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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The landscape of soil carbon data: Emerging questions, synergies and databases
Malhotra, Avni ; Todd-Brown, Katherine ; Nave, Lucas E. ; Batjes, Niels H. ; Holmquist, James R. ; Hoyt, Alison M. ; Iversen, Colleen M. ; Jackson, Robert B. ; Lajtha, Kate ; Lawrence, Corey ; Vindušková, Olga ; Wieder, William ; Williams, Mathew ; Hugelius, Gustaf ; Harden, Jennifer - \ 2019
Progress in Physical Geography 43 (2019)5. - ISSN 0309-1333 - p. 707 - 719.
long-term ecological research - model–data integration - root traits - Soil carbon data - soil carbon stabilization - soil chronosequence - soil database - soil radiocarbon - wetland carbon

Soil carbon has been measured for over a century in applications ranging from understanding biogeochemical processes in natural ecosystems to quantifying the productivity and health of managed systems. Consolidating diverse soil carbon datasets is increasingly important to maximize their value, particularly with growing anthropogenic and climate change pressures. In this progress report, we describe recent advances in soil carbon data led by the International Soil Carbon Network and other networks. We highlight priority areas of research requiring soil carbon data, including (a) quantifying boreal, arctic and wetland carbon stocks, (b) understanding the timescales of soil carbon persistence using radiocarbon and chronosequence studies, (c) synthesizing long-term and experimental data to inform carbon stock vulnerability to global change, (d) quantifying root influences on soil carbon and (e) identifying gaps in model–data integration. We also describe the landscape of soil datasets currently available, highlighting their strengths, weaknesses and synergies. Now more than ever, integrated soil data are needed to inform climate mitigation, land management and agricultural practices. This report will aid new data users in navigating various soil databases and encourage scientists to make their measurements publicly available and to join forces to find soil-related solutions.

Contribution of the land sector to a 1.5 °C world
Roe, Stephanie ; Streck, Charlotte ; Obersteiner, Michael ; Frank, Stefan ; Griscom, Bronson ; Drouet, Laurent ; Fricko, Oliver ; Gusti, Mykola ; Harris, Nancy ; Hasegawa, Tomoko ; Hausfather, Zeke ; Havlík, Petr ; House, Jo ; Nabuurs, Gert-Jan ; Popp, Alexander ; Sánchez, María José Sanz ; Sanderman, Jonathan ; Smith, Pete ; Stehfest, Elke ; Lawrence, Deborah - \ 2019
Nature Climate Change 9 (2019). - ISSN 1758-678X - p. 817 - 828.
The Paris Agreement introduced an ambitious goal of limiting warming to 1.5 °C above pre-industrial levels. Here we combine a review of modelled pathways and literature on mitigation strategies, and develop a land-sector roadmap of priority measures and regions that can help to achieve the 1.5 °C temperature goal. Transforming the land sector and deploying measures in agriculture, forestry, wetlands and bioenergy could feasibly and sustainably contribute about 30%, or 15 billion tonnes of carbon dioxide equivalent (GtCO2e) per year, of the global mitigation needed in 2050 to deliver on the 1.5 °C target, but it will require substantially more effort than the 2 °C target. Risks and barriers must be addressed and incentives will be necessary to scale up mitigation while maximizing sustainable development, food security and environmental co-benefits.
The Global Gridded Crop Model Intercomparison phase 1 simulation dataset
Müller, Christoph ; Elliott, Joshua ; Kelly, David ; Arneth, Almut ; Balkovic, Juraj ; Ciais, Philippe ; Deryng, Delphine ; Folberth, Christian ; Hoek, Steven ; Izaurralde, Roberto C. ; Jones, Curtis D. ; Khabarov, Nikolay ; Lawrence, Peter ; Liu, Wenfeng ; Olin, Stefan ; Pugh, Thomas A.M. ; Reddy, Ashwan ; Rosenzweig, Cynthia ; Ruane, Alex C. ; Sakurai, Gen ; Schmid, Erwin ; Skalsky, Rastislav ; Wang, Xuhui ; Wit, Allard de; Yang, Hong - \ 2019
Scientific Data 6 (2019). - ISSN 2052-4463 - 22 p.

