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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Genera of phytopathogenic fungi : GOPHY 2
Marin-Felix, Y. ; Hernández-Restrepo, Margarita ; Wingfield, M.J. ; Akulov, A. ; Carnegie, A.J. ; Cheewangkoon, R. ; Gramaje, D. ; Groenewald, J.Z. ; Guarnaccia, V. ; Halleen, F. ; Lombard, L. ; Luangsa-ard, J. ; Marincowitz, S. ; Moslemi, A. ; Mostert, L. ; Quaedvlieg, W. ; Schumacher, R.K. ; Spies, C.F.J. ; Thangavel, R. ; Taylor, P.W.J. ; Wilson, A.M. ; Wingfield, B.D. ; Wood, A.R. ; Crous, P.W. - \ 2019
Studies in Mycology 92 (2019). - ISSN 0166-0616 - p. 47 - 133.
26 new taxa - DNA barcodes - Fungal systematics - Six new typifications

This paper represents the second contribution in the Genera of Phytopathogenic Fungi (GOPHY) series. The series provides morphological descriptions and information regarding the pathology, distribution, hosts and disease symptoms for the treated genera. In addition, primary and secondary DNA barcodes for the currently accepted species are included. This second paper in the GOPHY series treats 20 genera of phytopathogenic fungi and their relatives including: Allantophomopsiella, Apoharknessia, Cylindrocladiella, Diaporthe, Dichotomophthora, Gaeumannomyces, Harknessia, Huntiella, Macgarvieomyces, Metulocladosporiella, Microdochium, Oculimacula, Paraphoma, Phaeoacremonium, Phyllosticta, Proxypiricularia, Pyricularia, Stenocarpella, Utrechtiana and Wojnowiciella. This study includes the new genus Pyriculariomyces, 20 new species, five new combinations, and six typifications for older names.

Legume abundance along successional and rainfall gradients in Neotropical forests
Gei, Maga ; Rozendaal, Danaë M.A. ; Poorter, Lourens ; Bongers, Frans ; Sprent, Janet I. ; Garner, Mira D. ; Aide, T.M. ; Andrade, José Luis ; Balvanera, Patricia ; Becknell, Justin M. ; Brancalion, Pedro H.S. ; Cabral, George A.L. ; César, Ricardo Gomes ; Chazdon, Robin L. ; Cole, Rebecca J. ; Colletta, Gabriel Dalla ; Jong, Ben De; Denslow, Julie S. ; Dent, Daisy H. ; Dewalt, Saara J. ; Dupuy, Juan Manuel ; Durán, Sandra M. ; Espírito Santo, Mário Marcos Do; Fernandes, G.W. ; Nunes, Yule Roberta Ferreira ; Finegan, Bryan ; Moser, Vanessa Granda ; Hall, Jefferson S. ; Hernández-Stefanoni, José Luis ; Junqueira, André B. ; Kennard, Deborah ; Lebrija-Trejos, Edwin ; Letcher, Susan G. ; Lohbeck, Madelon ; Marín-Spiotta, Erika ; Martínez-Ramos, Miguel ; Meave, Jorge A. ; Menge, Duncan N.L. ; Mora, Francisco ; Muñoz, Rodrigo ; Muscarella, Robert ; Ochoa-Gaona, Susana ; Orihuela-Belmonte, Edith ; Ostertag, Rebecca ; Peña-Claros, Marielos ; Pérez-García, Eduardo A. ; Piotto, Daniel ; Reich, Peter B. ; Reyes-García, Casandra ; Rodríguez-Velázquez, Jorge ; Romero-Pérez, I.E. ; Sanaphre-Villanueva, Lucía ; Sanchez-Azofeifa, Arturo ; Schwartz, Naomi B. ; Almeida, Arlete Silva De; Almeida-Cortez, Jarcilene S. ; Silver, Whendee ; Souza Moreno, Vanessa De; Sullivan, Benjamin W. ; Swenson, Nathan G. ; Uriarte, Maria ; Breugel, Michiel Van; Wal, Hans Van Der; Veloso, Maria Das Dores Magalhães ; Vester, Hans F.M. ; Vieira, Ima Célia Guimarães ; Zimmerman, Jess K. ; Powers, Jennifer S. - \ 2018
Nature Ecology & Evolution 2 (2018)7. - ISSN 2397-334X - p. 1104 - 1111.
