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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    Online drone education, a mapping review
    Velasco, Omar ; Valente, Joao - \ 2020
    In: Proceedings of the 2020 IEEE Global Engineering Education Conference, EDUCON 2020. - IEEE computer society (IEEE Global Engineering Education Conference, EDUCON ) - ISBN 9781728109312 - p. 1286 - 1289.
    Drones - M00C - Online Education - UAV

    As Unmanned Aerial Vehicles (UAV) increase in popularity, legislation, use and applications education becomes a paramount objective for safety reasons and correct usage of this technology. Online education is becoming one of the main sources of knowledge, especially thanks to the wider geographical and social reach. Online education regarding UAVs has become a crucial mean to transfer and spread this knowledge. This work presents a mapping review of the state of such education with the aim of finding knowledge gaps and areas of improvement.

    Development of an effective and stable genotype-matched live attenuated newcastle disease virus vaccine based on a novel naturally recombinant malaysian isolate using reverse genetics
    Bello, Muhammad Bashir ; Mahamud, Siti Nor Azizah ; Yusoff, Khatijah ; Ideris, Aini ; Hair-Bejo, Mohd ; Peeters, Ben P.H. ; Omar, Abdul Rahman - \ 2020
    Vaccines 8 (2020)2. - ISSN 2076-393X
    Genotype VII - Genotype-matched - Newcastle disease virus - Recombinant vaccine - Reverse genetics

    Genotype VII Newcastle disease viruses are associated with huge economic losses in the global poultry industry. Despite the intensive applications of vaccines, disease outbreaks caused by those viruses continue to occur frequently even among the vaccinated poultry farms. An important factor in the suboptimal protective efficacy of the current vaccines is the genetic mismatch between the prevalent strains and the vaccine strains. Therefore, in the present study, an effective and stable genotype-matched live attenuated Newcastle disease virus (NDV) vaccine was developed using reverse genetics, based on a recently isolated virulent naturally recombinant NDV IBS025/13 Malaysian strain. First of all, the sequence encoding the fusion protein (F) cleavage site of the virus was modified in silico from virulent polybasic (RRQKRF) to avirulent monobasic (GRQGRL) motif. The entire modified sequence was then chemically synthesized and inserted into pOLTV5 transcription vector for virus rescue. A recombinant virus termed mIBS025 was successfully recovered and shown to be highly attenuated based on OIE recommended pathogenicity assessment indices. Furthermore, the virus was shown to remain stably attenuated and retain the avirulent monobasic F cleavage site after 15 consecutive passages in specific-pathogen-free embryonated eggs and 12 passages in one-day-old chicks. More so, the recombinant virus induced a significantly higher hemagglutination inhibition antibody titre than LaSota although both vaccines fully protected chicken against genotype VII NDV induced mortality and morbidity. Finally, mIBS025 was shown to significantly reduce both the duration and quantity of cloacal and oropharyngeal shedding of the challenged genotype VII virus compared to the LaSota vaccine. These findings collectively indicate that mIBS025 provides a better protective efficacy than LaSota and therefore can be used as a promising vaccine candidate against genotype VII NDV strains.

    Exploring the prospects of engineered Newcastle disease virus in modern vaccinology
    Bashir Bello, Muhammad ; Yusoff, Khatijah ; Ideris, Aini ; Hair-Bejo, Mohd ; Hassan Jibril, Abdurrahman ; Peeters, Ben P.H. ; Rahman Omar, Abdul - \ 2020
    Viruses 12 (2020)4. - ISSN 1999-4915
    Cancer - Infectious diseases - Newcastle disease virus - Reverse genetics - Vaccines

    Many traditional vaccines have proven to be incapable of controlling newly emerging infectious diseases. They have also achieved limited success in the fight against a variety of human cancers. Thus, innovative vaccine strategies are highly needed to overcome the global burden of these diseases. Advances in molecular biology and reverse genetics have completely restructured the concept of vaccinology, leading to the emergence of state-of-the-art technologies for vaccine design, development and delivery. Among these modern vaccine technologies are the recombinant viral vectored vaccines, which are known for their incredible specificity in antigen delivery as well as the induction of robust immune responses in the vaccinated hosts. Although a number of viruses have been used as vaccine vectors, genetically engineered Newcastle disease virus (NDV) possesses some useful attributes that make it a preferable candidate for vectoring vaccine antigens. Here, we review the molecular biology of NDV and discuss the reverse genetics approaches used to engineer the virus into an efficient vaccine vector. We then discuss the prospects of the engineered virus as an efficient vehicle of vaccines against cancer and several infectious diseases of man and animals.

