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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    Life on earth? Yes! We are here, right? | WURcast
    Moene, A.F. - \ 2017
    Wageningen : Wageningen University & Research
    life - atmosphere
    A control model for object virtualization in supply chain management
    Verdouw, C.N. ; Beulens, A.J.M. ; Reijers, H.A. ; Vorst, J.G.A.J. van der - \ 2015
    Computers in Industry 68 (2015). - ISSN 0166-3615 - p. 116 - 131.
    information-systems - intelligent products - science research - design science - internet - things - life - technology - framework - demand
    Due to the emergence of the Internet of Things, supply chain control can increasingly be based on virtual objects instead of on the direct observation of physical objects. Object virtualization allows the decoupling of control activities from the handling and observing of physical products and resources. Moreover, virtual objects can be enriched with information that goes beyond human observation. This will allow for more advanced control capabilities, e.g. concerning tracking and tracing, quality monitoring and supply chain (re)planning. This paper proposes a control model for object virtualization in supply chain management, which is based on a multiple case study in the Dutch floriculture. It includes a typology of distinct mechanisms for object virtualization, which discerns reference objects and future projections next to the representation of real physical objects. The control model helps to define feasible redesign options for the virtualization of supply chain control. It is also of value as a basis to define the requirements for information systems that enable these redesign options.
    Consumption of unprocessed cow's milk protects infants from common respiratory infections
    Loss, G. ; Depner, M. ; Ulfman, L.H. ; Neerven, R.J.J. van; Hose, A.J. ; Genuneit, J. - \ 2015
    Journal of Allergy and Clinical Immunology 135 (2015)1. - ISSN 0091-6749 - p. 56 - 62.
    1st year - atopic sensitization - childhood asthma - viral-infections - birth-cohort - life - children - inflammation - prevention - proteins
    Background: Breast-feeding is protective against respiratory infections in early life. Given the co-evolutionary adaptations of humans and cattle, bovine milk might exert similar anti-infective effects in human infants. Objective: To study effects of consumption of raw and processed cow's milk on common infections in infants. Methods: The PASTURE birth cohort followed 983 infants from rural areas in Austria, Finland, France, Germany, and Switzerland, for the first year of life, covering 37,306 person-weeks. Consumption of different types of cow's milk and occurrence of rhinitis, respiratory tract infections, otitis, and fever were assessed by weekly health diaries. C-reactive protein levels were assessed using blood samples taken at 12 months. Results: When contrasted with ultra-heat treated milk, raw milk consumption was inversely associated with occurrence of rhinitis (adjusted odds ratio from longitudinal models [95% CI]: 0.71 [0.54-0.94]), respiratory tract infections (0.77 [0.59-0.99]), otitis (0.14 [0.05-0.42]), and fever (0.69 [0.47-1.01]). Boiled farm milk showed similar but weaker associations. Industrially processed pasteurized milk was inversely associated with fever. Raw farm milk consumption was inversely associated with C-reactive protein levels at 12 months (geometric means ratio [95% CI]: 0.66 [0.45-0.98]). Conclusions: Early life consumption of raw cow's milk reduced the risk of manifest respiratory infections and fever by about 30%. If the health hazards of raw milk could be overcome, the public health impact of minimally processed but pathogen-free milk might be enormous, given the high prevalence of respiratory infections in the first year of life and the associated direct and indirect costs.
    Quality of weight-loss counseling by Dutch practice nurses in primary care: an observational study
    Dillen, S. van; Noordman, J. ; Dulmen, S. van; Hiddink, G.J. - \ 2015
    European Journal of Clinical Nutrition 69 (2015). - ISSN 0954-3007 - p. 73 - 78.
    nutrition communication styles - physical-activity - general-practice - guidance practices - health-care - intervention - obesity - life - barriers - consultations
    Background/objective:To assess the quality of weight-loss counseling provided by Dutch primary care practice nurses (PNs) to overweight and obese patients including both PNs' compliance with the Five A's Model for behavioral counseling in primary care, and the use of different communication styles. In addition, relationships between PN/patient characteristics (including Five A's) and communication styles will be examined.Subjects/methods:In this observational study, 100 videotaped real-life consultations, collected in 2010/2011, were viewed using an observational checklist. Selection of consultations was based on PNs' registration of patient's complaint. The quality of weight-loss counseling was assessed by the Five A's Model (sequence of evidence-based practice behaviors that are effective for helping patients to change health behaviors) and by PNs' communication styles. Moreover, several PN and patient characteristics were registered. Descriptive statistics and logistic regression analysis were conducted with significance set at P
    Efficacy of repeated exposure and flavour-flavour learning as mechanisms to increase preschooler's vegetable intake and acceptance
    Wild, V.W.T. de; Graaf, C. de; Jager, G. - \ 2015
    Pediatric Obesity 10 (2015)3. - ISSN 2047-6310 - p. 205 - 212.
