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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Balanced harvest: concept, policies, evidence, and management implications
Zhou, Shijie ; Kolding, Jeppe ; Garcia, Serge M. ; Plank, Michael J. ; Bundy, Alida ; Charles, Anthony ; Hansen, Cecilie ; Heino, Mikko ; Howell, Daniel ; Jacobsen, Nis S. ; Reid, David G. ; Rice, Jake C. ; Zwieten, Paul A.M. van - \ 2019
Reviews in Fish Biology and Fisheries 29 (2019)3. - ISSN 0960-3166 - p. 711 - 733.
Ecological effect - Ecosystem approach to fishery - Ecosystem structure - Fishing intensity - Production - Selectivity - Sustainability

Balanced harvest has been proposed to reduce fishing impact on ecosystems while simultaneously maintaining or even increasing fishery yield. The concept has attracted broad interest, but also received criticisms. In this paper, we examine the theory, modelling studies, empirical evidence, the legal and policy frameworks, and management implications of balanced harvest. The examination reveals unresolved issues and challenges from both scientific and management perspectives. We summarize current knowledge and address common questions relevant to the idea. Major conclusions include: balanced harvest can be expressed in several ways and implemented on multiple levels, and with different approaches e.g. métier based management; it explicitly bridges fisheries and conservation goals in accordance with international legal and policy frameworks; modelling studies and limited empirical evidence reveal that balanced harvest can reduce fishing impact on ecosystem structure and increase the aggregate yield; the extent of balanced harvest is not purely a scientific question, but also a legal and social choice; a transition to balanced harvest may incur short-term economic costs, while in the long-term, economic results will vary across individual fisheries and for society overall; for its application, balanced harvest can be adopted at both strategic and tactical levels and need not be a full implementation, but could aim for a “partially-balanced” harvest. Further objective discussions and research on this subject are needed to move balanced harvest toward supporting a practical ecosystem approach to fisheries.

Money talk : How relations between farmers and advisors around financial management are shaped
Hilkens, Aniek ; Reid, Janet I. ; Klerkx, Laurens ; Gray, David I. - \ 2018
Journal of Rural Studies 63 (2018). - ISSN 0743-0167 - p. 83 - 95.
Agricultural advice - Agricultural entrepreneurship - Agricultural finance - Agricultural Knowledge and Innovation Systems (AKIS) - Dairy - Farm management - Farmer-advisor relationships - Financial management - Rural extension

The nature of interactions between farmers and advisors is the focus of a growing body of research. While many studies explore the potential role of advisors in facilitating farmers’ practice change in practices related to agricultural production such as soil, water, pest and animal health management, studies that specifically investigate how advisors support farmers with financial management (FM) are limited. The contribution this paper makes is to identify who farmers’ FM advisors are and to shed light on how farmer-advisor interactions about FM are shaped. Semi-structured interviews with both farmers and a range of advisors (bankers, accountants, farm management consultants, specialist financial advisors and industry funded advisors) were conducted. The main findings are that farm financial information and FM are considered to be sensitive topics and being good at FM is not central to farmers’ identity (relative to e.g. production management). Due to the sensitivity and taboo around the topic and the low level of interest in FM, most farmers do not actively seek to acquire financial advice. Farmers most openly discuss FM with their banker and accountant and some seek advice from farm management consultants. Advice seeking from other advisors was limited. Theoretical implications are that FM as a topic of advice introduces unique dynamics to interactions between farmer and advisor, which highlights the importance of better consideration of taboo and sensitive topics in advisory interactions. Furthermore, the findings on how the bankers’ authority impacts on the advisory relationship with farmers indicated that issues of power in view of such authoritative advisory relationships need to be better considered. To enhance effective provisioning on FM advice, policy could focus on improving the match between demand and supply, and help create awareness about the importance of discussing FM to reduce the sensitivity of the topic.

Moving beyond the MSY concept to reflect multidimensional fisheries management objectives
Rindorf, Anna ; Mumford, John ; Baranowski, Paul ; Clausen, Lotte Worsøe ; García, Dorleta ; Hintzen, Niels T. ; Kempf, Alexander ; Leach, Adrian ; Levontin, Polina ; Mace, Pamela ; Mackinson, Steven ; Maravelias, Christos ; Prellezo, Raúl ; Quetglas, Antoni ; Tserpes, George ; Voss, Rüdiger ; Reid, David G. - \ 2017
Marine Policy 85 (2017). - ISSN 0308-597X - p. 33 - 41.
Inclusive governance - Management objectives - MEY - MSOY - MSY - Sustainability pillars
Maximising the long term average catch of single stock fisheries as prescribed by the globally-legislated MSY objective is unlikely to ensure ecosystem, economic, social and governance sustainability unless an effort is made to explicitly include these considerations. We investigated how objectives to be maximised can be combined with sustainability constraints aiming specifically at one or more of these four sustainability pillars. The study was conducted as a three-year interactive process involving 290 participating science, industry, NGO and management representatives from six different European regions. Economic considerations and inclusive governance were generally preferred as the key objectives to be maximised in complex fisheries, recognising that ecosystem, social and governance constraints are also key aspects of sustainability in all regions. Relative preferences differed between regions and cases but were similar across a series of workshops, different levels of information provided and the form of elicitation methods used as long as major shifts in context or stakeholder composition did not occur. Maximising inclusiveness in governance, particularly the inclusiveness of affected stakeholders, was highly preferred by participants across the project. This suggests that advice incorporating flexibility in the interpretation of objectives to leave room for meaningful inclusiveness in decision-making processes is likely to be a prerequisite for stakeholder buy-in to management decisions.
A novel millet-based probiotic fermented food for the developing world
Stefano, Elisa Di; White, Jessica ; Seney, Shannon ; Hekmat, Sharareh ; McDowell, Tim ; Sumarah, Mark ; Reid, Gregor - \ 2017
Nutrients 9 (2017)5. - ISSN 2072-6643
Cereal - Fermentation - Millet - Probiotic - Sub-Saharan Africa - Yogurt

Probiotic yogurt, comprised of a Fiti sachet containing Lactobacillus rhamnosus GR-1 and Streptococcus thermophilus C106, has been used in the developing world, notably Africa, to alleviate malnutrition and disease. In sub-Saharan African countries, fermentation of cereals such as millet, is culturally significant. The aim of this study was to investigate the fermentation capability of millet when one gram of the Fiti sachet consortium was added. An increase of 1.8 and 1.4 log CFU/mL was observed for S. thermophilus C106 and L. rhamnosus GR-1 when grown in 8% millet in water. Single cultures of L. rhamnosus GR-1 showed the highest _max when grown in the presence of dextrose, galactose and fructose. Single cultures of S. thermophilus C106 showed the highest _max when grown in the presence of sucrose and lactose. All tested recipes reached viable counts of the probiotic bacteria, with counts greater than 106 colony-forming units (CFU)/mL. Notably, a number of organic acids were quantified, in particular phytic acid, which was shown to decrease when fermentation time increased, thereby improving the bioavailability of specific micronutrients. Millet fermented in milk proved to be the most favorable, according to a sensory evaluation. In conclusion, this study has shown that sachets being provided to African communities to produce fermented milk, can also be used to produce fermented millet. This provides an option for when milk supplies are short, or if communities wish to utilize the nutrient-rich qualities of locally-grown millet.

Inclusion of ecological, economic, social, and institutional considerations when setting targets and limits for multispecies fisheries
Rindorf, Anna ; Dichmont, Catherine M. ; Thorson, James ; Charles, Anthony ; Clausen, Lotte Worsøe ; Degnbol, Poul ; Garcia, Dorleta ; Hintzen, Niels T. ; Kempf, Alexander ; Levin, Phillip ; Mace, Pamela ; Maravelias, Christos ; Minto, Coilín ; Mumford, John ; Pascoe, Sean ; Prellezo, Raul ; Punt, André E. ; Reid, David G. ; Rockmann, Christine ; Stephenson, Robert L. ; Thebaud, Olivier ; Tserpes, George ; Voss, Rüdiger - \ 2017
ICES Journal of Marine Science 74 (2017)2. - ISSN 1054-3139 - p. 453 - 463.
ecosystem-based fisheries management - multiple objectives - reference points - sustainability - variability
Targets and limits for long-term management are used in fisheries advice to operationalize the way management reflects societal priorities on ecological, economic, social and institutional aspects. This study reflects on the available published literature as well as new research presented at the international ICES/Myfish symposium on targets and limits for long term fisheries management. We examine the inclusion of ecological, economic, social and institutional objectives in fisheries management, with the aim of progressing towards including all four objectives when setting management targets or limits, or both, for multispecies fisheries. The topics covered include ecological, economic, social and governance objectives in fisheries management, consistent approaches to management, uncertainty and variability, and fisheries governance. We end by identifying ten ways to more effectively include multiple objectives in setting targets and limits in ecosystem based fisheries management.
When experts disagree : the need to rethink indicator selection for assessing sustainability of agriculture
Olde, Evelien M. de; Moller, Henrik ; Marchand, Fleur ; McDowell, Richard W. ; MacLeod, Catriona J. ; Sautier, Marion ; Halloy, Stephan ; Barber, Andrew ; Benge, Jayson ; Bockstaller, Christian ; Bokkers, E.A.M. ; Boer, Imke J.M. de; Legun, Katharine A. ; Quellec, Isabelle Le; Merfield, Charles ; Oudshoorn, Frank W. ; Reid, John ; Schader, Christian ; Szymanski, Erika ; Sørensen, Claus A.G. ; Whitehead, Jay ; Manhire, Jon - \ 2017
Environment, Development and Sustainability 19 (2017)4. - ISSN 1387-585X - p. 1327 - 1342.
Indicator selection - Multi-criteria assessment - Ranking - Sustainability assessment - Temperate agriculture
Sustainability indicators are well recognized for their potential to assess and monitor sustainable development of agricultural systems. A large number of indicators are proposed in various sustainability assessment frameworks, which raises concerns regarding the validity of approaches, usefulness and trust in such frameworks. Selecting indicators requires transparent and well-defined procedures to ensure the relevance and validity of sustainability assessments. The objective of this study, therefore, was to determine whether experts agree on which criteria are most important in the selection of indicators and indicator sets for robust sustainability assessments. Two groups of experts (Temperate Agriculture Research Network and New Zealand Sustainability Dashboard) were asked to rank the relative importance of eleven criteria for selecting individual indicators and of nine criteria for balancing a collective set of indicators. Both ranking surveys reveal a startling lack of consensus amongst experts about how best to measure agricultural sustainability and call for a radical rethink about how complementary approaches to sustainability assessments are used alongside each other to ensure a plurality of views and maximum collaboration and trust amongst stakeholders. To improve the transparency, relevance and robustness of sustainable assessments, the context of the sustainability assessment, including prioritizations of selection criteria for indicator selection, must be accounted for. A collaborative design process will enhance the acceptance of diverse values and prioritizations embedded in sustainability assessments. The process by which indicators and sustainability frameworks are established may be a much more important determinant of their success than the final shape of the assessment tools. Such an emphasis on process would make assessments more transparent, transformative and enduring.
Discrete water quality sampling at open-water aquaculture sites: limitations and strategies
Jansen, H.M. ; Reid, G.K. ; Bannister, R.J. ; Husa, V. ; Robinson, S.M.C. ; Cooper, J.A. ; Quinton, C. ; Strand, Ø. - \ 2016
Aquaculture Environment Interactions 8 (2016). - ISSN 1869-215X - p. 463 - 480.
Sampling design - pelagic - IMTA - Nutrients - Cage aquaculture - Farm-scale
While environmental performance of cage-based aquaculture is most often monitored through benthic conditions, there may also be requirements that necessitate discrete, pelagic sampling. In the pelagic realm, adequately capturing the spatial and temporal dynamics of interest and attributing causality to aquaculture processes can be extremely challenging. Conditions are seldom ideal, and data adequacy concerns of discrete samples collected at open-water
aquaculture sites are not uncommon. Further exploration of these challenges is needed. Herein, we aim to explore considerations for study design, analysis, and data interpretation of discrete pelagic sampling. As examples, we present 2 case studies where limited sampling occurred under conditions of complex pelagic dynamics. A Norwegian case study quantified particle abundance
around salmon farms, and aimed to highlight the effects of spatial−temporal variation on sampling design, the need for inclusion of companion parameters, and the benefits of a priori and a posteriori data interpretation strategies. A Canadian case study collected discrete samples to measure ammonium concentrations with continuous current measurements at an Integrated Multi-Trophic Aquaculture (IMTA) farm, to explore issues of complex hydrodynamics, reference site suitability, sampling resolution, data pooling, and post hoc power tests. We further discuss lessons learned and the implications of study design, ambient conditions, physical processes, farm management, statistical analysis, companion parameters, and the potential for confounding effects. Pragmatic
consideration of these aspects will ultimately serve to better frame the costs and benefits of discrete pelagic sampling at open-water aquaculture sites.
Robotics in agriculture and forestry
Bergerman, M. ; Billingsley, J. ; Reid, J. ; Henten, E.J. van - \ 2016
In: Springer handbook of robotics / Siciliano, Bruno, Khatib, Oussama, Heidelberg : Springer Verlag - ISBN 9783319325507 - p. 1463 - 1492.
Robotics
Robotics for agriculture and forestry (A&F) represents the ultimate application of one of our society’s latest and most advanced innovations to its most ancient and important industries. Over the course of history, mechanization and automation increased crop output several orders of magnitude, enabling a geometric growth in population and an increase in quality of life across the globe. Rapid population growth and rising incomes in developing countries, however, require ever larger amounts of A&F output. This chapter addresses robotics for A&F in the form of case studies where robotics is being successfully applied to solve well-identified problems. With respect to plant crops, the focus is on the in-field or in-farm tasks necessary to guarantee a quality crop and, generally speaking, end at harvest time. In the livestock domain, the focus is on breeding and nurturing, exploiting, harvesting, and slaughtering and processing. The chapter is organized in four main sections. The first one explains the scope, in particular, what aspects of robotics for A&F are dealt with in the chapter. The second one discusses the challenges and opportunities associated with the application of robotics to A&F. The third section is the core of the chapter, presenting twenty case studies that showcase (mostly) mature applications of robotics in various agricultural and forestry domains. The case studies are not meant to be comprehensive but instead to give the reader a general overview of how robotics has been applied to A&F in the last 10 years. The fourth section concludes the chapter with a discussion on specific improvements to current technology and paths to commercialization.
Evaluating early-warning indicators of critical transitions in natural aquatic ecosystems
Gsell, A.S. ; Scharfenberger, Ulrike ; Özkundakci, Deniz ; Walters, Annika ; Hansson, Lars Anders ; Janssen, Annette B.G. ; Nõges, Peeter ; Reid, Philip C. ; Schindler, Daniel E. ; Donk, Ellen Van ; Dakos, Vasilis ; Adrian, Rita - \ 2016
Proceedings of the National Academy of Sciences of the United States of America 113 (2016)50. - ISSN 0027-8424 - p. E8089 - E8095.
Competition - Intraguild predation - Resilience indicators - Time series - Trophic cascade