    Global carbon budget 2019
    Friedlingstein, Pierre ; Jones, Matthew W. ; O'Sullivan, Michael ; Andrew, Robbie M. ; Hauck, Judith ; Peters, Glen P. ; Peters, Wouter ; Pongratz, Julia ; Sitch, Stephen ; Quéré, Corinne Le; Bakker, Dorothee C.E. ; Canadell1, Josep G. ; Ciais1, Philippe ; Jackson, Robert B. ; Anthoni, Peter ; Barbero, Leticia ; Bastos, Ana ; Bastrikov, Vladislav ; Becker, Meike ; Bopp, Laurent ; Buitenhuis, Erik ; Chandra, Naveen ; Chevallier, Frédéric ; Chini, Louise P. ; Currie, Kim I. ; Feely, Richard A. ; Gehlen, Marion ; Gilfillan, Dennis ; Gkritzalis, Thanos ; Goll, Daniel S. ; Gruber, Nicolas ; Gutekunst, Sören ; Harris, Ian ; Haverd, Vanessa ; Houghton, Richard A. ; Hurtt, George ; Ilyina, Tatiana ; Jain, Atul K. ; Joetzjer, Emilie ; Kaplan, Jed O. ; Kato, Etsushi ; Goldewijk, Kees Klein ; Korsbakken, Jan Ivar ; Landschützer, Peter ; Lauvset, Siv K. ; Lefèvre, Nathalie ; Lenton, Andrew ; Lienert, Sebastian ; Lombardozzi, Danica ; Marland, Gregg ; McGuire, Patrick C. ; Melton, Joe R. ; Metzl, Nicolas ; Munro, David R. ; Nabel, Julia E.M.S. ; Nakaoka, Shin Ichiro ; Neill, Craig ; Omar, Abdirahman M. ; Ono, Tsuneo ; Peregon, Anna ; Pierrot, Denis ; Poulter, Benjamin ; Rehder, Gregor ; Resplandy, Laure ; Robertson, Eddy ; Rödenbeck, Christian ; Séférian, Roland ; Schwinger, Jörg ; Smith, Naomi ; Tans, Pieter P. ; Tian, Hanqin ; Tilbrook, Bronte ; Tubiello, Francesco N. ; Werf, Guido R. Van Der; Wiltshire, Andrew J. ; Zaehle, Sönke - \ 2019
    Earth System Science Data 11 (2019)4. - ISSN 1866-3508 - p. 1783 - 1838.

    Accurate assessment of anthropogenic carbon dioxide (CO2) emissions and their redistribution among the atmosphere, ocean, and terrestrial biosphere-the "global carbon budget"-is important to better understand the global carbon cycle, support the development of climate policies, and project future climate change. Here we describe data sets and methodology to quantify the five major components of the global carbon budget and their uncertainties. Fossil CO2 emissions (EFF) are based on energy statistics and cement production data, while emissions from land use change (ELUC), mainly deforestation, are based on land use and land use change data and bookkeeping models. Atmospheric CO2 concentration is measured directly and its growth rate (GATM) is computed from the annual changes in concentration. The ocean CO2 sink (SOCEAN) and terrestrial CO2 sink (SLAND) are estimated with global process models constrained by observations. The resulting carbon budget imbalance (BIM), the difference between the estimated total emissions and the estimated changes in the atmosphere, ocean, and terrestrial biosphere, is a measure of imperfect data and understanding of the contemporary carbon cycle. All uncertainties are reported as ±1σ. For the last decade available (2009-2018), EFF was 9:5±0:5 GtC yr-1, ELUC 1:5±0:7 GtC yr-1, GATM 4:9±0:02 GtC yr-1 (2:3±0:01 ppm yr-1), SOCEAN 2:5±0:6 GtC yr-1, and SLAND 3:2±0:6 GtC yr-1, with a budget imbalance BIM of 0.4 GtC yr-1 indicating overestimated emissions and/or underestimated sinks. For the year 2018 alone, the growth in EFF was about 2.1% and fossil emissions increased to 10:0±0:5 GtC yr-1, reaching 10 GtC yr-1 for the first time in history, ELUC was 1:5±0:7 GtC yr-1, for total anthropogenic CO2 emissions of 11:5±0:9 GtC yr-1 (42:5±3:3 GtCO2). Also for 2018, GATM was 5:1±0:2 GtC yr-1 (2:4±0:1 ppm yr-1), SOCEAN was 2:6±0:6 GtC yr-1, and SLAND was 3:5±0:7 GtC yr-1, with a BIM of 0.3 GtC. The global atmospheric CO2 concentration reached 407:38±0:1 ppm averaged over 2018. For 2019, preliminary data for the first 6-10 months indicate a reduced growth in EFF of C0:6% (range of.0:2% to 1.5 %) based on national emissions projections for China, the USA, the EU, and India and projections of gross domestic product corrected for recent changes in the carbon intensity of the economy for the rest of the world. Overall, the mean and trend in the five components of the global carbon budget are consistently estimated over the period 1959-2018, but discrepancies of up to 1 GtC yr-1 persist for the representation of semi-decadal variability in CO2 fluxes. A detailed comparison among individual estimates and the introduction of a broad range of observations shows (1) no consensus in the mean and trend in land use change emissions over the last decade, (2) a persistent low agreement between the different methods on the magnitude of the land CO2 flux in the northern extra-tropics, and (3) an apparent underestimation of the CO2 variability by ocean models outside the tropics. This living data update documents changes in the methods and data sets used in this new global carbon budget and the progress in understanding of the global carbon cycle compared with previous publications of this data set (Le Quéré et al., 2018a, b, 2016, 2015a, b, 2014, 2013). The data generated by this work are available at https://doi.org/10.18160/gcp-2019 (Friedlingstein et al., 2019).

