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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    Genotypic variation in source and sink traits affects the response of photosynthesis and growth to elevated atmospheric CO2
    Fabre, Denis ; Dingkuhn, Michael ; Yin, Xinyou ; Clément-Vidal, Anne ; Roques, Sandrine ; Soutiras, Armelle ; Luquet, Delphine - \ 2020
    Plant, Cell & Environment 43 (2020)3. - ISSN 0140-7791 - p. 579 - 593.
    carbon assimilation - climate change - CO - enrichment - L. phenotypic plasticity - local source–sink ratio - Oryza sativa - sink limitation - triose phosphate utilization

    This study aimed to understand the response of photosynthesis and growth to e-CO2 conditions (800 vs. 400 μmol mol−1) of rice genotypes differing in source–sink relationships. A proxy trait called local C source–sink ratio was defined as the ratio of flag leaf area to the number of spikelets on the corresponding panicle, and five genotypes differing in this ratio were grown in a controlled greenhouse. Differential CO2 resources were applied either during the 2 weeks following heading (EXP1) or during the whole growth cycle (EXP2). Under e-CO2, low source–sink ratio cultivars (LSS) had greater gains in photosynthesis, and they accumulated less nonstructural carbohydrate in the flag leaf than high source–sink ratio cultivars (HSS). In EXP2, grain yield and biomass gain was also greater in LSS probably caused by their strong sink. Photosynthetic capacity response to e-CO2 was negatively correlated across genotypes with local C source–sink ratio, a trait highly conserved across environments. HSS were sink-limited under e-CO2, probably associated with low triose phosphate utilization (TPU) capacity. We suggest that the local C source–sink ratio is a potential target for selecting more CO2-responsive cultivars, pending validation for a broader genotypic spectrum and for field conditions.

    Undernutrition management and the role of protein-enriched meals for older adults
    Ziylan, Canan - \ 2016
    Wageningen University. Promotor(en): Lisette de Groot; Stefanie Kremer; Annemien Haveman-Nies. - Wageningen : Wageningen University - ISBN 9789462579323 - 148
    elderly - elderly nutrition - undernutrition - enrichment - protein - eating patterns - feeding behaviour - meals - nursing homes - ouderen - ouderenvoeding - ondervoeding - verrijking - eiwit - eetpatronen - voedingsgedrag - maaltijden - verpleeghuizen

    Undernutrition is a major health problem in the growing elderly population. It is estimated that one in ten Dutch community-dwelling older adults is suffering from undernutrition, and one in three Dutch older adults who receive home care. Undernutrition may lead to many negative consequences, ranging from fatigue and falls to impaired immune function and death. This makes undernutrition an obvious target for preventive measures.

    Undernutrition can be defined as “a state of nutrition in which a deficiency or excess (or imbalance) of energy, protein, and other nutrients causes measurable adverse effects on tissue/body form (body shape, size and composition) and function, and clinical outcome”. In addition, it is often described as protein energy malnutrition. Adequate protein intake may to some extent prevent and reverse this process. However, throughout ageing, it becomes increasingly difficult to reach adequate protein intake due to higher protein needs and lower protein intakes. Finding solutions to assist older adults in reaching their optimal protein intake is necessary.

    In our overall research project, we considered 1.2g protein per kg weight per day (g/kg/d) as adequate protein intake. In Dutch community-dwelling older adults, protein intake is around 1.0 g/kg/d, implying room for improvement. However, it is possible that many of these older adults deal with physiological changes, medical conditions, and physical and mental limitations that impair their appetite and food provision. For these older adults with higher protein needs, merely recommending that they eat more would not be realistic. It would be more realistic to explore strategies that increase protein intake without having to increase food intake. This calls for the exploration of instruments that match the needs and preferences of older adults: protein-enriched regular products.

    One particular group that can be identified as a target group for such products, are older adults who receive home care. Undernutrition prevalence is high in this group, which may be explained by their health problems that led to this dependence on home care. Likewise, many of these older adults also depend on meals-on-wheels. These meals-on-wheels recipients, regardless of whether they receive home care or not, often risk undernutrition too. In both these (overlapping) care-dependent groups, difficulties in adhering to energy and protein recommendations can be discerned. For this reason, enriching the readymade meals that these older adults receive may contribute to the prevention of protein undernutrition by increasing protein intake while keeping food intake the same. Here, protein enrichment instruments can be used to prevent undernutrition, but only when implemented in a timely manner. Adequate undernutrition management systems are therefore necessary to facilitate timely intervention, ensuring that the developed protein-enriched meals are actually offered and effective. For this reason, the overall aim of our research project was to gain insight into the current state of undernutrition management in community-dwelling older adults in the Netherlands and explore the role of protein-enriched regular products as a supportive instrument in protein undernutrition management.

    In Study 1 (chapter 2) we explored the experiences of 22 Dutch nutrition and care professionals and researchers with undernutrition awareness, monitoring, and treatment among community-dwelling older adults. This qualitative study among, for example, dietitians, general practitioners, nurse practitioners, and home care nurses provided insight into the current bottlenecks within the existing undernutrition management guidelines. In these telephone interviews, these experts also discussed the current dietary behaviour problems of older adults and their impact on undernutrition risk. The experts’ experiences implied that undernutrition awareness is limited, among both older adults and care professionals. In addition, the interviewees were unclear about which professionals are responsible for monitoring and which monitoring procedures are preferred. The dietitians feel that they become involved too late, leading to decreased treatment effectiveness. In general, the interviewees desired more collaboration and a coherent and feasible allocation of responsibilities regarding undernutrition monitoring and treatment. This implied that the available guidelines on undernutrition management require more attention and facilitation.