    childrens food preferences - mere exposure - fruit - consumption - childhood - variety - life - perspective - infants - obesity
    Background - Dutch children's diets, like the diets of many children in Europe and the US are not balanced, do not contain enough vegetables and have been associated with a high prevalence of childhood obesity. Promoting children's vegetable intake is challenging. Objective - We investigated the relative effectiveness of repeated exposure and flavour–flavour learning in increasing vegetable intake and acceptance in preschoolers. Methods - During an intervention period of 7 weeks, 39 toddlers (aged 1.5 to 4¿years) consumed red beet and parsnip crisps at day-care centres in Wageningen, the Netherlands. Half of the group received red beet crisps with a dip of tomato ketchup (Conditioned [C]) and parsnip with a neutral white sauce (Unconditioned, [UC]), whereas for the other half the order was reversed (red beet [UC], parsnip [C]). Preference and ad libitum consumption of vegetable crisps were measured once before and three times after the intervention over the course of a 6-month follow-up period to assess longer-term effects. Results - Intake increased significantly after the intervention for both vegetables (on average with 8¿g; an increase of approximately 300%), and this effect was persistent even 6 months afterwards. The increase was irrespective of crisps being offered with C or UC dip sauce. Conclusions These results suggest a robust and persistent effect of repeated exposure but no effect of flavour–flavour learning. Offering pure vegetable tastes repeatedly is sufficient to increase intake.
    Effect of antimicrobial compounds on cut Gerbera flowers: Poor relation between stem bending and numbers of bacteria in the vase water
    Witte, Y. van de; Harkema, H. ; Doorn, W.G. van - \ 2014
    Postharvest Biology and Technology 91 (2014). - ISSN 0925-5214 - p. 78 - 83.
    jamesonii flowers - essential oils - rose flowers - membranes - longevity - stress - sugars - plants - life - acid
    Gerbera flowers (Gerbera jamesonii) often show stem bending. In four cultivars (Tamara, Liesbeth, Cora, and Mickey), we tested the effects on bending of antimicrobial compounds (chlorine bleach, a slow release chlorine compound, 8-hydroxyquinoline citrate [HQC], silver nitrate, carvacrol and thymol), some combined with sugars. At concentrations used for other cut flowers, inclusion in the vase solution of several of the antimicrobial compounds delayed bending, had no effect, or hastened bending. Hastening of bending was found at higher concentrations. It was accompanied with visible damage on the stem ends. Results with HQC indicated high toxicity as it did not delay bending at any of the concentration tested (100-400 mg L-1). At 200 mg L-1 HQC induced growth of bacteria that were not found in the controls. The number of bacteria in the vase water showed a low correlation with bending. Visible toxicity on the stem surface was often associated with a high bacteria count. However, at relatively high concentrations of the antimicrobial compounds stem bending was associated with a low count. This indicated an effect other than bacteria. Water uptake was low in stems that bent early. It is hypothesized that material from dead stem cells resulted in a xylem blockage which led to early bending. Sucrose at 15 g L-1 in combination with an antimicrobial compound (slow release chlorine, HQC) resulted in the absence of stem damage and produced much less bending than the same concentration of the antimicrobial compounds alone. Sucrose apparently counteracted the toxic effects of the antimicrobial chemicals. (C) 2014 Published by Elsevier B.V.
    Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes
    Nielsen, H.B. ; Almeida, M. ; Sierakowska Juncker, A. ; Rasmussen, S. ; Li, J. ; Sunagawa, S. ; Plichta, D.R. ; Gautier, L. ; Pedersen, A.G. ; Chatelier, E. Le; Pelletier, E. ; Bonde, I. ; Nielsen, T. ; Manichanh, C. ; Arumugam, M. ; Batto, J.M. ; Quintanilha dos Santos, M.B. ; Blom, N. ; Borruel, N. ; Burgdorf, K.S. ; Boumezbeur, F. ; Casellas, F. ; Doré, J. ; Dworzynski, P. ; Guarner, F. ; Hansen, T. ; Hildebrand, F. ; Kaas, R.S. ; Kennedy, S. ; Kristiansen, K. ; Kultima, J.R. ; Leonard, P. ; Levenez, F. ; Lund, O. ; Moumen, B. ; Paslier, D. Le; Pons, N. ; Pedersen, O. ; Prifti, E. ; Qin, J. ; Raes, J. ; Sørensen, S. ; Tap, J. ; Tims, S. ; Ussery, D.W. ; Yamada, T. ; Jamet, A. ; Mérieux, A. ; Cultrone, A. ; Torrejon, A. ; Quinquis, B. ; Brechot, C. ; Delorme, C. ; M'Rini, C. ; Vos, W.M. de; Maguin, E. ; Varela, E. ; Guedon, E. ; Gwen, F. ; Haimet, F. ; Artiguenave, F. ; Vandemeulebrouck, G. ; Denariaz, G. ; Khaci, G. ; Blottière, H. ; Knol, J. ; Weissenbach, J. ; Hylckama Vlieg, J.E. van; Torben, J. ; Parkhil, J. ; Turner, K. ; Guchte, M. van de; Antolin, M. ; Rescigno, M. ; Kleerebezem, M. ; Derrien, M. ; Galleron, N. ; Sanchez, N. ; Grarup, N. ; Veiga, P. ; Oozeer, R. ; Dervyn, R. ; Layec, S. ; Bruls, T. ; Winogradski, Y. ; Zoetendal, E.G. ; Renault, D. ; Sicheritz-Ponten, ; Bork, P. ; Wang, J. ; Brunak, S. ; Ehrlich, S.D. - \ 2014
    Nature Biotechnology 32 (2014). - ISSN 1087-0156 - p. 822 - 828.
    short read alignment - sequences - systems - algorithms - microbiota - protein - life - sets - tree - tool
    Most current approaches for analyzing metagenomic data rely on comparisons to reference genomes, but the microbial diversity of many environments extends far beyond what is covered by reference databases. De novo segregation of complex metagenomic data into specific biological entities, such as particular bacterial strains or viruses, remains a largely unsolved problem. Here we present a method, based on binning co-abundant genes across a series of metagenomic samples, that enables comprehensive discovery of new microbial organisms, viruses and co-inherited genetic entities and aids assembly of microbial genomes without the need for reference sequences. We demonstrate the method on data from 396 human gut microbiome samples and identify 7,381 co-abundance gene groups (CAGs), including 741 metagenomic species (MGS). We use these to assemble 238 high-quality microbial genomes and identify affiliations between MGS and hundreds of viruses or genetic entities. Our method provides the means for comprehensive profiling of the diversity within complex metagenomic samples.
    Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi
    Schoch, C.L. ; Robbertse, B. ; Robert, V. ; Vu, D. ; Cardinali, G. ; Irinyi, L. ; Meyer, W. ; Nilsson, R.H. ; Hughes, K. ; Miller, A.N. ; Kirk, P.M. ; Abarenkov, K. ; Aime, M.C. ; Ariyawansa, H.A. ; Bidartondo, M. ; Boekhout, T. ; Buyck, B. ; Cai, Q. ; Chen, J. ; Crespo, A. ; Crous, P.W. ; Damm, U. ; Beer, Z.W. de; Dentinger, B.T.M. ; Divakar, P.K. ; Duenas, M. ; Feau, N. ; Fliegerova, K. ; Garcia, M.A. ; Ge, Z.W. ; Griffith, G.W. ; Groenewald, J.Z. ; Groenewald, M. ; Grube, M. ; Gryzenhout, M. ; Gueidan, C. ; Guo, L. ; Hambleton, S. ; Hamelin, R. ; Hansen, K. ; Hofstetter, V. ; Hong, S.B. ; Houbraken, J. ; Hyde, K.D. ; Inderbitzin, P. ; Johnston, P.A. ; Karunarathna, S.C. ; Koljalg, U. ; Kovacs, G.M. ; Kraichak, E. ; Krizsan, K. ; Kurtzman, C.P. ; Larsson, K.H. ; Leavitt, S. ; Letcher, P.M. ; Liimatainen, K. ; Liu, J.K. ; Lodge, D.J. ; Luangsa-ard, J.J. ; Lumbsch, H.T. ; Maharachchikumbura, S.S.N. ; Manamgoda, D. ; Martin, M.P. ; Minnis, A.M. ; Moncalvo, J.M. ; Mule, G. ; Nakasone, K.K. ; Niskanen, T. ; Olariaga, I. ; Papp, T. ; Petkovits, T. ; Pino-Bodas, R. ; Powell, M.J. ; Raja, H.A. ; Redecker, D. ; Sarmiento-Ramirez, J.M. ; Seifert, K.A. ; Shrestha, B. ; Stenroos, S. ; Stielow, B. ; Suh, S.O. ; Tanaka, K. ; Tedersoo, L. ; Telleria, M.T. ; Udayanga, D. ; Untereiner, W.A. ; Dieguez Uribeondo, J. ; Subbarao, K.V. ; Vagvolgyi, C. ; Visagie, C. ; Voigt, K. ; Walker, D.M. ; Weir, B.S. ; Weiss, M. ; Wijayawardene, N.N. ; Wingfield, M.J. ; Xu, J.P. ; Yang, Z.L. ; Zhang, N. ; Zhuang, W.Y. ; Federhen, S. - \ 2014
    Database : the Journal of Biological Databases and Curation 2014 (2014). - ISSN 1758-0463 - 21 p.