    Workshopbericht: Das Erbe der Gewalt in Französisch-Äquatorialafrika
    Vries, Lotje de; Mangarella, Joseph - \ 2019
    Afrika Spectrum 54 (2019)2. - ISSN 0002-0397 - p. 162 - 172.
    French Equatorial Africa - history - instability - marginality - violence

    This report offers an account of an international workshop held at the Omar Bongo University in Libreville, Gabon, from 23 November to 27 November 2018. Bringing together specialists on and from Cameroon, Central African Republic, Chad, Congo, Equatorial Guinea, and Gabon, participants reflected on the ways in which different forms of violence have historically had – and continue to have – an impact on social fabrics and several dimensions of politics. The workshop also sought to relate these legacies of violence to the region’s economies of extraction. The region is confronted with social and political turmoil that receives little international attention. The combination of simmering and open instability and the relatively marginal position of the region vis-à-vis the wider continent risks propelling several countries into outright political strife with regional repercussions. The debates concluded that further thinking on how violence permeates every aspect of social and political life is much needed.

    BrAPI-an application programming interface for plant breeding applications
    Selby, Peter ; Abbeloos, Rafael ; Backlund, Jan Erik ; Basterrechea Salido, Martin ; Bauchet, Guillaume ; Benites-Alfaro, Omar E. ; Birkett, Clay ; Calaminos, Viana C. ; Carceller, Pierre ; Cornut, Guillaume ; Vasques Costa, Bruno ; Edwards, Jeremy D. ; Finkers, Richard ; Yanxin Gao, Star ; Ghaffar, Mehmood ; Glaser, Philip ; Guignon, Valentin ; Hok, Puthick ; Kilian, Andrzej ; König, Patrick ; Lagare, Jack Elendil B. ; Lange, Matthias ; Laporte, Marie Angélique ; Larmande, Pierre ; LeBauer, David S. ; Lyon, David A. ; Marshall, David S. ; Matthews, Dave ; Milne, Iain ; Mistry, Naymesh ; Morales, Nicolas ; Mueller, Lukas A. ; Neveu, Pascal ; Papoutsoglou, Evangelia ; Pearce, Brian ; Perez-Masias, Ivan ; Pommier, Cyril ; Ramírez-González, Ricardo H. ; Rathore, Abhishek ; Raquel, Angel Manica ; Raubach, Sebastian ; Rife, Trevor ; Robbins, Kelly ; Rouard, Mathieu ; Sarma, Chaitanya ; Scholz, Uwe ; Sempéré, Guilhem ; Shaw, Paul D. ; Simon, Reinhard ; Verouden, Maikel - \ 2019
    Bioinformatics 35 (2019)20. - ISSN 1367-4803 - p. 4147 - 4155.

    MOTIVATION: Modern genomic breeding methods rely heavily on very large amounts of phenotyping and genotyping data, presenting new challenges in effective data management and integration. Recently, the size and complexity of datasets have increased significantly, with the result that data are often stored on multiple systems. As analyses of interest increasingly require aggregation of datasets from diverse sources, data exchange between disparate systems becomes a challenge. RESULTS: To facilitate interoperability among breeding applications, we present the public plant Breeding Application Programming Interface (BrAPI). BrAPI is a standardized web service API specification. The development of BrAPI is a collaborative, community-based initiative involving a growing global community of over a hundred participants representing several dozen institutions and companies. Development of such a standard is recognized as critical to a number of important large breeding system initiatives as a foundational technology. The focus of the first version of the API is on providing services for connecting systems and retrieving basic breeding data including germplasm, study, observation, and marker data. A number of BrAPI-enabled applications, termed BrAPPs, have been written, that take advantage of the emerging support of BrAPI by many databases. AVAILABILITY AND IMPLEMENTATION: More information on BrAPI, including links to the specification, test suites, BrAPPs, and sample implementations is available at https://brapi.org/. The BrAPI specification and the developer tools are provided as free and open source.

    Low-level stratiform clouds and dynamical features observed within the southern West African monsoon
    Dione, Cheikh ; Lohou, Fabienne ; Lothon, Marie ; Adler, Bianca ; Babić, Karmen ; Kalthoff, Norbert ; Pedruzo-Bagazgoitia, Xabier ; Bezombes, Yannick ; Gabella, Omar - \ 2019
    Atmospheric Chemistry and Physics 19 (2019)13. - ISSN 1680-7316 - p. 8979 - 8997.

    During the boreal summer, the monsoon season that takes place in West Africa is accompanied by low stratus clouds over land that stretch from the Guinean coast several hundred kilometers inland. Numerical climate and weather models need finer description and knowledge of cloud macrophysical characteristics and of the dynamical and thermodynamical structures occupying the lowest troposphere, in order to be properly evaluated in this region. The Dynamics-Aerosol-Chemistry-Cloud Interactions in West Africa (DACCIWA) field experiment, which took place in summer 2016, addresses this knowledge gap. Low-level atmospheric dynamics and stratiform low-level cloud macrophysical properties are analyzed using in situ and remote sensing measurements continuously collected from 20 June to 30 July at Savè, Benin, roughly 180 km from the coast. The macrophysical characteristics of the stratus clouds are deduced from a ceilometer, an infrared cloud camera, and cloud radar. Onset times, evolution, dissipation times, base heights, and thickness are evaluated. The data from an ultra-high-frequency (UHF) wind profiler, a microwave radiometer, and an energy balance station are used to quantify the occurrence and characteristics of the monsoon flow, the nocturnal low-level jet, and the cold air mass inflow propagating northward from the coast of the Gulf of Guinea. The results show that these dynamical structures are very regularly observed during the entire 41 d documented period. Monsoon flow is observed every day during our study period. The so-called "maritime inflow" and the nocturnal low-level jet are also systematic features in this area. According to synoptic atmospheric conditions, the maritime inflow reaches Savè around 18:00-19:00 UTC on average. This timing is correlated with the strength of the monsoon flow. This time of arrival is close to the time range of the nocturnal low-level jet settlement. As a result, these phenomena are difficult to distinguish at the Savè site. The low-level jet occurs every night, except during rain events, and is associated 65 % of the time with low stratus clouds. Stratus clouds form between 22:00 and 06:00 UTC at an elevation close to the nocturnal low-level jet core height. The cloud base height, 310±30 m above ground level (a.g.l.), is rather stationary during the night and remains below the jet core height. The cloud top height, at 640±100 m a.g.l., is typically found above the jet core. The nocturnal low-level jet, low-level stratiform clouds, monsoon flow, and maritime inflow reveal significant day-to-day and intra-seasonal variability during the summer given the importance of the different monsoon phases and synoptic atmospheric conditions. Distributions of strength, depth, onset time, breakup time, etc. are quantified here. These results contribute to satisfy the main goals of DACCIWA and allow a conceptual model of the dynamical structures in the lowest troposphere over the southern part of West Africa.

