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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    Differences exist in the faecal microbiota of domesticated equines
    Edwards, Joan ; Schennink, Angeline ; Burden, F. ; Long, S. ; Doorn, D.A. van; Pellikaan, Wilbert ; Dijkstra, Jan ; Saccenti, Edoardo ; Smidt, Hauke - \ 2020
    Wageningen University
    PRJEB32772 - ERP115488 - Metagenome - Equine species - faecal microbiota - Comparison
    Background: Compared to horses and ponies, donkeys have increased degradation of dietary fiber. The longer total mean retention time of feed in the donkey gut has been proposed to be the basis of this, because of the increased time available for feed to be acted upon by enzymes and the gut microbiota. However, differences in terms of microbial concentrations and/or community composition in the hindgut may also underpin this. Therefore, a study was conducted to determine the effect of equine type on the faecal microbiota of three types of domesticated equines: pony, donkey and pony × donkey hybrid (i.e. mule/hinny).Results: Equine type had no significant effect on faecal dry matter content or faecal concentrations of bacteria, archaea and anaerobic fungi. However, equine type did significantly affect the faecal community composition of prokaryotes and anaerobic fungi. Two bacterial genera were significantly higher in donkey compared to both pony and pony x donkey: Lachnoclostridium 10 and ‘probable genus 10’ from the Lachnospiraceae family. Equine type also significantly affected the anaerobic fungal community composition. Piromyces was significantly lower in donkey compared to pony × donkey, with pony not significantly differing from either equine type. In contrast, the uncultivated genus SK3 was only found in donkey (4 of the 8 animals), and not at all in pony or pony × donkey. Anaerobic fungal diversity, as indicated by the number of OTUs, was also significantly higher in donkey, with no significant differences found between pony and pony × donkey.Conclusions: Donkey faecal microbiota differed from that of both pony and pony × donkey. These differences related to an increase in the relative abundance and diversity of taxa with known, or speculated, roles in plant material degradation. These findings are consistent with the previously reported increased fiber degradation in donkeys compared to ponies, and suggests that the hindgut microbiota play a role as well as differences in total retention time of feed. This offers novel opportunities to generate more energy from dietary fiber, decreasing the need for energy dense feeds which are a risk factor for gut-mediated disease.
    Domesticated equine species and their derived hybrids differ in their fecal microbiota
    Edwards, J.E. ; Schennink, A. ; Burden, F. ; Long, S. ; Doorn, D.A. van; Pellikaan, W.F. ; Dijkstra, J. ; Saccenti, E. ; Smidt, H. - \ 2020
    Animal Microbiome 2 (2020). - ISSN 2524-4671
    Background: Compared to horses and ponies, donkeys have increased degradation of dietary fiber. The longer total mean retention time of feed in the donkey gut has been proposed to be the basis of this, because of the increased time available for feed to be acted upon by enzymes and the gut microbiota. However, differences in terms of microbial concentrations and/or community composition in the hindgut may also underpin the increased degradation of fiber in donkeys. Therefore, a study was conducted to assess if differences existed between the fecal microbiota of pony, donkey and hybrids derived from them (i.e. pony × donkey) when fed the same forage diet.
    Results: Fecal community composition of prokaryotes and anaerobic fungi significantly differed between equine types. The relative abundance of two bacterial genera was significantly higher in donkey compared to both pony and pony x donkey: Lachnoclostridium 10 and ‘probable genus 10’ from the Lachnospiraceae family. The relative abundance of Piromyces was significantly lower in donkey compared to pony × donkey, with pony not significantly differing from either of the other equine types. In contrast, the uncultivated genus SK3 was only found in donkey (4 of the 8 animals). The number of anaerobic fungal OTUs was also significantly higher in donkey than in the other two equine types, with no significant differences found between pony and pony × donkey. Equine types did not significantly differ with respect to prokaryotic alpha diversity, fecal dry matter content or fecal concentrations of bacteria, archaea and anaerobic fungi.
    Conclusions: Donkey fecal microbiota differed from that of both pony and pony × donkey. These differences related to a higher relative abundance and diversity of taxa with known, or speculated, roles in plant material degradation. These findings are consistent with the previously reported increased fiber degradation in donkeys compared to ponies, and suggest that the hindgut microbiota plays a role. This offers novel opportunities for pony and pony × donkey to extract more energy from dietary fiber via microbial mediated strategies. This could potentially decrease the need for energy dense feeds which are a risk factor for gut-mediated disease.
    Improving dietary intake during lunch through the provision of a healthy school lunch at Dutch primary schools : Design of a pretest-posttest effectiveness study
    Kleef, Ellen Van; Rongen, Frédérique C. ; Vingerhoeds, Monique H. ; Dijkstra, Coosje ; Seidell, Jaap C. - \ 2020
    BMC Public Health 20 (2020)1. - ISSN 1471-2458
    Primary school - School lunch - School-based intervention - Vegetables