    internal transcribed spacer - arbuscular mycorrhizal fungi - ribosomal dna - interspecific hybridization - sequence analyses - species complex - identification - evolution - barcode - life
    DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.
    Detecting leaf pulvinar movements on NDVI time series of desert trees: A new approach for water stress detection
    Chávez Oyanadel, R.O. ; Clevers, J.G.P.W. ; Verbesselt, J. ; Naulin, P. ; Herold, M. - \ 2014
    PLoS ONE 9 (2014)9. - ISSN 1932-6203 - 12 p.
    pampa del tamarugal - atacama desert - prosopis-tamarugo - canopy structure - northern chile - photoinhibition - landsat - plants - terra - life
    Heliotropic leaf movement or leaf ‘solar tracking’ occurs for a wide variety of plants, including many desert species and some crops. This has an important effect on the canopy spectral reflectance as measured from satellites. For this reason, monitoring systems based on spectral vegetation indices, such as the normalized difference vegetation index (NDVI), should account for heliotropic movements when evaluating the health condition of such species. In the hyper-arid Atacama Desert, Northern Chile, we studied seasonal and diurnal variations of MODIS and Landsat NDVI time series of plantation stands of the endemic species Prosopis tamarugo Phil., subject to different levels of groundwater depletion. As solar irradiation increased during the day and also during the summer, the paraheliotropic leaves of Tamarugo moved to an erectophile position (parallel to the sun rays) making the NDVI signal to drop. This way, Tamarugo stands with no water stress showed a positive NDVI difference between morning and midday (¿NDVImo-mi) and between winter and summer (¿NDVIW-S). In this paper, we showed that the ¿NDVImo-mi of Tamarugo stands can be detected using MODIS Terra and Aqua images, and the ¿NDVIW-S using Landsat or MODIS Terra images. Because pulvinar movement is triggered by changes in cell turgor, the effects of water stress caused by groundwater depletion can be assessed and monitored using ¿NDVImo-mi and ¿NDVIW-S. For an 11-year time series without rainfall events, Landsat ¿NDVIW-S of Tamarugo stands showed a positive linear relationship with cumulative groundwater depletion. We conclude that both ¿NDVImo-mi and ¿NDVIW-S have potential to detect early water stress of paraheliotropic vegetation.
    Associations of plant and animal protein intake with 5-year changes in blood pressure: The Zutphen Elderly Study
    Tielemans, S.M.A.J. ; Kromhout, D. ; Altorf-van der Kuil, W. ; Geleijnse, J.M. - \ 2014
    Nutrition, Metabolism & Cardiovascular Diseases 24 (2014)11. - ISSN 0939-4753 - p. 1228 - 1233.
    hypertension - prevention - intermap - health - risk - life
    Background and aim The aim of the present study was to investigate the association of plant and animal protein intake with 5-year changes in blood pressure (BP) level. Methods and results Analyses were based on 702 observations of 272 men participating in the Zutphen Elderly Study. Men did not use antihypertensive medication and were initially free of cardiovascular disease, diabetes mellitus and cancer. Physical and dietary examinations were performed in 1985, 1990, 1995, and 2000. Diet was assessed using the cross-check dietary history method. Men were categorised into tertiles according to their plant and animal protein intake. BP was measured twice at each examination. The associations of plant and animal protein intake with 5-year changes in BP level were investigated by a random intercept model with first-order autoregressive (AR [1]) serial correlation and a nugget effect. Adjustments were made for age, examination year, BMI, socioeconomic status, smoking, physical activity, prescribed diet, alcohol consumption and intake of energy and nutrients. In 1985, men were 70.1 ± 4.6 years old and had a mean BP of 147/84 mmHg. Mean protein intake was 15 en%, of which one-third consisted of plant protein. The higher-intake tertiles of plant protein intake were associated with a mean 5-year change of -2.9 mmHg (95% CI: -5.6, -0.2) systolic and -1.7 mmHg (95% CI: -3.2, -0.2) diastolic, compared with the lowest-intake tertile. No associations were observed for animal protein intake. Conclusion Intake of plant protein, but not animal protein, was inversely associated with 5-year changes in BP level in elderly men.