    Wet and dry tropical forests show opposite successional pathways in wood density but converge over time
    Poorter, L. ; Rozendaal, Danaë ; Bongers, F. ; Almeida-Cortez, Jarcilene S. ; Almeyda Zambrano, Angélica María ; Álvarez, Francisco S. ; Andrade, José Luís ; Villa, Luis Felipe Arreola ; Balvanera, Patricia ; Becknell, Justin M. ; Bentos, Tony V. ; Bhaskar, Radika ; Boukili, Vanessa ; Brancalion, Pedro H.S. ; Broadbent, Eben N. ; César, Ricardo Gomes ; Chave, Jerome ; Chazdon, Robin L. ; Colletta, Gabriel Dalla ; Craven, Dylan ; Jong, Ben H.J. de; Denslow, Julie S. ; Dent, Daisy H. ; DeWalt, Saara J. ; García, Elisa Díaz ; Dupuy, Juan M. ; Durán, Sandra M. ; Espírito Santo, Mário Marcos ; Fandiño, María C. ; Fernandes, Geraldo Wilson ; Finegan, Bryan ; Moser, Vanessa Granda ; Hall, Jefferson S. ; Hernández-Stefanoni, José Luis ; Jakovac, A.C. ; Junqueira, André B. ; Kennard, Deborah ; Lebrija-Trejos, Edwin ; Letcher, Susan G. ; Lohbeck, M.W.M. ; Lopez, Omar R. ; Marín-Spiotta, Erika ; Martínez-Ramos, Miguel ; Martins, Sebastião Venâncio ; Massoca, Paulo E.S. ; Meave, Jorge A. ; Mesquita, Rita ; Mora, Francisco ; Souza Moreno, Vanessa De; Müller, Sandra C. ; Muñoz, Rodrigo ; Muscarella, Robert ; Oliveira Neto, Silvio Nolasco De; Nunes, Yule Roberta Ferreira ; Ochoa-Gaona, Susana ; Paz, Horacio ; Pena Claros, M. ; Piotto, Daniel ; Ruíz, Jorge ; Sanaphre-Villanueva, Lucía ; Sanchez-Azofeifa, Arturo ; Schwartz, Naomi B. ; Steininger, Marc K. ; Thomas, William Wayt ; Toledo, Marisol ; Uriarte, Maria ; Breugel, Michiel van; Wal, Hans van der - \ 2019
    Wageningen University & Research
    secondary succession - community assembly - community-weighted mean - wood density - Neotropics - tropical forest - Latin America
    We analyse how community wood density (WD) recovers during secondary tropical forest succession. In wet forests succession proceeds from low to high WD, in dry forests from high to low WD, resulting in convergence of community WD of dry and wet forests over time, as vegetation cover builds up.
    Wet and dry tropical forests show opposite successional pathways in wood density but converge over time
    Poorter, Lourens ; Rozendaal, Danaë M.A. ; Bongers, Frans ; Almeida-Cortez, Jarcilene S. de; Almeyda Zambrano, Angélica María ; Álvarez, Francisco S. ; Andrade, José Luís ; Villa, Luis Felipe Arreola ; Balvanera, Patricia ; Becknell, Justin M. ; Bentos, Tony V. ; Bhaskar, Radika ; Boukili, Vanessa ; Brancalion, Pedro H.S. ; Broadbent, Eben N. ; César, Ricardo G. ; Chave, Jerome ; Chazdon, Robin L. ; Colletta, Gabriel Dalla ; Craven, Dylan ; Jong, Ben H.J. de; Denslow, Julie S. ; Dent, Daisy H. ; DeWalt, Saara J. ; García, Elisa Díaz ; Dupuy, Juan Manuel ; Durán, Sandra M. ; Espírito Santo, Mário M. ; Fandiño, María C. ; Fernandes, Geraldo Wilson ; Finegan, Bryan ; Moser, Vanessa Granda ; Hall, Jefferson S. ; Hernández-Stefanoni, José Luis ; Jakovac, Catarina C. ; Junqueira, André B. ; Kennard, Deborah ; Lebrija-Trejos, Edwin ; Letcher, Susan G. ; Lohbeck, Madelon ; Lopez, Omar R. ; Marín-Spiotta, Erika ; Martínez-Ramos, Miguel ; Martins, Sebastião V. ; Massoca, Paulo E.S. ; Meave, Jorge A. ; Mesquita, Rita ; Mora, Francisco ; Souza Moreno, Vanessa de; Müller, Sandra C. ; Muñoz, Rodrigo ; Muscarella, Robert ; Oliveira Neto, Silvio Nolasco de; Nunes, Yule R.F. ; Ochoa-Gaona, Susana ; Paz, Horacio ; Peña-Claros, Marielos ; Piotto, Daniel ; Ruíz, Jorge ; Sanaphre-Villanueva, Lucía ; Sanchez-Azofeifa, Arturo ; Schwartz, Naomi B. ; Steininger, Marc K. ; Thomas, William Wayt ; Toledo, Marisol ; Uriarte, Maria ; Utrera, Luis P. ; Breugel, Michiel van; Sande, Masha T. van der; Wal, Hans van der; Veloso, Maria D.M. ; Vester, Hans F.M. ; Vieira, Ima C.G. ; Villa, Pedro Manuel ; Williamson, G.B. ; Wright, S.J. ; Zanini, Kátia J. ; Zimmerman, Jess K. ; Westoby, Mark - \ 2019
    Nature Ecology & Evolution 3 (2019). - ISSN 2397-334X - p. 928 - 934.

