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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Spatial variation of carbon and nutrients stocks in Amazonian Dark Earth
Brazao Vieira Alho, C.F. ; Samuel Rosa, A. ; Coimbra Martins, Gilvan ; Hiemstra, T. ; Kuijper, T.W.M. ; Teixeira, Wenceslau G. - \ 2019
Geoderma 337 (2019). - ISSN 0016-7061 - p. 322 - 332.
Amazonian Dark Earths (ADE) are anthropic soils that are enriched in carbon (C) and several nutrients, particularly calcium (Ca) and phosphorus (P), when compared to adjacent soils from the Amazon basin. Studies on ADE empower the understanding of complex pre-Columbian cultural development in the Amazon and may also provide insights for future sustainable agricultural practices in the tropics. ADE are highly variable in size, depth and soil physico-chemical characteristics. Nonetheless, the differentiation between ADE and the adjacent soils is not standardized and is commonly done based on visual field observations. In this regard, the pretic horizon has been recently proposed as an attempt to classify ADE systematically. Spatial modelling techniques can be of great use to study the structure of the spatial variation of soil properties in highly variable areas. Here, we predicted the carbon and nutrients stocks in ADE by applying spatial modelling techniques using an environmental covariate (i.e. expected anthropic enrichment gradient) in our model. In addition, we used the pretic horizon criteria to classify pretic and non-pretic areas and evaluate their relative contribution to the total stocks. In this study, we collected soil samples from five 20-cm soil layers at n = 53 georeferenced points placed in a grid of about 10 to 60 m spacing in a study area located in Central Amazon (~9.4 ha). Ceramic fragments were weighed and quantified. Samples were analysed for: Total C, Total Ca, Total P, Exchangeable Ca + Mg, Extractable P, soil pH, potential CEC (pH = 7.0) and the clay content. The use of the pretic horizon criteria allowed us to clearly distinguish two unambiguous areas with a sharp transition, rather than a smooth continuum, in contrast to previous studies in ADE. Depth- and profile-wise linear regression model parameters indicated a greater importance of the chosen environmental covariate (i.e. expected anthropic enrichment gradient) to explain the spatial variation of Total Ca and Total P stocks than Total C stocks. The overall Total Ca and Total P stocks were twice as large in the pretic area when compared to the non-pretic area.
Nutrimetabolomics: An Integrative Action for Metabolomic Analyses in Human Nutritional Studies
Ulaszewska, Marynka M. ; Weinert, Christoph H. ; Trimigno, Alessia ; Portmann, Reto ; Andres Lacueva, Cristina ; Badertscher, René ; Brennan, Lorraine ; Brunius, Carl ; Bub, Achim ; Capozzi, Francesco ; Cialiè Rosso, Marta ; Cordero, Chiara E. ; Daniel, Hannelore ; Durand, Stéphanie ; Egert, Bjoern ; Ferrario, Paola G. ; Feskens, Edith J.M. ; Franceschi, Pietro ; Garcia-Aloy, Mar ; Giacomoni, Franck ; Giesbertz, Pieter ; González-Domínguez, Raúl ; Hanhineva, Kati ; Hemeryck, Lieselot Y. ; Kopka, Joachim ; Kulling, Sabine E. ; Llorach, Rafael ; Manach, Claudine ; Mattivi, Fulvio ; Migné, Carole ; Münger, Linda H. ; Ott, Beate ; Picone, Gianfranco ; Pimentel, Grégory ; Pujos-Guillot, Estelle ; Riccadonna, Samantha ; Rist, Manuela J. ; Rombouts, Caroline ; Rubert, Josep ; Skurk, Thomas ; Sri Harsha, Pedapati S.C. ; Meulebroek, Lieven Van; Vanhaecke, Lynn ; Vázquez-Fresno, Rosa ; Wishart, David ; Vergères, Guy - \ 2018
Molecular Nutrition & Food Research (2018). - ISSN 1613-4125
GC–MS - LC–MS - metabolomics - NMR - nutrition
The life sciences are currently being transformed by an unprecedented wave of developments in molecular analysis, which include important advances in instrumental analysis as well as biocomputing. In light of the central role played by metabolism in nutrition, metabolomics is rapidly being established as a key analytical tool in human nutritional studies. Consequently, an increasing number of nutritionists integrate metabolomics into their study designs. Within this dynamic landscape, the potential of nutritional metabolomics (nutrimetabolomics) to be translated into a science, which can impact on health policies, still needs to be realized. A key element to reach this goal is the ability of the research community to join, to collectively make the best use of the potential offered by nutritional metabolomics. This article, therefore, provides a methodological description of nutritional metabolomics that reflects on the state-of-the-art techniques used in the laboratories of the Food Biomarker Alliance (funded by the European Joint Programming Initiative “A Healthy Diet for a Healthy Life” (JPI HDHL)) as well as points of reflections to harmonize this field. It is not intended to be exhaustive but rather to present a pragmatic guidance on metabolomic methodologies, providing readers with useful “tips and tricks” along the analytical workflow.