The Global Gridded Crop Model Intercomparison (GGCMI) phase 1 dataset of the Agricultural Model Intercomparison and Improvement Project (AgMIP) provides an unprecedentedly large dataset of crop model simulations covering the global ice-free land surface. The dataset consists of annual data fields at a spatial resolution of 0.5 arc-degree longitude and latitude. Fourteen crop modeling groups provided output for up to 11 historical input datasets spanning 1901 to 2012, and for up to three different management harmonization levels. Each group submitted data for up to 15 different crops and for up to 14 output variables. All simulations were conducted for purely rainfed and near-perfectly irrigated conditions on all land areas irrespective of whether the crop or irrigation system is currently used there. With the publication of the GGCMI phase 1 dataset we aim to promote further analyses and understanding of crop model performance, potential relationships between productivity and environmental impacts, and insights on how to further improve global gridded crop model frameworks. We describe dataset characteristics and individual model setup narratives.

Meta-analysis of epigenome-wide association studies in neonates reveals widespread differential DNA methylation associated with birthweight
Küpers, Leanne K. ; Monnereau, Claire ; Sharp, Gemma C. ; Yousefi, Paul ; Salas, Lucas A. ; Ghantous, Akram ; Page, Christian M. ; Reese, Sarah E. ; Wilcox, Allen J. ; Czamara, Darina ; Starling, Anne P. ; Novoloaca, Alexei ; Lent, Samantha ; Roy, Ritu ; Hoyo, Cathrine ; Breton, Carrie V. ; Allard, Catherine ; Just, Allan C. ; Bakulski, Kelly M. ; Holloway, John W. ; Everson, Todd M. ; Xu, Cheng Jian ; Huang, Rae Chi ; Plaat, Diana A. van der; Wielscher, Matthias ; Merid, Simon Kebede ; Ullemar, Vilhelmina ; Rezwan, Faisal I. ; Lahti, Jari ; Dongen, Jenny van; Langie, Sabine A.S. ; Richardson, Tom G. ; Magnus, Maria C. ; Nohr, Ellen A. ; Xu, Zongli ; Duijts, Liesbeth ; Zhao, Shanshan ; Zhang, Weiming ; Plusquin, Michelle ; DeMeo, Dawn L. ; Solomon, Olivia ; Heimovaara, Joosje H. ; Jima, Dereje D. ; Gao, Lu ; Bustamante, Mariona ; Perron, Patrice ; Wright, Robert O. ; Hertz-Picciotto, Irva ; Zhang, Hongmei ; Karagas, Margaret R. ; Gehring, Ulrike ; Marsit, Carmen J. ; Beilin, Lawrence J. ; Vonk, Judith M. ; Jarvelin, Marjo Riitta ; Bergström, Anna ; Örtqvist, Anne K. ; Ewart, Susan ; Villa, Pia M. ; Moore, Sophie E. ; Willemsen, Gonneke ; Standaert, Arnout R.L. ; Håberg, Siri E. ; Sørensen, Thorkild I.A. ; Taylor, Jack A. ; Räikkönen, Katri ; Yang, Ivana V. ; Kechris, Katerina ; Nawrot, Tim S. ; Silver, Matt J. ; Gong, Yun Yun ; Richiardi, Lorenzo ; Kogevinas, Manolis ; Litonjua, Augusto A. ; Eskenazi, Brenda ; Huen, Karen ; Mbarek, Hamdi ; Maguire, Rachel L. ; Dwyer, Terence ; Vrijheid, Martine ; Bouchard, Luigi ; Baccarelli, Andrea A. ; Croen, Lisa A. ; Karmaus, Wilfried ; Anderson, Denise ; Vries, Maaike de; Sebert, Sylvain ; Kere, Juha ; Karlsson, Robert ; Arshad, Syed Hasan ; Hämäläinen, Esa ; Routledge, Michael N. ; Boomsma, Dorret I. ; Feinberg, Andrew P. ; Newschaffer, Craig J. ; Govarts, Eva ; Moisse, Matthieu ; Fallin, M.D. ; Melén, Erik ; Prentice, Andrew M. ; Kajantie, Eero ; Almqvist, Catarina ; Oken, Emily ; Dabelea, Dana ; Boezen, H.M. ; Melton, Phillip E. ; Wright, Rosalind J. ; Koppelman, Gerard H. ; Trevisi, Letizia ; Hivert, Marie France ; Sunyer, Jordi ; Munthe-Kaas, Monica C. ; Murphy, Susan K. ; Corpeleijn, Eva ; Wiemels, Joseph ; Holland, Nina ; Herceg, Zdenko ; Binder, Elisabeth B. ; Davey Smith, George ; Jaddoe, Vincent W.V. ; Lie, Rolv T. ; Nystad, Wenche ; London, Stephanie J. ; Lawlor, Debbie A. ; Relton, Caroline L. ; Snieder, Harold ; Felix, Janine F. - \ 2019
