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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A novel method for the quantification, characterisation and speciation of silver nanoparticles in earthworms exposed in soil
Makama, S.I. ; Peters, R.J.B. ; Undas, A.K. ; Brink, N.W. van den - \ 2015
Environmental Chemistry 12 (2015)6. - ISSN 1448-2517 - p. 643 - 651.
accumulation - enzymatic digestion - particle characterisation - sp-ICP-MS - tissue concentrations
Currently, metal engineered nanoparticles (ENPs) in tissues are generally quantified based on total concentrations after acid digestion of samples. Electron microscopy has also been used for non-quantitative characterisation of NPs in situ, and can be enhanced with tissue-processing methods that can extract NPs with minimal destruction. For a proper risk assessment, it is essential to quantify and characterise the ENPs in both exposure media and organisms. For this, we developed a method using a combination of enzymatic tissue processing, followed by single particle inductively coupled plasma–mass spectrometry (sp-ICP-MS) to characterise and quantify AgNPs in tissues of earthworms after in vivo exposure in soil to 50-nm AgNPs or AgNO3. Tissue concentration of Ag in worms exposed to 250 mg AgNP kg–1 soil (dry weight) was 0.502 ± 0.219 mg kg–1 (dry weight) reflecting a bioaccumulation factor of 0.002. In both AgNP- and AgNO3-treated groups, the metal-rich granule fraction contained the highest Ag concentrations (77 and 64 % respectively). Total Ag contained in the earthworm tissue of the AgNP- and AgNO3-treated groups comprised ~34 and <5 % particulate Ag respectively. Average particle size of AgNPs extracted from tissues was consistent with exposure material (44 v. 43 nm respectively). High resolution field-emission gun scanning electron microscopy in combination with energy-dispersive X-ray (FEG-SEM/EDX) identified individual AgNPs in tissue extracts with corresponding spectral elemental peaks, providing further evidence of tissue particle uptake and composition.
Rain events decrease boreal peatland net CO2 uptake through reduced light availability
Nijp, J.J. ; Limpens, J. ; Metselaar, K. ; Peichl, M. ; Nilsson, M. ; Zee, S.E.A.T.M. van der; Berendse, F. - \ 2015
Global Change Biology 21 (2015)6. - ISSN 1354-1013 - p. 23309 - 2320.
carbon-dioxide - soil respiration - sphagnum mosses - water-content - solar-radiation - climate-change - precipitation - accumulation - drought - balance
Boreal peatlands store large amounts of carbon, reflecting their important role in the global carbon cycle. The short-term exchange and the long-term storage of atmospheric carbon dioxide (CO2) in these ecosystems are closely associated with the permanently wet surface conditions and are susceptible to drought. Especially, the single most important peat forming plant genus, Sphagnum, depends heavily on surface wetness for its primary production. Changes in rainfall patterns are expected to affect surface wetness, but how this transient rewetting affects net ecosystem exchange of CO2 (NEE) remains unknown. This study explores how the timing and characteristics of rain events during photosynthetic active periods, that is daytime, affect peatland NEE and whether rain event associated changes in environmental conditions modify this response (e.g. water table, radiation, vapour pressure deficit, temperature).
Isolation and identification of 4-a-rhamnosyloxy benzyl glucosinolate in Noccaea caerulescens showing intraspecific variation
Graaf, R.M. de; Krosse, S. ; Swolfs, A.E.M. ; Brinke, E. te; Prill, N. ; Leimu, R. ; Galen, P.M. van; Wang, Y. ; Aarts, M.G.M. ; Dam, N.M. van - \ 2015
Phytochemistry 110 (2015). - ISSN 0031-9422 - p. 166 - 171.
