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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    No to Neocosmospora: Phylogenomic and Practical Reasons for Continued Inclusion of the Fusarium solani Species Complex in the Genus Fusarium
    O'Donnell, Kerry ; Al-Hatmi, Abdullah M.S. ; Aoki, Takayuki ; Brankovics, Balázs ; Cano-Lira, Jose F. ; Coleman, Jeffrey J. ; Hoog, G.S. de; Pietro, A. Di; Frandsen, R.J.N. ; Geiser, D.M. ; Lee, T.A.J. van der; Diepeningen, A.D. van; Waalwijk, C. - \ 2020
    mSphere 5 (2020)5. - ISSN 2379-5042
    clinical mycology - evolution - fungi - phylogenetics - taxonomy
    This article is to alert medical mycologists and infectious disease specialists of recent name changes of medically important species of the filamentous mold Fusarium. Fusarium species can cause localized and life-threating infections in humans. Of the 70 Fusarium species that have been reported to cause infections, close to one-third are members of the Fusarium solani species complex (FSSC), and they collectively account for approximately two-thirds of all reported Fusarium infections. Many of these species were recently given scientific names for the first time by a research group in the Netherlands, but they were misplaced in the genus Neocosmospora. In this paper, we present genetic arguments that strongly support inclusion of the FSSC in Fusarium. There are potentially serious consequences associated with using the name Neocosmospora for Fusarium species because clinicians need to be aware that fusaria are broadly resistant to the spectrum of antifungals that are currently available.
    Effects of folic acid withdrawal on transcriptomic profiles in murine triple-negative breast cancer cell lines
    Kok, Dieuwertje E. ; O'Flanagan, Ciara H. ; Coleman, Michael F. ; Ashkavand, Zahra ; Hursting, Stephen D. ; Krupenko, Sergey A. - \ 2020
    Biochimie 173 (2020). - ISSN 0300-9084 - p. 114 - 122.
    Epithelial-to-mesenchymal transition - Folic acid - Interferon signaling - Metastasis - Transcriptomics - Triple-negative breast cancer

    We have previously shown that withdrawal of folic acid led to metabolic reprogramming and a less aggressive phenotype in a mouse cell model of triple-negative breast cancer (TNBC). Herein, we evaluate the effects of folic acid withdrawal on transcriptomic profiles in these cells. Murine cell lines were originally derived from a pool of spontaneous mammary tumors grown in MMTV-Wnt1 transgenic mice. Based on their differential molecular characteristics and metastatic potential, these cell lines were previously characterized as non-metastatic epithelial (E-Wnt), non-metastatic mesenchymal (M-Wnt) and metastatic mesenchymal (metM-Wntliver) cells. Using custom two-color 180K Agilent microarrays, we have determined gene expression profiles for three biological replicates of each subtype kept on standard medium (2.2 μM folic acid) or folic acid-free medium for 72 h. The analyses revealed that more genes were differentially expressed upon folic acid withdrawal in M-Wnt cells (1884 genes; Benjamini-Hochberg-adjusted P-value <0.05) compared to E-Wnt and metM-Wntliver cells (108 and 222 genes, respectively). Pathway analysis has identified that type I interferon signaling was strongly affected by folic acid withdrawal, with interferon-responsive genes consistently being upregulated upon folic acid withdrawal in M-Wnt cells. Of note, repressed interferon signaling has been established as one of the characteristics of aggressive human TNBC, and hence reactivation of this pathway may be a promising therapeutic approach. Overall, while our study indicates that the response to folic acid withdrawal varies by molecular subtype and cellular phenotype, it also underscores the necessity to further investigate one-carbon metabolism as a potential therapeutic means in the treatment of advanced TNBC.

