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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Research data supporting "Genetic manipulation of structural colour in bacterial colonies"
Johansen, Villads Egede ; Catón, Laura ; Hamidjaja, Raditijo ; Oosterink, E. ; Wilts, Bodo D. ; Rasmussen, Torben Sølbeck ; Sherlock, Michael Mario ; Ingham, Colin J. ; Vignolini, Silvia - \ 2018
photonics - microbiology - structural colour
This data supports the publication "Living colours: Genetic manipulation of structural colour in bacterial colonies" and consists of electron microscopy images, a microscope video and goniometer data.
Effects of steaming on contaminants of emerging concern levels in seafood
Barbosa, Vera ; Maulvault, Ana Luísa ; Alves, Ricardo N. ; Kwadijk, Christian ; Kotterman, Michiel ; Tediosi, Alice ; Fernández-Tejedor, Margarita ; Sloth, Jens J. ; Granby, Kit ; Rasmussen, Rie R. ; Robbens, Johan ; Witte, Bavo De; Trabalón, Laura ; Fernandes, José O. ; Cunha, Sara C. ; Marques, António - \ 2018
Food and Chemical Toxicology 118 (2018). - ISSN 0278-6915 - p. 490 - 504.
Musk fragrances and UV-Filters - PAHs - PFCs - Seafood - Steaming - Toxic elements
Seafood consumption is a major route for human exposure to environmental contaminants of emerging concern (CeCs). However, toxicological information about the presence of CeCs in seafood is still insufficient, especially considering the effect of cooking procedures on contaminant levels. This study is one among a few who evaluated the effect of steaming on the levels of different CeCs (toxic elements, PFCs, PAHs, musk fragrances and UV-filters) in commercially relevant seafood in Europe, and estimate the potential risks associated with its consumption for consumers. In most cases, an increase in contaminant levels was observed after steaming, though varying according to contaminant and seafood species (e.g. iAs, perfluorobutanoate, dibenzo(ah)anthracene in Mytilus edulis, HHCB-Lactone in Solea sp., 2-Ethylhexyl salicylate in Lophius piscatorius). Furthermore, the increase in some CeCs, like Pb, MeHg, iAs, Cd and carcinogenic PAHs, in seafood after steaming reveals that adverse health effects can never be excluded, regardless contaminants concentration. However, the risk of adverse effects can vary. The drastic changes induced by steaming suggest that the effect of cooking should be integrated in food risk assessment, as well as accounted in CeCs regulations and recommendations issued by food safety authorities, in order to avoid over/underestimation of risks for consumer health.
Enhancing the Saliency of climate services for marine mobility sectors in European Arctic seas (SALIENSEAS) : Stakeholder Advisory Group workshop report
Lamers, M.A.J. ; Knol, Maaike ; Müller, Malte ; Blair, Berill ; Jeuring, J.H.G. ; Rasmussen, Till ; Sivle, Anders - \ 2018
Wageningen : - 28 p.
SALIENSEAS brings together a team of social and natural scientists, metocean service personnel, and end-users, with the aim to 1). Better understand the mobility patterns, constraints, challenges, decision-making contexts and information needs of end-users in different European Arctic marine sectors; 2). Develop and apply participatory tools for co-producing salient weather and sea ice services with Arctic marine end-users, and 3). Co-develop user-relevant and sector specific weather and sea ice services and dissemination systems dedicated to Arctic marine end-users tailored to key social, environmental and economic needs. This report provides an overview of the activities and discussions that took place during the first SALIENSEAS Stakeholder Advisory Group (SAG) workshop, held on 25 January 2018 at UiT The Arctic University of Norway in Tromsø, Norway. Participants of the SAG represented a wide variety of perspectives and needs related to maritime activities in the European Arctic, including expedition cruising, ice pilotage, ice breaking, fishing and hunting, and shipping. During this participatory workshop participants reflected on important information needs pertinent to planning and operations in their sectors. The core purpose of the workshop was twofold: 1) to identify the most pressing issues around metocean information availability and access, in terms of sector-specific needs to increase safety and efficiency of operations; and 2) to formulate a plan for efficient and relevant data collection from end users.