hyperaccumulator thlaspi-praecox - moringa-oleifera l. - mustard oil bomb - arabidopsis-thaliana - plants - isothiocyanates - stenopetala - accumulation - brassicaceae - profiles
Glucosinolates are secondary plant compounds typically found in members of the Brassicaceae and a few other plant families. Usually each plant species contains a specific subset of the ~130 different glucosinolates identified to date. However, intraspecific variation in glucosinolate profiles is commonly found. Sinalbin (4-hydroxybenzyl glucosinolate) so far has been identified as the main glucosinolate of the heavy metal accumulating plant species Noccaea caerulescens (Brassicaceae). However, a screening of 13 N. caerulescens populations revealed that in 10 populations a structurally related glucosinolate was found as the major component. Based on nuclear magnetic resonance (NMR) and mass spectrometry analyses of the intact glucosinolate as well as of the products formed after enzymatic conversion by sulfatase or myrosinase, this compound was identified as 4-a-rhamnosyloxy benzyl glucosinolate (glucomoringin). So far, glucomoringin had only been reported as the main glucosinolate of Moringa spp. (Moringaceae) which are tropical tree species. There was no apparent relation between the level of soil pollution at the location of origin, and the presence of glucomoringin. The isothiocyanate that is formed after conversion of glucomoringin is a potent antimicrobial and antitumor agent. It has yet to be established whether glucomoringin or its breakdown product have an added benefit to the plant in its natural habitat
Carryover of cadmium from feed in growing pigs
Hoogenboom, L.A.P. ; Hattink, J. ; Polanen, A. van; Oostrom, J.J. van; Verbunt, J.T. ; Traag, W.A. ; Kan, K.A. ; Eijkeren, J.C.H. ; Boeck, G. de; Zeilmaker, M.J. - \ 2015
Food Additives & Contaminants. Pt. A, Chemistry, Analysis, Control, Exposure & Risk Assessment 32 (2015)1. - ISSN 1944-0049 - p. 1 - 12.
cd-saturation method - sludge-amended soil - metallothionein - tissues - growth - swine - accumulation - dioxins - protein - cortex
Growing male pigs were exposed to cadmium (Cd) at levels around 1 and 10 mg kg–1 feed for up to 12 weeks, administered as CdCl2 or Cd-cysteine (CdCys). Pigs exposed to 10 mg kg–1 showed decreased growth during the last 3 weeks. Liver and kidney concentrations of Cd continuously increased over the entire 12-week exposure, exceeding the European Union limits of 1.0 mg kg–1 (kidney) and 0.5 mg kg–1 (liver) within 3 weeks at the feed level of 10 mg kg–1. A switch to clean feed after 3 weeks for 5 or 9 weeks resulted in steadily decreased levels in kidney and liver, which could be completely attributed to organ growth. At the lower feed level, the level in kidney exceeded the limit almost twofold after 12 weeks, but not after 3 weeks. Liver levels remained below the limit. Metallothionein (MT) levels in livers showed a steady decrease in both untreated and treated animals over time. In kidney such a decrease was only observed in control animals, whereas in the highest-dosed animals the MT concentrations steadily increased. The observed carryover of Cd from feed to liver and kidney was modelled by means of a simple transfer model relating levels in feed via MT levels to accumulation of Cd. Using this model, it was shown that the exposure period of growing pigs to feed containing the European Union limit of 0.5 mg kg–1 feed should be less than 12 weeks in order to prevent Cd levels in the kidneys to exceed the European Union limit.
Selecting microalgae with high lipid productivity and photosynthetic activity under nitrogen starvation
Benvenuti, G. ; Bosma, R. ; Cuaresma Franco, M. ; Janssen, M.G.J. ; Barbosa, M.J. ; Wijffels, R.H. - \ 2015
Journal of Applied Phycology 27 (2015)4. - ISSN 0921-8971 - p. 1425 - 1431.
neochloris-oleoabundans - parietochloris-incisa - marine-phytoplankton - biodiesel production - nutrient stress - fatty-acids - light - accumulation - efficiency - biofuels
An economically feasible microalgal lipid industry heavily relies on the selection of suitable strains. Because microalgae lipid content increases under a range of adverse conditions (e.g. nutrient deprivation, high light intensity), photosynthetic activity is usually strongly reduced. As a consequence, lipid productivity rapidly declines overtime, after reaching a maximum within the first days of cultivation. The microalgae Chlorella vulgaris, Chlorococcum littorale, Nannochloropsis oculata, Nannochloropsis sp., Neochloris oleoabundans, Stichococcus bacillaris and Tetraselmis suecica were compared on fatty acid content and productivity, and also on photosynthetic activity under nitrogen (N) starvation. Cultures in N-replete conditions were used as reference. Photosystem II (PSII) maximumefficiency was followed during the experiment, as proxy for the change in photosynthetic activity of the cells. Strains with a high capacity for both lipid accumulation as well as high photosynthetic activity under N starvation exhibited a high lipid productivity over time. Among the tested strains, Nannochloropsis sp. showed highest fatty acid content (45%w/w) and productivity (238 mg L-1 day-1) aswell as PSII maximum efficiency, demonstrating to be the most suitable strain, of those tested, for lipid production. This study highlights that for microalgae, maintaining a high photosynthetic efficiency during stress is the key to maintain high fatty acid productivities overtime and should be considered when selecting strains for microalgal lipid production.