Considerations and consequences of allowing DNA sequence data as types of fungal taxa
Zamora, Juan Carlos ; Svensson, Måns ; Kirschner, Roland ; Olariaga, Ibai ; Ryman, Svengunnar ; Parra, Luis Alberto ; Geml, József ; Rosling, Anna ; Adamčík, Slavomír ; Ahti, Teuvo ; Aime, M.C. ; Ainsworth, A.M. ; Albert, László ; Albertó, Edgardo ; García, Alberto Altés ; Ageev, Dmitry ; Agerer, Reinhard ; Aguirre-Hudson, Begoña ; Ammirati, Joe ; Andersson, Harry ; Angelini, Claudio ; Antonín, Vladimír ; Aoki, Takayuki ; Aptroot, André ; Argaud, Didier ; Sosa, Blanca Imelda Arguello ; Aronsen, Arne ; Arup, Ulf ; Asgari, Bita ; Assyov, Boris ; Atienza, Violeta ; Bandini, Ditte ; Baptista-Ferreira, João Luís ; Baral, Hans-Otto ; Baroni, Tim ; Barreto, Robert Weingart ; Beker, Henry ; Bell, Ann ; Bellanger, Jean-Michel ; Bellù, Francesco ; Bemmann, Martin ; Bendiksby, Mika ; Bendiksen, Egil ; Bendiksen, Katriina ; Benedek, Lajos ; Bérešová-Guttová, Anna ; Berger, Franz ; Berndt, Reinhard ; Bernicchia, Annarosa ; Biketova, Alona Yu. ; Bizio, Enrico ; Bjork, Curtis ; Boekhout, Teun ; Boertmann, David ; Böhning, Tanja ; Boittin, Florent ; Boluda, Carlos G. ; Boomsluiter, Menno W. ; Borovička, Jan ; Brandrud, Tor Erik ; Braun, Uwe ; Brodo, Irwin ; Bulyonkova, Tatiana ; Burdsall, Harold H. ; Buyck, Bart ; Burgaz, Ana Rosa ; Calatayud, Vicent ; Callac, Philippe ; Campo, Emanuele ; Candusso, Massimo ; Capoen, Brigitte ; Carbó, Joaquim ; Carbone, Matteo ; Castañeda-ruiz, Rafael F. ; Castellano, Michael A. ; Chen, Jie ; Clerc, Philippe ; Consiglio, Giovanni ; Corriol, Gilles ; Courtecuisse, Régis ; Crespo, Ana ; Cripps, Cathy ; Crous, Pedro W. ; Silva, Gladstone Alves Da ; Silva, Meiriele Da ; Dam, Marjo ; Dam, Nico ; Dämmrich, Frank ; Das, Kanad ; Davies, Linda ; Crop, Eske De; Kesel, Andre De; Kuijper, T.W.M. - \ 2018
IMA fungus 9 (2018)1. - ISSN 2210-6340 - p. 167 - 185.
Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.
LED or HPS in ornamentals? A case study in roses and campanulas
Ouzounis, Theoharis ; Giday, Habtamu ; Kjaer, Katrine H. ; Ottosen, Carl-Otto - \ 2018
European Journal of Horticultural Science 83 (2018)3. - ISSN 1611-4434 - p. 166 - 172.
Energy saving - Greenhouses - Light sources - Ornamentals

The aim of the experiment was to evaluate the effect of novel top-installed high-output light-emitting diodes (LEDs) on ornamental plant production both in terms of productivity and energy use in comparison with conventional HPS lamps in two standard greenhouse compartments. The experiments were performed in late winter period using three varieties of potted miniature roses (Rosa hybrida) and two cultivars of Campanula grown in identical installed supplemental light levels (75–85 µmol m-2 s-1 of PPFD) with temperature set points 18°C at night, 24°C during the day, while 800 ppm of CO2 was supplied. Due to the winter being relatively cold, the set points were equal to the realized temperature as ventilation rarely occurred. The leaf temperature was maintained at the same level by adjusting the top pipe temperature. Two harvests were performed in February and in March to show the potential effect of winter-or early spring-grown plants. The results showed relatively small differences with respect to plant performance between the HPS and LED treatments, and most significant differences were found only in the 1st batch of roses harvested in February regarding plant height and stem fresh and dry weight, indicating that growth was favored under HPS lamps for three out of four cultivars. Both the 2nd batches for roses and campanulas harvested in March showed very limited or no differences between treatments. The energy saving on the electricity side was 60% in LEDs compared to HPS, but due to the increased heat use from top pipes the energy used for heating increased by around 50% over the whole experimental period.

Using a system innovation's approach for stimulating agroforestry adoption
Cuperus, Fogelina ; Schoutsen, M.A. ; Sukkel, W. ; Selin Norén, Isabella ; Wijnands, F.G. - \ 2018
In: Agroforestry as sustainable land use. - - p. 35 - 39.