    In the following mixed-methods study (chapter 3), with interviews, we qualitatively explored the dietary behaviour and undernutrition risk of 12 Dutch elderly meals-on-wheels clients, one of the largest at-risk groups. We followed up on this information by quantifying the topics that emerged from the qualitative exploration of experienced bottlenecks in performing adequate dietary behaviour. For this, we used a survey among 333 meals-on-wheels clients. The interviews with elderly meals-on-wheels clients made clear that they have fixed and habitual eating patterns, while at the same time their appetite had decreased throughout the years. This was confirmed by the survey finding that regular portion size meals were perceived as too large by the oldest group aged over 75y. In addition, as the professionals suggested earlier, the interviewed elderly clients indeed showed limited awareness of undernutrition risk. Simultaneously, the survey showed that almost one in four elderly meals-on-wheels clients was undernourished. These findings led to the conclusion that staying close to the identified dietary habits may facilitate small yet effective modifications within these habits to prevent inadequate nutritional intake. Still, the limited awareness of undernutrition risk was expected to play a limiting role in whether clients believe they need dietary modifications. Consequently, informing them about this need could facilitate their motivation to implement modifications.

    After learning about the general dietary behaviour of these older adults, we used this information for Study 3 (chapter 4). We developed two kinds of protein-enriched readymade meals that are in line with the needs and preferences of older adults: one of regular size (450g) and one of reduced size (400g). We tested these meals in a lab setting in 120 community-dwelling older adults in a single-blind randomised crossover trial. One day a week at lunchtime, for four weeks, participants had to consume and evaluate a readymade meal. Overall, regardless of portion size, the protein-enriched meals led to higher protein intakes in vital older adults in a lab setting during lunch. In this crossover study, the participants liked the protein-enriched meals and the regular meals equally. However, we did not find the expected lower ratings of satiety after the reduced-size meals, while one reduced-size enriched meal and another regular-size enriched meal led to higher ratings of subsequent satiety. This higher satiety in the enriched meals could lead to compensational behaviour on the remainder of the day.

    After establishing that the protein-enriched meals were effective and acceptable in the lab setting, we moved to the homes of older adults to test the meals in a longer-term study in Study 4 (chapter 5). In this double-blind randomised controlled trial of two weeks, we also included protein-enriched bread to assess whether both this bread and the meals could increase daily protein intake to 1.2g/kg/d in 42 community-dwelling older adults to reach optimal protein intake. We found that the enriched products again led to higher protein intakes and a high liking. The mean protein intake per day was 14.6g higher in the intervention group, which amounted to a protein intake of 1.25g/kg/d, compared with 0.99g/kg/d in the control group. In addition, the meals scored 7.7 out of 10, while the bread scored 7.8 out of 10, which both were comparable with their regular counterparts. Lastly, we found no negative effect of compensational behaviour throughout the day. These promising findings indicated that we achieved a good match between older adults’ needs and preferences regarding protein intake.

    In the general discussion of this thesis (chapter 6), we combined our learnings from the four studies to reflect on protein undernutrition management in community-dwelling older adults and the possible role of protein-enriched regular products. We have discussed a conceptual framework consisting of three wheels of protein undernutrition management. In the first wheel regarding awareness, we proposed that limited awareness of adequate nutrition and body composition forms the largest bottleneck in undernutrition management. When this awareness is generated among both older adults and professionals, it will benefit the second wheel of monitoring. Here, we argued that a policy and the actual facilitation of that policy are required for this monitoring to succeed. When the monitoring is performed adequately, in the third wheel, the appropriate treatment can be carried out. We discussed that personalisation and evaluation of this treatment are important conditions. All in all, the public health implications that we have discussed on the basis of our findings can be summarised by the three key messages that could help us ace in adequate protein undernutrition management: address awareness in both older adults and professionals, facilitate continuous collaboration between professionals, and offer protein-enriched products expediently.

    Standardising the assessment of environmental enrichment and tail-docking legal requirements for finishing pigs in Europe
    Hothersall, B. ; Whistance, L.K. ; Zedlacher, H. ; Algers, B. ; Andersson, E. ; Bracke, M.B.M. ; Courboulay, V. ; Ferrari, P. ; Leeb, C. ; Mullan, S. ; Nowicki, J. ; Meunier-Salaün, M.C. ; Schwarz, T. ; Stadig, L. ; Main, D. - \ 2016
    Animal Welfare 25 (2016)4. - ISSN 0962-7286 - p. 499 - 515.
