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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Desiccation sensitive seeds: understanding their evolution, genetics and physiology
Correia Silva de Santana Marques, Alexandre - \ 2018
University. Promotor(en): Richard Immink, co-promotor(en): Henk Hilhorst; Wilco Ligterink. - Wageningen : Wageningen University - ISBN 9789463438599 - 189
Adaptation to climate change at local level in Europe: An overview
Aguiar, F.C. ; Bentz, J. ; Silva, J.M.N. ; Fonseca, A.L. ; Swart, R.J. ; Santos, F.D. ; Penha-Lopes, Gil - \ 2018
Environmental Science & Policy 86 (2018). - ISSN 1462-9011 - p. 38 - 63.
Europe’s climate change vulnerability pushes for initiatives such as the European Adaptation Strategy and the associated Covenant of Mayors for Climate and Energy. What are the triggers and barriers, for which sectors and for which risks and how is adaptation funded? This paper examines 147 Local Adaptation Strategies in Europe. Key triggers were incentives via research projects, implementation of EU policies and the increasing frequency of extreme climate events. Insufficient resources, capacity, political commitment and uncertainty were the main barriers. Prioritized sectors reflected the main local vulnerabilities - flood protection and water management, built environment and urban planning. Differing patterns of adaptation planning and adaptive capacity were identified among different regions in Europe. Large municipalities generally fund adaptation locally, whereas international and national funding appears to be more important for adaptation in less urban or densely populated territories. The database of LAS described in the present study can be expanded and used to increase the understanding of and promotion of local adaptation action in Europe and beyond.
Propagating annotations of molecular networks using in silico fragmentation
Silva, Ricardo R. da; Wang, Mingxun ; Nothias, Louis Félix ; Hooft, Justin J.J. van der; Caraballo-Rodríguez, Andrés Mauricio ; Fox, Evan ; Balunas, Marcy J. ; Klassen, Jonathan L. ; Lopes, Norberto Peporine ; Dorrestein, Pieter C. - \ 2018
PLoS Computational Biology 14 (2018)4. - ISSN 1553-734X

The annotation of small molecules is one of the most challenging and important steps in untargeted mass spectrometry analysis, as most of our biological interpretations rely on structural annotations. Molecular networking has emerged as a structured way to organize and mine data from untargeted tandem mass spectrometry (MS/MS) experiments and has been widely applied to propagate annotations. However, propagation is done through manual inspection of MS/MS spectra connected in the spectral networks and is only possible when a reference library spectrum is available. One of the alternative approaches used to annotate an unknown fragmentation mass spectrum is through the use of in silico predictions. One of the challenges of in silico annotation is the uncertainty around the correct structure among the predicted candidate lists. Here we show how molecular networking can be used to improve the accuracy of in silico predictions through propagation of structural annotations, even when there is no match to a MS/MS spectrum in spectral libraries. This is accomplished through creating a network consensus of re-ranked structural candidates using the molecular network topology and structural similarity to improve in silico annotations. The Network Annotation Propagation (NAP) tool is accessible through the GNPS web-platform https://gnps.ucsd.edu/ProteoSAFe/static/gnps-theoretical.jsp.

Erratum to “Investigation of Clostridium botulinum group III's mobilome content” [Anaerobe 49 (2018) 71–77]
Woudstra, Cédric ; Maréchal, Caroline Le; Souillard, Rozenn ; Anniballi, Fabrizio ; Auricchio, Bruna ; Bano, Luca ; Bayon-Auboyer, Marie Hélène ; Koene, Miriam ; Mermoud, Isabelle ; Brito, Roseane B. ; Lobato, Francisco C.F. ; Silva, Rodrigo O.S. ; Dorner, Martin B. ; Fach, Patrick - \ 2018
Anaerobe (2018). - ISSN 1075-9964
Genetic correlations between feed efficiency traits, and growth performance and carcass traits in purebred and crossbred pigs
Godinho, R.M. ; Bergsma, R. ; Silva, F.F. ; Sevillano, C.A. ; Knol, E.F. ; Lopes, M.S. ; Lopes, P.S. ; Bastiaansen, J.W.M. ; Guimarães, S.E.F. - \ 2018
Journal of Animal Science 96 (2018)3. - ISSN 0021-8812 - p. 817 - 829.