    Tropical forests are converted at an alarming rate for agricultural use and pastureland, but also regrow naturally through secondary succession. For successful forest restoration, it is essential to understand the mechanisms of secondary succession. These mechanisms may vary across forest types, but analyses across broad spatial scales are lacking. Here, we analyse forest recovery using 1,403 plots that differ in age since agricultural abandonment from 50 sites across the Neotropics. We analyse changes in community composition using species-specific stem wood density (WD), which is a key trait for plant growth, survival and forest carbon storage. In wet forest, succession proceeds from low towards high community WD (acquisitive towards conservative trait values), in line with standard successional theory. However, in dry forest, succession proceeds from high towards low community WD (conservative towards acquisitive trait values), probably because high WD reflects drought tolerance in harsh early successional environments. Dry season intensity drives WD recovery by influencing the start and trajectory of succession, resulting in convergence of the community WD over time as vegetation cover builds up. These ecological insights can be used to improve species selection for reforestation. Reforestation species selected to establish a first protective canopy layer should, among other criteria, ideally have a similar WD to the early successional communities that dominate under the prevailing macroclimatic conditions.

    Experimental design of a mobile landing platform to Assist Aerial Surveys in fluvial environments
    Borreguero, David ; Velasco, Omar ; Valente, João - \ 2019
    Applied Sciences 9 (2019)1. - ISSN 2076-3417
    Field robotics - Fluvial environments - Mechatronics - Unmanned aerial vehicles - Unmanned surface vehicles

    Sampling aquatic ecosystems is a laborious and expensive task, especially when covering large areas. This can be improved using unmanned aerial vehicles (UAVs) equipped with various remote sensing sensors. However, the UAV performance and autonomy may vary due to external factors when it is operated outdoors. In some cases, an emergency landing maneuver is necessary to avoid an accident, since in fluvial environments, the UAV control landing becomes a difficult operation. Therefore, it is important to have a backup platform on the water to fix this problem. This paper presents the design and development of a custom-built unmanned surface vehicle using open-source tools and with two types of operation-remotely piloted and autonomous-to support remote sensing practices with UAVs in fluvial environments. Finally, part of the software developed within this project was released in an open-source repository.

    Characterization of phenology, physiology, morphology and biomass traits across a broad Euro-Mediterranean ecotypic panel of the lignocellulosic feedstock Arundo donax
    Fabbrini, Francesco ; Ludovisi, Riccardo ; Alasia, Omar ; Flexas, Jaume ; Douthe, Cyril ; Ribas Carbó, Miquel ; Robson, Paul ; Taylor, Gail ; Scarascia-Mugnozza, Giuseppe ; Keurentjes, Joost J.B. ; Harfouche, Antoine - \ 2019
    Global change biology Bioenergy 11 (2019)1. - ISSN 1757-1693 - p. 152 - 170.
    Arundo donax - biomass - ecotype variability - growth traits - lignocellulosic biomass - multivariate analysis - perennial grasses - phenology - physiology

    Giant reed (Arundo donax L.) is a perennial rhizomatous grass, which has attracted great attention as a potential lignocellulosic feedstock for bioethanol production due to high biomass yield in marginal land areas, high polysaccharide content and low inhibitor levels in microbial fermentations. However, little is known about the trait variation that is available across a broad ecotypic panel of A. donax nor the traits that contribute most significantly to yield and growth in drought prone environments. A collection of 82 ecotypes of A. donax sampled across the Mediterranean basin was planted in a common garden experimental field in Savigliano, Italy. We analysed the collection using 367 clumps representing replicate plantings of 82 ecotypes for variation in 21 traits important for biomass accumulation and to identify the particular set of ecotypes with the most promising potential for biomass production. We measured morpho-physiological, phenological and biomass traits and analysed causal relationships between traits and productivity characteristics assessed at leaf and canopy levels. The results identified differences among the 82 ecotypes for all studied traits: those showing the highest level of variability included stomatal resistance, stem density (StN), stem dry mass (StDM) and total biomass production (TotDM). Multiple regression analysis revealed that leaf area index, StDM, StN, number of nodes per stem, stem height and diameter were the most significant predictors of TotDM and the most important early selection criteria for bioenergy production from A. donax. These traits were used in a hierarchical cluster analysis to identify groups of similar ecotypes, and a selection was made of promising ecotypes for multiyear and multisite testing for biomass production. Heritability estimates were significant for all traits. The potential of this ecotype collection as a resource for studies of germplasm diversity and for the analysis of traits underpinning high productivity of A. donax is highlighted.