The nutrient demands of regrowing tropical forests are partly satisfied by nitrogen-fixing legume trees, but our understanding of the abundance of those species is biased towards wet tropical regions. Here we show how the abundance of Leguminosae is affected by both recovery from disturbance and large-scale rainfall gradients through a synthesis of forest inventory plots from a network of 42 Neotropical forest chronosequences. During the first three decades of natural forest regeneration, legume basal area is twice as high in dry compared with wet secondary forests. The tremendous ecological success of legumes in recently disturbed, water-limited forests is likely to be related to both their reduced leaflet size and ability to fix N2, which together enhance legume drought tolerance and water-use efficiency. Earth system models should incorporate these large-scale successional and climatic patterns of legume dominance to provide more accurate estimates of the maximum potential for natural nitrogen fixation across tropical forests.
Optimizing air flow distribution in maritime refrigerated containers
Lukasse, L.J.S. ; Staal, M.G. - \ 2018
In: 8th International Postharvest Symposium. - International Society for Horticultural Science (Acta Horticulturae ) - ISBN 9789462611900 - p. 1391 - 1398.
Cover - Gradient - Homogeneity - Reefer - T-bar - Temperature - Uniformity
Ever more intercontinental fruit transport takes place in reefer containers. The global installed fleet of 40 ft high cube reefer containers counts approximately 1,000,000 units. The reefer market has generally realized a compound annual growth (CAGR) of 5%. Product temperature requirements are very tight for highly temperature-sensitive fruit like grape and kiwi. Another application where temperature requirements are particularly tight is in cold treatment shipments, required as a quarantine measure by authorities of importing countries. In cold treatment shipments it is often hard to maintain the warmest product temperature below the regulatory imposed treatment limit, without causing chilling injury in the cold spots. Temperature gradients are reduced by good air flow distribution. T-bars make up the air ducts of reefer containers. Unfortunately most air escapes from the ducts before reaching the container door-end if no further measures are taken. An appropriate T-floor cover could help to guide more air to the locations where it is needed most. This paper reports on an experimental study with the aim to design an optimised T-floor cover and assess its effect on fruit temperature distribution. In a series of climate chamber tests it is investigated how temperature gradients are affected by four different T-bar cover designs. During the tests the container is stuffed with palletized empty cartons, with zero autonomous heat production. The results show clear positive effects of T-bar covers. The best of the four covers is non-perforated, of a trapezoidal-like shape, installed in the container with the narrowest end towards the door-end. It reduces the temperature difference between warmest and coldest measurement location by nearly 50%, and also accelerates temperature recovery after a power off period. In view of the promising results it is recommended to follow-up with real transport tests.
Apples from Monalisa – Biological variation of firmness behaviour in storage and shelf life
Tijskens, L.M.M. ; Schouten, R.E. ; Zanella, A. ; Sadar, N. - \ 2018
In: 8th International Postharvest Symposium. - International Society for Horticultural Science (Acta Horticulturae ) - ISBN 9789462611900 - p. 1415 - 1420.
Attitude - CA storage - Crop load - Probelation - Quantile regression - Shelf-life
Apples are long-term stored in quite similar CA conditions, expecting the behaviour during that storage to be the similar for all apples, only affected by cultivar and picking time. The aim of this study, within the Monalisa project, is the effect of growing conditions on the firmness behaviour of apples during postharvest CA storage and shelf-life. Apples of two cultivars (‘Braeburn’, ‘Kanzi’) were harvested from four orchards (different altitudes and different crop loads) and stored in commercial CA storage for nine months. Samples of 30 apples were taken from CA storage every one or two months and subjected to storage at room temperature. Apples were assessed on firmness shelf-life. Firmness measurements were carried out using the (destructive) puncture test and the (non-destructive) Aweta firmness meter. The first and overwhelming outcome of this study is the huge variation in firmness and the almost absence of firmness decrease of ‘Kanzi’ apples both during CA and shelf-life. The huge variation was tackled by novel statistical analysis techniques (probelation, quantile regression) and assuming a logistic behaviour. Data sets were analysed including the biological variation between individual fruit with explained variation (R2 adj) often over 90%. Only minor effects of the CA duration on the rate of firmness loss during shelf life could be indicated. Altitude has a major effect on the level of firmness while crop load has less effect. Likely, higher altitudes result in lower growing temperatures and therefore in a lower rate of cell division during the early growth phase, which results in smaller and firmer apples. Crop load likely affects the amount of available photo assimilates per fruit. Higher crop load results therefore in smaller and firmer apples. These results clearly show that, up to now, the huge biological variation in the orchard prohibited progress in orchard dependant storage management.
Techniques to assess biological variation in destructive data
Tijskens, L.M.M. ; Schouten, R.E. ; Jongbloed, G. ; Konopacki, P.J. - \ 2018
In: 8th International Postharvest Symposium. - International Society for Horticultural Science (Acta Horticulturae ) - ISBN 9789462611900 - p. 1383 - 1390.