Breeding program - Carcass traits - Feed efficiency - Genetic correlations - Growing-Finishing pigs - Growth
Selection for feed efficiency (FE) is a strategy to reduce the production costs per unit of animal product, which is one of the major objectives of current animal breeding programs. In pig breeding, selection for FE and other traits traditionally takes place based on purebred pig (PB) performance at the nucleus level, while pork production typically makes use of crossbred animals (CB). The success of this selection, therefore, depends on the genetic correlation between the performance of PB and CB (rpc) and on the genetic correlation (rg) between FE and the other traits that are currently under selection. Different traits are being used to account for FE, but the rpc has been reported only for feed conversion rate. Therefore, this study aimed 1) to estimate the rpc for growth performance, carcass, and FE traits; 2) to estimate rg between traits within PB and CB populations; and 3) to compare three different traits representing FE: feed conversion rate, residual energy intake (REI), and residual feed intake (RFI). Phenotypes of 194,445 PB animals from 23 nucleus farms, and 46,328 CB animals from three farms where research is conducted under near commercial production conditions were available for this study. From these, 22,984 PB and 8,657 CB presented records for feed intake. The PB population consisted of five sire and four dam lines, and the CB population consisted of terminal cross-progeny generated by crossing sires from one of the five PB sire lines with commercially available two-way maternal sow crosses. Estimates of rpc ranged from 0.61 to 0.71 for growth performance traits, from 0.75 to 0.82 for carcass traits, and from 0.62 to 0.67 for FE traits. Estimates of rg between growth performance, carcass, and FE traits differed within PB and CB. REI and RFI showed substantial positive rg estimates in PB (0.84) and CB (0.90) populations. The magnitudes of rpc estimates indicate that genetic progress is being realized in CB at the production level from selection on PB performance at nucleus level. However, including CB phenotypes recorded on production farms, when predicting breeding values, has the potential to increase genetic progress for these traits in CB. Given the genetic correlations with growth performance traits and the genetic correlation between the performance of PB and CB, REI is an attractive FE parameter for a breeding program.
Effects of rumen-undegradable protein on intake, performance, and mammary gland development in prepubertal and pubertal dairy heifers
Silva, A.L. ; Detmann, E. ; Dijkstra, J. ; Pedroso, A.M. ; Silva, L.H.P. ; Machado, A.F. ; Sousa, F.C. ; Santos, G.B. dos; Marcondes, M.I. - \ 2018
Journal of Dairy Science (2018). - ISSN 0022-0302
growth - mammary gland ultrasound - nitrogen retention
The objective of this study was to evaluate the influence of different amounts of rumen-undegradable protein (RUP) on intake, N balance, performance, mammary gland development, carcass traits, and hormonal status of Holstein heifers at different physiological stages (PS). Sixteen prepubertal (PRE) heifers (initial BW = 106 ± 7.6 kg; age = 4.3 ± 0.46 mo) and 16 pubertal (PUB) heifers (initial BW = 224 ± 7.9 kg; age = 12.6 ± 0.45 mo) were used in an experiment over a period of 84 d. Four diets with increasing RUP contents (38, 44, 51, and 57% of dietary crude protein) and heifers at 2 PS (PRE or PUB) were used in a 4 × 2 factorial arrangement of treatments in a completely randomized design. Throughout the experiment, 2 digestibility trials were performed over 5 consecutive days (starting at d 36 and 78) involving feed and ort sampling and spot collections of feces and urine. At d 0 and 83, body ultrasound images were obtained for real-time carcass trait evaluation. The mammary gland was ultrasonically scanned at d 0 and every 3 wk during the experiment. Blood samples were taken at d 0 and 84 to determine serum concentrations of progesterone, estrogen, insulin-like growth factor I (IGF-I), and insulin. No interaction between PS and the level of RUP was found for any trait. Apparent digestibility of dry matter, organic matter, and neutral detergent fiber corrected for ash and protein was not affected by RUP level but was lower for PRE compared with PUB heifers. Sorting against neutral detergent fiber corrected for ash and protein (tendency only) and for crude protein was greater for PUB than PRE heifers. Pubertal heifers had greater average daily gain (905 vs. 505 g/d) and N retention (25.9 vs. 12.5 g/d) than PRE heifers. In addition, average daily gain and N retention were greatest at 51% RUP of dietary protein. Mammary ultrasonography indicated no effects of RUP amounts on mammary gland composition, whereas PRE heifers had greater pixel values than PUB, indicating higher contents of fat rather than protein in the mammary glands of PRE heifers. Serum progesterone and IGF-I concentration was affected only by PS, and PRE heifers had greater values of progesterone and IGF-I concentrations than PUB heifers. Serum insulin concentration was unaffected by PS but tended to be higher at 51% of RUP. In conclusion, an RUP level of 51% increases body weight, average daily gain, feed efficiency, and N retention in heifers regardless of the PS. In addition, PRE heifers have a lower sorting ability and reduced intake, total-tract digestibility, and N retention. They also have higher amounts of fat in their mammary glands, even at moderate growth rates.
