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.

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Side by Side Comparison of Chemical Compounds Generated by Aqueous Pretreatments of Maize Stover, Miscanthus and Sugarcane Bagasse
Gomez, L.D. ; Vanholme, R. ; Bird, S. ; Goeminne, G. ; Trindade, L.M. ; Polikarpov, I. ; Simister, R. ; Morreel, K. ; Boerjan, W. ; McQueen-Mason, S.J. - \ 2014
Bio Energy Research 7 (2014)4. - ISSN 1939-1234 - p. 1466 - 1480.
cell-walls - bioethanol production - ferulic acid - wheat-straw - energy crop - lignin - saccharification - ethanol - delignification - technologies
In order to examine the potential for coproduct generation, we have characterised chemical compounds released by a range of alkaline and acidic aqueous pretreatments as well as the effect of these pretreatments on the saccharification ability of the lignocellulosic material. Comparative experiments were performed using three biomass types chosen for their potential as second-generation biofuel feedstocks: maize stover, miscanthus and sugarcane bagasse. The release of lignin from the feedstock correlated with the residual biomass saccharification potential, which was consistently higher after alkaline pretreament for all three feedstock types. Alkaline pretreatment released more complex mixtures of pentose and hexose sugars into the pretreatment liquor than did acid pretreatment. In addition, complex mixtures of aromatic and aliphatic compounds were released into pretreatment liquors under alkaline conditions, in a temperature-dependent manner, but far less so under acidic conditions. We show that the three feedstocks characterised interact with the pretreatment conditions in a specific manner to generate different ranges of products, highlighting the need to tailor pretreatments to both the starting feedstock and desired outcomes.
Using management information in broiler supply chains
Yassin, H. - \ 2012
Wageningen University. Promotor(en): Alfons Oude Lansink, co-promotor(en): Annet Velthuis; M. Boerjan. - S.l. : s.n. - ISBN 9789461732996 - 142
vleeskuikenproductie - vleeskuikens - bedrijfsinformatiesystemen - ketenmanagement - broiler production - broilers - management information systems - supply chain management

The Dutch broiler supply chain involves several interdependent firms such as breeding and feed companies, rearing farms, breeder farms, broiler hatcheries and broiler farms. To stay competitive and sustain continuity, evaluation of production at each level of the chain is crucial. Good quality data and the use of management information systems (MIS) can facilitate this process. Firms in the Dutch broiler supply chain collect data as a routine practice. However, the data are not often analysed and not fully used to support management decisions. The focus of this thesis is on the broiler breeder farms, because eggs are the origin of broiler production. Thus, improving the management at broiler breeder farms could contribute to the improvement of the performance of subsequent firms and the whole supply chain. The objective of this research is, therefore, to develop MIS based on available data in the broiler supply chain to support management decisions at breeder farms. The thesis is composed of three parts.
In the first part, management factors at breeder farms that are related to the performance indicators at the subsequent levels of the broiler production chain are explored. For this, field data from three Dutch hatcheries of 2004, 2005 and 2006 were analysed. Hatchability and first week mortality (FWM) of chicks are considered as performance indicators as these are related to the performance at the breeder farms, hatcheries and broiler farms. A significant difference in hatchability and FWM among eggs from different breeder flocks was found. Furthermore FWM differ significantly between broiler farms. Hatchability and FWM are significantly related with breeder flock age, egg storage length, strain, feed company of the breeder farm, season, year, as well as hatchery. It is concluded that breeder farm management factors are related to the performance in the subsequent levels of the chain next to hatchery and broiler farm factors.
In the second part of this thesis, the availability and quality of data in the Dutch broiler supply chain was assessed. The data quality of the hatchery dataset (from part one) was assessed based on the intuitive approach whereby the quality attitudes are selected by the researcher intuitively. Results showed that the datasets had some fields with inaccurate, incorrect, inconsistent, non-uniform, incomprehensible, and/or incomplete data. In addition, a protocol was proposed and validated for standardization of data to improve the quality of data in the chain.