Ecosystems can show sudden and persistent changes in state despite only incremental changes in drivers. Such critical transitions are difficult to predict, because the state of the system often shows little change before the transition. Early-warning indicators (EWIs) are hypothesized to signal the loss of system resilience and have been shown to precede critical transitions in theoretical models, paleo-climate time series, and in laboratory as well as whole lake experiments. The generalizability of EWIs for detecting critical transitions in empirical time series of natural aquatic ecosystems remains largely untested, however. Here we assessed four commonly used EWIs on long-term datasets of five freshwater ecosystems that have experienced sudden, persistent transitions and for which the relevant ecological mechanisms and drivers are well understood. These case studies were categorized by three mechanisms that can generate critical transitions between alternative states: competition, trophic cascade, and intraguild predation. Although EWIs could be detected in most of the case studies, agreement among the four indicators was low. In some cases, EWIs were detected considerably ahead of the transition. Nonetheless, our results show that at present, EWIs do not provide reliable and consistent signals of impending critical transitions despite using some of the best routinely monitored freshwater ecosystems. Our analysis strongly suggests that a priori knowledge of the underlying mechanisms driving ecosystem transitions is necessary to identify relevant state variables for successfully monitoring EWIs.

Encouraging results for controlling an Agricultural pest on St. Eustatius
Debrot, A.O. ; Reid, A. ; Leslie, T.W. ; Madden, H. ; Stapel, J. ; Dalm, Friso ; Uphoff, Lara ; Zwet, Leonie van der - \ 2016
BioNews (2016)26. - p. 8 - 8.
In 2013, the invasive Giant African Land Snail, Achatina fulica was found in a small part of urban St. Eustatius. In collaboration with local government agencies and Dutch universities, IMARES* conducted field and laboratory pilot trials of control methods from October 2015 to June 2016.
Grazing lands in Sub-Saharan Africa and their potential role in climate change mitigation: What we do and don't know
Milne, E. ; Aynekulu, E. ; Bationo, A. ; Batjes, N.H. ; Boone, R. ; Conant, R. ; Davies, J. ; Hanan, N. ; Hoag, D. ; Herrick, J.E. ; Knausenberger, W. ; Neely, C. ; Njoka, J. ; Ngugi, M. ; Parton, B. ; Paustian, K. ; Reid, K. ; Said, M. ; Shepherd, K. ; Swift, D. ; Thornton, P. ; Williams, S. ; Miller, S. ; Nkonya, Ephraim - \ 2016
Environmental Development 19 (2016). - ISSN 2211-4645 - p. 70 - 74.
In 2014, the USAID project ‘Grazing lands, livestock and climate resilient mitigation in Sub-Saharan Africa’ held two workshops, hosted by the Colorado State University, which brought together experts from around the world. Two reports resulted from these workshops, one an assessment of the state of the science, and the other an inventory of related activities in the region to date.. In this short communication we summarize the main points of the first report – The state of the science (Milne and Williams, 2015). A second report is in preparation.
Vlakvaaggrond : Ameland, Neerlands Reid in wording. ´Kwelder als buffer bij zeespiegelstijging´
Mantel, S. ; Slim, P.A. ; Krol, J. - \ 2016
Natuurcentrum Ameland
Map-based estimates of present carbon stocks of grazing lands in Sub-Sahara Africa
Batjes, N.H. ; Milne, E. ; Williams, S. - \ 2015
In: Grazing Lands, Livestock and Climate Resilient Mitigation in Sub-Saharan Africa: The State of the Science United States Agency for International Development (USAID) - p. 31 - 33, 97-100.
This report is a detailed review, synthesis, and analysis of the current “state of the science” concerning the potential for carbon sequestration in grazing lands through improved land management practices in Sub-Saharan Africa (SSA). It aims to provide an up-to-date assessment of the science of C sequestration from improved land management, including the current levels of uncertainty, major gaps in knowledge and data, areas for near term research and development, major determinants of sequestration potential, and current and potential scientific monitoring tools. The report firstly gives an overview of current grazing lands in SSA (Chapter 1) and explores the major determinants of C sequestration in grass/rangeland systems (Chapter 2). It then considers current research work on C impacts of grazing land management systems (Chapter 3). Available measurement techniques are summarized in Chapter 4 and a map based approach is then used in Chapter 5 to estimate present C stocks in grazing lands in SSA. This is followed by Chapter 6 which looks at available modeling techniques and Chapter 7 which presents a model based estimate of C sequestration potential in grass/rangelands in SSA. The final chapter (Chapter 8) provides a synthesis of the report’s findings. > Authors of the respective chapters: Eleanor Milne · Stephen Williams · Andre Bationo · Robin Reid · David Swift · Rich Conant · Niall Hanan · Constance Neely · Ermias Aynekulu · Keith D. Shepherd · Niels Batjes · Randall Boone
A novel consortium of Lactobacillus rhamnosus and Streptococcus thermophilus for increased access to functional fermented foods
Kort, Remco ; Westerik, Nieke ; Mariela Serrano, L. ; Douillard, François P. ; Gottstein, Willi ; Mukisa, Ivan M. ; Tuijn, Coosje J. ; Basten, Lisa ; Hafkamp, Bert ; Meijer, Wilco C. ; Teusink, Bas ; Vos, Willem de; Reid, Gregor ; Sybesma, Wilbert - \ 2015
Microbial Cell Factories 14 (2015)1. - ISSN 1475-2859
Bacterial fermentation - Consortium - Enrichment - Fermented foods - Functional foods - Lactobacillus rhamnosus GG - Lactobacillus rhamnosus yoba 2012 - Streptococcus thermophilus C106 - Yoghurt

Background: The lactic acid bacterium Lactobacillus rhamnosus GG is the most studied probiotic bacterium with proven health benefits upon oral intake, including the alleviation of diarrhea. The mission of the Yoba for Life foundation is to provide impoverished communities in Africa increased access to Lactobacillus rhamnosus GG under the name Lactobacillus rhamnosus yoba 2012, world's first generic probiotic strain. We have been able to overcome the strain's limitations to grow in food matrices like milk, by formulating a dried starter consortium with Streptococcus thermophilus that enables the propagation of both strains in milk and other food matrices. The affordable seed culture is used by people in resource-poor communities. Results: We used S. thermophilus C106 as an adjuvant culture for the propagation of L. rhamnosus yoba 2012 in a variety of fermented foods up to concentrations, because of its endogenous proteolytic activity, ability to degrade lactose and other synergistic effects. Subsequently, L. rhamnosus could reach final titers of 1E+09CFUml-1, which is sufficient to comply with the recommended daily dose for probiotics. The specific metabolic interactions between the two strains were derived from the full genome sequences of L. rhamnosus GG and S. thermophilus C106. The piliation of the L. rhamnosus yoba 2012, required for epithelial adhesion and inflammatory signaling in the human host, was stable during growth in milk for two rounds of fermentation. Sachets prepared with the two strains, yoba 2012 and C106, retained viability for at least 2 years. Conclusions: A stable dried seed culture has been developed which facilitates local and low-cost production of a wide range of fermented foods that subsequently act as delivery vehicles for beneficial bacteria to communities in east Africa.