    Genotype Diversity of Newcastle Disease Virus in Nigeria : Disease Control Challenges and Future Outlook
    Bello, Muhammad Bashir ; Yusoff, Khatijah Mohd ; Ideris, Aini ; Hair-Bejo, Mohd ; Peeters, Ben P.H. ; Jibril, Abdurrahman Hassan ; Tambuwal, Farouk Muhammad ; Omar, Abdul Rahman - \ 2018
    Advances in Virology 2018 (2018). - ISSN 1687-8639

    Newcastle disease (ND) is one of the most important avian diseases with considerable threat to the productivity of poultry all over the world. The disease is associated with severe respiratory, gastrointestinal, and neurological lesions in chicken leading to high mortality and several other production related losses. The aetiology of the disease is an avian paramyxovirus type-1 or Newcastle disease virus (NDV), whose isolates are serologically grouped into a single serotype but genetically classified into a total of 19 genotypes, owing to the continuous emergence and evolution of the virus. In Nigeria, molecular characterization of NDV is generally very scanty and majorly focuses on the amplification of the partial F gene for genotype assignment. However, with the introduction of the most objective NDV genotyping criteria which utilize complete fusion protein coding sequences in phylogenetic taxonomy, the enormous genetic diversity of the virus in Nigeria became very conspicuous. In this review, we examine the current ecological distribution of various NDV genotypes in Nigeria based on the available complete fusion protein nucleotide sequences (1662 bp) in the NCBI database. We then discuss the challenges of ND control as a result of the wide genetic distance between the currently circulating NDV isolates and the commonest vaccines used to combat the disease in the country. Finally, we suggest future directions in the war against the economically devastating ND in Nigeria.

    Diagnostic and Vaccination Approaches for Newcastle Disease Virus in Poultry : The Current and Emerging Perspectives
    Bello, Muhammad Bashir ; Yusoff, Khatijah ; Ideris, Aini ; Hair-Bejo, Mohd ; Peeters, Ben P.H. ; Omar, Abdul Rahman - \ 2018
    BioMed Research International 2018 (2018). - ISSN 2314-6133 - 18 p.

    Newcastle disease (ND) is one of the most devastating diseases that considerably cripple the global poultry industry. Because of its enormous socioeconomic importance and potential to rapidly spread to naïve birds in the vicinity, ND is included among the list of avian diseases that must be notified to the OIE immediately upon recognition. Currently, virus isolation followed by its serological or molecular identification is regarded as the gold standard method of ND diagnosis. However, this method is generally slow and requires specialised laboratory with biosafety containment facilities, making it of little relevance under epidemic situations where rapid diagnosis is seriously needed. Thus, molecular based diagnostics have evolved to overcome some of these difficulties, but the extensive genetic diversity of the virus ensures that isolates with mutations at the primer/probe binding sites escape detection using these assays. This diagnostic dilemma leads to the emergence of cutting-edge technologies such as next-generation sequencing (NGS) which have so far proven to be promising in terms of rapid, sensitive, and accurate recognition of virulent Newcastle disease virus (NDV) isolates even in mixed infections. As regards disease control strategies, conventional ND vaccines have stood the test of time by demonstrating track record of protective efficacy in the last 60 years. However, these vaccines are unable to block the replication and shedding of most of the currently circulating phylogenetically divergent virulent NDV isolates. Hence, rationally designed vaccines targeting the prevailing genotypes, the so-called genotype-matched vaccines, are highly needed to overcome these vaccination related challenges. Among the recently evolving technologies for the development of genotype-matched vaccines, reverse genetics-based live attenuated vaccines obviously appeared to be the most promising candidates. In this review, a comprehensive description of the current and emerging trends in the detection, identification, and control of ND in poultry are provided. The strengths and weaknesses of each of those techniques are also emphasised.

    Extreme precipitation in the Netherlands : An event attribution case study
    Eden, Jonathan M. ; Kew, Sarah F. ; Bellprat, Omar ; Lenderink, Geert ; Manola, Iris ; Omrani, Hiba ; Oldenborgh, Geert Jan van - \ 2018
    Weather and Climate Extremes 21 (2018). - ISSN 2212-0947 - p. 90 - 101.

    Attributing the change in likelihood of extreme weather events, particularly those occurring at small spatiotemporal scales, to anthropogenic forcing is a key challenge in climate science. While a warmer world is associated with an increase in atmospheric moisture on a global scale, the impact on the magnitude of extreme precipitation episodes has substantial regional variability. Analysis of individual cases is important in understanding the extent of these changes on spatial scales relevant to stakeholders. Here, we present a probabilistic attribution analysis of the extreme precipitation that fell in large parts of the Netherlands on 28 July 2014. Using a step-by-step approach, we aim to identify changes in intensity and likelihood of such an event as a result of anthropogenic global warming while highlighting the challenges in performing robust event attribution on high-impact precipitation events that occur at small scales. A method based on extreme value theory is applied to observational data in addition to global and regional climate model ensembles that pass a robust model evaluation process. Results based on observations suggest a strong and significant increase in the intensity and frequency of a 2014-type event as a result of anthropogenic climate change but trends in the model ensembles used are considerably smaller. Our results are communicated alongside considerable uncertainty, highlighting the difficulty in attributing events of this nature. Application of our approach to convection-resolving models may produce a more robust attribution.