Sequence diversity of CV777 PEDV strains
Rasmussen, Thomas Bruun ; Boniotti, Maria Beatrice ; Papetti, Alice ; Grasland, Béatrice ; Frossard, Jean Pierre ; Dastjerdi, Akbar ; Hulst, M.M. ; Hanke, Dennis ; Pohlmann, Anne ; Blome, Sandra ; Poel, W.H.M. van der; Steinbach, Falko ; Blanchard, Yannick ; Lavazza, Antonio ; Bøtner, Anette ; Belsham, Graham J. - \ 2018
PRJEB20818 - ERP023004
The influence of microplastics and halogenated contaminants in feed on toxicokinetics and gene expression in European seabass (Dicentrarchus labrax)
Granby, Kit ; Rainieri, Sandra ; Rasmussen, Rie Romme ; Kotterman, Michiel J.J. ; Sloth, Jens Jørgen ; Cederberg, Tommy Licht ; Barranco, Alex ; Marques, António ; Larsen, Bodil Katrine - \ 2018
Environmental Research 164 (2018). - ISSN 0013-9351 - p. 430 - 443.
Elimination - Gene expression - Microplastics - PBDE - PCB
When microplastics pollute fish habitats, it may be ingested by fish, thereby contaminating fish with sorbed contaminants. The present study investigates how combinations of halogenated contaminants and microplastics associated with feed are able to alter toxicokinetics in European seabass and affect the fish. Microplastic particles (2%) were added to the feed either with sorbed contaminants or as a mixture of clean microplastics and chemical contaminants, and compared to feed containing contaminants without microplastics. For the contaminated microplastic diet, the accumulation of polychlorinated biphenyls (PCBs) and brominated flame retardants (BFRs) in fish was significantly higher, increasing up to 40 days of accumulation and then reversing to values comparable to the other diets at the end of accumulation. The significant gene expression results of liver (cyp1a, il1β gstα) after 40 days of exposure indicate that microplastics might indeed exacerbate the toxic effects (liver metabolism, immune system, oxidative stress) of some chemical contaminants sorbed to microplastics. Seabass quickly metabolised BDE99 to BDE47 by debromination, probably mediated by deiodinase enzymes, and unlike other contaminants, this metabolism was unaffected by the presence of microplastics. For the other PCBs and BFRs, the elimination coefficients were significantly lower in fish fed the diet with contaminants sorbed to microplastic compared to the other diets. The results indicate that microplastics affects liver detoxification and lipid distribution, both of which affect the concentration of contaminants.
Genetic manipulation of structural color in bacterial colonies
Johansen, Villads Egede ; Catón, Laura ; Hamidjaja, Raditijo ; Oosterink, Els ; Wilts, Bodo D. ; Rasmussen, Torben Sølbeck ; Sherlock, Michael Mario ; Ingham, Colin J. ; Vignolini, Silvia - \ 2018
Proceedings of the National Academy of Sciences of the United States of America 115 (2018)11. - ISSN 0027-8424 - p. 2652 - 2657.
Disorder - Flavobacteria - Genetics - Self-organization - Structural color
Naturally occurring photonic structures are responsible for the bright and vivid coloration in a large variety of living organisms. Despite efforts to understand their biological functions, development, and complex optical response, little is known of the underlying genes involved in the development of these nanostructures in any domain of life. Here, we used Flavobacterium colonies as a model system to demonstrate that genes responsible for gliding motility, cell shape, the stringent response, and tRNA modification contribute to the optical appearance of the colony. By structural and optical analysis, we obtained a detailed correlation of how genetic modifications alter structural color in bacterial colonies. Understanding of genotype and phenotype relations in this system opens the way to genetic engineering of on-demand living optical materials, for use as paints and living sensors.