    animal welfare - enrichment - inspector - legislation - pig - tail-docking - animal welfare - enrichment - inspector - legisation - pig - tail-docking
    An online training package providing a concise synthesis of the scientific data underpinning EU legislation on enrichment and tail-docking of pigs was produced in seven languages, with the aim of improving consistency of professional judgements regarding legislation compliance on farms. In total, 158 participants who were official inspectors, certification scheme assessors and advisors from 16 EU countries completed an initial test and an online training package. Control group participants completed a second identical test before, and Training group participants after, viewing the training. In Section 1 of the test participants rated the importance of modifying environmental enrichment defined in nine scenarios from 1 (not important) to 10 (very important). Training significantly increased participants' overall perception of the need for change. Participants then rated nine risk factors for tail-biting from 1 (no risk) to 10 (high risk). After training scores were better correlated with risk rankings already described by scientists. Scenarios relating to tail-docking and management were then described. Training significantly increased the proportion of respondents correctly identifying that a farm without tail lesions should stop tail-docking. Finally, participants rated the importance of modifying enrichment in three further scenarios. Training increased ratings in all three. The pattern of results indicated that participants' roles influenced scores but overall the training improved: i) recognition of enrichments that, by virtue of their type or use by pigs, may be insufficient to achieve legislation compliance; ii) knowledge on risk factors for tail-biting; and iii) recognition of when routine tail-docking was occurring.
    Glass transitions of barley starch and protein in the endosperm and isolated form
    Donkelaar, L.H.G. van; Martinez, J.T. ; Frijters, H. ; Noordman, T.R. ; Boom, R.M. ; Goot, A.J. van der - \ 2015
    Food Research International 72 (2015). - ISSN 0963-9969 - p. 241 - 246.
    air classification - temperature - enrichment - fractions - flours
    When studying the glass-to-rubber transition inside natural materials, it is important to take into account not only the moisture content but also the moisture distribution over the components in the material. We measured the Tg of protein and starch isolated from barley at different moisture contents using differential scanning calorimetry (DSC) (heating rate 10 °C/min) and by thermo mechanical compression tests (TMCT) (heating rate 2 °C/min). The measurement of the Tg of partially crystalline materials, such as barley starch, is more difficult using TMCT because the mechanical effect of expansion of these materials is smaller. For both measurement sets the glass transition lines were modeled using the Gordon–Taylor equation. The lines were adapted for the differences in moisture content over the endosperm by using the sorption isotherms of isolated barley starch and protein and whole barley endosperm. The glass transition lines measured by TMCT were closer together than the ones measured by DSC
    High rates of anaerobic oxidation of methane, ethane and propane coupled to thiosulphate reduction
    Suarez Zuluaga, D.A. ; Weijma, J. ; Timmers, P.H.A. ; Buisman, C.J.N. - \ 2015
    Environmental Science and Pollution Research 22 (2015)5. - ISSN 0944-1344 - p. 3697 - 3704.
    sulfate-reducing bacteria - marine-sediments - electron-donor - sulfur cycle - aarhus bay - consumption - denmark - disproportionation - bioreactor - enrichment
    Anaerobic methane oxidation coupled to sulphate reduction and the use of ethane and propane as electron donors by sulphate-reducing bacteria represent new opportunities for the treatment of streams contaminated with sulphur oxyanions. However, growth of microbial sulphate-reducing populations with methane, propane or butane is extremely slow, which hampers research and development of bioprocesses based on these conversions. Thermodynamic calculations indicate that the growth rate with possible alternative terminal electron acceptors such as thiosulphate and elemental sulphur may be higher, which would facilitate future research. Here, we investigate the use of these electron acceptors for oxidation of methane, ethane and propane, with marine sediment as inoculum. Mixed marine sediments originating from Aarhus Bay (Denmark) and Eckernförde Bay (Germany) were cultivated anaerobically at a pH between 7.2 and 7.8 and a temperature of 15 °C in the presence of methane, ethane and propane and various sulphur electron acceptors. The sulphide production rates in the conditions with methane, ethane and propane with sulphate were respectively 2.3, 2.2 and 1.8 µmol S L-1 day-1. For sulphur, no reduction was demonstrated. For thiosulphate, the sulphide production rates were up to 50 times higher compared to those of sulphate, with 86.2, 90.7 and 108.1 µmol S L-1 day-1 for methane, ethane and propane respectively. This sulphide production was partly due to disproportionation, 50 % for ethane but only 7 and 14 % for methane and propane respectively. The oxidation of the alkanes in the presence of thiosulphate was confirmed by carbon dioxide production. This is, to our knowledge, the first report of thiosulphate use as electron acceptor with ethane and propane as electron donors. Additionally, these results indicate that thiosulphate is a promising electron acceptor to increase start-up rates for sulphate-reducing bioprocesses coupled to short-chain alkane oxidation.
