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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Monitoring mosselgroei Flakkeese spuisluis : resultaten T1 bemonstering 2017
Wijsman, Jeroen ; Gool, Ad van; Pool, Jesse van der - \ 2017
Yerseke : Wageningen Marine Research (Wageningen Marine Research rapport C106/17) - 30
Schelpdierwateronderzoek 2016
Kotterman, M. ; Gool, A.C.M. van; Poelman, M. - \ 2017
Yerseke : Wageningen Marine Research (Wageningen Marine Research rapport C072/17) - 34
Taking multi-morbidity into account when attributing DALYs to risk factors : comparing dynamic modeling with the GBD2010 calculation method
Boshuizen, Hendriek C. ; Nusselder, Wilma J. ; Plasmans, Marjanne H.D. ; Hilderink, Henk H. ; Snijders, Bianca E.P. ; Poos, René ; Gool, Coen H. van - \ 2017
BMC Public Health 17 (2017). - ISSN 1471-2458
Comorbidity - Disability weights - Incidence - Multi-morbidity - Prevalence - Risk factor attribution

Background: Disability Adjusted Life Years (DALYs) quantify the loss of healthy years of life due to dying prematurely and due to living with diseases and injuries. Current methods of attributing DALYs to underlying risk factors fall short on two main points. First, risk factor attribution methods often unjustly apply incidence-based population attributable fractions (PAFs) to prevalence-based data. Second, it mixes two conceptually distinct approaches targeting different goals, namely an attribution method aiming to attribute uniquely to a single cause, and an elimination method aiming to describe a counterfactual situation without exposure. In this paper we describe dynamic modeling as an alternative, completely counterfactual approach and compare this to the approach used in the Global Burden of Disease 2010 study (GBD2010). Methods: Using data on smoking in the Netherlands in 2011, we demonstrate how an alternative method of risk factor attribution using a pure counterfactual approach results in different estimates for DALYs. This alternative method is carried out using the dynamic multistate disease table model DYNAMO-HIA. We investigate the differences between our alternative method and the method used by the GBD2010 by doing additional analyses using data from a synthetic population in steady state. Results: We observed important differences between the outcomes of the two methods: in an artificial situation where dynamics play a limited role, DALYs are a third lower as compared to those calculated with the GBD2010 method (398,000 versus 607,000 DALYs). The most important factor is newly occurring morbidity in life years gained that is ignored in the GBD2010 approach. Age-dependent relative risks and exposures lead to additional differences between methods as they distort the results of prevalence-based DALY calculations, but the direction and magnitude of the distortions depend on the particular situation. Conclusions: We argue that the GBD2010 approach is a hybrid of an attributional and counterfactual approach, making the end result hard to understand, while dynamic modelling uses a purely counterfactual approach and thus yields better interpretable results.

Monitoring mosselgroei Flakkeese spuisluis : resultaten T0 bemonstering 2016
Wijsman, J.W.M. ; Brummelhuis, E. ; Gool, A.C.M. van - \ 2016
Yerseke : Wageningen Marine Research (Wageningen Marine Research rapport C126/16) - 33
mossels - mosselteelt - groei - monitoring - zuid-holland - mussels - mussel culture - growth
In de winter van 2016/2017 zal de Flakkeese spuisluis in de Grevelingendam weer in gebruik worden genomen. De spuisluis, bestaande uit een hevel, vormt een verbinding tussen het Grevelingenmeer en de Oosterschelde. Door het openen van de hevel zal als gevolg van het getij op de Oosterschelde water heen en weer worden getransporteerd tussen de Oosterschelde en het Grevelingenmeer. De verwachting is dat door de toename in waterbeweging de waterkwaliteit in het Grevelingenmeer zal verbeteren, met name nabij de bodem waar zuurstofloosheid optreedt. Om deze veranderingen te kunnen monitoren zijn er mosselen uitgezet in speciale mandjes op twee locaties in het Grevelingenmeer en twee locaties in de Oosterschelde. De groei en ontwikkeling van de mosselen kan worden gebruikt als een indicator voor de waterkwaliteit en -productiviteit. Doordat de mosselen gedurende een periode van enkele maanden zijn uitgezet, zijn de groeimetingen de resultante van de waterkwaliteit over die hele periode. Ook zijn in het Grevelingenmeer continue-metingen verricht voor zuurstofconcentratie (alleen bij de bodem) en temperatuur (nabij de bodem en het wateroppervlak). Dit rapport beschrijft de situatie in 2016 vóór de ingebruikname van de hevel.