    Background: Since there is a shift from eating lunch at home to eating lunch at primary schools in the Netherlands, providing a school lunch may be an important opportunity to improve the diet quality of Dutch children. Therefore, the aim of this Healthy School Lunch project is to encourage healthy eating behavior of children at primary schools by offering a healthy school lunch, based on the guidelines for a healthy diet. In this study, two research questions will be addressed. The first research question is: What and how much do children consume from a self-served school lunch and how do they evaluate the lunch? The second research question is: Do children compensate healthier school lunches by eating less healthy outside school hours? The purpose of this paper is to report the rationale and study design of this study. Methods: In the Healthy School Lunch project children in grades 5-8 (aged 8-12 years) of three primary schools in the Netherlands will receive a healthy school lunch for a 6-month period. To answer research question 1, lunch consumption data will be collected at baseline and again at 3- A nd 6-months. This will be measured with lunch photos and questionnaires among children. To answer the second research question, a quasi-experimental, pre-test post-test intervention-comparison group design (3 intervention schools and 3 comparison schools) will be carried out. Potential compensation effects will be measured with a single brief questionnaire among parents at the three intervention and three comparison schools at month 6 of the lunch period. The school lunch will also be evaluated by parents (discussion groups) and teachers and support staff (brief questionnaires). Discussion: Results of this study will provide valuable information to influence future school lunch interventions and policies. Trial registration: This study is registered at the Netherlands trial register (NTR): Trialregister.nl, Trial NL7402 (NTR7618), registered retrospectively at 2018-11-13.

    Multi-kingdom characterization of the core equine fecal microbiota based on multiple equine (sub)species
    Edwards, J.E. ; Shetty, S.A. ; Berg, P. van den; Burden, F. ; Doorn, D.A. van; Pellikaan, W.F. ; Dijkstra, J. ; Smidt, H. - \ 2020
    Animal Microbiome 2 (2020).
    Background: Equine gut microbiology studies to date have primarily focused on horses and ponies, which represent only one of the eight extant equine species. This is despite asses and mules comprising almost half of the world’s domesticated equines, and donkeys being superior to horses/ponies in their ability to degrade dietary fiber. Limited attention has also been given to commensal anaerobic fungi and archaea even though anaerobic fungi are potent fiber degrading organisms, the activity of which is enhanced by methanogenic archaea. Therefore, the objective of this study was to broaden the current knowledge of bacterial, anaerobic fungal and archaeal diversity of the equine fecal microbiota to multiple species of equines. Core taxa shared by all the equine fecal samples (n = 70) were determined and an overview given of the microbiota across different equine types (horse, donkey, horse × donkey and zebra).
    Results: Equine type was associated with differences in both fecal microbial concentrations and community composition. Donkey was generally most distinct from the other equine types, with horse and zebra not differing. Despite this, a common bacterial core of eight OTUs (out of 2070) and 16 genus level groupings (out of 231) was found in all the fecal samples. This bacterial core represented a much larger proportion of the equine fecal microbiota than previously reported, primarily due to the detection of predominant core taxa belonging to the phyla Kiritimatiellaeota (formerly Verrucomicrobia subdivision 5) and Spirochaetes. The majority of the core bacterial taxa lack cultured representation. Archaea and anaerobic fungi were present in all animals, however, no core taxon was detected for either despite several taxa being prevalent and predominant.
    Conclusions: Whilst differences were observed between equine types, a core fecal microbiota existed across all the equines. This core was composed primarily of a few predominant bacterial taxa, the majority of which are novel and lack cultured representation. The lack of microbial cultures representing the predominant taxa needs to be addressed, as their availability is essential to gain fundamental knowledge of the microbial functions that underpin the equine hindgut ecosystem.
    Vragen en antwoorden over stikstof
    Dijkstra, Jan - \ 2020
    Can unhealthy food purchases at checkout counters be discouraged by introducing healthier snacks? A real-life experiment in supermarkets in deprived urban areas in the Netherlands
    Huitink, Marlijn ; Poelman, Maartje P. ; Seidell, Jacob C. ; Pleus, Milan ; Hofkamp, Tom ; Kuin, Carlijn ; Dijkstra, S.C. - \ 2020
    BMC Public Health 20 (2020)1. - ISSN 1471-2458
    Checkout counter - Food environment - Food purchases - Impulsive behavior - Purchase behavior - Snacks - Supermarkets