The debate on food sovereignty theory: agrarian capitalism, dispossession and agroecology
Jansen, K. - \ 2015
The Journal of Peasant Studies 42 (2015)1. - ISSN 0306-6150 - p. 213 - 232.
organic agriculture - latin-america - gm crops - accumulation - technology - question - poor - 21st-century - revolution - knowledge
This contribution reviews recent critiques of the food sovereignty framework. In particular it engages with the debate between Henry Bernstein and Philip McMichael and analyzes their different conceptualizations of agrarian capitalism. It critically identifies tendencies in food sovereignty approaches to assume a food regime crisis, to one-sidedly emphasize accumulation by dispossession and enclosure and thereby to overlook the importance of expanded reproduction, and to espouse a romantic optimism about farmer-driven agroecological knowledge which is devoid of modern science. Alternatives to current modernization trajectories cannot simply return to the peasant past and to the local. Instead, they need to recognize the desires of farmers to be incorporated into larger commodity networks, the importance of industrialization and complex chains for feeding the world population, and the support of state and science, as well as social movements, for realizing a food sovereign alternative.
The genome of the stress-tolerant wild tomato species Solanum pennellii
Bolger, A. ; Scossa, F. ; Bolger, M.E. ; Aflitos, S.A. ; Schijlen, E.G.W.M. ; Ham, R.C.H.J. van; Klein Lankhorst, R.M. - \ 2014
Nature Genetics 46 (2014)9. - ISSN 1061-4036 - p. 1034 - 1038.
introgression lines - gene-expression - fruit - qtl - accumulation - evolution - trichomes - responses - plants - traits
Solanum pennellii is a wild tomato species endemic to Andean regions in South America, where it has evolved to thrive in arid habitats. Because of its extreme stress tolerance and unusual morphology, it is an important donor of germplasm for the cultivated tomato Solanum lycopersicum(1). Introgression lines (ILs) in which large genomic regions of S. lycopersicum are replaced with the corresponding segments from S. pennellii can show remarkably superior agronomic performance(2). Here we describe a high-quality genome assembly of the parents of the IL population. By anchoring the S. pennellii genome to the genetic map, we define candidate genes for stress tolerance and provide evidence that transposable elements had a role in the evolution of these traits. Our work paves a path toward further tomato improvement and for deciphering the mechanisms underlying the myriad other agronomic traits that can be improved with S. pennellii germplasm.
Evaluation of two commercial, rapid, ELISA kits testing or scrapie in retro-pharyngeal lymph nodes in sheep
Kittelberger, R. ; McIntuyre, L. ; Watts, S. ; MacDiarmid, S. ; Hannah, M.J. ; Jenner, J. ; Bueno, R. ; Swainsbury, R. ; Langeveld, J.P.M. ; Keulen, L.J.M. van; Zijderveld, F.G. van; Wemheuer, W.M. ; Richt, J.A. ; Sorenson, S.J. ; Pigott, C.J. ; O'Keefe, J.S. - \ 2014
New Zealand Veterinary Journal 62 (2014)6. - ISSN 0048-0169 - p. 343 - 350.
