Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Optimal dairy feed input selection under alternative feeds availability and relative prices
    Alqaisi, Othman ; Moraes, Luis Eduardo ; Ndambi, Oghaiki Asaah ; Williams, Ryan Blake - \ 2019
    Information Processing in Agriculture 6 (2019)4. - ISSN 2214-3173 - p. 438 - 453.
    Diet formulation - Feed availability - Feed prices - Feed switch - LP modelling

    Feed formulation is essential in the dairy production chain from economic, nutritional, and environmental perspectives. Optimizing the feed formulation across those three domains – given uncertainty of input prices, input availability, and regional climatic conditions – is a challenge for those in the industry. The diet formulation method that is widely used by trading firms and feed production facilities employs a static linear programming (LP) approach. This approach does not allow for intertemporal feed formulations and switches between dietary feed commodities under feed availability conditions, which result in foregone economic gains for feed producers. The current study develops a multi-period LP feed model that uses historical data to capture ration switch opportunities between available feed resources for dairy cows and demonstrates the potential use of the method in different commodity feed availability situations. We apply 14 diet formulations, each covering 150 months, representing a total of 2100 diets. The diet formulation considers a specific milk production level for a “model cow”, alternative feed formulations available, and volatility in feed prices. The results demonstrate that there is an opportunity for efficiency gains in the dairy industry with respect to feed formulation. Based on dietary feed inclusion and price spreads, barley can be an important dairy feed grain which completely replaces wheat, corn, and sorghum at price spreads of less than 94%, less than 78%, and less than 67%, respectively. Grain-based feed scenarios represent the lowest nutrient variation while multiple meal feeds had the lowest costs. Furthermore, and on average, multiple meal feed scenarios provided 10% higher dietary crude protein contents compared to grain based feed scenarios (i.e. 163 vs 179 g/kg DM formulated feed). Meanwhile, multiple meal feeding cost was 11% lower than that in the grain based feeding scenarios. Additionally, the use of multiple meals reduces alfalfa dietary inclusion by 7% on dry matter basis. Our analysis shows a strong reduction in feed cost associated with dietary crude protein reduction equivalent to 7.6 USD/tonne per 1% reduction in dietary crude protein level. The modeling approach allows for the interaction between feed components over time taking into consideration volatile global feed prices, thereby improving feed availability and feed formulation. Overall, the model provides a decision making tool to improve the use of feed resources in the dairy sector.

    Remote sensing and signaling in kidney proximal tubules stimulates gut microbiome-derived organic anion secretion
    Jansen, Jitske ; Jansen, Katja ; Neven, Ellen ; Poesen, Ruben ; Othman, Amr ; Mil, Alain van; Sluijter, Joost ; Torano, Javier Sastre ; Zaal, Esther A. ; Berkers, Celia R. ; Esser, Diederik ; Wichers, Harry J. ; Ede, Karin van; Duursen, Majorie van; Burtey, Stéphane ; Verhaar, Marianne C. ; Meijers, Björn ; Masereeuw, Rosalinde - \ 2019
    Proceedings of the National Academy of Sciences of the United States of America 116 (2019)32. - ISSN 0027-8424 - p. 16105 - 16110.
    Indoxyl sulfate - Kidney proximal tubule - Organic anion transporter 1 - Remote sensing and signaling

    Membrane transporters and receptors are responsible for balancing nutrient and metabolite levels to aid body homeostasis. Here, we report that proximal tubule cells in kidneys sense elevated endogenous, gut microbiome-derived, metabolite levels through EGF receptors and downstream signaling to induce their secretion by up-regulating the organic anion transporter-1 (OAT1). Remote metabolite sensing and signaling was observed in kidneys from healthy volunteers and rats in vivo, leading to induced OAT1 expression and increased removal of indoxyl sulfate, a prototypical microbiome-derived metabolite and uremic toxin. Using 2D and 3D human proximal tubule cell models, we show that indoxyl sulfate induces OAT1 via AhR and EGFR signaling, controlled by miR-223. Concomitantly produced reactive oxygen species (ROS) control OAT1 activity and are balanced by the glutathione pathway, as confirmed by cellular metabolomic profiling. Collectively, we demonstrate remote metabolite sensing and signaling as an effective OAT1 regulation mechanism to maintain plasma metabolite levels by controlling their secretion.

    Genetic diversity of endangered terrestrial orchids Spathoglottis plicata in Peninsular Malaysia based on AFLP markers
    Ginibun, Florence C. ; Arens, Paul ; Vosman, Ben ; Bhassu, Subha ; Khalid, Norzulaani ; Othman, Rofina Yasmin - \ 2018
    Plant OMICS 11 (2018)3. - ISSN 1836-0661 - p. 135 - 144.
    AFLP - Genetic diversity - Spathoglottis plicata - Terrestrial orchids