Relationship between the estimated breeding values for litter traits at birth and ovarian and embryonic traits and their additive genetic variance in gilts at 35 days of pregnancy
Silva, Carolina L.A. Da; Mulder, Han A. ; Broekhuijse, Marleen L.W.J. ; Kemp, Bas ; Soede, Nicoline M. ; Knol, Egbert F. - \ 2018
Frontiers in Genetics 9 (2018)APR. - ISSN 1664-8021
Corpora lutea weight - Embryo - Gilts - Ovulation rate - Precision phenotyping
We investigated (1) the relationship between the estimated breeding values (EBVs) for litter traits at birth and ovulation rate (OR), average corpora luteal weight, uterine length and embryonic survival and development traits in gilts at 35 days of pregnancy by linear regression, (2) the genetic variance of OR, average corpora lutea (CL) weight, uterine length and embryonic survival and development traits at 35 days of pregnancy, and (3) the genetic correlations between these traits. Landrace (n = 86) and Yorkshire × Landrace (n = 304) gilts were inseminated and slaughtered at 35 days of pregnancy. OR was assessed by dissection of the CL on both ovaries. Individual CL was weighed and the average CL weight calculated. The number of embryos (total and vital) were counted and the vital embryos were individually weighed for calculation of within litter average and standard deviation (SD) of the embryo weight. Length of the uterine implantation site of the vital embryos was measured and the average per gilt calculated. Results suggests that increasing the EBV for total number of piglets born would proportionally increase OR and number of embryos, while decreasing the average CL weight. On the contrary, increasing the EBV for average piglet birth weight and for within litter birth weight standard deviation would increase the average CL weight. There was no relationship between the EBVs for BW and for BWSD and vital embryonic weight at 35 days of pregnancy. OR, average CL weight, number of embryos, average weight and implantation length of the vital embryos had all moderate to high heritabilities, ranging from 0.36 (±0.18) to 0.70 (±0.17). Thus, results indicate that there is ample genetic variation in OR, average CL weight and embryonic development traits. This knowledge could be used to optimize the balance between selection for litter size, average piglets birth weight and within litter birth weight uniformity.
Relations between ovarian & embryonic traits in pigs : effects of genetic selection for litter traits at birth
Lima Alvares Da Silva, Carolina - \ 2018
University. Promotor(en): Bas Kemp, co-promotor(en): Nicoline Nieuwenhuizen-Soede; E.F. Knol. - Wageningen : Wageningen University - ISBN 9789463438858 - 196
Timing belangrijk voor hogere opbrengsten
Nunes Vieira da Silva, Joao - \ 2018

Artikel naar aanleiding van proefschrift

Affymetrix SNP array data for wild Dutch great tits (Parus major)
Silva, Vinicius Da; Laine, Veronika N. ; Bosse, M. ; Oers, C.H.J. ; Dibbits, B.W. ; Visser, M.E. ; Crooijmans, R.P.M.A. ; Groenen, M. - \ 2018
GSE105131 - Parus major - PRJNA415009
The great tit is a widely studied passerine bird species in ecology that, in the past decades, has provided important insights into speciation, phenology, behavior and microevolution. After completion of the great tit genome sequence, a customized high density 650k SNP array was developed enabling more detailed genomic studies in this species.