natural scrapie - prion protein - immunohistochemical detection - new-zealand - prp - accumulation - diagnosis - genotypes - tissues - brain
AIMS: To estimate the number of cases of scrapie that would occur in sheep of different prion protein (PrP) genotypes if scrapie was to become established in New Zealand, and to compare the performance of two commercially available, rapid ELISA kits using ovine retro-pharyngeal lymph nodes (RLN) from non-infected and infected sheep of different PrP genotypes. METHODS: Using published data on the distribution of PrP genotypes within the New Zealand sheep flock and the prevalence of cases of scrapie in these genotypes in the United Kingdom, the annual expected number of cases of scrapie per genotype was estimated, should scrapie become established in New Zealand, assuming a total population of 28 million sheep. A non-infected panel of RLN was collected from 737 sheep from New Zealand that had been culled, found in extremis or died. Brain stem samples were also collected from 131 of these sheep. A second panel of infected samples comprised 218 and 117 RLN from confirmed scrapie cases that had originated in Europe and the United States of America, respectively. All samples were screened using two commercial, rapid, transmissible spongiform encephalopathy ELISA kits: Bio-Rad TeSeE ELISA (ELISA-BR), and IDEXX HerdChek BSE-Scrapie AG Test (ELISA-ID). RESULTS: If scrapie became established in New Zealand, an estimated 596 cases would occur per year; of these 234 (39%) and 271 (46%) would be in sheep carrying ARQ/ARQ and ARQ/VRQ PrP genotypes, respectively. For the non-infected samples from New Zealand the diagnostic specificity of both ELISA kits was 100%. When considering all infected samples, the diagnostic sensitivity was 70.4 (95% CI=65.3-75.3)% for ELISA-BR and 91.6 (95% CI=88.2-94.4)% for ELISA-ID. For the ARQ/ARQ genotype (n=195), sensitivity was 66.2% for ELISA-BR and 90.8% for ELISA-ID, and for the ARQ/VRQ genotype (n=107), sensitivity was 81.3% for ELISA-BR and 98.1% for ELISA-ID. CONCLUSIONS: In this study, the ELISA-ID kit demonstrated a higher diagnostic sensitivity for detecting scrapie in samples of RLN from sheep carrying scrapie-susceptible PrP genotypes than the ELISA-BR kit at comparable diagnostic specificity.
Control of anthocyanin and non-flavonoid compounds by anthocyanin-regulating MYB and bHLH transcription factors in Nicotiana benthamiana leaves
Outchkourov, N.S. ; Carollo, C.A. ; Gomez Roldan, M.V. ; Vos, C.H. de; Bosch, H.J. ; Hall, R.D. ; Beekwilder, M.J. - \ 2014
Frontiers in Plant Science 5 (2014). - ISSN 1664-462X - 9 p.
r2r3-myb gene family - mass-spectrometry - tomato fruit - arabidopsis-thaliana - biosynthesis - tobacco - accumulation - metabolomics - plants - health
Coloration of plant organs such as fruit, leaves and flowers through anthocyanin production is governed by a combination of MYB and bHLH type transcription factors (TFs). In this study we introduced Rosea1 (ROS1, a MYB type) and Delila (DEL, a bHLH type), into Nicotiana benthamiana leaves by agroinfiltration. ROS1 and DEL form a pair of well-characterized TFs from Snapdragon (Antirrhinum majus), which specifically induce anthocyanin accumulation when expressed in tomato fruit. In N. benthamiana, robust induction of a single anthocyanin, delphinidin-3-rutinoside (D3R) was observed after expression of both ROS1 and DEL. Surprisingly in addition to D3R, a range of additional metabolites were also strongly and specifically up-regulated upon expression of ROS1 and DEL. Except for the D3R, these induced compounds were not derived from the flavonoid pathway. Most notable among these are nornicotine conjugates with butanoyl, hexanoyl, and octanoyl hydrophobic moieties, and phenylpropanoid-polyamine conjugates such as caffeoyl putrescine. The defensive properties of the induced molecules were addressed in bioassays using the tobacco specialist lepidopteran insect Manduca sexta. Our study showed that the effect of ROS1 and DEL expression in N. benthamiana leaves extends beyond the flavonoid pathway. Apparently the same transcription factor may regulate different secondary metabolite pathways in different plant species.