    Genome-wide survey indicates involvement of loci on canine chromosomes 7 and 31 in patellar luxation in flat-coated retrievers
    Lavrijsen, I.C.M. ; Leegwater, P.A.J. ; Wangdee, C. ; Steenbeek, F.G. van; Schwencke, M. ; Breur, G.J. ; Meutstege, F.J. ; Nijman, I.J. ; Cuppen, E. ; Heuven, H.C.M. ; Hazewinkel, H.A.W. - \ 2014
    BMC Genetics 15 (2014). - ISSN 1471-2156
    dogs - breed - frequency - association - enrichment
    Background: Patellar luxation is an orthopedic disorder in which the patella moves out of its normal location within the femoral trochlea of the knee and it can lead to osteoarthritis, lameness, and pain. In dogs it is a heritable trait, with both environmental and genetic factors contributing to the phenotype. The prevalence of patellar luxation in the Dutch Flat-Coated Retriever population is 24%. In this study, we investigated the molecular genetics of the disorder in this population. Results: Genome-wide association analysis of 15,823 single nucleotide polymorphisms (SNPs) in 45 cases and 40 controls revealed that patellar luxation was significantly associated with a region on chromosome CFA07, and possibly with regions on CFA03, CFA31, and CFA36. The exons of the genes in these regions, 0.5 Mb combined, were analyzed further. These exons from 15 cases and a pooled sample from 15 controls were enriched using custom genomic hybridization arrays and analyzed by massive parallel DNA sequencing. In total 7257 variations were detected. Subsequently, a selection of 144 of these SNPs were genotyped in 95 Flat-Coated Retrievers. Nine SNPs, in eight genes on CFA07 and CFA31, were associated with patellar luxation (P <10(-4)). Genotyping of these SNPs in samples from a variety of breeds revealed that the disease-associated allele of one synonymous SNP in a pseudogene of FMO6 was unique to Flat-Coated Retrievers. Conclusion: Genome-wide association analysis followed by targeted DNA sequencing identified loci on chromosomes 7 and 31 as being involved in patellar luxation in the Flat-Coated Retriever breed.
    Effect of temperature on denitrifying methanotrophic activity of 'Candidatus Methylomirabilis oxyfera'
    Kampman, C. ; Piai, L. ; Hendrickx, T.L.G. ; Temmink, B.G. ; Zeeman, G. ; Buisman, C.J.N. - \ 2014
    Water Science and Technology 70 (2014)10. - ISSN 0273-1223 - p. 1683 - 1689.
    waterzuivering - denitrificatie - biologische behandeling - water treatment - denitrification - biological treatment - anaerobic methane oxidation - municipal waste-water - nitrogen removal - membrane bioreactor - sewage-treatment - uasb-digester - degrees-c - bacteria - enrichment - nitrite
    The activity of denitrifying methanotrophic bacteria at 11-30 degrees C was assessed in short-term experiments. The aim was to determine the feasibility of applying denitrifying methanotrophic bacteria in low-temperature anaerobic wastewater treatment. This study showed that biomass enriched at 21 degrees C had an optimum temperature of 20-25 degrees C and that activity dropped as temperature was increased to 30 degrees C. Biomass enriched at 30 degrees C had an optimum temperature of 25-30 degrees C. These results indicated that biomass from low-temperature inocula adjusted to the enrichment temperature and that low-temperature enrichment is suitable for applications in low-temperature wastewater treatment. Biomass growth at
    vanI: a novel d-Ala-d-Lac vancomycin resistance gene cluster found in Desulfitobacterium hafniense
    Kruse, T. ; Levisson, M. ; Vos, W.M. de; Smidt, H. - \ 2014
    Microbial Biotechnology 7 (2014)5. - ISSN 1751-7907 - p. 456 - 466.
    comparative-analysis system - antibiotic-resistance - enterococcus-faecium - genome sequence - streptomyces-coelicolor - bacteria - enrichment - evolution - resistome - alignment
    The glycopeptide vancomycin was until recently considered a drug of last resort against Gram-positive bacteria. Increasing numbers of bacteria, however, are found to carry genes that confer resistance to this antibiotic. So far, 10 different vancomycin resistance clusters have been described. A chromosomal vancomycin resistance gene cluster was previously described for the anaerobic Desulfitobacterium hafniense Y51. We demonstrate that this gene cluster, characterized by its d-Ala-d-Lac ligase-encoding vanI gene, is present in all strains of D.¿hafniense, D.¿chlororespirans and some strains of Desulfosporosinus spp. This gene cluster was not found in vancomycin-sensitive Desulfitobacterium or Desulfosporosinus spp., and we show that this antibiotic resistance can be exploited as an intrinsic selection marker for Desulfitobacterium hafniense and D.¿chlororespirans. The gene cluster containing vanI is phylogenetically only distantly related with those described from soil and gut bacteria, but clusters instead with vancomycin resistance genes found within the phylum Actinobacteria that include several vancomycin-producing bacteria. It lacks a vanH homologue, encoding a D-lactate dehydrogenase, previously thought to always be present within vancomycin resistance gene clusters. The location of vanH outside the resistance gene cluster likely hinders horizontal gene transfer. Hence, the vancomycin resistance cluster in D.¿hafniense should be regarded a novel one that we here designated vanI after its unique d-Ala-d-Lac ligase
    A Next-Generation Sequencing Method for Genotyping-by-Sequencing of Highly Heterozygous Autotetraploid Potato
    Uitdewilligen, J.G.A.M.L. ; Wolters, A.M.A. ; hoop, B.B. D'; Borm, T.J.A. ; Visser, R.G.F. ; Eck, H.J. van - \ 2013
    PLoS ONE 8 (2013)5. - ISSN 1932-6203 - 14 p.