    Wellbeing for homeless people: a Salutogenic approach
    Dunleavy, A. ; Kennedy, L.A. ; Vaandrager, L. - \ 2014
    Health Promotion International 29 (2014)1. - ISSN 0957-4824 - p. 144 - 154.
    health-promotion - coherence scale - qualitative research - antonovskys sense - model - life
    Homelessness affects considerable numbers in the UK and is caused by poverty and social exclusion. Much of the literature on housing and health is disease centric, where the experience of homelessness is described as traumatic, disempowering and socially isolating. Based on the Salutogenic approach, which calls for a positive orientation on health, the aim of this study was to explore the subjective lived experiences of wellbeing in the situated context of homeless people's lives. Nine in-depth qualitative interviews with temporarily housed adults (>25 years) in a socio-economically deprived region of North-west England were held. Accounts of renewed self-confidence, perceived resourcefulness and continual personal participation are said to be supporting wellbeing. A strong belief, or sense of coherence, in internal and external general resistance resources was a critical enabling factor for those living in temporary accommodation. Wellbeing was consistently linked with both social and formal activities; keeping occupied and having a strong sense of purpose were essential to wellbeing. In utilizing a Salutogenic approach we demonstrate how the ‘context and meaning’ of health actions can improve the understanding about the kinds of factors influencing wellbeing.
    Effects of repeated exposure to either vegetables or fruits on infant's vegetable and fruit acceptance at the beginning of weaning
    Barends, C. ; Vries, J. de; Mojet, J. ; Graaf, C. de - \ 2013
    Food Quality and Preference 29 (2013)2. - ISSN 0950-3293 - p. 157 - 165.
    developmental-changes - food preferences - variety - children - life - experience - formula
    This study investigated the effects of repeated exposure to either vegetables or fruits on an infant's vegetable and fruit acceptance during the first 18 days of weaning. We hypothesized that repeated exposure to a type of vegetable or fruit, would increase its intake. Furthermore, we expected that being exclusively weaned with vegetables would result in a higher acceptance of vegetables than being exclusively weaned with fruits. To investigate this, a 19-day intervention study was conducted in 101 healthy infants, aged 4-6 months. Infants were randomly assigned to one of four treatment groups. Two groups received exclusively vegetable purees as targets every other day for 18 consecutive days; green beans was the target for one group and artichoke for the other group. The other two groups received exclusively fruit purees including either apple or plums as the target fruit. On day 19, the vegetable groups consumed their first fruit pur e and the fruit groups their first vegetable pur e. At the beginning of the study on days 1 and 2 and at the end on days 17, 18 and 19, the infants were fed fruit or vegetable pur e in our laboratory. On days 3-16, the parents fed their infants the fruit or vegetable purees at home. Outcome variables were vegetable and fruit intake over time. Mean vegetable intake in the vegetable group increased significantly from 24 28 g (mean +/- SD) on days 1 and 2 to 45 +/- 44 g on days 17 and 18. Fruit intake in the fruit group increased significantly from 46 +/- 40 to 66 +/- 42 g. Fruit intake was significantly higher than vegetable intake from the start. Repeated exposure to fruit had no effect on the vegetable intake. The first intake of green beans in the fruit groups at day 19, was 24 +/- 29 g and on average as low as the green beans intake in the vegetable groups at the 1st exposure on days 1 or 2. Similarly, the first apple intake in the fruit groups on days 1 or 2 of 47 +/- 48 g did on average not differ from the first apple intake of 45 +/- 49 g in the vegetable groups on day 19. The mean intake of green beans and plums increased significantly after repeated exposure. The intake of the target food artichoke stayed low and the intake of apple only increased slightly. These findings confirm that at the first exposure fruit acceptance is higher than vegetable acceptance. Weaning with vegetables, but not with fruits, may promote vegetable acceptance in infants. (C) 2013 Elsevier Ltd. All rights reserved.