    Background: The checkout area in supermarkets is an unavoidable point of purchase where impulsive food purchases are likely to be made. However, the product assortment at the checkout counters is predominantly unhealthy. The aim of this real life experiment was to investigate if unhealthy food purchases at checkout counters in supermarkets in deprived urban areas in the Netherlands can be discouraged by the introduction of the Healthy Checkout Counter (HCC). In addition, we examined customers' perceptions towards the HCC. Methods: The HCC was an initiative of a leading supermarket chain in the Netherlands that consisted of displays with a selection of healthier snacks that were placed at the checkouts. We used a real life quasi-experimental design with 15 intervention and 9 control supermarkets. We also performed a cross-sectional customer evaluation in 3 intervention supermarkets using oral surveys to investigate customers' perceptions towards the HCC (n=134). The purchases of unhealthy and healthier snacks at checkouts were measured with sales data. Results: During the intervention period, customers purchased on average 1.7 (SD: 0.08) unhealthy snacks per 100 customers in the intervention supermarket and 1.4 (SD: 0.10) in the control supermarket. Linear regression analyses revealed no statistically significant difference in the change during the control and intervention period of sales of unhealthy snacks between the control and intervention supermarkets (B = - 0.008, 95% CI = - 0.15 to 0.14). The average number of healthier snacks purchased was 0.2 (SD: 0.3) items per 100 customers in the intervention supermarkets during the intervention period. Of the intervention customers, 41% noticed the HCC and 80% of them were satisfied or very satisfied with the intervention. Conclusions: This real life experiment in supermarkets showed that the placement of healthier snacks at checkouts did not lead to the substitution of unhealthy snack purchases with healthier alternatives. Although supermarket customers positively evaluated the HCC, future studies are needed to investigate other strategies to encourage healthier food purchases in supermarkets.

    Soils in lakes : the impact of inundation and storage on surface water quality
    Vink, Jos P.M. ; Comans, Rob N.J. ; Dijkstra, Joris J. ; Lamers, Leon P.M. - \ 2020
    Environmental Monitoring and Assessment 192 (2020)6. - ISSN 0167-6369
    Bioavailability - Biotic ligand models - Chemical extraction - Risk assessment - Sediment fluxes - Speciation - Suspended matter - Toxicity

    The large-scale storage and inundation of contaminated soils and sediments in deep waterlogged former sand pits or in lakes have become a fairly common practice in recent years. Decreasing water depth potentially promotes aquatic biodiversity, but it also poses a risk to water quality as was shown in a previous study on the impact on groundwater. To provide in the urgent need for practical and robust risk indicators for the storage of terrestrial soils in surface waters, the redistribution of metals and nutrients was studied in long-term mesocosm experiments. For a range of surface water turbidity (suspended matter concentrations ranging from 0 to 3000 mg/L), both chemical partitioning and toxicity of pollutants were tested for five distinctly different soils. Increasing turbidity in surface water showed only marginal response on concentrations of heavy metals, phosphorus (P) and nitrogen (N). Toxicity testing with bioluminescent bacteria, and biotic ligand modelling (BLM), indicated no or only minor risk of metals in the aerobic surface water during aerobic mixing under turbid conditions. Subsequent sedimentation of the suspended matter revealed the chemical speciation and transport of heavy metals and nutrients over the aerobic and anaerobic interface. Although negative fluxes occur for Cd and Cu, most soils show release of pollutants from sediment to surface waters. Large differences in fluxes occur for PO4, SO4, B, Cr, Fe, Li, Mn and Mo between soils. For an indicator of aerobic chemical availability, dilute nitric acid extraction (0.43 M HNO3; Aqua nitrosa) performed better than the conventional Aqua regia destruction. Both the equilibrium concentrations in surface waters, and fluxes from sediment, were adequately (r2 = 0.81) estimated by a 1 mM CaCl2 soil extraction procedure. This study has shown that the combination of 0.43 M HNO3 and 1 mM CaCl2 extraction procedures can be used to adequately estimate emissions from sediment to surface waters, and assess potential water quality changes, when former sand pits are being filled with soil materials.