Accounting for multimorbidity can affect the estimation of the Burden of Disease : A comparison of approaches
Hilderink, Henk B.M. ; Plasmans, Marjanne H.D. ; Snijders, Bianca E.P. ; Boshuizen, Hendriek C. ; René Poos, M.J.J.C. ; Gool, Coen H. van - \ 2016
Archives of Public Health 74 (2016). - ISSN 0778-7367 - 16 p.
Disability weights - Disease burden - Multimorbidity - Prevalence

Background: Various Burden of Disease (BoD) studies do not account for multimorbidity in their BoD estimates. Ignoring multimorbidity can lead to inaccuracies in BoD estimations, particularly in ageing populations that include large proportions of persons with two or more health conditions. The objective of this study is to improve BoD estimates for the Netherlands by accounting for multimorbidity. For this purpose, we analyzed different methods for 1) estimating the prevalence of multimorbidity and 2) deriving Disability Weights (DWs) for multimorbidity by using existing data on single health conditions. Methods: We included 25 health conditions from the Dutch Burden of Disease study that have a high rate of prevalence and that make a large contribution to the total number of Years Lived with a Disability (YLD). First, we analyzed four methods for estimating the prevalence of multimorbid conditions (i.e. independent, independent age-and sex-specific, dependent, and dependent sex-and age-specific). Secondly, we analyzed three methods for calculating the Combined Disability Weights (CDWs) associated with multimorbid conditions (i.e. additive, multiplicative and maximum limit). A combination of these two approaches was used to recalculate the number of YLDs, which is a component of the Disability-Adjusted Life Years (DALY). Results: This study shows that the YLD estimates for 25 health conditions calculated using the multiplicative method for Combined Disability Weights are 5 % lower, and 14 % lower when using the maximum limit method, than when calculated using the additive method. Adjusting for sex-and age-specific dependent co-occurrence of health conditions reduces the number of YLDs by 10 % for the multiplicative method and by 26 % for the maximum limit method. The adjustment is higher for health conditions with a higher prevalence in old age, like heart failure (up to 43 %) and coronary heart diseases (up to 33 %). Health conditions with a high prevalence in middle age, such as anxiety disorders, have a moderate adjustment (up to 13 %). Conclusions: We conclude that BoD calculations that do not account for multimorbidity can result in an overestimation of the actual BoD. This may affect public health policy strategies that focus on single health conditions if the underlying cost-effectiveness analysis overestimates the intended effects. The methodology used in this study could be further refined to provide greater insight into co-occurrence and the possible consequences of multimorbid conditions in terms of disability for particular combinations of health conditions.

Innovatieve reproductie Europese aal : VIP report
Palstra, A.P. ; Graziano, Marco ; Mes, Daan ; Heide, M. van der; Böhm, Thijs ; Blom, E. ; Hofman, A.R.T. ; Es, Y. van; Gool, A.C.M. van; Brummelhuis, E.B.M. - \ 2016
IMARES Wageningen UR (IMARES report C061/16) - 35 p.
Op het grensvlak van chemie en biotechnologie (interview met Harry Bitter)
Gool, J. van; Bitter, J.H. - \ 2015
Petrochem 2015 (2015)6. - ISSN 1380-6386 - p. 8 - 9.
Harry Bitter, sinds twee jaar hoogleraar Biobased Chemistry & Technology aan de Wageningen Universiteit, pleit voor meer chemie en katalyse in het onderzoek naar biobased producten. ‘Mijn onderzoeksfocus ligt op hoe je de omzettingen van biomassa naar product zo optimaal mogelijk kunt uitvoeren. Voor mij zijn de reacties een vehikel om nieuwe, betere katalysatoren te ontwikkelen.’