The whole genome effects of the PPARα agonist fenofibrate on livers of hepatocyte humanized mice
Rosa Rodriguez, M.A. de la; Sugahara, Go ; Ishida, Yuji ; Tateno, Chise ; Kersten, A.H. - \ 2018
Mus musculus - GSE107041 - PRJNA418862
The role of PPARα in gene regulation in mouse liver is well characterized. However, less is known about the effect of PPARα activation in human liver. The aim of the present study was to better characterize the impact of PPARα activation on gene regulation in human liver by combining transcriptomics with the use of hepatocyte humanized livers. To that end, chimeric mice containing hepatocyte humanized livers were given an oral dose of 300 mg/kg fenofibrate daily for 4 days. Livers were collected and analysed by hematoxilin and eosin staining, qPCR, and transcriptomics. Transcriptomics data were compared with existing datasets on fenofibrate treatment in normal mice. The human hepatocytes exhibited excessive lipid accumulation. Fenofibrate increased the size of the mouse but not human hepatocytes, and tended to reduce steatosis in the human hepatocytes. Quantitative PCR indicated that induction of PPARα targets by fenofibrate was less pronounced in the human hepatocytes than in the residual mouse hepatocytes. Transcriptomics analysis indicated that, after filtering, a total of 282 genes was significantly different between fenofibrate- and control-treated mice (P<0.01). 123 genes were significantly lower and 159 genes significantly higher in the fenofibrate-treated mice, including many established PPARα targets such as FABP1, HADHB, HADHA, VNN1, PLIN2, ACADVL and HMGCS2. According to gene set enrichment analysis, fenofibrate upregulated interferon/cytokine signaling-related pathways in hepatocyte humanized liver, but downregulated these pathways in normal mouse liver. Also, fenofibrate downregulated pathways related to DNA synthesis in hepatocyte humanized liver but not in normal mouse liver. The results support the major role of PPARα in regulating hepatic lipid metabolism, and underscore the more modest effect of PPARα activation on gene regulation in human liver compared to mouse liver. The data suggest that PPARα may have a suppressive effect on DNA synthesis in human liver, and a stimulatory effect on interferon/cytokine signalling.
A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits
Hibrand Saint-Oyant, L. ; Ruttink, T. ; Hamama, L. ; Kirov, I. ; Lakhwani, D. ; Zhou, N.N. ; Bourke, P.M. ; Daccord, N. ; Leus, L. ; Schulz, D. ; Geest, H. van de; Hesselink, T. ; Laere, K. Van; Debray, K. ; Balzergue, S. ; Thouroude, T. ; Chastellier, A. ; Jeauffre, J. ; Voisine, L. ; Gaillard, S. ; Borm, T.J.A. ; Arens, P. ; Voorrips, R.E. ; Maliepaard, C. ; Neu, E. ; Linde, M. ; Paslier, M.C. Le; Bérard, A. ; Bounon, R. ; Clotault, J. ; Choisne, N. ; Quesneville, H. ; Kawamura, K. ; Aubourg, S. ; Sakr, S. ; Smulders, M.J.M. ; Schijlen, E. ; Bucher, E. ; Debener, T. ; Riek, J. De; Foucher, F. - \ 2018
Nature Plants 4 (2018). - ISSN 2055-026X - p. 473 - 484.

Rose is the world’s most important ornamental plant, with economic, cultural and symbolic value. Roses are cultivated worldwide and sold as garden roses, cut flowers and potted plants. Roses are outbred and can have various ploidy levels. Our objectives were to develop a high-quality reference genome sequence for the genus Rosa by sequencing a doubled haploid, combining long and short reads, and anchoring to a high-density genetic map, and to study the genome structure and genetic basis of major ornamental traits. We produced a doubled haploid rose line (‘HapOB’) from Rosa chinensis ‘Old Blush’ and generated a rose genome assembly anchored to seven pseudo-chromosomes (512 Mb with N50 of 3.4 Mb and 564 contigs). The length of 512 Mb represents 90.1–96.1% of the estimated haploid genome size of rose. Of the assembly, 95% is contained in only 196 contigs. The anchoring was validated using high-density diploid and tetraploid genetic maps. We delineated hallmark chromosomal features, including the pericentromeric regions, through annotation of transposable element families and positioned centromeric repeats using fluorescent in situ hybridization. The rose genome displays extensive synteny with the Fragaria vesca genome, and we delineated only two major rearrangements. Genetic diversity was analysed using resequencing data of seven diploid and one tetraploid Rosa species selected from various sections of the genus. Combining genetic and genomic approaches, we identified potential genetic regulators of key ornamental traits, including prickle density and the number of flower petals. A rose APETALA2/TOE homologue is proposed to be the major regulator of petal number in rose. This reference sequence is an important resource for studying polyploidization, meiosis and developmental processes, as we demonstrated for flower and prickle development. It will also accelerate breeding through the development of molecular markers linked to traits, the identification of the genes underlying them and the exploitation of synteny across Rosaceae.