Full-length genome sequences of porcine epidemic diarrhoea virus strain CV777; use of NGS to analyse genomic and sub-genomic RNAs
Rasmussen, Thomas Bruun ; Boniotti, Maria Beatrice ; Papetti, Alice ; Grasland, Béatrice ; Frossard, Jean Pierre ; Dastjerdi, Akbar ; Hulst, Marcel ; Hanke, Dennis ; Pohlmann, Anne ; Blome, Sandra ; Poel, Wim H.M. Van Der; Steinbach, Falko ; Blanchard, Yannick ; Lavazza, Antonio ; Bøtner, Anette ; Belsham, Graham J. - \ 2018
PLoS One 13 (2018)3. - ISSN 1932-6203
Porcine epidemic diarrhoea virus, strain CV777, was initially characterized in 1978 as the causative agent of a disease first identified in the UK in 1971. This coronavirus has been widely distributed among laboratories and has been passaged both within pigs and in cell culture. To determine the variability between different stocks of the PEDV strain CV777, sequencing of the full-length genome (ca. 28kb) has been performed in 6 different laboratories, using different protocols. Not surprisingly, each of the different full genome sequences were distinct from each other and from the reference sequence (Accession number AF353511) but they are >99% identical. Unique and shared differences between sequences were identified. The coding region for the surface-exposed spike protein showed the highest proportion of variability including both point mutations and small deletions. The predicted expression of the ORF3 gene product was more dramatically affected in three different variants of this virus through either loss of the initiation codon or gain of a premature termination codon. The genome of one isolate had a substantially rearranged 5´-terminal sequence. This rearrangement was validated through the analysis of sub-genomic mRNAs from infected cells. It is clearly important to know the features of the specific sample of CV777 being used for experimental studies.
Oral bioaccessibility of toxic and essential elements in raw and cooked commercial seafood species available in European markets
Alves, Ricardo N. ; Maulvault, Ana L. ; Barbosa, Vera L. ; Fernandez-Tejedor, Margarita ; Tediosi, Alice ; Kotterman, Michiel ; Heuvel, Fredericus H.M. van den; Robbens, Johan ; Fernandes, José O. ; Romme Rasmussen, Rie ; Sloth, Jens J. ; Marques, António - \ 2018
Food Chemistry 267 (2018). - ISSN 0308-8146 - p. 15 - 27.
Bioaccessibility - Seafood - Steaming - Toxic/essential elements
The oral bioaccessibility of several essential and toxic elements was investigated in raw and cooked commercially available seafood species from European markets. Bioaccessibility varied between seafood species and elements. Methylmercury bioaccessibility varied between 10 (octopus) and 60% (monkfish). Arsenic (>64%) was the toxic element showing the highest bioaccessibility. Concerning essential elements bioaccessibility in raw seafood, selenium (73%) and iodine (71%) revealed the highest percentages. The bioaccessibility of elements in steamed products increased or decreased according to species. For example, methylmercury bioaccessibility decreased significantly after steaming in all species, while zinc bioaccessibility increased in fish (tuna and plaice) but decreased in molluscs (mussel and octopus).Together with human exposure assessment and risk characterization, this study could contribute to the establishment of new maximum permissible concentrations for toxic elements in seafood by the European food safety authorities, as well as recommended intakes for essential elements.
Assessing the effects of seawater temperature and pH on the bioaccumulation of emerging chemical contaminants in marine bivalves
Maulvault, Ana Luísa ; Camacho, Carolina ; Barbosa, Vera ; Alves, Ricardo ; Anacleto, Patrícia ; Fogaça, Fabiola ; Kwadijk, Christiaan ; Kotterman, Michiel ; Cunha, Sara C. ; Fernandes, José O. ; Rasmussen, Rie R. ; Sloth, Jens J. ; Aznar-Alemany, Òscar ; Eljarrat, Ethel ; Barceló, Damià ; Marques, António - \ 2018
Environmental Research 161 (2018). - ISSN 0013-9351 - p. 236 - 247.
