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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Untargeted mass spectrometry-based metabolomics approach unveils molecular changes in raw and processed foods and beverages
Gauglitz, Julia M. ; Aceves, Christine M. ; Aksenov, Alexander A. ; Aleti, Gajender ; Almaliti, J. ; Bouslimani, A. ; Brown, Elizabeth A. ; Campeau, Anaamika ; Caraballo-Rodríguez, Andrés Mauricio ; Chaar, Rama ; Silva, Ricardo R. da; Demko, Alyssa M. ; Ottavio, Francesca Di; Elijah, Emmanuel ; Ernst, Madeleine ; Ferguson, L.P. ; Holmes, Xavier ; Jarmusch, Alan K. ; Jiang, Lingjing ; Kang, Kyo Bin ; Koester, I. ; Kwan, B. ; Li, Jie ; Li, Yueying ; Melnik, Alexey V. ; Molina-Santiago, Carlos ; Ni, B. ; Oom, Aaron L. ; Panitchpakdi, Morgan W. ; Petras, Daniel ; Quinn, Robert ; Sikora, Nicole ; Spengler, Katharina ; Teke, B. ; Tripathi, Anupriya ; Ul-Hasan, S. ; Hooft, Justin J.J. van der; Vargas, Fernando ; Vrbanac, Alison ; Vu, Anthony Q. ; Wang, Steven C. ; Weldon, K. ; Wilson, K. ; Wozniak, Jacob M. ; Yoon, Michael ; Bandeira, Nuno ; Dorrestein, Pieter C. - \ 2020
Food Chemistry 302 (2020). - ISSN 0308-8146
Fermentation - Food - LC-MS/MS - Metabolomics - Molecular networking - Tea - Untargeted mass spectrometry - Yogurt

In our daily lives, we consume foods that have been transported, stored, prepared, cooked, or otherwise processed by ourselves or others. Food storage and preparation have drastic effects on the chemical composition of foods. Untargeted mass spectrometry analysis of food samples has the potential to increase our chemical understanding of these processes by detecting a broad spectrum of chemicals. We performed a time-based analysis of the chemical changes in foods during common preparations, such as fermentation, brewing, and ripening, using untargeted mass spectrometry and molecular networking. The data analysis workflow presented implements an approach to study changes in food chemistry that can reveal global alterations in chemical profiles, identify changes in abundance, as well as identify specific chemicals and their transformation products. The data generated in this study are publicly available, enabling the replication and re-analysis of these data in isolation, and serve as a baseline dataset for future investigations.

Red LED streetlights make UK road bat-friendly
Ramakers, J.J.C. ; Ferguson, K.B. ; Veenendaal, E.M. ; Visser, M.E. - \ 2019
Effect of mass rearing on the genetic diversity of the predatory mite Amblyseius swirskii
Paspati, Angeliki ; Ferguson, Kim B. ; Verhulst, Eveline C. ; Urbaneja, Alberto ; González‐Cabrera, Joel ; Pannebakker, Bart A. - \ 2019
Entomologia Experimentalis et Applicata 167 (2019)7. - ISSN 0013-8703 - p. 670 - 681.
Amblyseius swirskii Athias‐Henriot (Acari: Phytoseiidae) is a predatory mite used to control whiteflies and thrips in protected crops. This biocontrol agent, originating from the Eastern Mediterranean region, has been mass‐reared for commercial use since 2005 and is widely used in augmentative biocontrol programs. As a polyphagous predator, it has to cope with different biotic and abiotic factors. However, possible adaptation to mass rearing for production might be hindering its resilience and capacity for optimum performance in the field. In this study, we investigated the effect of long‐term mass rearing on the genetic diversity of A. swirskii. We identified six microsatellite loci from whole‐genome nanopore sequencing of A. swirskii and used these in a comparative analysis of the genetic diversity and differentiation in eight wild populations collected from Israel in 2017 and a commercially available population. Our results indicate that the commercial population is 2.5× less heterozygous than the wild A. swirskii. Furthermore, the commercial population has the highest genetic differentiation from all the natural populations, as indicated by higher pairwise Fst values. Overall, we show that commercially reared A. swirskii have reduced genetic variation compared to their wild counterparts, which may reduce their performance when released to control pests in an integrated pest management (IPM) context.
Twenty-three unsolved problems in hydrology (UPH)–a community perspective
Blöschl, Günter ; Bierkens, Marc F.P. ; Chambel, Antonio ; Cudennec, Christophe ; Destouni, Georgia ; Fiori, Aldo ; Kirchner, James W. ; McDonnell, Jeffrey J. ; Savenije, Hubert H.G. ; Sivapalan, Murugesu ; Stumpp, Christine ; Toth, Elena ; Volpi, Elena ; Carr, Gemma ; Lupton, Claire ; Salinas, Josè ; Széles, Borbála ; Viglione, Alberto ; Aksoy, Hafzullah ; Allen, Scott T. ; Amin, Anam ; Andréassian, Vazken ; Arheimer, Berit ; Aryal, Santosh K. ; Baker, Victor ; Bardsley, Earl ; Barendrecht, Marlies H. ; Bartosova, Alena ; Batelaan, Okke ; Berghuijs, Wouter R. ; Beven, Keith ; Blume, Theresa ; Bogaard, Thom ; Borges de Amorim, Pablo ; Böttcher, Michael E. ; Boulet, Gilles ; Breinl, Korbinian ; Brilly, Mitja ; Brocca, Luca ; Buytaert, Wouter ; Castellarin, Attilio ; Castelletti, Andrea ; Chen, Xiaohong ; Chen, Yangbo ; Chen, Yuanfang ; Chifflard, Peter ; Claps, Pierluigi ; Clark, Martyn P. ; Collins, Adrian L. ; Croke, Barry ; Dathe, Annette ; David, Paula C. ; Barros, Felipe P.J. de; Rooij, Gerrit de; Baldassarre, Giuliano Di; Driscoll, Jessica M. ; Duethmann, Doris ; Dwivedi, Ravindra ; Eris, Ebru ; Farmer, William H. ; Feiccabrino, James ; Ferguson, Grant ; Ferrari, Ennio ; Ferraris, Stefano ; Fersch, Benjamin ; Finger, David ; Foglia, Laura ; Fowler, Keirnan ; Gartsman, Boris ; Gascoin, Simon ; Gaume, Eric ; Gelfan, Alexander ; Geris, Josie ; Gharari, Shervan ; Gleeson, Tom ; Glendell, Miriam ; Gonzalez Bevacqua, Alena ; González-Dugo, María P. ; Grimaldi, Salvatore ; Gupta, A.B. ; Guse, Björn ; Han, Dawei ; Hannah, David ; Harpold, Adrian ; Haun, Stefan ; Heal, Kate ; Helfricht, Kay ; Herrnegger, Mathew ; Hipsey, Matthew ; Hlaváčiková, Hana ; Hohmann, Clara ; Holko, Ladislav ; Hopkinson, Christopher ; Hrachowitz, Markus ; Illangasekare, Tissa H. ; Inam, Azhar ; Innocente, Camyla ; Istanbulluoglu, Erkan ; Jarihani, Ben ; Kalantari, Zahra ; Kalvans, Andis ; Khanal, Sonu ; Khatami, Sina ; Kiesel, Jens ; Kirkby, Mike ; Knoben, Wouter ; Kochanek, Krzysztof ; Kohnová, Silvia ; Kolechkina, Alla ; Krause, Stefan ; Kreamer, David ; Kreibich, Heidi ; Kunstmann, Harald ; Lange, Holger ; Liberato, Margarida L.R. ; Lindquist, Eric ; Link, Timothy ; Liu, Junguo ; Loucks, Daniel Peter ; Luce, Charles ; Mahé, Gil ; Makarieva, Olga ; Malard, Julien ; Mashtayeva, Shamshagul ; Maskey, Shreedhar ; Mas-Pla, Josep ; Mavrova-Guirguinova, Maria ; Mazzoleni, Maurizio ; Mernild, Sebastian ; Misstear, Bruce Dudley ; Montanari, Alberto ; Müller-Thomy, Hannes ; Nabizadeh, Alireza ; Nardi, Fernando ; Neale, Christopher ; Nesterova, Nataliia ; Nurtaev, Bakhram ; Odongo, Vincent O. ; Panda, Subhabrata ; Pande, Saket ; Pang, Zhonghe ; Papacharalampous, Georgia ; Perrin, Charles ; Pfister, Laurent ; Pimentel, Rafael ; Polo, María J. ; Post, David ; Prieto Sierra, Cristina ; Ramos, Maria Helena ; Renner, Maik ; Reynolds, José Eduardo ; Ridolfi, Elena ; Rigon, Riccardo ; Riva, Monica ; Robertson, David E. ; Rosso, Renzo ; Roy, Tirthankar ; Sá, João H.M. ; Salvadori, Gianfausto ; Sandells, Mel ; Schaefli, Bettina ; Schumann, Andreas ; Scolobig, Anna ; Seibert, Jan ; Servat, Eric ; Shafiei, Mojtaba ; Sharma, Ashish ; Sidibe, Moussa ; Sidle, Roy C. ; Skaugen, Thomas ; Smith, Hugh ; Spiessl, Sabine M. ; Stein, Lina ; Steinsland, Ingelin ; Strasser, Ulrich ; Su, Bob ; Szolgay, Jan ; Tarboton, David ; Tauro, Flavia ; Thirel, Guillaume ; Tian, Fuqiang ; Tong, Rui ; Tussupova, Kamshat ; Tyralis, Hristos ; Uijlenhoet, Remko ; Beek, Rens van; Ent, Ruud J. van der; Ploeg, Martine van der; Loon, Anne F. Van; Meerveld, Ilja van; Nooijen, Ronald van; Oel, Pieter R. van; Vidal, Jean Philippe ; Freyberg, Jana von; Vorogushyn, Sergiy ; Wachniew, Przemyslaw ; Wade, Andrew J. ; Ward, Philip ; Westerberg, Ida K. ; White, Christopher ; Wood, Eric F. ; Woods, Ross ; Xu, Zongxue ; Yilmaz, Koray K. ; Zhang, Yongqiang - \ 2019
Hydrological Sciences Journal 64 (2019)10. - ISSN 0262-6667 - p. 1141 - 1158.
hydrology - interdisciplinary - knowledge gaps - research agenda - science questions

This paper is the outcome of a community initiative to identify major unsolved scientific problems in hydrology motivated by a need for stronger harmonisation of research efforts. The procedure involved a public consultation through online media, followed by two workshops through which a large number of potential science questions were collated, prioritised, and synthesised. In spite of the diversity of the participants (230 scientists in total), the process revealed much about community priorities and the state of our science: a preference for continuity in research questions rather than radical departures or redirections from past and current work. Questions remain focused on the process-based understanding of hydrological variability and causality at all space and time scales. Increased attention to environmental change drives a new emphasis on understanding how change propagates across interfaces within the hydrological system and across disciplinary boundaries. In particular, the expansion of the human footprint raises a new set of questions related to human interactions with nature and water cycle feedbacks in the context of complex water management problems. We hope that this reflection and synthesis of the 23 unsolved problems in hydrology will help guide research efforts for some years to come.

Identifying Dietary Strategies to Improve Nutrient Adequacy among Ethiopian Infants and Young Children Using Linear Modelling
Samuel, Aregash ; Osendarp, Saskia J.M. ; Ferguson, Elaine ; Borgonjen, Karin ; Alvarado, Brenda M. ; Neufeld, Lynnette M. ; Adish, Abdulaziz ; Kebede, Amha ; Brouwer, Inge D. - \ 2019
Nutrients 11 (2019)6. - ISSN 2072-6643
complementary food - Ethiopia - food-based dietary recommendations - nutrient adequacy - Optifood analysis

Nutrient adequacy of young children's diet and best possible strategies to improve nutrient adequacy were assessed. Data from the Ethiopian National Food Consumption Survey were analysed using Optifood (software for linear programming) to identify nutrient gaps in diets for children (6-8, 9-11 and 12-23 months), and to formulate feasible Food-Based Dietary Recommendations (FBDRs) in four regions which differ in culture and food practices. Alternative interventions including a local complementary food, micronutrient powders (MNPs), Small quantity Lipid-based Nutrient Supplement (Sq-LNS) and combinations of these were modelled in combination with the formulated FBDRs to compare their relative contributions. Risk of inadequate and excess nutrient intakes was simulated using the Estimated Average Requirement cut-point method and the full probability approach. Optimized local diets did not provide adequate zinc in all regions and age groups, iron for infants <12 months of age in all regions, and calcium, niacin, thiamine, folate, vitamin B12 and B6 in some regions and age-groups. The set of regional FBDRs, considerably different for four regions, increased nutrient adequacy but some nutrients remained sub-optimal. Combination of regional FBDRs with daily MNP supplementation for 6-12 months of age and every other day for 12-23 months of age, closed the identified nutrient gaps without leading to a substantial increase in the risk of excess intakes.

Repurposing isoxazoline veterinary drugs for control of vector-borne human diseases
Miglianico, Marie ; Eldering, Maarten ; Slater, Hannah ; Ferguson, Neil ; Ambrose, Pauline ; Lees, Rosemary S. ; Koolen, Karin M.J. ; Pruzinova, Katerina ; Jancarova, Magdalena ; Volf, Petr ; Koenraadt, Constantianus J.M. ; Duerr, Hans Peter ; Trevitt, Graham ; Yang, Baiyuan ; Chatterjee, Arnab K. ; Wisler, John ; Sturm, Angelika ; Bousema, Teun ; Sauerwein, Robert W. ; Schultz, Peter G. ; Tremblay, Matthew S. ; Dechering, Koen J. - \ 2018
Proceedings of the National Academy of Sciences of the United States of America 115 (2018)29. - ISSN 0027-8424 - p. E6920 - E6926.
Insecticide - Isoxazoline - Malaria - Vector control - Zika fever

Isoxazolines are oral insecticidal drugs currently licensed fo ectoparasite control in companion animals. Here we propose thei use in humans for the reduction of vector-borne disease incidence Fluralaner and afoxolaner rapidly killed Anopheles, Aedes, an Culex mosquitoes and Phlebotomus sand flies after feeding on drug-supplemented blood meal, with IC50 values ranging from 33 to 575 nM, and were fully active against strains with preexist ing resistance to common insecticides. Based on allometric scalin of preclinical pharmacokinetics data, we predict that a single hu man median dose of 260 mg (IQR, 177–407 mg) for afoxolaner, o 410 mg (IQR, 278–648 mg) for fluralaner, could provide an insecti cidal effect lasting 50–90 days against mosquitoes and Phleboto mus sand flies. Computational modeling showed that seasona mass drug administration of such a single dose to a fraction of regional population would dramatically reduce clinical cases o Zika and malaria in endemic settings. Isoxazolines therefore rep resent a promising new component of drug-based vector control.