CNVs are associated with genomic architecture in a songbird
Silva, Vinicius H. da; Laine, Veronika N. ; Bosse, Mirte ; Oers, Kees van; Dibbits, Bert ; Visser, Marcel E. ; Crooijmans, Richard P.M.A. ; Groenen, Martien A.M. - \ 2018
BMC Genomics 19 (2018)Supplement 2. - ISSN 1471-2164
Duplication - Genetic variation - Inheritance - Parus major - Recombination

Background: Understanding variation in genome structure is essential to understand phenotypic differences within populations and the evolutionary history of species. A promising form of this structural variation is copy number variation (CNV). CNVs can be generated by different recombination mechanisms, such as non-allelic homologous recombination, that rely on specific characteristics of the genome architecture. These structural variants can therefore be more abundant at particular genes ultimately leading to variation in phenotypes under selection. Detailed characterization of CNVs therefore can reveal evolutionary footprints of selection and provide insight in their contribution to phenotypic variation in wild populations. Results: Here we use genotypic data from a long-term population of great tits (Parus major), a widely studied passerine bird in ecology and evolution, to detect CNVs and identify genomic features prevailing within these regions. We used allele intensities and frequencies from high-density SNP array data from 2,175 birds. We detected 41,029 CNVs concatenated into 8,008 distinct CNV regions (CNVRs). We successfully validated 93.75% of the CNVs tested by qPCR, which were sampled at different frequencies and sizes. A mother-daughter family structure allowed for the evaluation of the inheritance of a number of these CNVs. Thereby, only CNVs with 40 probes or more display segregation in accordance with Mendelian inheritance, suggesting a high rate of false negative calls for smaller CNVs. As CNVRs are a coarse-grained map of CNV loci, we also inferred the frequency of coincident CNV start and end breakpoints. We observed frequency-dependent enrichment of these breakpoints at homologous regions, CpG sites and AT-rich intervals. A gene ontology enrichment analyses showed that CNVs are enriched in genes underpinning neural, cardiac and ion transport pathways. Conclusion: Great tit CNVs are present in almost half of the genes and prominent at repetitive-homologous and regulatory regions. Although overlapping genes under selection, the high number of false negatives make neutrality or association tests on CNVs detected here difficult. Therefore, CNVs should be further addressed in the light of their false negative rate and architecture to improve the comprehension of their association with phenotypes and evolutionary history.

Adapting forest management to climate change in Europe : Linking perceptions to adaptive responses
Sousa-Silva, Rita ; Verbist, Bruno ; Lomba, Ângela ; Valent, Peter ; Suškevičs, Monika ; Picard, Olivier ; Hoogstra-Klein, Marjanke A. ; Cosofret, Vasile Cosmin ; Bouriaud, Laura ; Ponette, Quentin ; Verheyen, Kris ; Muys, Bart - \ 2018
Forest Policy and Economics 90 (2018). - ISSN 1389-9341 - p. 22 - 30.
Adaptive capacity - Awareness - Climate change - Europe - Forest management - Regional differences
Climate change will impact forests and may impair their ability to provide essential ecosystem services in the decades to come. Addressing this challenge requires adjustments to forest management strategies as of now, but it is still unclear to what extent this is already in progress. Using data from surveys of 1131 forest owners and managers from seven European countries, we assessed how they perceive their role in adapting forest management to climate change. The surveys focused on foresters' observations of climate change impacts, the degree to which climate change is a part of their operational and strategic management, and their ability to address related risks and opportunities. We found evidence of a strong continent-wide climate change awareness among respondents, with 73% foresters convinced that climate change will impact their forest. However, only about one-third (36%) reported having modified their management practices, though figures vary widely between countries, from 14% in Portugal to 57% in Slovakia. Among the constraints limiting their actions, lack of knowledge and information emerged as a major barrier towards forest adaptation. Differences between countries could be linked to their socio-economic and political contexts. Our results further suggest that severely damaging events, such as windstorms, fires and pest outbreaks, present relevant opportunities to engage people with climate change and encourage action. Further work needs to be done in strengthening the relationship between scientific research and practice, working out context dependent measures to foster adaptation to changing climate and disturbance regimes in forest management.
Molecular characterization of biochar from five Brazilian agricultural residues obtained at different charring temperatures
Schellekens, Judith ; Silva, Carlos Alberto ; Buurman, Peter ; Rittl, Tatiana F. ; Domingues, Rimena R. ; Justi, Marina ; Vidal-Torrado, Pablo ; Trugilho, Paulo Fernando - \ 2018
Journal of Analytical and Applied Pyrolysis 130 (2018). - ISSN 0165-2370 - p. 249 - 255.
