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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Erratum to : Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study
Hellenkamp, Björn ; Schmid, Sonja ; Doroshenko, Olga ; Opanasyuk, Oleg ; Kühnemuth, Ralf ; Adariani, Soheila Rezaei ; Ambrose, Benjamin ; Aznauryan, Mikayel ; Barth, Anders ; Birkedal, Victoria ; Bowen, Mark E. ; Chen, Hongtao ; Cordes, Thorben ; Eilert, Tobias ; Fijen, Carel ; Gebhardt, Christian ; Götz, Markus ; Gouridis, Giorgos ; Gratton, Enrico ; Ha, Taekjip ; Hao, Pengyu ; Hanke, Christian A. ; Hartmann, Andreas ; Hendrix, Jelle ; Hildebrandt, Lasse L. ; Hirschfeld, Verena ; Hohlbein, Johannes ; Hua, Boyang ; Hübner, Christian G. ; Kallis, Eleni ; Kapanidis, Achillefs N. ; Kim, Jae Yeol ; Krainer, Georg ; Lamb, Don C. ; Lee, Nam Ki ; Lemke, Edward A. ; Levesque, Brié ; Levitus, Marcia ; McCann, James J. ; Naredi-Rainer, Nikolaus ; Nettels, Daniel ; Ngo, Thuy ; Qiu, Ruoyi ; Robb, Nicole C. ; Röcker, Carlheinz ; Sanabria, Hugo ; Schlierf, Michael ; Schröder, Tim ; Schuler, Benjamin ; Seidel, Henning - \ 2018
Nature Methods : techniques for life scientists and chemists 15 (2018)11. - ISSN 1548-7091 - p. 984 - 984.

This paper was originally published under standard Springer Nature copyright. As of the date of this correction, the Analysis is available online as an open-access paper with a CC-BY license. No other part of the paper has been changed.

Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study
Hellenkamp, Björn ; Schmid, Sonja ; Doroshenko, Olga ; Opanasyuk, Oleg ; Kühnemuth, Ralf ; Rezaei Adariani, Soheila ; Ambrose, Benjamin ; Aznauryan, Mikayel ; Barth, Anders ; Birkedal, Victoria ; Bowen, Mark E. ; Chen, Hongtao ; Cordes, Thorben ; Eilert, Tobias ; Fijen, Carel ; Gebhardt, Christian ; Götz, Markus ; Gouridis, Giorgos ; Gratton, Enrico ; Ha, Taekjip ; Hao, Pengyu ; Hanke, Christian A. ; Hartmann, Andreas ; Hendrix, Jelle ; Hildebrandt, Lasse L. ; Hirschfeld, Verena ; Hohlbein, Johannes ; Hua, Boyang ; Hübner, Christian G. ; Kallis, Eleni ; Kapanidis, Achillefs N. ; Kim, Jae Yeol ; Krainer, Georg ; Lamb, Don C. ; Lee, Nam Ki ; Lemke, Edward A. ; Levesque, Brié ; Levitus, Marcia ; McCann, James J. ; Naredi-Rainer, Nikolaus ; Nettels, Daniel ; Ngo, Thuy ; Qiu, Ruoyi ; Robb, Nicole C. ; Röcker, Carlheinz ; Sanabria, Hugo ; Schlierf, Michael ; Schröder, Tim ; Schuler, Benjamin ; Seidel, Henning ; Streit, Lisa ; Thurn, Johann ; Tinnefeld, Philip ; Tyagi, Swati ; Vandenberk, Niels ; Vera, Andrés Manuel ; Weninger, Keith R. ; Wünsch, Bettina ; Yanez-Orozco, Inna S. ; Michaelis, Jens ; Seidel, Claus A.M. ; Craggs, Timothy D. ; Hugel, Thorsten - \ 2018
Nature Methods : techniques for life scientists and chemists 15 (2018)9. - ISSN 1548-7091 - p. 669 - 676.

Single-molecule Förster resonance energy transfer (smFRET) is increasingly being used to determine distances, structures, and dynamics of biomolecules in vitro and in vivo. However, generalized protocols and FRET standards to ensure the reproducibility and accuracy of measurements of FRET efficiencies are currently lacking. Here we report the results of a comparative blind study in which 20 labs determined the FRET efficiencies (E) of several dye-labeled DNA duplexes. Using a unified, straightforward method, we obtained FRET efficiencies with s.d. between ±0.02 and ±0.05. We suggest experimental and computational procedures for converting FRET efficiencies into accurate distances, and discuss potential uncertainties in the experiment and the modeling. Our quantitative assessment of the reproducibility of intensity-based smFRET measurements and a unified correction procedure represents an important step toward the validation of distance networks, with the ultimate aim of achieving reliable structural models of biomolecular systems by smFRET-based hybrid methods.

Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals
Bouwman, Aniek C. ; Daetwyler, Hans D. ; Chamberlain, Amanda J. ; Ponce, Carla Hurtado ; Sargolzaei, Mehdi ; Schenkel, Flavio S. ; Sahana, Goutam ; Govignon-Gion, Armelle ; Boitard, Simon ; Dolezal, Marlies ; Pausch, Hubert ; Brøndum, Rasmus F. ; Bowman, Phil J. ; Thomsen, Bo ; Guldbrandtsen, Bernt ; Lund, Mogens S. ; Servin, Bertrand ; Garrick, Dorian J. ; Reecy, James ; Vilkki, Johanna ; Bagnato, Alessandro ; Wang, Min ; Hoff, Jesse L. ; Schnabel, Robert D. ; Taylor, Jeremy F. ; Vinkhuyzen, Anna A.E. ; Panitz, Frank ; Bendixen, Christian ; Holm, Lars Erik ; Gredler, Birgit ; Hozé, Chris ; Boussaha, Mekki ; Sanchez, Marie Pierre ; Rocha, Dominique ; Capitan, Aurelien ; Tribout, Thierry ; Barbat, Anne ; Croiseau, Pascal ; Drögemüller, Cord ; Jagannathan, Vidhya ; Vander Jagt, Christy ; Crowley, John J. ; Bieber, Anna ; Purfield, Deirdre C. ; Berry, Donagh P. ; Emmerling, Reiner ; Götz, Kay Uwe ; Frischknecht, Mirjam ; Russ, Ingolf ; Sölkner, Johann ; Tassell, Curtis P. van; Fries, Ruedi ; Stothard, Paul ; Veerkamp, Roel F. ; Boichard, Didier ; Goddard, Mike E. ; Hayes, Ben J. - \ 2018
Nature Genetics 50 (2018). - ISSN 1061-4036 - p. 362 - 367.
Stature is affected by many polymorphisms of small effect in humans1. In contrast, variation in dogs, even within breeds, has been suggested to be largely due to variants in a small number of genes2,3. Here we use data from cattle to compare the genetic architecture of stature to those in humans and dogs. We conducted a meta-analysis for stature using 58,265 cattle from 17 populations with 25.4 million imputed whole-genome sequence variants. Results showed that the genetic architecture of stature in cattle is similar to that in humans, as the lead variants in 163 significantly associated genomic regions (P < 5 × 10−8) explained at most 13.8% of the phenotypic variance. Most of these variants were noncoding, including variants that were also expression quantitative trait loci (eQTLs) and in ChIP–seq peaks. There was significant overlap in loci for stature with humans and dogs, suggesting that a set of common genes regulates body size in mammals.
Deliverable No. 10.1: Quantified SUSFANS scenario drivers ready to be used by the modeling toolbox
Havlik, P. ; Dijk, M. van; Achterbosch, T.J. ; Batka, M. ; Boere, E. ; Folberth, C. ; Frank, S. ; Götz, C. ; Heckelei, T. ; Valin, H. ; Ziegler, F. ; Zurek, M. - \ 2017
SUSFANS - 24 p.
Deliverable No. D4.7: Database on farm-level production and sutainability indices assessing sustainable diets
Zimmermann, A. ; Götz, Christian ; Leip, A. ; Zanten, H.H.E. van; Hornborg, Sara ; Ziegler, Friederike - \ 2017
SUSFANS - 45 p.
This paper demonstrates that SUSFANS metrics for assessing the environmental sustainability of the European food system can be effectively produced and applied to assess policy measures and potential innovations that aim at achieving sustainable food and nutrition security in the European Union. The analysis points at important issues that need to be taken into account for the further development and application of metrics.