A New Method to Infer Causal Phenotype Networks Using QTL and Phenotypic Information
Wang, H. ; Eeuwijk, F. van - \ 2014
PLoS One 9 (2014)8. - ISSN 1932-6203
quantitative trait loci - bayesian networks - tomato fruits - multi-trait - environment - model - accumulation - volatiles - genomics
In the context of genetics and breeding research on multiple phenotypic traits, reconstructing the directional or causal structure between phenotypic traits is a prerequisite for quantifying the effects of genetic interventions on the traits. Current approaches mainly exploit the genetic effects at quantitative trait loci (QTLs) to learn about causal relationships among phenotypic traits. A requirement for using these approaches is that at least one unique QTL has been identified for each trait studied. However, in practice, especially for molecular phenotypes such as metabolites, this prerequisite is often not met due to limited sample sizes, high noise levels and small QTL effects. Here, we present a novel heuristic search algorithm called the QTL+phenotype supervised orientation (QPSO) algorithm to infer causal directions for edges in undirected phenotype networks. The two main advantages of this algorithm are: first, it does not require QTLs for each and every trait; second, it takes into account associated phenotypic interactions in addition to detected QTLs when orienting undirected edges between traits. We evaluate and compare the performance of QPSO with another state-of-the-art approach, the QTL-directed dependency graph (QDG) algorithm. Simulation results show that our method has broader applicability and leads to more accurate overall orientations. We also illustrate our method with a real-life example involving 24 metabolites and a few major QTLs measured on an association panel of 93 tomato cultivars. Matlab source code implementing the proposed algorithm is freely available upon request.
Circadian rhythms in the cell cycle and biomass composition of Neochloris oleoabundans under nitrogen limitation
Winter, L. de; Schepers, L.W. ; Cuaresma Franco, M. ; Barbosa, M.J. ; Martens, D.E. ; Wijffels, R.H. - \ 2014
Journal of Biotechnology 187 (2014). - ISSN 0168-1656 - p. 25 - 33.
chlamydomonas-reinhardtii - nutrient starvation - microalgae - division - growth - accumulation - quadricauda - clock - death
The circadian clock schedules processes in microalgae cells at suitable times in the day/night cycle. To gain knowledge about these biological time schedules, Neochloris oleoabundans was grown under constant light conditions and nitrogen limitation. Under these constant conditions, the only variable was the circadian clock. The results were compared to previous work done under nitrogen-replete conditions, in order to determine the effect of N-limitation on circadian rhythms in the cell cycle and biomass composition of N. oleoabundans. The circadian clock was not affected by nitrogen-limitation, and cell division was timed in the natural night, despite of constant light conditions. However, because of nitrogen-limitation, not the entire population was able to divide every day. Two subpopulations were observed, which divided alternately every other day. This caused oscillations in biomass yield and composition. Starch and total fatty acids (TFA) were accumulated during the day. Also, fatty acid composition changed during the cell cycle. Neutral lipids were built up during the day, especially in cells that were arrested in their cell cycle (G2 and G3). These findings give insight in the influence of circadian rhythms on the cell cycle and biomass composition.
Optimizing soaking and germination conditions to improve gamma-aminobutyric acid content in japonica and indica germinated brown rice
Zhang, Q. ; Xiang, J. ; Zhang, L. ; Zhu, X. ; Evers, J.B. ; Werf, W. van der; Duan, L. - \ 2014
Journal of Functional Foods 10 (2014). - ISSN 1756-4646 - p. 283 - 291.
glutamate-decarboxylase - protease activities - blood-pressure - water soaking - giant-embryo - gaba - accumulation - metabolism - beans - rats
Germinated brown rice is a well-known functional food due to its high content of gamma-aminobutyric acid (GABA). This study was designed to test the difference of producing GABA in two domesticated rice genotypes (indica and japonica rice), and the effects of adding exogenous glutamic acid or gibberellin, and processing conditions. Soaking at 30¿°C and germination at 35¿°C during 36¿h resulted in the highest GABA in distilled soaking water with pH¿7. The indica rice showed higher GABA levels than japonica rice. GABA was increased under acidic soaking conditions or by adding L-glutamic acid (L-Glu) at the optimal concentration of 1.0¿g¿L-1 and gibberellin A3 (GA3) at the optimal concentration of 0.25¿mg¿L-1. The lower accumulation of GABA in japonica rice could be remedied by adding exogenous L-Glu and GA3, and providing acidic soaking conditions. The results help to efficiently produce GABA enriched functional food.