Nature Communications 10 (2019)1. - ISSN 2041-1723

Birthweight is associated with health outcomes across the life course, DNA methylation may be an underlying mechanism. In this meta-analysis of epigenome-wide association studies of 8,825 neonates from 24 birth cohorts in the Pregnancy And Childhood Epigenetics Consortium, we find that DNA methylation in neonatal blood is associated with birthweight at 914 sites, with a difference in birthweight ranging from −183 to 178 grams per 10% increase in methylation (P Bonferroni < 1.06 x 10 −7 ). In additional analyses in 7,278 participants, <1.3% of birthweight-associated differential methylation is also observed in childhood and adolescence, but not adulthood. Birthweight-related CpGs overlap with some Bonferroni-significant CpGs that were previously reported to be related to maternal smoking (55/914, p = 6.12 x 10 −74 ) and BMI in pregnancy (3/914, p = 1.13x10 −3 ), but not with those related to folate levels in pregnancy. Whether the associations that we observe are causal or explained by confounding or fetal growth influencing DNA methylation (i.e. reverse causality) requires further research.

State-of-the-art global models underestimate impacts from climate extremes
Schewe, Jacob ; Gosling, Simon N. ; Reyer, Christopher ; Zhao, Fang ; Ciais, Philippe ; Elliott, Joshua ; Francois, Louis ; Huber, Veronika ; Lotze, Heike K. ; Seneviratne, Sonia I. ; Vliet, Michelle T.H. Van; Vautard, Robert ; Wada, Yoshihide ; Breuer, Lutz ; Büchner, Matthias ; Carozza, David A. ; Chang, Jinfeng ; Coll, Marta ; Deryng, Delphine ; Wit, Allard De; Eddy, Tyler D. ; Folberth, Christian ; Frieler, Katja ; Friend, Andrew D. ; Gerten, Dieter ; Gudmundsson, Lukas ; Hanasaki, Naota ; Ito, Akihiko ; Khabarov, Nikolay ; Kim, Hyungjun ; Lawrence, Peter ; Morfopoulos, Catherine ; Müller, Christoph ; Müller Schmied, Hannes ; Orth, René ; Ostberg, Sebastian ; Pokhrel, Yadu ; Pugh, Thomas A.M. ; Sakurai, Gen ; Satoh, Yusuke ; Schmid, Erwin ; Stacke, Tobias ; Steenbeek, Jeroen ; Steinkamp, Jörg ; Tang, Qiuhong ; Tian, Hanqin ; Tittensor, Derek P. ; Volkholz, Jan ; Wang, Xuhui ; Warszawski, Lila - \ 2019
Nature Communications 10 (2019). - ISSN 2041-1723
Global impact models represent process-level understanding of how natural and human systems may be affected by climate change. Their projections are used in integrated assessments of climate change. Here we test, for the first time, systematically across many important systems, how well such impact models capture the impacts of extreme climate conditions. Using the 2003 European heat wave and drought as a historical analogue for comparable events in the future, we find that a majority of models underestimate the extremeness of impacts in important sectors such as agriculture, terrestrial ecosystems, and heat-related human mortality, while impacts on water resources and hydropower are overestimated in some river basins; and the spread across models is often large. This has important implications for economic assessments of climate change impacts that rely on these models. It also means that societal risks from future extreme events may be greater than previously thought.