Land-atmosphere interactions the LoCo perspective
Santanello, Joseph A. ; Dirmeyer, Paul A. ; Ferguson, Craig R. ; Findell, Kirsten L. ; Tawfik, Ahmed B. ; Berg, Alexis ; Ek, Michael ; Gentine, Pierre ; Guillod, Benoit P. ; Heerwaarden, Chiel van; Roundy, Joshua ; Wulfmeyer, Volker - \ 2018
Bulletin of the American Meteorological Society 99 (2018)6. - ISSN 0003-0007 - p. 1253 - 1272.

Metrics derived by the LoCo working group have matured and begun to enter the mainstream, signaling the success of the GEWEX approach to foster grassroots participation.

BIOFOS: A micro-ring resonator-based biophotonic system for food analysis - Application to olive oil contaminants
Romero, A. ; Ninot, A. ; Hermoso, J.F. ; Zergioti, I. ; Kouloumentas, C. ; Avramopoulos, H. ; Leeuwis, H. ; Schreuder, E. ; Graf, S. ; Knapp, H. ; Barthelmebs, L. ; Noguer, T. ; Tsekenis, G. ; Scheres, L. ; Smulders, M. ; Zuilhof, H. ; Heesink, G. ; Reguillo, L. - \ 2018
In: Proceedings of the 8th International Olive Symposium. - International Society for Horticultural Science (Acta Horticulturae ) - ISBN 9789462611955 - p. 505 - 509.
Analysis of pesticides and heavy metals - Copper - Oil quality - Organophosphates

Current detection methods for contaminants in food use high-tech equipment sited in specialized laboratories. This makes online quality control along the food chain difficult. Official regulations limit pesticide and heavy-metal contamination, mainly for organic production, although their analysis is quite expensive, requires skilled personnel and is very difficult to apply to a large number of oil batches. The BIOFOS Project (ICT-FP7-GA.N.611528) aims to develop and validate a Lab-on-a-Chip (LoC) multianalyser, based on micro-biophotonic sensors, for in-situ food contaminant analysis. This device includes biosensors for milk analysis (aflatoxin M1, antibiotic and lactose), nuts (aflatoxin B1), dried fruits (ochratoxin A) and olive oil (organophosphates and metals). BIOFOS combines four high-tech platforms: (1) a photonic platform based on micro-ring resonators (MRR) for signal quantification, (2) a biological platform based on aptamers for analyte detection, (3) a nanochemical platform to immobilize aptamers onto the chip surface and (4) a microfluidic platform for sample pre-treatment and its loading into the biosensor. The project is organized in work packages in order to develop the technological platforms. End-user requirements are also considered, as well as existing fast analysis kits that will be compared against the device. Validation protocols and exploitation plans are also included. BIOFOS applications for olive oil analysis are discussed, in terms of accuracy, sensitivity, time-to-result and cost per sample.

Reconfiguration of Hydrosocial Territories and Struggles for Water Justice : from Part II - Hydrosocial De-Patterning and Re-Composition
Hommes, L.M. ; Boelens, R.A. ; Duarte Abadia, Bibiana ; Hidalgo, Jean Pablo ; Hoogesteger van Dijk, J.D. - \ 2018
In: Water Justice / Boelens, R., Perreault, T., Vos, J., Cambridge : Cambridge University Press - ISBN 9781107179080 - p. 151 - 168.
Introduction A vast and growing body of scholarly studies has shown how large-scale hydraulic and hydro-managerial projects, such as large dam and irrigation developments or market-environmentalist ecosystem payment schemes, have diverse socio-cultural and political-economic implications beyond merely altering water flows and raising socio-economic productivity. Concepts such as the hydrosocial cycle (Boelens, 2014; Linton and Budds, 2014), waterscapes (Baviskar, 2007; Budds and Hinojosa-Valencia, 2012; Swyngedouw, 1999) and water as socio-nature (Barnes and Alatout, 2012; Perreault, 2014) express connected insights about water being coproduced by social relations and in turn shaping these relations. The hydrosocial cycle, for instance, is described as a socio-natural process in which “water and society make and remake each other over space and time” cyclically (Linton and Budds, 2014: 170). Such coproduction of water and society is also reflected in the notion of waterscapes, conceptualized as socio-spatial configurations of water flows, artifacts, institutions and imaginaries embodying a particular world view (Budds and Hinojosa-Valencia, 2012; Zwarteveen 2015). However, these notions have so far largely focused on established hegemonic structures and discourses that drive and succeed from waterscape configurations. Less attention has been given to the multiplicity of diverging and overlapping hydrosocial territories that exist within one and the same space. To address this, we employ the hydrosocial territories approach, analyzing water territories not merely as materializations of dominant discourses and interests, but as multi-scalar networks in which water flows, hydraulic infrastructure, legal-administrative and financial systems, and socio-cultural institutions and practices are interactively produced, aligned, negotiated and contested (Boelens et al., 2016). Furthermore, combining the hydrosocial territories notion with Foucault’s governmentality approach highlights different forms of “government rationalities” and how they are entwined with hydraulic and hydro-managerial projects. We focus specifically on analyzing how ruling groups’ efforts to “conduct the conduct” of the governed (Foucault, 2008: 313) penetrate, operate through, and assimilate the rationality of the governed to advance neoliberal projects (Fletcher, 2010; Hommes et al., 2016; Zwarteveen and Boelens, 2014). Building on the work of Agnew (1994), Gupta and Ferguson (1992) and Elden (2010), we understand territories not as fixed spaces, but as spatially entrenched multi-scalar networks evolving from social interactions and practices, and materializations of these practices (see also Baletti, 2012; Brighenti, 2010). Social encounters and acts, including legal-administrative arrangements, technical reconfigurations and symbolic, cultural and political mechanisms of boundary-and place-making, actively produce territories.
Going for the dough : Engaging governmental funds in the Ciénega de Zacapu, Mexico
Servin Juárez, Fidencio - \ 2018
Wageningen University. Promotor(en): L.E. Visser, co-promotor(en): G.M. Verschoor. - Wageningen : Wageningen University - ISBN 9789463438292 - 167

This study follows a planned development intervention involving greenhouse production systems for tomatoes. The intervention played out in Mexico, where the Planning Sub- Committee for Regional Development (SUPLADER) promoted a strategy for the "development" of the Zacapu region in Michoacán, from 2002 to 2005. The intervention is illustrated through a detailed, in-depth ethnographic case study of the way in which the Unión de Invernaderos Ruta de la Libertad (a USPR or Union of Rural Producers Association) sought to materialize a greenhouse project.

Using an actor-oriented perspective (Long, 2001; Nuijten, 2001; Diego, 1997) and the concepts of actor’s agency, networks, associations, collectives and organizing processes, the study aims to understand the character of intervention, and shows how programs and development projects serve different purposes – purposes which symbiotically relate to the prevailing social conditions. As a general conclusion, I argue that what is called “the dough” (la lana) is what drives the dynamics of development intervention. While important, it is central to understand the different roles “the dough” plays in these intervention settings: for planners, it is the means to accomplish development, whereas for project beneficiaries it is a goal in itself.

Chapter 1 elaborates on the general context of planned intervention in Michoacán’s Zacapu region, delineates the theoretical framework, presents the main research question (How do stakeholders organize themselves around the greenhouse project, and how do they redefine the view of planned development by the local government?) and elaborates on the methodology employed.

Chapter 2 describes the organizing processes underlying implementation of the greenhouse project in the Zacapu - Ciénega region. It explains how, in order to acquire resources for the project, stakeholders organized into groups, forming Rural Production Associations (SPRs) and Unions of Rural Producers’ Associations (USPRs). As a result, a total of 28 SPRs were formed. For the most part, members of these SPRs had extensive, prior experience in organizing and participating in programs similar to those promoted by SUPLADER.

Chapter 3 describes the practices of the eight groups (SPR) who got no resources from SUPLADER and seek to compensate for an initial investment from the Alliance for the Countryside (Alianza). To complete the project file, the groups were linked to government agencies, municipalities and communities as well as with external agents (firms) to use the register as a professional services provider (PSP) and enter the file to the Alianza program. In addition, power differences and conflict relationships were evident (Lukes, 1974); conditions that led to negotiation (Diego, 1997).

Advisor firms were considered necessary for the negotiations since their capabilities were required and considered essential for the expected benefit of the Asociación, although they appeared to be a very powerful party. Despite the regulations established by the State to exercise governmental programs, the parties responsible for exercising them applied ambiguous criteria.

Chapter 4 describes the development of an ideal configuration of greenhouses that included technological, social and cultural elements associated with safety practices, automation and demanding consumers located in an international market. This perception was far from the project conditions of greenhouses in La Ciénega; however, it did not prevent generating expectations among the SPRs. For these actors, the greenhouse became an alternative livelihood, income, and development opportunity.

To interpret the processes described I used Latour’s (2008) notion of a sociology of associations; this allowed me to interpret how actor-networks were incorporated in the greenhouse project.

Chapter 5 describes a breakaway attempt from the Asociación spearheaded by 17 SPRs that chose to build their greenhouses with an alternative hardware supplier (ACEA). To obtain the necessary funds new negotiations were started with a range of agencies. The move eventually strengthened the Asociación and its institutional embeddedness.

In Chapter 6, the Asociación is shown to be a heterogeneous collective with different agendas. This resulted in several conflicts, some of them, involving the advisory offices that intended to take the resources (“the dough”) from the project. Nonetheless, a regional bank authorized a cash disbursement for the initial stage of the greenhouse project.

Chapter 7 presents the final stage of SUPLADER Zacapu’s greenhouse project. After complex negotiations and conflicts within the Asociación, complementary credit was obtained for the construction of the greenhouse. However, during a municipal election campaign key figures in charge of implementation changed position; this led to a change in project conditions, and the Asociación had to face interventions from external actors. The negotiation game restarted and triggered a new set of strategies (amongst others to obtain money directly through the new SEPLADE delegate). Eventually, some of the Asociación’s funds were reappropriated and assigned to USPR Agrícola Tsakapu and different factions (vying for of resources) resulted fom this.

Chapter 8 provides the discussion and conclusion to this thesis, with insights that build on Mosse’s (2005) argument that policies to promote development are associated to organizational demands and needs to maintain existing relationships (rather than promoting a previously defined policy). However, in the case of La Ciénega, the agents of change (including the Michoacán Congress) supported and pushed through planners’ development initiatives. In line with Ferguson (1994), I conclude that development must be understood in relation to the political-economic-cultural interests of those behind its design and implementation. Rather than linear, hegemonic and rigid, however, actors’ practices and strategies mould and twist planned development intervention to suit their needs and desires.

Seagrass ecosystem trajectory depends on the relative timescales of resistance, recovery and disturbance
O'Brien, Katherine R. ; Waycott, Michelle ; Maxwell, Paul ; Kendrick, Gary A. ; Udy, James W. ; Ferguson, Angus J.P. ; Kilminster, Kieryn ; Scanes, Peter ; McKenzie, Len J. ; McMahon, Kathryn ; Adams, Matthew P. ; Samper-Villarreal, Jimena ; Collier, Catherine ; Lyons, Mitchell ; Mumby, Peter J. ; Radke, Lynda ; Christianen, Marjolijn J.A. ; Dennison, William C. - \ 2018
Marine Pollution Bulletin 134 (2018). - ISSN 0025-326X - p. 166 - 176.
Colonizing - Opportunistic - Persistent - Recovery - Resilience - Resistance - Seagrass - Trajectory
Seagrass ecosystems are inherently dynamic, responding to environmental change across a range of scales. Habitat requirements of seagrass are well defined, but less is known about their ability to resist disturbance. Specific means of recovery after loss are particularly difficult to quantify. Here we assess the resistance and recovery capacity of 12 seagrass genera. We document four classic trajectories of degradation and recovery for seagrass ecosystems, illustrated with examples from around the world. Recovery can be rapid once conditions improve, but seagrass absence at landscape scales may persist for many decades, perpetuated by feedbacks and/or lack of seed or plant propagules to initiate recovery. It can be difficult to distinguish between slow recovery, recalcitrant degradation, and the need for a window of opportunity to trigger recovery. We propose a framework synthesizing how the spatial and temporal scales of both disturbance and seagrass response affect ecosystem trajectory and hence resilience.
The potential contribution of yellow cassava to dietary nutrient adequacy of primary-school children in Eastern Kenya; the use of linear programming
Talsma, Elise F. ; Borgonjen-van den Berg, Karin J. ; Melse-Boonstra, Alida ; Mayer, Eva V. ; Verhoef, Hans ; Demir, Ayşe Y. ; Ferguson, Elaine L. ; Kok, Frans J. ; Brouwer, Inge D. - \ 2018
Public Health Nutrition 21 (2018)2. - ISSN 1368-9800 - p. 365 - 376.
Biofortification - Linear programming - Optifood - Vitamin A deficiency - Yellow cassava

Objective: Introduction of biofortified cassava as school lunch can increase vitamin A intake, but may increase risk of other deficiencies due to poor nutrient profile of cassava. We assessed the potential effect of introducing a yellow cassava-based school lunch combined with additional food-based recommendations (FBR) on vitamin A and overall nutrient adequacy using Optifood (linear programming tool). Design: Cross-sectional study to assess dietary intakes (24 h recall) and derive model parameters (list of foods consumed, median serving sizes, food and food (sub)group frequency distributions, food cost). Three scenarios were modelled, namely daily diet including: (i) no school lunch; (ii) standard 5d school lunch with maize/beans; and (iii) 5d school lunch with yellow cassava. Each scenario and scenario 3 with additional FBR were assessed on overall nutrient adequacy using recommended nutrient intakes (RNI). Setting: Eastern Kenya. Subjects: Primary-school children (n 150) aged 7–9 years. Results: Best food pattern of yellow cassava-based lunch scenario achieved 100 % RNI for six nutrients compared with no lunch (three nutrients) or standard lunch (five nutrients) scenario. FBR with yellow cassava and including small dried fish improved nutrient adequacy, but could not ensure adequate intake of fat (52 % of average requirement), riboflavin (50 % RNI), folate (59 % RNI) and vitamin A (49 % RNI). Conclusions: Introduction of yellow cassava-based school lunch complemented with FBR potentially improved vitamin A adequacy, but alternative interventions are needed to ensure dietary adequacy. Optifood is useful to assess potential contribution of a biofortified crop to nutrient adequacy and to develop additional FBR to address remaining nutrient gaps.