Gene Expression Differences between Noccaea caerulescens Ecotypes Help to Identify Candidate Genes for Metal Phytoremediation
Halimaa, P. ; Lin, Y.F. ; Ahonen, V.H. ; Blande, D. ; Clemens, S. ; Gyenesei, A. ; Haikio, E. ; Karenlampi, S.O. ; Laiho, A. ; Aarts, M.G.M. ; Pursiheimo, J.P. ; Schat, H. ; Schmidt, H. ; Tuomainen, M.H. ; Tervahauta, A.I. - \ 2014
Environmental Science and Technology 48 (2014)6. - ISSN 0013-936X - p. 3344 - 3353.
hyperaccumulator thlaspi-caerulescens - arabidopsis-halleri - commercial phytoextraction - cadmium tolerance - cd tolerance - copy number - key role - accumulation - transporter - plants
Populations of Noccaea caerulescens show tremendous differences in their capacity to hyperaccumulate and hypertolerate metals. To explore the differences that could contribute to these traits, we undertook SOLiD high-throughput sequencing of the root transcriptomes of three phenotypically well-characterized N. caerulescens accessions, i.e., Ganges, La Calamine, and Monte Prinzera. Genes with possible contribution to zinc, cadmium, and nickel hyperaccumulation and hypertolerance were predicted. The most significant differences between the accessions were related to metal ion (di-, trivalent inorganic cation) transmembrane transporter activity, iron and calcium ion binding, (inorganic) anion transmembrane transporter activity, and antioxidant activity. Analysis of correlation between the expression profile of each gene and the metal-related characteristics of the accessions disclosed both previously characterized (HMA4, HMA3) and new candidate genes (e.g., for nickel IRT1, ZIP10, and PDF2.3) as possible contributors to the hyperaccumulation/tolerance phenotype. A number of unknown Noccaea-specific transcripts also showed correlation with Zn2+, Cd2+, or Ni2+ hyperaccumulation/tolerance. This study shows that N. caerulescens populations have evolved great diversity in the expression of metal-related genes, facilitating adaptation to various metalliferous soils. The information will be helpful in the development of improved plants for metal phytoremediation.
Long-term acclimation of anaerobic sludges for high-rate methanogenesis from LCFA
Silva, S.A. ; Cavaleiro, A.J. ; Pereira, M.A. ; Stams, A.J.M. ; Alves, M.M. ; Sousa, D.Z. - \ 2014
Biomass and Bioenergy 67 (2014). - ISSN 0961-9534 - p. 297 - 303.
chain fatty-acids - oleic-acid - oxidizing bacteria - methane production - waste-water - digestion - lipids - quantification - hybridization - accumulation
Inhibition of methanogens by long chain fatty acids (LCFA) and the low numbers of LCFA-degrading bacteria are limitations to exploit biogas production from fat-rich wastewaters. Generally reactors fail due to excessive LCFA accumulation onto the sludge. Here, long-term acclimation and bioaugmentation with a LCFA-degrading coculture were hypothesized as strategies to enhance methanogenic conversion of these compounds. Anaerobic sludges previously exposed to LCFA for more than 100 days converted a specific biomass-associated substrate of (3.2 ± 0.1) kg·kg-1 with very short lag phases (
On the relation between tree crown morphology and particulate matter deposition on urban tree leaves: a ground-based LiDAR approach
Hofman, J. ; Bartholomeus, H. ; Calders, K. ; Wittenberghe, S. van; Wuyts, K. ; Samson, R. - \ 2014
Atmospheric Environment 99 (2014). - ISSN 1352-2310 - p. 130 - 139.