    Spathoglottis plicata is an endangered terrestrial orchid species that have experienced severe threats to its habitat as wild forest sites come under pressure from industrialisation and natural disasters. This orchid species chosen to evaluate their levels of genetic diversity and population genetic structure, which 25-30 accession collected in the different location with different geographical, altitude and habitat. Genomic DNA was extracted from six natural populations (n=172) in Peninsular Malaysia using eleven AFLP markers of EcoRI+3 bases/MseI+3 base primer combinations. Based on 279 polymorphic bands, a significant degree of genetic population differentiation was found, with a 78.5% variation within populations as measured by AMOVA, indicating a potential restricted gene flow. Two distinct clades generated from a UPGMA dendrogram were further investigated through a Bayesian analysis using STRUCTURE software, producing an estimated population structure at optimal value K=4. These results point to the presence of four genetic structures in the Spathoglottis plicata population. The Pahang and Terengganu population revealed a higher than average genetic variation (60.25%), indicating that there may be a robust structural division between the population samples and a possible hybridisation between the Northern (Kedah), Southern (Negeri Sembilan and Johor) and Central (Selangor) region populations. In sum, these results suggest that geographical distance is the primary factor contributing to differences among populations and the need for conservation measures to protect the Spathoglottis plicata species.

    Effects of pre and post-calving feed supplementation on milk yield, reproductive performance and farm profitability of Ethiopian dairy cows
    Ndambi, O.A. ; Wassink, G. ; Abebe, Kiros ; Alqaisi, Othman - \ 2018
    Wageningen : Wageningen University & Research (DairyBISS Research Brief 001) - 3 p.
    Time series livestock diet optimization : cost-effective broiler feed substitution using the commodity price spread approach
    Alqaisi, Othman ; Ndambi, Oghaiki Asaah ; Williams, Ryan Blake - \ 2017
    Agricultural and Food Economics 5 (2017)1. - ISSN 2193-7532
    Broiler diet - Byproducts - Feed industry - Multi-stage linear-programming - Price spread - Trading
    Sustainable feed formulation (defined here as nutritional and economic feed optimization) is substantial in feed chain production from crop farmers to livestock producers. Diet formulation employing a static linear programming (LP) approach, which is widely used in trading firms and feed production facilities, does not allow for intertemporal flexibility. Our approach allows the interaction between feed components over time, considering the volatile global feed prices, thereby improving sustainability in feed formulation and feed availability. The objectives of this study were to (1) develop a multi-stage LP feed model, (2) demonstrate its potential use in broiler feeding, and (3) illustrate the impact of feed input price spread (variation) on the composition of broiler diets. Modeling resulted in reciprocal relationships between conventional feeds and byproducts at different rates. Based on the price spreads expressed as a percentage of DDGS (distiller’s dried grains with solubles) price compared to corn price, three positions of dietary switch were identified; corn-DDGS price spreads of higher than 94%, between 76 and 94%, and lower than 76% corresponding to limited/no inclusion, partial inclusion, and maximum replacement of corn by DDGS, respectively. Rapeseed meal inclusion was 4, 5, and 6% in the corn-based starter, grower, and finisher diets, respectively, and its potential to replace soybean meal was limited by its higher fiber content. Based on the simulated compound feed prices, the global broiler feed industry could gain 1.7 billion USD through improved resources planning.
    A preliminary amplified fragment length polymorphism (AFLP) primers selection for spathoglottis species
    Ginibun, F.C. ; Bhassu, S. ; Khalid, N. ; Arens, P. ; Vosman, B. ; Othman, R.Y. - \ 2015
    Acta Horticulturae 1078 (2015). - ISSN 0567-7572 - p. 167 - 173.
    AFLP primer - Molecular marker - Terrestrial orchid

    Spathoglottis is a native terrestrial orchid that attracting horticultural interest as a landscaping plant. Distinguishing orchid at species level based on morphological characteristics is unconvincing as some characteristic may sensitive to environmental. Therefore, molecular characterization could be an alternative method in characterizing Spathoglottis species. Amplified Fragment Length Polymorphism (AFLP) marker was selected to characterize the Spathoglottis species. Among 56 AFLP primer combinations tested on Spathoglottis plicata, only eight primer combinations gave clear scorable polymorphic bands. A total of 60 accessions of Spathoglottis species, hybrid and outgroup (Dendrobium) were analysed using the eight primer combinations and generated 891 polymorphic bands with 98.41% in average. The AFLP patterns showed that the Spathoglottis species sampled were clearly different.

    Allantoin and amino acid composition in xylem exudates of nodulated and nitrate dependent cowpea plants.
    Wan Othman, W.M. ; Lie, T.A. ; Mannetje, L. 't - \ 1993
    Pertanika journal of tropical agricultural science 16 (1993)1. - p. 53 - 63.
    Low level phosphorus supply affecting nodulation, N2 fixation and growth of cowpea (Vigna anguiculata L. Walp).
    Wan Othman, W.M. ; Lie, T.A. ; Mannetje, L. 't; Wassink, G.Y. - \ 1991
    Plant and Soil 135 (1991). - ISSN 0032-079X - p. 67 - 74.
    Physiological aspects of biological nitrogen fixation: Actual and potential nitrogen fixation.
    Mil, M. van; Lie, T.A. - \ 1988
    In: Proc. UNESCO Symp. Biotechnology of nitrogen fixation in the tropics, Z.H. Shamsuddin, W.M.W. Othman, M. Marzia, J. Sundram (eds.). Univ. Pertanian Malaysia, Kuala Lumpur - p. 171 - 176.
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