Development of a dichotomous indicator for population-level assessment of dietary diversity in women of reproductive age
Martin-Prevel, Yves ; Arimond, Mary ; Allemand, Pauline ; Wiesmann, Doris ; Ballard, Terri J. ; Deitchler, Megan ; Dop, Marie Claude ; Kennedy, Gina ; Lartey, Anna ; Lee, Warren T.K. ; Moursi, Mourad ; Becquey, Elodie ; Brouwer, Inge D. ; Carriquiry, Alicia ; Daniels, Melissa C. ; Fanou-Fogny, Nadia ; Ferguson, Elaine ; Joseph, Maria L. ; Ruel, Marie T. ; Torheim, Liv Elin - \ 2017
Current Developments in Nutrition 1 (2017)12. - ISSN 2475-2991
Developing countries - Diet quality - Dietary diversity - Food groups - Indicator - Nutrition-sensitive interventions - Resource-poor settings - Women of reproductive age

Background: Dietary diversity is a key element of diet quality, but diets of women of reproductive age (WRA; aged 15-49 y) in resource-poor settings are often deficient in a range of micronutrients. Previous work showed associations between simple food-group diversity indicators (FGIs) and micronutrient adequacy among WRA. For operational and advocacy purposes, however, there is strong demand for a dichotomous indicator reflecting an acceptable level of dietary diversity. Objective: The aim of the study was to develop a dichotomous indicator of dietary diversity inWRA. Methods: We performed a secondary analysis of 9 data sets containing quantitative dietary data from WRA in resource-poor settings (total n = 4166). From the raw dietary data, we calculated an individual "mean probability of adequacy" (MPA) across 11 micronutrients. Several candidate FGIs were constructed. Indicator performance in predicting an MPA > 0.60 was assessed within each data set by using receiver-operating characteristic analysis and sensitivity and specificity analysis at various FGI cutoffs. The analysis was performed separately for nonpregnant and nonlactating (NPNL) women and for lactating women. Results: We identified 2 "best candidate" dichotomous indicators on the basis of 9- or 10-point food-group scores (FGI-9 and FGI-10) with a cutoff of ≥ 5 food groups. Both were significantly correlated to MPA in each site (P < 0.001). Areas under the curve were moderate, ranging from 0.62 to 0.82 among NPNL women and from 0.56 to 0.90 among lactating women. Comparisons of results slightly favored FGI-10 for all women. Conclusions: When resource-intensive dietary methods are not feasible, a simple dichotomous indicator based on a cutoff of ≥ 5 of 10 defined food groups reflects "minimum dietary diversity for women of reproductive age." According to the conclusions of a consensus meeting of experts, this indicator is well suited for population-level assessment, advocacy, and possibly also for tracking of change in dietary diversity across time.

Data from: Response of bats to light with different spectra: light-shy and agile bat presence is affected by white and green, but not red light
Spoelstra, K. ; Grunsven, R.H.A. van; Ramakers, Jip J.C. ; Ferguson, Kim B. ; Raap, Thomas ; Donners, Maurice ; Veenendaal, E.M. ; Visser, Marcel E. - \ 2017
light pollution - experimental light at night - bats - light colour
Artificial light at night has shown a remarkable increase over the past decades. Effects are reported for many species groups, and include changes in presence, behaviour, physiology and life-history traits. Among these, bats are strongly affected, and how bat species react to light is likely to vary with light colour. Different spectra may therefore be applied to reduce negative impacts. We used a unique set-up of eight field sites to study the response of bats to three different experimental light spectra in an otherwise dark and undisturbed natural habitat. We measured activity of three bat species groups around transects with light posts emitting white, green and red light with an intensity commonly used to illuminate countryside roads. The results reveal a strong and spectrum-dependent response for the slow-flying Myotis and Plecotus and more agile Pipistrellus species, but not for Nyctalus and Eptesicus species. Plecotus and Myotis species avoided white and green light, but were equally abundant in red light and darkness. The agile, opportunistically feeding Pipistrellus species were significantly more abundant around white and green light, most likely because of accumulation of insects, but equally abundant in red illuminated transects compared to dark control. Forest-dwelling Myotis and Plecotus species and more synanthropic Pipistrellus species are thus least disturbed by red light. Hence, in order to limit the negative impact of light at night on bats, white and green light should be avoided in or close to natural habitat, but red lights may be used if illumination is needed.
Nutritional strategies to establish a responsible use of antibiotics in swine
Hartog, L.A. den; Hees, H. van; Ferguson, N. ; Smits, C. - \ 2017
In: Proceedings Banff Pork Seminar. - University of Alberta (Advances in Pork Production ) - p. 177 - 188.
Response of bats to light with different spectra : Light-shy and agile bat presence is affected by white and green, but not red light
Spoelstra, Kamiel ; Grunsven, Roy H.A. van; Ramakers, Jip J.C. ; Ferguson, Kim B. ; Raap, Thomas ; Donners, Maurice ; Veenendaal, Elmar M. ; Visser, Marcel E. - \ 2017
Proceedings of the Royal Society. B: Biological Sciences 284 (2017)1855. - ISSN 0962-8452
Bats - Experimental light at night - Light colour - Light pollution

Artificial light at night has shown a remarkable increase over the past decades. Effects are reported for many species groups, and include changes in presence, behaviour, physiology and life-history traits. Among these, bats are strongly affected, and how bat species react to light is likely to vary with light colour. Different spectra may therefore be applied to reduce negative impacts. We used a unique set-up of eight field sites to study the response of bats to three different experimental light spectra in an otherwise dark and undisturbed natural habitat. We measured activity of three bat species groups around transects with light posts emitting white, green and red light with an intensity commonly used to illuminate countryside roads. The results reveal a strong and spectrum-dependent response for the slowflying Myotis and Plecotus and more agile Pipistrellus species, but not for Nyctalus and Eptesicus species. Plecotus and Myotis species avoided white and green light, but were equally abundant in red light and darkness. The agile, opportunistically feeding Pipistrellus species were significantly more abundant around white and green light, most likely because of accumulation of insects, but equally abundant in red illuminated transects compared to dark control. Forest-dwelling Myotis and Plecotus species and more synanthropic Pipistrellus species are thus least disturbed by red light. Hence, in order to limit the negative impact of light at night on bats, white and green light should be avoided in or close to natural habitat, but red lights may be used if illumination is needed.