First records of the dwarf surf clam Mulinia lateralis (Say, 1822) in Europe
Craeymeersch, J.A. ; Faasse, M.A. ; Gheerardyn, H. ; Troost, K. ; Nijland, R. ; Engelberts, A. ; Perdon, K.J. ; Ende, D. Van Den; Zwol, J. Van - \ 2019
Marine Biodiversity Records 12 (2019)1. - ISSN 1755-2672 - 11 p.
Mulinia lateris - Bivalvia - Marine - North Sea - Invasive - Competition
This paper reports the first records of the dwarf surf clam Mulinia lateralis (Say, 1822) outside its native area, which is the western Atlantic Ocean, ranging from the Gulf of St Lawrence to the Gulf of Mexico. In 2017 and 2018 specimens were found in the Dutch coastal waters (North Sea), in the Wadden Sea and in the
Westerschelde estuary, in densities of up to almost 6000 individuals per square meter. In view of its ecology and distributional range in the native area M. lateralis has the potential to become an invasive species. Its ability to quickly colonize defaunated areas, its high fecundity and short generation time, its tolerance for anoxia and temperature extremes and its efficient exploitation of the high concentrations of phytoplankton and natural seston at the sediment-water interface may bring it into competition with native species for food
and space.
How to slow the global spread of small hive beetles, Aethina tumida
Schäfer, M.O. ; Cardaio, Ilaria ; Cilia, Giovanni ; Cornelissen, A.C.M. ; Crailsheim, Karl ; Formato, Giovanni ; Lawrence, A.K. ; Conte, Y. Le; Mutinelli, Franco ; Nanetti, Antonio ; Rivera-Gomis, Jorge ; Teepe, Anneke ; Neumann, P. - \ 2019
Biological Invasions 21 (2019)5. - ISSN 1387-3547 - p. 1451 - 1459.
Apis mellifera - Apiculture - Bees - Contingency plan - Honeybee - Parasite
Small hive beetles (SHBs) are parasites of social bee colonies endemic to sub-Saharan Africa and have become a widespread invasive species. In the new ranges, SHBs can cause damage to apiculture and wild bees. Although the further spread seems inevitable, eradication of new introductions and containment of established ones are nevertheless urgently required to slow down the invasion speed until better mitigation options are available. However, at present there is no adequate action plan at hand. Here, we propose to take advantage of SHB invasion history and biology to enrol a feasible plan involving all stakeholders. Raising awareness, education and motivation of stakeholders (incl. adequate and timely compensation of beekeepers) is essential for success. Moreover, sentinel apiaries are recommended in areas at risk, because early detection is crucial for the success of eradication efforts. Given that introductions are detected early, SHB eradication is recommended, incl. destruction of all infested apiaries, installation of sentinel colonies to lure escaped SHBs and a ban on migratory beekeeping. If wild perennial social bee colonies are infested, eradication programs are condemned to fail and a strategic switch to a containment strategy is recommended. Containment includes adequate integrated pest management and a strict ban on migratory beekeeping. Despite considerable gaps in our knowledge of SHBs, the proposed action plan will help stakeholders to slow down the global spread of SHBs.