    Exploring the effects of a healthy school lunch on cognitive performance in Dutch primary school children within the Healthy School Lunch project
    Dijkstra, Coosje ; Haar, Sandra van der; Bergen, Geertje van; Kleef, Ellen van; Vingerhoeds, Monique - \ 2020
    Wageningen : Wageningen Food & Biobased Research (Wageningen Food & Biobased Research report 2041) - ISBN 9789463953832 - 17
    The ‘Healthy School Lunch’ project (PPS Een gezonde schoollunch - TKI AF-16098) aimed to study the feasibility and impact of offering a healthy school lunch in Dutch primary schools. In the first phase of the project we studied the support for a healthy school lunch among a wide range of stakeholders and we explored what they thought a healthy school lunch should look like. The next phase aimed to study the effects of a healthy school lunch on dietary intake and cognitive performance. In order to investigate the effects of providing a healthy school lunch on the dietary intake of children during lunch, a longitudinal intervention study with three schools was designed, where a healthy school lunch was offered for six months. Due to various financial and methodological reasons that were not fully considered when starting this project, it was not possible to combine the dietary intake and cognition study in the school lunch intervention. Instead, we explored the possibilities and requirements to perform a solid experimental cross-over study on the effects of a healthy school lunch on cognitive performance within the Healthy School Lunch Project. This process is described in the current report. We started with a review of the literature on the effects of a healthy school lunch on cognitive performance of children. Studies on the immediate and transient effects of a healthy school lunch versus skipping lunch showed, on a variety of cognitive measures, small and inconsistent effects on alertness and working memory of children. Studies on the long-term effects of a healthy school lunch versus habitual lunch showed small improvements in concentration and language processing ability of children. Given the restriction that long term effects of a school lunch on cognitive performance could not be examined within the scope of this project, the focus shifted to understanding immediate effects. A well-designed study to capture immediate effects of a healthy school lunch on cognitive performance of children within our project would require a strictly controlled cross-over design in a school setting. The intervention should consist of an ad libitum buffet-style healthy school lunch, compared with a control condition in which children eat ad libitum from a provided lunch comparable to the common relatively unhealthy packed school lunch of Dutch children. Finding an adequate measure for cognitive performance is hampered by the great variation of previously used measures across studies. These ranged from relatively indirect measures of concentration and disengagement to standardized computerized tests assessing specific cognitive domains such as alertness and higher-level executive functions. Hence, a comprehensive battery of tests would be advisable to explore various potential effects. Power calculations would be needed to determine the sample size of such a study, but it is clear that large numbers of children would be needed, given the small expected effects and methodological challenges. As more than one participating school would be needed, multilevel statistical models would be required to handle grouped and individual children’s data. More research on the effects of a healthy school lunch on cognition in primary school children would be very useful. However, a well-designed study that would provide convincing evidence of the effects of a healthy school lunch on cognitive performance in primary school children, would require a high cost set-up that places a very high burden on both the children and the schools. Therefore, we decided that it is not realistic to perform this study within the Healthy School Lunch project. In this report we would like to share our findings, considerations and recommendations to researchers of future studies on the effect of healthy school lunches on cognitive performance in children.
    Social norm nudges in shopping trolleys to promote vegetable purchases : A quasi-experimental study in a supermarket in a deprived urban area in the Netherlands
    Huitink, Marlijn ; Poelman, Maartje P. ; Eynde, Emma van den; Seidell, Jacob C. ; Dijkstra, S.C. - \ 2020
    Appetite 151 (2020). - ISSN 0195-6663
    Deprived urban area - Nudging - Purchase behaviour - Shopping trolleys - Social norm - Supermarkets - Vegetables

    Background: Supermarkets are a key point of purchase for groceries and can therefore have a considerable influence on eating behaviours. Evidence suggests that descriptive social norm nudges in shopping trolleys can be effective in stimulating vegetable purchases in supermarkets. Objective: We investigated the effect of a combination of two nudging strategies in shopping trolleys – a social norm about vegetable purchases and a designated place to put vegetables – on the amount of vegetables purchased in a supermarket in a deprived urban area in the Netherlands. Design: A quasi-experimental study was conducted with two conditions: 1) intervention days on which the shopping trolleys in the supermarket had a green nudge inlay indicating a place for vegetables and a social norm message and 2) control days on which the regular shopping trolleys (no inlay or social norm) were used in the supermarket. During both the intervention and control days, vegetable purchases were measured by means of the cash receipts collected from customers at the checkouts. In addition, individual and purchase characteristics were assessed by means of short surveys. Results: In total, 244 customers participated in the study. Ordinal logistic regression analyses showed that customers on the intervention days (n = 123) were in a higher tertile for grams of vegetables purchased compared to the customers on the control days (OR: 1.66, 95% CI: 1.03–2.69, p = 0.03), especially those who bought groceries for less than three days (OR: 3.24, 95% CI: 1.43–7.35, p = 0.003). Sensitivity analyses also showed that intervention customers who noticed the green inlay were even more likely to purchase more vegetables (OR: 1.86, 95% CI: 1.06–3.25, p = 0.02). Conclusions: This quasi-experimental study showed that a nudge inlay in shopping trolleys communicating a social norm on vegetable purchases and indicating a distinct place to put vegetables in the trolley increased vegetable purchases among supermarket customers.

    Effect of arginine or glutamine supplementation and milk feeding allowance on small intestine development in calves
    Keulen, P. van; Khan, M.A. ; Dijkstra, J. ; Knol, F. ; McCoard, S.A. - \ 2020
    Journal of Dairy Science 103 (2020)5. - ISSN 0022-0302 - p. 4754 - 4764.
    L-arginine - L-glutamine - milk allowance - small intestine development