    Mapping Geospatial Processes Affecting the Environmental Fate of Agricultural Pesticides in Africa
    Hendriks, Chantal M.J. ; Gibson, Harry S. ; Trett, Anna ; Python, André ; Weiss, Daniel J. ; Vrieling, Anton ; Coleman, Michael ; Gething, Peter W. ; Hancock, Penny A. ; Moyes, Catherine L. - \ 2019
    International Journal of Environmental Research and Public Health 16 (2019)19. - ISSN 1660-4601
    artificial compound - crop protection - environmental data - insecticide residue - satellite data - tropics

    The application of agricultural pesticides in Africa can have negative effects on human health and the environment. The aim of this study was to identify African environments that are vulnerable to the accumulation of pesticides by mapping geospatial processes affecting pesticide fate. The study modelled processes associated with the environmental fate of agricultural pesticides using publicly available geospatial datasets. Key geospatial processes affecting the environmental fate of agricultural pesticides were selected after a review of pesticide fate models and maps for leaching, surface runoff, sedimentation, soil storage and filtering capacity, and volatilization were created. The potential and limitations of these maps are discussed. We then compiled a database of studies that measured pesticide residues in Africa. The database contains 10,076 observations, but only a limited number of observations remained when a standard dataset for one compound was extracted for validation. Despite the need for more in-situ data on pesticide residues and application, this study provides a first spatial overview of key processes affecting pesticide fate that can be used to identify areas potentially vulnerable to pesticide accumulation.

    Multi-objective optimization as a tool to identify possibilities for future agricultural landscapes
    Todman, Lindsay C. ; Coleman, Kevin ; Milne, Alice E. ; Gil, Juliana D.B. ; Reidsma, Pytrik ; Schwoob, Marie Hélène ; Treyer, Sébastien ; Whitmore, Andrew P. - \ 2019
    Science of the Total Environment 687 (2019). - ISSN 0048-9697 - p. 535 - 545.

    Agricultural landscapes provide many functions simultaneously including food production, regulation of water and regulation of greenhouse gases. Thus, it is challenging to make land management decisions, particularly transformative changes, that improve on one function without unintended consequences for other functions. To make informed decisions the trade-offs between different landscape functions must be considered. Here, we use a multi-objective optimization algorithm with a model of crop production that also simulates environmental effects such as nitrous oxide emissions to identify trade-off frontiers and associated possibilities for agricultural management. Trade-offs are identified in three soil types, using wheat production in the UK as an example, then the trade-off for combined management of the three soils is considered. The optimization algorithm identifies trade-offs between different objectives and allows them to be visualised. For example, we observed a highly non-linear trade-off between wheat yield and nitrous oxide emissions, illustrating where small changes might have a large impact. We used a cluster analysis to identify distinct management strategies with similar management actions and use these clusters to link the trade-off curves to possibilities for management. There were more possible strategies for achieving desirable environmental outcomes and remaining profitable when the management of different soil types was considered together. Interestingly, it was on the soil capable of the highest potential profit that lower profit strategies were identified as useful for combined management. Meanwhile, to maintain average profitability across the soils, it was necessary to maximise the profit from the soil with the lowest potential profit. These results are somewhat counterintuitive and so the range of strategies supplied by the model could be used to stimulate discussion amongst stakeholders. In particular, as some key objectives can be met in different ways, stakeholders could discuss the impact of these management strategies on other objectives not quantified by the model.