Acidification - Bioaccumulation - Emerging chemical contaminants - Flame retardants - Perfluorinated compounds - Toxic elements - Warming
Emerging chemical contaminants [e.g. toxic metals speciation, flame retardants (FRs) and perfluorinated compounds (PFCs), among others], that have not been historically recognized as pollutants nor their toxicological hazards, are increasingly more present in the marine environment. Furthermore, the effects of environmental conditions (e.g. temperature and pH) on bioaccumulation and elimination mechanisms of these emerging contaminants in marine biota have been poorly studied until now. In this context, the aim of this study was to assess, for the first time, the effect of warmer seawater temperatures (Δ = + 4 °C) and lower pH levels (Δ = − 0.4 pH units), acting alone or combined, on the bioaccumulation and elimination of emerging FRs (dechloranes 602, 603 and 604, and TBBPA), inorganic arsenic (iAs), and PFCs (PFOA and PFOS) in two estuarine bivalve species (Mytilus galloprovincialis and Ruditapes philippinarum). Overall, results showed that warming alone or combined with acidification promoted the bioaccumulation of some compounds (i.e. dechloranes 602, 604, TBBPA), but also facilitated the elimination of others (i.e. iAs, TBBPA). Similarly, lower pH also resulted in higher levels of dechloranes, as well as enhanced iAs, PFOA and PFOS elimination. Data also suggests that, when both abiotic stressors are combined, bivalves' capacity to accumulate contaminants may be time-dependent, considering significantly drastic increase observed with Dec 602 and TBBPA, during the last 10 days of exposure, when compared to reference conditions. Such changes in contaminants' bioaccumulation/elimination patterns also suggest a potential increase of human health risks of some compounds, if the climate continues changing as forecasted. Therefore, this first study pointed out the urgent need for further research on the effects of abiotic conditions on emerging contaminants kinetics, to adequately estimate the potential toxicological hazards associated to these compounds and develop recommendations/regulations for their presence in seafood, considering the prevailing environmental conditions expected in tomorrow's ocean.
Non-Chemical Weed Management
Melander, Bo ; Liebman, Matt ; Davis, Adam S. ; Gallandt, Eric R. ; Bàrberi, Paolo ; Moonen, Anna Camilla ; Rasmussen, Jesper ; Weide, Rommie van der; Vidotto, Francesco - \ 2017
In: Weed Research / Hatcher, Paul E., Froud-Williams, Robert J., Wiley - ISBN 9781119969143 - p. 245 - 270.
Crop competition - Cultural methods - European weed research - Non-chemical weed management - North America - Organic crop production - Weed control methods - Weed germination

Non-chemical weed management covers all management practices that influence weeds except herbicides. This chapter summarises the major achievements in European research, as well as work undertaken in North America. Research groups from both continents have interacted strongly on the topic over the years and shared common interests on the development of non-chemical tactics. The chapter encompasses preventive, cultural and direct weed control methods, explaining the basic principles and the integration of these tactics in weed management strategies for agricultural and horticultural crops and in some cases amenity areas as well. Preventive methods reduce weed germination, cultural methods improve crop competition and direct physical weed control reduces weed survival. Non-chemical weed management is mainly adopted in organic crop production, as conventional growers still perceive it as more costly and less reliable than herbicide-based weed control programmes.

Plant Cytokinesis : Terminology for Structures and Processes
Smertenko, Andrei ; Assaad, Farhah ; Baluška, František ; Bezanilla, Magdalena ; Buschmann, Henrik ; Drakakaki, Georgia ; Hauser, Marie Theres ; Janson, Marcel ; Mineyuki, Yoshinobu ; Moore, Ian ; Müller, Sabine ; Murata, Takashi ; Otegui, Marisa S. ; Panteris, Emmanuel ; Rasmussen, Carolyn ; Schmit, Anne Catherine ; Šamaj, Jozef ; Samuels, Lacey ; Staehelin, L.A. ; Damme, Daniel Van; Wasteneys, Geoffrey ; Žárský, Viktor - \ 2017
Trends in Cell Biology 27 (2017)12. - ISSN 0962-8924 - p. 885 - 894.
Cell plate - Cytokinesis - Division plane - Phragmoplast - Preprophase band

Plant cytokinesis is orchestrated by a specialized structure, the phragmoplast. The phragmoplast first occurred in representatives of Charophyte algae and then became the main division apparatus in land plants. Major cellular activities, including cytoskeletal dynamics, vesicle trafficking, membrane assembly, and cell wall biosynthesis, cooperate in the phragmoplast under the guidance of a complex signaling network. Furthermore, the phragmoplast combines plant-specific features with the conserved cytokinetic processes of animals, fungi, and protists. As such, the phragmoplast represents a useful system for understanding both plant cell dynamics and the evolution of cytokinesis. We recognize that future research and knowledge transfer into other fields would benefit from standardized terminology. Here, we propose such a lexicon of terminology for specific structures and processes associated with plant cytokinesis. A large number of phragmoplast proteins have been identified.Electron microscopy/tomography studies have produced nanoscale information about the architecture of phragmoplast and cell plate assembly stages in cryofixed cells.Novel components of the cortical division zone and cell plate fusion site have been discovered. This information lays a foundation for understanding how plant cells memorize the division plane throughout mitosis and how the cell plate is guided to its predetermined attachment site.MAP65 and plus end-directed kinesins contribute to the maintenance of the antiparallel overlap of phragmoplast microtubules. In addition, the MAP65-TRAPPII interaction plays a key role in cell plate assembly.Actin filaments align parallel to microtubules in the phragmoplast, while some microfilaments extend from cell plate margin to guide its expansion towards the fusion site.