    single-nucleotide polymorphisms - genome-wide association - chloroplast dna - solanum-tuberosum - agronomic traits - hybrid selection - discovery - enrichment - resistance - diversity
    Assessment of genomic DNA sequence variation and genotype calling in autotetraploids implies the ability to distinguish among five possible alternative allele copy number states. This study demonstrates the accuracy of genotyping-by-sequencing (GBS) of a large collection of autotetraploid potato cultivars using next-generation sequencing. It is still costly to reach sufficient read depths on a genome wide scale, across the cultivated gene pool. Therefore, we enriched cultivar-specific DNA sequencing libraries using an in-solution hybridisation method (SureSelect). This complexity reduction allowed to confine our study to 807 target genes distributed across the genomes of 83 tetraploid cultivars and one reference (DM 1–3 511). Indexed sequencing libraries were paired-end sequenced in 7 pools of 12 samples using Illumina HiSeq2000. After filtering and processing the raw sequence data, 12.4 Gigabases of high-quality sequence data was obtained, which mapped to 2.1 Mb of the potato reference genome, with a median average read depth of 63× per cultivar. We detected 129,156 sequence variants and genotyped the allele copy number of each variant for every cultivar. In this cultivar panel a variant density of 1 SNP/24 bp in exons and 1 SNP/15 bp in introns was obtained. The average minor allele frequency (MAF) of a variant was 0.14. Potato germplasm displayed a large number of relatively rare variants and/or haplotypes, with 61% of the variants having a MAF below 0.05. A very high average nucleotide diversity (p = 0.0107) was observed. Nucleotide diversity varied among potato chromosomes. Several genes under selection were identified. Genotyping-by-sequencing results, with allele copy number estimates, were validated with a KASP genotyping assay. This validation showed that read depths of ~60–80× can be used as a lower boundary for reliable assessment of allele copy number of sequence variants in autotetraploids. Genotypic data were associated with traits, and alleles strongly influencing maturity and flesh colour were identified.
    Genomic Treasure Troves: Complete Genome Sequencing of Herbarium and Insect Museum Specimens
    Staats, M. ; Erkens, R.H.J. ; Vossenberg, B. van de; Wieringa, J.J. ; Kraaijeveld, K. ; Stielow, B. ; Geml, J. ; Richardson, J.E. ; Bakker, F.T. - \ 2013
    PLoS ONE 8 (2013)7. - ISSN 1932-6203
    ancient dna-sequences - miscoding lesions - extraction - amplification - patterns - fungi - plant - enrichment - evolution - alignment
    Unlocking the vast genomic diversity stored in natural history collections would create unprecedented opportunities for genome-scale evolutionary, phylogenetic, domestication and population genomic studies. Many researchers have been discouraged from using historical specimens in molecular studies because of both generally limited success of DNA extraction and the challenges associated with PCR-amplifying highly degraded DNA. In today's next-generation sequencing (NGS) world, opportunities and prospects for historical DNA have changed dramatically, as most NGS methods are actually designed for taking short fragmented DNA molecules as templates. Here we show that using a standard multiplex and paired-end Illumina sequencing approach, genome-scale sequence data can be generated reliably from dry-preserved plant, fungal and insect specimens collected up to 115 years ago, and with minimal destructive sampling. Using a reference-based assembly approach, we were able to produce the entire nuclear genome of a 43-year-old Arabidopsis thaliana (Brassicaceae) herbarium specimen with high and uniform sequence coverage. Nuclear genome sequences of three fungal specimens of 22–82 years of age (Agaricus bisporus, Laccaria bicolor, Pleurotus ostreatus) were generated with 81.4–97.9% exome coverage. Complete organellar genome sequences were assembled for all specimens. Using de novo assembly we retrieved between 16.2–71.0% of coding sequence regions, and hence remain somewhat cautious about prospects for de novo genome assembly from historical specimens. Non-target sequence contaminations were observed in 2 of our insect museum specimens. We anticipate that future museum genomics projects will perhaps not generate entire genome sequences in all cases (our specimens contained relatively small and low-complexity genomes), but at least generating vital comparative genomic data for testing (phylo)genetic, demographic and genetic hypotheses, that become increasingly more horizontal. Furthermore, NGS of historical DNA enables recovering crucial genetic information from old type specimens that to date have remained mostly unutilized and, thus, opens up a new frontier for taxonomic research as well.
    Climate Change and Potato Production in Contrasting South African Agro-ecosystems 1. Effects on Land and Water Use Efficiencies
    Haverkort, A.J. ; Franke, A.C. ; Engelbrecht, F.A. ; Steyn, J.M. - \ 2013
    Potato Research 56 (2013)1. - ISSN 0014-3065 - p. 31 - 50.
    elevated carbon-dioxide - solanum-tuberosum l. - co2 concentration - atmospheric co2 - crop yields - model - growth - simulation - enrichment - quality
    Explorations of the impact of climate change on potential potato yields were obtained by downscaling the projections of six different coupled climate models to high spatial resolution over southern Africa. The simulations of daily maximum and minimum temperatures, precipitation, wind speed, and solar radiation were used as input to run the crop growth model LINTUL-Potato. Pixels representative for potato growing areas were selected for four globally occurring agro-ecosystems: rainy and dry winter and summer crops. The simulated inter-annual variability is much greater for rainfall than for temperature. Reference evapotranspiration and radiation are projected to hardly decline over the 90-year period, whilst temperatures are projected to rise significantly by about 1.9 °C. From literature, it was found that radiation use efficiency of potato increased with elevated CO2 concentrations by almost 0.002 g¿MJ-1¿ppm-1. This ratio was used to calculate the CO2 effect on yields between 1960 and 2050, when CO2 concentration increases from 315 to 550 ppm. Within this range, evapotranspiration by the potato crop was reduced by about 13% according to literature. Simulated yield increase was strongest in the Mediterranean-type winter crop (+37%) and least under Mediterranean summer (+12%) and relatively warm winter conditions (+14%) closer to the equator. Water use efficiency also increased most in the cool rainy Mediterranean winter (+45%) and least so in the winter crop closer to the equator (+14%). It is concluded from the simulations that for all four agro-ecosystems possible negative effects of rising temperatures and reduced availability of water for potato are more than compensated for by the positive effect of increased CO2 levels on water use efficiency and crop productivity.