The whole transcriptome effects of the PPARα agonist fenofibrate on livers of hepatocyte humanized mice
Rosa Rodriguez, Montserrat A. de la; Sugahara, Go ; Hooiveld, Guido J.E.J. ; Ishida, Yuji ; Tateno, Chise ; Kersten, Sander - \ 2018
BMC Genomics 19 (2018). - ISSN 1471-2164
DNA synthesis - Fenofibrate - Hepatocyte humanized mice - Lipid metabolism - PPARα - Transcriptomics

Background: The role of PPARα in gene regulation in mouse liver is well characterized. However, less is known about the role of PPARα in human liver. The aim of the present study was to better characterize the impact of PPARα activation on gene regulation in human liver. To that end, chimeric mice containing hepatocyte humanized livers were given an oral dose of 300 mg/kg fenofibrate daily for 4 days. Livers were collected and analyzed by hematoxilin and eosin staining, qPCR, and transcriptomics. Transcriptomics data were compared with existing datasets on PPARα activation in normal mouse liver, human primary hepatocytes, and human precision cut liver slices. Results: Of the different human liver models, the gene expression profile of hepatocyte humanized livers most closely resembled actual human liver. In the hepatocyte humanized mouse livers, the human hepatocytes exhibited excessive lipid accumulation. Fenofibrate increased the size of the mouse but not human hepatocytes, and tended to reduce steatosis in the human hepatocytes. Quantitative PCR indicated that induction of PPARα targets by fenofibrate was less pronounced in the human hepatocytes than in the residual mouse hepatocytes. Transcriptomics analysis indicated that, after filtering, a total of 282 genes was significantly different between fenofibrate- and control-treated mice (P < 0.01). 123 genes were significantly lower and 159 genes significantly higher in the fenofibrate-treated mice, including many established PPARα targets such as FABP1, HADHB, HADHA, VNN1, PLIN2, ACADVL and HMGCS2. According to gene set enrichment analysis, fenofibrate upregulated interferon/cytokine signaling-related pathways in hepatocyte humanized liver, but downregulated these pathways in normal mouse liver. Also, fenofibrate downregulated pathways related to DNA synthesis in hepatocyte humanized liver but not in normal mouse liver. Conclusion: The results support the major role of PPARα in regulating hepatic lipid metabolism, and underscore the more modest effect of PPARα activation on gene regulation in human liver compared to mouse liver. The data suggest that PPARα may have a suppressive effect on DNA synthesis in human liver, and a stimulatory effect on interferon/cytokine signalling.

Independent data for transparent monitoring of greenhouse gas emissions from the land use sector – What do stakeholders think and need?
Romijn, Erika ; Sy, Veronique De; Herold, Martin ; Böttcher, Hannes ; Roman-Cuesta, Rosa Maria ; Fritz, Steffen ; Schepaschenko, Dmitry ; Avitabile, Valerio ; Gaveau, David ; Verchot, Louis ; Martius, Christopher - \ 2018
Environmental Science & Policy 85 (2018). - ISSN 1462-9011 - p. 101 - 112.
The agriculture, forestry and other land use (AFOLU) sectors contribute substantially to the net global anthropogenic greenhouse gas (GHG) emissions. To reduce these emissions under the Paris Agreement, effective mitigation actions are needed that require engagement of multiple stakeholders. Emission reduction also requires that accurate, consistent and comparable datasets are available for transparent reference and progress monitoring. Availability of free and open datasets and portals (referred to as independent data) increases, offering opportunities for improving and reconciling estimates of GHG emissions and mitigation options. Through an online survey, we investigated stakeholders’ data needs for estimating forest area and change, forest biomass and emission factors, and AFOLU GHG emissions. The survey was completed by 359 respondents from governmental, intergovernmental and non-governmental organizations, research institutes and universities, and public and private companies. These can be grouped into data users and data providers. Our results show that current open and freely available datasets and portals are only able to fulfil stakeholder needs to a certain degree. Users require a) detailed documentation regarding the scope and usability of the data, b) comparability between alternative data sources, c) uncertainty estimates for evaluating mitigation options, d) more region-specific and detailed data with higher accuracy for sub-national application, e) regular updates and continuity for establishing consistent time series. These requirements are found to be key elements for increasing overall transparency of data sources, definitions, methodologies and assumptions, which is required under the Paris
Agreement. Raising awareness and improving data availability through centralized platforms are important for increasing engagement of data users. In countries with low capacities, independent data can support countries’
mitigation planning and implementation, and related GHG reporting. However, there is a strong need for further guidance and capacity development (i.e.‘
readiness support’) on how to make proper use of independent datasets. Continued investments will be needed to sustain programmes and keep improving datasets to serve the objectives of the many stakeholders involved in climate change mitigation and should focus on increased accessibility and transparency of data to encourage stakeholder involvement.
Fusarium riograndense sp. nov., a new species in the Fusarium solani species complex causing fungal rhinosinusitis
Dallé Rosa, P. ; Ramirez-Castrillon, M. ; Valente, P. ; Meneghello Fuentefria, A. ; Diepeningen, A.D. Van; Goldani, L.Z. - \ 2018
Journal de Mycologie Medicale 28 (2018)1. - ISSN 1156-5233 - p. 29 - 35.
Antifungal susceptibility - Fusarium - MLST - Molecular phylogeny - Morphology
Invasive fusariosis has a high mortality and is predominantly observed in patients with leukemia. We report the first case of a novel species of Fusarium, Fusarium riograndense sp. nov, isolated from a lesion in the nasal cavity lesion of a patient with acute lymphoblastic leukemia. The etiological agent was identified by Multilocus Sequencing Typing (MLST), including RPB2, TEF-1α, and ITS-LSU sequences, the gold standard technique to identify new species of Fusarium. MLST and phenotypic data strongly supported its inclusion in the F. solani species complex (FSSC). The new species produced a red pigment in the Sabouraud Dextrose Agar similar to other members of the complex. The macroconiodia developed from phialides on multibranched conidiophores which merge to form effuse sporodochia with a basal foot-cell instead of papilla in basal cell shape. The microconidia were ellipsoidal, 0-1-septated, produced from long monophialides. Chlamydospores were produced singly or in pairs. Amphotericin B (MIC 1. μg/mL) was the most active drug, followed by voriconazole (MIC 8. μg/mL). The patient was successfully treated with voriconazole. Our findings indicate another lineage within FSSC capable causing of invasive human infection.