Molucular Epidemiology and Evolution of Influenza Viruses Circulating within European Swine between 2009 and 2013
Watson, S.J. ; Langat, P. ; Reid, S. ; Lam, T. ; Cotten, M. ; Kelly, M. ; Reeth, K. Van; Qiu, Y. ; Simon, G. ; Bonin, E. ; Foni, E. ; Chiapponi, C. ; Larsen, L. ; Hjulsager, C. ; Markowska-Daniel, I. ; Urbaniak, K. ; Durrwald, R. ; Schlegel, M. ; Huovilainen, A. ; Davidson, I. ; Dan, A. ; Loeffen, W.L.A. ; Edwards, S. ; Bublot, M. ; Vila, T. ; Maldonado, J. ; Valls, L. ; Brown, I.H. ; Pybus, O.G. ; Kellam, P. - \ 2015
Journal of Virology 89 (2015)19. - ISSN 0022-538X - p. 9920 - 9931.
The emergence in humans of the A(H1N1)pdm09 influenza virus, a complex reassortant virus of swine origin, highlighted the importance of worldwide influenza virus surveillance in swine. To date, large-scale surveillance studies have been reported for southern China and North America, but such data have not yet been described for Europe. We report the first large-scale genomic characterization of 290 swine influenza viruses collected from 14 European countries between 2009 and 2013. A total of 23 distinct genotypes were identified, with the 7 most common comprising 82% of the incidence. Contrasting epidemiological dynamics were observed for two of these genotypes, H1huN2 and H3N2, with the former showing multiple long-lived geographically isolated lineages, while the latter had short-lived geographically diffuse lineages. At least 32 human-swine transmission events have resulted in A(H1N1)pdm09 becoming established at a mean frequency of 8% across European countries. Notably, swine in the United Kingdom have largely had a replacement of the endemic Eurasian avian virus-like (“avian-like”) genotypes with A(H1N1)pdm09-derived genotypes. The high number of reassortant genotypes observed in European swine, combined with the identification of a genotype similar to the A(H3N2)v genotype in North America, underlines the importance of continued swine surveillance in Europe for the purposes of maintaining public health. This report further reveals that the emergences and drivers of virus evolution in swine differ at the global level.
Validation of the effects of a single one second hypochlorite floral dip on Bortytis cinerea incidence following long-term shipment of cut roses
Woltering, E.J. ; Boerrigter, H.A.M. ; Mensink, M.G.J. ; Harkema, H. ; Macnish, A.J. ; Reid, M.S. ; Jiang, C.Z. - \ 2015
Acta Horticulturae 1064 (2015). - ISSN 0567-7572 - p. 211 - 220.
The effect of a pre-shipment hypochlorite treatment on botrytis incidence was evaluated in a large number of rose cultivars and under different long-term storage conditions. Application parameters, stability and sources of hypochlorite were investigated. Irrespective of the type of packaging and shipment conditions, roses that received a pre-shipment treatment with 100 to 150 mg/L hypochlorite showed a significantly decreased botrytis incidence compared to non-hypochlorite treated roses. The hypochlorite treatment generally was more effective than a comparable treatment with commercial fungicides. Dipping the flower heads for approximately one second in a hypochlorite solution was more effective than spraying the heads. In few cases minor hypochlorite-induced damage on the petal tips was observed at higher concentrations (>200 mg/L). Apart from the effect on botrytis incidence, the treatment resulted in reduced water loss that may have an additional beneficial effect on the eventual flower quality. It is concluded that, apart from other obvious measures to reduce botrytis incidence (prevention of high humidity at the flower heads) a pre-shipment floral dip in 100 to 150 mg/L hypochlorite from commercial household bleach is an easy and cost effective way to reduce botrytis incidence following long term storage/transportation of roses.
Pedestrian Safety and the Built Environment : A Review of the Risk Factors
Stoker, Philip ; Garfinkel-Castro, Andrea ; Khayesi, Meleckidzedeck ; Odero, Wilson ; Mwangi, M.N. ; Peden, Margie ; Ewing, Reid - \ 2015
Journal of Planning Literature 30 (2015)4. - ISSN 0885-4122 - p. 377 - 392.
built environment - pedestrian safety - risk factors

Urban and regional planning has a contribution to make toward improving pedestrian safety, particularly in view of the fact that about 273,000 pedestrians were killed in road traffic crashes in 2010. The road is a built environments that should enhance safety and security for pedestrians, but this ideal is not always the case. This article presents an overview of the evidence on the risks that pedestrians face in the built environment. This article shows that design of the roadway and development of different land uses can either increase or reduce pedestrian road traffic injury. Planners need to design or modify the built environment to minimize risk for pedestrians.

Balanced Harvest in the Real World. Scientific, Policy and Operational Issues in an Ecosystem Approach to Fisheries
Garcia, S.M. ; Bianchi, G. ; Charles, A. ; Kolding, J. ; Rice, J. ; Rochet, M.J. ; Zhou, S. ; Delius, G. ; Reid, D. ; Zwieten, P.A.M. van; Atcheson, M. ; Bartley, D. ; Borges, L. ; Bundy, A. ; Dagorn, L. ; Dunn, D. ; Hall, M. ; Heino, M. ; Jacobsen, B. ; Jacobsen, N.S. ; Law, R. ; Makino, M. ; Martin, F. ; Skern-Mauritzen, M. ; Suuronen, P. ; Symons, D. - \ 2015
Gland, Switzerland : IUCN - 94 p.
The concept of the Ecosystem Approach has entered the fishery harvesting discussions both from fishery perspectives (Reykjavik Declaration; FAO 2003 Annex to the Code of Conduct and from the principles of the Ecosystem Approach adopted by the CBD in 1995. Both perspectives establish the need to maintain ecosystem structure and functioning, whether for sustainable use of biodiversity (CBD) or simply to keep exploited ecosystems healthy and productive (fisheries). In response, the “Balanced Harvest” (BH) concept was suggested by a group of scientists brought together by the IUCN Fisheries Experts Group during the CBD CoP 10 in 2010. The meeting and the BH concept as consolidated there highlighted some of the collateral ecological effects of current fishing patterns and unbalanced removals of particular components of the food web, stimulating a critical rethinking of current approaches to fisheries management. The meeting on “Balanced Harvest in the real world - Scientific, policy and operational issues in an ecosystem approach to fisheries” (Rome, September 29-October 2, 2014) examined the progress made since 2010 on a number of fronts. It considered questions related to the scientific underpinning of the BH concept, including theory, modelling, and empirical observations. It began to explore the economic, policy and management implications of harvesting in a more balanced way.
Does vegetation in restored salt marshes equal naturally developed vegetation
Loon-Steensma, J.M. van; Dobben, H.F. van; Slim, P.A. ; Huiskes, H.P.J. ; Dirkse, G.M. - \ 2015
Applied Vegetation Science 18 (2015)4. - ISSN 1402-2001 - p. 674 - 682.
Question: Do low stone dams built to prevent erosion and to restore salt marshes through increased sedimentation affect plant species composition? Location: Dutch Wadden Sea area (ca. 53°N 5°E). Methods: Relevés (N = 170) were made of the vegetation of two restored salt marsh sites on the barrier islands Terschelling (Grië) and Ameland (Neerlands Reid). Existing relevés of salt-marsh vegetation (N = 6198) made along the entire Dutch Wadden Sea coast (both the mainland and the barrier islands) were used as a reference. The vegetation of the two restored sites (Grië NLR data) was compared with the reference by (1) simple species-by-species analysis based on frequencies in both data sets, and by (2) ordination, where relevés of the restored sites were projected into a multivariate space defined by the species' abundances in the reference relevés. Results: Out of the 37 species that are common (i.e. have a frequency >5%) in either the Grië NLR data or the reference data, 31 have frequencies that differ by less than a factor of five, and 23 differ by less than a factor of two. Furthermore, the Grië NLR data occupy a space that is well in the centre of the ordination space defined by the reference data. Conclusions: There are no conspicuous differences between salt-marsh vegetation behind low dams and the vegetation that has naturally developed on unprotected mudflats. We conclude that measures targeting salt marsh development in view of flood protection do not interfere with nature conservation.
Identifying marine pelagic ecoystem management objectives and indicators
Trenkel, V.M. ; Hintzen, N.T. ; Farnsworth, K. ; Olesen, C. ; Reid, D. ; Rindorf, A. ; Shephard, S. ; Dickey-Collas, M. - \ 2015
Marine Policy 55 (2015). - ISSN 0308-597X - p. 23 - 32.
north-sea - fisheries management - celtic sea - continental-shelf - functional-groups - fish communities - forage fish - atlantic - seabirds - impacts
International policy frameworks such as the Common Fisheries Policy and the European Marine Strategy Framework Directive define high-level strategic goals for marine ecosystems. Strategic goals are addressed via general and operational management objectives. To add credibility and legitimacy to the development of objectives, for this study stakeholders explored intermediate level ecological, economic and social management objectives for Northeast Atlantic pelagic ecosystems. Stakeholder workshops were undertaken with participants being free to identify objectives based on their own insights and needs. Overall 26 objectives were proposed, with 58% agreement in proposed objectives between two workshops. Based on published evidence for pressure-state links, examples of operational objectives and suitable indicators for each of the 26 objectives were then selected. It is argued that given the strong species-specific links of pelagic species with the environment and the large geographic scale of their life cycles, which contrast to demersal systems, pelagic indicators are needed at the level of species (or stocks) independent of legislative region. Pelagic community indicators may be set at regional scale in some cases. In the evidence-based approach used in this study, the selection of species or region specific operational objectives and indicators was based on demonstrated pressure-state links. Hence observed changes in indicators can reliably inform on appropriate management measures.
Making progress towards integration of existing sampling activities to establish Joint Monitoring Programmes in support of the MSFD
Shephard, S. ; Hal, R. van; Boois, I.J. de; Birchenough, S.N.R. ; Foden, J. ; O'Connor, J. ; Geelhoed, S.C.V. ; Hoey, G. van; Marco-Rius, F. ; Reid, D.G. ; Schaber, M. - \ 2015
Marine Policy 59 (2015). - ISSN 0308-597X - p. 105 - 111.
marine - management
Data support for GES assessment under the MSFD will require subregion-scale Joint Monitoring Programmes (JMPs). These JMPs must be cost-efficient and produce the necessary evidence-base to support management decisions. This review summarises the outputs of a 2.5-day multidisciplinary workshop where scientists and programme managers developed monitoring scenarios as examples of how current sampling activities could be extended and combined into framework JMPs. The objective was to explore opportunities for improved i) integration of monitoring, ii) international collaboration and iii) multi-disciplinary use of platforms. The workshop identified opportunities to upgrade current monitoring programmes, to include additional sampling activities, and to support integration of resources and activities. We found that developing JMPs using this bottom-up approach has potential benefits but requires commitment and expert coordination. Coordination needs include definition of data requirements, common sampling methodologies and data exchange.
Phylogeography and population dynamics of the white-sided dolphin (Lagenorhynchus acutus) in the North Atlantic
Banguera-Hinestroza, E. ; Evans, P.G.H. ; Mirimin, L. ; Reid, R.J. ; Mikkelsen, B. ; Couperus, A.S. ; Deaville, R. ; Rogan, E. ; Hoelzel, A.R. - \ 2014
Conservation Genetics 15 (2014)4. - ISSN 1566-0621 - p. 789 - 802.
Highly mobile species in the marine environment may be expected to show little differentiation at the population level, but this is often not the case. Instead cryptic population structure is common, and effective conservation will require an understanding of how these patterns evolve. Here we present an assessment from both sides of the North Atlantic of differentiation among populations of a dolphin species that inhabits mainly pelagic waters, the Atlantic white-sided dolphin. We compare eleven putative populations in the western and eastern North Atlantic at mtDNA and microsatellite DNA loci and find reduced nucleotide diversity and signals for historical bottlenecks and post-bottleneck expansions in all regions. We calculate expansion times to have occurred during the early Holocene, following the last glacial maximum (LGM). We find evidence for connectivity among populations from either side of the North Atlantic, and differentiation between putative populations in the far northeast compared with all other areas sampled. Some data suggest the possibility of separate refugia during the LGM explaining this pattern, although ongoing ecological processes may also be a factor. We discuss the implications for developing effective programs of conservation and management in the context of ongoing anthropogenic impact.
European surveillance network for influenza in pigs : Surveillance programs, diagnostic tools and swine influenza virus subtypes identified in 14 European countries from 2010 to 2013
Simon, Gaëlle ; Larsen, Lars E. ; Dürrwald, Ralf ; Foni, Emanuela ; Harder, Timm ; Reeth, Kristien Van; Markowska-Daniel, Iwona ; Reid, Scott M. ; Dan, Adam ; Maldonado, Jaime ; Huovilainen, Anita ; Billinis, Charalambos ; Davidson, Irit ; Agüero, Montserrat ; Vila, Thaïs ; Hervé, Séverine ; Breum, Solvej Østergaard ; Chiapponi, Chiara ; Urbaniak, Kinga ; Kyriakis, Constantinos S. ; Brown, Ian H. ; Loeffen, Willie ; Meulen, Karen Van der; Schlegel, Michael ; Bublot, Michel ; Kellam, Paul ; Watson, Simon ; Lewis, Nicola S. ; Pybus, Oliver G. ; Webby, Richard ; Chen, Hualan ; Vincent, Amy L. - \ 2014
PLoS ONE 9 (2014)12. - ISSN 1932-6203