In the third part of this thesis, two management information systems were developed aiming to support decisions at broiler breeder farms. The first management information system evaluates the tactical management at broiler breeder farms using individual farm analysis combined with a deterministic simulation model (IFAS). With IFAS, the performance of a breeder farm is compared with an average of similar farms or other standards, and relevant deviations are determined based on economic and statistical importance. According to the relevance of the identified deviations the strong and weak management practices are indicated. The second management information system determines the economic optimal replacement age of the broiler breeder flock using the marginal net revenue approach. A well informed replacement decision for breeder flocks improves profitability, not only at the breeder farms but also at hatcheries and broiler farms.

Standardized data in the broiler value chain
Yassin, H. ; Velthuis, A.G.J. ; Boerjan, M. ; Lourens, A. ; Oude Lansink, A.G.J.M. - \ 2011
Poultry Science 90 (2011)2. - ISSN 0032-5791 - p. 498 - 506.
information-systems - chick quality - hatching eggs - hatchability - breeders - performance - incubation - mortality - storage - weight
In the Dutch broiler chain, data are collected as a routine practice. However, there is wide variation in the content of data collected and in data collection systems. This variability hampers the use of field data in management information systems to support decisions. The objective of this study was to analyze the quality of data and to standardize the content of data sets in the broiler production chain. To evaluate the quality of data, data sets from 3 Dutch hatcheries, from 23,637 batches of eggs, were assessed. The quality of data was assessed intuitively based on 7 quality attributes. To standardize the content of the data set, a protocol was proposed and validated. The protocol was validated at 30 breeder farms, 3 hatcheries, and 104 broiler farms by using 3 quality attributes: consistency, uniformity, and completeness. Results of the data quality analysis of the 3 Dutch hatcheries showed that the data sets had some fields with inaccurate, incorrect, inconsistent, nonuniform, incomprehensible, missing relevant, or incomplete data. Results of the validation protocol were as follows: feedback was obtained from 23 (77%) breeder farms, 3 (100%) hatcheries, and 7 (7%) broiler farms. Of all the questions, on average 88% were answered on breeder farms; 57, 65, and 82% were answered at each of the 3 hatcheries, respectively; and 79% were answered on the broiler farms. Data collected at 2 hatcheries were more consistent than those collected at the third hatchery. Hatchery data were less consistent than breeder farm data, but the number of data entries at hatcheries far exceeded the number at the farm level. Data from the hatcheries, breeder farms, and broiler farms were not always uniform, possibly because of differences in management strategies. This protocol enables the listing of relevant and standard contents of a data set whereby information exchange along the chain can be simplified. However, it is recommended that the protocol be supplemented with some rules for data collection and management, for example, that variables must be recorded in the provided fields, and that a variable must have one and only one name or code, the same unit of measurement, and the same definition
Management information system for the Dutch broiler breeder farms: individual farm analysis
Yassin, H. ; Velthuis, A.G.J. ; Boerjan, M. ; Giesen, G.W.J. ; Oude Lansink, A.G.J.M. - \ 2010
In: Proceedings of the International Workshop Farm Animal Health Economics, Nantes, France, 14-15 January 2010. - Nantes, France : INRA - p. 73 - 77.
Management information system for the Dutch broiler breeder farms: individual farm analysis
Yassin, H. ; Velthuis, A.G.J. ; Giesen, G.W.J. ; Oude Lansink, A.G.J.M. ; Boerjan, M. - \ 2010
Structural elucidation of cell wall polysaccharides from Okra (Abelmoschus esculentus (L.) Moench)
Schols, H.A. ; Vanholme, R. ; Storme, V. ; Boerjan, W. - \ 2010
Een goed ei heet broedei
Yassin, H. ; Boerjan, M. ; Velthuis, A.G.J. - \ 2010
De Pluimveehouderij 6/7 (2010)40. - ISSN 0166-8250 - p. 31 - 31.
pluimveehouderij - pluimvee - eieren - voedselkwaliteit - poultry farming - poultry - eggs - food quality
Een goede eikwaliteit bij aankomst op de boerderij is de basis voor een goed resultaat in de keten. Een enquête heeft inzicht gegeven in het eimanagement in de vermeerdering.