Biological variation - Cross-sectional data - Non-destructive data - Technical variation
Variation is present in all measured data, due to variation between individuals (biological variation) and variation induced by the measuring system (technical variation). Biological variation present in experimental data is not the result of a random process but strictly subject to deterministic rules as found on non-destructive data. The majority of data obtained in research are obtained by destructive techniques. The rules on behaviour and magnitude of variation should however, also apply to these cross sectional data. New techniques have been developed for analysing cross sectional data including the assessment of variation: 1) Probelation. In a set of cross-sectional data, the individual with the highest value at some point in time will resemble the individual with the highest value at previous or future times, and the second highest the second highest at previous times, and so on. One can assign an identification number based on the sorted order of the measured values per measuring point in time. This number can be used as a pseudo fruit number in indexed or mixed effects regression analysis, similar to the data analysis of longitudinal data; 2) Density assessment. For not too complex kinetic processes the density function can be deduced. Measuring a large number of individuals (on a single point in time) provides the possibility to assess directly the variation in the data; 3) Quantile regression. This technique also relies on ranking the data per measuring time. The probelation number is now converted into a probability, and the mean and standard deviation is estimated directly along with the kinetic parameter, using simple non-linear regression. Based on simulated data sets, all three techniques are demonstrated, and the results compared with the input values. Explained parts (R2 adj) obtained are generally well over 90%, provided that the technical variation is not excessively large.
Scaling-up biofortified beans high in iron and zinc through the school-feeding program : A sensory acceptance study with schoolchildren from two departments in southwest Colombia
Beintema, Joni J.S. ; Gallego-Castillo, Sonia ; Londoño-Hernandez, Luis F. ; Restrepo-Manjarres, José ; Talsma, Elise F. - \ 2018
Food Science and Nutrition 6 (2018)4. - ISSN 2048-7177 - p. 1138 - 1145.
Beans - Biofortification - Colombia - Micronutrients - Sensory acceptability
Iron and zinc deficiencies are global health problems, affecting mostly pregnant women and young children. In 2016, biofortified iron and zinc beans were introduced in Colombia. The incorporation of biofortified beans into the national school-feeding program could facilitate adoption and potentially improve the nutritional status of large populations. However, biofortified beans have to be accepted in order to be consumed by populations. We therefore studied the sensory acceptability of two biofortified beans, BIO-101 and BIO-107, and local beans at schools with free feeding services in two departments of southwest Colombia. Measured on a five-point Likert scale, the mean overall scores were 3.88 ± 0.64, 3.79 ± 0.74, and 3.81 ± 0.76, for BIO-101, BIO-107, and the local bean varieties, respectively, without significant differences. The children in Piendamó (Cauca) slightly preferred BIO-107 over the local bean (p < .05) based on color, smell, and taste. The children in Caicedonia (Valle del Cauca) slightly favored the local bean over BIO-107 (p < .05), regarding size, smell, and taste. Overall acceptability in schoolchildren was good for all beans without significant differences. This study advocates incorporation of accepted biofortified beans in the school-feeding program, in order to reach large groups of schoolchildren and potentially improve their nutritional statuses.
Micropollutant removal from black water and grey water sludge in a UASB-GAC reactor
Butkovskyi, A. ; Sevenou, L. ; Meulepas, R.J.W. ; Hernandez Leal, L. ; Zeeman, G. ; Rijnaarts, H.H.M. - \ 2018
Water Science and Technology 77 (2018)4. - ISSN 0273-1223 - p. 1137 - 1148.
Activated carbon - Black water - Grey water sludge - Micropollutants - UASB reactor
The effect of granular activated carbon (GAC) addition on the removal of diclofenac, ibuprofen, metoprolol, galaxolide and triclosan in a up-flow anaerobic sludge blanket (UASB) reactor was studied. Prior to the reactor studies, batch experiments indicated that addition of activated carbon to UASB sludge can decrease micropollutant concentrations in both liquid phase and sludge. In continuous experiments, two UASB reactors were operated for 260 days at an HRT of 20 days, using a mixture of source separated black water and sludge from aerobic grey water treatment as influent. GAC (5.7 g per liter of reactor volume) was added to one of the reactors on day 138. No significant difference in COD removal and biogas production between reactors with and without GAC addition was observed. In the presence of GAC, fewer micropollutants were washed out with the effluent and a lower accumulation of micropollutants in sludge and particulate organic matter occurred, which is an advantage in micropollutant emission reduction from wastewater. However, the removal of micropollutants by adding GAC to a UASB reactor would require more activated carbon compared to effluent post-treatment. Additional research is needed to estimate the effect of bioregeneration on the lifetime of activated carbon in a UASB-GAC reactor.