Swine influenza causes concern for global veterinary and public health officials. In continuing two previous networks that initiated the surveillance of swine influenza viruses (SIVs) circulating in European pigs between 2001 and 2008, a third European Surveillance Network for Influenza in Pigs (ESNIP3, 2010-2013) aimed to expand widely the knowledge of the epidemiology of European SIVs. ESNIP3 stimulated programs of harmonized SIV surveillance in European countries and supported the coordination of appropriate diagnostic tools and subtyping methods. Thus, an extensive virological monitoring, mainly conducted through passive surveillance programs, resulted in the examination of more than 9 000 herds in 17 countries. Influenza A viruses were detected in 31% of herds examined from which 1887 viruses were preliminary characterized. The dominating subtypes were the three European enzootic SIVs: avian-like swine H1N1 (53.6%), human-like reassortant swine H1N2 (13%) and human-like reassortant swine H3N2 (9.1%), as well as pandemic A/H1N1 2009 (H1N1pdm) virus (10.3%). Viruses from these four lineages co-circulated in several countries but with very different relative levels of incidence. For instance, the H3N2 subtype was not detected at all in some geographic areas whereas it was still prevalent in other parts of Europe. Interestingly, H3N2-free areas were those that exhibited highest frequencies of circulating H1N2 viruses. H1N1pdm viruses were isolated at an increasing incidence in some countries from 2010 to 2013, indicating that this subtype has become established in the European pig population. Finally, 13.9% of the viruses represented reassortants between these four lineages, especially between previous enzootic SIVs and H1N1pdm. These novel viruses were detected at the same time in several countries, with increasing prevalence. Some of them might become established in pig herds, causing implications for zoonotic infections.