Orde in de cijferbrij
Yassin, H. ; Velthuis, A.G.J. ; Boerjan, M. - \ 2010
De Pluimveehouderij 40 (2010)3. - ISSN 0166-8250 - p. 30 - 31.
pluimveehouderij - pluimvee - agrarische bedrijfsvoering - bedrijfseconomie - poultry farming - poultry - farm management - business economics
Vermeerderingsbedrijven verzamelen veel productiegegevens, blijkt uit een enquête van Wageningen Universiteit, maar elk op zijn eigen wijze. Dat belemmert het ketenmanagement
Field study on broilers' first-week mortality
Yassin, H. ; Velthuis, A.G.J. ; Boerjan, M. ; Rielt, J. van - \ 2009
Poultry Science 88 (2009). - ISSN 0032-5791 - p. 798 - 804.
day-old chick - live performance - egg storage - dietary-fat - breeder age - flock age - hatchability - incubation - nutrition - quality
In the Dutch poultry meat production chain, first week mortality (FWM) of the chicks is an important measure to quality and is therefore highly related to the price of the chicks that the broiler farm has to pay to the hatchery. Therefore, next to the total number of broiler eggs produced per hen and hatchability, this figure is often used as a measure of efficiency in the breeder-hatchery-broiler production chain. In this study, factors that are related to chick mortality in the first week at broiler farms were investigated. Field data obtained from 2 commercial Dutch hatcheries, for which 482 broiler farms voluntarily recorded FWM of 16,365 flocks of broiler chicks over the years 2004, 2005, and 2006, were analyzed. These represented 79% of the total number of day-old chicks delivered to separate broiler farms. First week mortality was significantly related to breeder age, egg storage length at the hatchery, season, strain, feed company of the breeder farm, year, and hatchery. Furthermore, FWM differed significantly between chicks originating from eggs of different breeder flocks and which were kept for grow-out at different broiler farms
Field study on broiler eggs hatchability
Yassin, H. ; Velthuis, A.G.J. ; Boerjan, M. ; Riel, J.W. van; Huirne, R.B.M. - \ 2008
Poultry Science 87 (2008). - ISSN 0032-5791 - p. 2408 - 2417.
flock age - chick quality - hatching eggs - breeder age - incubation-temperature - storage time - laying hens - weight - growth - model
The aim of this research was to explore factors that are related with hatchability in the field. Data from 3 Dutch hatcheries for the years 2004, 2005, and 2006 were analyzed using a random regression model with the method of restricted maximum likelihood. In total, 24,234 batches of 724,750,444 eggs, originating from 511 breeder flocks, were included. Annually, 241,583,481 eggs were set on average, which is 37% of the total annual eggs set in the Netherlands. A significant difference in hatchability among eggs from different breeder flocks was found. Hatchability was significantly related with flock age, egg storage length, strain, feed company, season, year, as well as hatchery (P <0.001). There was also significant interaction between flock age and age at first delivery, egg storage length at hatchery, strain, feed company, and season. Other 3-way interaction terms were also significant. The variation in hatchability was larger among the breeder farms than within breeder farms. The average estimated difference in hatchability among the hatcheries was 8%. The average estimated hatchability at 25 wk of age was 66%; it increased to 86% between 31 and 36 wk and decreased to 50% at 65 wk of age. On average, an extra day of storage until d 7 reduced hatchability by 0.2% and from d 7 to 14 by 0.5%. Eggs from older flocks were less sensitive to prolonged storage, whereas they were more sensitive to season. Hatchability was greater during late summer than during spring. The average estimated differences in hatchability among strains and feed companies of the breeder farms were 8 and 2%, respectively. Based on the relations found, optimization of hatchery results depends not only on good management at the hatchery but also on the hatching egg quality and therefore on the breeder farm management. It can be concluded that production data that are collected by the hatcheries can be used to adjust the management decisions at hatcheries as well as breeder farms
A field study on broiler hatchability: which factors are related to hatchability
Yassin, H. ; Velthuis, A.G.J. ; Boerjan, M. ; Huirne, R.B.M. - \ 2008
In: XXIII World's Poultry Congress 2008, Brisbane, Qld., Australia, 30 June-4 July 2008. - Brisbane : - p. 176 - 176.