Force and Scale Dependence of the Elasticity of Self-Assembled DNA Bottle Brushes
Rocha, Márcio Santos ; Storm, Ingeborg M. ; Bazoni, Raniella Falchetto ; Ramos, Ésio Bessa ; Hernandez-Garcia, Armando ; Cohen Stuart, Martien A. ; Leermakers, Frans ; Vries, Renko De - \ 2018
Macromolecules 51 (2018)1. - ISSN 0024-9297 - p. 204 - 212.
As a model system to study the elasticity of bottle-brush polymers, we here introduce self-assembled DNA bottle brushes, consisting of a DNA main chain that can be very long and still of precisely defined length, and precisely monodisperse polypeptide side chains that are physically bound to the DNA main chains. Polypeptide side chains have a diblock architecture, where one block is a small archaeal nucleoid protein Sso7d that strongly binds to DNA. The other block is a net neutral, hydrophilic random coil polypeptide with a length of exactly 798 amino acids. Light scattering shows that for saturated brushes the grafting density is one side chain per 5.6 nm of DNA main chain. According to small-angle X-ray scattering, the brush diameter is D = 17 nm. By analyzing configurations of adsorbed DNA bottle brushes using AFM, we find that the effective persistence of the saturated DNA bottle brushes is Peff = 95 nm, but from force-extension curves of single DNA bottle brushes measured using optical tweezers we find Peff = 15 nm. The latter is equal to the value expected for DNA coated by the Sso7d binding block alone. The apparent discrepancy between the two measurements is rationalized in terms of the scale dependence of the bottle-brush elasticity using theory previously developed to analyze the scale-dependent electrostatic stiffening of DNA at low ionic strengths.
Calcium addition to increase the production of phosphate granules in anaerobic treatment of black water
Cunha, Jorge Ricardo ; Schott, Chris ; Weijden, Renata D. van der; Leal, Lucía Hernández ; Zeeman, Grietje ; Buisman, Cees - \ 2018
Water Research 130 (2018). - ISSN 0043-1354 - p. 333 - 342.
Anaerobic treatment - Black water - Calcium phosphate - Phosphate recovery - UASB reactor
Simultaneous recovery of calcium phosphate granules (CaP granules) and methane from vacuum collected black water (BW), using an upflow anaerobic sludge blanket (UASB) reactor was previously investigated. It was calculated that only 2% of the total phosphorus (P) fed was present as CaP granules whereas 51% of the P accumulated dispersed in the reactor, limiting the applicability of this process for recovery of phosphate. This study proposes adding calcium to increase the P accumulation in the reactor and the production of CaP granules. Calcium was added in a lab-scale UASB reactor fed with BW. An identical UASB reactor was used as reference, to which no calcium was added. The treatment performance was evaluated by weekly monitoring of influent, effluent and produced biogas. Sludge bed development and CaP granulation were assessed through particle size analysis. The composition and structure of CaP granules were chemically and optically assessed. Calcium addition increased accumulation of P in the reactor and formation and growth of granules with size > 0.4 mm diameter (CaP granules). Moreover, with calcium addition, CaP granules contained 5.6 ± 1.5 wt% of P, while without calcium a lower P content was observed (3.7 ± 0.3 wt%). By adding Ca, 89% of the incoming P from BW accumulated in the reactor and 31% was sampled as CaP granules (> 0.4 mm diameter). Addition of 250 mgCa L−1 of BW was the optimum loading found in this study. Furthermore, no significant reduction in CODTotal removal (> 80%) and CH4 production (0.47 ± 0.10 gCOD-CH4 g−1CODTotal-BW) was observed. Therefore, adding calcium can significantly increase the CaP granulation without inhibiting the simultaneous CH4 recovery. This further indicates the potential of this process for phosphate recovery.
Simultaneous recovery of calcium phosphate granules and methane in anaerobic treatment of black water : Effect of bicarbonate and calcium fluctuations
Cunha Costa, J.M.R. da; Tervahauta, T. ; Weijden, R.D. van der; Hernández Leal, L. ; Zeeman, G. ; Buisman, C.J.N. - \ 2018
Journal of Environmental Management 216 (2018). - ISSN 0301-4797 - p. 399 - 405.