    Pseudo-starvation driven energy expenditure negatively affects ovarian follicle development
    Coleman, V. ; Meng, L. ; Teerds, K.J. ; Keijer, J. ; Bunschoten, J.E. ; Zhao, Y. ; Ost, M. ; Voigt, A. - \ 2018
    Objective: Conditions of reduced energy availability negatively affect female fertility. We examined whether a change in whole body energy fluxes away from the ovary could affect follicular development, employing mice ectopically expressing uncoupling protein 1 in skeletal muscle (UCP1-TG). We especially addressed insulin-like growth factor 1 (IGF1), a growth factor playing an important role in the regulation of both substrate metabolism and female fertility. Methods: Female UCP1-TG and wild-type (WT) mice were killed at 12 weeks postpartum. Energy intake, expenditure, activity, body weight and length, and body composition were measured. Plasma insulin, glucose, leptin and IGF1 levels were analysed. Ovaries were serial sectioned and follicle and corpora lutea numbers were counted. IGF1 signalling was analysed by immunohistochemical staining for activation of insulin receptor substrate 1/2 (IRS1/2) and AKT. Results: UCP1-TG female mice had increased energy expenditure, reduced body size, maintained adiposity, and decreased IGF1 concentrations compared to their WT littermates. Preantral and antral follicle numbers were reduced by 40% and 60%, respectively, in UCP1-TG mice, compared to WT mice. Corpora lutea (CL) were absent in 40% of the ovaries of UCP1-TG mice. No difference in total and phospho-IRS2 immunostaining was observed between WT and UCP1-TG ovaries. Phospho-IRS1, phosho-AKT -Ser473 and -Thr308 immunostaining was present in granulosa cells of antral follicles in WT ovaries, but faint to absent in antral follicles of UCP1-TG mice.Conclusion: The reduction in circulating IGF1 levels due to ectopic expression of UCP1 leads to areduced activation of the IRS1-PI3/AKT pathway negatively affecting normal ovarian follicle development and ovulation.
    Ecological networks in managed ecosystems: Connecting structure to services
    Mulder, Christian ; Sechi, Valentina ; Woodward, Guy ; Bohan, David Andrew - \ 2017
    In: Adaptive Food Webs Cambridge University Press - ISBN 9781107182110 - p. 214 - 227.

    Introduction Ecological networks represent a cornerstone of ecology: they describe and evaluate the links between form and function in multispecies systems, such as food-web structure and dynamics, and they connect different scales and levels of biological organization (Moore and de Ruiter, 2012; Wall et al., 2015). These properties of being able to elucidate both the structure within complex systems and their scaling indicate that ecological networks and network theory could be widely applied to practical problems, including management decision-making processes such as the design of nature reserves and the preservation of ecosystem services. While the study of networks – initially food-web compartments, then community assemblages, and more recently mutualistic networks – is now firmly embedded in ecology (Levins, 1974; Cohen, 1978; Hunt et al., 1987; Beare et al., 1992; Solé and Montoya, 2001; Berlow et al., 2004; Moore et al., 2004; Cohen and Carpenter, 2005; Thébault and Fontaine, 2010; Moore and de Ruiter, 2012; Pocock et al., 2012; Neutel and Thorne, 2014), the application of such approaches to managed ecosystems has lagged far behind. There are many explanations for this disconnection between agro-ecology and ecology, not least the pervasive view that because they are human managed and disturbed agro-systems are fundamentally “unnatural” and different from natural ecosystems: most ecologists prefer to study so-called natural ecosystems, even though most of these have in fact been heavily influenced by mankind for centuries either directly by local activity or indirectly by long-distance pollution. Network approaches have rarely been applied to agriculture and forestry, which is perhaps surprising given that much of the early, integrated management research (e.g., from the seminal works by Von Carlowitz, 1713, and Von Liebig, 1840, onwards) and the study of networks that stimulated major advances in ecological theory was grounded in attempts to improve agricultural and timber production (Wardle, 2002; Schröter et al., 2003; Coleman et al., 2004; Moore and de Ruiter, 2012, and the references therein). The last two decades have seen a hiatus in advances in agro-ecology in this area, while new network theory and empirical studies have elucidated the roles of body size in ecosystems and the study of plant–pollinator networks and other mutualistic webs have redefined our understanding of general ecology.