Biochar - Chicken manure - Coffee husk - Pine bark - Pyrolysis-GC/MS - Sugarcane bagasse
Important parameters that influence biochar properties include charring temperature and biomass type. We characterized the molecular properties of biochars from five agricultural residues with pyrolysis gas chromatography mass/spectrometry (pyrolysis-GC/MS) in comparison with atomic H/C and N/C ratios. Feedstocks included chicken manure, eucalyptus sawdust, coffee husk, sugarcane bagasse and pine bark. Biochars produced at three different temperatures (Tchar) were analyzed, including 350, 450 and 750 °C, as well as the uncharred materials. The optimum temperature during analysis with pyrolysis-GC/MS (Tpy) was examined. Tpy 600 °C gave the best results for all Tchar by showing a larger diversity of pyrolysis products compared to Tpy 700 °C and 800 °C; Tpy 600 °C was therefore used for qualitative and quantitative comparison of the samples. Charring temperature was the dominant factor that determined the chemical composition of the biochar pyrolysates. Uncharred feedstocks had the largest contribution from carbohydrates, lignin phenols and long chain n-alkanes, all of which rapidly decreased with charring; biochars produced at Tchar 350 and 450 °C showed the largest contribution from phenols, mid-chain n-alkanes, benzofurans, indenes, biphenyls and PAHs, from which the benzofurans, indenes, biphenyls and PAHs were particular abundant in samples produced at Tchar 450 °C; pyrolysates of biochars produced at Tchar 750 °C were characterized by branched aliphatics, short chain n-alkanes/n-alkenes and low molecular weight (LMW) benzenes. Factor analysis showed that the variation of products differed largely within some chemical groups. For the N-containing compounds, caffeine, C16 alkylnitrile and diketopiperazines were associated with uncharred materials, benzonitriles and quinolines were associated with Tchar 350–450 °C. Another part of the variation of N-containing compounds was associated with chicken manure, and to a lesser extend also coffee husk, independently of Tchar. For all five agricultural residues, the highest chemical diversity was found for biochar produced at Tchar 350 °C. As the charring temperature increased, the diversity of pyrolysis products diminished.
Species Distribution Modelling: Contrasting presence-only models with plot abundance data
Gomes, Vitor H.F. ; Ijff, Stéphanie D. ; Raes, Niels ; Amaral, Iêda Leão ; Salomão, Rafael P. ; Coelho, Luiz De Souza ; Matos, Francisca Dionízia De Almeida ; Castilho, Carolina V. ; Filho, Diogenes De Andrade Lima ; López, Dairon Cárdenas ; Guevara, Juan Ernesto ; Magnusson, William E. ; Phillips, Oliver L. ; Wittmann, Florian ; Carim, Marcelo De Jesus Veiga ; Martins, Maria Pires ; Irume, Mariana Victória ; Sabatier, Daniel ; Molino, Jean François ; Bánki, Olaf S. ; Guimarães, José Renan Da Silva ; Pitman, Nigel C.A. ; Piedade, Maria Teresa Fernandez ; Mendoza, Abel Monteagudo ; Luize, Bruno Garcia ; Venticinque, Eduardo Martins ; de Leão Novo, E.M.M. ; Vargas, Percy Núñez ; Silva, Thiago Sanna Freire ; Manzatto, Angelo Gilberto ; Terborgh, John ; Reis, Neidiane Farias Costa ; Montero, Juan Carlos ; Montero, Juan Carlos ; Casula, Katia Regina ; Marimon, Beatriz S. ; Marimon, Ben Hur ; Honorio Coronado, Euridice N. ; Feldpausch, Ted R. ; Duque, Alvaro ; Zartman, Charles Eugene ; Arboleda, Nicolás Castaño ; Killeen, Timothy J. ; Mostacedo, Bonifacio ; Vasquez, Rodolfo ; Schöngart, Jochen ; Assis, Rafael L. ; Medeiros, Marcelo Brilhante ; Simon, Marcelo Fragomeni ; Andrade, Ana ; Laurance, William F. ; Camargo, José Luís ; Demarchi, Layon O. ; Laurance, Susan G.W. ; Farias, Emanuelle De Sousa ; Nascimento, Henrique Eduardo Mendonça ; Revilla, Juan David Cardenas ; Quaresma, Adriano ; Costa, Flavia R.C. ; Vieira, Ima Célia Guimarães ; Cintra, Bruno Barçante Ladvocat ; Cintra, Bruno Barçante Ladvocat ; Castellanos, Hernán ; Brienen, Roel ; Stevenson, Pablo R. ; Feitosa, Yuri ; Duivenvoorden, Joost F. ; Aymard, Gerardo A.C. ; Mogollón, Hugo F. ; Targhetta, Natalia ; Comiskey, James A. ; Vicentini, Alberto ; Lopes, Aline ; Damasco, Gabriel ; Dávila, Nállarett ; García-Villacorta, Roosevelt ; Levis, Carolina ; Levis, Carolina ; Schietti, Juliana ; Souza, Priscila ; Emilio, Thaise ; Alonso, Alfonso ; Neill, David ; Dallmeier, Francisco ; Ferreira, Leandro Valle ; Araujo-Murakami, Alejandro ; Praia, Daniel ; Amaral, Dário Dantas Do; Carvalho, Fernanda Antunes ; Souza, Fernanda Coelho De - \ 2018