    The development of the small intestine (SI) is important for the health and growth of neonatal calves. This study evaluated the effect of arginine (Arg) and glutamine (Gln) supplementation and 2 levels of milk allowance on the histomorphological development of the SI in preweaning calves. Sixty mixed-sex Friesian × Jersey calves (3–5 d of age) were offered reconstituted whole milk (125 g/L, 26% fat, 26% protein) at either high (20% of arrival body weight/d; HM) or low (10% of arrival body weight/d; LM) milk allowance without (Ctrl) or with supplementary Arg or Gln (at 1% of milk dry matter) in a 2 × 3 factorial design (n = 10/treatment). After 35 d on the diets, all calves were slaughtered to collect tissues for examination of SI development. Calves in the HM group had higher milk intake, total weight gain, and average daily gain compared with LM calves, but no effect of AA supplementation nor an interaction between milk allowance and AA supplementation was observed. For the duodenum, we observed an AA by milk allowance interaction for villus height and width, and goblet cell number per villus (HM-Arg > HM-Gln > HM-Ctrl), and villus height to crypt depth ratio (HM-Arg > HM-Gln = HM-Ctrl), but no effect of AA supplementation in the LM group. Goblet cell numbers per 100 μm of SI were greater in Arg-supplemented calves than in unsupplemented controls, with Gln-supplemented calves intermediate to but not different from the other groups. Epithelium thickness was greater in LM than in HM calves. Villus density, crypt depth, and muscle thickness did not differ between groups. For the jejunum, there was an AA by milk allowance interaction for villus height, villus surface area, and villus height to crypt depth ratio (HM-Arg = HM-Gln > HM-Ctrl), with no effect of AA supplementation in the LM groups. Amino acid supplementation affected goblet cell number per villus (HM-Gln > HM-Ctrl calves, HM-Arg intermediate), and both LM-Arg and LM-Gln calves had greater numbers than LM-Ctrl calves. Villus width, crypt depth, and muscle thickness were greater in HM than LM calves but there was no effect of AA supplementation. Villus density, goblet cell number per 100 μm of SI, and epithelium thickness were unaffected by AA supplementation and milk allowance. Milk allowance and AA supplementation had no effect on SI morphology in the ileum. Increasing milk allowance improved villus height, width, and surface area but only in Arg- or Gln-supplemented calves, not in control calves. The observed changes in development may be important for intestinal functionality, integrity, and barrier function in preweaning calves, potentially through increased cell growth and proliferation or reduced levels of cellular atrophy.

    Review : Synergy between mechanistic modelling and data-driven models for modern animal production systems in the era of big data
    Ellis, J.L. ; Jacobs, M. ; Dijkstra, J. ; Laar, H. van; Cant, J.P. ; Tulpan, D. ; Ferguson, N. - \ 2020
    Animal (2020). - ISSN 1751-7311 - 15 p.
    animal production - digital agriculture - hybridization - machine learning - mechanistic modelling

    Mechanistic models (MMs) have served as causal pathway analysis and 'decision-support' tools within animal production systems for decades. Such models quantitatively define how a biological system works based on causal relationships and use that cumulative biological knowledge to generate predictions and recommendations (in practice) and generate/evaluate hypotheses (in research). Their limitations revolve around obtaining sufficiently accurate inputs, user training and accuracy/precision of predictions on-farm. The new wave in digitalization technologies may negate some of these challenges. New data-driven (DD) modelling methods such as machine learning (ML) and deep learning (DL) examine patterns in data to produce accurate predictions (forecasting, classification of animals, etc.). The deluge of sensor data and new self-learning modelling techniques may address some of the limitations of traditional MM approaches - access to input data (e.g. sensors) and on-farm calibration. However, most of these new methods lack transparency in the reasoning behind predictions, in contrast to MM that have historically been used to translate knowledge into wisdom. The objective of this paper is to propose means to hybridize these two seemingly divergent methodologies to advance the models we use in animal production systems and support movement towards truly knowledge-based precision agriculture. In order to identify potential niches for models in animal production of the future, a cross-species (dairy, swine and poultry) examination of the current state of the art in MM and new DD methodologies (ML, DL analytics) is undertaken. We hypothesize that there are several ways via which synergy may be achieved to advance both our predictive capabilities and system understanding, being: (1) building and utilizing data streams (e.g. intake, rumination behaviour, rumen sensors, activity sensors, environmental sensors, cameras and near IR) to apply MM in real-time and/or with new resolution and capabilities; (2) hybridization of MM and DD approaches where, for example, a ML framework is augmented by MM-generated parameters or predicted outcomes and (3) hybridization of the MM and DD approaches, where biological bounds are placed on parameters within a MM framework, and the DD system parameterizes the MM for individual animals, farms or other such clusters of data. As animal systems modellers, we should expand our toolbox to explore new DD approaches and big data to find opportunities to increase understanding of biological systems, find new patterns in data and move the field towards intelligent, knowledge-based precision agriculture systems.