    Priorities for research in soil ecology
    Eisenhauer, Nico ; Antunes, Pedro M. ; Bennett, Alison E. ; Birkhofer, Klaus ; Bissett, Andrew ; Bowker, Matthew A. ; Caruso, Tancredi ; Chen, Baodong ; Coleman, David C. ; Boer, Wietse de; Ruiter, Peter de; DeLuca, Thomas H. ; Frati, Francesco ; Griffiths, Bryan S. ; Hart, Miranda M. ; Hättenschwiler, Stephan ; Haimi, Jari ; Heethoff, Michael ; Kaneko, Nobuhiro ; Kelly, Laura C. ; Leinaas, Hans Petter ; Lindo, Zoë ; Macdonald, Catriona ; Rillig, Matthias C. ; Ruess, Liliane ; Scheu, Stefan ; Schmidt, Olaf ; Seastedt, Timothy R. ; Straalen, Nico M. van; Tiunov, Alexei V. ; Zimmer, Martin ; Powell, Jeff R. - \ 2017
    Pedobiologia 63 (2017). - ISSN 0031-4056 - p. 1 - 7.
    Aboveground-belowground interactions - Biodiversity–ecosystem functioning - Biogeography - Chemical ecology - Climate change - Ecosystem services - Global change - Microbial ecology - Novel environments - Plant-microbe interactions - Soil biodiversity - Soil food web - Soil management - Soil processes
    The ecological interactions that occur in and with soil are of consequence in many ecosystems on the planet. These interactions provide numerous essential ecosystem services, and the sustainable management of soils has attracted increasing scientific and public attention. Although soil ecology emerged as an independent field of research many decades ago, and we have gained important insights into the functioning of soils, there still are fundamental aspects that need to be better understood to ensure that the ecosystem services that soils provide are not lost and that soils can be used in a sustainable way. In this perspectives paper, we highlight some of the major knowledge gaps that should be prioritized in soil ecological research. These research priorities were compiled based on an online survey of 32 editors of Pedobiologia – Journal of Soil Ecology. These editors work at universities and research centers in Europe, North America, Asia, and Australia. The questions were categorized into four themes: (1) soil biodiversity and biogeography, (2) interactions and the functioning of ecosystems, (3) global change and soil management, and (4) new directions. The respondents identified priorities that may be achievable in the near future, as well as several that are currently achievable but remain open. While some of the identified barriers to progress were technological in nature, many respondents cited a need for substantial leadership and goodwill among members of the soil ecology research community, including the need for multi-institutional partnerships, and had substantial concerns regarding the loss of taxonomic expertise.
    Regulation of lipid droplet-associated proteins by peroxisome proliferator-activated receptors
    Rosa Rodriguez, Montserrat A. de la; Kersten, Sander - \ 2017
    Biochimica et Biophysica Acta. Molecular and Cell Biology of Lipids 1862 (2017)10. - ISSN 1388-1981 - p. 1212 - 1220.
    Lipid droplet - Lipid droplet-associated proteins - Perilipins - PPARs
    Excess fatty acids are stored in cells as triglycerides in specialized organelles called lipid droplets (LD). LD can be found in nearly all cell types and may expand during certain (patho)physiological conditions. The synthesis and breakdown of triglycerides and their deposition in LD is governed by a diverse set of enzymes and LD-associated proteins. These proteins serve structural roles in and around LD and regulate the activity of key lipogenic and lipolytic enzymes. The LD-associated proteins are subject to multiple regulatory mechanisms at the protein and gene expression level. A group of transcription factors that govern the expression of many LD-associated proteins are the Peroxisome Proliferator-Activated Receptors (PPARs). PPARs are lipid-activated transcription factors that play a key role in the regulation of lipid metabolism in liver (PPARα), adipose tissue (PPARγ), and skeletal muscle (PPARδ). This review provides an overview of the regulation of LD-associated proteins by PPARα, PPARδ, and PPARγ in adipose tissue, liver, macrophages, and skeletal muscle. It is concluded that many LD-associated proteins, including members of the PLIN family, CIDEC, CIDEA, HILPDA, FITM1, FITM2, and G0S2 are under direct transcriptional control of PPARs. Upregulation of LD-associated proteins by PPARs provides a mechanism to link uptake of lipids to regulation of lipid storage capacity. This article is part of a Special Issue entitled: Recent Advances in Lipid Droplet Biology edited by Rosalind Coleman and Matthijs Hesselink.
    Distributed Temperature Sensing as a downhole tool in hydrogeology
    Bense, V.F. ; Read, T. ; Bour, O. ; Borgne, T. Le; Coleman, T. ; Krause, S. ; Chalari, A. ; Mondanos, M. ; Ciocca, F. ; Selker, J.S. - \ 2016
    Water Resources Research 52 (2016)12. - ISSN 0043-1397 - p. 9259 - 9273.
    Distributed Temperature Sensing - Subsurface hydrology