Calcium phosphate recovery - Granules - Methane - Source separated black water - UASB reactor
Calcium phosphate (CaP) granules were discovered in the anaerobic treatment of vacuum collected black water (BW), using upflow anaerobic sludge blanket (UASB) technology. This allows simultaneous recovery of CaP granules and methane in the UASB reactor. However, the role of BW composition on CaP granulation is not yet understood. Moreover, CaP granulation was not observed in previous research on anaerobic treatment of BW, although similar treatment conditions were applied. Therefore, this study shows specifically the influence of bicarbonate and calcium fluctuations in BW on the phosphorus accumulation in the UASB reactor, which directly affects CaP granulation. Without calcium addition, 5% of the total phosphorus (P) fed was found as CaP granules in the reactor (61 mgP g-1dried matter), after 260 days of operation. Simultaneously, 65% of the COD in BW was efficiently converted into methane at 25 °C. Variations of bicarbonate and calcium concentrations in raw BW showed a significant influence on phosphorus accumulation in the UASB reactor. Geochemical modelling showed that the increase of soluble calcium from 39 to 54 mg L-1 in BW triggers supersaturation for calcium phosphate precursors (Cax(PO4)y). Concurrently, bicarbonate decreased from 2.7 to 1.2 g L-1, increasing further the ionic activity of calcium. Formation and accumulation of seed particles possibly enhanced CaP granulation. Preliminary results showed that addition of calcium (Ca2+/PO4 3- molar ratio of 3) increased the accumulation of total P in the UASB reactor to more than 85%. This further increases the granulation rate and consequently, the process feasibility.
Removal of emerging organic contaminants in a poplar vegetation filter
Martínez Hernández, V. ; Lealb, M. ; Meffe, R. ; Miguel Garcia, Angel de; Alonso-Alonso, C. ; Bustamante, I. de; Lillo, J. ; Martín, I. ; Salas, J.J. - \ 2018
Journal of Hazardous Materials 342 (2018). - ISSN 0304-3894 - p. 482 - 491.
Emerging organic contaminants - Groundwater - Unsaturated zone - Vegetation filter - Wastewater treatment

Vegetation filters (VFs), a type of land application system, are a robust technology based on natural treatment mechanisms for the removal of wastewater contaminants. Their capacity to attenuate emerging organic contaminants (EOCs) has not yet been evaluated. The present study reports the results of a 2-year EOC monitoring carried out using a poplar VF receiving wastewater primarily treated by an Imhoff tank. The compounds selected included analgesics, a β-adrenergic blocker, stimulants, an anticonvulsant, an anti-depressant, an anti-inflammatory, an antibiotic and analgesic and stimulant metabolites. EOCs were analysed in the Imhoff tank effluent, in the infiltrated water at a depth of 90 cm and in the groundwater at a depth of 10 m. The results demonstrated that EOC attenuation was more significant in the first 90 cm than in the rest of the soil profile. The removal efficiency for all of the selected EOCs was higher than 90% with the exception of ketoprofen, which may pose a higher threat of groundwater contamination. The observed attenuation correlated with the hydrophobicity and charge state of the EOCs. The higher persistence of the metabolites 4-AAA and 4-FAA shows that progression in the degradation pathway does not always imply a mitigation of contamination.

Templated co-assembly into nanorods of polyanions and artificial virus capsid proteins
Hernandez-Garcia, A. ; Cohen Stuart, M.A. ; Vries, R. De - \ 2017
Soft Matter 14 (2017)1. - ISSN 1744-683X - p. 132 - 139.
Recombinant triblock polypeptides C-Sn-B, where C is a 400 amino acid long hydrophilic random coil block, Sn is a multimer of the silk-like octapeptide S = (GAGAGAGQ), and B = K12 is an oligolysine, have previously been shown to encapsulate double stranded DNA into rod-shaped, virus-like particles. In order to gain insight of the co-assembly process, and in order to be able to use these proteins for templating other types of nanorods, we here explore their co-assembly with a range of polyanionic templates: poly(acrylic acids) (PAA) of a wide range of lengths, poly(styrene sulphonate) (PSS) and the stiff anionic polysaccharide xanthan. The formation of the complexes was characterized using Dynamic Light Scattering (DLS), cryogenic Transmission Electronic Microscopy (Cryo-TEM) and Atomic Force Microscopy (AFM). Except at very high molar masses, we find that flexible anionic PAA and PSS lead to co-assembly of proteins with single polyanion chains into nanorods, with a packing factor as expected on the basis of charge stochiometry. Only for very long PAA templates (8 × 105 Da) we find evidence for heterogeneous complexes with thin and thick sections. For the very stiff xanthan chains, we find that its stiffness precludes co-assembly with the artificial viral capsid proteins into condensed and regular nanorods. Given the simple and robust formation of rod-like structures with a range of polyanionic templates, we anticipate that the artificial virus proteins will be useful for preparing high-aspect ratio nanoparticles and scaffolds of precise size and find applications in nanotechnology and materials science for which currently natural rod-like viruses are being explored.
Scientific Opinion addressing the state of the science on risk assessment of plant protection products for in-soil organisms
Ockleford, C. ; Adriaanse, P.I. ; Berny, P. ; Brock, T.C.M. ; Duquesne, S. ; Grilli, S. ; Hernandez-Jerez, A.F. ; Hougaard Bennekou, S. ; Klein, M. ; Kuhl, T. - \ 2017
EFSA Journal 15 (2017)2. - 225 p.