    OliveCan : A process-based model of development, growth and yield of olive orchards
    López-Bernal, Álvaro ; Morales, Alejandro ; García-Tejera, Omar ; Testi, Luca ; Orgaz, Francisco ; Melo-Abreu, J.P. De; Villalobos, Francisco J. - \ 2018
    Frontiers in Plant Science 9 (2018). - ISSN 1664-462X
    Carbon assimilation - Crop model - Olea europaea L. - SPAC model - Water stress - Water uptake
    Several simulation models of the olive crop have been formulated so far, but none of them is capable of analyzing the impact of environmental conditions and management practices on water relations, growth and productivity under both well-irrigated and water-limiting irrigation strategies. This paper presents and tests OliveCan, a process-oriented model conceived for those purposes. In short, OliveCan is composed of three main model components simulating the principal elements of the water and carbon balances of olive orchards and the impacts of some management operations. To assess its predictive power, OliveCan was tested against independent data collected in two 3-year field experiments conducted in Córdoba, Spain, each of them applying different irrigation treatments. An acceptable level of agreement was found between measured and simulated values of seasonal evapotranspiration (ET, range 393 to 1016 mm year−1; RMSE of 89 mm year−1), daily transpiration (Ep, range 0.14–3.63 mm d−1; RMSE of 0.32 mm d−1) and oil yield (Yoil, range 13–357 g m−2; RMSE of 63 g m−2). Finally, knowledge gaps identified during the formulation of the model and further testing needs are discussed, highlighting that there is additional room for improving its robustness. It is concluded that OliveCan has a strong potential as a simulation platform for a variety of research applications.
    The Ozone Monitoring Instrument : Overview of 14 years in space
    Levelt, Pieternel F. ; Joiner, Joanna ; Tamminen, Johanna ; Veefkind, J.P. ; Bhartia, Pawan K. ; Zweers, Deborah C.S. ; Duncan, Bryan N. ; Streets, David G. ; Eskes, Henk ; Der, Ronald A. Van; McLinden, Chris ; Fioletov, Vitali ; Carn, Simon ; Laat, Jos De; Deland, Matthew ; Marchenko, Sergey ; McPeters, Richard ; Ziemke, Jerald ; Fu, Dejian ; Liu, Xiong ; Pickering, Kenneth ; Apituley, Arnoud ; Abad, Gonzalo González ; Arola, Antti ; Boersma, Folkert ; Miller, Christopher Chan ; Chance, Kelly ; Graaf, Martin De; Hakkarainen, Janne ; Hassinen, Seppo ; Ialongo, Iolanda ; Kleipool, Quintus ; Krotkov, Nickolay ; Li, Can ; Lamsal, Lok ; Newman, Paul ; Nowlan, Caroline ; Suleiman, Raid ; Tilstra, Lieuwe Gijsbert ; Torres, Omar ; Wang, Huiqun ; Wargan, Krzysztof - \ 2018
    Atmospheric Chemistry and Physics 18 (2018)8. - ISSN 1680-7316 - p. 5699 - 5745.
    This overview paper highlights the successes of the Ozone Monitoring Instrument (OMI) on board the Aura satellite spanning a period of nearly 14 years. Data from OMI has been used in a wide range of applications and research resulting in many new findings. Due to its unprecedented spatial resolution, in combination with daily global coverage, OMI plays a unique role in measuring trace gases important for the ozone layer, air quality, and climate change. With the operational very fast delivery (VFD; direct readout) and near real-time (NRT) availability of the data, OMI also plays an important role in the development of operational services in the atmospheric chemistry domain.
    Variability in size at maturity and reproductive season of queen conch Lobatus gigas (Gastropoda : Strombidae) in the Wider Caribbean Region
    Boman, Erik Maitz ; Graaf, Martin de; Nagelkerke, Leopold A.J. ; Stoner, Allan W. ; Bissada, Caroline E. ; Avila-Poveda, Omar Hernando ; Baqueiro-Cardenas, Erick Raul ; Smaal, Aad C. - \ 2018
    Fisheries Research 201 (2018). - ISSN 0165-7836 - p. 18 - 25.
    Caribbean - Fisheries management - Mollusks - Reproductive biology - Sexual dimorphism
    Queen conch (Lobatus gigas), is an economically and culturally important marine gastropod. The species is subject to extensive exploitation throughout large parts of the Caribbean which has led to a decrease in population densities across much of the species’ distribution range. Hence, there is a need for protective measures to safeguard the reproductive stock. This requires a better estimation of its size at maturity, which is best quantified as the thickness of the lip that the shell develops after reaching its maximum length. The lip thickness at 50% maturity (LT50) was determined using a logistic and an accumulation model, from seven representative location of distribution of this species in the Wider Caribbean Region. LT50 of both females (7–14 mm) and males (4–11.5 mm) varied between different locations in the Caribbean, although it did not correspond with variation in water temperature. In most cases females had a larger LT50 than males indicating sexual dimorphism. LT50 values estimated with the logistic model were smaller (7–14 mm for females, 4–11.5 mm for males) than values estimated with the accumulation model (13–26 mm for females, 16–24 mm for males), showing an overestimation of LT50 in queen conch in previous studies which used the accumulation model to estimate LT50. Locations with a relatively high variation in water temperature had a significantly shorter reproductive season. The implementation of adequate minimum size regulation based on lip thickness (ca. 15 mm) and a Caribbean wide seasonal closure (May–September) using the most recent biological information from this study, taking into consideration the local differences in LT50 and reproductive season, will assist in developing a long term sustainable queen conch fishery in the Caribbean.
    Brushes of Linear and Dendritically Branched Polyelectrolytes
    Zhulina, E.B. ; Leermakers, F.A.M. ; Borisov, O.V. - \ 2017
    In: Polymer and Biopolymer Brushes / Azzaroni, Omar, Szleifer, Igal, Wiley-Blackwell - ISBN 9781119455011 - p. 223 - 241.
    We present an analytical self‐consistent field model of planar brushes formed by linear or regularly branched charged macromolecules (dendrons with long flexible polyelectrolyte spacers). The macromolecules are tethered by a terminal root monomer to an impermeable surface at grafting densities at which intermolecular interactions dominate over intramolecular ones and lead to the elastic stretching of dendrons normally to the surface. Under the conditions of linear (Gaussian) elasticity for tethered chains, the architecture of polyion can be explicitly accounted for through the so‐called topological coefficient k. The topological coefficient k does not depend on the system parameters such as a fraction of ionized monomers, chain‐grafting density, salt concentration in solution, and thermodynamic quality of the solvent and provides a unified description of dendron brushes with various architectures. We focus here on symmetric polyelectrolyte dendrons with a number of generations, g = 1, 2, and 3, short comb‐like polymers, and also include for comparison linear polyions with g = 0. The analytical theory is complemented with the numerical Scheutjens‐Fleer self‐consistent field (SF‐SCF) calculations of electrostatic potential, polymer density profile, and end‐point distribution in brushes with selected architectures of dendrons. It is shown that both models are in good agreement under the conditions of linear (Gaussian) elasticity for the tethered polyions. An onset of nonlinear elasticity leads to noticeable deviations between the analytical and numerical results.
    Residual uncertainty estimation using instance-based learning with applications to hydrologic forecasting
    Wani, Omar ; Beckers, Joost V.L. ; Weerts, Albrecht H. ; Solomatine, Dimitri P. - \ 2017
    Hydrology and Earth System Sciences 21 (2017)8. - ISSN 1027-5606 - p. 4021 - 4036.