Interreg Safeguard - Food safety mapping of mussels and oysters (Crassostrea gigas) in the Dutch Wadden Sea
Glorius, S.T. ; Poelman, M. ; Zweeden, C. van; Gool, A.C.M. van - \ 2014
Den Helder : IMARES (Report / IMARES Wageningen UR C0104/14) - 71
waddenzee - oesters - crassostrea gigas - besmetting - pathogenen - verontreiniging - voedselveiligheid - mossels - voedselbesmetting - wadden sea - oysters - contamination - pathogens - pollution - food safety - mussels - food contamination
The areal coverage and biomass of the invasive Pacific oyster has increased in both the Dutch and German part of the Wadden Sea area since its introduction in the late seventies. In the Dutch part of the Wadden Sea oyster beds have increased in areal coverage in the period 2003 –2008. The Pacific oyster has relevance for commercial exploitation since 2009. This arises special interest for food safety aspects. A joint monitor program named ‘Interreg Safeguard’ has been set up with German partners to firstly identify oyster bed location and subsequently obtain insight in the temporal and areal variation in both the level of chemical contamination as well as contamination with pathogens. Measured levels were compared with legislation standards currently in force and it was also researched what the relation of pollution levels found in oysters were with those found in mussels collected in the near vicinity. This report describes the results of the work carried within the Dutch part of the Wadden Sea and include; results of the mapping effort of oyster beds, concentrations of chemical and microbiological parameters in oyster and mussel tissue and the comparison of the contaminant levels found in oyster with those found in mussels.
Schelpdierwateronderzoek 2013
Poelman, M. ; Hoek-van Nieuwenhuizen, M. van; Gool, A.C.M. van - \ 2014
Yerseke : IMARES (Rapport / IMARES Wageningen UR C091/14) - 33
schaaldieren - schaal- en schelpdierenvisserij - waterverontreiniging - westerschelde - oosterschelde - noordzee - waddenzee - monitoring - voordelta - shellfish - shellfish fisheries - water pollution - western scheldt - eastern scheldt - north sea - wadden sea
In november en december 2013 is onderzoek verricht naar de schelpdierwaterkwaliteit in de Nederlandse kustwatergebieden. Doel hiervan is het vaststellen van de gehalten aan fecale coliformen, E. coli (aanvullend), zware metalen en gehalogeneerde organische stoffen in schelpdiervlees. Daarnaast zijn zintuiglijke waarnemingen op het schelpdiervlees en veldmetingen voor de verschillende parameters in het oppervlaktewater uitgevoerd. De monitoringdata is getoetst aan de bestaande normen. De monitoring heeft plaatsgevonden op 12 locaties in gebieden waar schelpdierproductie/visserij voorkomt, namelijk de Westerschelde, Grevelingen, Oosterschelde, Voordelta en de Waddenzee.
MZI - mosselgewicht als indicator van voedselomstandigheden
Kamermans, P. ; Brummelhuis, E.B.M. ; Gool, A.C.M. van - \ 2014
Yerseke : IMARES (Rapport / IMARES Wageningen UR C190/13) - 19
schaal- en schelpdierenteelt - mosselteelt - aquatische biomassa - voedselbeperking - effecten - monitoring - shellfish culture - mussel culture - aquatic biomass - food restriction - effects
MZI-activiteiten hebben tot gevolg dat de Waddenzee en Oosterschelde meer biomassa aan mosselen zal gaan bevatten. Dit kan bij opschaling effect hebben op de voedselomstandigheden en dus draagkracht voor schelpdieren. Dat er geen negatieve effecten zullen optreden kan alleen aangetoond worden als er ook gericht gemeten wordt in de betreffende natuurgebieden. Daarom is onderzoek gedaan naar het gebruik van impact-indicatoren die iets kunnen zeggen over de huidige toestand van de draagkracht en die kunnen worden opgenomen in een monitoringsprogramma.