Following a request from EFSA, the Panel on Plant Protection Products and their Residues developed an opinion on the science behind the risk assessment of plant protection products for in-soil organisms. The current risk assessment scheme is reviewed, taking into account new regulatory frameworks and scientific developments. Proposals are made for specific protection goals for in-soil organisms being key drivers for relevant ecosystem services in agricultural landscapes such as nutrient cycling, soil structure, pest control and biodiversity. Considering the time-scales and biological processes related to the dispersal of the majority of in-soil organisms compared to terrestrial non-target arthropods living above soil, the Panel proposes that in-soil environmental risk assessments are made at in- and off-field scale considering field boundary levels. A new testing strategy which takes into account the relevant exposure routes for in-soil organisms and the potential direct and indirect effects is proposed. In order to address species recovery and long-term impacts of PPPs, the use of population models is also proposed.
Are forest disturbances amplifying or canceling out climate change-induced productivity changes in European forests?
Reyer, Christopher Paul Oliver ; Bathgate, Stephan ; Blennow, K. ; Borges, J.G. ; Bugmann, Harald ; Delzon, Sylvain ; Faias, Sonia P. ; Garcia-Gonzalo, Jordi ; Gardiner, Barry ; Gonzalez-Olabarria, J.R. ; Gracia, Carlos ; Guerra Hernandez, Jordi ; Kellomaki, Seppo ; Kramer, K. ; Lexer, M.J. ; Lindner, Marcus ; Maaten, Ernest van der; Maroschek, M. ; Muys, Bart ; Nicoll, B. ; Palahi, M. ; Palma, J.H.N. ; Paulo, Joana A. ; Peltola, H. ; Pukkala, T. ; Rammer, W. ; Ray, D. ; Sabaté, S. ; Schelhaas, M. ; Seidl, R. ; Temperli, Christian ; Tomé, Margarida ; Yousefpour, R. ; Zimmerman, N.E. ; Hanewinkel, Marc - \ 2017
Environmental Research Letters 12 (2017)3. - ISSN 1748-9326
Recent studies projecting future climate change impacts on forests mainly consider either the effects of climate change on productivity or on disturbances. However, productivity and disturbances are intrinsically linked because 1) disturbances directly affect forest productivity (e.g. via a reduction in leaf area, growing stock or resource-use efficiency), and 2) disturbance susceptibility is often coupled to a certain development phase of the forest with productivity determining the time a forest is in this specific phase of susceptibility. The objective of this paper is to provide an overview of forest productivity changes in different forest regions in Europe under climate change, and partition these changes into effects induced by climate change alone and by climate change and disturbances. We present projections of climate change impacts on forest productivity from state-of-the-art forest models that dynamically simulate forest productivity and the effects of the main European disturbance agents (fire, storm, insects), driven by the same climate scenario in seven forest case studies along a large climatic gradient throughout Europe. Our study shows that, in most cases, including disturbances in the simulations exaggerate ongoing productivity declines or cancel out productivity gains in response to climate change. In fewer cases, disturbances also increase productivity or buffer climate-change induced productivity losses, e.g. because low severity fires can alleviate resource competition and increase fertilization. Even though our results cannot simply be extrapolated to other types of forests and disturbances, we argue that it is necessary to interpret climate change-induced productivity and disturbance changes jointly to capture the full range of climate change impacts on forests and to plan adaptation measures.
Multiscale scenarios for nature futures
Rosa, Isabel M.D. ; Pereira, Henrique Miguel ; Ferrier, Simon ; Alkemade, J.R.M. ; Acosta, Lilibeth A. ; Resit Akcakaya, H. ; Belder, E. den; Fazel, Asghar M. ; Fujimori, Shinichiro ; Harfoot, Mike ; Harhash, Khaled A. ; Harrison, Paula A. ; Hauck, Jennifer ; Hendriks, Rob J.J. ; Hernández, Gladys ; Jetz, Walter ; Karlsson-Vinkhuyzen, S.I.S.E. ; Kim, Hyejin ; King, Nicholas ; Kok, Marcel ; Kolomytsev, Grygoriy O. ; Lazarova, Tanya ; Leadley, Paul ; Lundquist, Carolyn J. ; García Márquez, Jaime ; Meyer, Carsten ; Navarro, Laetitia M. ; Nesshöver, Carsten ; Ngo, Hien T. ; Ninan, Karachepone N. ; Palomo, Maria G. ; Pereira, Laura ; Peterson, G.D. ; Pichs, Ramon ; Popp, Alexander ; Purvis, Andy ; Ravera, Federica ; Rondinini, Carlo ; Sathyapalan, Jyothis ; Schipper, Aafke ; Seppelt, Ralf ; Settele, Josef ; Sitas, Nadia ; Vuuren, D. van - \ 2017
Nature Ecology & Evolution 1 (2017)10. - ISSN 2397-334X - p. 1416 - 1419.