    Distributed Temperature Sensing (DTS) technology enables downhole temperature monitoring to study hydrogeological processes at unprecedentedly high frequency and spatial resolution. DTS has been widely applied in passive mode in site investigations of groundwater flow, in-well flow, and subsurface thermal property estimation. However, recent years have seen the further development of the use of DTS in an active mode (A-DTS) for which heat sources are deployed. A suite of recent studies using A-DTS downhole in hydrogeological investigations illustrate the wide range of different approaches and creativity in designing methodologies. The purpose of this review is to outline and discuss the various applications and limitations of DTS in downhole investigations for hydrogeological conditions and aquifer geological properties. To this end, we first review examples where passive DTS has been used to study hydrogeology via downhole applications. Secondly, we discuss and categorize current A-DTS borehole methods into three types. These are thermal advection tests, hybrid cable flow logging, and heat pulse tests. We explore the various options with regards to cable installation, heating approach, duration, and spatial extent in order to improve their applicability in a range of settings. These determine the extent to which each method is sensitive to thermal properties, vertical in-well flow, or natural gradient flow. Our review confirms that the application of DTS has significant advantages over discrete point temperature measurements, particularly in deep wells, and highlights the potential for further method developments in conjunction with other emerging hydrogeophysical tools.

    Temporal trends in childhood mortality in Ghana: impacts and challenges of health policies and programs
    Kayode, Gbenga A. ; Grobbee, Diederick E. ; Koduah, Augustina ; Amoakoh-Coleman, Mary ; Agyepong, Irene A. ; Ansah, Evelyn ; Dijk, Han van; Klipstein-grobusch, Kerstin - \ 2016
    Global Health Action 9 (2016). - ISSN 1654-9716
    neonatal - Infant - under-five mortality - Ghana
    Background: Following the adoption of the Millennium Development Goal 4 (MDG 4) in Ghana to reduce under-five mortality by two-thirds between 1990 and 2015, efforts were made towards its attainment. However, impacts and challenges of implemented intervention programs have not been examined to inform implementation of Sustainable Development Goal 3.2 (SDG 3.2) that seeks to end preventable deaths of newborns and children aged under-five. Thus, this study aimed to compare trends in neonatal, infant, and under-five mortality over two decades and to highlight the impacts and challenges of health policies and intervention programs implemented.

    Design: Ghana Demographic and Health Survey data (1988–2008) were analyzed using trend analysis. Poisson regression analysis was applied to quantify the incidence rate ratio of the trends. Implemented health policies and intervention programs to reduce childhood mortality in Ghana were reviewed to identify their impact and challenges.

    Results: Since 1988, the annual average rate of decline in neonatal, infant, and under-five mortality in Ghana was 0.6, 1.0, and 1.2%, respectively. From 1988 to 1989, neonatal, infant, and under-five mortality declined from 48 to 33 per 1,000, 72 to 58 per 1,000, and 108 to 83 per 1,000, respectively, whereas from 1989 to 2008, neonatal mortality increased by 2 per 1,000 while infant and under-five mortality further declined by 6 per 1,000 and 17 per 1,000, respectively. However, the observed declines were not statistically significant except for under-five mortality; thus, the proportion of infant and under-five mortality attributed to neonatal death has increased. Most intervention programs implemented to address childhood mortality seem not to have been implemented comprehensively.