    Hungerwinter: Food & Famine : Forum Library Exhibition 27 January 2020 until 29 May 2020
    Dijkstra, A.G. ; Donselaar, D.H.P.A. van - \ 2020
    Wageningen : Wageningen University & Research - Library - 16 p.
    Phenylthiourea binding to human tyrosinase-related protein 1
    Lai, Xuelei ; Wichers, Harry J. ; Soler-Lopez, Montserrat ; Dijkstra, Bauke W. - \ 2020
    International Journal of Molecular Sciences 21 (2020)3. - ISSN 1661-6596
    Albinism - Crystal structure - Human tyrosinase - Human tyrosinase-related protein - Inhibitor - Melanogenesis - N-glycosylation - Phenylthiourea - Zinc-Copper enzymes

    Tyrosinase-related protein 1 (TYRP1) is one of the three human melanogenic enzymes involved in the biosynthesis of melanin, a pigment responsible for the color of the skin, hair, and eyes. It shares high sequence identity with tyrosinase, but has two zinc ions in its active site rather than two copper ions as in tyrosinase. Typical tyrosinase inhibitors do not directly coordinate to the zinc ions of TYRP1. Here, we show, from an X-ray crystal structure determination, that phenylthiourea, a highly potent tyrosinase inhibitor, does neither coordinate the active site zinc ions, but binds differently from other structurally characterized TYRP1-inhibitor complexes. Its aromatic ring is directed outwards from the active site, apparently as a result from the absence of polar oxygen substituents that can take the position of water molecules bound in the active site. The compound binds via hydrophobic interactions, thereby blocking substrate access to the active site.

    Review: Rumen sensors: Data and interpretation for key rumen metabolic processes
    Dijkstra, J. ; Gastelen, S. Van; Dieho, K. ; Nichols, K. ; Bannink, A. - \ 2020
    Animal 14 (2020)S1. - ISSN 1751-7311 - p. S176 - S186.
    data analysis - diurnal variation - fermentation - ruminants

    Rumen sensors provide specific information to help understand rumen functioning in relation to health disorders and to assist in decision-making for farm management. This review focuses on the use of rumen sensors to measure ruminal pH and discusses variation in pH in both time and location, pH-associated disorders and data analysis methods to summarize and interpret rumen pH data. Discussion on the use of rumen sensors to measure redox potential as an indication of the fermentation processes is also included. Acids may accumulate and reduce ruminal pH if acid removal from the rumen and rumen buffering cannot keep pace with their production. The complexity of the factors involved, combined with the interactions between the rumen and the host that ultimately determine ruminal pH, results in large variation among animals in their pH response to dietary or other changes. Although ruminal pH and pH dynamics only partially explain the typical symptoms of acidosis, it remains a main indicator and may assist to optimize rumen function. Rumen pH sensors allow continuous monitoring of pH and of diurnal variation in pH in individual animals. Substantial drift of non-retrievable rumen pH sensors, and the difficulty to calibrate these sensors, limits their application. Significant within-day variation in ruminal pH is frequently observed, and large distinct differences in pH between locations in the rumen occur. The magnitude of pH differences between locations appears to be diet dependent. Universal application of fixed conversion factors to correct for absolute pH differences between locations should be avoided. Rumen sensors provide high-resolution kinetics of pH and a vast amount of data. Commonly reported pH characteristics include mean and minimum pH, but these do not properly reflect severity of pH depression. The area under the pH × time curve integrates both duration and extent of pH depression. The use of this characteristic, as well as summarizing parameters obtained from fitting equations to cumulative pH data, is recommended to identify pH variation in relation to acidosis. Some rumen sensors can also measure the redox potential. This measurement helps to understand rumen functioning, as the redox potential of rumen fluid directly reflects the microbial intracellular redox balance status and impacts fermentative activity of rumen microorganisms. Taken together, proper assessment and interpretation of data generated by rumen sensors requires consideration of their limitations under various conditions.