A field study on first week chick mortality: which factors are related?
Yassin, H. ; Velthuis, A.G.J. ; Boerjan, M. ; Huirne, R.B.M. - \ 2008
In: XXIII World's poultry congress 2008, Brisbane, Qld., Australia, 30 June-4 July 2008. - Brisbane : - p. 235 - 235.
The relationship between chick characteristics, broiler welfare and growth
Jong, I.C. de; Fillerup, M. ; Riedstra, B. ; Boerjan, M.L. ; Hopster, H. - \ 2008
pluimveehouderij - kippen - dierenwelzijn - huisvesting van kippen - broedplaatsen - vleeskuikens - poultry farming - fowls - animal welfare - chicken housing - breeding places - broilers
In hatchery management, one-day-old chick quality is related to breeding and hatching conditions. However, it is likely that one-day-old chick quality is also related to broiler welfare and growth. Therefore, the authors studied if day-old chicks of optimal quality differ from day-old chicks of suboptimal quality in welfare aspects (behaviour, walking ability) and production aspects (growth) between 1-8 and 35-42 days of age
Structure of the genetic diversity in Black poplar (Populus nigra L.) populations across European river systems: consequences for conservation and restoration
Smulders, M.J.M. ; Cottrell, J.E. ; Lefevre, F. ; Schoot, J. van der; Arens, P.F.P. ; Vosman, B. ; Tabbener, H.E. ; Grassi, F. ; Fossati, T. ; Castiglione, S. ; Krystufek, V. ; Fluch, S. ; Burg, K. ; Vornam, B. ; Pohl, A. ; Gebhardt, K. ; Alba, N. ; Agúndez, D. ; Maestro, C. ; Notivol, E. ; Volosyanchuck, R. ; Pospiskova, M. ; Bordacs, S. ; Bovenschen, J. ; Dam, B.C. van; Koelewijn, H.P. ; Halfmaerten, D. ; Ivens, B. ; Slycken, J. Van; Vanden Broeck, A. ; Storme, V. ; Boerjan, W. - \ 2008
Forest Ecology and Management 255 (2008)5-6. - ISSN 0378-1127 - p. 1388 - 1399.
fragment length polymorphism - microsatellite markers - natural-populations - aflp markers - linkage maps - dispersal - stands - reproduction - tremuloides - salicaceae
Black poplar (Populus nigra L.) is a keystone species for riparian ecosystems in Europe. We analysed the structure of genetic diversity of 17 populations from 11 river valleys that are part of seven catchment systems (Danube, Ebro, Elbe, Po, Rhine, Rhone, and Usk) in Europe, in relation to geography and river management. In total, 1069 trees were genotyped using AFLP and microsatellite markers. The trees had an observed heterozygosity of 0.74 (range 0.59¿0.82 across microsatellite loci). The majority (72.6¿90.8%, depending on the marker system) of the genetic variation was present within populations. Most pairs of populations along a river were relatively similar (pairwise Fst 0.042¿0.135 based on AFLP, 0.002¿0.037 based on microsatellites). Overall population differentiation among rivers was considerable (Fst among populations was 0.268 based on AFLP, and 0.081 based on microsatellites). An analysis using the program Structure indicated that all populations recruited plants from several clusters. Geographically close populations tended to draw from the same Structure clusters, including populations from adjacent catchments. The Danube and Inn populations in Austria were genetically more similar to the Vltava population (Elbe catchment) in Czech Republic than the geographically more distant populations along the Tisa and Prut rivers of the Danube catchment in Ukraine. This indicates that gene flow and dispersal takes place across fairly large distances and between river catchments. Consistent with this result, a principal coordinate analysis of genetic distances among individual trees based on AFLP bands showed large overlap of populations, although the French and Spanish samples formed distinct clusters, and the samples from the Ticino (Italy) were at an intermediate position. The extent of clonal duplication was highest along regulated rivers, with e.g., 41% clonal duplication along the Rhine in The Netherlands (up to 32 trees for one genet). The Usk contained a man-made population (two genotypes along the entire river, one genet present as 70 trees out of 72 trees sampled). No clonal duplication was found along dynamic rivers, such as the Ebro (Spain), the Drome (France), and the Tisa and Prut (Ukraine).