    Conclusion: Progress towards attaining MDG 4 in Ghana was below the targeted rate, particularly for neonatal mortality as most health policies and programs targeted infant and under-five mortality. Implementing neonatal-specific interventions and improving existing programs will be essential to attain SDG 3.2 in Ghana and beyond.
    Muscle mitochondrial stress adaptation operates independently of endogenous FGF21 action
    Ost, Mario ; Coleman, Verena ; Voigt, Anja ; Schothorst, E.M. van; Keipert, Susanne ; Stelt, Inge van der; Ringel, Sebastian ; Graja, Antonia ; Ambrosi, Thomas ; Kipp, A.P. ; Jastroch, Martin ; Schulz, T.J. ; Keijer, Jaap ; Klaus, Susanne - \ 2016
    Molecular Metabolism 5 (2016)2. - ISSN 2212-8778 - p. 79 - 90.
    Browning - FGF21 - GDF15 - Mitochondrial disease - Muscle mitohormesis - Myokine

    Objective: Fibroblast growth factor 21 (FGF21) was recently discovered as stress-induced myokine during mitochondrial disease and proposed as key metabolic mediator of the integrated stress response (ISR) presumably causing systemic metabolic improvements. Curiously, the precise cell-non-autonomous and cell-autonomous relevance of endogenous FGF21 action remained poorly understood. Methods: We made use of the established UCP1 transgenic (TG) mouse, a model of metabolic perturbations made by a specific decrease in muscle mitochondrial efficiency through increased respiratory uncoupling and robust metabolic adaptation and muscle ISR-driven FGF21 induction. In a cross of TG with Fgf21-knockout (FGF21-/-) mice, we determined the functional role of FGF21 as a muscle stress-induced myokine under low and high fat feeding conditions. Results: Here we uncovered that FGF21 signaling is dispensable for metabolic improvements evoked by compromised mitochondrial function in skeletal muscle. Strikingly, genetic ablation of FGF21 fully counteracted the cell-non-autonomous metabolic remodeling and browning of subcutaneous white adipose tissue (WAT), together with the reduction of circulating triglycerides and cholesterol. Brown adipose tissue activity was similar in all groups. Remarkably, we found that FGF21 played a negligible role in muscle mitochondrial stress-related improved obesity resistance, glycemic control and hepatic lipid homeostasis. Furthermore, the protective cell-autonomous muscle mitohormesis and metabolic stress adaptation, including an increased muscle proteostasis via mitochondrial unfolded protein response (UPRmt) and amino acid biosynthetic pathways did not require the presence of FGF21. Conclusions: Here we demonstrate that although FGF21 drives WAT remodeling, the adaptive pseudo-starvation response under elevated muscle mitochondrial stress conditions operates independently of both WAT browning and FGF21 action. Thus, our findings challenge FGF21 as key metabolic mediator of the mitochondrial stress adaptation and powerful therapeutic target during muscle mitochondrial disease.