Integere relaties: wetenschappelijke integriteit en de verhouding tussen wetenschap en samenleving
Turnhout, E. - \ 2017
Beleid en maatschappij 44 (2017)1. - ISSN 0165-1625
Wetenschap staat onder druk. Dat lijken althans wetenschappers zelf in groten getale te vinden. Wetenschap moet haar autoriteit en geloofwaardigheid terugkrijgen, zichzelf opnieuw uitvinden en ze moet haar publieke functie in de democratie weer gaan vervullen. Hoewel de verschillende bijdragen aan het debat hierover allemaal het huidige wetenschapssysteem bekritiseren, is het belangrijk om te beseffen dat ze niet allemaal hetzelfde zeggen of dezelfde doelen voor ogen hebben. Sommigen lijken vooral uit te zijn op het (her)winnen van respect en autoriteit voor de wetenschap (Nurse, 2012; Van Dijck & Saarloos, 2017). Anderen uiten kritiek op de over-gemanagede universiteit en de nadruk op kwantitatieve prestatie-indicatoren (Benedictus, Miedema & Ferguson, 2016; Halffman &Radder, 2013). Weer anderen leggen de nadruk op de relatie tussen wetenschap en samenleving en suggereren dat het tijd is voor een nieuw contract tussen wetenschap en samenleving (Gibbons, 1999; Sarewitz, 2016). In dit essay richt ik me op dit laatste onderwerp: de relatie tussen wetenschap en maatschappij. Ik geef eerst een overzicht van dominante idealen over hoe deze relatie het beste kan worden georganiseerd en van de kritiek die is geuit tegen deze idealen. Vervolgens illustreer ik, aan de hand van een voorbeeld over statiegeldonderzoek, de risico’s en knelpunten die kunnen optreden als niet zorgvuldig wordt nagedacht over welke rol wetenschap in verschillende vraagstukken kan spelen. Op basis daarvan pleit ik voor een verbreding van het begrip ‘wetenschappelijke integriteit’, zodat die niet alleen betrekking heeft op het gedrag van individuele wetenschappers, maar ook op de institutionele relaties en maatschappelijke context waarin wetenschappers handelen.
Loss of animal seed dispersal increases extinction risk in a tropical tree species due to pervasive negative density dependence across life stages
Caughlin, T.T. ; Ferguson, J.M. ; Lichstein, J.W. ; Zuidema, P.A. ; Bunyavejchewin, S. ; Levey, D.J. - \ 2015
Proceedings of the Royal Society. B: Biological Sciences 282 (2015)1798. - ISSN 0962-8452 - 9 p.
spatial-patterns - rain-forest - recruitment - consequences - neighborhood - defaunation - habitat - uncertainty - diversity - abundance
Overhunting in tropical forests reduces populations of vertebrate seed dispersers. If reduced seed dispersal has a negative impact on tree population viability, overhunting could lead to altered forest structure and dynamics, including decreased biodiversity. However, empirical data showing decreased animal-dispersed tree abundance in overhunted forests contradict demographic models which predict minimal sensitivity of tree population growth rate to early life stages. One resolution to this discrepancy is that seed dispersal determines spatial aggregation, which could have demographic consequences for all life stages. We tested the impact of dispersal loss on population viability of a tropical tree species, Miliusa horsfieldii, currently dispersed by an intact community of large mammals in a Thai forest. We evaluated the effect of spatial aggregation for all tree life stages, from seeds to adult trees, and constructed simulation models to compare population viability with and without animal-mediated seed dispersal. In simulated populations, disperser loss increased spatial aggregation by fourfold, leading to increased negative density dependence across the life cycle and a 10-fold increase in the probability of extinction. Given that the majority of tree species in tropical forests are animal-dispersed, overhunting will potentially result in forests that are fundamentally different from those existing now.
Data from: Loss of animal seed dispersal increases extinction risk in a tropical tree species due to pervasive negative density dependence across life stages
Caughlin, T.T. ; Ferguson, J.M. ; Lichstein, J.W. ; Zuidema, Pieter ; Bunyavejchewin, S. ; Levey, D.J. - \ 2014
University of Florida
tropical forests - Anthropocene - fruit production - neighborhood model - seed addition experment - Saccopetalum - extinction - germination - tree demography - seedling demography - tree population - seedlings - neighborhood - tropical forest dynamics - negative density dependence - Miliusa - Annonaceae - seed dispersal - spatial model - Frugivory - Miliusa horsfieldii - overhunting
Overhunting in tropical forests reduces populations of vertebrate seed dispersers. If reduced seed dispersal has a negative impact on tree population viability, overhunting could lead to altered forest structure and dynamics, including decreased biodiversity. However, empirical data showing decreased animal-dispersed tree abundance in overhunted forests contradict demographic models which predict minimal sensitivity of tree population growth rate to early life stages. One resolution to this discrepancy is that seed dispersal determines spatial aggregation, which could have demographic consequences for all life stages. We tested the impact of dispersal loss on population viability of a tropical tree species, Miliusa horsfieldii, currently dispersed by an intact community of large mammals in a Thai forest. We evaluated the effect of spatial aggregation for all tree life stages, from seeds to adult trees, and constructed simulation models to compare population viability with and without animal-mediated seed dispersal. In simulated populations, disperser loss increased spatial aggregation by fourfold, leading to increased negative density dependence across the life cycle and a 10-fold increase in the probability of extinction. Given that the majority of tree species in tropical forests are animal-dispersed, overhunting will potentially result in forests that are fundamentally different from those existing now.
Association of total mixed ration particle fractions retained on the Penn State Particle Separator with milk, fat, and protein yield lactation curves at the cow level
Caccamo, M. ; Ferguson, J.D. ; Veerkamp, R.F. ; Schadt, I. ; Petriflieri, R. ; Azzaro, G. ; Pozzebon, A. ; Licitra, G. - \ 2014
Journal of Dairy Science 97 (2014)4. - ISSN 0022-0302 - p. 2502 - 2511.
physically effective fiber - neutral detergent fiber - dairy-cows - grain fermentability - rumen fermentation - midlactation cows - corn-silage - ruminal ph - size - forage
As part of a larger project aiming to develop management evaluation tools based on results from test-day (TD) models, the objective of this study was to examine the effect of physical composition of total mixed rations (TMR) tested quarterly from March 2006 through December 2008 on milk, fat, and protein yield curves for 25 herds in Ragusa, Sicily. A random regression sire-maternal grandsire model was used to estimate variance components for milk, fat, and protein yields fitted on a full data set, including 241,153 TD records from 9,809 animals in 42 herds recorded from 1995 through 2008. The model included parity, age at calving, year at calving, and stage of pregnancy as fixed effects. Random effects were herd × test date, sire and maternal grandsire additive genetic effect, and permanent environmental effect modeled using third-order Legendre polynomials. Model fitting was carried out using ASREML. Afterward, for the 25 herds involved in the study, 9 particle size classes were defined based on the proportions of TMR particles on the top (19-mm) and middle (8-mm) screen of the Penn State Particle Separator. Subsequently, the model with estimated variance components was used to examine the influence of TMR particle size class on milk, fat, and protein yield curves. An interaction was included with the particle size class and days in milk. The effect of the TMR particle size class was modeled using a ninth-order Legendre polynomial. Lactation curves were predicted from the model while controlling for TMR chemical composition (crude protein content of 15.5%, neutral detergent fiber of 40.7%, and starch of 19.7% for all classes), to have pure estimates of particle distribution not confounded by nutrient content of TMR. We found little effect of class of particle proportions on milk yield and fat yield curves. Protein yield was greater for sieve classes with 10.4 to 17.4% of TMR particles retained on the top (19-mm) sieve. Optimal distributions different from those recommended may reflect regional differences based on climate and types and quality of forages fed.
Harvesting normative potential for nutrigenomic research
Penders, B. ; Korthals, M. - \ 2013
In: Nutrigenetics and nutrigenomics in functional foods and personalised nutrition / Ferguson, L.R., Boca Raton : CRC Press - ISBN 9781439876800 - p. 361 - 374.
Ecologia del paesaggio del Monte di Portofino / Landscape Ecology of the Monte di Portofino
Pedroli, G.B.M. ; Tagliasacchi, S. ; Sluis, T. van der - \ 2013
Wageningen : FERGUSON (Portus Delphini 2) - ISBN 9789077634028 - 457
landschapsecologie - ecologie - ecosystemen - geschiedenis - italië - landscape ecology - ecology - ecosystems - history - italy
Merino ewes can be bred for body weight change to be more tolerant to uncertain feed supply
Rose, I.J. ; Kause, A. ; Mulder, H.A. ; Werf, J.H.J. van der; Thompson, A.N. ; Ferguson, M.B. ; Arendonk, J.A.M. van - \ 2013
Journal of Animal Science 91 (2013)6. - ISSN 0021-8812 - p. 2555 - 2565.
random regression-models - parameter-estimation - heat-stress - environment - covariance - liveweight - survival - climate - cattle
Sheep in Australia experience periods with different feed supply causing them to gain and lose BW during the year. It is more efficient if ewes lose less BW during periods of poor nutrition and gain more BW during periods of good nutrition. We investigated whether BW loss during periods of poor nutrition and BW gain during periods of good nutrition are genetically different traits. We used BW measurements from 2,336 adult Merino ewes managed over 5 yr in a Mediterranean climate in Katanning, Australia. Body weight loss is the difference between 2 BW measured 42 d apart during mating, a period of poor nutrition. Body weight gain is the difference between 2 BW measured 131 d apart during a period of good nutrition between prelambing and weaning. We estimated variance compnents of BW change using 3 methods: 1) as a trait calculated by subtracting the first BW from the second, 2) multivariate analysis of BW traits, and 3) random regression analysis of BW. The h(2) and genetic correlations (rg) estimated using the multivariate analysis of BW and the BW change trait were very similar whereas the random regression analysis estimated lower heritabilities and more extreme negative genetic correlations between BW loss and gain. The multivariate model fitted the data better than random regression based on Akaike and Bayesian information criterion so we considered the results of the multivariate model to be more reliable. The heritability of BW loss (h(2) = 0.05-0.16) was smaller than that of BW gain (h(2) = 0.14-0.37). Body weight loss and gain can be bred for independently at 2 and 4 yr of age (rg = 0.03 and -0.04) whereas at 3 yr of age ewes that genetically lost more BW gained more BW (rg = -0.41). Body weight loss is genetically not the same trait at different ages (rg range 0.13-0.39). Body weight gain at age 3 yr is genetically the same trait at age 4 yr (rg = 0.99) but is different between age 2 yr and the older ages (rg = 0.53 and 0.51). These results suggest that as the ewes reach their mature BW, BW gain at different ages becomes the same trait. This does not apply to BW loss. We conclude that BW change could be included in breeding programs to breed adult Merino ewes that are more tolerant to variation in feed supply.
Diagnosing evaporative fraction over land from boundary-layer clouds
Gentine, P. ; Ferguson, C.R. ; Holtslag, A.A.M. - \ 2013
Journal of Geophysical Research: Atmospheres 118 (2013)15. - ISSN 2169-897X - p. 8185 - 8196.
large-aperture scintillometer - large-eddy simulation - relative-humidity - mixed-layer - cumulus convection - diurnal behavior - soil-moisture - atmosphere interaction - surface-temperature - spatial variability
The potential use of continental fair-weather shallow cumuli as a way to retrieve the daily surface evaporative fraction over land is evaluated in convective conditions. The proposed method utilizes the fact that both the timing of cloud occurrence and the cloud base height at the time of occurrence provide strong constraints on the surface energy balance and evaporative fraction. The retrieval is especially reliable in the presence of relatively stable and humid free troposphere profiles. The advantage of the method is that it provides a more direct estimate of the surface evaporative fraction than indirect estimation based on inversion of a highly parameterized land surface model. In addition, the evaporative fraction is obtained at a scale of a few kilometers, which is more pertinent for weather and climate studies. The retrieval strategy is tested and validated for three contrasting climates: the U.S. southern Great Plains, West Africa, and the Netherlands. We suggest that the use of satellite observations of shallow cumuli can help constrain the retrieval of the surface evaporative fraction within a data assimilation scheme/reanalysis
Estimating the Economic Value of Narwhal and Beluga Hunts in Hudson Bay, Nunavut
Hoover, C. ; Bailey, M.L. ; Higdon, J. ; Ferguson, S.H. ; Sumaila, R. - \ 2013
Arctic 66 (2013)1. - ISSN 0004-0843 - p. 1 - 16.
inuit - growth - foods - diet
Hunting of narwhal (Monodon monoceros) and beluga (Delphinapterus leucas) in Hudson Bay is an important activity, providing food and income in northern communities, yet few studies detail the economic aspects of these hunts. We outline the uses of narwhal and beluga and estimate the revenues, costs, and economic use value associated with the hunt on the basis of the harvests in 2007. We also explore the effects of cost sharing and inclusion of opportunity cost of labour on model outputs. For the communities participating in each hunt, the average economic use value was negative (-$9399) for beluga and positive ($133 278) for narwhal. The corresponding per capita value estimates were -$1 for beluga and $44 for narwhal. Including the effects of cost sharing with one other hunting activity in the model increased the economic use values to $266 504 for beluga and $321 500 for narwhal. Narwhals provide a higher value per whale, in addition to a higher per capita total economic value to the community, compared to belugas because resources are shared among fewer communities. However, the beluga hunt overall provides greater revenue because more belugas are harvested. In keeping with literature on other hunting activities in the Arctic, our results indicate that the value of whales to communities is largely due to their food value.
Genetics show that adaptation to drought periods means less lambs for young ewes and more for old
Rose, I.J. ; Mulder, H.A. ; Thompson, P.N. ; Ferguson, M. ; Werf, J.H.J. van der; Arendonk, J.A.M. van - \ 2012
In: Book of Abstracts of the 63rd Annual Meeting of the European Association for Animal Production, Bratislava, 27-31 August 2012. - Wageningen Academic Publishers - p. 239 - 239.
Selection of mosquito life-histories: a hidden weapon against malaria?
Ferguson, H.M. ; Maire, N. ; Takken, W. ; Lyimo, I.N. ; Briet, O. ; Lindsay, S.W. ; Smith, T.A. - \ 2012
Malaria Journal 11 (2012). - ISSN 1475-2875
anopheles-gambiae giles - plasmodium-falciparum - resistance status - endemic area - evolution - populations - arabiensis - culicidae - vectors - diptera
Background There has recently been a substantial decline in malaria incidence in much of Africa. While the decline can clearly be linked to increasing coverage of mosquito vector control interventions and effective drug treatment in most settings, the ubiquity of reduction raises the possibility that additional ecological and associated evolutionary changes may be reinforcing the effectiveness of current vector control strategies in previously unanticipated ways. Presentation of hypothesis Here it is hypothesized that the increasing coverage of insecticide-treated bed nets and other vector control methods may be driving selection for a shift in mosquito life history that reduces their ability to transmit malaria parasites. Specifically it is hypothesized that by substantially increasing the extrinsic rate of mortality experienced in vector populations, these interventions are creating a fitness incentive for mosquitoes to re-allocate their resources towards greater short-term reproduction at the expense of longer-term survival. As malaria transmission is fundamentally dependent on mosquito survival, a life history shift in this direction would greatly benefit control. Testing the hypothesis At present, direct evaluation of this hypothesis within natural vector populations presents several logistical and methodological challenges. In the meantime, many insights can be gained from research previously conducted on wild Drosophila populations. Long-term selection experiments on these organisms suggest that increasing extrinsic mortality by a magnitude similar to that anticipated from the up-scaling of vector control measures generated an increase in their intrinsic mortality rate. Although this increase was small, a change of similar magnitude in Anopheles vector populations would be predicted to reduce malaria transmission by 80%. Implications of hypothesis The hypothesis presented here provides a reminder that evolutionary processes induced by interventions against disease vectors may not always act to neutralize intervention effectiveness. In the search for new intervention strategies, consideration should be given to both the potential disadvantages and advantages of evolutionary processes resulting from their implementation, and attempts made to exploit those with greatest potential to enhance control.
Management parameters from the random regressions testday model to advic farmers on cow nutrition
Caccamo, M. - \ 2012
Wageningen University. Promotor(en): Johan van Arendonk; Roel Veerkamp, co-promotor(en): J.D. Ferguson; G. Licitra. - S.l. : s.n. - ISBN 9789461734198 - 143
melkkoeien - melkveevoeding - dairy cows - dairy cattle nutrition

Accurate monitoring and adequate planning of activities at modern dairy farms are important to improve farm profitability. The aim of this study was to investigate the use of test-day information to support farmers in management of Sicilian dairy herds. To this purpose, a test-day random regression model was developed for the analysis of production data of Sicilian dairy herds. Highest between-herd variation found in the variance components analysis using the test day model showed clear evidence of benefits in using a random regression TD model for management improvement. To identify sources of variation able to explain differences between herds in milk and milk components production herd curves, a field study was conducted in Southern Italy (Ragusa province) where diets and chemical composition of the diet was collected at herd level (every 3 months) and testday milk yield records at individual cow level (every month). Data collection was performed from March 2006 through December 2008 on 40 cooperating farms. Animal breed, feeding system, and total mixed ration chemical composition were identified to influence between-herd variation. At the individual cow level, test day model was further used to investigate the production response to changes in chemical and physical composition of diets in Ragusa province. Starch had the greatest effect on milk, fat, and protein production when crude protein and neutral detergent fiber contents were at a high and low value, respectively. Effects of a nutrition component on production changed when the other nutrients were included in the model, suggesting the confounding response one can have when multiple nutrients are not accounted for.