Scientific Reports 8 (2018)1. - ISSN 2045-2322
Species distribution models (SDMs) are widely used in ecology and conservation. Presence-only SDMs such as MaxEnt frequently use natural history collections (NHCs) as occurrence data, given their huge numbers and accessibility. NHCs are often spatially biased which may generate inaccuracies in SDMs. Here, we test how the distribution of NHCs and MaxEnt predictions relates to a spatial abundance model, based on a large plot dataset for Amazonian tree species, using inverse distance weighting (IDW). We also propose a new pipeline to deal with inconsistencies in NHCs and to limit the area of occupancy of the species. We found a significant but weak positive relationship between the distribution of NHCs and IDW for 66% of the species. The relationship between SDMs and IDW was also significant but weakly positive for 95% of the species, and sensitivity for both analyses was high. Furthermore, the pipeline removed half of the NHCs records. Presence-only SDM applications should consider this limitation, especially for large biodiversity assessments projects, when they are automatically generated without subsequent checking. Our pipeline provides a conservative estimate of a species' area of occupancy, within an area slightly larger than its extent of occurrence, compatible to e.g. IUCN red list assessments.
Water-soluble chitosan derivatives and pH-responsive hydrogels by selective C-6 oxidation mediated by TEMPO-laccase redox system
Botelho da Silva, Suse ; Krolicka, Malgorzata ; Broek, Lambertus A.M. van den; Frissen, August E. ; Boeriu, Carmen Gabriela - \ 2018
Carbohydrate Polymers 186 (2018). - ISSN 0144-8617 - p. 299 - 309.
2,2,6,6-Tetramethylpiperidinoxyl radical (TEMPO) - Chitosan - Laccase - Oxidation - pH-responsive hydrogel - Soluble chitosan
Chitosan is a polysaccharide with recognized antioxidant, antimicrobial and wound healing activities. However, this polymer is soluble only in dilute acidic solutions, which restricts much of its applications. A usual strategy for improving the functionality of polysaccharides is the selective oxidation mediated by 2,2,6,6-tetra-methyl-1-piperidinidyloxy (TEMPO) using laccase as a co-oxidant. In this work, the TEMPO-laccase redox system was used for the first time to selectively oxidize chitosan in order to produce tailored derivatives. The reaction was performed at pH 4.5 under continuous air supply and the oxidized products were characterized structurally and functionally. The TEMPO-laccase oxidation successfully added aldehyde and carboxylate groups to chitosan structure resulting in derivatives with oxidation between 4 and 7%. These derivatives showed increased solubility and decreased viscosity in solution. If chitosan is dissolved in diluted hydrochloric acid prior to TEMPO-laccase oxidation, a crosslinked chitosan derivative was produced, which was able to form a pH-responsive hydrogel.
Mechanism and structural diversity of exoribonuclease-resistant RNA structures in flaviviral RNAs
Macfadden, Andrea ; O’Donoghue, Zoe ; Silva, Patricia A.G.C. ; Chapman, Erich G. ; Olsthoorn, René C. ; Sterken, Mark G. ; Pijlman, Gorben P. ; Bredenbeek, Peter J. ; Kieft, Jeffrey S. - \ 2018
Nature Communications 9 (2018)1. - ISSN 2041-1723
Flaviviruses such as Yellow fever, Dengue, West Nile, and Zika generate disease-linked viral noncoding RNAs called subgenomic flavivirus RNAs. Subgenomic flavivirus RNAs result when the 5′–3′ progression of cellular exoribonuclease Xrn1 is blocked by RNA elements called Xrn1-resistant RNAs located within the viral genome’s 3′-untranslated region that operate without protein co-factors. Here, we show that Xrn1-resistant RNAs can halt diverse exoribonucleases, revealing a mechanism in which they act as general mechanical blocks that ‘brace’ against an enzyme’s surface, presenting an unfolding problem that confounds further enzyme progression. Further, we directly demonstrate that Xrn1-resistant RNAs exist in a diverse set of flaviviruses, including some specific to insects or with no known arthropod vector. These Xrn1-resistant RNAs comprise two secondary structural classes that mirror previously reported phylogenic analysis. Our discoveries have implications for the evolution of exoribonuclease resistance, the use of Xrn1-resistant RNAs in synthetic biology, and the development of new therapies.