A Diurnal Rhythm in Brown Adipose Tissue Causes Rapid Clearance and Combustion of Plasma Lipids at Wakening
Berg, Rosa van den; Kooijman, Sander ; Noordam, Raymond ; Ramkisoensing, Ashna ; Abreu-Vieira, Gustavo ; Tambyrajah, Lauren L. ; Dijk, Wieneke ; Ruppert, Philip ; Mol, Isabel M. ; Kramar, Barbara ; Caputo, Rosanna ; Puig, Laura Sardón ; Ruiter, Evelien M. de; Kroon, Jan ; Hoekstra, Menno ; Sluis, Ronald J. van der; Meijer, Onno C. ; Willems van Dijk, Ko ; Kerkhof, Linda W.M. van; Christodoulides, Constantinos ; Karpe, Fredrik ; Gerhart-Hines, Zachary ; Kersten, Sander ; Meijer, Johanna H. ; Coomans, Claudia P. ; Heemst, Diana van; Biermasz, Nienke R. ; Rensen, Patrick C.N. - \ 2018
Cell Reports 22 (2018)13. - ISSN 2211-1247 - p. 3521 - 3533.
angiopoietin-like 4 - APOE3-Leiden.CETP mice - brown adipose tissue - circadian rhythm - diurnal rhythm - fatty acids - lipoprotein lipase - postprandial lipid response - triglycerides
Many favorable metabolic effects have been attributed to thermogenic activity of brown adipose tissue (BAT). Yet, time of day has rarely been considered in this field of research. Here, we show that a diurnal rhythm in BAT activity regulates plasma lipid metabolism. We observed a high-amplitude rhythm in fatty acid uptake by BAT that synchronized with the light/dark cycle. Highest uptake was found at the onset of the active period, which coincided with high lipoprotein lipase expression and low angiopoietin-like 4 expression by BAT. Diurnal rhythmicity in BAT activity determined the rate at which lipids were cleared from the circulation, thereby imposing the daily rhythm in plasma lipid concentrations. In mice as well as humans, postprandial lipid excursions were nearly absent at waking. We anticipate that diurnal BAT activity is an important factor to consider when studying the therapeutic potential of promoting BAT activity. van den Berg et al. show a strong circadian rhythm in fatty acid uptake by brown adipose tissue that peaks at wakening regardless of the light exposure period. Consequently, postprandial lipid handling by brown adipose tissue is highest at wakening, resulting in the lowest postprandial plasma lipid excursions.
Hypoxia-inducible lipid droplet-associated protein inhibits adipose triglyceride lipase
Padmanabha Das, Krishna M. ; Wechselberger, Lisa ; Liziczai, Márton ; La Rosa Rodriguez, Montserrat De; Grabner, Gernot F. ; Heier, Christoph ; Viertlmayr, Roland ; Radler, Claudia ; Lichtenegger, Jörg ; Zimmermann, Robert ; Borst, Jan Willem ; Zechner, Rudolf ; Kersten, Sander ; Oberer, Monika - \ 2018
Journal of Lipid Research 59 (2018)3. - ISSN 0022-2275 - p. 531 - 541.
Adipocytes - Hypoxia-inducible gene-2 - Intracellular lipolysis - Lipolysis and fatty acid metabolism - Triglycerides
Elaborate control mechanisms of intracellular triacylglycerol (TAG) breakdown are critically involved in the maintenance of energy homeostasis. Hypoxia-inducible lipid droplet-associated protein (HILPDA)/hypoxia-inducible gene-2 (Hig-2) has been shown to affect intracellular TAG levels, yet, the underlying molecular mechanisms are unclear. Here, we show that HILPDA inhibits adipose triglyceride lipase (ATGL), the enzyme catalyzing the first step of intracellular TAG hydrolysis. HILPDA shares structural similarity with G0/G1 switch gene 2 (G0S2), an established inhibitor of ATGL. HILPDA inhibits ATGL activity in a dose-dependent manner with an IC50 value of ∼2 μM. ATGL inhibition depends on the direct physical interaction of both proteins and involves the N-terminal hydrophobic region of HILPDA and the N-terminal patatin domain-containing segment of ATGL. Finally, confocal microscopy combined with Förster resonance energy transfer-fluorescence lifetime imaging microscopy analysis indicated that HILPDA and ATGL colocalize and physically interact intracellularly. These findings provide a rational biochemical explanation for the tissue-specific increased TAG accumulation in HILPDA-overexpressing transgenic mouse models.
Guidelines for Biomarker of Food Intake Reviews (BFIRev) : How to conduct an extensive literature search for biomarker of food intake discovery
Praticò, Giulia ; Gao, Qian ; Scalbert, Augustin ; Vergères, Guy ; Kolehmainen, Marjukka ; Manach, Claudine ; Brennan, Lorraine ; Pedapati, Sri Harsha ; Afman, Lydia A. ; Wishart, David S. ; Vázquez-Fresno, Rosa ; Lacueva, Cristina Andres ; Garcia-Aloy, Mar ; Verhagen, Hans ; Feskens, Edith J.M. ; Dragsted, Lars O. - \ 2018
Genes & Nutrition 13 (2018)1. - ISSN 1555-8932
Biomarkers - Food exposure markers - Literature search methodology - Metabolomics - Systematic review
Identification of new biomarkers of food and nutrient intake has developed fast over the past two decades and could potentially provide important new tools for compliance monitoring and dietary intake assessment in nutrition and health science. In recent years, metabolomics has played an important role in identifying a large number of putative biomarkers of food intake (BFIs). However, the large body of scientific literature on potential BFIs outside the metabolomics area should also be taken into account. In particular, we believe that extensive literature reviews should be conducted and that the quality of all suggested biomarkers should be systematically evaluated. In order to cover the literature on BFIs in the most appropriate and consistent manner, there is a need for appropriate guidelines on this topic. These guidelines should build upon guidelines in related areas of science while targeting the special needs of biomarker methodology. This document provides a guideline for conducting an extensive literature search on BFIs, which will provide the basis to systematically validate BFIs. This procedure will help to prioritize future work on the identification of new potential biomarkers and on validating these as well as other biomarker candidates, thereby providing better tools for future studies in nutrition and health.