air-quality - marquardt algorithm - magnetic-properties - leaf surfaces - street canyon - pollution - particles - canopy - accumulation - vegetation
Urban dwellers often breathe air that does not meet the European and WHO standards. Next to legislative initiatives to lower atmospheric pollutants, much research has been conducted on the potential of urban trees as mitigation tool for atmospheric particles. While leaf-deposited dust has shown to vary significantly throughout single tree crowns, this study evaluated the influence of micro-scale tree crown morphology (leaf density) on the amount of leaf-deposited dust. Using a ground-based LiDAR approach, the three-dimensional tree crown morphology was obtained and compared to gravimetric measurements of leaf-deposited dust within three different size fractions (>10, 3–10 and 0.2–3 µm). To our knowledge, this is the first application of ground-based LiDAR for comparison with gravimetric results of leaf-deposited particulate matter. Overall, an increasing leaf density appears to reduce leaf-deposition of atmospheric particles. This might be explained by a reduced wind velocity, suppressing turbulent deposition of atmospheric particles through impaction. Nevertheless, the effect of tree crown morphology on particulate deposition appears almost negligible (7% AIC decrease) compared to the influence of physical factors like height, azimuth and tree position.
Integrative cross-omics analysis in primary mouse hepatocytes unravels mechanisms of cyclosporin A-induced hepatotoxicity
Hof, W.F.P.M. ; Summeren, A. van; Lommen, A. ; Coonen, M.L.J. ; Brauers, K. ; Herwijnen, M. van; Wodzig, W.K.W.H. ; Kleinjans, J.C.S. - \ 2014
Toxicology 324 (2014). - ISSN 0300-483X - p. 18 - 26.
drug-induced hepatotoxicity - gene-expression - micrornas - repression - normalization - accumulation - metabonomics - translation - activation - biomarkers
The liver is responsible for drug metabolism and drug-induced hepatotoxicity is the most frequent reason for drug withdrawal, indicating that better pre-clinical toxicity tests are needed. In order to bypass animal models for toxicity screening, we exposed primary mouse hepatocytes for exploring the prototypical hepatotoxicant cyclosporin A. To elucidate the mechanisms underlying cyclosporin A-induced hepatotoxicity, we analyzed expression levels of proteins, mRNAs, microRNAs and metabolites.
What cost mitochondria? The maintenance of functional mitochondrial DNA within and across generations
Aanen, D.K. ; Spelbrink, J.N. ; Beekman, M. - \ 2014
Philosophical Transactions of the Royal Society. Series B, Biological Sciences 369 (2014)1646. - ISSN 0962-8436
hereditary optic neuropathy - cytoplasmic inheritance - deletion mutants - evolution - mtdna - mutations - selection - disease - genomes - accumulation
The peculiar biology of mitochondrial DNA (mtDNA) potentially has detrimental consequences for organismal health and lifespan. Typically, eukaryotic cells contain multiple mitochondria, each with multiple mtDNA genomes. The high copy number of mtDNA implies that selection on mtDNA functionality is relaxed. Furthermore, because mtDNA replication is not strictly regulated, within-cell selection may favour mtDNA variants with a replication advantage, but a deleterious effect on cell fitness. The opportunities for selfish mtDNA mutations to spread are restricted by various organism-level adaptations, such as uniparental transmission, germline mtDNA bottlenecks, germline selection and, during somatic growth, regular alternation between fusion and fission of mitochondria. These mechanisms are all hypothesized to maintain functional mtDNA. However, the strength of selection for maintenance of functional mtDNA progressively declines with age, resulting in age-related diseases. Furthermore, organismal adaptations that most probably evolved to restrict the opportunities for selfish mtDNA create secondary problems. Owing to predominantly maternal mtDNA transmission, recombination among mtDNA from different individuals is highly restricted or absent, reducing the scope for repair. Moreover, maternal inheritance precludes selection against mtDNA variants with male-specific effects. We finish by discussing the consequences of life-history differences among taxa with respect to mtDNA evolution and make a case for the use of microorganisms to experimentally manipulate levels of selection
Heterosis is prevalent among domesticated but not wild strains of Saccharomyces cerevisiae
Plech, M. ; Visser, J.A.G.M. de; Korona, R. - \ 2014
G3 : Genes Genomes Genetics 4 (2014). - ISSN 2160-1836 - p. 315 - 323.