Deliverable No. 1.4: A modelling strategy for quantifying the sustainability of food and nutrition security in the EU
Kuiper, M.H. ; Zurek, Monika ; Havlik, Petr ; Deppermann, Andre ; Valin, Hugo ; Kuijsten, A. ; Geleijnse, J.M. ; Veer, P. van 't; Heckelei, T. ; Götz, Christian ; Leip, Adrian ; Zimmermann, A. ; Soler, L.G. ; Irz, Xavier ; Cuaresma, Jesus Crespo ; Hlouskova, Jaroslava ; Obersteiner, Michael - \ 2017
SUSFANS - 83 p.
Deliverable No. 1.3: Sustainability metrics for the EU food system: a review across economic, environmental and social considerations
Zurek, Monika ; Leip, Adrian ; Kuijsten, Anneleen ; Wijnands, Jo ; Terluin, Ida ; Shutes, Lindsay ; Hebinck, Aniek ; Zimmermann, Andrea ; Götz, Christian ; Hornborg, Sara ; Zanten, Hannah van; Ziegler, Friederike ; Havlik, Petr ; Garrone, Maria ; Geleijnse, Marianne ; Kuiper, Marijke ; Turrini, Aida ; Dofkova, Marcela ; Trolle, Ellen ; Mistura, Lorenza ; Dubuisson, Carine ; Veer, Pieter van 't; Achterbosch, Thom ; Ingram, John ; Brem-Wilson, Joshua ; Franklin, Alex ; Fried, Jana ; Guzman Rodriguez, Paola ; Owen, Luke ; Saxena, Lopa ; Trenchard, Liz ; Wright, Julia - \ 2017
SUSFANS - 78
One of the main objectives of the SUSFANS project is to develop a set of concepts and tools to help policy and decision makers across Europe make sense of the outcomes and trends of the EU food system. This paper proposes a set of metrics for assessing the performance of the EU food system in delivering sustainable food and nutrition security. The performance metrics have been built up through the aggregation of a wide range of variables, which together help to monitor the achievement of four overarching policy goals for the EU food system, namely a balanced diet for EU citizens, reduced environmental impacts, competitive agri-food businesses and equitable outcomes of the food system. The project decided to take a hierarchical approach to aggregating from Individual Variables to Derived Variables to Aggregate Indicators to Performance Metrics. This approach aims at marrying the notion that decision makers want only a small but powerful set of metrics to communicate the findings of the assessment, with the need to substantiate these metrics with the best available data from a large number of sources in a transparent way. In this deliverable the current set up of the performance metrics focus on each individual policy goal. In a related report, the team explores if and how the performance metrics presented here can be quantified using available data and modelling tools, and which of the models of the SUSFANS tool box can estimate which ones of the performance metrics and how (report D1.4). In a final step the SUSFANS team will bring all performance metrics together in an integrated set that will allow a view across all four policy goals and thus across all aspects of sustainable food and nutrition security (forthcoming report D1.5). Further work is the quantification of metrics using case studies and prospective scenario analysis. In addition to their use for monitoring, the proposed metrics are geared towards quantification using selected computational modelling tools. As such, SUSFANS aims to assist in foresight on and the evaluation of transformative changes in the food system with rigour and consistency.
Kinetic study of butanol production from various sugars by Clostridium acetobutylicum using a dynamic model
Raganati, Francesca ; Procentese, Alessandra ; Olivieri, Giuseppe ; Götz, Peter ; Salatino, Piero ; Marzocchella, Antonio - \ 2015
Biochemical Engineering Journal 99 (2015). - ISSN 1369-703X - p. 156 - 166.
Biokinetics - Clostridium acetobutylicum - COPASI - Dynamic modelling - Product inhibition - Substrate inhibition

This paper presents a kinetic dynamic model of acetone-butanol-ethanol production by Clostridium acetobutylicum DSM 792 developed with the biochemical networks simulator COPASI. This model is an evolution of previous models described in the literature, updated by including various mono-, di-, hexose and pentose sugars: glucose, mannose, fructose, sucrose, lactose, xylose and arabinose. The kinetic relationships of uptake of substrate, butanol production, cell growth and cell death are also included.The batch fermentation tests were carried out at an initial sugar concentration ranging from 5 to 100. g/L. The data from the batch tests were used to assess the kinetic parameters of the model. This model gave satisfactory results for each sugar, both in terms of simulation of fermentation - the square correlation coefficient of metabolite concentrations, calculated by comparing experiments and simulations, ranged between 0.87 and 0.925 - and of comparison with the models reported in the literature.The effects of mono-, di-, hexose and pentose sugars on the growth and production of metabolites, including acids and solvents, were reviewed according to the proposed model. The low fermentation performance measured for xylose and lactose were interpreted taking into account the sugar uptake, the acid production and the hydrolysis path.

