito, J. Postma, I. de Bruijn and J.M. Raaijmakers, 2016. Microbiome studies give new insights in Rhizoctonia-suppressive microbial communities
. KNPV Working group Soil-borne pathogens en microbiology, Oosterwolde
Postma, Joeke - \ 2016
• R. Gomez Exposito, J. Postma, I. de Bruijn and J.M. Raaijmakers, 2016. Microbiome studies give new insights in Rhizoctonia-suppressive microbial communities. (lezing)
Mass Spectrometric Characterization of Benzoxazinoid Glycosides from Rhizopus-Elicited Wheat (Triticum aestivum) Seedlings
Bruijn, Wouter J.C. de; Vincken, Jean Paul ; Duran, Katharina ; Gruppen, Harry - \ 2016
Journal of Agricultural and Food Chemistry 64 (2016)32. - ISSN 0021-8561 - p. 6267 - 6276.
benzoxazinoid classification - cereal grain - elicitation - germination - LC-MS - phytoalexin - plant defense - Rhizopus oryzae

Benzoxazinoids function as defense compounds and have been suggested to possess health-promoting effects. In this work, the mass spectrometric behavior of benzoxazinoids from the classes benzoxazin-3-ones (with subclasses lactams, hydroxamic acids, and methyl derivatives) and benzoxazolinones was studied. Wheat seeds were germinated with simultaneous elicitation by Rhizopus. The seedling extract was screened for the presence of benzoxazinoid (glycosides) using reversed-phase ultra-high-performance liquid chromatography with photodiode array detection coupled in line to multiple-stage mass spectrometry (RP-UHPLC-PDA-MSn). Benzoxazin-3-ones from the different subclasses showed distinctly different ionization and fragmentation behaviors. These features were incorporated into a newly proposed decision guideline to aid the classification of benzoxazinoids. Glycosides of the methyl derivative 2-hydroxy-4-methoxy-1,4-benzoxazin-3-one were tentatively identified for the first time in wheat. We conclude that wheat seedlings germinated with simultaneous fungal elicitation contain a diverse array of benzoxazinoids, mainly constituted by benzoxazin-3-one glycosides.

PanTools: representation, storage and exploration of pan-genomic data
Sheikhizadeh Anari, S. ; Schranz, M.E. ; Akdel, Mehmet ; Ridder, D. de; Smit, S. - \ 2016
Bioinformatics 32 (2016)17. - ISSN 1367-4803 - p. i487 - i493.
Motivation: Next-generation sequencing technology is generating a wealth of highly similar genome sequences for many species, paving the way for a transition from single-genome to pangenome analyses. Accordingly, genomics research is going to switch from reference-centric to pan-genomic approaches. We define the pan-genome as a comprehensive representation of multiple
annotated genomes, facilitating analyses on the similarity and divergence of the constituent genomes at the nucleotide, gene and genome structure level. Current pan-genomic approaches do not thoroughly address scalability, functionality and usability.
Results: We introduce a generalized De Bruijn graph as a pan-genome representation, as well as an online algorithm to construct it. This representation is stored in a Neo4j graph database, which makes our approach scalable to large eukaryotic genomes. Besides the construction algorithm, our software package, called PanTools, currently provides functionality for annotating pan-genomes,
adding sequences, grouping genes, retrieving gene sequences or genomic regions, reconstructing genomes and comparing and querying pan-genomes. We demonstrate the performance of the tool using datasets of 62 E. coli genomes, 93 yeast genomes and 19 Arabidopsis thaliana genomes.
Availability and Implementation: The Java implementation of PanTools is publicly available at
Observing Boundary-Layer Winds from Hot-Air Balloon Flights
Bruijn, E.I.F. de; Haan, S. de; Bosveld, F.C. ; Wichers Schreur, B.G.J. ; Holtslag, A.A.M. - \ 2016
Weather and Forecasting 31 (2016)5. - ISSN 0882-8156 - p. 1451 - 1463.
High-resolution upper-air wind observations are sparse, and additional observations are a welcome source of meteorological information. In this paper the potential of applying balloon flights for upper-air wind measurements is explored, and the meteorological content of this information is investigated. The displacement of a hot-air balloon is a measure for the wind speed and direction and thus a potential source for wind observations in the lower part of the troposphere. The response time of the balloon on the changing wind is fast in the beginning and levels off for smaller relative wind speeds. Four case studies are presented, and the balloon-derived winds are compared with other wind observations and with results from the HIRLAM–ALADIN Research on Mesoscale Operational NWP in Europe (HARMONIE) model. It turns out that hot-air balloon tracks can indeed produce useful wind observations just above and in the atmospheric boundary layer (ABL).
Effects of rye inclusion in diets on broiler performance, gut morphology and microbiota composition
Krimpen, M.M. van; Torki, Mehran ; Borgijink, S.M. ; Schokker, D. ; Vastenhouw, S.A. ; Bree, F.M. de; Bossers, A. ; Fabri, T. ; Bruijn, Naomi de; Jansman, A.J.M. ; Rebel, J.M.J. ; Smits, M.A. ; Emous, R.A. van - \ 2016
- 1 p.
It has been hypothesized that dietary inclusion of rye would increase viscosity of intestinal
digesta, consequently resulting in an effect on nutrient absorption, gut wall morphology,
composition of microbiota, and immunity-related processes in the gut wall, and it might be a
helpful model ingredient to investigate the negative effects of nutrition on immune competence
parameters of the birds. In this experiment the effects of dietary inclusion of three levels (0, 5,
and 10%) of rye between 14 and 28 days of age on gut health, digesta microbiota composition,
expression of genes in the small intestinal tissue and performance in broilers were investigated.
A total of 960 day-old male Ross 308 chicks were allocated to 24 pens (40 birds per pen).
Inclusion of 10% rye in the diet did not affect feed intake, but decreased body weight gain, and
increased feed conversion ratio. Litter quality was inversely related to the level of rye inclusion
in the diet. Providing rye-rich diets resulted in increased jejunal villus height and crypt depth
during the first week of provision, whereas the villus-crypt ratio was not affected. During the
second week of the experiment, however, the level of rye inclusion had no effect on jejunal
gut morphology. Inclusion of rye into the diet did not affect the number and size of jejunal
goblet cells. Dietary inclusion of rye did not affect the diversity of the jejunal microbiota,
as determined by the Shannon index, although specific microbial strains were affected by
rye inclusion. Lactobacillus species made about 75-80% of the jejunal microbiota, and rye
inclusion resulted in an exchange between the different lactobacillus species. At d28, the share
of Lactobacillus reuteri, Staphylococcus saporphyticus and Aerococcaceae in the microbiota in jejunal digesta decreased with increasing dietary rye. Dietary rye inclusion affected expression of genes in the small intestinal tissue involved in cell cycle processes of the epithelial cells, including proliferation, differentiation, motility, and survival, as well as in the complement and coagulation cascade. At 28 d of age, effects were more pronounced in birds fed the 10% rye diet, compared to birds fed the 5% rye diet. In conclusion, inclusion of 5% or 10% rye to the grower diet of broilers have limited effects on performance. Ileal gut morphology, microbiota composition of jejunal digesta, and gene expression profiles of jejunal tissue; however, were affected by dietary rye inclusion level.
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