Volatile organic molecules from Fusarium oxysporum strain 21 with nematicidal activity against Meloidogyne incognita
Terra, Willian César ; Campos, Vicente Paulo ; Martins, Samuel Julio ; Costa, Lilian Simara Abreu S. ; Silva, Júlio Carlos Pereira da; Barros, Aline Ferreira ; Lopez, Liliana Estupiñan ; Santos, Thaisa Conrado Nunes ; Smant, Geert ; Oliveira, Denilson Ferreira - \ 2018
Crop Protection 106 (2018). - ISSN 0261-2194 - p. 125 - 131.
Bioprospecting - Fusarium oxysporum - Plant-parasitic nematodes - Volatiles
Volatile organic compounds (VOCs) produced by microorganisms are potential alternatives for the development of new nematicides. In a previous study, we identified VOCs produced by Fusarium oxysporum strain 21 (F.o–21). In this study, we tested the eight most abundant VOCs produced by F.o-21 against Meloidogyne incognita. Compounds 2-methylbutyl acetate (1), 3-methylbutyl acetate (2), ethyl acetate (7), and 2-methylpropyl acetate (8) led to in vitro mortality of 100%, 91%, 100%, and 82%, respectively, in second-stage juveniles (J2) of M. incognita at a concentration of 500 μg/mL. The lethal concentration (LC50) for compounds 1, 2, 7, and 8 in M. incognita J2, was 236, 198, 213, and 218 μg/mL, respectively. Under the same conditions, the commercial nematicide called carbofuran (2,3-dihydro-2,2-dimethyl-1-benzofuran-7-yl N-methyl carbamate) showed an LC50 of 191 μg/mL. Eggs exposed to compounds 2 and 7, for 72 h showed up to a 90% reduction in hatching, and the compounds 1, 2, 7, and 8 reduced M. incognita infectivity by 52%, 52%, 36% and 41%, respectively. When the compounds were applied in tomato seedlings infested by M. incognita, compound 1 reduced the number of galls per root gram by 22% when compared to the negative control (without the application of nematicide). The compound 2-methylbutyl acetate (1) showed potential to be used in the field after improvements in the application technology.
Investigation of Clostridium botulinum group III's mobilome content
Woudstra, Cédric ; Maréchal, Caroline Le; Souillard, Rozenn ; Anniballi, Fabrizio ; Auricchio, Bruna ; Bano, Luca ; Bayon-Auboyer, Marie Hélène ; Koene, Miriam ; Mermoud, Isabelle ; Brito, Roseane B. ; Lobato, Francisco C.F. ; Silva, Rodrigo O.S. ; Dorner, Martin B. ; Fach, Patrick - \ 2018
Anaerobe 49 (2018). - ISSN 1075-9964 - p. 71 - 77.
Animal botulism - Clostridium botulinum group III - Phage - Plasmid
Clostridium botulinum group III is mainly responsible for botulism in animals. It could lead to high animal mortality rates and, therefore, represents a major environmental and economic concern. Strains of this group harbor the botulinum toxin locus on an unstable bacteriophage. Since the release of the first complete C. botulinum group III genome sequence (strain BKT015925), strains have been found to contain others mobile elements encoding for toxin components. In this study, seven assays targeting toxin genes present on the genetic mobile elements of C. botulinum group III were developed with the objective to better characterize C. botulinum group III strains. The investigation of 110 C. botulinum group III strains and 519 naturally contaminated samples collected during botulism outbreaks in Europe showed alpha-toxin and C2-I/C2-II markers to be systematically associated with type C/D bont-positive samples, which may indicate an important role of these elements in the pathogenicity mechanisms. On the contrary, bont type D/C strains and the related positive samples appeared to contain almost none of the markers tested. Interestingly, 31 bont-negative samples collected on farms after a botulism outbreak revealed to be positive for some of the genetic mobile elements tested. This suggests loss of the bont phage, either in farm environment after the outbreak or during laboratory handling.