    International scientists formulate a roadmap for insect conservation and recovery
    Harvey, Jeffrey A. ; Heinen, Robin ; Armbrecht, Inge ; Basset, Yves ; Baxter-Gilbert, James H. ; Bezemer, T.M. ; Böhm, Monika ; Bommarco, Riccardo ; Borges, Paulo A.V. ; Cardoso, Pedro ; Clausnitzer, Viola ; Cornelisse, Tara ; Crone, Elizabeth E. ; Dicke, Marcel ; Dijkstra, Klaas Douwe B. ; Dyer, Lee ; Ellers, Jacintha ; Fartmann, Thomas ; Forister, Mathew L. ; Furlong, Michael J. ; Garcia-Aguayo, Andres ; Gerlach, Justin ; Gols, Rieta ; Goulson, Dave ; Habel, Jan Christian ; Haddad, Nick M. ; Hallmann, Caspar A. ; Henriques, Sérgio ; Herberstein, Marie E. ; Hochkirch, Axel ; Hughes, Alice C. ; Jepsen, Sarina ; Jones, T.H. ; Kaydan, Bora M. ; Kleijn, David ; Klein, Alexandra Maria ; Latty, Tanya ; Leather, Simon R. ; Lewis, Sara M. ; Lister, Bradford C. ; Losey, John E. ; Lowe, Elizabeth C. ; Macadam, Craig R. ; Montoya-Lerma, James ; Nagano, Christopher D. ; Ogan, Sophie ; Orr, Michael C. ; Painting, Christina J. ; Pham, Thai Hong ; Potts, Simon G. ; Rauf, Aunu ; Roslin, Tomas L. ; Samways, Michael J. ; Sanchez-Bayo, Francisco ; Sar, Sim A. ; Schultz, Cheryl B. ; Soares, António O. ; Thancharoen, Anchana ; Tscharntke, Teja ; Tylianakis, Jason M. ; Umbers, Kate D.L. ; Vet, Louise E.M. ; Visser, Marcel E. ; Vujic, Ante ; Wagner, David L. ; Wallis DeVries, Michiel F. ; Westphal, Catrin ; White, Thomas E. ; Wilkins, Vicky L. ; Williams, Paul H. ; Wyckhuys, Kris A.G. ; Zhu, Zeng Rong ; Kroon, Hans de - \ 2020
    Nature Ecology & Evolution 4 (2020)4. - ISSN 2397-334X - p. 174 - 176.
    Effects of an artificial hay aroma and compound feed formulation on feed intake pattern, rumen function and milk production in lactating dairy cows
    Binti Abd Rahim, Sholeha ; Laar, Harmen van; Dijkstra, J. ; Navarro-Villa, A. ; Fowers, R. ; Hendriks, W.H. ; Pellikaan, W.F. ; Leen, F. ; Martín-Tereso, J. - \ 2020
    Animal 14 (2020)3. - ISSN 1751-7311 - p. 529 - 537.
    The Kempen system is a dairy feeding system in which diet is provided in the form of a compound feed (CF) and hay offered ad libitum. Ad libitum access to CF and hay allows cows in this system to achieve a high DM intake (DMI). Out of physiological concerns, the voluntary hay intake could be increased and the consumption pattern of CF could be manipulated to maintain proper rumen functioning and health. This study investigated the effects of an artificial hay aroma and CF formulation on feed intake pattern, rumen function and milk production in mid- to late-lactating dairy cows. Twenty Holstein–Friesian cows were assigned to four treatments in a 4 × 4 Latin square design. Diet consisted of CF and grass hay (GH), fed separately, and both offered ad libitum, although CF supply was restricted in maximum meal size and speed of supply by an electronic system. Treatments were the combination of two CF formulations – high in starch (CHS) and fibre (CHF); and two GH – untreated (UGH) and the same hay treated with an artificial aroma (TGH). Meal criteria were determined using three-population Gaussian–Gaussian–Weibull density functions. No GH × CF interaction effects on feed intake pattern characteristics were found. Total DMI and CF intake, but not GH intake, were greater (P < 0.01) in TGH treatment, and feed intake was not affected by type of CF. Total visits to feeders per day, visits to the GH feeder, visits to the CF feeder and CF eating time (all P < 0.01) were significantly greater in cows fed with TGH. Meal frequency, meal size and meal duration were unaffected by treatments. Cows fed CHF had a greater milk fat (P = 0.02), milk urea content (P < 0.01) and a greater milk fat yield (P < 0.01). Cows fed TGH had a greater milk lactose content and lactose yield (P < 0.05), and milk urea content (P < 0.01). Cows fed TGH had smaller molar proportions of acetic acid and greater molar proportions of propionic acid compared with UGH. In conclusion, treatment of GH with an artificial aroma increased CF intake and total DMI, but did not affect hay intake. Additionally, GH treatment increased the frequency of visits to both feeders, and affected rumen volatile fatty acid profile. Type of CF did not affect meal patterns, ruminal pH, nor fermentation profiles.
    Effect of dimethyl disulfide on the sulfur formation and microbial community composition during the biological H2S removal from sour gas streams
    Kiragosyan, Karine ; Picard, Magali ; Sorokin, Dimitry Y. ; Dijkstra, Jelmer ; Klok, Johannes B.M. ; Roman, Pawel ; Janssen, Albert J.H. - \ 2020
    Journal of Hazardous Materials 386 (2020). - ISSN 0304-3894
    Biodesulfurization - Biosulfur - Dimethyl disulfide - Selective inhibition - Sulfur-oxidizing bacteria