Estimation of above-ground biomass of large tropical trees with terrestrial LiDAR
Gonzalez De Tanago, Jose ; Lau, Alvaro ; Bartholomeus, Harm ; Herold, Martin ; Avitabile, Valerio ; Raumonen, Pasi ; Martius, Christopher ; Goodman, Rosa C. ; Disney, Mathias ; Manuri, Solichin ; Burt, Andrew ; Calders, Kim - \ 2018
Methods in Ecology and Evolution 9 (2018)2. - ISSN 2041-210X - p. 223 - 234.
1. Tropical forest biomass is a crucial component of global carbon emission estimations. However, calibration and validation of such estimates require accurate and effective methods to estimate in situ above-ground biomass (AGB). Present methods rely on allometric models that are highly uncertain for large tropical trees. Terrestrial laser scanning (TLS) tree modelling has demonstrated to be more accurate than these models to infer forest AGB. Nevertheless, applying TLS methods on tropical large trees is still challenging. We propose a method to estimate AGB of large tropical trees by three-dimensional (3D) tree modelling of TLS point clouds. 2. Twenty-nine plots were scanned with a TLS in three study sites (Peru, Indonesia and Guyana). We identified the largest tree per plot (mean diameter at breast height of 73.5 cm), extracted its point cloud and calculated its volume by 3D modelling its structure using quantitative structure models (QSM) and converted to AGB using species-specific wood density. We also estimated AGB using pantropical and local allometric models. To assess the accuracy of our and allometric methods, we harvest the trees and took destructive measurements. 3. AGB estimates by the TLS–QSM method showed the best agreement in comparison to destructive harvest measurements (28.37% coefficient of variation of root mean square error [CV-RMSE] and concordance correlation coefficient [CCC] of 0.95), outperforming the pantropical allometric models tested (35.6%–54.95% CV-RMSE and CCC of 0.89–0.73). TLS–QSM showed also the lowest bias (overall underestimation of 3.7%) and stability across tree size range, contrasting with the allometric models that showed a systematic bias (overall underestimation ranging 15.2%–35.7%) increasing linearly with tree size. The TLS–QSM method also provided accurate tree wood volume estimates (CV RMSE of 23.7%) with no systematic bias regardless the tree structural characteristics. 4. Our TLS–QSM method accounts for individual tree biophysical structure more effectively than allometric models, providing more accurate and less biased AGB estimates for large tropical trees, independently of their morphology. This non-destructive method can be further used for testing and calibrating new allometric models, reducing the current under-representation of large trees in and enhancing present and past estimates of forest biomass and carbon emissions from tropical forests.
Fire effects and ecological recovery pathways of tropical montane cloud forests along a time chronosequence
Oliveras, Imma ; Román-Cuesta, Rosa M. ; Urquiaga-Flores, Erickson ; Quintano Loayza, Jose A. ; Kala, Jose ; Huamán, Vicky ; Lizárraga, Nohemi ; Sans, Guissela ; Quispe, Katia ; Lopez, Efrain ; Lopez, David ; Cuba Torres, Israel ; Enquist, Brian J. ; Malhi, Yadvinder - \ 2018
Global Change Biology 24 (2018)2. - ISSN 1354-1013 - p. 758 - 772.
carbon allocation - forest structure - metabolic scaling theory - regeneration - species diversity
Tropical montane cloud forests (TMCFs) harbour high levels of biodiversity and large carbon stocks. Their location at high elevations make them especially sensitive to climate change, because a warming climate is enhancing upslope species migration, but human disturbance (especially fire) may in many cases be pushing the treeline downslope. TMCFs are increasingly being affected by fire, and the long-term effects of fire are still unknown. Here, we present a 28-year chronosequence to assess the effects of fire and recovery pathways of burned TMCFs, with a detailed analysis of carbon stocks, forest structure and diversity. We assessed rates of change of carbon (C) stock pools, forest structure and tree-size distribution pathways and tested several hypotheses regarding metabolic scaling theory (MST), C recovery and biodiversity. We found four different C stock recovery pathways depending on the selected C pool and time since last fire, with a recovery of total C stocks but not of aboveground C stocks. In terms of forest structure, there was an increase in the number of small stems in the burned forests up to 5–9 years after fire because of regeneration patterns, but no differences on larger trees between burned and unburned plots in the long term. In support of MST, after fire, forest structure appears to approximate steady-state size distribution in less than 30 years. However, our results also provide new evidence that the species recovery of TMCF after fire is idiosyncratic and follows multiple pathways. While fire increased species richness, it also enhanced species dissimilarity with geographical distance. This is the first study to report a long-term chronosequence of recovery pathways to fire suggesting faster recovery rates than previously reported, but at the expense of biodiversity and aboveground C stocks.