Targets for human development are increasingly connected with targets for nature, however, existing scenarios do not explicitly address this relationship. Here, we outline a strategy to generate scenarios centred on our relationship
with nature to inform decision-making at multiple scales.
Numerical simulation of the effect of different mulches on the heat storage capacity of a Mediterranean greenhouse soil
Baeza, E.J. ; Sapounas, A. ; Stanghellini, C. ; Bonachela CastaAo, S. ; Hernández, J. ; Montero, J.I. ; López, J.C. ; Granados, M.R. ; Muñoz, P. ; Lorenzo, P. ; Fernández-Del Olmo, P. - \ 2017
In: International Symposium on New Technologies and Management for Greenhouses - GreenSys2015 International Society for Horticultural Science (Acta Horticulturae ) - ISBN 9789462611665 - p. 119 - 127.
Black film - CFD - Sand - Semi-transparent film - Temperature
In the Mediterranean greenhouse areas, a large majority of growers rely on passive techniques to improve the microclimate of the greenhouse during the winter period, rather than using more expensive systems such as active heating. Some of these techniques such as different types of mulch (sand, plastic films, etc.) are used to improve the heat storage capacity of the greenhouse soil. A proper modeling of the role of the greenhouse soil a heat store would allow the verification of which techniques have a larger positive effect on the heat store capacity of the soil (i.e. type, color and thickness of the mulch, soil moisture content, etc.) and how to optimize their management by the grower. In recent years, CFD has been successfully used to model the greenhouse microclimate under very different scenarios, but little has been done to include in the simulations the role of passive techniques in the winter period microclimate, such as the role of the soil as a heat store. In the present work, a CFD model of a Mediterranean greenhouse and its soil has been developed, and the effect on the heat storage capacity of the soil as well as in the ambient of 2 different types of mulch (black plastic film, semi-transparent plastic film) was evaluated, by comparing the temperature measured at 4 different depths and ambient temperature (at two heights), during daytime period with the values provided by the model. The evolution of the temperatures at different soil depths followed the same pattern in both the experiments and the simulations. Good quantitative agreement was found between values predicted by the model and the measurements with differences being always lower than 2°C.
Integrated QTL detection for key breeding traits in multiple peach progenies
Hernández Mora, José R. ; Micheletti, Diego ; Bink, Marco ; Weg, Eric Van de; Cantín, Celia ; Nazzicari, Nelson ; Caprera, Andrea ; Dettori, Maria Teresa ; Micali, Sabrina ; Banchi, Elisa ; Campoy, José Antonio ; Dirlewanger, Elisabeth ; Lambert, Patrick ; Pascal, Thierry ; Troggio, Michela ; Bassi, Daniele ; Rossini, Laura ; Verde, Ignazio ; Quilot-Turion, Bénédicte ; Laurens, François ; Arús, Pere ; Aranzana, Maria José - \ 2017
BMC Genomics 18 (2017). - ISSN 1471-2164 - 15 p.
FlexQTL - PBA - Peach breeding - Peach QTL - Pedigre-based Analysis

Background: Peach (Prunus persica (L.) Batsch) is a major temperate fruit crop with an intense breeding activity. Breeding is facilitated by knowledge of the inheritance of the key traits that are often of a quantitative nature. QTLs have traditionally been studied using the phenotype of a single progeny (usually a full-sib progeny) and the correlation with a set of markers covering its genome. This approach has allowed the identification of various genes and QTLs but is limited by the small numbers of individuals used and by the narrow transect of the variability analyzed. In this article we propose the use of a multi-progeny mapping strategy that used pedigree information and Bayesian approaches that supports a more precise and complete survey of the available genetic variability. Results: Seven key agronomic characters (data from 1 to 3 years) were analyzed in 18 progenies from crosses between occidental commercial genotypes and various exotic lines including accessions of other Prunus species. A total of 1467 plants from these progenies were genotyped with a 9 k SNP array. Forty-seven QTLs were identified, 22 coinciding with major genes and QTLs that have been consistently found in the same populations when studied individually and 25 were new. A substantial part of the QTLs observed (47%) would not have been detected in crosses between only commercial materials, showing the high value of exotic lines as a source of novel alleles for the commercial gene pool. Our strategy also provided estimations on the narrow sense heritability of each character, and the estimation of the QTL genotypes of each parent for the different QTLs and their breeding value. Conclusions: The integrated strategy used provides a broader and more accurate picture of the variability available for peach breeding with the identification of many new QTLs, information on the sources of the alleles of interest and the breeding values of the potential donors of such valuable alleles. These results are first-hand information for breeders and a step forward towards the implementation of DNA-informed strategies to facilitate selection of new cultivars with improved productivity and quality.