    A non-parametric method is applied to quantify residual uncertainty in hydrologic streamflow forecasting. This method acts as a post-processor on deterministic model forecasts and generates a residual uncertainty distribution. Based on instance-based learning, it uses a k nearest-neighbour search for similar historical hydrometeorological conditions to determine uncertainty intervals from a set of historical errors, i.e. discrepancies between past forecast and observation. The performance of this method is assessed using test cases of hydrologic forecasting in two UK rivers: the Severn and Brue. Forecasts in retrospect were made and their uncertainties were estimated using kNN resampling and two alternative uncertainty estimators: quantile regression (QR) and uncertainty estimation based on local errors and clustering (UNEEC). Results show that kNN uncertainty estimation produces accurate and narrow uncertainty intervals with good probability coverage. Analysis also shows that the performance of this technique depends on the choice of search space. Nevertheless, the accuracy and reliability of uncertainty intervals generated using kNN resampling are at least comparable to those produced by QR and UNEEC. It is concluded that kNN uncertainty estimation is an interesting alternative to other post-processors, like QR and UNEEC, for estimating forecast uncertainty. Apart from its concept being simple and well understood, an advantage of this method is that it is relatively easy to implement.

    Two maize Kip-related proteins differentially interact with, inhibit and are phosphorylated by cyclin D-cyclin-dependent kinase complexes
    Godínez-Palma, Silvia K. ; Rosas-Bringas, Fernando R. ; Rosas-Bringas, Omar G. ; García-Ramírez, Elpidio ; Zamora-Zaragoza, Jorge ; Vázquez-Ramos, Jorge M. - \ 2017
    Journal of Experimental Botany 68 (2017)7. - ISSN 0022-0957 - p. 1585 - 1597.
    CDKs - Cyclins D - ICK/KRPs - Kinase inhibition - KRP phosphorylation - Zea mays

    The family of maize Kip-related proteins (KRPs) has been studied and a nomenclature based on the relationship to rice KRP genes is proposed. Expression studies of KRP genes indicate that all are expressed at 24 h of seed germination but expression is differential in the different tissues of maize plantlets. Recombinant KRP1;1 and KRP4;2 proteins, members of different KRP classes, were used to study association to and inhibitory activity on different maize cyclin D (CycD)-cyclin-dependent kinase (CDK) complexes. Kinase activity in CycD2;2-CDK, CycD4;2-CDK, and CycD5;3- CDK complexes was inhibited by both KRPs; however, only KRP1;1 inhibited activity in the CycD6;1-CDK complex, not KRP4;2. Whereas KRP1;1 associated with either CycD2;2 or CycD6;1, and to cyclin-dependent kinase A (CDKA) recombinant proteins, forming ternary complexes, KRP4;2 bound CDKA and CycD2;2 but did not bind CycD6;1, establishing a differential association capacity. All CycD-CDK complexes included here phosphorylated both the retinoblastoma- related (RBR) protein and the two KRPs; interestingly, while KRP4;2 phosphorylated by the CycD2;2-CDK complex increased its inhibitory capacity, when phosphorylated by the CycD6;1-CDK complex the inhibitory capacity was reduced or eliminated. Evidence suggests that the phosphorylated residues in KRP4;2 may be different for every kinase, and this would influence its performance as a cyclin-CDK inhibitor.

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