Pushing nuclear magnetic resonance sensitivity limits with microfluidics and photo-chemically induced dynamic nuclear polarization
Mompeán, Miguel ; Sánchez-Donoso, Rosa M. ; La Hoz, Antonio De; Saggiomo, Vittorio ; Velders, Aldrik H. ; Gomez, M.V. - \ 2018
Nature Communications 9 (2018)1. - ISSN 2041-1723
Among the methods to enhance the sensitivity of nuclear magnetic resonance (NMR) spectroscopy, small-diameter NMR coils (microcoils) are promising tools to tackle the study of mass-limited samples. Alternatively, hyperpolarization schemes based on dynamic nuclear polarization techniques provide strong signal enhancements of the NMR target samples. Here we present a method to effortlessly perform photo-chemically induced dynamic nuclear polarization in microcoil setups to boost NMR signal detection down to sub-picomole detection limits in a 9.4T system (400 MHz 1H Larmor frequency). This setup is unaffected by current major drawbacks such as the use of high-power light sources to attempt uniform irradiation of the sample, and accumulation of degraded photosensitizer in the detection region. The latter is overcome with flow conditions, which in turn open avenues for complex applications requiring rapid and efficient mixing that are not easily achievable on an NMR tube without resorting to complex hardware.
Global environmental change effects on plant community composition trajectories depend upon management legacies
Perring, Michael P. ; Bernhardt-Römermann, Markus ; Baeten, Lander ; Midolo, Gabriele ; Blondeel, Haben ; Depauw, Leen ; Landuyt, Dries ; Maes, Sybryn L. ; Lombaerde, Emiel De; Carón, Maria Mercedes ; Vellend, Mark ; Brunet, Jörg ; Chudomelová, Markéta ; Decocq, Guillaume ; Diekmann, Martin ; Dirnböck, Thomas ; Dörfler, Inken ; Durak, Tomasz ; Frenne, Pieter De; Gilliam, Frank S. ; Hédl, Radim ; Heinken, Thilo ; Hommel, Patrick ; Jaroszewicz, Bogdan ; Kirby, Keith J. ; Kopecký, Martin ; Lenoir, Jonathan ; Li, Daijiang ; Máliš, František ; Mitchell, Fraser J.G. ; Naaf, Tobias ; Newman, Miles ; Petřík, Petr ; Reczyńska, Kamila ; Schmidt, Wolfgang ; Standovár, Tibor ; Świerkosz, Krzysztof ; Calster, Hans Van; Vild, Ondřej ; Wagner, Eva Rosa ; Wulf, Monika ; Verheyen, Kris - \ 2018
Global Change Biology 24 (2018)4. - ISSN 1354-1013 - p. 1722 - 1740.
Biodiversity change - Climate change - Disturbance regime - ForestREplot - Herbaceous layer - Management intensity - Nitrogen deposition - Plant functional traits - Time lag - Vegetation resurvey
The contemporary state of functional traits and species richness in plant communities depends on legacy effects of past disturbances. Whether temporal responses of community properties to current environmental changes are altered by such legacies is, however, unknown. We expect global environmental changes to interact with land-use legacies given different community trajectories initiated by prior management, and subsequent responses to altered resources and conditions. We tested this expectation for species richness and functional traits using 1814 survey-resurvey plot pairs of understorey communities from 40 European temperate forest datasets, syntheses of management transitions since the year 1800, and a trait database. We also examined how plant community indicators of resources and conditions changed in response to management legacies and environmental change. Community trajectories were clearly influenced by interactions between management legacies from over 200 years ago and environmental change. Importantly, higher rates of nitrogen deposition led to increased species richness and plant height in forests managed less intensively in 1800 (i.e., high forests), and to decreases in forests with a more intensive historical management in 1800 (i.e., coppiced forests). There was evidence that these declines in community variables in formerly coppiced forests were ameliorated by increased rates of temperature change between surveys. Responses were generally apparent regardless of sites' contemporary management classifications, although sometimes the management transition itself, rather than historic or contemporary management types, better explained understorey responses. Main effects of environmental change were rare, although higher rates of precipitation change increased plant height, accompanied by increases in fertility indicator values. Analysis of indicator values suggested the importance of directly characterising resources and conditions to better understand legacy and environmental change effects. Accounting for legacies of past disturbance can reconcile contradictory literature results and appears crucial to anticipating future responses to global environmental change.
Impact of Changes in Groundwater Extractions and Climate Change on Groundwater-Dependent Ecosystems in a Complex Hydrogeological Setting
Engelenburg, Jolijn van; Hueting, Rosa ; Rijpkema, Sjoerd ; Teuling, Adriaan J. ; Uijlenhoet, Remko ; Ludwig, Fulco - \ 2018
Water Resources Management 32 (2018)1. - ISSN 0920-4741 - p. 259 - 272.