    Genetic control of interactions among individuals: contrasting outcomes of indirect genetic effects arising from neighbour disease infection and competition in a forest tree
    Costa e Silva, J. ; Potts, B.M. ; Bijma, P. ; Kerr, R.J. ; Pilbeam, D.J. - \ 2013
    New Phytologist 197 (2013)2. - ISSN 0028-646X - p. 631 - 641.
    eucalyptus-globulus - multilevel selection - mycosphaerella-nubilosa - ecological interactions - arabidopsis-thaliana - heritable variation - evolution - model - life - consequences
    Indirect genetic effects (IGEs) are heritable effects of individuals on trait values of their conspecifics. IGEs may substantially affect response to selection, but empirical studies on IGEs are sparse and their magnitude and correlation with direct genetic effects are largely unknown in plants. Here we used linear mixed models to estimate genetic (co)variances attributable to direct and indirect effects for growth and foliar disease damage in a large pedigreed population of Eucalyptus globulus. We found significant IGEs for growth and disease damage, which increased with age for growth. The correlation between direct and indirect genetic effects was highly negative for growth, but highly positive for disease damage, consistent with neighbour competition and infection, respectively. IGEs increased heritable variation by 71% for disease damage, but reduced heritable variation by 85% for growth, leaving nonsignificant heritable variation for later age growth. Thus, IGEs are likely to prevent response to selection in growth, despite a considerable ordinary heritability. IGEs change our perspective on the genetic architecture and potential response to selection. Depending on the correlation between direct and indirect genetic effects, IGEs may enhance or diminish the response to natural or artificial selection compared with that predicted from ordinary heritability.
    Metagenomic species profiling using universal phylogenetic marker genes
    Sunagawa, S. ; Mende, D.R. ; Zeller, G. ; Izquierdo-Carrasco, F. ; Berger, S.A. ; Kultima, J.R. ; Coelho, L.P. ; Arumugam, M. ; Tap, J. ; Nielsen, H.B. ; Rasmussen, S. ; Brunak, S. ; Pedersen, O. ; Guarner, F. ; Vos, W.M. de; Wang, J. ; Li, J. ; Doré, J. ; Ehrlich, S.D. ; Stamatakis, A. ; Bork, P. - \ 2013
    Nature Methods : techniques for life scientists and chemists 10 (2013)12. - ISSN 1548-7091 - p. 1196 - 1199.
    maximum-likelihood - human microbiome - gut microbiome - alignments - accurate - catalog - reads - life - tree - ibd
    To quantify known and unknown microorganisms at species-level resolution using shotgun sequencing data, we developed a method that establishes metagenomic operational taxonomic units (mOTUs) based on single-copy phylogenetic marker genes. Applied to 252 human fecal samples, the method revealed that on average 43% of the species abundance and 58% of the richness cannot be captured by current reference genome-based methods. An implementation of the method is available at http://www.bork.embl.de/software/mOTU/
    Bovine biopolitics and the promise of monsters in the rewilding of Heck cattle
    Lorimer, J. ; Driessen, C.P.G. - \ 2013
    Geoforum 48 (2013)8. - ISSN 0016-7185 - p. 249 - 259.
    nature conservation - livestock - politics - wolf - life - technologies - biosecurity - management - openness - science
    In the early 1980s the Dutch ecologist Frans Vera began an ambitious ecological restoration experiment on a polder in the Netherlands. He introduced herds of ‘back-bred’ Heck cattle and other large herbivores and encouraged them to ‘de-domesticate’ themselves and ‘rewild’ the landscape they inhabit. His intervention has triggered a great deal of interest and controversy. It is being replicated and adapted across Europe as part of a wider interest in ‘rewilding’ in nature conservation. This innovative approach rubs up against powerful and prevalent practices of environmental management. This paper examines these frictions by mapping the character and exploring the interface between different modes of nonhuman biopolitics – in this case the powerful ways in which modern humans live with and govern cattle. Focusing on the story of Heck cattle and the bovine biopolitics of their rewilding it attends in particular to the character, place and promise of monsters. It first outlines a conceptual framework for examining nonhuman biopolitics and teratology (the study of monsters), identifying fertile tensions between the work of Haraway, Derrida and Deleuze. It then provides a typology of four prevalent modes of bovine biopolitics – namely agriculture, conservation, welfare and biosecurity – and their associated monsters. This paper identifies rewilding as a fifth mode and examines frictions at its interfaces with the other four. Developing the conceptual framework the paper examines what these frictions tell us about the understandings of life that circulate in the ontological politics of contemporary environmentalisms. In conclusion the paper critically examines the monstrous promise of rewilding, in relation to tensions between the convivial aspirations of Haraway and Deleuze.