Dynamic-HIA-2: a tool to calculate the complete counterfactual disability-adjusted life-years (DALYs) of risk factor exposure
Boshuizen, H.C. ; Gool, C.H. ; Nusselder, W.J. - \ 2013
The Lancet 381 (2013)Suppl.2. - ISSN 0140-6736 - p. S21 - S21.
Background Many risk factors, such as smoking, affect multiple diseases. Calculating a disability-adjusted life-year (DALY) for such risk factors should take comorbidity into account. We aim to provide a tool for such calculations, using a counterfactual approach. Methods We defined a DALY in the original terms as a metric “to quantify loss of healthy years of life due to dying prematurely or to living with the health consequences of diseases, injuries or risk factors”, rather than use its operational form (the sum of healthy years lost through mortality and through disease). As a DALY reflects the effect of risk factor exposure in a particular year only, we calculate this by comparing future population health in the current situation and in the situation where the risk factor is absent in the particular year but returns to the value it would have had in the current situation after 1 year. We derived disability weights for comorbidity by multiplying (1 — disability weight) of the separate diseases. We also included disability weights greater than 0 for those without risk-factor-related disease, reflecting disability from all other diseases. We incorporated the calculation in the DYNAMO-HIA-2 programme, which implements a risk factor—disease Markov model. This reduces the computational burden on the user from entering the data. Findings Our method delivers a lower DALY than the WHO burden of disease approach, as the latter assumes that the years gained by elimination of the risk factor would all have been healthy years, while our method takes into account that part of these years would have been spent with disease. Interpretation The proposed method delivers a straightforward metric in terms of interpretation, fully taking competing mortality, morbidity, and comorbidity into account. However, handling of interaction effects (that is, those spared in one year are at risk in later years) needs further discussion. Funding This research was funded by the National Institute for Public Health and the Environment (RIVM) and partly by the Netherlands Organisation for Health Research and Development. The first version of DYNAMO-HIA was partly funded by the Directorate General for Health and Consumers of the European Commission.
De voedselveiligheid van Japanse oesters en mosselen in de Waddenzee
Poelman, M. ; Glorius, S.T. ; Gool, A.C.M. van; Linden, A. van der - \ 2013
Aquacultuur 28 (2013)2. - ISSN 1382-2764 - p. 10 - 16.
oesters - crassostrea gigas - mossels - mytilidae - voedselveiligheid - volksgezondheid - monitoring - bemonsteren - monsters - waddenzee - oysters - mussels - food safety - public health - sampling - samples - wadden sea
De laatste decennia is het areaal aan Japanse oesters in de Duitse en Nederlandse Waddenzee toegenomen. Dit leidt tot een zekere mate van concurrentie in ruimte en voedsel tussen onder andere mosselen en oesters. Naast de ecologische effecten zijn er ook directe economische effecten, er wordt inmiddels al dankbaar gebruik gemaakt door bedrijfsmatig oester in de Waddenzee te rapen. Over de voedselveiligheid van deze oesters in het Wad is nog niet veel bekend, reden dus om een monitoring uit te voeren op oesters en als vergelijking mosselen. Dit alles om beter zicht te hebben op de voedselveiligheid van Waddenzee oesters.
Distinct roles of carbohydrate esterase family CE16 acetyl esterases and polymer-acting acetyl xylan esterases in xylan deacetylation
Koutaniemi, S. ; Gool, M.P. van; Juvonen, M. ; Hinz, S.W.A. ; Schols, H.A. ; Tenkanen, M. - \ 2013
Journal of Biotechnology 168 (2013)4. - ISSN 0168-1656 - p. 684 - 692.