Sedimentatiemodel kwelders Ameland Fase 1: ontwerp en haalbaarheid
Groot, A.V. de; Duin, W.E. van; Brinkman, A.G. ; Vries, P. de - \ 2014
Den Helder : IMARES (Rapport / IMARES Wageningen UR C025/14) - 47
kweldergronden - waterstand - bodemdaling - aardgas - overstromingen - risicoschatting - fauna - watervogels - nederlandse waddeneilanden - salt marsh soils - water level - subsidence - natural gas - floods - risk assessment - waterfowl - dutch wadden islands
Op Ameland vindt bodemdaling plaats als gevolg van gaswinning. Dit heeft consequenties voor de opslibbingsbalans en daarmee de maaiveldhoogte van de oostelijke kwelders Neerlands Reid en De Hon, vergeleken met wanneer er geen bodemdaling zou hebben plaatsgevonden. Dit kan weer gevolgen hebben voor het broedsucces van grondbroedende vogels, dat mede afhankelijk is van het overstromingsrisico. Om de impact van gaswinning op het ecosysteem te bepalen, is het dus mede van belang om inzicht te krijgen in hoe het overstromingsrisico op de kwelders op Ameland zou zijn geweest vanaf 1986 zónder de opgetreden bodemdaling. Daarvoor is het nodig de hoogteligging zonder bodemdaling te reconstrueren.
Genomic characterisation of the effector complement of the potato cyst nematode Globodera pallida
Thorpe, P. ; Mantelin, S. ; Cock, P.J.A. ; Blok, V.C. ; Coke, M.C. ; Evers-van den Akker, S. ; Guzeeva, E. ; Lilley, C.J. ; Smant, G. ; Reid, A.J. ; Wright, K.M. ; Urwin, P.E. ; Jones, J.T. - \ 2014
BMC Genomics 15 (2014). - ISSN 1471-2164 - 15 p.
plant-parasitic nematodes - esophageal gland-cells - heterodera-glycines - meloidogyne-incognita - phytophthora-infestans - arabidopsis-thaliana - chorismate mutase - giant-cells - protein - sequence
Background The potato cyst nematode Globodera pallida has biotrophic interactions with its host. The nematode induces a feeding structure – the syncytium – which it keeps alive for the duration of the life cycle and on which it depends for all nutrients required to develop to the adult stage. Interactions of G. pallida with the host are mediated by effectors, which are produced in two sets of gland cells. These effectors suppress host defences, facilitate migration and induce the formation of the syncytium. Results The recent completion of the G. pallida genome sequence has allowed us to identify the effector complement from this species. We identify 128 orthologues of effectors from other nematodes as well as 117 novel effector candidates. We have used in situ hybridisation to confirm gland cell expression of a subset of these effectors, demonstrating the validity of our effector identification approach. We have examined the expression profiles of all effector candidates using RNAseq; this analysis shows that the majority of effectors fall into one of three clusters of sequences showing conserved expression characteristics (invasive stage nematode only, parasitic stage only or invasive stage and adult male only). We demonstrate that further diversity in the effector pool is generated by alternative splicing. In addition, we show that effectors target a diverse range of structures in plant cells, including the peroxisome. This is the first identification of effectors from any plant pathogen that target this structure. Conclusion This is the first genome scale search for effectors, combined to a life-cycle expression analysis, for any plant-parasitic nematode. We show that, like other phylogenetically unrelated plant pathogens, plant parasitic nematodes deploy hundreds of effectors in order to parasitise plants, with different effectors required for different phases of the infection process.
Production of Entomopathogenic Viruses
Reid, S. ; Chan, L. ; Oers, M.M. van - \ 2014
In: Mass Production of Beneficial Organisms / Morales-Ramos, J.A., Rojas, M.G., Shapiro-Ilan, David, Amsterdam : Elsevier - ISBN 9780123914538 - p. 437 - 482.
Agriculture applications
Bergerman, M. ; Billingsley, J. ; Henten, E.J. van; Evert, F.K. van; Hamner, B. ; Reid, J. ; Singh, S. ; Moorehead, S. - \ 2014
In: Autonomous Technologies: Applications That Matter / Messner, William C., Warrendale PA : SAE International - ISBN 9780768077186 - p. 69 - 88.
autonomous - agriculture - Applications
Assessing the state of pelagic fish communities within an ecosystem approach and the European Marine Strategy Framework Directive
Shephard, S. ; Rindorf, A. ; Dickey-Collas, M. ; Hintzen, N.T. ; Farnsworth, K. ; Reid, D.G. - \ 2014
ICES Journal of Marine Science 71 (2014)7. - ISSN 1054-3139 - p. 1572 - 1585.
cod gadus-morhua - north-sea - celtic sea - southern benguela - condition indexes - energy reserves - horse mackerel - forage fish - indicators - management
Pelagic fish are key elements in marine foodwebs and thus comprise an important part of overall ecosystem health. We develop a suite of ecological indicators that track pelagic fish community state and evaluate state of specific objectives against Good Environmental Status (GES) criteria. Indicator time-series are calculated for the EU Marine Strategy Framework Directive “Celtic Seas” (CS) and “Greater North Sea” subregions. Precautionary reference points are proposed for each indicator and a simple decision process is then used to aggregate indicators into a GES assessment for each subregion. The pelagic fish communities of both subregions currently appear to be close to GES, but each remains vulnerable. In the CS subregion, fishing mortality is close to the precautionary reference point, although the unknown dynamics of sandeel, sprat, and sardine in the subregion may reduce the robustness of this evaluation. In the North Sea, sandeel stocks have been in poor state until very recently. Pelagic fish community biomass is slightly below the precautionary reference point in both subregions.
Assessing the impacts of livestock production on biodiversity in rangeland ecosystems
Alkemade, R. ; Reid, R.S. ; Berg, M. van den; Leeuw, J. de; Jeuken, M. - \ 2013
Proceedings of the National Academy of Sciences of the United States of America 110 (2013)52. - ISSN 0027-8424 - p. 20900 - 20905.
land-use changes - south-africa - diversity - conservation - assemblages - grassland - management - scenarios - responses - savanna
Biodiversity in rangelands is decreasing, due to intense utilization for livestock production and conversion of rangeland into cropland; yet the outlook of rangeland biodiversity has not been considered in view of future global demand for food. Here we assess the impact of future livestock production on the global rangelands area and their biodiversity. First we formalized existing knowledge about livestock grazing impacts on biodiversity, expressed in mean species abundance (MSA) of the original rangeland native species assemblages, through metaanalysis of peer-reviewed literature. MSA values, ranging from 1 in natural rangelands to 0.3 in man-made grasslands, were entered in the IMAGE-GLOBIO model. This model was used to assess the impact of change in food demand and livestock production on future rangeland biodiversity. The model revealed remarkable regional variation in impact on rangeland area and MSA between two agricultural production scenarios. The area of used rangelands slightly increases globally between 2000 and 2050 in the baseline scenario and reduces under a scenario of enhanced uptake of resource-efficient production technologies increasing production [high levels of agricultural knowledge, science, and technology (high-AKST)], particularly in Africa. Both scenarios suggest a global decrease in MSA for rangelands until 2050. The contribution of livestock grazing to MSA loss is, however, expected to diminish after 2030, in particular in Africa under the high-AKST scenario. Policies fostering agricultural intensification can reduce the overall pressure on rangeland biodiversity, but additional measures, addressing factors such as climate change and infrastructural development, are necessary to totally halt biodiversity loss.
IEEE Robotics and Automation Society Technical Committee on Agricultural Robotics and Automation
Bergerman, M. ; Henten, E. van; Billingsley, J. ; Reid, J. ; Deng, M.C. - \ 2013
IEEE Robot. Autom. Mag. 20 (2013)2. - ISSN 1070-9932 - p. 20 - 125.
field
An assessment of the variation of manure nitrogen efficiency throughout Europe and an appraisal of means to increase manure-N efficiency
Webb, J. ; Sorensen, P. ; Velthof, G.L. ; Amon, B. ; Pinto, M. ; Rodhe, L. ; Salomon, E. ; Hutchings, N. ; Burczyk, J. ; Reid, J.E. - \ 2013
Advances in Agronomy 119 (2013). - ISSN 0065-2113 - p. 371 - 442.
fertilizer replacement value - reducing ammonia emissions - greenhouse-gas emissions - treated cattle slurry - pig slurry - organic nitrogen - animal manures - short-term - mineral fertilizer - plant utilization
Using the nitrogen (N) in organic manures more effectively reduces losses to the environment. A requirement to take allowance of the N conserved by reduced ammonia (NH3)-emission techniques would increase manure-N efficiency by up to 15%. Covering manure stores and land application of slurry by injection beneath the soil surface and by rapid incorporation of both slurries and solid manures into uncropped soil reduce NH3 emissions. Injection of cattle slurry also reduces N immobilization compared with application methods, which mix the slurry with soil and increases manure-N efficiency by ca 10–15%. In growing cereals, NH3 emissions can be reduced by band spreading within the canopy. Anaerobic digestion of slurry may also increase manure-N availability in the season of application by 10–20%, compared with undigested slurry. Slurry acidification may increase manure-N efficiency by 35–65% by reducing total NH3 losses by 70% compared with unacidified slurry stored without cover and not incorporated after spreading. To fully utilize the fertilizer value of manure-N, uptake over more than 1 year needs to be accounted for. This is particularly important for solid manures which provide less-available N in the season after application than slurries but release more N to crops in subsequent years. Using manure-N as a sole N source may limit overall manure-N efficiency. Applying manures at reduced rates over a larger crop area, using N fertilizer at times when crop recovery of manure-N may be limited, may give the greatest overall manure-N efficiency.
Human Microbiota in Health and Disease
Vos, W.M. de; Engstrand, L. ; Drago, L. ; Reid, G. ; Schauber, J. ; Hay, R. ; Mendling, W. ; Schaller, M. ; Spiller, R. ; Gahan, C.G.M. ; Rowland, I. - \ 2012
SelfCare Journal 3 (2012)6. - ISSN 2042-7018 - p. 1 - 68.
Each human body plays host to a microbial population which is both numerically vast (at around 1014 microbial cells) and phenomenally diverse (over 1,000 species). The majority of the microbial species in the gut have not been cultured but the application of culture-independent approaches for high throughput diversity and functionality analysis has allowed characterisation of the diverse microbial phylotypes present in health and disease
Challenges to the Future - Conservation of the Antarctic
Chown, S.L. ; Lee, J.E. ; Hughes, K.A. ; Barnes, J. ; Bergstrom, D.M. ; Convey, P. ; Cowan, D.A. ; Crosbie, K. ; Dyer, G. ; Frenot, Y. ; Grant, S.M. ; Herr, D. ; Kennicutt, M.C. ; Lamers, M.A.J. ; Murray, A. ; Possingham, H.P. ; Reid, K. ; Riddle, M.J. ; Ryan, P.G. ; Sanson, L. ; Shaw, J.D. ; Sparrow, M.D. ; Summerhayes, C. ; Terauds, A. ; Wall, D.H. - \ 2012
Science 337 (2012)6091. - ISSN 0036-8075 - p. 158 - 159.
The Antarctic Treaty System, acknowledged as a successful model of cooperative regulation of one of the globe's largest commons (1), is under substantial pressure. Concerns have been raised about increased stress on Antarctic systems from global environmental change and growing interest in the region's resources (2, 3). Although policy-makers may recognize these challenges, failure to respond in a timely way can have substantial negative consequences. We provide a horizon scan, a systematic means for identifying emerging trends and assisting decision-makers in identifying policies that address future challenges (2, 3). Previous analyses of conservation threats in the Antarctic have been restricted to matters for which available evidence is compelling (4). We reconsider these concerns because they might escalate quickly, judging from recent rapid environmental change in parts of Antarctica and increasing human interest in the region (see the map). We then focus on a more distant time horizon.
Utility of 18-kHz acoustic data for abundance estimation of Atlantic herring (Clupea harengus)
Saunders, R.A. ; O'Donnell, C. ; Korneliussen, R.J. ; Fassler, S.M.M. ; Clarke, M.W. ; Egan, A.R. ; Reid, D. - \ 2012
ICES Journal of Marine Science 69 (2012)6. - ISSN 1054-3139 - p. 1086 - 1098.
target-strength - high-frequencies - fish - identification - oceanography - swimbladder - mackerel - krill
Current acoustic survey protocols for Atlantic herring (Clupea harengus) abundance estimation are principally dependent upon 38-kHz backscatter data. This can constitute a substantial problem for robust stock assessment when 38-kHz data are compromised. Research vessels now typically collect multifrequency data during acoustic surveys, which could be used to remediate such situations. Here, we investigate the utility of using 18- and 120-kHz data for herring abundance estimation when the standard 38-kHz approach is not possible. Estimates of herring abundance/biomass in the Celtic Sea (2007–2010) were calculated at 18, 38, and 120 kHz using the standard 38-kHz target-strength (TS) model and geometrically equivalent TS models at 18 and 120 kHz. These estimates were compared to assess the level of coherence between the three frequencies, and 18-kHz-derived estimates were subsequently input into standard 38-kHz-based population models to evaluate the impact on the assessment. Results showed that estimates of herring abundance/biomass from 18 and 38 kHz acoustic integration varied by only 0.3–5.4%, and acoustically derived numbers-at-age estimates were not significantly (p > 0.05) different from 1:1. Estimates at 120 kHz were also robust. Furthermore, 18-kHz-derived estimates did not significantly change the assessment model output, indicating that 18-kHz data can be used for herring stock assessment purposes
Strengthening Coastal Pollution Management in the Wider Caribbean Region
Lavieren, H. van; Metcalfe, C.D. ; Drouillard, K. ; Sale, P. ; Gold-Bouchot, G. ; Reid, R. ; Vermeulen, L.C. - \ 2011
In: Proceedings of the Sixty Four Annual Gulf and Caribbean Fisheries Institute, Puerto Morelos, Mexico, 31 October - 5 November 2011. - Puerto Morelos, Mexico : Gulf and Caribbean Fisheries Institute - p. 17 - 27.
Control of aquatic pollution is critical for improving coastal zone management and for the conservation of fisheries resources. Countries in the Wider Caribbean Region (WCR) generally lack monitoring capacity and do not have reliable information on the levels and distribution of pollutants, particularly chemical contaminants, and the ecological and/or human health risks. Given the substantial cultural and economic importance of coastal environments to WCR communities, this should be cause for serious concern. This paper describes two studies determining persistent organic pollutants (POPs) in 1) the white grunt fish (Haemulon plumieri) and 2) three oyster species. It highlights lessons learned on improving capacity for environmental monitoring of POPs and how to build an effective south-south network involving academic institutions, laboratories and management agencies. Data are reported for Jamaica, St. Lucia, Trinidad and Tobago, Belize, and the Caribbean coast of Mexico. Overall, PCB and organochlorine concentrations were low relative to consumption guidelines used to protect the health of humans consuming contaminated seafood. However, since both monitoring organisms occupy low to mid-trophic levels in the marine food web, there is a risk of higher contaminant concentrations accumulating in top trophic levels, such as piscivorous fish and birds. Identified sources of contaminants include domestic sewage, agriculture and industry, large continental rivers and atmospheric deposition. For example, data indicate that atmospheric deposition is a likely source of POPs in Belize, while there is evidence of point sources of POPs in St. Lucia. Currently, these are the only data available on POPs contamination in fish and oysters distributed across the WCR, but will hopefully lead to future studies, increased awareness and strengthening of coastal pollution management
Study on variation of manure N efficiency throughout Europe
Webb, J. ; Sorensen, P. ; Velthof, G.L. ; Amon, B. ; Pinto, M. ; Rodhe, L. ; Salomon, E. ; Hutchings, N. ; Burczyk, J. ; Reid, J.E. - \ 2011
Didcot, United Kingdom : AEA Technology plc (Final report ) - 114 p.
Is there a decline in marine phytoplankton?
McQuatters-Gollop, A. ; Reid, P.C. ; Edwards, M. ; Burkill, P.H. ; Castellani, C. ; Batten, S. ; Gieskes, W. ; Beare, D.J. ; Bidigare, R.R. ; Head, E. ; Johnson, R. ; Kahru, M. ; Koslow, J.A. ; Pena, A. - \ 2011
Nature 472 (2011)7342. - ISSN 0028-0836 - p. E6 - E7.
long-term - northeast atlantic - ocean - chlorophyll - plankton - biomass - variability - trends - sea
Construction of an integrated microsatellite and key morphological characteristic database of potato varieties on the EU common catalogue
Reid, A. ; Hof, L. ; Felix, G. ; Rucker, B. ; Tams, S. ; Milczynska, E. ; Esselink, G. ; Uenk-Stunnenberg, G.E. ; Vosman, B. ; Weitz, A. - \ 2011
Euphytica 182 (2011)2. - ISSN 0014-2336 - p. 239 - 249.
identification - markers - tomato - plants
The European Union Common Catalogue (EUCC) for potato contains over 1000 varieties. Each year member states add varieties to the list after they have undergone Distinctness, Uniformity and Stability (DUS) testing according to international guidelines. A rapid and robust method for variety identification to aid the management and maintenance of existing variety collections and for the screening of new candidate varieties would therefore be a highly useful tool for DUS testing stations. A database containing key morphological characteristics and microsatellite data was constructed for varieties on the 2006 list of the EUCC for potato. Rules for scoring SSR markers in different laboratories were established to allow a harmonized scoring of markers. Almost all varieties (99.5%) were shown to have unique molecular profiles and in pair wise comparisons 99.99% of all variety pairs could be distinguished. This clearly shows the versatility of the markers and database for identifying potato samples.
A high intake of industrial or ruminant trans fatty acids does not affect the plasma proteome in healthy men
Roos, B. de; Wanders, A.J. ; Wood, S. ; Horgan, G. ; Rucklige, G. ; Reid, M. ; Siebelink, E. ; Brouwer, I.A. - \ 2011
Proteomics 11 (2011)19. - ISSN 1615-9853 - p. 3928 - 3934.
conjugated linoleic-acid - lipid-peroxidation - insulin-resistance - biomarker discovery - risk-factors - cholesterol - disease - serum - supplementation - inflammation
Consumption of industrial trans fat raises the risk of cardiovascular disease, but it is unclear whether cis9,trans11-conjugated linoleic acid (CLA) – a trans fatty acid in dairy products – modulates disease development. We investigated the effects of complete diets providing 7% of energy as industrial trans fat or cis9, trans11 CLA, compared with oleic acid, on regulation of plasma proteins in 12 healthy men. Diets were provided for 3¿wk each, in random order. Plasma was collected at the end of each 3 wk intervention period, depleted of its 12 most abundant proteins and analyzed by 2-DE. Principal component analysis of protein spot intensity values revealed that the nature of the dietary intervention did not significantly affect the plasma proteome. The intervention provided in the 1st period produced a significant treatment effect compared with the interventions provided in the other two periods, and there was a significant subject effect. In conclusion, the nature of an extreme dietary intervention, i.e. 7% of energy provided by industrial trans fat or cis9,trans11 CLA, did not markedly affect the plasma proteome. Thus plasma proteomics using 2-DE appears, by and large, an unsuitable approach to detect regulation of plasma proteins due to changes in the diet
Responses of marine benthos to climate change
Birchenough, S.N.R. ; Degraer, S. ; Reiss, H. ; Craeymeersch, J.A.M. ; Mesel, I.G. de - \ 2011
In: ICES status report on climate change in the North Atlantic / Reid, P.C., Valdes, L., Copenhagen : ICES (ICES cooperative Research Report 310) - ISBN 9788774820963 - p. 123 - 146.
Effects of climate variability and change on fish
Kulka, D.W. ; Simpson, S.D. ; Hal, R. van; Duplisea, D.E. ; Sell, A.L. ; Teal, L.R. - \ 2011
In: ICES Status report on climate change in the North Atlantic / Reid, P.C., Valdes, L., Copenhagen : ICES (ICES Cooperative Research Report 310) - ISBN 9788774820963 - p. 147 - 158.
Collagen-inspired self-assembling materals
Skrzeszewska, P.J. - \ 2011
Wageningen University. Promotor(en): Martien Cohen Stuart, co-promotor(en): Jasper van der Gucht; Frits de Wolf. - [S.l.] : S.n. - ISBN 9789085858690 - 151
zelf-assemblage - polypeptiden - biodegradatie - pichia pastoris - genetische modificatie - genetisch gemanipuleerde micro-organismen - aminozuursequenties - biomedische techniek - self assembly - polypeptides - biodegradation - pichia pastoris - genetic engineering - genetically engineered microorganisms - amino acid sequences - biomedical engineering