    Letter to the Editor : One Fungus, One Name: Defining the Genus Fusarium in a Scientifically Robust Way That Preserves Longstanding Use
    Geiser, D.M. ; Aoki, T. ; Bacon, C.W. ; Baker, S.E. ; Bhattacharyya, M.K. ; Brandt, M.E. ; Brown, D.W. ; Burgess, L.W. ; Chulze, S. ; Coleman, J.J. ; Correll, J.C. ; Covert, S.F. ; Crous, P.W. ; Waalwijk, C. - \ 2013
    Phytopathology 103 (2013). - ISSN 0031-949X - p. 400 - 408.
    solani species complex - sudden-death syndrome - phylogeny - tucumaniae - taxonomy - reveals - genera
    In this letter, we advocate recognizing the genus Fusarium as the sole name for a group that includes virtually all Fusarium species of importance in plant pathology, mycotoxicology, medicine, and basic research. This phylogenetically guided circumscription will free scientists from any obligation to use other genus names, including teleomorphs, for species nested within this clade, and preserve the application of the name Fusarium in the way it has been used for almost a century. Due to recent changes in the International Code of Nomenclature for algae, fungi, and plants, this is an urgent matter that requires community attention. The alternative is to break the longstanding concept of Fusarium into nine or more genera, and remove important taxa such as those in the F. solani species complex from the genus, a move we believe is unnecessary. Here we present taxonomic and nomenclatural proposals that will preserve established research connections and facilitate communication within and between research communities, and at the same time support strong scientific principles and good taxonomic practice.
    Complete genome sequence of the sulfate-reducing firmicute Desulfotomaculum ruminis type strain (DLT)
    Spring, S. ; Visser, M. ; Lu, M. ; Copeland, A. ; Lapidus, A. ; Lucas, S. ; Cheng, J.F. ; Han, C. ; Tapia, R. ; Goodwin, L.A. ; Pitluck, S. ; Ivanova, N. ; Land, M. ; Hauser, L. ; Larimer, F. ; Rohde, M. ; Göker, M. ; Detter, J.C. ; Kyrpides, N. ; Woyke, T. ; Schaap, P.J. ; Plugge, C.M. ; Muyzer, G. ; Kuever, J. ; Pereira, I.A.C. ; Parshina, S.N. ; Bernier-Latmani, R. ; Stams, A.J.M. ; Klenk, H.P. - \ 2012
    Standards in Genomic Sciences 7 (2012). - ISSN 1944-3277 - p. 304 - 319.
    bacterial names - classification - hydrogenases - database - archaea - system - site - tool
    Strain DLT (= DSM 2154 = ATCC 23193 = NCIMB 8452) is the type strain of the species Desulfotomaculum ruminis [1], one out of current-ly 30 species with validly published names in the paraphyletic genus Desulfotomaculum [2,3]. Strain DLT was initially isolated by G. S. Coleman in the 1950s from the rumen of hay-fed sheep [4]. Dissimilatory reduction of sulfate to sulfide in the rumen was first demonstrated by Lewis [5], who dosed fistulated sheep with sulfate and deter-mined the amount of sulfide produced. As high amounts of sulfide may be toxic to animals, bacte-rial sulfate-reduction in ruminants was a concern due to the presence of sulfate in grass and hay. D. ruminis represented the first pure culture of a sul-fate-reducing bacterium isolated from the rumen. The genus name was derived from the Latin words 'de', from, ‘sulfur’, sulfur, and 'tomaculum', a kind of sausage, meaning 'a sausage-shaped sul-fate reducer' [2,6]. The species epithet is derived from the Latin word 'rumen', throat, first stomach (rumen) of a ruminant, meaning of a rumen [1,2]. Here, we present a summary classification and a set of features for D. ruminis strain DLT, together with the description of the complete genomic se-quencing and annotation. The complete genome sequence of strain DLT will provide valuable in-formation for defining a more adequate descrip-tion of the currently paraphyletic genus Desulfotomaculum
    "Quality Handling" : a multimedia training program for animal handing
    Boivin, X. ; Ruis, M.A.W. ; Waiblinger, S. ; Mounaix, B. ; Windschnurer, I. ; Coleman, G. - \ 2012
    dierlijke productie - varkens - melkvee - vleesvee - hennen - diergedrag - diergezondheid - opleiding - onderwijs - dierenwelzijn - animal production - pigs - dairy cattle - beef cattle - hens - animal behaviour - animal health - training - education - animal welfare
    Poster van het trainingsprogramma "Quality Handling."
    "Quality Handling" of farm animals
    Boivin, X. ; Ruis, M.A.W. ; Waiblinger, S. ; Mounaix, B. ; Windschnurer, I. ; Coleman, G. - \ 2012
    dierlijke productie - varkens - melkvee - vleesvee - hennen - diergedrag - diergezondheid - opleiding - onderwijs - mens-dier relaties - dierenwelzijn - animal production - pigs - dairy cattle - beef cattle - hens - animal behaviour - animal health - training - education - human-animal relationships - animal welfare
    Poster over de "Quality Handling training" methode.