Virus-Like Particles of mRNA with Artificial Minimal Coat Proteins : Particle Formation, Stability, and Transfection Efficiency
Jekhmane, Shehrazade ; Haas, Rob De; Paulino Da Silva Filho, Omar ; Asbeck, Alexander H. van; Favretto, Marco Emanuele ; Hernandez Garcia, Armando ; Brock, Roland ; Vries, Renko De - \ 2017
Nucleic Acid Therapeutics 27 (2017)3. - ISSN 2159-3337 - p. 159 - 167.
mRNA delivery - self-assembly - Virus-like particles

RNA has enormous potential as a therapeutic, yet, the successful application depends on efficient delivery strategies. In this study, we demonstrate that a designed artificial viral coat protein, which self-assembles with DNA to form rod-shaped virus-like particles (VLPs), also encapsulates and protects mRNA encoding enhanced green fluorescent protein (EGFP) and luciferase, and yields cellular expression of these proteins. The artificial viral coat protein consists of an oligolysine (K12) for binding to the oligonucleotide, a silk protein-like midblock S10 = (GAGAGAGQ)10 that self-assembles into stiff rods, and a long hydrophilic random coil block C that shields the nucleic acid cargo from its environment. With mRNA, the C-S10-K12 protein coassembles to form rod-shaped VLPs each encapsulating about one to five mRNA molecules. Inside the rod-shaped VLPs, the mRNAs are protected against degradation by RNAses, and VLPs also maintain their shape following incubation with serum. Despite the lack of cationic surface charge, the mRNA VLPs transfect cells with both EGFP and luciferase, although with a much lower efficiency than obtained by a lipoplex transfection reagent. The VLPs have a negligible toxicity and minimal hemolytic activity. Our results demonstrate that VLPs yield efficient packaging and shielding of mRNA and create the basis for implementation of additional virus-like functionalities to improve transfection and cell specificity, such as targeting functionalities.

Engineered Diblock Polypeptides Improve DNA and Gold Solubility during Molecular Assembly
Estrich, Nicole A. ; Hernandez-Garcia, Armando ; Vries, Renko De; LaBean, Thomas H. - \ 2017
ACS Nano 11 (2017)1. - ISSN 1936-0851 - p. 831 - 842.
diblock polypeptide - directed self-assembly - DNA nanotechnology - molecular assembly - protein engineering - protein polymer - solution compatibilization

Programmed molecular recognition is being developed for the bionanofabrication of mixed organic/inorganic supramolecular assemblies for applications in electronics, photonics, and medicine. For example, DNA-based nanotechnology seeks to exploit the easily programmed complementary base-pairing of DNA to direct assembly of complex, designed nanostructures. Optimal solution conditions for bionanofabrication, mimicking those of biological systems, may involve high concentrations of biomacromolecules (proteins, nucleic acids, etc.) and significant concentrations of various ions (Mg2+, Na+, Cl-, etc.). Given a desire to assemble diverse inorganic components (metallic nanoparticles, quantum dots, carbon nanostructures, etc.), it will be increasingly difficult to find solution conditions simultaneously compatible with all components. Frequently, the use of chemical surfactants is undesirable, leaving a need for the development of alternative strategies. Herein, we discuss the use of artificial, diblock polypeptides in the role of solution compatibilizing agents for molecular assembly. We describe the use of two distinct diblock polypeptides with affinity for DNA in the stabilization of DNA origami and DNA-functionalized gold nanoparticles (spheres and rods) in solution, protection of DNA from enzymatic degradation, as well as two 3D tetrahedral DNA origamis. We present initial data showing that the diblock polypeptides promote the formation in the solution of desired organic/inorganic assemblies.

Micropollutants in source separated wastewater streams and recovered resources of source separated sanitation
Butkovskyi, A. ; Hernandez Leal, L. ; Zeeman, G. ; Rijnaarts, H.H.M. - \ 2017
Environmental Research 156 (2017). - ISSN 0013-9351 - p. 434 - 442.
Black water - Grey water - Micropollutants - Sludge - Struvite

The quality of anaerobic sludge and struvite from black water treatment system, aerobic sludge from grey water treatment system and effluents of both systems was assessed for organic micropollutant content in order to ensure safety when reusing these products. Use of anaerobic black water sludge and struvite as soil amendments is recommended based on the low micropollutant content. Aerobic grey water sludge is recommended for disposal, because of the relatively high micropollutant concentrations, exceeding those in sewage sludge. Effluents of black and grey water treatment systems require post-treatment prior to reuse, because the measured micropollutant concentrations in the effluents are above ecotoxicological thresholds.

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