The rapid increase of the quality of life together with the progress of medical science asks for the development of new, tuneable and controllable materials. For the same reason, materials used for biomedical applications have to be increasingly biocompatible, biodegradable and biofunctional. Most of the available systems, however, lack one property or the other. For example, conventional animal-derived gelatin that is often used in biomedicine, is susceptible to a risk of contamination with prions or viruses and has a risk of bringing out allergic reactions, particularly against the non helix-forming domains of collagen [1]. Furthermore, gelatin is composed of a variety of molecules and structures with different thermal stabilities and molecular sizes. This, in combination with the impossibility to change the molecular structure at will, limits the chances to elucidate the relation between the structure and function. On the other hand, synthetic materials that have a rather well-controlled size distribution often lack biocompatibility, biofunctionality or biodegradability. In addition to that, as their synthesis often requires toxic solvents, their application in the human body is restricted. All the drawbacks of the presently used materials have brought scientists towards a new approach in designing materials viz. genetic engineering. Rapid progress in recombinant techniques has led to new ways of producing molecules with well-defined composition and structure and with full control over the length and sequence of the biopolymer and its constituent blocks. These methods thus combine the advantages of natural and synthetic polymers. Using molecular biology tools, unique molecules can be created by merging in a desired manner naturally occurring self-assembling motifs such as elastin, silk or collagen [2-4], or entirely artificial fragments. As we show in this thesis, the precise control over the molecular design of these biotechnologically produced block polypeptides is extremely valuable as it also leads to control over their physicochemical properties.

In this thesis we present a new class of monodisperse, biodegradable and biocompatible network-forming block polymers that are produced by genetically modified strain of yeast, Pichia pastoris (Chapter 2). Trimer-forming end blocks, abbreviated as T, consisting of nine Pro-Gly-Pro amino acid triplets, are symmetrically flanking a random coil-like middle block composed of four or eight repeats of highly hydrophilic R or P sequences (Figure 8.1). R and P are identical with respect to length (99 amino acids) and composition but have different amino acid sequences. The P block has a glycine in every third position (as in collagen) but does not form any supramolecular structures and maintains a random coil-like conformation at any temperature [5]. The R block is a shuffled version of the P block. Four recombinant gelatins are reported in this thesis, denoted as TR4T, TR8T, TP4T and TP8T (Figure 8.1). All of these were successfully produced with high yields (1-3 g/l of fermentation broth) by the Pichia pastoris GS115 strain transformed with a pPIC9 vector with the gene of interest in its expression cassette.

Figure 8.1 Schematic representation of collagen-inspired telechelic polypeptides: TR4T, TR8T, TP4T and TP8T.

In Chapter 3 we described the linear rheological properties of hydrogels formed by TR4T polypeptides. At a temperature of 50 °C, the solution does not show any viscoelastic response. However, upon cooling, the collagen-like trimer-forming domains (T) start to assemble into triple helical nodes and a well-defined network, with a node multiplicity of three, is formed. In the beginning of the gelation process, viscous properties are predominant, but as the network formation progresses, the elastic properties prevail. A plateau storage modulus is reached within a few hours. At this point the triple helices are in equilibrium with the free T blocks. An equilibrium or near-equilibrium state is reached, contrary to natural gelatin, because the collagen-like (T) assembling domains are relatively short and well-defined. The T blocks are solely responsible for the network formation. We have shown that a solution of the middle blocks only (i.e. R4) does not demonstrate any elastic response at any time and temperature. In addition, differential scanning calorimetry (DSC) (Chapter 5) proved that the collagen-like side blocks are near-quantitatively responsible for trimerization, as the observed melting enthalpies are in good agreement with values obtained by Frank et al. [6] for free (Pro-Gly-Pro)10 peptides. The equilibrium fraction of T blocks involved in triple helices shifts with temperature. By lowering the temperature, the fraction of triple helices increases, while the fraction of free ends decreases. There are two possibilities to form a triple helix. It can be formed either by three T blocks from three different chains, or by three T blocks from two different chains, so that two side blocks come from the same polypeptide. As a consequence, the network is composed of dangling ends, elastically active bridges and inactive loops (Figure 8.2). Because of the precisely-known junction multiplicity of three, we could develop an analytical model that links the internal structure of the gel, with dangling ends, loops, and bridges, to the physicochemical properties. This model uses a limited set of input parameters that can all be measured independently. It describes the experimental data quantitatively without further adjustable parameters. Using this model, we could show that the observed strong dependency of the storage modulus, the relaxation time and the viscosity on concentration and temperature is related to the changes in the number of loops, active bridges, and dangling ends in the gel matrix.

Figure 8.2 Network formation by collagen-inspired telechelic biopolymers.

In Chapter 4 we show that the number of intermolecular junctions and intramolecular loops depends not only on protein concentration and temperature but also on the length and the stiffness of the middle block. We synthesised new triblock copolymers with middle blocks, of different lengths and amino acid sequences, named TP4T, TR8T and TP8T (Figure 8.1). For all new proteins, there is a strong dependency of the storage modulus, the relaxation time and the viscosity on concentration and temperature (as for TR4T). However at comparable molar concentrations, the longer versions of polypeptides i.e. TR8T and TP8T show a significantly higher storage modulus and relaxation time than their counterparts TR4T and TP4T. This is because a longer middle block leads to a larger radius of gyration (Rg), which decreases the probability that two end blocks from the same molecule associate with each other, and form a loop. The consequence of fewer loops in the system is a higher storage modulus and a higher overall relaxation time.

TR8T

TP8T

Besides the effect of polymer length, we also observed that the R series, i.e. TR4T and TR8T, show a higher storage modulus than their P counterparts, i.e. TP4T and TP8T, at the same concentration and temperature. This can be explained by differences in coil flexibility. Although the P and R blocks have exactly the same amino acid composition, their amino acid sequence is different. Fitzkee et al. [7] have shown that even a polypeptide chain that assumes a random coil conformation still has locally folded conformations that contribute to the overall flexibility of the chain. This apparently leads to a smaller radius of gyration for the P middle block than for the R middle block and thus to a higher probability of loop formation.

Even though the melting behaviour obtained with DSC is the same for all four polypeptides (as the end blocks stay the same), the temperature at which the G0 value approaches zero and the gel completely loses its elastic properties varies with the length of the middle block. Shorter molecules, i.e. TP4T and TR4T, melt at lower temperatures. A solution of 1.2 mM TP4T melts at 298 K, while TP8T at a comparable molar concentration melts at a temperature which is 15 degrees higher. Furthermore, the R versions show slightly higher melting temperatures than the P versions. These differences in melting behaviour are related to the gel structure and the relative probabilities of forming intramolecular and intermolecular assemblies. We could account for these findings with the help of the analytical model presented in Chapter 3. The only parameter that had to be varied in the model was the coil size of the polymer, since the enthalpy and the melting temperatures of the triple helices did not change with the length of the middle block. The theoretical calculations clearly show that the molecules with smaller Rg form up to 30 % more loops than their bigger counterparts. Loops that act as gel stoppers do not contribute to the network elasticity and significantly lower the melting temperatures detected with rheology.

The network junctions in our gels are solely formed by triple helices. The mechanism of junction formation by the T blocks can be well-described by a two-step kinetic model (Chapter 5). Prior to triple helix propagation, a trimeric nucleus has to be formed. For dilute systems, nucleation is the limiting step, giving an apparent reaction order of three. These results indicate that only triple helices are stable. For more concentrated solutions, when nucleation is relatively fast, propagation of triple helices becomes rate-limiting and the apparent reaction order is close to unity. The propagation of triple helices is probably limited by cis-trans isomerization of peptide bonds, in which proline residues are involved.

Above overlap concentration (C*) the measured enthalpy for stable gels (~15 hours) indicates that almost 100 % of the T blocks are involved in triple helices. Values obtained by us are in good agreement with values obtained by Frank et al. [6] for single (Gly-Pro-Gly)10 peptides. Conversely, at concentrations below C*, the enthalpy per mole of protein is becoming less, suggesting that the fraction of free ends or mismatched helices becomes more pronounced. The apparent melting temperature increases slightly with increasing concentration. This can be explained on the basis of the reaction stoichiometry under equilibrium conditions [8, 9]. Except for the highest measured concentration (2.4 mM), the apparent melting temperature revealed a dependence on the scan rate, indicating that it was not possible to maintain equilibrium during the heating step. At a concentration of 2.4 mM concentration there is no scan rate dependence, since the melting occurs at a higher temperature, where the dissociation kinetics is faster [4, 10].

The kinetics of triple helix formation determines the rate of gel formation. The gelation starts when the first triple helical node is formed. At that time viscous properties (loss modulus) predominate, but as the network formation evolves the elastic response (storage modulus) becomes more pronounced. The storage modulus (G’) reaches a plateau value within a few hours. Changes in network structure and mechanical properties of the gel in time can be predicted from the kinetics of triple helix formation, using the model presented in Chapter 3. By comparing the kinetics obtained with rheology and with DSC we could see that for our system, the helix content is not simply proportional to the network progress and that the relation between the elastic properties (G’) and the helix content (pH) depends on the protein concentration. The reason for this concentration dependence is the formation of loops, which is more likely at low concentrations.

The investigated hydrogels undergo time-dependent macroscopic fracturing when a constant shear rate or shear stress is applied (start-up and creep experiments, respectively) (Chapter 6). Observations with particle image velocimetry (PIV) showed that in the beginning of a start-up (or creep) experiment the sample flows homogenously. After some time, the gel fractures, and is separated into two fractions. The inner region moves at the same velocity as the moving bob, while the outer fraction does not move at all. From the rate-dependence of the fracture strength we can conclude that gel fracture is due to stress-activated rupture of the triple helical nodes in the network.When the deformation is taken away, the gel can heal (Chapter 6). The capacity of self-healing is due to the transient character of the network nodes with a finite relaxation time. Such behaviour, impossible for most permanent gels, is highly desired in many applications, as hydrogels are often subjected to deformations, which easily go beyond the linear regime. As we present in Figure 8.3, TR4T gels cut into small pieces (grey and transparent), can heal within 2 hours. As measured with rheology the broken gel can recover up to 100 % of its initial elastic properties, even after several fracturing cycles. Interestingly, the kinetics of healing differs from the kinetics of fresh gel formation (Chapter 5). The latter is characterized by a lag-phase before elastic properties start to appear. This lag-phase occurs because at low degrees of crosslinking there is not yet a percolated network, so that the storage modulus is undetectable. By contrast, the recovery of the gel after rupturing is much faster and does not show a lag-phase. The elastic modulus, depending on the rupturing history, comes back to its initial value within 1-5 hours. These findings indicate that outside the fracture zone, the network nodes have not dissociated significantly, so that healing only requires the reformation of junctions that connect the undamaged pieces of the network (gel clusters).