Association of total-mixed-ration chemical composition with milk, fat, and protein yield lactation curves at the individual level
Caccamo, M. ; Veerkamp, R.F. ; Licitra, G. ; Petriglieri, R. ; Terra, F. La; Pozzebon, A. ; Ferguson, J.D. - \ 2012
Journal of Dairy Science 95 (2012)10. - ISSN 0022-0302 - p. 6171 - 6183.
test-day model - dairy-cows - dietary-protein - starch - management
The objective of this study was to examine the effect of the chemical composition of a total mixed ration (TMR) tested quarterly from March 2006 through December 2008 for milk, fat, and protein yield curves for 27 herds in Ragusa, Sicily. Before this study, standard yield curves were generated on data from 241,153 test-day records of 9,809 animals from 42 herds in Ragusa province collected from 1995 to 2008. A random regression sire-maternal grandsire model was used to develop variance components for yields. The model included parity, age at calving, year at calving, and stage of pregnancy as fixed effects. Random effects were herd × test date, sire and maternal grandsire additive genetic effect, and permanent environmental effect modeled using third-order Legendre polynomials. Model fitting was carried out using ASReml. Subsequently, the model with estimated variance components was used to examine the influence of TMR crude protein, soluble N, acid detergent lignin, neutral detergent fiber, acid detergent fiber, starch, and ash on milk, fat, and protein yield curves. The data set contained 46,531 test-day milk yield records from 3,554 cows in the 27 herds recorded during the study period. Initially, an analysis was performed using one dietary component (one-component analysis) within each model as a fixed effect associated with the test-day record closest to the months the TMR was sampled within each herd. An interaction was included with the nutrient component and days in milk. The effect of the TMR chemical component(s) was modeled using a ninth-order Legendre polynomial. The conditional Wald F-statistic for the fixed effects revealed significant effects for acid detergent fiber, neutral detergent fiber, crude protein, starch, and their interactions with days in milk on milk, fat, and protein yield. On the basis of these results, a multicomponent analysis was performed in which crude protein, neutral detergent fiber, and starch were simultaneously included in the model with days in milk interactions. Although both analyses revealed that diet composition influenced production responses depending on lactation stage, the multiple-component analysis showed more pronounced effects of starch and neutral detergent fiber relative to crude protein for all traits throughout lactation.
Analysis of nanomaterials in complex matrices (environment and biota): general considerations and conceptual case studies
Kammer, F. von der; Ferguson, P.L. ; Holden, P. ; Masion, A. ; Rogers, K. ; Klaine, S.J. ; Koelmans, A.A. ; Horne, N. ; Unrine, J. - \ 2012
Environmental Toxicology and Chemistry 31 (2012)1. - ISSN 0730-7268 - p. 32 - 49.
walled carbon nanotubes - field-flow fractionation - plasma-mass spectrometry - x-ray-fluorescence - cdse quantum dots - silver nanoparticles - electron-microscopy - colloid analysis - icp-ms - pseudomonas-aeruginosa
This paper evolved from discussions held at a SETAC-endorsed Technical Workshop held at Clemson University in August, 2010. The workshop was sponsored by the United States Environmental Protection Agency (U.S. EPA), Arcadis-US, and the Clemson University Institute of Environmental Toxicology.
Adult Merino ewes can be bred for live weight change to be more tolerant to climate change
Rose, I.J. ; Kause, A. ; Werf, J.H.J. van der; Thompson, A.N. ; Ferguson, M.B. ; Arendonk, J.A.M. van - \ 2011
In: Proceedings of the Association for the Advancement of Animal Breeding and Genetics. - Perth, Australia : Association for the Advancement of Animal Breeding and - ISBN 9780646559155 - p. 311 - 314.
Climate change is going to complicate sheep management in Mediterranean climates due to increased variation in the supply of pasture and crop stubbles for grazing during summer and autumn. Farmers will rely more on providing supplementary feed which is expensive. Therefore liveweight loss during periods of low nutrition and subsequent liveweight gain are likely to be economically important traits. We estimated the genetic parameters for liveweight loss and liveweight gain on 2700 fully pedigreed 2 to 4 years old Merino ewes. When data for ewes from all ages was analysed together with age fitted as a fixed effect, liveweight gain had a heritability of 0.18 whilst liveweight loss had a heritability of 0.06. Loss and gain also had a moderate negative genetic correlation, showing that high weight loss was related to high weight gain. When liveweight change is analysed to be a different trait at each age using a multivariate model, heritability for live weight gain was 0.37 for ewes aged 2 years and 0.20 for ewes aged 3 and 4 years. Heritability for live weight loss was around 0.15 for all ages. These results suggest that liveweight change could be included in breeding programs to breed adult Merino ewes that are more tolerant to variation in feed supply.
Local Land-Atmosphere Coupling (LoCo) Research: Status and Results
Santanello, J.A. ; Ferguson, C. ; Ek, M.B. ; Dirmeyer, P. ; Tuinenburg, O.A. ; Jacobs, C.M.J. ; Heerwaarden, C. van; Findell, B. - \ 2011
GEWEX news 21 (2011)4. - p. 7 - 9.
Linking individual phenotype to density-dependent population growth: the influence of body size on the population dynamics of malaria vectors
Russell, T.L. ; Lwetoijera, D.W. ; Knols, B.G.J. ; Takken, W. ; Killeen, G.F. ; Ferguson, H.M. - \ 2011
Proceedings of the Royal Society. B: Biological Sciences 278 (2011)1721. - ISSN 0962-8452 - p. 3142 - 3151.
plasmodium-falciparum malaria - anopheles-gambiae - multimodel inference - culicidae - diptera - transmission - arabiensis - mosquitos - fecundity - abundance
Understanding the endogenous factors that drive the population dynamics of malaria mosquitoes will facilitate more accurate predictions about vector control effectiveness and our ability to destabilize the growth of either low- or high-density insect populations. We assessed whether variation in phenotypic traits predict the dynamics of Anopheles gambiae sensu lato mosquitoes, the most important vectors of human malaria. Anopheles gambiae dynamics were monitored over a six-month period of seasonal growth and decline. The population exhibited density-dependent feedback, with the carrying capacity being modified by rainfall (97% wAICc support). The individual phenotypic expression of the maternal (p = 0.0001) and current (p = 0.040) body size positively influenced population growth. Our field-based evidence uniquely demonstrates that individual fitness can have population-level impacts and, furthermore, can mitigate the impact of exogenous drivers (e.g. rainfall) in species whose reproduction depends upon it. Once frontline interventions have suppressed mosquito densities, attempts to eliminate malaria with supplementary vector control tools may be attenuated by increased population growth and individual fitness
Merino ewes can be selected to lose less weight during periods of low nutrition
Rose, I.J. ; Kause, A. ; Werf, J.H.J. van der; Thompson, A.N. ; Ferguson, M. - \ 2010
Animal Production Science 50 (2010)11-12. - ISSN 1836-0939 - p. xxxi - xxxi.
Establishment of a self-propagating population of the African malaria vector Anopheles arabiensis under semi-field conditions
Ng'habi, K.R.N. ; Mwasheshi, D. ; Knols, B.G.J. ; Ferguson, H.M. - \ 2010
Malaria Journal 9 (2010). - ISSN 1475-2875
insecticide-treated bednets - gambiae-sensu-stricto - western kenya - mating-behavior - swarming behavior - s.l. diptera - s.s. diptera - mosquitos - culicidae - survival
Background: The successful control of insect disease vectors relies on a thorough understanding of their ecology and behaviour. However, knowledge of the ecology of many human disease vectors lags behind that of agricultural pests. This is partially due to the paucity of experimental tools for investigating their ecology under natural conditions without risk of exposure to disease. Assessment of vector life-history and demographic traits under natural conditions has also been hindered by the inherent difficulty of sampling these seasonally and temporally varying populations with the limited range of currently available tools. Consequently much of our knowledge of vector biology comes from studies of laboratory colonies, which may not accurately represent the genetic and behavioural diversity of natural populations. Contained semi-field systems (SFS) have been proposed as more appropriate tools for the study of vector ecology. SFS are relatively large, netting-enclosed, mesocosms in which vectors can fly freely, feed on natural plant and vertebrate host sources, and access realistic resting and oviposition sites. Methods: A self-replicating population of the malaria vector Anopheles arabiensis was established within a large field cage (21 x 9.1 x 7.1 m) at the Ifakara Health Institute, Tanzania that mimics the natural habitat features of the rural village environments where these vectors naturally occur. Offspring from wild females were used to establish this population whose life-history, behaviour and demography under semi-field conditions was monitored over 24 generations. Results: This study reports the first successful establishment and maintenance of an African malaria vector population under SFS conditions for multiple generations (> 24). The host-seeking behaviour, time from blood feeding to oviposition, larval development, adult resting and swarming behaviour exhibited by An. arabiensis under SFS conditions were similar to those seen in nature. Conclusions: This study presents proof-of-principle that populations of important African malaria vectors can be established within environmentally realistic, contained semi-field settings. Such SFS will be valuable tools for the experimental study of vector ecology and assessment of their short-term ecological and longer-term evolutionary responses to existing and new vector control interventions.
What do local communities say about fences?
Chaminuka, P. - \ 2010
In: Fencing Impacts: a review of the environmental, social and economic impacts of game and veterinary fencing in Africa with particular reference to the great Limpopo and Kavango-Zambezi Transfrontier Conservaton Areas / Ferguson, K., Hanks, J., Pretoria, South Africa : Mammal Research Institute, University of Pretoria - p. 53 - 55.
Modelling and valuating the effects of landscape management on the ecosystem service of biological control - a spatial dynamic perspective
Werf, W. van der - \ 2010
In: IOBC/WPRS Landscape management for functional biodiversity, Cambridge, UK, 29 June - 1 July 2010. - Darmstadt, Germany : IOBC/WPRS - ISBN 9789290672302 - p. 121 - 124.
Biological control of crop pests is affected by a broad range of organisms which need a variety of resources in the crop and non-crop elements in the landscape to complete their life cycles. The effect of enemies on the population dynamics of pests depends on enemy density and diversity, and is critically affected by spatial and temporal scales. Recent studies illustrate how models can help to bridge those scales and quantify: (1) the relationship between sink-source distance in the landscape and time of colonization; (2) the relationship between time of colonization and enemy impact on pest population dynamics; (3) the relationship between enemy impacts, crop damage, and economic loss. Such models help to predict the effect of landscape and crop management on the effectiveness of ecosystem services. They are indispensible tools for integrating information across spatial and temporal scales, and translate ecological thinking into economic valuation
IOBC/WPRS Landscape management for functional biodiversity
Holland, J. ; Helden, M. van; Rossing, W.A.H. ; Poehling, H.M. ; Werf, W. van der; Ferguson, A. ; Lavigne, C. - \ 2010
Darmstadt, Germany : IOBC/WPRS (IOBC wprs Bulletin 56) - ISBN 9789290672302 - 146 p.
Predicting the time to colonization of Diadegma semiclausum using spatial dispersal kernels
Bianchi, F.J.J.A. ; Schellhorn, N.A. ; Werf, W. van der - \ 2010
In: IOBC/WPRS Working Group Landscape management for functional biodiversity, Cambridge, UK, 29 June - 1 July 2010. - Darmstadt, Germany : IOBC/WPRS - ISBN 9789290672302 - p. 21 - 24.
The predatory staphylinid beetle, Atheta coriaria, can be reared easily and cheaply on turkey feed. This creates opportunities for inundative release of the predator at relatively low cost for biological control of pests with ground-dwelling life stages. A. coriaria was mass-released into a commercial cauliflower crop, in a field trial to investigate its potential for biological control of cabbage root fly (CRF) (Delia radicum). Significantly fewer dead plants due to CRF damage and higher root weights of surviving plants were recorded in plots treated with A. coriaria or with chlorpyrifos or spinosad than in untreated control plots. If use of A. coriaria for biological control of CRF is developed for commercial uptake, its potential interactions with other immigrant and resident beetles should be investigated. Initial data on beetle activity in the trial field was collected and these preliminary results are discussed
Ground beetle dispersal: how to bridge the scales?
Allema, A.B. ; Rossing, W.A.H. ; Werf, W. van der; Volker, D. ; Marsan, D. ; Steingröver, E.G. ; Lenteren, J.C. van - \ 2010
In: IOBC/WPRS Working Group Landscape management for functional biodiversity, Cambridge, UK, 22 June – 1 July, 2010. - Darmstadt : IOBC/WPRS - ISBN 9789290672302 - p. 5 - 8.
Beneficial arthropods that provide biological control of aphids or weed seeds use a variety of habitats in agricultural landscapes. Information on the movement behaviour of these arthropods between these habitats is needed to develop conservation strategies that sustain pest suppression in agricultural landscapes. Models for movement behaviour may help to understand and explore biocontrol functions. As measurements of behaviour at the landscape scale are technically difficult to make, measurements are often made at smaller scales. It is then necessary to upscale to larger scales, using movement models. Here we present a case study on such upscaling. The first results indicate that upscaling from small scales to large scales, using a correlated random movement model, may result in errors. An alternative approach, to be tested in further work, is to fit the movement model directly to the large scale data
Associations of breed and feeding management with milk production curves at herd level using a random regression test-day model
Caccamo, M. ; Veerkamp, R.F. ; Ferguson, J.D. ; Petriglieri, R. ; Terra, F. La; Licitra, G. - \ 2010
Journal of Dairy Science 93 (2010)10. - ISSN 0022-0302 - p. 4986 - 4995.
somatic-cell score - dairy-cows - dietary-protein - brown-swiss - performance - yield - fat - lactation - systems - prediction
Earlier studies identified large between-herd variation in estimated lactation curve parameters from test-day milk yield and milk composition records collected in Ragusa province, Italy. The objective of this study was to identify sources of variation able to explain these between-herd differences in milk production curves, by estimating associations of animal breed (Holstein Friesian vs. Brown Swiss), feeding system [separate feeding (SF) vs. total mixed ration (TMR)], and TMR chemical composition on milk and milk components herd curves. Data recorded from 1992 through 2007 for test-day (TD) milk, fat, and protein yields from 1,287,019 records of 148,951 lactations of 51,489 cows in 427 herds were processed using a random regression TD model. Random herd curves (HCUR) for milk, fat, and protein yields were estimated from the model per herd, year, and parity (1, 2, and 3+) using 4-order Legendre polynomials. From March 2006 through December 2007, samples of TMR were collected every 3 mo from 37 farms in Ragusa province. Samples were analyzed for dry matter, ash, crude protein, soluble nitrogen, acid detergent lignin, neutral detergent fiber, acid detergent fiber, and starch. Traits used to describe milk production curves were peak, days in milk at peak, persistency, and mean. Association of feeding system and animal breed with HCUR traits was investigated using a general mixed model procedure. Association of TMR chemical composition with HCUR traits was investigated using multivariate analysis with regression and stepwise model selection. Results were consistent for all traits and parities. Feeding system was significantly associated with HCUR peak and mean, with higher values for TMR. Animal breed was significantly associated with HCUR persistency, with higher values for Brown Swiss herds. Furthermore, animal breed influenced HCUR peak and mean, with higher values for Holstein Friesian herds. Crude protein had the largest effect on HCUR peak and mean, whereas the interaction between crude protein and dry matter mainly affected persistency. When provided by a national evaluation system, HCUR can be used as an indicator of herd feeding management.
Clarification of anomalies in the application of a 2La molecular karyotyping method for the malaria vector Anopheles gambiae
Ng'habi, K.R.N. ; Meneses, C.R. ; Cornel, A.J. ; Slotman, M.A. ; Knols, B.G.J. ; Ferguson, H.M. ; Lanzaro, G.C. - \ 2008
Parasites & Vectors 1 (2008). - ISSN 1756-3305 - 8 p.
incipient speciation - complex - inversion - area - identification - polymorphisms - transmission - resistance - genes - forms
Background - Chromosomal inversions have been considered to be potentially important barriers to gene flow in many groups of animals through their effect on recombination suppression in heterokaryotypic individuals. Inversions can also enhance local adaptation in different groups of organisms and may often represent species-specific differences among closely related taxa. We conducted a study to characterize the 2La inversion karyotypes of An. gambiae sensu stricto mosquitoes sampled from the Kilombero Valley (Tanzania) using a newly designed PCR assay. Results - We frequently encountered a (687 bp) fragment which was only present in the Kilombero Valley populations. Laboratory crossing between An. gambiae s.s. from Njage (Tanzania) and Kisumu (Western Kenya) populations resulted in F1 offspring carrying the observed fragment. Karyotype analysis did not indicate differences in 2La region chromosome morphology between individuals carrying the PCR fragments, the 207 bp fragment, or the 687 bp fragement. Conclusion - The observed insertion/deletion polymorphism within the region amplified by the 2La PCR diagnostic test may confound the interpretation of this assay and should be well considered in order to maintain an acceptable level of reliability in studies using this assay to describe the distribution and frequency of the 2La inversion among natural populations of An. gambiae s.s.
Establishment of a large semi-field system for experimental study of African malaria vector ecology and control in Tanzania
Ferguson, H.M. ; Ng'habi, K.R. ; Walder, T. ; Kadungula, D. ; Moore, S.J. ; Lyimo, I. ; Russell, T.L. ; Urassa, H. ; Mshinda, H. ; Killeen, G.F. ; Knols, B.G.J. - \ 2008
Malaria Journal 7 (2008). - ISSN 1475-2875 - 15 p.
anopheles-gambiae diptera - germ-line transformation - insecticide-treated nets - genetic-control systems - aedes-aegypti - western kenya - plasmodium-falciparum - transgenic mosquitos - transmitting mosquitos - laboratory populations
Background - Medical entomologists increasingly recognize that the ability to make inferences between laboratory experiments of vector biology and epidemiological trends observed in the field is hindered by a conceptual and methodological gap occurring between these approaches which prevents hypothesis-driven empirical research from being conducted on relatively large and environmentally realistic scales. The development of Semi-Field Systems (SFS) has been proposed as the best mechanism for bridging this gap. Semi-field systems are defined as enclosed environments, ideally situated within the natural ecosystem of a target disease vector and exposed to ambient environmental conditions, in which all features necessary for its life cycle completion are present. Although the value of SFS as a research tool for malaria vector biology is gaining recognition, only a few such facilities exist worldwide and are relatively small in size (<100 m2). Methods - The establishment of a 625 m2 state-of-the-art SFS for large-scale experimentation on anopheline mosquito ecology and control within a rural area of southern Tanzania, where malaria transmission intensities are amongst the highest ever recorded, is described. Results A greenhouse frame with walls of mosquito netting and a polyethylene roof was mounted on a raised concrete platform at the Ifakara Health Institute. The interior of the SFS was divided into four separate work areas that have been set up for a variety of research activities including mass-rearing for African malaria vectors under natural conditions, high throughput evaluation of novel mosquito control and trapping techniques, short-term assays of host-seeking behaviour and olfaction, and longer-term experimental investigation of anopheline population dynamics and gene flow within a contained environment that simulates a local village domestic setting. Conclusion - The SFS at Ifakara was completed and ready for use in under two years. Preliminary observations indicate that realistic and repeatable observations of anopheline behaviour are obtainable within the SFS, and that habitat and climatic features representative of field conditions can be simulated within it. As work begins in the SFS in Ifakara and others around the world, the major opportunities and challenges to the successful application of this tool for malaria vector research and control are discussed.
Sexual selection in mosquito swarms: may the best man lose?
Ng'habi, K.R. ; Huho, B.J. ; Nkwengulila, G. ; Killeen, G.F. ; Knols, B.G.J. ; Ferguson, H.M. - \ 2008
Animal Behaviour 76 (2008)1. - ISSN 0003-3472 - p. 105 - 112.
male body-size - anopheles-gambiae females - mating success - adult size - stabilizing selection - reproductive success - larval density - aedes-aegypti - sao-tome - behavior
One of the greatest paradoxes in evolutionary biology is the continued maintenance of genetic variation for phenotypic traits that appear to confer strong fitness advantages. Of these traits, body size is perhaps the one that has been most consistently linked to increased longevity and reproductive success in males. We investigated two hypotheses for how events occurring during mating in the mosquito Anopheles gambiae could impede directional selection on male body size: (1) whether male copulation probability is random with respect to body size in aerial swarms, and (2) whether large males are less competitive during mating than smaller, shorter-lived rivals. By manipulation of larval nutritional conditions (low, intermediate and high food allocation), we generated cohorts of male A. gambiae mosquitoes that differed in adult body size and energy reserves (body size and energy reserves being positively correlated with larval nutrition). When competing against one another in aerial swarms, males from the intermediate food treatment were six and two times more successful at acquiring mates than those from the high and low food treatments, respectively. The median survival of males from this most sexually competitive group was approximately 13% lower than that of the larger males with high larval nutrition. We conclude that phenotypic determinants of long-term survival and mating success may not be correlated in this system, and thus that stabilizing selection as well as environmental condition-dependent expression of traits could account for the maintenance of variation in male body size in this species and in other