eucalyptus-globulus labill - trichoderma-reesei - alpha-glucuronidase - schizophyllum-commune - catalytic-properties - purification - aspen - mode - wood
Mass spectrometric analysis was used to compare the roles of two acetyl esterases (AE, carbohydrate esterase family CE16) and three acetyl xylan esterases (AXE, families CE1 and CE5) in deacetylation of natural substrates, neutral (linear) and 4-O-methyl glucuronic acid (MeGlcA) substituted xylooligosaccharides (XOS). AEs were similarly restricted in their action and apparently removed in most cases only one acetyl group from the non-reducing end of XOS, acting as exo-deacetylases. In contrast, AXEs completely deacetylated longer neutral XOS but had difficulties with the shorter ones. Complete deacetylation of neutral XOS was obtained after the combined action of AEs and AXEs. MeGlcA substituents partially restricted the action of both types of esterases and the remaining acidic XOS were mainly substituted with one MeGlcA and one acetyl group, supposedly on the same xylopyranosyl residue. These resisting structures were degraded to great extent only after inclusion of a-glucuronidase, which acted with the esterases in a synergistic manner. When used together with xylan backbone degrading endoxylanase and ß-xylosidase, both AE and AXE enhanced the hydrolysis of complex XOS equally.
Two novel GH11 endo-xylanases from Myceliophthora thermophila C1 act differently toward soluble and insoluble xylans
Gool, M.P. van; Muiswinkel, G.C.J. van; Hinz, S.W.A. ; Schols, H.A. ; Sinitsyn, A.P. ; Gruppen, H. - \ 2013
Enzyme and Microbial Technology 53 (2013)1. - ISSN 0141-0229 - p. 25 - 32.
chrysosporium-lucknowense - families - arabinoxylan - hydrolases
Two novel GH11 endo-xylanases from Myceliophthora thermophila C1 (C1), Xyl7 and Xyl8, were purified and the influence of solubility and molecular structure of various xylans on their efficiency was investigated. Both endo-xylanases were hindered by a high degree of substitution of a xylan. The two GH11 xylanases released different products from the xylans, in which Xyl7 displayed a degradation product composition closer to GH10 xylanases. A correlation of the degradation product composition with a specific residue at position 163 in the amino acid sequence of Xyl8 is suggested: tyrosine in Xyl8; valine in Xyl7. This is confirmed with examples of various endo-xylanases reported in literature. The C1 GH11 xylanases were more efficient on self-associated xylan compared to C1 GH10 endo-xylanases and they released more small xylooligomers from these xylans. This is contrary to the general assumption that GH10 xylanases degrade xylans to a higher degree than GH11 xylanases
Diversity in Production of Xylan-Degrading Enzymes Among Species Belonging to the Trichoderma Section Longibrachiatum
Toth, K. ; Gool, M.P. van; Schols, H.A. ; Samuels, G.J. ; Gruppen, H. ; Szakacs, G. - \ 2013
Bio Energy Research 6 (2013)2. - ISSN 1939-1234 - p. 631 - 643.
wheat-flour arabinoxylan - industrial applications - h-1-nmr spectroscopy - aspergillus-awamori - beta-glucosidase - biofuels - reesei - fermentation - hypocrea - endo-beta-1,4-xylanases
Xylan is an important part of plant biomass and represents a renewable raw material for biorefineries. Contrary to cellulose, the structure of hemicellulose is quite complex. Therefore, the biodegradation of xylan needs the cooperation of many enzymes. For industrial production of xylanase multienzyme complexes (cocktails) and selected monocomponent xylanases, different Trichoderma reesei mutants and recombinants are used. T. reesei QM 6a (wild-type parent of best existing mutants) was selected as a starting material in the 1960s when the modern in-depth analytical methods were not yet in use. Therefore, screening of fungi genetically close to T. reesei in biodegradation of xylan may have a scientific value. Fifteen different strains from Trichoderma section Longibrachiatum have been tested for extracellular xylan-degrading enzyme production on three carbon sources (wheat straw, corn fiber, and eucalyptus wood) in shake flask cultivation. The enzyme activities were evaluated by traditional colorimetric enzyme assays and by HPLC and matrix assisted laser desorption/ionization time-of-flight mass