    The influence of genetic selection on the milk fatty acid profile of spring calving dairy cows
    Mc Parland, S. ; Berry, D.P. ; Coleman, J. ; Veerkamp, R.F. ; Soyeurt, H. - \ 2010
    In: Proceedings of the British Society of Animal Science and the Agricultural Research Forum 2010, 12-14 April 20120, Belfast, UK. - - p. 306 - 306.
    A multimedia-based cognitive-behavioural intervention program improves attitudes and handling behaviours of stockpeople in livestock farming
    Ruis, M.A.W. ; Coleman, G.J. ; Waiblinger, S. ; Windschnurer, I. ; Boivin, X. - \ 2010
    In: Proceedings of the British Society of Animal Science Meeting on Food, Feed, Energy and Fibre from land - a vision for 2020, Belfast, Northern Ireland, 12-14 April 2010. - Penicuik, Scotland : BSAS - ISBN 9780906562673 - p. 175 - 175.
    A multimedia-based cognitive-behavioural intervention programme improves the attitude of stockpeople to handling pigs
    Ruis, M.A.W. ; Coleman, G. ; Waiblinger, S. ; Boivin, X. - \ 2009
    In: Proceedings of the 43rd Congress of the International Society for Applied Ethology, Cairns, Australia, 6-10 July 2009. - - p. 139 - 139.
    Multimedia-based training packages (Quality Handling®) for livestock handlers to improve human-animal interactions are currently being developed in Europe (within Welfare Quality®) for beef and dairy cattle farmers, pig farmers and laying hen farmers. Each training package comprises a computerized cognitive-behavioural intervention programme, using voice-overs, images and videos. Such programmes have shown, in Australia, to be appropriate for people with limited formal education and to be the preferred method of learning for stockpeople. Most importantly, such a training method has been shown to improve stockperson animal handling, farm animal production and farm animal welfare. The effectiveness of the pig stockperson training package was tested in a field test with Dutch pig farmers. Two groups of stockpeople were used. In one group the stockpeople were trained, and their farms were visited twice (treatment group: 6 farms, 6 stockpeople): one visit shortly before and one visit 6 to 8 weeks after the training. Farms of the other group of stockpeople were visited twice, and these stockpeople were not trained (control group: 9 farms, 12 stockpeople). Part of a farm visit was the use of a questionnaire to determine the stockperson's beliefs about pigs in general, and on attitudes towards interacting with pigs. Relative to control stockpeople, trained stockpeople showed no change in general attitudes towards pigs, but showed a greater improvement in attitude to handling pigs (GLM; p
    A multimedia-besed cognitive-behavioural intervention program improves attitudes and handling behaviours of stockpeople on dairy farms
    Windschnurer, I. ; Boivin, X. ; Coleman, G. ; Ruis, M.A.W. ; Mounaix, B. ; Brulé, A. ; Waiblinger, S. - \ 2009
    Soil fauna and soil function in the fabric of the food web
    Brussaard, L. ; Pulleman, M.M. ; Ouédraogo, E. ; Mando, A. ; Six, J. - \ 2007
    Pedobiologia 50 (2007)6. - ISSN 0031-4056 - p. 447 - 462.
    organic-matter dynamics - semi-permanent cultivation - sudano-sahelian conditions - habitable pore-space - crusted soil - phosphorus allocation - earthworm activity - microaggregate formation - nitrogen mineralization - ecosystem engineers
    Over the last four decades, spanning David Coleman's career, and in no small measure thanks to him, soil ecologists have made tremendous progress in describing and understanding the overwhelming complexity of biological, biophysical and biochemical interactions in soil. These interactions shape the soil as a habitat for the soil food web and the vegetation and, thereby, regulate the two main life-supporting processes on Planet Earth: production and decomposition. Changes in decomposition and production processes are governed by (human-induced) changes in vegetation composition/cover, the amounts and quality of organic residues and (in)organic fertilizers entering the soil. Such modifications alter the physical environment and the soil biota. Hence, decomposition and production processes cannot be understood and/or manipulated without explicitly addressing the composition and activity of the soil food web. Using a conceptual model, we argue that quantitative understanding of biophysical interactions, in particular those between soil fauna and soil structure, are paramount to understanding biological and biochemical processes in soil and the availability of water and nutrients to plants. The need to increase the efficiency of crop production worldwide, to reverse soil degradation and to increase soil resilience will set the agenda for soil ecologists in the near future
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