    CAMPFIRE and human-wildlife conflicts in local communities bordering northern Gonarezhou National Park, Zimbabwe
    Gandiwa, E. ; Heitkonig, I.M.A. ; Lokhorst, A.M. ; Prins, H.H.T. ; Leeuwis, C. - \ 2013
    Ecology and Society 18 (2013)4. - ISSN 1708-3087 - 15 p.
    health-promotion - psychology - dimensions - framework - ecosystem - justice - science - life
    Human-wildlife conflicts are a global problem, and are occurring in many countries where human and wildlife requirements overlap. Conflicts are particularly common near protected areas where societal unrest is large. To ease conflict, integrated conservation and development projects (ICDPs) have been implemented. The Communal Areas Management Programme for Indigenous Resources (CAMPFIRE) is an example of an ICDP. We hypothesized that (i) a higher perceived effectiveness of CAMPFIRE would be associated with a decline in human-wildlife conflicts, and (ii) local communities with higher perceived effectiveness of CAMPFIRE programs would have more favorable attitudes towards problematic wild animals. Four focus group discussions and interviews with 236 respondents were conducted in four local communities adjacent to northern Gonarezhou National Park, Zimbabwe from December 2010 to August 2011. Moreover, we included data on recorded incidences of human-wildlife conflicts and CAMPFIRE financial returns to study communities between 2000 and 2010. Our results indicate that local communities showed considerable differences in how CAMPFIRE effectiveness was perceived. Local communities with higher ratings of CAMPFIRE effectiveness generally perceived a decline in human-wildlife conflicts, although some people had experienced problems with wild animals. Attitudes towards main problematic wild animals varied across the study communities and were partly associated with perceived CAMPFIRE effectiveness. Our findings partly support both of our study hypotheses. Contextual factors across the four local communities seemed to influence the perceived effectiveness of CAMPFIRE programs and attitudes towards problematic wildlife species. We recommend that decisions and actions regarding the control of problem animals be devolved to the community level in order to help reduce human-wildlife conflicts in community-based natural resources management programs.
    Influence of temperature and food availability on juvenile European anchovy Engraulis encrasicolus at its northern boundary
    Raab, K.E. ; Llope, M. ; Nagelkerke, L.A.J. ; Rijnsdorp, A.D. ; Teal, L.R. ; Licandro, P. ; Ruardij, P. ; Dickey-Collas, M. - \ 2013
    Marine Ecology Progress Series 488 (2013). - ISSN 0171-8630 - p. 233 - 245.
    growth-selective predation - climate-change - sea - bay - energy - biscay - fish - japonicus - life - variability
    The European anchovy Engraulis encrasicolus population of the North Sea has increased and spread in recent decades, probably in response to the relaxation of limiting factors in its life history. We use models and empirical data to explore the effects of temperature and food availability during the first growing season on the adult anchovy population across the North Sea. First, we compare simulated growth during summer and autumn, from a dynamic energy budget model, with trends in the time series of anchovy survey catch per unit effort. The proportion of the area of the North Sea in which anchovy can grow to 10 cm (the potential growth habitat) correlates with the abundance of anchovy caught in surveys the following year. Second, spatio-temporal statistical modeling is used to show that anchovy abundance in surveys is related to environmental variables (temperature and food availability). Temperature explains the distribution and abundance of anchovy in the North Sea better than food availability or a combination of both environmental factors. We conclude that variations in growth during the first months of life can impact anchovy life cycle closure. Specifically for the North Sea anchovy, changes in temperature are more important than changes in food availability in allowing the fish to grow to overwintering size, under probably non-food-limited conditions.