Migratory preferences of humpback whales between feeding and breeding grounds in the eastern South Pacific
Acevedo, Jorge ; Aguayo-lobo, Anelio ; Allen, Judith ; Botero-acosta, Natalia ; Capella, Juan ; Castro, Cristina ; Rosa, Luciano Dalla ; Denkinger, Judith ; Félix, Fernando ; Flórez-gonzález, Lilian ; Garita, Frank ; Guzmán, Héctor M. ; Haase, Ben ; Kaufman, Gregory ; Llano, Martha ; Olavarría, Carlos ; Pacheco, Aldo S. ; Plana, Jordi ; Rasmussen, Kristin ; Scheidat, Meike ; Secchi, Eduardo R. ; Silva, Sebastian ; Stevick, Peter T. - \ 2017
Marine Mammal Science 33 (2017)4. - ISSN 0824-0469 - p. 1035 - 1052.
megaptera novaeangliae - migratory destinations - breeding stock G - photo-identifiaction - feeding ground - Antarctic Peninsula - Fueguian Archipelago
Latitudinal preferences within the breeding range have been suggested for Breeding Stock G humpback whales that summer in different feeding areas of the eastern South Pacific. To address this hypothesis, humpback whales photo-identified from the Antarctic Peninsula and the Fueguian Archipelago (southern Chile) were compared with whales photo-identified from lower latitudes extending from northern Peru to Costa Rica. This comparison was performed over a time span that includes 18 austral seasons. A total of 238 whales identified from the Antarctic Peninsula and 25 whales from the Fueguian Archipelago were among those photo-identified at the breeding grounds. Our findings showed that humpback whales from each feeding area were resighted unevenly across the breeding grounds, which suggests a degree of spatial structuring in the migratory pathway. Humpback whales that feed at the
Antarctic Peninsula were more likely to migrate to the southern breeding range
between northern Peru and Colombia, whereas whales that feed at the Fueguian
Archipelago were more likely to be found in the northern range of the breeding
ground off Panama. Further photo-identification efforts and genetic sampling from poorly sampled or unsampled areas are recommended to confirm these reported connectivity patterns.
Dairy proteins, dairy lipids, and postprandial lipemia in persons with abdominal obesity (DairyHealth) : A 12-wk, randomized, parallel-controlled, double-blinded, diet intervention study
Bohl, Mette ; Bjørnshave, Ann ; Rasmussen, Kia V. ; Schioldan, Anne Grethe ; Amer, Bashar ; Larsen, Mette K. ; Dalsgaard, Trine K. ; Holst, Jens J. ; Herrmann, Annkatrin ; O'Neill, Sadhbh ; O'Driscoll, Lorraine ; Afman, Lydia ; Jensen, Erik ; Christensen, Merete M. ; Gregersen, Søren ; Hermansen, Kjeld - \ 2015
American Journal of Clinical Nutrition 101 (2015)4. - ISSN 0002-9165 - p. 870 - 878.