Breeding progress and preparedness for mass-scale deployment of perennial lignocellulosic biomass crops switchgrass, miscanthus, willow and poplar
Clifton-Brown, John ; Harfouche, Antoine ; Casler, Michael D. ; Dylan Jones, Huw ; Macalpine, William J. ; Murphy-Bokern, Donal ; Smart, Lawrence B. ; Adler, Anneli ; Ashman, Chris ; Awty-Carroll, Danny ; Bastien, Catherine ; Bopper, Sebastian ; Botnari, Vasile ; Brancourt-Hulmel, Maryse ; Chen, Zhiyong ; Clark, Lindsay V. ; Cosentino, Salvatore ; Dalton, Sue ; Davey, Chris ; Dolstra, Oene ; Donnison, Iain ; Flavell, Richard ; Greef, Joerg ; Hanley, Steve ; Hastings, Astley ; Hertzberg, Magnus ; Hsu, Tsai Wen ; Huang, Lin S. ; Iurato, Antonella ; Jensen, Elaine ; Jin, Xiaoli ; Jørgensen, Uffe ; Kiesel, Andreas ; Kim, Do Soon ; Liu, Jianxiu ; McCalmont, Jon P. ; McMahon, Bernard G. ; Mos, Michal ; Robson, Paul ; Sacks, Erik J. ; Sandu, Anatolii ; Scalici, Giovanni ; Schwarz, Kai ; Scordia, Danilo ; Shafiei, Reza ; Shield, Ian ; Slavov, Gancho ; Stanton, Brian J. ; Swaminathan, Kankshita ; Trindade, Luisa M. - \ 2019
Global change biology Bioenergy 11 (2019)1. - ISSN 1757-1693 - p. 118 - 151.
bioenergy - feedstocks - lignocellulose - M. sacchariflorus - M. sinensis - Miscanthus - Panicum virgatum - perennial biomass crop - Populus spp. - Salix spp.

Genetic improvement through breeding is one of the key approaches to increasing biomass supply. This paper documents the breeding progress to date for four perennial biomass crops (PBCs) that have high output–input energy ratios: namely Panicum virgatum (switchgrass), species of the genera Miscanthus (miscanthus), Salix (willow) and Populus (poplar). For each crop, we report on the size of germplasm collections, the efforts to date to phenotype and genotype, the diversity available for breeding and on the scale of breeding work as indicated by number of attempted crosses. We also report on the development of faster and more precise breeding using molecular breeding techniques. Poplar is the model tree for genetic studies and is furthest ahead in terms of biological knowledge and genetic resources. Linkage maps, transgenesis and genome editing methods are now being used in commercially focused poplar breeding. These are in development in switchgrass, miscanthus and willow generating large genetic and phenotypic data sets requiring concomitant efforts in informatics to create summaries that can be accessed and used by practical breeders. Cultivars of switchgrass and miscanthus can be seed-based synthetic populations, semihybrids or clones. Willow and poplar cultivars are commercially deployed as clones. At local and regional level, the most advanced cultivars in each crop are at technology readiness levels which could be scaled to planting rates of thousands of hectares per year in about 5 years with existing commercial developers. Investment in further development of better cultivars is subject to current market failure and the long breeding cycles. We conclude that sustained public investment in breeding plays a key role in delivering future mass-scale deployment of PBCs.

Lawrence Jones-Walters - Challenge, opportunity or dilemma?
Jones-Walters, Lawrence - \ 2018
sustainable development
Introducing Adaptive Flood Risk Management in England, New Zealand, and the Netherlands : The Impact of Administrative Traditions
Buuren, Arwin van; Lawrence, Judy ; Potter, Karen ; Warner, Jeroen F. - \ 2018
Review of Policy Research 35 (2018)6. - ISSN 1541-132X - p. 907 - 929.
adaptive flood risk management - administrative traditions - climate change adaptation - implementation - policy change

Climate change adaptation creates significant challenges for decision makers in the flood risk-management policy domain. Given the complex characteristics of climate change, adaptive approaches (which can be adjusted as circumstances evolve) are deemed necessary to deal with a range of uncertainties around flood hazard and its impacts and associated risks. The question whether implementing adaptive approaches is successful highly depends upon how the administrative tradition of a country enable or hinder applying a more adaptive approach. In this article, we discern how the administrative tradition in the Netherlands, England, and New Zealand impact upon the introduction of adaptive flood risk management approaches. Using the concept of administrative traditions, we aim to explain the similarities and/or differences in how adaptive strategies are shaped and implemented in the three different state flood management regimes and furthermore, which aspects related to administrative traditions are enablers or barriers to innovation in these processes.