Integrating Agricultural Landscapes with Biodiversity Conservation in the Mesoamerican Hotspot
Harvey, C.A. ; Komar, O. ; Chazdon, R.L. ; Ferguson, B.G. ; Finegan, B. ; Griffith, D.M. ; Martínez-Ramos, M. ; Morales, H. ; Nigh, R. ; Soto-Pinto, L. ; Breugel, M. van; Wishnie, M. - \ 2008
Conservation Biology 22 (2008)1. - ISSN 0888-8892 - p. 8 - 15.
environmental services help - costa-rica - latin-america - countryside biogeography - forest fragments - los-tuxtlas - rain-forest - mexico - coffee - diversity
Denitrification and agriculture
Munch, J.C. ; Velthof, G.L. - \ 2007
In: Biology of the Nitrogen Cycle / Bothe, H, Ferguson, SJ, Newton, WE, Amsterdam : Elsevier - ISBN 9780444528575 - p. 331 - 341.
The cultural dimension of learning. Learning experiences from Wageningen University
Brinkman, B. ; Rodenburg, J. ; Chevallier, A. - \ 2007
In: The Proceedings of GIIC 2005, The 4th Global International Internship Congress, Amsterdam, the Netherlands, 5 - 8 April, 2005. - Amsterdam : Inholland University Diemen - p. 97 - 108.
Nature beats nurture: a case study of the physiological fitness of free-living and laboratory-reared male Anopheles gambiae s.l.
Hubo, B.J. ; Ng'habi, K.R. ; Killeen, G.F. ; Nkwengulila, G. ; Knols, B.G.J. ; Ferguson, H.M. - \ 2007
Journal of Experimental Biology 210 (2007)18. - ISSN 0022-0949 - p. 2939 - 2947.
mosquito species diptera - aedes-aegypti mosquitos - female body-size - wing length - transgenic mosquitos - larval development - adult mosquitos - genetic manipulation - reproductive-system - rapid-determination
Laboratory experimentation forms the basis for most of our knowledge of the biology of many organisms, in particular insects. However, the accuracy with which laboratory-derived estimates of insect life history and behaviour can predict their fitness and population dynamics in the wild is rarely validated. Such comparison is especially important in cases where laboratory-derived information is used to formulate and implement strategies for the genetic control of insects in nature. We have conducted a comparative study of the reproductive potential and life history of male Anopheles gambiae Gilies sensu lato mosquitoes from both standardized laboratory conditions and from natural field settings. We measured three indirect indicators of male mosquito fitness: energetic reserves, body size and survival, in a bid to determine whether the demographics and energetic limitations of wild males can be correctly predicted from their laboratory counterparts. Crucially, the body size and lipid reserves of wild males were substantially greater than those reared under standard laboratory conditions. We caution that the energetic limitations of insects as identified in the laboratory may underestimate their resilience in the wild, and discuss the implications of this phenomenon with respect to vector-borne disease control programmes based on genetic control of mosquitoes.
Male Anopheles gambiae mating success in a swarm: 'May the best man lose'
Ng'habi, K.R.N. ; John, B. ; Nkwengulila, G. ; Killeen, G. ; Knols, B.G.J. ; Ferguson, H.M. - \ 2006
American Journal of Tropical Medicine and Hygiene 75 (2006)5. - ISSN 0002-9637 - p. 305 - 305.
A reliable morphological method to assess the age of male Anopheles gambiae
Huho, B.J. ; Ng'habi, K.R. ; Killeen, G.F. ; Nkwengulila, G. ; Knols, B.G.J. ; Ferguson, H.M. - \ 2006
Malaria Journal 5 (2006). - ISSN 1475-2875 - 11 p.
plasmodium-falciparum - chloroquine resistance - transgenic mosquitos - reproductive-system - population ecology - malaria parasite - southern african - temporal changes - diptera - culicifacies
Background - Release of genetically-modified (GM) or sterile male mosquitoes for malaria control is hampered by inability to assess the age and mating history of free-living male Anopheles. Methods - Age and mating-related changes in the reproductive system of male Anopheles gambiae were quantified and used to fit predictive statistical models. These models, based on numbers of spermatocysts, relative size of sperm reservoir and presence/absence of a clear area around the accessory gland, were evaluated using an independent sample of mosquitoes whose status was blinded during the experiment. Results - The number of spermatocysts in male testes decreased with age, and the relative size of their sperm reservoir increased. The presence of a clear area around accessory glands was also linked to age and mating status. A quantitative model was able to categorize males from the blind trial into age groups of young (¿ 4 days) and old (> 4 days) with an overall efficiency of 89%. Using the parameters of this model, a simple table was compiled that can be used to predict male age. In contrast, mating history could not be reliably assessed as virgins could not be distinguished from mated males
Epidemiological analysis of data for scrapie in Great Britain
Hagenaars, T.H.J. ; Donnelly, C. ; Ferguson, N.M. - \ 2006
Epidemiology and Infection 134 (2006)2. - ISSN 0950-2688 - p. 359 - 367.
bovine spongiform encephalopathy - sheep flock - british sheep - transmission - bse - infection - program
In recent years, the control or eradication of scrapie and any other transmissible spongiform encephalopathies (TSEs) possibly circulating in the sheep population has become a priority in Britain and elsewhere in Europe. A better understanding of the epidemiology of scrapie would greatly aid the development and evaluation of control and eradication strategies. Here we bound the range of key epidemiological parameters using a combination of relatively detailed pathogenesis and demography data, more limited data on susceptibility and incubation times, and recent survey data on scrapie incidence in Great Britain. These data are simultaneously analysed using mathematical models describing scrapie transmission between sheep and between flocks. Our analysis suggests that occurrence of scrapie in a flock typically provokes changes in flock management that promote termination of the outbreak, such as the adoption of selective breeding, and that a large fraction of cases (possibly over 80%) goes undetected. We show that the data analysed are consistent with the within-flock reproduction number of scrapie lying in the range 1·5¿6, consistent with previous epidemiological studies
The case for strategic international alliances to harness nutritional genomics for public and personal health
Kaput, J. ; Ordovas, J.M. ; Ferguson, L. ; Ommen, B. van; Müller, M.R. - \ 2005
The British journal of nutrition 94 (2005)5. - ISSN 0007-1145 - p. 623 - 632.
diabetes-related traits - coronary-heart-disease - genetic association - population stratification - carbohydrate ingestion - complex diseases - immune function - hapmap project - messenger-rna - dietary fiber
Nutrigenomics is the study of how constituents of the diet interact with genes, and their products, to alter phenotype and, conversely, how genes and their products metabolise these constituents into nutrients, antinutrients, and bioactive compounds. Results from molecular and genetic epidemiological studies indicate that dietary unbalance can alter gene-nutrient interactions in ways that increase the risk of developing chronic disease. The interplay of human genetic variation and environmental factors will make identifying causative genes and nutrients a formidable, but not intractable, challenge. We provide specific recommendations for how to best meet this challenge and discuss the need for new methodologies and the use of comprehensive analyses of nutrient-genotype interactions involving large and diverse populations. The objective of the present paper is to stimulate discourse and collaboration among nutrigenomic researchers and stakeholders, a process that will lead to an increase in global health and wellness by reducing health disparities in developed and developing countries
Variance components of test-day milk, fat, and protein production, and somatic cell score from all parities of dairy cows in South-eastern Sicily estimated with a random regression model
Roos, P.G. ; Pool, M.H. ; Caccamo, M. ; Azzaro, G. ; Ferguson, J.D. ; Licitra, G. - \ 2005
In: Proceedings of the 2005 Joint Meeting of ADSA, ASAS, and CSAS, July 24-28, 2005, Cincinnati, Ohio Cincinnati Ohio : - p. 202 no.252 - 202 no.252.
The presence of Plasmodium falciparum gametocytes in human blood increases the gravidity of Anopheles gambiae mosquitoes
Ferguson, H.M. ; Gouagna, L.C. ; Obare, P. ; Read, A.F. ; Babiker, H. ; Githure, J.I. ; Beier, J.C. - \ 2005
American Journal of Tropical Medicine and Hygiene 73 (2005)2. - ISSN 0002-9637 - p. 312 - 320.
western kenya - yoelii-nigeriensis - aedes-aegypti - seasonal transmission - malaria transmission - egg development - body-size - infection - fecundity - stephensi
We conducted a field study in an area of endemic malaria transmission in western Kenya to determine whether mosquitoes that feed on gametocyte-infected blood but do not become infected have reduced or enhanced fecundity in comparison to mosquitoes fed on uninfected blood. Fifteen paired membrane-feeding experiments were conducted in which two strains of Anopheles gambiae mosquitoes were simultaneously fed on either Plasmodium falciparum¿infected blood from children or uninfected control blood from adults. The presence of noninfecting gametocytes in blood increased the probability that An. gambiae would produce eggs after one blood meal by sixfold (odds ratio for control relative to infected blood group 0.16; 95% CI 0.10¿0.23). This result could not be explained by variation in blood meal size or hemoglobin content between hosts. When children cleared their infections, the difference in gravidity between mosquitoes fed on their blood and uninfected adults disappeared, suggesting this phenomenon is due to the presence of Plasmodium gametocytes in blood and not to host-specific factors such as age. This result was observed in two mosquito strains that differ in their innate fecundity, suggesting it may apply generally. To our knowledge, this is the first time that Plasmodium has been implicated as enhancing vector gravidity
Effect of larval crowding on mating competitiveness of Anopheles gambiae mosquitoes
Ng'habi, K.R. ; John, B. ; Nkwengulila, G. ; Knols, B.G.J. ; Killeen, G.F. ; Ferguson, H.M. - \ 2005
Malaria Journal 4 (2005). - ISSN 1475-2875 - 9 p.
genetically-modified mosquitos - aedes-aegypti diptera - treated bed nets - western kenya - adult size - malaria transmission - transgenic mosquitos - wing length - insecticide resistance - swarming behavior
Background: The success of sterile or transgenic Anopheles for malaria control depends on their mating competitiveness within wild populations. Current evidence suggests that transgenic mosquitoes have reduced fitness. One means of compensating for this fitness deficit would be to identify environmental conditions that increase their mating competitiveness, and incorporate them into laboratory rearing regimes. Methods: Anopheles gambiae larvae were allocated to three crowding treatments with the same food input per larva. Emerged males were competed against one another for access to females, and their corresponding longevity and energetic reserves measured. Results: Males from the low-crowding treatment were much more likely to acquire the first mating. They won the first female approximately 11 times more often than those from the high-crowding treatment (Odds ratio = 11.17) and four times more often than those from the medium-crowding treatment (Odds ratio = 3.51). However, there was no overall difference in the total number of matings acquired by males from different treatments (p = 0.08). The survival of males from the low crowding treatment was lower than those from other treatments. The body size and teneral reserves of adult males did not differ between crowding treatments, but larger males were more likely to acquire mates than small individuals. Conclusion: Larval crowding and body size have strong, independent effects on the mating competitiveness of adult male An. gambiae. Thus manipulation of larval crowding during mass rearing could provide a simple technique for boosting the competitiveness of sterile or transgenic male mosquitoes prior to release
Redressing the sex imbalance in knowledge of vector biology
Ferguson, H.M. ; John, B. ; Ng'habi, K.R. ; Knols, B.G.J. - \ 2005
Trends in Ecology and Evolution 20 (2005)4. - ISSN 0169-5347 - p. 202 - 209.
mediterranean fruit-flies - genetically-modified mosquitos - cucurbitae coquillett diptera - anopheles-culicifacies giles - accessory-gland substances - mass-reared males - aedes-aegypti l - cytoplasmic incompatibility - mating competitiveness - larval density
The recent development of transgenic mosquitoes that are resistant to infection by the Plasmodium malarial parasite is a promising new tool in the fight against malaria. However, results of large-scale field releases of alternatively modified mosquitoes carried out during the 1970s and 1980s suggest that this approach could be difficult to implement in the field. These past attempts to control mosquito populations largely floundered as a result of our insufficient understanding of the behavioural ecology of released males. In spite of this, contemporary research on genetic control strategies has concentrated predominantly on molecular aspects, with little progress being made toward resolving key ecological uncertainties, male mosquito ecology being the most important. Here, we review the state of knowledge of male mosquito ecology, and highlight priorities for further research. Case studies of two crop pests, the Mediterranean fruit fly and melon fly, are given as examples of how knowledge of male ecology facilitates successful control in other species. Unless similar information becomes available for mosquitoes, any future genetic control strategy will risk failure
Spatial heternogeneity and the persistence of infectious diseases
Hagenaars, T.H.J. ; Donelly, C.A. ; Ferguson, N.M. - \ 2004
Journal of Theoretical Biology 229 (2004)3. - ISSN 0022-5193 - p. 349 - 359.
stochastic epidemics - extinction times - community size - endemic period - metapopulation - dynamics - measles - models - transmission - duration
The endemic persistence of infectious diseases can often not be understood without taking into account the relevant heterogeneities of host mixing. Here, we consider spatial heterogeneity, defined as `patchiness¿ of the host population. After briefly reviewing how disease persistence is influenced by population size, reproduction number and infectious period, we explore its dependence on the level of spatial heterogeneity. Analysis and simulation of disease transmission in a symmetric meta-population suggest that disease persistence typically becomes worse as spatial heterogeneity increases, although local persistence optima can occur for infections with oscillatory population dynamics. We obtain insight into the dynamics that underlie the observed persistence patterns by studying the infection prevalence correlation between patches and by comparing full-model simulations to results obtained using simplified patch-level descriptions of the interplay between local extinctions and between-patch transmissions. The observed patterns are interpreted in terms of rescue effects for strong spatial heterogeneity and in terms of between-patch coherence and synchronization effects at intermediate and weak levels of heterogeneity.
Mosquito appetite for blood is stimulated by Plasmodium chabaudi infections in themselves and their vertebrate hosts
Ferguson, H.M. ; Read, A.F. - \ 2004
Malaria Journal 3 (2004). - ISSN 1475-2875 - 8 p.
leishmania-mexicana-amazonensis - anopheles-stephensi mosquitos - la-crosse virus - malaria parasite - aedes-aegypti - yoelii-nigeriensis - brugia-malayi - fecundity - gallinaceum - gambiae
Background - Arthropod vectors of disease may encounter more than one infected host during the course of their lifetime. The consequences of super-infection to parasite development are rarely investigated, but may have substantial epidemiological and evolutionary consequences. Methods - Using a rodent malaria model system, behavioural avoidance of super-infection was tested by examining whether already-infected Anopheles stephensi mosquitoes were less responsive to new vertebrate hosts if they were infected. Additionally, a second dose of parasites was given to malaria-infected mosquitoes on a biologically realistic time scale to test whether it impeded the development of a first infection. Results - No effect of a second infected blood meal on either the prevalence or parasite burden arising from a first was found. Furthermore, it was found that not only were infected mosquitoes more likely to take a second blood meal than their uninfected counterparts, they were disproportionately drawn to infected hosts. Conclusions - The alterations in mosquito feeding propensity reported here would occur if parasites have been selected to make infected vertebrate hosts more attractive to mosquitoes, and infected mosquitoes are more likely to seek out new blood meals. Although such a strategy might increase the risk of super-infection, this study suggests the cost to parasite development is not high and as such would be unlikely to outweigh the potential benefits of increasing the contact rate between the parasite's two obligate hosts.
Unveiling the burden of pertussis
Boven, R.M. van; Ferguson, N.M. ; Rie, A. van - \ 2004
Trends in Microbiology 12 (2004). - ISSN 0966-842X - p. 116 - 119.
bordetella-pertussis - united-states - adults - transmission - vaccination - population - infection - epidemic - booster - england
Increasing incidence has led to pertussis re-emerging as a public health problem in developed countries over the past decade. Obtaining a better understanding of the epidemiological factors underlying the transmission dynamics of Bordetella pertussis in highly vaccinated populations is key to explaining this increasing incidence. This has prompted attempts to improve age-stratified estimates of pertussis disease and infection incidence and has led to the development of a new generation of epidemiological models that take into account waning of immunity. Combining these approaches offers the potential to unravel the causes of the resurgence and to predict the impact of novel vaccination strategies.
Molecular cytogenetic definition of the chicken genome: the first complete Avian Karyotype
Masabanda, J.S. ; Burt, D.W. ; O'Brien, P.C.M. ; Vignal, A. ; Fillon, V. ; Walsh, P.S. ; Cox, H. ; Tempest, H.G. ; Smit, J. ; Habermann, F. ; Schmidt, M. ; Matsuda, Y. ; Ferguson-Smith, M.A. ; Crooijmans, R.P.M.A. ; Groenen, M.A.M. ; Griffin, D.K. - \ 2004
Genetics 166 (2004)3. - ISSN 0016-6731 - p. 1367 - 1373.
dna microarrays - comparative map - gene family - cell-line - chromosome - fish - microchromosomes - macrochromosome - identification - localization
Chicken genome mapping is important for a range of scientific disciplines. The ability to distinguish chromosomes of the chicken and other birds is thus a priority. Here we describe the molecular cytogenetic characterization of each chicken chromosome using chromosome painting and mapping of individual clones by FISH. Where possible, we have assigned the chromosomes to known linkage groups. We propose, on the basis of size, that the NOR chromosome is approximately the size of chromosome 22; however, WC Suggest that its original assignment of 16 should be retained. We also suggest a definitive chromosome classification system and propose that the probes developed here will find wide utility in the fields of developmental biology, DT40 studies, agriculture, vertebrate genome organization, and comparative mapping of avian species.
Dynamics of a scrapie outbreak in a flock of Romanov sheep-estimation of transmission parameters
Hagenaars, T.H.J. ; Donelly, C.A. ; Ferguson, N.M. ; Anderson, R.M. - \ 2003
Epidemiology and Infection 131 (2003). - ISSN 0950-2688 - p. 1015 - 1022.
population-dynamics - mathematical-model - great-britain - epidemiology - infection - disease - virus - uk
Knowledge of epidemiological mechanisms and parameters underlying scrapie transmission in sheep flocks remains very limited at present. Here we introduce a method for fitting stochastic transmission models to outbreak data to estimate bounds on key transmission parameters. We apply this method to data describing an outbreak of scrapie in a closed flock of Romanov sheep. The main findings are that the relative infectiousness of infected animals in this outbreak becomes appreciable early into disease incubation and that the mean incubation period is less than 1·5 years. We also find that the data are consistent with a broad range of values for the basic reproduction number R0 and describe how the boundaries of this range depend on assumptions about the mean incubation period and the contribution to transmission of a long-lived environmental reservoir of infectivity.
Comparison of media for enumeration of Clostridium perfringens from foods
Jong, A.E.I. de; Eijhusen, G.P. ; Brouwer-Post, E.J.F. ; Grand, M. ; Johansson, T. ; Kärkkäinen, T. ; Marugg, J. ; Veld, P.H. in 't; Warmerdam, F.H.M. ; Wörner, G. ; Zicavo, A. ; Rombouts, F.M. ; Beumer, R.R. - \ 2003
Journal of Microbiological Methods 54 (2003)3. - ISSN 0167-7012 - p. 359 - 366.
sporulation
Many media have been developed to enumerate Clostridium perfringens from foods. In this study, six media [iron sulfite (IS) agar, tryptose sulfite cycloserine (TSC) agar, Shahidi Ferguson perfringens (SFP) agar, sulfite cycloserine azide (SCA), differential clostridial agar (DCA), and oleandomycin polymyxin sulfadiazine perfringens (OPSP) agar] were compared in a prestudy, of which four (IS, TSC, SCA, and DCA) were selected for an international collaborative trial. Recovery of 15 pure strains was tested in the prestudy and recovery of one strain from foodstuffs was tested in the collaborative trial. Results from the prestudy did reveal statistical difference of the media but recoveries on all media were within the microbiological limits (+/- 30%) of IS, which was set as a reference medium. Recoveries on the media tested in the collaborative trial were statistically different as well, but these differences were of no microbiological-analytical relevance. Food matrices did not affect the recovery of C perfringens in general. DCA and SCA, in particular, are labor-intensive to prepare and DCA frequently failed to produce black colonies; gray colonies were quite common. Since IS medium is nonselective, it was concluded that TSC was the most favorable medium for the enumeration of C. perfringens from foods. (C) 2003 Elsevier Science B.V. All rights reserved.
Structural studies on metal-containing enzymes: T4 endonuclease VII and D. gigas formate dehydrogenase
Raaijmakers, H.C.A. - \ 2001
Wageningen University. Promotor(en): N.C.M. Laane; D. Suck. - S.l. : S.n. - ISBN 9789058084125 - 85
enzymen - röntgenkristallografie - desulfovibrio - oxidoreductasen - wolfraam - enzymes - x ray crystallography - desulfovibrio - oxidoreductases - tungsten