history trade-offs - inbreeding depression - deleterious mutations - outbreeding depression - population genomics - yeast - evolution - load - consequences - accumulation
Crosses between inbred but unrelated individuals often result in an increased fitness of the progeny. This phenomenon is known as heterosis and has been reported for wild and domesticated populations of plants and animals. Analysis of heterosis is often hindered by the fact that the genetic relatedness between analyzed organisms is only approximately known. We studied a collection of Saccharomyces cerevisiae isolates from wild and human-created habitats whose genomes were sequenced and thus their relatedness was fully known. We reasoned that if these strains accumulated different deleterious mutations at an approximately constant rate, then heterosis should be most visible in F1 heterozygotes from the least related parents. We found that heterosis was substantial and positively correlated with sequence divergence, but only in domesticated strains. More than 80% of the heterozygous hybrids were more fit than expected from the mean of their homozygous parents, and approximately three-quarters of those exceeded even the fittest parent. Our results support the notion that domestication brings about relaxation of selection and accumulation of deleterious mutations. However, other factors may have contributed as well. In particular, the observed build-up of genetic load might be facilitated by a decrease, and not increase, in the rate of inbreeding
Deepwater marine litter densities and compsoition from submersible video-gransects around the ABC-islands, Dutch Caribbean
Debrot, A.O. ; Vinke, E. ; Wende, G. van der; Hylkema, A. ; Reed, J.K. - \ 2014
Marine Pollution Bulletin 88 (2014)1-2. - ISSN 0025-326X - p. 361 - 365.
sea-floor - plastic debris - accumulation - california - curacao - bottom - coast
Baseline data on anthropogenic seafloor debris contamination in the year 2000 is provided for 24 submersible video transects at depths of 80–900 m, off the Dutch ABC-islands (Aruba, Bonaire, Curaçao), in the southeastern Caribbean Sea. In total, 202 objects were documented from a combined 21,184 m of transect, ranging from sandy lower island-slope to rocky upper island-slope habitat. Debris densities differed significantly with depth. Highest debris accumulation (0.459 items 100 m-2 or 4590 items per km2) occurred at depths of 300–600 m on more shallow-sloping (20–30°) sand and silt bottoms. The overall average debris density was 0.27 objects per 100 m2 (or 2700 items per km2), which is an order of magnitude higher than most other deepwater debris studies. What we describe may be representative for other small, populated, steep volcanic Caribbean islands. Food and beverage-related items were the single largest usage category identified (44% of objects; mostly glass beverage bottles).
Lanthanum from a modified clay used in eutrophication control is bioavailable to the marbled crayfish (Procambarus fallax f. virginalis)
Oosterhout, F. van; Goitom, E. ; Roessink, I. ; Lurling, M. - \ 2014
PLoS One 9 (2014)7. - ISSN 1932-6203 - 9 p.
phosphorus binding clay - copper nickel smelters - rare-earth-elements - heavy-metals - fresh-water - lakes - toxicity - accumulation - phoslock(r) - sediment
To mitigate eutrophication in fresh standing waters the focus is on phosphorus (P) control, i.e. on P inflows to a lake as well as a lake's sediment as internal P source. The in-lake application of the lanthanum (La) modified clays – i.e. La modified bentonite (Phoslock) or La modified kaolinite, aim at dephosphatising the water column and at reducing the release of P from a lake's sediment. Application of these clays raises the question whether La from these clays can become bioavailable to biota. We investigated the bioavailability of La from Phoslock in a controlled parallel groups experiment in which we measured the La in carapace, gills, ovaries, hepatopancreas and abdominal muscle after 0, 14 and 28 days of exposure to Phoslock. Expressing the treatment effect as the difference of the median concentration between the two treatment groups (Phoslock minus control group) yield the following effects, the plus sign (+) indicating an increase, concentrations in µg g-1 dry weight: Day 14: carapace +10.5 µg g-1, gills +112 µg g-1, ovaries +2.6 µg g-1, hepatopancreas +32.9 µg g-1 and abodminal muscle +3.2 µg g-1. Day 28: carapace +17.9 µg g-1; gills +182 µg g-1; ovaries +2.2 µg g-1; hepatopancreas +41.9 µg g-1 and abodminal muscle +7.6 µg g-1, all effects were statistically significant. As La from Phoslock is bio-available to and taken up by the marbled crayfishes (Procambarus fallax f. virginalis), we advocate that the application of in-lake chemical water treatments to mitigate eutrophication should be accompanied by a thorough study on potential side effects
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