Figure 8.3 Self-healing of TR4T hydrogels. (A) Pieces of broken gel. (B) Two gel pieces healed after 2 hours.

In Chapter 7 we demonstrated the shape-memory effects in hydrogels formed by permanently crosslinked TR4T molecules. The programmed shape of these hydrogels was achieved by chemical crosslinking of lysine residues present in the random coil. The chemical network could be stretched up to 200 % and “pinned” in a temporary shape by lowering the temperature and allowing the collagen-like end blocks to assemble into the physical nodes. The deformed shape of hydrogel can be maintained, at room temperature, for several days, or relaxed within few minutes upon heating to 50 ºC or higher. The presented hydrogels could return to their programmed shape even after several thermo-mechanical cycles, hence indicating that they remember the programmed shape. We have studied in more detail the shape recovery process by describing our hydrogels by a mechanical model composed of two springs and a dashpot. With the help of this model we showed that above the melting temperature of the triple helices, the recovery is exponential and that the decay time is roughly ten times slower than the relaxation of the physical network.

1.Biomedical applications - perspectives and considerations

The class of collagen-inspired self-assembling materials, which we present in this thesis are nice model systems for a systematic study of physical networks, but they also have a lot of potential for biomedical applications. In this section we discuss the possibilities for these self- assembling hydrogels in biomedicine.

Drug delivery systems

One of the major goals of modern medicine is to ensure that the required amount of an active substance is available at the desired time at the desired location in the body. Consequently, a lot of effort is put into designing delivery systems with precisely adapted release profiles, sensitive to external stimuli such as temperature or pH. A frequently used group of materials in this field are hydrogels, both chemically and physically crosslinked. In the case of covalently crosslinked networks the release of the drug is mostly via diffusion of the drug out of the gel particle after it swells. The rate of drug release is governed by the resistance of the network to volume increase [11]. Although permanent networks are widely used as drug carriers they have some disadvantages such as incomplete release of active substances and poor biodegradability in the body. The problem can be partially solved by introducing enzymatic cleavage or hydrolysis sites into the main chain, but still the hydrogel erosion cannot be precisely controlled and complete material degradation can not be guaranteed.

These obstacles can be overcome by using physical hydrogels that are formed by weak interactions. These can dissociate in a controlled manner and completely release the active component. In contrast to chemical gels, erosion of physical gels occurs spontaneously. The erosion rate is determined by the life time of the junctions, but it depends also on the relative amount of intramolecular loops and intermolecular junctions, as demonstrated by Shen et al. [12]. These authors showed that, by using triblock polymers with dissimilar coiled-coil side domains rather than identical ones, loop formation could be suppressed, leading to a lower erosion rate [12].

The potential of our gels for drug delivery applications was tested by Teles et al. [13]. It was shown that trapped proteins (BSA) can be completely released from TR4T and TR8T gels, both at 37 ºC and 20 ºC. The release at 37 ºC from 20 % gels was completed within 48 hours while at 20 ºC it took about 5 times longer. At body temperature the release was mostly driven by dissociation of trimeric junction and dissolution of the separate polymer chains (gel erosion). At 20 ºC the junction life time was long so that erosion was slower and swelling and diffusion played a more important role. The observations of Teles are in agreement with studies of several groups that demonstrated the importance of hydrogel erosion for controlled release [12, 14].

The erosion rate of physical hydrogels is governed by the junction relaxation time. The mean relaxation time of transient networks can be manipulated either by varying the gel architecture (Chapter 3 and 4) or by changing the relaxation time of a single triple helix. The gel architecture (i.e. the number of loops and bridges) can be altered either as we show in Chapter 3 by changing the protein concentration or as we demonstrate in Chapter 4 by manipulating the design of the middle block. The number of loops becomes lower as the spacer length and stiffness increase (Chapter 4). The lifetime of a single node can be changed by enzymatic hydroxylation of proline to hydroxyproline, [15] which leads to more hydrogen bonds among adjacent T blocks, or by changing the length of the collagen-like T domains. Preliminary results showed that average relaxation time of the network is roughly hounded times higher for molecules with collagen-like domains composed of sixteen Pro-Gly-Pro repeats instead of nine (unpublished data).

For these biotechnologically produced collagen-inspired polymers, the length or the composition of the blocks can be changed simply by changing the DNA template. This, in combination with the model elaborated in Chapter 3 and 4 that links the internal gel architecture with the physicochemical gel behaviour, gives ample possibilities to design materials with custom-desired release profiles of active components.

Tissue engineering

Materials for tissue engineering scaffolds have to mimic the in vivo extracellular matrix environment. They provide physical support, but also have to guarantee proper adhesion of cells and controlled release of growth factors. A very important role in scaffolds design is played by the mechanical properties of the matrix [16-18]. As shown by Engler et al. [17], the elasticity of the matrix directs stem cell development to different lineages. Soft networks (0.1-1 kPa), which mimic brain tissue, promote neuron development, stiffer scaffolds (8-17 kPa) are myogenic, while gels with an elastic modulus of 24-40 kPa promote growth of bone cells. The stiffness of the matrix affects focal-adhesions and the organization of the cytoskeleton structure, and thus contractility, motility and spreading [16, 18]. Another significant factor, which plays a role in tissue growth is the degradation rate of the scaffold. The degradation should be synchronized with cellular repair in such a way, that tissue replaces the material within the desired time interval. The scaffold disintegration also controls the release of growth factors. For naturally derived materials such as alginate, the degradation rate could be influenced by partial oxidation of the polymer chain or via a bimodal molecular weight distribution [19]. For synthetic polymers different degradation profiles can be realized by incorporating in the polymer backbone groups with different susceptibility to hydrolysis [19].

Presently the most widely used scaffolds for tissue engineering are natural polymers such as collagen, gelatin, and polysaccharides [20] or synthetic, biodegradable polymers such as poly (L-lactic acid) (PLLA), poly(glycolic acid) (PGA), and poly(ethylene glycol) (PEG). [21-23]. Although these materials show promising properties, their use is limited as they suffer from batch to batch variations, polydispersity, viral contamination, allergic reactions or toxic byproducts after degradation. Also their mechanical properties are poorly-controlled and it is difficult to relate the molecular structure to the resulting properties. Furthermore, in the case of synthetic polymers, there is no intrinsic mechanism to interact with cells and to propagate cell adhesion proliferation or migration. This problem can be partially solved by functionalizing synthetic materials with bioactive molecules, such as collagen [24] or short peptides (for example arginine-glycine-aspartic (RGD) or tyrosine-isoleucine-glycine-serine-arginine (YIGSR) [25]). It remains difficult, however, to precisely control the spatial distribution, of these biofunctional domains [25].

A very promising alternative for the currently used scaffolds are hydrogels formed by self-assembling protein polymers [2, 26-28], including the collagen-inspired polypeptides presented in this thesis. Our block polymers form physical gels with precisely controlled elastic properties. As discussed in Chapter 3 and 4, the gel structure and the resulting mechanical properties strongly depend on concentration, temperature and on the molecular design of the polymer. Within the investigated range of conditions our gels have an elastic modulus between 0.03 and 5 kPa. Thus they seem most appropriate for neuron cell growth [17]. Moreover, it is also possible to incorporate specific short adhesive peptide sequences (such as RGD) in the middle block to improve attachment and cell propagation.

The presently investigated proteins, with T domains composed of nine Pro-Gly-Pro repeats, still need some enhancement in terms of stability. As shown by Teles et al. the currently available molecules erode within 2 days [13]. For tissue engineering applications, this is too fast. We therefore propose some strategies to stabilize our hydrogels. A first possibility alternative is to introduce amino acids which can form chemical bonds such as cysteines that can form disulfide bridges under oxidizing conditions [29], or lysines, which can be functionalized with acrylate and then photo-crosslinked with UV radiation [30-32]. However, one has to be aware that this additional procedure may have negative side effects such as toxic byproducts, incomplete polymer degradation in the body, or loss of responsiveness to external stimuli. Alternatively, the erosion can be moderately slowed down by increasing the relaxation time of the network (as discussed in section on drug delivery systems).

Wound dressing materials

Under normal circumstances wound healing is a very long process. In order to speed it up, so that bacterial infections or wound dehydration can be avoided, wound dressing materials are used [33-37]. These materials should fulfil several general requirements such as biocompability, ease of application and removal, proper adherence (to avoid fluid pockets, in which bacteria could proliferate), ease in gas exchange between tissue and environment, and controlled release of active components such as antimicrobial agents or wound repair agents (for example Epidermal Growth Factor (EGF)) [37].

All above-mentioned requirements can be fulfilled by the collagen-inspired hydrogels presented in this thesis. The advantage of our materials is that they can follow the contour of the wound and entirely fill it, thus forming an efficient barrier for microbes, but at the same time being permeable for water vapour and oxygen. Furthermore they can entrap active components and release them in a controlled way during the healing process, as discussed above. Depending on the circumstances, the release profile can be synchronised with the wound healing process. An additional advantage of our genetically engineered molecules is that adhesion domains can be introduced along the middle block, assuring better integration of the gel with the damaged tissue.

8.3 Final conclusions and outlook

In this final chapter we have discussed the potential of our collagen-inspired materials in biomedical applications. They are biocompatible and biodegradable, whilst offering numerous possibilities to change the molecular design in order to meet the desired mechanical or biological properties. Furthermore, the well-defined nature of the triple helical junctions allows us to predict the mechanical properties of the gel from the molecular design of polypeptides. This exclusive feature of our system makes it unique and offers great flexibility to design custom biomedical materials.

Biomedical needs, however, are very variable and often require an individual approach. That is why in our group we have created a family of genetically engineered block copolypeptides. Besides collagen we use other motifs present in nature, such as silk or elastin. We can combine these motifs in various ways in order to create unique stimuli-responsive (often multi-responsive) molecules that can meet individual application needs.

The silk-like domains consist of (Gly-Ala-Gly-Ala-Gly-Ala-Gly-Xxx)n repeats. Position Xxx is occupied by charged amino acids such as histidine, lysine or glutamic acid. When the charge is screened, the molecules assemble, forming first β sheet-like secondary structures, and then long fibres. As shown by Martens et al. [38], block polymers comprising silk-like domains with glutamic acid or histidine in the Xxx position form fibre-like gels at a pH of 2 or 12, respectively. They also assemble when mixed with oppositely charged (coordination) polymers [3, 38]. Probably, the assembling conditions can be tuned even more precisely by adjusting the isoelectric point of the assembling domain. This will allow the production of hydrogels that are formed after being injected into the body, while they disassemble (releasing the drug) when exposed to the acidic or the alkaline conditions. The nanofibre gels are also stable enough to serve as scaffolds for tissue engineering [39-41].