Many biological processes require metal ions, and many of these metal-ion functions involve metalloproteins. The metal ions in metalloproteins are often critical to the protein's function, structure, or stability. This thesis focuses on two of these proteins, bacteriophage T4 endonuclease VII (EndoVII) and D. gigas fonnate dehydrogenase, which are studied by X-ray crystallography. The structure of EndoVII reveals how a magnesium or calcium ion is used to cleave several kinds of irregular but flexible DNA, while a zinc ion maintains the structural integrity of this DNase.

The formate dehydrogenase contains a tungsten ion and a seleno-cysteine at the active site, that catalyses the oxidation of formate to carbon dioxide. The two released electrons are transferred through four [4Fe-4S] clusters before they can be handed over to another protein. Two of the [4Fe-4S] and the selenium have been overlooked by other techniques, but could be localised and identified by crystallography.

Chapter 1 gives a general introduction on metals in biological systems, X-ray crystallography and also describes the biological background of both proteins.

Chapter 2 presents the structure of the four-way DNA-junction resolving enzyme T4 endonuclease VII, and that of the inactive N62D mutant. The betterexpressed mutant was solved first, using seleno-methionine, mercury and gold derivatives. These mercury and gold derivatives bind to the sulphurs that also ligand the zinc. The wild-type was solved with help of a single mercury derivative since molecular replacement with the mutant structure failed.

On its own, the EndoVII monomer would not represent a stable fold, as it exposes many hydrophobic residues to the solvent. But two monomers intertwine to form a dimer without this problem. In this dimer, the monomers are aligned head-to-tail; the N-terminus of one monomer interacts with the C-terminus of the other monomer and vice versa . The major dimerization element, unique to EndoVII, is the "four-helix-cross" domain, which consists of helix-2 and helix-3 from each monomer. It contains an extended hydrophobic core.

Another feature is the "beta-finger", residues 38-56. Its stability depends critically on the zinc. This zinc ion is tetrahedrally co-ordinated to four cysteines, linking helix- I through residues C23 and C26 firmly to the N-terminal part of helix-2 (C58, C61). Indeed, interfering mutations inactivate the protein. Finally, the calcium ion, which marks the active site, is liganded to aspartate-40 and asparagine-62. Mutation studies show that these amino acids are essential for activity: The N62D mutant is completely inactive.

The EndoVII structure has been docked to a "stacked-X" four-way DNA junction, one of its many substrates. This model is not refined, since both the DNA and the protein are known to be flexible and might undergo conformational changes. However, its overall features confirm experimental data: 1) The EndoVII dimer binds to the minor groove side of the four-way junction; 11) Basic residues on helix-2 can interact with phosphates on the exchanging strands and those on the C-terminal domain can interact with phosphates in the continuous strands, consistent with observed foot-printing patterns; 111) The C-terminus binds up to nine base pairs away from the junction, confirming the minimal length of two arms of the substrate; IV). The active sites do not cleave both the scissile phosphates simultaneously.

Surprisingly, the N62D mutant shows a major rearrangement in the "four-helixcross" domain, when compared to the wild-type: helices-2 are translated by half a turn each, in opposite direction and the opening of the "bays", between each helix-2 and betafinger, is wider. These differences might be attributed to the point-mutation, which introduces an extra charge in the active site, to differences in crystallisation conditions, to the different pH employed, to crystal contacts or perhaps they are simply a sign of the intrinsic flexibility of EndoVII.

This dilemma is partly solved in chapter 3, which presents the crystal structure of wild-type EndoVII in a different space group, which contains less solvent. It crystallised in the same drop, so that differences observed between the two wild-type structures cannot be attributed to the mutation, pH or salt concentrations. Since the helical-cross region of this second structure is very similar to that of the mutant, rearrangements in this region must be seen as a consequence of intrinsic flexibility of EndoVII. The widening of the "bays", however, might still be a consequence of the mutation, different pH, absence of Ca 2+ or crystal packing. An investigation of the flexibility of EndoVII with TLS- refinement, i.e. anisotropic refinement of rigid bodies, provides only limited insight. However, it confirms that rotations along the axes of the helices 2 and 4 and along the beta-finger are a main source of flexibility and also that the C-terminus, helix-4, 5 and 6, behave as a rigid body.

The high-resolution structure of the N62D mutant brings more clarity towards the reaction mechanism of the nuclease. This model contains important water molecules and reveals the position and orientation of 14 sulphate ions, which may indicate favoured phosphate (DNA) binding sites. Supported by new mutation data (Birkenbihl, unpublished), these sulphate and water positions, combined with the Ca 2+ positions in the wild-type structures, suggest a reaction-mechanism similar to those proposed for some other magnesium dependent nucleases.

2 Asparagine-62, glutamate-65 and aspartate-40 are important to position Mg 2+ or Ca 2+ next to the scissile phosphate of the DNA substrate. Histidine-41 activates a water molecule, which in turn executes a nucleophilic attack on the phosphor atom. Histidine-43 stabilises this phosphate directly through a hydrogen bond. Unfortunately it is still unclear why the N62D shows no DNase activity at all; an aspartate would also be able to ligand/position a divalent cation. The extra charge that this mutation introduces in the active site might distort the geometry of the active site, and repel the DNA. A more attractive, albeit more speculative hypothesis, assumes that the amino group of asparagine-62 donates a hydrogen-bond to the phosphate, which would also stabilise the transition state.

At present, there are no known proteins with significant sequence homology to EndoVII, though nucleases with structural similarities do exist. One group consists of magnesium-dependent nucleases, which have a similar geometry of liganding sidechains around the magnesium (or calcium) ion in the active site; e.g. the E. coli proteins RuvC (Ariyosi et al., 1994) and RNase H (Katayanagi et al., 1990). However, these nucleases have no resembling fold. Most likely, this just shows that magnesium-dependent nucleases need a certain geometry to function.

A more interesting group shares a folding motif similar to the beta finger and helix-2: Serratia Nuclease (Miller et al., 1994), Ppol (Flick et al., 1998) and perhaps even Colicin E9 (Kleanthous et al., 1999). Asparagine-62 and histidine-41 are conserved between Serratia nuclease, Ppol and T4 endonuclease VII. Ppol has also been crystallised in complex with DNA. If one superimposes this with the EndoVII structure, it turns out that the Ca 2+ in EndoVII is buried deeper within the protein, but small rotations (10-20 degrees) along helix 2 and the beta-finger suffice to superimpose them. These two nucleases act on different substrates, and maybe the larger DNA junctions of EndoVII need a wider and deeper binding groove than the double stranded DNA of Ppol. However, it could also be the source of EndoVII's specificity; flexible DNA might impose this conformational change of EndoVII upon binding, readying the enzyme for cleavage, while the magnesium or calcium ion might be too far away if EndoVII approaches more rigid DNA. A structure of EndoVII in complex with DNA would solve these questions.