spectrometry. Degradation of xylan was studied on four different xylan-rich model substrates. T. reesei CPK 155, Trichoderma parareesei TUB F-2535, and Trichoderma gracile TUB F-2543 isolates were equally good or better in degradation of the wheat arabinoxylan (WAX) and corn fiber alcohol insoluble solids as hydolysis substrates than the well-known T. reesei QM 6a and RUT C30 strains. Though Trichoderma saturnisporum ATCC 18903 gave relatively low volumetric enzyme activities by traditional colorimetric assays, it could release quite large amount of hydrolysis products (mono- and oligosaccharides) from WAX. Therefore, these fungi may be potential candidates for further experiments. Enzyme production on wheat straw and corn fiber carbon sources was more effective than on eucalyptus wood
Schelpdierwateronderzoek 2012
Poelman, M. ; Hoek-van Nieuwenhuizen, M. van; Gool, A.C.M. van - \ 2013
Yerseke : IMARES (Rapport / IMARES Wageningen UR C065/13) - 36
schaaldieren - schaal- en schelpdierenvisserij - verontreiniging - waterverontreiniging - westerschelde - oosterschelde - noordzee - waddenzee - monitoring - voordelta - shellfish - shellfish fisheries - pollution - water pollution - western scheldt - eastern scheldt - north sea - wadden sea
Rijkswaterstaat heeft IMARES verzocht om de gehalten aan fecale coliformen, E. coli (aanvullend), zware metalen en gehalogeneerde organische stoffen vast te stellen in schelpdiervlees in de productiegebieden. Ook is verzocht zintuiglijke waarnemingen op het schelpdiervlees en veldmetingen voor de verschillende parameters in het oppervlaktewater uit te voeren. IMARES heeft op 12 locaties waar schelpdierproductie/visserij voorkomt, namelijk in de Westerschelde, Grevelingen, Oosterschelde, Voordelta en de Waddenzee deze bepalingen uitgevoerd. Toetsing aan de bestaande normen leert dat de normen niet worden overschreden.
Production of oligosaccharides from extruded wheat and rye biomass using enzymatic treatment
Makaravicius, T. ; Basinskiene, L. ; Juodeikiene, G. ; Gool, M.P. van; Schols, H.A. - \ 2012
Catalysis today 196 (2012)1. - ISSN 0920-5861 - p. 16 - 25.
secale-cereale l. - dietary fiber - nonstarch polysaccharides - extrusion-cooking - physicochemical properties - extractable arabinoxylans - xylo-oligosaccharides - functional-properties - eucalyptus wood - harvest year
Research on prebiotics and other novel healthpromoting food components has been active for over a decade. Arabinoxylan (AX) derived arabinoxylooligosaccharides (AXOS), which may have various chemical structures, depending on the xylan source and the degradation method used, stand increasingly in the spotlight as potential prebiotics. During the past decade, the studies of the possibilities to produce the AXOS by using biocatalytic conversion have received more attention. In addition, there is an interest in the use of novel cereal biomass for the production of AXOS. The aim of this study was to investigate the influence of various commercial enzyme preparations on the degradability of insoluble arabinoxylans in wheat and rye wholemeal treated by extrusion, identify and quantify xylooligosaccharides (XOS) and arabinoxylooligosaccharides (AXOS) in treated media. The enzymatic degradation of rye and wheat cell wall materials was monitored by HPSEC, HPAEC and MALDITOFMS techniques. It was noticed that there is no significant difference between extruded and natural cereals, and type of cereals had not significant influence on XOS and AXOS production. The most effective biocatalysts were hemicellulases expressed in the enzyme preparations from Trichoderma and Aspergillus spp. (Depol 692), Humicola and Bacillus spp. (Ceremix Plus). Degradability of rye and wheat cell wall materials by these enzyme preparations obtained break down percentages of 70–87% and 67–77%, respectively. After enzymatic treatment, only small amounts of xylose, xylobiose, and xylotriose was eluted compare to the amount of more complex oligosaccharides with higher degree of polymerization (DP). The mass spectra of oligosaccharides indicated the presence of a homologous series of pentoses ranging from DP 4 to 15. This indicates that chosen enzyme preparations acted well on wheat and rye biomass, and released quite high amounts of XOS and AXOS.