Bos taurus strain:dairy beef (cattle): 1000 Bull Genomes Run 2, Bovine Whole Genome Sequence
Bouwman, A.C. ; Daetwyler, H.D. ; Chamberlain, Amanda J. ; Ponce, Carla Hurtado ; Sargolzaei, Mehdi ; Schenkel, Flavio S. ; Sahana, Goutam ; Govignon-Gion, Armelle ; Boitard, Simon ; Dolezal, Marlies ; Pausch, Hubert ; Brøndum, Rasmus F. ; Bowman, Phil J. ; Thomsen, Bo ; Guldbrandtsen, Bernt ; Lund, Mogens S. ; Servin, Bertrand ; Garrick, Dorian J. ; Reecy, James M. ; Vilkki, Johanna ; Bagnato, Alessandro ; Wang, Min ; Hoff, Jesse L. ; Schnabel, Robert D. ; Taylor, Jeremy F. ; Vinkhuyzen, Anna A.E. ; Panitz, Frank ; Bendixen, Christian ; Holm, Lars-Erik ; Gredler, Birgit ; Hozé, Chris ; Boussaha, Mekki ; Sanchez, Marie Pierre ; Rocha, Dominique ; Capitan, Aurelien ; Tribout, Thierry ; Barbat, Anne ; Croiseau, Pascal ; Drögemüller, Cord ; Jagannathan, Vidhya ; Vander Jagt, Christy ; Crowley, John J. ; Bieber, Anna ; Purfield, Deirdre C. ; Berry, Donagh P. ; Emmerling, Reiner ; Götz, Kay Uwe ; Frischknecht, Mirjam ; Russ, Ingolf ; Sölkner, Johann ; Tassell, Curtis P. van; Fries, Ruedi ; Stothard, Paul ; Veerkamp, R.F. ; Boichard, Didier ; Goddard, Mike E. ; Hayes, Ben J. - \ 2014
Bos taurus - PRJNA238491
Whole genome sequence data (BAM format) of 234 bovine individuals aligned to UMD3.1. The aim of the study was to identify genetic variants (SNPs and indels) for downstream analysis such as imputation, GWAS, and detection of lethal recessives. Additional sequences for later 1000 bull genomes runs can be found at partners individual projects including PRJEB9343, PRJNA176557, PRJEB18113, PRNJA343262, PRJNA324822, PRJNA324270, PRJNA277147, PRJEB5462.
Evaluatie microvezeldoekjes.
Duisterwinkel, A.E. ; Götz, C.M. ; Schmits, R. ; Zundert, L. van; Vrielink, H. ; Terpstra, P.M.J. - \ 1997
Unknown Publisher - 82 p.
Detection and characterization of broad-host-range plasmids in environmental bacteria by PCR
Götz, A. ; Pukall, R. ; Smit, E. ; Tietze, E. ; Prager, R. ; Tschäpe, H. ; Elsas, J.D. van; Smalla, K. - \ 1996
Applied and Environmental Microbiology 62 (1996). - ISSN 0099-2240 - p. 2621 - 2628.
Protein engineering of lantibiotics.
Kuipers, O.P. ; Bierbaum, G. ; Ottenwälder, G. ; Dodd, H.M. ; Horn, N. ; Metzger, J. ; Kupke, T. ; Gnau, V. ; Bongers, R. ; Boogaard, P. van den; Kosters, H. ; Rollema, H.S. ; Vos, W.M. de; Siezen, R.J. ; Jung, G. ; Götz, F. ; Sahl, H.G. ; Gasson, M.J. - \ 1996
Antonie van Leeuwenhoek: : Nederlandsch tijdschrift voor hygiëne, microbiologie en serologie 69 (1996). - ISSN 0003-6072 - p. 161 - 169.
PCR-based detection of broad host range plasmids in environmental bacteria
Smalla, K. ; Gotz, A. ; Pukall, R. ; Tschape, H. ; Elsas, J.D. van - \ 1995
Molecular diversity of IncP-type plasmids isolated from different soils and related habitats
Smalla, K. ; Götz, A. ; Hill, K. ; Fry, J.C. ; Derore, H. ; Top, E. ; Wilmotte, A. ; Mergeay, M. ; Elsas, J.D. van; Tschäpe, H. - \ 1995
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