Abdominal obesity - Adipose tissue gene expression - ApoB-48 - Casein - Dairy - Incretin - Mediumchain saturated fatty acid - Milk fat - Milk protein - Postprandial lipemia - Whey

Background: Abdominal obesity and exaggerated postprandial lipemia are independent risk factors for cardiovascular disease (CVD) and mortality, and both are affected by dietary behavior. Objective: We investigated whether dietary supplementation with whey protein and medium-chain saturated fatty acids (MC-SFAs) improved postprandial lipid metabolism in humans with abdominal obesity. Design: We conducted a 12-wk, randomized, double-blinded, diet intervention study. Sixty-three adults were randomly allocated to one of 4 diets in a 2 3 2 factorial design. Participants consumed 60 g milk protein (whey or casein) and 63 g milk fat (with high or low MCSFA content) daily. Before and after the intervention, a high-fat meal test was performed. We measured changes from baseline in fasting and postprandial triacylglycerol, apolipoprotein B-48 (apoB-48; reflecting chylomicrons of intestinal origin), free fatty acids (FFAs), insulin, glucose, glucagon, glucagon-like peptide 1 (GLP-1), and gastric inhibitory polypeptide (GIP). Furthermore, changes in the expression of adipose tissue genes involved in lipid metabolism were investigated. Two-factor ANOVA was used to examine the difference between protein types and fatty acid compositions, as well as any interaction between the two. Results: Fifty-two participants completed the study. We found that the postprandial apoB-48 response decreased significantly after whey compared with casein (P = 0.025) independently of fatty acid composition. Furthermore, supplementation with casein resulted in a significant increase in the postprandial GLP-1 response compared with whey (P = 0.003). We found no difference in postprandial triacylglycerol, FFA, insulin, glucose, glucagon, or GIP related to protein type or MC-SFA content. We observed no interaction between milk protein and milk fat on postprandial lipemia. Conclusion: We found that a whey protein supplement decreased the postprandial chylomicron response compared with casein in persons with abdominal obesity, thereby indicating a beneficial impact on CVD risk.

Toxic elements and speciation in seafood samples from different contaminated sites in Europe
Maulvault, A.L. ; Anacleto, P. ; Barbosa, V. ; Sloth, J.J. ; Rasmussen, R. ; Tediosi, A. ; Fernandez-Tejedor, M. ; Heuvel, F.H.M. ; Kotterman, M.J.J. ; Marques, A. - \ 2015
Environmental Research 143 (2015)Part B. - ISSN 0013-9351 - p. 72 - 81.
The presence of cadmium (Cd), lead (Pb), mercury (THg), methylmercury (MeHg), arsenic (TAs), inorganic arsenic (iAs), cobalt (Co), copper (Cu), zinc (Zn), nickel (Ni), chromium (Cr) and iron (Fe) was investigated in seafood collected from European marine ecosystems subjected to strong anthropogenic pressure, i.e. hotspot areas. Different species (Mytilus galloprovincialis, n=50; Chamelea gallina, n=50; Liza aurata, n=25; Platichthys flesus, n=25; Laminaria digitata, n=15; and Saccharina latissima, n=15) sampled in Tagus estuary, Po delta, Ebro delta, western Scheldt, and in the vicinities of a fish farm area (Solund, Norway), between September and December 2013, were selected to assess metal contamination and potential risks to seafood consumers, as well as to determine the suitability of ecologically distinct organisms as bioindicators in environmental monitoring studies. Species exhibited different elemental profiles, likely as a result of their ecological strategies, metabolism and levels in the environment (i.e. seawater and sediments). Higher levels of Cd (0.15–0.94 mg kg-1), Pb (0.37-0.89 mg kg-1), Co (0.48–1.1 mg kg-1), Cu (4.8–8.4 mg kg-1), Zn (75–153 mg kg-1), Cr (1.0–4.5 mg kg-1) and Fe (283–930 mg kg-1) were detected in bivalve species, particularly in M. galloprovincialis from Ebro and Po deltas, whereas the highest content of Hg was found in P. flesus (0.86 mg kg-1). In fish species, most Hg was organic (MeHg; from 69 to 79%), whereas lower proportions of MeHg were encountered in bivalve species (between 20 and 43%). The highest levels of As were found in macroalgae species L. digitata and S. latissima (41 mg kg-1 and 43 mg kg-1, respectively), with iAs accounting almost 50% of the total As content in L. digitata but not with S. latissima nor in the remaining seafood samples. This work highlights that the selection of the most appropriate bioindicator species is a fundamental step in environmental monitoring of each contaminant, especially in coastal areas. Furthermore, data clearly shows that the current risk assessment and legislation solely based on total As or Hg data is limiting, as elemental speciation greatly varies according to seafood species, thus playing a key role in human exposure assessment via food.