Two GH10 endo-xylanases from Myceliophthora thermophila C1 with and without cellulose binding module act differently towards soluble and insoluble xylans
Gool, M.P. van; Muiswinkel, G.C.J. van; Hinz, S.W.A. ; Schols, H.A. ; Sinitsyn, A.P. ; Gruppen, H. - \ 2012
Bioresource Technology 119 (2012). - ISSN 0960-8524 - p. 123 - 132.
chrysosporium-lucknowense - hydrolase family - substrate - arabinoxylans - hydrolysis - efficiency - residues - domains - bran
Xylanases are mostly classified as belonging to glycoside hydrolase (GH) family 10 and 11, which differ in catalytic properties and structures. However, within one family, differences may also be present. The influence of solubility and molecular structure of substrates towards the efficiency of two GH10 xylanases from Myceliophthora thermophila C1 was investigated. The xylanases differed in degradation of high and low substituted substrate and the substitution pattern was an important factor influencing their efficiency. Alkali-labile interactions, as well as the presence of cellulose within the complex cell wall structure hindered efficient hydrolysis for both xylanases. The presence of a carbohydrate binding module did not enhance the degradation of the substrates. The differences in degradation could be related to the protein structure of the two xylanases. The study shows that the classification of enzymes does not predict their performance towards various substrates.
Targeted discovery and functional characterisation of complex-xylan degrading enzymes
Gool, M.P. van - \ 2012
University. Promotor(en): Harry Gruppen, co-promotor(en): Henk Schols. - S.l. : s.n. - ISBN 9789461733528 - 224
enzymen - xylaan - xylanolytische micro-organismen - myceliophthora thermophila - bodemschimmels - enzymes - xylan - xylanolytic microorganisms - soil fungi

This thesis describes the development of a screening method to discover efficient hemicellulase producers in a wide range of fungi. The method is based on the potential of soil fungi to degrade soluble and insoluble xylan-rich substrates, by assigning various individual enzyme activities. Released mono- and oligosaccharides were monitored by high performance anion exchange chromatography and matrix assisted laser desorption/ionisation time-of-flight mass spectrometry. In addition, the released amounts of acetic acid were measured. Fungal strains, grown on wheat straw, with an efficient production of hemicellulolytic enzymes were Aspergillus lentulus, Penicllium pinophilum, and Trichoderma harzianum.

Next, two glycoside hydrolase (GH) family 10 endo-xylanases and two GH11 endo-xylanases of Myceliophthora thermophila C1 (C1) were subjected to a detailed characterisation. The degradation products from xylan-rich substrates, varying in type and degree of substituents, displayed that both intra- and interfamily differences occurred for these endo-xylanases. The different degradation profiles were correlated with a difference in the predicted secondary protein structure of the GH10 xylanases and with a minor difference in the primary protein structure of the GH11 xylanases. An additional cellulose binding domain attached to the endo-xylanases did not enhance the degradation of insoluble substrates.

In addition, synergy studies were performed on acetyl (xylan) esterases with glucuronidases. A concerted action of acetyl (xylan) esterases from different carbohydrate esterase families as well as synergy with glucuronidases of different GH families was observed.

Single-tube linear DNA amplification for genome-wide studies using a few thousand cells
Shankaranarayanan, P. ; Mendoza-Parra, M.A. ; Gool, W. van; Trindade, L.M. ; Gronemeyer, H. - \ 2012
Nature protocols 7 (2012)2. - ISSN 1754-2189 - p. 328 - 338.
t7 rna-polymerase - chip-seq - displacement amplification - limited numbers - chromatin - methylation - challenges - principles - samples - domain
Linear amplification of DNA (LinDA) by T7 polymerase is a versatile and robust method for generating sufficient amounts of DNA for genome-wide studies with minute amounts of cells. LinDA can be coupled to a great number of global profiling technologies. Indeed, chromatin immunoprecipitation coupled to massive parallel sequencing (ChIP-seq) has been achieved for transcription factors and epigenetic modification of chromatin histones with 1,000 to 5,000 cells. LinDA largely simplifies reChIP-seq experiments to monitor co-binding at chromatin target sites. The single-tube design of LinDA is ideal for handling ultrasmall amounts of DNA (
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