Climate change - Desiccation - Drinking water - Groundwater extraction - Groundwater resources - Hydrological modelling - Veluwe
Climate change and other future developments can influence the availability of groundwater resources for drinking water. The uncertainty of the projected impact is a challenge given the urgency to decide on adaptation measures to secure the drinking water supply. Improved understanding on how climate change affects the groundwater system is necessary to develop adaptation strategies. AZURE is used, a detailed, well-calibrated hydrological model to study the projected impact of climate change scenarios on the large Veluwe aquifer in the Netherlands. The Veluwe area is an important source of drinking water. However, some existing groundwater extractions in the area affect nearby groundwater-dependent ecosystems. Redistribution of the licensed extraction volumes of these sites is considered to reduce the impact on these ecosystems. The projected impact of climate change and redistribution to groundwater levels is studied. The research shows that in a slowly responding large aquifer the projected climate change may cause rising groundwater levels despite the projected increase in summer dryness. The results indicate that this impact may exceed the impact of redistribution of extraction volumes. In addition, it is shown that the combined effect strongly depends on local conditions, thus highlighting the need for high-resolution modelling.
Weed suppression greatly increased by plant diversity in intensively managed grasslands: a continental-scale experiment
Connolly, J. ; Sebastià, M.T. ; Kirwan, L. ; Finn, John A. ; Llurba, Rosa ; Suter, M. ; Collins, Rosemary P. ; Porqueddu, C. ; Helgadóttir, A. ; Baadshaug, Ole H. ; Bélanger, Gilles ; Black, A. ; Brophy, C. ; Čop, Jure ; Dalmannsdóttir, S. ; Delgado, I. ; Elgersma, A. ; Fothergill, M. ; Frankow-Lindberg, Bodil E. ; Ghesquiere, A. ; Golinski, P. ; Grieu, P. ; Gustavsson, A.M. ; Höglind, M. ; Huguenin-Elie, O. ; Jørgensen, M. ; Kadziuliene, Z. ; Lunnan, T. ; Nykanen-Kurki, P. ; Ribas, A. ; Taube, F. ; Thumm, U. ; Vliegher, A. de; Lüscher, A. - \ 2018
Journal of Applied Ecology 55 (2018)2. - ISSN 0021-8901 - p. 852 - 862.
1.Grassland diversity can support sustainable intensification of grassland production through increased yields, reduced inputs and limited weed invasion. We report the effects of diversity on weed suppression from three years of a 31-site continental-scale field experiment.

2.At each site, fifteen grassland communities comprising four monocultures and 11 4-species mixtures based on a wide range of species’ proportions were sown at two densities and managed by cutting. Forage species were selected according to two crossed functional traits, ‘method-of-nitrogen-acquisition’ and ‘pattern-of-temporal- development’.

3.Across sites, years, and sown densities, annual weed biomass in mixtures and monocultures was 0.5 and 2.0 t DM ha−1 (7% and 33% of total biomass respectively). Over 95% of mixtures had weed biomass lower than the average of monocultures, and, in two thirds of cases, lower than in the most suppressive monoculture (transgressive suppression). Suppression was significantly transgressive for 58% of site-years. Transgressive suppression by mixtures was maintained across years, independent of site productivity.

4.Based on models, average weed biomass in mixture over the whole experiment was 52% less (95% confidence interval 30% to 75%) than in the most suppressive monoculture. Transgressive suppression of weed biomass was significant at each year across all mixtures and for each mixture.

5.Weed biomass was consistently low across all mixtures and years and was in some cases significantly but not largely different from that in the equiproportional mixture. The average variability (standard deviation) of annual weed biomass within a site was much lower for mixtures (0.42) than for monocultures (1.77).

6.Synthesis and applications. Weed invasion can be diminished through a combination of forage species selected for complementarity and persistence traits in systems designed to reduce reliance on fertilizer nitrogen. In this study, effects of diversity on weed suppression were consistently strong across mixtures varying widely in species proportions and over time. The level of weed biomass did not vary greatly across mixtures varying widely in proportions of sown species. These diversity benefits in intensively managed grasslands are relevant for the sustainable intensification of agriculture and, importantly, are achievable through practical farm-scale actions.
Major satellite repeat RNA stabilize heterochromatin retention of Suv39h enzymes by RNA-nucleosome association and RNA : DNA hybrid formation
Camacho, Oscar Velazquez ; Galan, Carmen ; Swist-Rosowska, Kalina ; Ching, Reagan ; Gamalinda, Michael ; Karabiber, Fethullah ; La Rosa-Velazquez, Inti De; Engist, Bettina ; Koschorz, Birgit ; Shukeir, Nicholas ; Onishi-Seebacher, Megumi ; De Nobelen, Suzanne Van; Jenuwein, Thomas - \ 2017
eLife 6 (2017). - ISSN 2050-084X
The Suv39h1 and Suv39h2 histone lysine methyltransferases are hallmark enzymes at mammalian heterochromatin. We show here that the mouse Suv39h2 enzyme differs from Suv39h1 by containing an N-terminal basic domain that facilitates retention at mitotic chromatin and provides an additional affinity for major satellite repeat RNA. To analyze an RNA-dependent interaction with chromatin, we purified native nucleosomes from mouse ES cells and detect that Suv39h1 and Suv39h2 exclusively associate with poly-nucleosomes. This association was attenuated upon RNaseH incubation and entirely lost upon RNaseA digestion of native chromatin. Major satellite repeat transcripts remain chromatin-associated and have a secondary structure that favors RNA:DNA hybrid formation. Together, these data reveal an RNA-mediated mechanism for the stable chromatin interaction of the Suv39h KMT and suggest a function for major satellite noncoding RNA in the organization of an RNA-nucleosome scaffold as the underlying structure of mouse heterochromatin.
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