Erratum: Postglacial migration of Populus nigra L.: Lessons learnt from chloroplast DNA
Cottrell, J.E. ; Krystufek, V. ; Tabbener, H.E. ; Milner, A.D. ; Connolly, T. ; Sing, L. ; Fluch, S. ; Burg, K. ; Lefèvre, F. ; Achard, P. ; Bordács, S. ; Gebhardt, K. ; Vornam, B. ; Smulders, M.J.M. ; Vanden Broeck, A.H. ; Slycken, J. Van; Storme, V. ; Boerjan, W. ; Castiglione, S. ; Fossati, T. ; Alba, N. ; Agúndez, D. ; Maestro, C. ; Notivol, E. ; Bovenschen, J. ; Dam, B.C. van - \ 2005
Forest Ecology and Management 219 (2005)2-3. - ISSN 0378-1127 - p. 292 - 312.
Eleven laboratories have collaborated to study chloroplast DNA (cpDNA) variation in black poplar (Populus nigra L.) across Europe in order to improve our understanding of the location of glacial refugia and the subsequent postglacial routes of recolonisation. A common analysis based on the restricted fragments produced by five primer pairs was used to determine the cpDNA haplotype of 637 samples obtained from genebank collections established in nine European countries. Haplotype 2 was particularly common and was found in 46% of the non-hybrid samples. A total of 81 non-hybrid chloroplast variants were detected. Three haplotypes (from four trees believed to originate from Eastern Europe) clustered together and were very different from the rest of the samples. The remaining samples were divided into two groups, one of which had a largely eastern distribution and samples from the other group were mostly located in the west. This, along with the fact that Spain in the southwest and Austria and Italy in the southeast had high diversity, suggest that there were ice age refugia of black poplar in both southwestern (Spain) and southeastern Europe (Italy and/or Balkan). Results also indicate that the Pyrenees formed a significant
barrier, since only 7 of the 45 haplotypes in Spain exist elsewhere in Europe
Postglacial migration of Populus nigra L.: lessons learnt from chloroplast DNA
Cottrell, J.E. ; Krystufek, V. ; Tabbener, H.E. ; Milner, A.D. ; Connolly, T. ; Sing, L. ; Fluch, S. ; Burg, K. ; Lefèvre, F. ; Achard, P. ; Bordács, S. ; Gebhardt, K. ; Vornam, B. ; Smulders, M.J.M. ; Vanden Broeck, A.H. ; Slycken, J. Van; Storme, V. ; Boerjan, W. ; Castiglione, S. ; Fossati, T. ; Alba, N. ; Agúndez, D. ; Maestro, C. ; Notivol, E. ; Bovenschen, J. ; Dam, B.C. van - \ 2005
Forest Ecology and Management 206 (2005)1-3. - ISSN 0378-1127 - p. 71 - 90.
european white oaks - genetic-variation - colonization routes - noncoding regions - universal primers - x-canadensis - phylogeography - polymorphisms - deltoides - diversity
Eleven laboratories have collaborated to study chloroplast DNA (cpDNA) variation in black poplar (Populus nigra L.) across Europe in order to improve our understanding of the location of glacial refugia and the subsequent postglacial routes of recolonisation. A common analysis based on the restricted fragments produced by five primer pairs was used to determine the cpDNA haplotype of 637 samples obtained from genebank collections established in nine European countries. Haplotype 2 was particularly common and was found in 46% of the non-hybrid samples. A total of 81 non-hybrid chloroplast variants were detected. Three haplotypes (from four trees believed to originate from Eastern Europe) clustered together and were very different from the rest of the samples. The remaining samples were divided into two groups, one of which had a largely eastern distribution and samples from the other group were mostly located in the west. This, along with the fact that Spain in the southwest and Austria and Italy in the southeast had high diversity, suggest that there were ice age refugia of black poplar in both southwestern (Spain) and southeastern Europe (Italy and/or Balkan). Results also indicate that the Pyrenees formed a significant barrier, since only 7 of the 45 haplotypes in Spain exist elsewhere in Europe
The relationship between chick characteristics, broiler welfare and growth
Jong, I.C. de; Wolthuis-Fillerup, M. ; Riedstra, B. ; Boerjan, M.L. ; Hopster, H. - \ 2004
In: Proceedings of the 38th International Congress of the ISAE, Helsinki, Finland, 3-7 August 2004 / Hanninen, M., Valros, A., - p. 222 - 222.