Another motif that has been used is elastin. It consists of (Val-Pro-Gly-Xxx-Gly)n repeats and it self-assembles above a lower critical solution temperature (LCST). The transition temperature can be tuned by introducing more or less polar amino acid residues in position Xxx. By combining elastin-like or collagen-like blocks with silk-like blocks, thermo and pH responsive networks can be obtained. This may allow us toswitch from fibre-like gels to associative networks.

Block polypeptides, produced using recombinant techniques, besides biocompability and biodegradability offer many possibilities to adjust the molecular design in will, to realize the desired mechanical or biological properties. Three dimensional structures with different thermal stabilities can be programmed by combining in a precise manner various amino acid sequences. The obtained materials can respond to external stimuli such as pH, ionic strength or temperature. They can also carry peptides fragments that can enhance cells adhesion and proliferation or induce crystallization.

The new approach in material science, which we present in this thesis, opens a new world of polymers, in which the main constraint is imagination.

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Altered Host-Microbe Interaction in HIV: A Target for Intervention with Pro- and Prebiotics
Hummelen, R. ; Vos, A.P. ; Land, B. van 't; Norren, K. van; Reid, G. - \ 2010
International Reviews of Immunology 29 (2010)5. - ISSN 0883-0185 - p. 485 - 513.
human-immunodeficiency-virus - randomized controlled-trial - placebo-controlled trial - coli nissle 1917 - chain galacto-oligosaccharides - active antiretroviral therapy - inflammatory bowel diseases - intestinal epithelial-cells - lactobacillus-rhamnosus-gg - ele
The intestinal immune system is severely affected by HIV and circulating microbial products from the intestinal tract that provide an ongoing source of systemic inflammation and concomitant viral replication. In addition, HIV-infected individuals can have a deregulated immune response that may hamper the anti-viral capacity of the host. Various probiotic organisms and prebiotic agents have been shown to enhance intestinal epithelial barrier functions, reduce inflammation, and support effective Th-1 responses. As these characteristics may benefit HIV patients, this review aims to provide a theoretical framework for the development of probiotic and prebiotic interventions specifically for this population.
Sodium hypochlorite: A promising agent for reducing Botrytis cinerea infection on rose flowers
Macnish, A.J. ; Morris, K.L. ; Theije, A. de; Mensink, M.G.J. ; Boerrigter, H.A.M. ; Reid, M.S. ; Jiang, C.Z. ; Woltering, E.J. - \ 2010
Postharvest Biology and Technology 58 (2010)3. - ISSN 0925-5214 - p. 262 - 267.
cut roses - chlorine - conidia - preharvest - resistance - bacteria - humidity - disease - mold
Botrytis cinerea is a fungal pathogen that greatly reduces the postharvest quality of rose flowers. A postharvest dip in 200 µL L-1 sodium hypochlorite (NaOCl) for 10 s at 20 °C provided the greatest control of B. cinerea on ‘Akito’ and ‘Gold Strike’ flowers. NaOCl derived from Clorox® Ultra household bleach solution was more effective than laboratory grade NaOCl in reducing disease symptoms. Lowering the pH of the NaOCl solution from pH 9.7 (unadjusted) to pH 7.0 greatly improved its efficacy. Treating ‘Gold Strike’ flowers in this pH-adjusted NaOCl solution was more effective in reducing the level of infection on petals than postharvest dips in the conventional fungicides Medallion®, Phyton®, Switch® and Vangard®. Applying NaOCl prior to a 3- or 10-d commercial shipment also provided the most consistent disease control for a wide range of rose cultivars as compared to conventional fungicides. Of particular interest, the efficacy of NaOCl and Phyton® was greatest when these compounds were applied to ‘Gold Strike’ flowers after incubation at 20 °C and 90% RH for 6–9 h. Our findings highlight NaOCl as a promising new candidate for the control of B. cinerea on rose flowers.
An unintended experiment in fisheries science: a marine area protected by war results in Mexican waves in fish numbers-at-age
Beare, D.J. ; Hoelker, F. ; Engelhard, G.H. ; McKenzie, E. ; Reid, D.G. - \ 2010
Naturwissenschaften 97 (2010)9. - ISSN 0028-1042 - p. 797 - 808.
ocean ecosystem services - biodiversity loss - impacts - conservation - management
Marine protected areas (MPAs) are attaining increasing importance in the management of marine ecosystems. They are effective for conservation in tropical and subtropical areas (mainly coral and rocky reefs), but it is debated whether they are useful in the management of migratory fish stocks in open temperate regions. World War II created a large marine area within which commercial fishing was prevented for 6 years. Here we analyse scientific trawl data for three important North Sea gadoids, collected between 1928 and 1958. Using statistical models to summarise the data, we demonstrate the potential of MPAs for expediting the recovery of over-exploited fisheries in open temperate regions. Our age-structured data and population models suggest that wild fish stocks will respond rapidly and positively to reductions in harvesting rates and that the numbers of older fish in a population will react before, and in much greater proportion, than their younger counterparts in a kind of Mexican wave. Our analyses demonstrate both the overall increase in survival due to the lack of harvesting in the War and the form of the age-dependent wave in numbers. We conclude that large closed areas can be very useful in the conservation of migratory species from temperate areas and that older fish benefit fastest and in greater proportion. Importantly, any rise in spawning stock biomass may also not immediately result in better recruitment, which can respond more slowly and hence take longer to contribute to higher future harvestable biomass levels
Investigating agreement between different data sources using Bayesian state-space model: an application to estimating NE Atlantic mackerel catch and stock abundance
Simmonds, E.J. ; Portilla, E. ; Skagen, D. ; Beare, D.J. ; Reid, D.G. - \ 2010
ICES Journal of Marine Science 67 (2010)6. - ISSN 1054-3139 - p. 1138 - 1153.
egg mortality - age data - parameters - management - indexes
Bayesian Markov chain Monte Carlo methods are ideally suited to analyses of situations where there are a variety of data sources, particularly where the uncertainties differ markedly among the data and the estimated parameters can be correlated. The example of Northeast Atlantic (NEA) mackerel is used to evaluate the agreement between available data from egg surveys, tagging, and catch-at-age using multiple models within the Bayesian framework WINBUGS. The errors in each source of information are dealt with independently, and there is extensive exploration of potential sources of uncertainty in both the data and the model. Model options include variation by age and over time of both selectivity in the fishery and natural mortality, varying the precision and calculation method for spawning-stock biomass derived from an egg survey, and the extent of missing catches varying over time. The models are compared through deviance information criterion and Bayesian posterior predictive p-values. To reconcile mortality estimated from the different datasets the landings and discards reported would have to have been between 1.7 and 3.6 times higher than the recorded catches.
Molecular mobility interpretation of water sorption isotherms of food materials by means of gravimetric NMR
Weglarz, W. ; Witek, M.M. ; Inoue, C. ; As, H. van; Duynhoven, J.P.M. van - \ 2010
In: Water properties in food, health, pharmaceutical and biological systems: ISOPOW 10 / Reid, D.S., Sajjaanantakul, T., Lillford, P.J., Charoenrein, S., Wiley-Blackwell - ISBN 9780813812731 - p. 411 - 418.
A review of RT-PCR technologies used in veterinary virology and disease control: sensitive and specific diagnosis of five livestock diseases notifiable to the World Organisation for Animal Health
Hoffmann, B. ; Beer, M. ; Reid, S.M. ; Mertens, P. ; Oura, C.A.L. ; Rijn, P.A. van; Slomka, M.J. ; Banks, J. ; Brown, I.H. ; Alexander, D.J. ; King, D.P. - \ 2009
Veterinary Microbiology 139 (2009)1-2. - ISSN 0378-1135 - p. 1 - 23.
polymerase-chain-reaction - foot-and-mouth - classical-swine-fever - real-time pcr - reverse-transcription-pcr - avian influenza-viruses - resonance energy-transfer - hog-cholera virus - internal positive control - mediated isothermal amplification
Real-time, reverse transcription polymerase chain reaction (rRT-PCR) has become one of the most widely used methods in the field of molecular diagnostics and research. The potential of this format to provide sensitive, specific and swift detection and quantification of viral RNAs has made it an indispensable tool for state-of-the-art diagnostics of important human and animal viral pathogens. Integration of these assays into automated liquid handling platforms for nucleic acid extraction increases the rate and standardisation of sample throughput and decreases the potential for cross-contamination. The reliability of these assays can be further enhanced by using internal controls to validate test results. Based on these advantageous characteristics, numerous robust rRT-PCRs systems have been developed and validated for important epizootic diseases of livestock. Here, we review the rRT-PCR assays that have been developed for the detection of five RNA viruses that cause diseases that are notifiable to the World Organisation for Animal Health (OIE), namely: foot-and-mouth disease, classical swine fever, bluetongue disease, avian influenza and Newcastle disease. The performance of these tests for viral diagnostics and disease control and prospects for improved strategies in the future are discussed.
Consumer Acceptability in Flower Chains: How Can We Determine What the Final Customers Really Want?
Kooten, O. van; Kuiper, W.E. - \ 2009
Acta Horticulturae 847 (2009). - ISSN 0567-7572 - p. 17 - 26.
When we look at the ornamental supply chain in the Netherlands as a Value Chain (Porter, 1998) it strikes us that most actors in the chain are obsessed by the product and have no idea how the value of these products is developed throughout the entire production and supply chain. Any value chain starts with the value a group of consumers attributes to the product. So it all starts with finding out what consumers want and then finding the most cost effective way of delivering that product with the desired attributes to these consumers. In the USA the South American producers expected to be able to compete with the local production by offering the product (cut flowers) at a lower price (Reid, 2002). In the first instance this worked very well and the local production virtually disappeared. However the quality of the imported product was a dismal failure and while imports surged, total flower consumption plummeted in the 90s. In the UK the retail chains such as Sainsbury’s and Tesco wanted to improve their ornamental categories. They invented the ‘Vase Life Guarantee’ and improved their quality considerably. This resulted in an increase in market share from 18 to 60% over 15 years, while the total flower consumption in the UK doubled in the past 15 years. A research will be shown on the response of stakeholders in the ornamental industry and consumers on the question whether they would see the ‘Vase Life Guarantee’ as a value addition in the supply chain. This research was done in the UK and the Netherlands (where no vase life guarantee was used explicitly in the retail) at the turn of the millennium. It clearly shows the difference between the judgements of the stakeholders versus the opinions of the consumers. If we want to create Value Added Chains in the ornamental industry it is about time to find out what the consumer really wants!
Potato Cultivar Genome Analysis
Reid, A. ; Hof, L. ; Esselink, D. ; Vosman, B. - \ 2009
In: Methods in Molecular Biology, Plant Pathology / Burns, R., - p. 295 - 309.
Due to the yearly increase in the numbers of new potato varieties obtaining Plant Breeders’ Rights the reliable maintenance of large culture collections of reference varieties for DUS testing is becoming more and more difficult, as accidental mix ups might occur. Efficient identification methods and databases can act as an aid to overcome this problem. Identification of cultivars by morphological characteristics is a highly skilled and time-consuming task, and for these reasons a rapid and robust method for variety differentiation has become extremely desirable. By use of a set of nine microsatellite (SSR) markers we can differentiate over 1,000 cultivars, including the majority of varieties on the European Union Common Catalogue, but excluding somaclonal variants (e.g. Red King Edward and King Edward) and mutants. The whole identification process from DNA extraction to accurate identification can be carried out in a single day.
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