    Removal of organic and inorganic sulfur compounds from sour gases is required because of their toxicity and atmospheric pollution. The most common are hydrogen sulfide (H2S) and methanethiol (MT). Under oxygen-limiting conditions about 92 mol% of sulfide is oxidized to sulfur by haloalkaliphilic sulfur-oxidizing bacteria (SOB), whilst the remainder is oxidized either biologically to sulfate or chemically to thiosulfate. MT is spontaneously oxidized to dimethyl disulfide (DMDS), which was found to inhibit the oxidation of sulfide to sulfate. Hence, we assessed the effect of DMDS on product formation in a lab-scale biodesulfurization setup. DMDS was quantified using a newly, in-house developed analytical method. Subsequently, a chemical reaction mechanism was proposed for the formation of methanethiol and dimethyl trisulfide from the reaction between sulfide and DMDS. Addition of DMDS resulted in significant inhibition of sulfate formation, leading to 96 mol% of sulfur formation. In addition, a reduction in the dominating haloalkaliphilic SOB species, Thioalkalivibrio sulfidiphilus, was observed in favor of Thioalkaibacter halophilus as a more DMDS-tolerant with the 50 % inhibition coefficient at 2.37 mM DMDS.

    Relationships between chemical composition and in vitro gas production parameters of maize leaves and stems
    He, Yuan ; Cone, John W. ; Hendriks, Wouter H. ; Dijkstra, Jan - \ 2020
    Journal of Animal Physiology and Animal Nutrition 104 (2020)1. - ISSN 0931-2439 - p. 12 - 21.
    cell wall degradation - in vitro gas production - maize leaves - maize stems

    This study investigated the chemical composition (proximate and Van Soest analysis) and in vitro gas production parameters of maize leaves and stems separately, and related the in vitro gas production parameters with the chemical composition, of thirteen maize cultivars. After harvest in September 2016, all plants were separated into two morphological fractions: leaves and stems. The crude protein (CP) content was greater, and the ratio of acid detergent lignin (ADL) to potentially rumen degradable fibre (calculated as the difference between neutral detergent fibre and ADL; ADL:pRDF) was lower in the leaves than in the stems in all 13 cultivars. For the leaves, the cumulative gas production between 3 and 20 hr (A2), representing cell wall fermentation in the rumen fluid, and the cumulative 72-hr gas production (GP72), representing total organic matter (OM) degradation, were moderately to weakly correlated with the chemical composition, including hemicellulose, cellulose, ADL and CP content (R2 < 0.40), whilst the best relationship between the half-time value (B2), representing the rate of cell wall degradation, and chemical composition had an R2 of 0.63. For the stems, the best relationship between A2, B2 and GP72 with chemical composition was greater (R2 ≥ 0.74) and the best relationship included hemicellulose (A2 only), cellulose and ADL (GP72 and A2 only) contents. In conclusion, maize leaves and stems differed in chemical composition, in particular CP content and ADL:pRDF. The A2 and GP72 of the stems, but not of the leaves, were highly correlated with the chemical composition, indicating that the cell wall and OM degradation of maize stems can be better predicted by its chemical composition.

    Acquisition and regeneration of Spinacia turkestanica Iljin and S. tetrandra Steven ex M. Bieb. to improve a spinach gene bank collection
    Treuren, R. van; Groot, E.C. de; Hisoriev, H. ; Khassanov, F. ; Farzaliyev, V. ; Melyan, G. ; Gabrielyan, I. ; Soest, L.J.M. ; Tulmans, C. ; Courand, D. de; Visser, J. de; Kimura, R. ; Boshoven, J.C. ; Kanda, T. ; Goossens, R. ; Verhoef, M. ; Dijkstra, Jan ; Kik, C. - \ 2020
    Genetic Resources and Crop Evolution 67 (2020). - ISSN 0925-9864 - p. 549 - 559.
    Spinach (Spinacia oleracea L.) is a highly nutritious leafy vegetable and an economically important food crop. The wild species S. turkestanica Iljin and S. tetrandra Steven ex M. Bieb. are inter-fertile with cultivated spinach and constitute important sources of novel characters to improve spinach varieties, such as for their resistance to pests and diseases. Despite their relevance in plant breeding, S. turkestanica and S. tetrandra are poorly represented in genetic resources collections. Among the reasons for these collection gaps are the difficulties in propagating these species ex situ. Here we report on the results of collecting expeditions for S. turkestanica in Central Asia and for S. tetrandra in the Trans-Caucasus, which were organized by the Dutch gene bank in collaboration with several breeding companies. Furthermore, we also present efficient protocols for the ex situ regeneration of these species. These protocols were used to successfully regenerate 66 S. turkestanica and 36 S. tetrandra samples from the collecting expeditions. These new accessions fill up important collection gaps in ex situ conserved genetic resources of spinach and can be used for exploitation in crop improvement.
    Study title: Comparison of the faecal microbiota of different types of domesticated equines
    Edwards, J.E. ; Schennink, A. ; Burden, F. ; Long, S. ; Doorn, D.A. van; Pellikaan, W.F. ; Dijkstra, J. ; Saccenti, E. ; Smidt, H. - \ 2019
    Wageningen University & Research
    This repository contains codes for analysis done in the research article by Edwards JE, et al (2019) Comparison of the faecal microbiota of different types of domesticated equines.
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