Ex-situ conservation of black poplar in Europe: genetic diversity in nine gene bank collections and their value for nature development
Storme, V. ; Vanden Broeck, A. ; Ivens, B. ; Halfmaerten, D. ; Slycken, J. Van; Castiglione, S. ; Grassi, F. ; Fossati, T. ; Cottrell, J.E. ; Tabbener, H.E. ; Lefèvre, F. ; Saintagne, C. ; Fluch, S. ; Krystufek, V. ; Burg, K. ; Bordács, S. ; Borovics, A. ; Gebhardt, K. ; Vornam, B. ; Pohl, A. ; Alba, N. ; Agúndez, D. ; Maestro, C. ; Notivol, E. ; Bovenschen, J. ; Dam, B.C. van; Schoot, J. van der; Vosman, B.J. ; Boerjan, W. ; Smulders, M.J.M. - \ 2004
Theoretical and Applied Genetics 108 (2004)6. - ISSN 0040-5752 - p. 969 - 981.
populus-nigra l. - microsatellite markers - eukaryotic genomes - dna - construction - varieties - database - polymorphisms - deltoides - cultivars
Populus nigra L. is a pioneer tree species of riparian ecosystems that is threatened with extinction because of the loss of its natural habitat. To evaluate the existing genetic diversity of P. nigra within ex-situ collections, we analyzed 675 P. nigra L. accessions from nine European gene banks with three amplified fragment length polymorphism (AFLP) and five microsatellite [or simple sequence repeat (SSR)] primer combinations, and 11 isozyme systems. With isozyme analysis, hybrids could be detected, and only 3% were found in the gene bank collection. AFLP and SSR analyses revealed effectively that 26% of the accessions were duplicated and that the level of clonal duplication varied from 0% in the French gene bank collection up to 78% in the Belgian gene bank collection. SSR analysis was preferred because AFLP was technically more demanding and more prone to scoring errors. To assess the genetic diversity, we grouped material from the gene banks according to topography of the location from which the accessions were originally collected (river system or regions separated by mountains). Genetic diversity was expressed in terms of the following parameters: percentage of polymorphic loci, observed and effective number of alleles, and Neis expected heterozygosity or gene diversity (for AFLP). Genetic diversity varied from region to region and depended, to some extent, on the marker system used. The most unique alleles were identified in the Danube region (Austria), the Rhône region (France), Italy, the Rijn region (The Netherlands), and the Ebro region (Spain). In general, the diversity was largest in the material collected from the regions in Southern Europe. Dendrograms and principal component analysis resulted in a clustering according to topography. Material from the same river systems, but from different countries, clustered together. The genetic differentiation among the regions (Fst/Gst) was moderate.
The potential reproductive effects of exposure of domestic ruminants to endocrine disrupting compounds
Boerjan, M.L. ; Freijnagel, S. ; Rhind, S.M. ; Meijer, G.A.L. - \ 2002
Animal Science 74 (2002)1. - ISSN 1357-7298 - p. 3 - 12.
Ex-situ conservation black poplar in Belgium, the margin of the geographical distribution area of the species
Storme, V. ; Vanden Broeck, A. ; Ivens, B. ; Smulders, M.J.M. ; Halfmaerten, D. ; Slycken, J. van; Boerjan, W. - \ 2002
In: Genetic diversity in river populations of European black poplar : implications for riparian eco-system management : proceedings of an international symposium held in Szekszárd, Hungary from 16-20-May, 2001 / van Dam, B.C., Bordács, S., Budapest : Nyomda - p. 61 - 72.
Ex-situ - Belgium
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