    Does predator interference cause alternative stable states in multispecies communities?
    Feng, J. ; Dakos, V. ; Nes, E.H. van - \ 2012
    Theoretical Population Biology 82 (2012)3. - ISSN 0040-5809 - p. 170 - 176.
    mutual interference - marine ecosystems - shallow lakes - regime shifts - thresholds - enrichment - paradox - stabilization - resilience - stability
    Whereas it is well known that simple ecological mechanisms may promote stability in simple species models, their consequences for stability and resilience in multispecies communities are largely unexplored. Here, we studied the effect of predator interference on the occurrence of alternative attractors and complex dynamics in randomly constructed multispecies predator-prey communities. We studied three types of interference: random interference ("asymmetric"), random interference but symmetrical between pairs of predators ("symmetric"), and interference among only the same species ("conspecific"). In all cases predator interference increased the average number of alternative attractors, whereas at the same time it reduced the emergence of oscillatory or chaotic dynamics. Our findings demonstrate a contrasting effect of predator interference on the stability of a community: on the one hand it reduces cycles and chaos in the dynamics, on the other hand predator interference increases the likelihood that communities may undergo critical transitions between multiple stable states.
    Effects of irradiance and light spectrum on growth of the scleractinian coral Galaxea
    Wijgerde, T.H.M. ; Henkemans, P. ; Osinga, R. - \ 2012
    Aquaculture 344-349 (2012). - ISSN 0044-8486 - p. 188 - 193.
    carbonate-ion concentration - stylophora-pistillata - ocean acidification - skeletal growth - climate-change - photosynthesis - calcification - zooxanthellae - temperature - enrichment
    Due to global degradation of coral reefs and high demand for scleractinian corals, aquaculture of these marine organisms is gaining importance. To make coral aquaculture economically viable, optimisation of culture protocols is vital. We determined the effects of irradiance and light spectrum on the growth of a model scleractinian coral species, Galaxea fascicularis (Linnaeus 1767). Single polyps (n=10) were cultured under six different treatments; LED (light emitting diode) at a PPFD of 40-60, 125-150 and 275-325 mu mol m(-2) s(-1); and LEP (light emitting plasma) at a PPFD of 40-60, 125-150 and 275-325 mu mol m (2) s (1). Specific growth and survival rates were monitored over a 69-day interval. Mean specific growth rates were 0.031 +/- 0.006 day(-1) for the LED 40-60 treatment, 0.030 +/- 0.007 day(-1) for LED 125-150, 0.022 +/- 0.009 day(-1) for LED 275-325, 0.024 +/- 0.011 day(-1) for LEP 40-60, 0.040 +/- 0.008 day(-1) for LEP 125-150, and 0.031 +/- 0.006 day(-1) for LEP 275-325. Coral survival rate at the end of the growth interval was 95%. A significant main effect of irradiance on coral specific growth rate was found (factorial ANOVA, P=0.018), whereas spectrum did not show a significant main effect (factorial ANOVA, P=0.085). A significant interactive effect between irradiance and spectrum was found (factorial ANOVA, P=0.013), as LEP lighting resulted in higher coral growth rates at the two higher irradiance levels applied. The effect of irradiance and its interaction with spectrum were likely modulated by water flow rates. Our results show that balanced as well as light sources skewed towards the blue part of the spectrum result in high coral growth. Specifically, LEP and LED have shown to be suitable lighting technologies for coral aquaculture, where LEP yields higher G. fascicularis growth rates at higher irradiance levels. (c) 2012 Elsevier B.V. All rights reserved.
    Serum protein profiles as potential biomarkers for infectious disease status in pigs
    Koene, M.G.J. ; Mulder, H.A. ; Stockhofe, N. ; Kruijt, L. ; Smits, M.A. - \ 2012
    BMC Veterinary Research 8 (2012). - ISSN 1746-6148 - 14 p.
    low-abundance proteins - acute-phase proteins - clinical proteomics - mass-spectrometry - ovine serum - discovery - classification - technology - enrichment - samples
    Background: In veterinary medicine and animal husbandry, there is a need for tools allowing the early warning of diseases. Preferably, tests should be available that warn farmers and veterinarians during the incubation periods of disease and before the onset of clinical signs. The objective of this study was to explore the potential of serum protein profiles as an early biomarker for infectious disease status. Serum samples were obtained from an experimental pig model for porcine circovirus-associated disease (PCVAD), consisting of Porcine Circovirus type 2 (PCV2) infection in combination with either Porcine Parvovirus (PPV) or Porcine Reproductive and Respiratory Syndrome virus (PRRSV). Sera were collected before and after onset of clinical signs at day 0, 5 and 19 post infection. Serum protein profiles were evaluated against sera from non-infected control animals. Results: Protein profiles were generated by SELDI-TOF mass spectrometry in combination with the Proteominer (TM) technology to enrich for low-abundance proteins. Based on these protein profiles, the experimentally infected pigs could be classified according to their infectious disease status. Before the onset of clinical signs 88% of the infected animals could be classified correctly, after the onset of clinical sigs 93%. The sensitivity of the classification appeared to be high. The protein profiles could distinguish between separate infection models, although specificity was moderate to low. Classification of PCV2/PRRSV infected animals was superior compared to PCV2/PPV infected animals. Limiting the number of proteins in the profiles (ranging from 568 to 10) had only minor effects on the classification performance. Conclusions: This study shows that serum protein profiles have potential for detection and identification of viral infections in pigs before clinical signs of the disease become visible.