Assessing drivers of vegetation changes in drylands from time series of earth observation data
Fensholt, R. ; Horion, S. ; Tagesson, T. ; Ehammer, A. ; Grogan, K. ; Tian, F. ; Huber, S. ; Verbesselt, J. ; Prince, S.D. ; Tucker, C.J. ; Rasmussen, K. - \ 2015
In: Remote Sensing Time Series : Revealing Land Surface Dynamics / Kuenzer, C., Dech, S., Wagner, W., Springer International Publishing (Remote sensing and digital image processing 22) - ISBN 9783319159676 - p. 183 - 202.
This chapter summarizes methods of inferring information about drivers of global dryland vegetation changes observed from remote sensing time series data covering from the 1980s until present time. Earth observation (EO) based time series of vegetation metrics, sea surface temperature (SST) (both from the AVHRR (Advanced Very High Resolution Radiometer) series of instruments) and precipitation data (blended satellite/rain gauge) are used for determining the mechanisms of observed changes. EO-based methods to better distinguish between climate and human induced (land use) vegetation changes are reviewed. The techniques presented include trend analysis based on the Rain-Use Efficiency (RUE) and the Residual Trend Analysis (RESTREND) and the methodological challenges related to the use of these. Finally, teleconnections between global sea surface temperature (SST) anomalies and dryland vegetation productivity are illustrated and the associated predictive capabilities are discussed.
Assessment of vegetation trends in drylands from time series of earth observation data
Fensholt, R. ; Horion, S. ; Tagesson, T. ; Ehammer, A. ; Grogan, K. ; Tian, F. ; Huber, S. ; Verbesselt, J. ; Prince, S.D. ; Tucker, C.J. ; Rasmussen, K. - \ 2015
In: Remote Sensing Time Series : Revealing Land Surface Dynamics / Kuenzer, C., Dech, S., Wagner, W., Springer International Publishing (Remote Sensing and Digital Image Processing 22) - ISBN 9783319159676 - p. 159 - 182.
This chapter summarizes approaches to the detection of dryland vegetation change and methods for observing spatio-temporal trends from space. An overview of suitable long-term Earth Observation (EO) based datasets for assessment of global dryland vegetation trends is provided and a status map of contemporary greening and browning trends for global drylands is presented. The vegetation metrics suitable for per-pixel temporal trend analysis is discussed, including seasonal parameterisation and the appropriate choice of trend indicators. Recent methods designed to overcome assumptions of long-term linearity in time series analysis (Breaks For Additive Season and Trend(BFAST)) are discussed. Finally, the importance of the spatial scale when performing temporal trend analysis is introduced and a method for image downscaling (Spatial and Temporal Adaptive Reflectance Fusion Model (STARFM)) is presented.
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.
Molecular double-check strategy for the identification and characterization of European Lyssaviruses
Fischer, M. ; Freuling, C.M. ; Müller, T. ; Wegelt, A. ; Kooi, E.A. ; Rasmussen, T.B. ; Voller, K. ; Marston, D.A. ; Fooks, A.R. ; Beer, M. ; Hoffmann, B. - \ 2014
Journal of Virological Methods 203 (2014). - ISSN 0166-0934 - p. 23 - 32.
real-time - rt-pcr - developing-countries - virus detection - bat lyssavirus - human rabies - diagnosis - assay - infection - germany
The “gold standard” for post-mortem rabies diagnosis is the direct fluorescent antibody test (FAT). However, in the case of ante-mortem non-neural sample material or decomposed tissues, the FAT reaches its limit, and the use of molecular techniques can be advantageous. In this study, we developed and validated a reverse transcription PCR cascade protocol feasible for the classification of samples, even those for which there is no epidemiological background knowledge. This study emphasises on the most relevant European lyssaviruses. In a first step, two independent N- and L-gene based pan-lyssavirus intercalating dye assays are performed in a double-check application to increase the method's diagnostic safety. For the second step, characterization of the lyssavirus positive samples via two independent multiplex PCR-systems was performed. Both assays were probe-based, species-specific multiplex PCR-systems for Rabies virus, European bat lyssavirus type 1 and 2 as well as Bokeloh bat lyssavirus. All assays were validated successfully with a comprehensive panel of lyssavirus positive samples, as well as negative material from various host species. This double-check strategy allows for both safe and sensitive screening, detection and characterization of all lyssavirus species of humans and animals, as well as the rapid identification of currently unknown lyssaviruses in bats in Europe.