Characterization of the Theileria parva sporozoite proteome
Nyagwange, James ; Tijhaar, Edwin ; Ternette, Nicola ; Mobegi, Fredrick ; Tretina, Kyle ; Silva, Joana C. ; Pelle, Roger ; Nene, Vishvanath - \ 2018
International Journal for Parasitology 48 (2018)3-4. - ISSN 0020-7519 - p. 265 - 273.
Antigens - East Coast fever - MudPIT - Proteomics - Sporozoites - Theileria
East Coast fever is a lymphoproliferative disease caused by the tick-borne protozoan parasite Theileria parva. The sporozoite stage of this parasite, harboured and released from the salivary glands of the tick Rhipicephalus appendiculatus during feeding, invades and establishes infection in bovine lymphocytes. Blocking this initial stage of invasion presents a promising vaccine strategy for control of East Coast fever and can in part be achieved by targeting the major sporozoite surface protein p67. To support research on the biology of T. parva and the identification of additional candidate vaccine antigens, we report on the sporozoite proteome as defined by LC-MS/MS analysis. In total, 4780 proteins were identified in an enriched preparation of sporozoites. Of these, 2007 were identified as T. parva proteins, representing close to 50% of the total predicted parasite proteome. The remaining 2773 proteins were derived from the tick vector. The identified sporozoite proteins include a set of known T. parva antigens targeted by antibodies and cytotoxic T cells from cattle that are immune to East Coast fever. We also identified proteins predicted to be orthologs of Plasmodium falciparum sporozoite surface molecules and invasion organelle proteins, and proteins that may contribute to the phenomenon of bovine lymphocyte transformation. Overall, these data establish a protein expression profile of T. parva sporozoites as an important starting point for further study of a parasitic species which has considerable agricultural impact.
Attraction of Three Mirid Predators to Tomato Infested by Both the Tomato Leaf Mining Moth Tuta absoluta and the Whitefly Bemisia tabaci
Silva, Diego B. ; Bueno, Vanda H.P. ; Loon, Joop J.A. van; Peñaflor, Maria Fernanda G.V. ; Bento, José Maurício S. ; Lenteren, Joop C. van - \ 2018
Journal of Chemical Ecology 44 (2018)1. - ISSN 0098-0331 - p. 29 - 39.
Campyloneuropsis infumatus - Engytatus varians - Macrolophus basicornis - Multiple herbivory - Predator foraging behavior - Tomato pests
Plants emit volatile compounds in response to insect herbivory, which may play multiple roles as defensive compounds and mediators of interactions with other plants, microorganisms and animals. Herbivore-induced plant volatiles (HIPVs) may act as indirect plant defenses by attracting natural enemies of the attacking herbivore. We report here the first evidence of the attraction of three Neotropical mirid predators (Macrolophus basicornis, Engytatus varians and Campyloneuropsis infumatus) toward plants emitting volatiles induced upon feeding by two tomato pests, the leaf miner Tuta absoluta and the phloem feeder Bemisia tabaci, in olfactometer bioassays. Subsequently, we compared the composition of volatile blends emitted by insect-infested tomato plants by collecting headspace samples and analyzing them with GC-FID and GC-MS. Egg deposition by T. absoluta did not make tomato plants more attractive to the mirid predators than uninfested tomato plants. Macrolophus basicornis is attracted to tomato plants infested with either T. absoluta larvae or by a mixture of B. tabaci eggs, nymphs and adults. Engytatus varians and C. infumatus responded to volatile blends released by tomato plants infested with T. absoluta larvae over uninfested plants. Also, multiple herbivory by T. absoluta and B. tabaci did not increase the attraction of the mirids compared to infestation with T. absoluta alone. Terpenoids represented the most important class of compounds in the volatile blends and there were significant differences between the volatile blends emitted by tomato plants in response to attack by T. absoluta, B. tabaci, or by both insects. We, therefore, conclude that all three mirids use tomato plant volatiles to find T. absoluta larvae. Multiple herbivory did neither increase, nor decrease attraction of C. infumatus, E. varians and M. basicornis. By breeding for higher rates of emission of selected terpenes, increased attractiveness of tomato plants to natural enemies may improve the effectiveness of biological control.
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