    Kinetics of ferrous iron oxidation by batch and continuous cultures of thermoacidophilic Archaea at extremely low pH of 1.1–1.3
    Gonzalez-Contreras, P.A. ; Weijma, J. ; Buisman, C.J.N. - \ 2012
    Applied Microbiology and Biotechnology 93 (2012)3. - ISSN 0175-7598 - p. 1295 - 1303.
    sulfolobus-metallicus - acidianus-sulfidivorans - metallosphaera-sedula - microorganisms - concentrate - pyrite - chalcopyrite - biooxidation - acidophiles - enrichment
    The extreme acid conditions required for scorodite (FeAsO4·2H2O) biomineralization (pH below 1.3) are suboptimal for growth of most thermoacidophilic Archaea. With the objective to develop a continuous process suitable for biomineral production, this research focuses on growth kinetics of thermoacidophilic Archaea at low pH conditions. Ferrous iron oxidation rates were determined in batch-cultures at pH 1.3 and a temperature of 75°C for Acidianus sulfidivorans, Metallosphaera prunea and a mixed Sulfolobus culture. Ferrous iron and CO2 in air were added as sole energy and carbon source. The highest growth rate (0.066 h-1) was found with the mixed Sulfolobus culture. Therefore, this culture was selected for further experiments. Growth was not stimulated by increase of the CO2 concentration or by addition of sulphur as an additional energy source. In a CSTR operated at the suboptimal pH of 1.1, the maximum specific growth rate of the mixed culture was 0.022 h-1, with ferrous iron oxidation rates of 1.5 g L-1 d-1. Compared to pH 1.3, growth rates were strongly reduced but the ferrous iron oxidation rate remained unaffected. Influent ferrous iron concentrations above 6 g L-1 caused instability of Fe2+ oxidation, probably due to product (Fe3+) inhibition. Ferric-containing, nano-sized precipitates of K-jarosite were found on the cell surface. Continuous cultivation stimulated the formation of an exopolysaccharide-like substance. This indicates that biofilm formation may provide a means of biomass retention. Our findings showed that stable continuous cultivation of a mixed iron-oxidizing culture is feasible at the extreme conditions required for continuous biomineral formation.
    Two new effective semiselective crystal violet pectate media for isolation of Pectobacterium and Dickeya
    Hélias, V. ; Hamon, P. ; Huchet, E. ; Wolf, J.M. van der; Andrivon, D. - \ 2012
    Plant Pathology 61 (2012)2. - ISSN 0032-0862 - p. 339 - 345.
    soft-rot erwinias - carotovora subsp atroseptica - selective medium - sp-nov. - potato - chrysanthemi - enrichment - soil
    Pectolytic bacteria, including Pectobacterium spp. and Dickeya spp., are best isolated on crystal violet pectate (CVP), a semiselective medium containing pectin. The source of pectin is essential, because pectolytic bacteria are not able to degrade all of them. The aims of this study were to identify a new pectin source and to perfect formulations of semiselective CVP media to isolate the pectolytic bacteria Pectobacterium spp. and Dickeya spp. from different environmental compartments (plants, soil and water). The AG366 pectin, selected after screening six different formulations, was incorporated into single-layer (SL-CVPAG366) and double-layer (DL-CVPAG366) CVP media. Both media were compared with those based on Bulmer, Sigma-Aldrich and Slendid-Burger pectins, using 39 Pectobacterium and Dickeya strains. All strains formed deep cavities on AG366-CVPs, whereas nine did not produce cavities on Bulmer or Sigma-Aldrich media. Recovery rates were similar on DL-CVPAG366, Sigma-Aldrich and Bulmer CVPs for a given taxon, and did not differ significantly between SL- and DL-CVPAG366. Pectolytic bacteria were successfully isolated on both media from field samples of diseased potatoes, carrots, tobacco, onions, radishes and ornamentals. AG366 is thus a high-performance pectin source for the elaboration of CVP media suitable to isolate Dickeya and Pectobacterium. It is also efficient for enrichment purposes in liquid medium. The validation of AG366 as an improved source of pectin to recover the polyphagous Pectobacterium and Dickeya in different environmental compartments is essential given the current worldwide emergence and recrudescence of these bacteria.