Sub-chronic toxicity study in rats orally exposed to nanostructured silica
Zande, M. van der; Vandebriel, R.J. ; Groot, M.J. ; Kramer, E.H.M. ; Herrera Riviera, Z.E. ; Rasmussen, K. ; Ossenkoppele, J.S. ; Tromp, P. ; Gremmer, E.R. ; Peters, R.J.B. ; Hendriksen, P.J. ; Marvin, H.J.P. ; Hoogenboom, L.A.P. ; Peijnenburg, A.A.C.M. ; Bouwmeester, H. - \ 2014
Particle and Fibre Toxicology 11 (2014). - ISSN 1743-8977
in-vivo biodistribution - expression profiles - liver fibrosis - nanoparticles - absorption - elimination - injection - foods - acid - size
Synthetic Amorphous Silica (SAS) is commonly used in food and drugs. Recently, a consumer intake of silica from food was estimated at 9.4 mg/kg bw/day, of which 1.8 mg/kg bw/day was estimated to be in the nano-size range. Food products containing SAS have been shown to contain silica in the nanometer size range (i.e. 5 – 200 nm) up to 43% of the total silica content. Concerns have been raised about the possible adverse effects of chronic exposure to nanostructured silica.
Pig Domestication and Human-Mediated Dispersal in Western Eurasia Revealed through Ancient DNA and Geometric Morphometrics
Ottoni, C. ; Flink, L.G. ; Evin, A. ; Georg, C. ; Cupere, B. De; Neer, W. van; Bartosiewicz, L. ; Linderholm, A. ; Barnett, R. ; Peters, J. ; Decorte, R. ; Waelkens, M. ; Vanderheyden, N. ; Ricaut, F.X. ; Cakirlar, C. ; Cevik, O. ; Hoelzel, A.R. ; Mashkour, M. ; Karimlu, A.F.M. ; Seno, S.S. ; Daujat, J. ; Brock, F. ; Pinhasi, R. ; Hongo, H. ; Perez-Enciso, M. ; Rasmussen, M. ; Frantz, L.A.F. ; Megens, H.J.W.C. ; Crooijmans, R.P.M.A. ; Groenen, M.A.M. ; Arbuckle, B. ; Benecke, N. ; Vidarsdottir, U.S. ; Burger, J. ; Cucchi, T. ; Dobney, K. ; Larson, G. - \ 2013
Molecular Biology and Evolution 30 (2013)4. - ISSN 0737-4038 - p. 824 - 832.
origins - history - agriculture - shape - wild - expansions - likelihood - insights - farmers - europe
Zooarcheological evidence suggests that pigs were domesticated in Southwest Asia ~8,500 BC. They then spread across the Middle and Near East and westward into Europe alongside early agriculturalists. European pigs were either domesticated independently or more likely appeared so as a result of admixture between introduced pigs and European wild boar. As a result, European wild boar mtDNA lineages replaced Near Eastern/Anatolian mtDNA signatures in Europe and subsequently replaced indigenous domestic pig lineages in Anatolia. The specific details of these processes, however, remain unknown. To address questions related to early pig domestication, dispersal, and turnover in the Near East, we analyzed ancient mitochondrial DNA and dental geometric morphometric variation in 393 ancient pig specimens representing 48 archeological sites (from the Pre-Pottery Neolithic to the Medieval period) from Armenia, Cyprus, Georgia, Iran, Syria, and Turkey. Our results reveal the first genetic signatures of early domestic pigs in the Near Eastern Neolithic core zone. We also demonstrate that these early pigs differed genetically from those in western Anatolia that were introduced to Europe during the Neolithic expansion. In addition, we present a significantly more refined chronology for the introduction of European domestic pigs into Asia Minor that took place during the Bronze Age, at least 900 years earlier than previously detected. By the 5th century AD, European signatures completely replaced the endemic lineages possibly coinciding with the widespread demographic and societal changes that occurred during the Anatolian Bronze and Iron Ages.
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