Chapter 4 presents the major part of the determination of the 3D structure of the tungsten-containing formate dehydrogenasc (W-FDH) from Desulfovibrio gigas, one of the first tungsten-containing enzymes isolated from a mesophile. The large subunit (92 kDa) is structurally related to several tungsten- and molybdenumcontaining enzymes and X-ray structures have been determined for two of them. One of these, the periplasmic nitrate reductase (Dias et al, 1999), could be used to obtain a molecular replacement solution. But the quality of phasing was not sufficient to generate a clear, interpretable electron density map. Furthermore, the amino acid sequence of W-FDH has not yet been determined, what makes model building complicated. Multiple wavelength diffraction (MAD) measurements were undertaken at the absorption edges of W and Fe to define unambiguously the number, positions and identity of these anomalous scatterers and to improve the X-ray phases. The MAD-analysis revealed one W-atom with a Se-cys ligand and one [4Fe-4S] cluster bound to the large subunit, and three [4Fe-4S] clusters in the small subunit. The four [4Fe-4S] clusters are ca. 10 Å apart, creating a feasible electron transfer pathway, which connects the exterior of the protein to the W/Se site in the large subunit. Two of the four iron-sulphur clusters had not been predicted before by spectroscopic techniques (Almendra et al., 1999). A reinvestigation of the spectroscopic data was performed, but gave the same results as before. If these data were correct, this means that the [4Fe-4S] clusters are instable, and that only protein with fully occupied clusters crystallises.

The formate dehydrogenase H (FDH-H) from E. coli catalyses the same reaction as W-FDH, but uses a molybdenum instead of tungsten. Both are liganded to two molybdopterin-cofactors and to a seleno-cysteine, so the question remains why W-FDH prefers tungsten to the more common molybdenum. The full structure will allow a comparison of the two enzymes in atomic detail, and perhaps, it will shed some light on this phenomenon.

X-ray crystallography has been used to characterise the nature of metal-centres in proteins, their coordination geometry and even their identity. Sometimes, the way metal ions are bound to the protein already clarifies its role in the protein. In other cases it has to be supplemented with other studies before the role can be fully understood. Either way, crystallography provides a powerful tool for the study of metalloproteins.

References
Almendra, M.J., Brondino, C.D., Gavel, 0., Pereira, A.S., Tavares, P., Bursakov, S., Duarte, R., Caldeira, J., Moura, J.J.G., Moura, 1. (1999) Biochemistry, 38 , 16366-16372
Ariyosi, M., Vassylyev, D., Iwasaki, H., Shinagawa, H. and Morikawa, K. (1994) Cell, 78 , 1063-1072.
Flick, K.E., Jurica, M.S., Monnart Jr, R.J. and Stoddard, B.L. (1998), Nature, 394 , 96-101.
Katayanagi, M., Miyagawa, M., Matsushima, M., Ishikawa, M., Kanaya, S., Ikehara, M., Matsuzaki, M. and Morikawa, K. (1990) Nature, 347 , 306-309.
Kleanthous, C., Kuhlmann, U.C., Pornmer, A.J., Ferguson, N., Radford, S.E., Moore, G.R., James, R. and Hemmings, A.M. (1999) Nature Struct. Biol., 6 , 243-252.
Miller, M.D., Tanner, J., Alpaugh, M., Benedik, M.J. and Krause, K.L. (1994) Nature Struct Biol., 1 , 461-468.
Anaerobic hydrolysis during digestion of complex substrates
Sanders, W.T.M. - \ 2001
Wageningen University. Promotor(en): G. Lettinga; G. Zeeman. - S.l. : S.n. - ISBN 9789058083753 - 101
hydrolyse - organische verbindingen - afvalwater - rioolwater - kinetica - industrieel afval - aardappelfabrieksafvalwater - slachthuisafval - mest - hydrolysis - organic compounds - waste water - sewage - kinetics - industrial wastes - potato factory effluent - slaughterhouse waste - manures

Complex waste(water) such as, raw sewage, dairy wastewater, slaughterhouse wastewater, fish processing wastewater, primary sludge and the organic fraction of municipal solid waste have been proven to be degradable under anaerobic conditions. However, during the digestion process the conversion of the complex organic molecules into mono- and dimer components, also called the hydrolysis, is often the rate-limiting step. For design and optimization of the anaerobic conversion of complex waste(water) a good knowledge of the hydrolysis kinetics is therefore essential. The scope of this thesis was therefore to clarify the hydrolysis kinetics during the anaerobic digestion of complex waste(water), with emphasis on the hydrolysis of particles, dissolved macromolecules and lipids in coherence with the process conditions during the digestion. The mechanisms of the hydrolysis were elucidated by lab experiments and simulations with mechanistic hydrolysis models. For the hydrolysis of particulate substrates the results presented in this thesis revealed that, at constant pH and digestion temperature, the amount of surface available for the hydrolysis is the most important parameter for the hydrolysis rate and all other parameters are of minor importance.

With respect to dissolved polymers, such as gelatine and dissolved starch, the results indicate that the mechanism of the enzymatic hydrolysis in batch experiments can be described as a random polymerisation process. Moreover, the hydrolysis rate of dissolved components is linearly related to the sludge concentration in the batch experiment. The hydrolysis of neutral lipids under acidogenic conditions is slower as compared to the hydrolysis under methanogenic conditions. Based on the results presented in this thesis it was hypothesised that this is due to positive effect of the methane production on maintaining the lipid-water interface and subsequent higher volumetric hydrolysis rate.

In practice the hydrolysis rate is most commonly described by an empirical first order relation, in which the hydrolysis rate is linearly related to the amount of biodegradable substrate that is available (Eastman and Ferguson, 1981).

The identification of the essential parameters of the hydrolysis mechanisms in this thesis made it possible to evaluate the first order approach and designate the limitations of the relation. The evaluation revealed that the hydrolysis only proceeds according to first order kinetics if no changes in the rate limiting step or the biodegradability occur during the degradation of a substrate. Moreover, the first order hydrolysis constant seems system and substrate specific and the use of literature values for the hydrolysis constant is therefore not advised.

For assessment of a hydrolysis constant in a lab experiment the following guidelines were presented: (1) For waste(water) containing mainly protein and carbohydrates, first order kinetics can be established under acidic and methanogenic conditions in batch or completely stirred tank reactor (CSTR) system. (2) For waste(water) that contains high concentrations of lipids the assessment of the hydrolysis constant for neutral lipids under acid conditions is impossible due to coagulation of the lipid. Under methanogenic conditions the hydrolysis constant can be assessed in a 'multiple flask' batch system. However as (gas) mixing can differ between a laboratory batch and a full-scale CSTR-system, the subsequent effect on the lipid-water interface might cause a difference in the prevailing k h value of the two systems.

Colophospermum reduced to Hardwickia (Leguminosae-Caesalpinioideae).
Breteler, F.J. ; Ferguson, I.K. ; Gasson, P.E. ; Welle, B.J.H. ter - \ 1997
Adansonia 19 (1997)2. - ISSN 1280-8571 - p. 279 - 291.
Growth stategie for maximum lifetime profitability.
Galligan, D.T. ; Ramberg, C. ; Ferguson, J. ; Huirne, R.B.M. ; Dijkhuizen, A.A. - \ 1996
In: Proc. National Conf. on Calves, heifers, and dairy profitability, Harrisburg, Pennsylvania - p. 64 - 72.
Optimal economic goals in reproduction: underlying concepts from semen to culling.
Galligan, D.T. ; Ferguson, J. ; Dijkhuizen, A.A. ; Huirne, R.B.M. - \ 1995
In: Proc. Conf. on Animal Reproduction,C.R. Jordan (ed.). 1994, Philadelphia - p. 55 - 64.
Cereal trade systems and food security.
Amonoo, E. ; Jongkamp, C. ; Tilburg, A. van - \ 1991
In: Sustainability of food security in Central West Africa / Oomen, A., Ferguson, E., - p. 1 - 14.
Light absorption of pollen and pollen walls.
Willemse, M.T.M. - \ 1986
In: Pollen and spores. Form and function / Blackmore, S., Ferguson, I.K., London : Academic Press - p. 393 - 395.
Adam Ferguson en de dienst aan de samenleving
Munters, Q.J. - \ 1984
Omkeer 2 (1984)1. - p. 10 - 11.
Effects of external pH on dry matter production, chemical composition and ion uptake of maize plants grown on NO-3 and NH+4-N
Keltjens, W.G. - \ 1979
In: Proc. 8th Int. Colloq. Plant Anal. Fert. Probl., A.R. Ferguson, R.L. Bieleski and I.B. Ferguson (eds), Auckland, New Zealand - p. 239 - 240.
Earliness of flowering and fruiting of forty strawberry varieties : a statistical study
Ferguson, J.H.A. - \ 1971
Wageningen : [s.n.] (Mededeling / I.V.T. no. 331) - 9
plantkunde - teelt - cultuurmethoden - fragaria - aardbeien - botany - cultivation - cultural methods - strawberries
Beproeving Massey - Ferguson maaidorser type 510
Anonymous, - \ 1967
Wageningen : [s.n.] (Bulletin / Instituut voor landbouwtechniek en rationalisatie no. 344) - 15
maaidorsers - graansoorten - voedselgewassen - brassica napus var. oleifera - koolzaad - plantenvermeerdering - voedergrassen - combine harvesters - cereals - food crops - rape - propagation - fodder grasses
Rassenproeven met tuinbouwgewassen
Ferguson, J.H.A. - \ 1967
Wageningen : IVT (Mededeling / Instituut voor de veredeling van tuinbouwgewassen no. 261) - 27
tuinbouw - landbouw - teelt - cultuurmethoden - laboratoria - voorzieningen - horticulture - agriculture - cultivation - cultural methods - laboratories - facilities
Beproeving Massey - Ferguson aanbouwzaaimachine
Anonymous, - \ 1966
Wageningen : [s.n.] (Bulletin / Instituut voor landbouwtechniek en rationalisatie no. 339) - 6
zaaimachines - ruggenzaaimachines - seed drills - ridge drills
Tabel van de tweedimensionale normale kansverdeling
Ferguson, J.H.A. - \ 1965
Wageningen : [s.n.] (Mededeling / Instituut voor de Veredeling van Tuinbouwgewassen no. 245) - 16
graphics - wiskundige tafels - waarschijnlijkheidstheorie - tabellen - mathematical tables - probability theory - tables
Statistische achtergrond van een proefopzet
Ferguson, J.H.A. - \ 1964
Wageningen : [s.n.] (Mededeling / Instituut voor de veredeling van tuinbouwgewassen, Wageningen no. 219) - 8
proefopzet - landbouw - onderzoek - experimental design - agriculture - research
Invloed van orientatie en vorm van boomhagen op de hoeveelheid opgevangen straling
Ferguson, J.H.A. - \ 1963
Wageningen : IVT (Mededeling / Instituut voor de Veredeling van Tuinbouwgewassen 199)
Random variability in horticultural experiments
Ferguson, J.H.A. - \ 1963
Wageningen : IVT (Mededeling / Instituut voor de Veredeling van Tuinbouwgewassen 196)
Beproeving Massey - Ferguson opraappers type 10
Anonymous, - \ 1963
Wageningen : [s.n.] (Bulletin / Instituut voor landbouwtechniek en rationalisatie no. 229) - 9
laders - persen - opraappersen - balenpers - graansoorten - voedselgewassen - voedergrassen - loaders - presses - pickup balers - balers - cereals - food crops - fodder grasses
Verslag van een studiereis naar Engeland van 8-20 september 1963
Ferguson, J.H.A. ; Verdooren, L.R. - \ 1963
Wageningen : [s.n.] (Rapport / Instituut voor de veredeling van tuinbouwgewassen, Wageningen no. 28) - 7
biometrie - landbouw - groot-brittannië - virologie - laboratoria - statistische analyse - voorzieningen - biometry - agriculture - great britain - laboratories - statistical analysis - ? - facilities
Nomogram voor het onderscheidingsvermogen van de F - toets gemodificeerd naar Keuls
Ferguson, J.H.A. - \ 1962
Wageningen : I.V.T. (Mededeling / Instituut voor de Veredeling van Tuinbouwgewassen 187)
comparison of two planting systems in orchards as regards the amount of radiation intercepted by the trees
Ferguson, J.H.A. - \ 1961
Wageningen : IVT (Mededeling / Instituut voor de Veredeling van Tuinbouwgewassen 168)
Beproeving Massey - Ferguson centrifugaalstrooier
Anonymous, - \ 1958
Wageningen : [s.n.] (Bulletin / Instituut voor landbouwtechniek en rationalisatie no. 60) - 6
korrels - kunstmeststrooiers - granules - fertilizer distributors
Beproeving S en S Simplex aanbouwmaaier voor Ferguson trekkers
Anonymous, - \ 1958
Wageningen : [s.n.] (Bulletin / Instituut voor landbouwtechniek en rationalisatie no. 63) - 4
maaiers - groenvoeders - boerderij uitrusting - landbouwwerktuigen - mowers - green fodders - farm equipment - farm machinery
Empirical estimation of thermoreaction curves for the rate development
Ferguson, J.H.A. - \ 1958
Wageningen : IVT (Mededeling / Instituut voor de Veredeling van Tuinbouwgewassen 134)
Beproeving Ferguson stalmeststrooier
Anonymous, - \ 1957
Wageningen : [s.n.] (Bulletin / Instituut voor landbouwtechniek en rationalisatie no. 36) - 4
mestverspreiders - stalmest - manure spreaders - farmyard manure
Photothermographs : a tool for climate studies in relation to the ecology of vegetable varieties
Ferguson, J.H.A. - \ 1957
Wageningen : IVT (Mededeling / Instituut voor de Veredeling van Tuinbouwgewassen 111)
Some applications of binomial probability paper in genetic analysis
Ferguson, J.H.A. - \ 1957
Wageningen : IVT (Mededeling / Instituut voor de Veredeling van Tuinbouwgewassen 95)
wiskunde - waarschijnlijkheidsanalyse - statistiek - mathematics - probability analysis - statistics
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