    Chromothripsis is a common mechanism driving genomic rearrangements in primary and metastatic colorectal cancer
    Kloosterman, W.P. ; Hoogstraat, M. ; Paling, O. ; Tavakoli-Yaraki, M. ; Renkens, I. ; Vermaat, J.S. ; Roosmalen, M.J. van; Lieshout, S. van; Nijman, I.J. ; Roessingh, W. ; Slot, R. van 't; Belt, J. van de - \ 2011
    Genome Biology 12 (2011)10. - ISSN 1474-7596 - 11 p.
    human breast - pancreatic-cancer - resolution - evolution - patterns - mutation - progression - landscapes - enrichment - genes
    Background - Structural rearrangements form a major class of somatic variation in cancer genomes. Local chromosome shattering, termed chromothripsis, is a mechanism proposed to be the cause of clustered chromosomal rearrangements and was recently described to occur in a small percentage of tumors. The significance of these clusters for tumor development or metastatic spread is largely unclear. Results - We used genome-wide long mate-pair sequencing and SNP array profiling to reveal that chromothripsis is a widespread phenomenon in primary colorectal cancer and metastases. We find large and small chromothripsis events in nearly every colorectal tumor sample and show that several breakpoints of chromothripsis clusters and isolated rearrangements affect cancer genes, including NOTCH2, EXO1 and MLL3. We complemented the structural variation studies by sequencing the coding regions of a cancer exome in all colorectal tumor samples and found somatic mutations in 24 genes, including APC, KRAS, SMAD4 and PIK3CA. A pairwise comparison of somatic variations in primary and metastatic samples indicated that many chromothripsis clusters, isolated rearrangements and point mutations are exclusively present in either the primary tumor or the metastasis and may affect cancer genes in a lesion-specific manner. Conclusions - We conclude that chromothripsis is a prevalent mechanism driving structural rearrangements in colorectal cancer and show that a complex interplay between point mutations, simple copy number changes and chromothripsis events drive colorectal tumor development and metastasis
    An intracellular pH gradient in the anammox bacterium Kuenenia stuttgartiensis as evaluated by P-31 NMR
    Star, W.R.L. van der; Dijkema, C. ; Waard, P. de; Picioreanu, C. ; Strous, M. ; Loosdrecht, M.C.M. van - \ 2010
    Applied Microbiology and Biotechnology 86 (2010)1. - ISSN 0175-7598 - p. 311 - 317.
    ammonium-oxidizing bacteria - nuclear-magnetic-resonance - proton gradients - 4 genera - compartmentation - enrichment - oxidation - reactor - cells - identification
    The cytoplasm of anaerobic ammonium oxidizing (anammox) bacteria consists of three compartments separated by membranes. It has been suggested that a proton motive force may be generated over the membrane of the innermost compartment, the "anammoxosome". P-31 nuclear magnetic resonance (NMR) spectroscopy was employed to investigate intracellular pH differences in the anammox bacterium Kuenenia stuttgartiensis. With in vivo NMR, spectra were recorded of active, highly concentrated suspensions of K. stuttgartiensis in a wide-bore NMR tube. At different external pH values, two stable and distinct phosphate peaks were apparent in the recorded spectra. These peaks were equivalent with pH values of 7.3 and 6.3 and suggested the presence of a proton motive force over an intracytoplasmic membrane in K. stuttgartiensis. This study provides for the second time-after discovery of acidocalcisome-like compartments in Agrobacterium tumefaciens-evidence for an intracytoplasmic pH gradient in a chemotrophic prokaryotic cell
    Hokverrijking om in de knaagbehoefte van konijnen te voorzien: een literatuurstudie = Environmental enrichment to fulfill gnawing requirements in rabbits: a literature study
    Rommers, J.M. ; Jong, I.C. de - \ 2010
    Lelystad : Wageningen UR Livestock Research (Rapport / Wageningen UR Livestock Research 396) - 16
    dierenwelzijn - konijnen - verrijking - hokken - zachthout - ruwvoer (forage) - animal welfare - rabbits - enrichment - pens - softwoods - forage
    This report is a literature study to environmental enrichment in rabbits, that possibly fulfills the gnawing requirements
    Food Quality in Producer-Grazer Models: A Generalized Analysis
    Stiefs, D. ; Voorn, G.A.K. van; Kooi, B.W. ; Feudel, U. ; Gross, T. - \ 2010
    American Naturalist 176 (2010)3. - ISSN 0003-0147 - p. 367 - 380.
    predator-prey interactions - population-dynamics - functional-response - stability - systems - stoichiometry - enrichment - connectance - coexistence - competition
    Stoichiometric constraints play a role in the dynamics of natural populations but are not explicitly considered in most mathematical models. Recent theoretical works suggest that these constraints can have a significant impact and should not be neglected. However, it is not yet resolved how stoichiometry should be integrated in population dynamical models, as different modeling approaches are found to yield qualitatively different results. Here we investigate a unifying framework that reveals the differences and commonalities between previously proposed models for producer-grazer systems. Our analysis reveals that stoichiometric constraints affect the dynamics mainly by increasing the intraspecific competition between producers and by introducing a variable biomass conversion efficiency. The intraspecific competition has a strongly stabilizing effect on the system, whereas the variable conversion efficiency resulting from a variable food quality is the main determinant for the nature of the instability once destabilization occurs. Only if the food quality is high can an oscillatory instability, as in the classical paradox of enrichment, occur. While the generalized model reveals that the generic insights remain valid in a large class of models, we show that other details such as the specific sequence of bifurcations encountered in enrichment scenarios can depend sensitively on assumptions made in modeling stoichiometric constraints.
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