    Twenty-four hour urinary urea excretion and 9-year risk of hypertension: the PREVEND study
    Tielemans, S.M.A.J. ; Geleijnse, J.M. ; Baak, M.A. van; Engberink, M.F. ; Brink, E.J. ; Jong, P.E. ; Gansevoort, R.T. ; Bakker, S.J.A. - \ 2013
    Journal of Hypertension 31 (2013)8. - ISSN 0263-6352 - p. 1564 - 1569.
    blood-pressure - protein-intake - association - nutrients - nitrogen - cohort - trial - life - men
    OBJECTIVES:: It is not yet clear whether dietary protein could help maintaining a healthy blood pressure (BP). We investigated the association between total protein intake, estimated from 24-h urinary urea excretion, and incident hypertension in Dutch men and women. METHODS:: We analyzed data of 3997 men and women (aged 28-75 years) who participated in the Prevention of Renal and Vascular Endstage Disease (PREVEND) study, a prospective cohort study. Urea excretion was assessed in two consecutive 24-h urine collections at baseline and approximately 4 years later, from which total protein intake was estimated using the Maroni method. Participants were followed for 9 years for hypertension incidence, defined as BP at least 140/90¿mmHg or initiation of antihypertensive medication. Hazard ratios (HR) were obtained in sex-specific quintiles of protein intake using time-dependent Cox regression, adjusted for age, sex, BMI, smoking, alcohol use, and 24-h urinary excretions of sodium and potassium. RESULTS:: Baseline BP was on average 119/70¿mmHg and 976 participants developed hypertension during follow-up. Mean protein intake (in g/kg ideal body weight) was 1.18¿±¿0.26 for men and 1.12¿±¿0.25 for women. Estimated protein intake was nonlinearly inversely associated with incident hypertension in the fully adjusted model, with nonsignificant HR of 0.77, 0.75, 0.82, and 0.83 in consecutive quintiles compared with the lowest quintile (P-trend: 0.52). CONCLUSION:: Protein intake, as assessed by urinary urea excretion, was not significantly associated with 9-year hypertension incidence in Dutch men and women.
    Intestinal Microbiota of Infants With Colic: Development and Specific Signatures
    Weerth, C. de; Fuentes Enriquez de Salamanca, S. ; Puylaert, P.G.B. ; Vos, W.M. de - \ 2013
    Pediatrics 131 (2013)2. - ISSN 0031-4005 - p. e550 - e558.
    gastrointestinal-tract microbiota - human gut microbiome - phylogenetic microarray - bacterial - microflora - succession - diversity - life - age
    OBJECTIVES:To provide a comprehensive analysis of the fecal microbiota in infants with colic, as compared with control infants, during their first 100 days of life.METHODS:Microbial DNA of >200 samples from 12 infants with colic and 12 age-matched control infants was extracted and hybridized to a phylogenetic microarray.RESULTS:Microbiota diversity gradually increased after birth only in the control group; moreover, in the first weeks, the diversity of the colic group was significantly lower than that of the control group. The stability of the successive samples also appeared to be significantly lower in the infants with colic for the first weeks. Further analyses revealed which bacterial groups were responsible for colic-related differences in microbiota at age 1 or 2 weeks, the earliest ages with significant differences. Proteobacteria were significantly increased in infants with colic compared with control infants, with a relative abundance that was more than twofold. In contrast, bifidobacteria and lactobacilli were significantly reduced in infants with colic. Moreover, the colic phenotype correlated positively with specific groups of proteobacteria, including bacteria related to Escherichia, Klebsiella, Serratia, Vibrio, Yersinia, and Pseudomonas, but negatively with bacteria belonging to the Bacteroidetes and Firmicutes phyla, the latter of which includes some lactobacilli and canonical groups known to produce butyrate and lactate.CONCLUSIONS:The results indicate the presence of microbial signatures in the first weeks of life in infants who later develop colic. These microbial signatures may be used to understand the excessive crying. The results offer opportunities for early diagnostics as well as for developing specific therapies
    Types of cell death and methods of their detection in yeast Saccharomyces cerevisiae
    Wloch-Salamon, D.M. ; Bem, A.E. - \ 2013
    Journal of Applied Microbiology 114 (2013)2. - ISSN 1364-5072 - p. 287 - 298.
    monitoring autophagy - programmed necrosis - global analysis - budding yeast - acetic-acid - apoptosis - proteins - biology - life - mitochondria
    The occurrence of programmed cell death in unicellular organisms is a subject that arouses great interest of theoreticians and experimental scientists. Already found evolutionarily conserved genes and metabolic pathways confirmed its existence in yeast, protozoa and even bacteria. In the yeast Saccharomyces cerevisiae, at least three main types of death are distinguished: apoptosis, necrosis and autophagy. Their classification suggested by the Nomenclature Committee on Cell Death initially based on the morphological characteristics has now been extended to include the measurable biochemical characteristics. Several laboratory methods previously used to detect the types of cell death of higher eucaryotes and later developed and successfully used for the analysis of yeast cells are here critically reviewed. Their advantages and limitations are described.
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