How private are Europe’s private forests? A comparative property rights analysis
Nichiforel, Liviu ; Keary, Kevin ; Deuffic, Philippe ; Weiss, Gerhard ; Thorsen, Bo Jellesmark ; Winkel, Georg ; Avdibegović, Mersudin ; Dobšinská, Zuzana ; Feliciano, Diana ; Gatto, Paola ; Gorriz Mifsud, Elena ; Hoogstra-klein, Marjanke ; Hrib, Michal ; Hujala, Teppo ; Jager, Laszlo ; Jarský, Vilém ; Jodłowski, Krzysztof ; Lawrence, Anna ; Lukmine, Diana ; Pezdevšek Malovrh, Špela ; Nedeljković, Jelena ; Nonić, Dragan ; Krajter Ostoić, Silvija ; Pukall, Klaus ; Rondeux, Jacques ; Samara, Theano ; Sarvašová, Zuzana ; Scriban, Ramona Elena ; Šilingienė, Rita ; Sinko, Milan ; Stojanovska, Makedonka ; Stojanovski, Vladimir ; Stoyanov, Nickola ; Teder, Meelis ; Vennesland, Birger ; Vilkriste, Lelde ; Wilhelmsson, Erik ; Wilkes-Allemann, Jerylee ; Bouriaud, Laura - \ 2018
Land Use Policy 76 (2018). - ISSN 0264-8377 - p. 535 - 552.
Private forests are widespread in Europe providing a range of ecosystem services of significant value to society, and there are calls for novel policies to enhance their provision and to face the challenges of environmental changes. Such policies need to acknowledge the importance of private forests, and importantly they need to be based on a deep understanding of how property rights held by private forest owners vary across Europe. We collected and analysed data on the content of property rights based on formal legal requirements existing in 31 European jurisdictions. To allow a comparison across jurisdictions, we constructed an original Property Rights Index for Forestry encompassing five rights domains (access, withdrawal, management, exclusion and alienation). We documented substantial variation of the private forest owners’ rights, and notably to i) make decisions in operational management and the formulation of management goals, ii) withdraw timber resources from their forest, and iii) exclude others from the use of forest resources. We identified broad relations between the scope for decision making of private forest owners and jurisdictions’ former socio-political background and geographical distribution. The variation in the content of property rights has implications for the implementation of international environmental policies, and stresses the need for tailored policy instruments, when addressing European society’s rural development, the bioeconomy, climate change mitigation measures and nature protection strategies.
Data from: Genome-wide SNP data unveils the globalization of domesticated pigs
Yang, Bin ; Cui, Leilei ; Pérez-Enciso, M. ; Traspov, Aleksei ; Crooijmans, R.P.M.A. ; Zinovieva, Natalia ; Schook, Lawrence B. ; Gatphayak, Kesinee ; Knorr, Christophe ; Triantafyllidis, Alex ; Alexandri, Panoraia ; Semiadi, Gono ; Hanotte, Olivier ; Dias, Deodália ; Dovč, Peter ; Uimari, Pekka ; Iacolina, Laura ; Scandura, Massimo ; Groenen, M. ; Huang, L. ; Megens, H.J.W.C. - \ 2017
pig - domestication - genome - selection
Background: Pigs were domesticated independently in Eastern and Western Eurasia early during the agricultural revolution, and have since been transported and traded across the globe. Here, we present a worldwide survey on 60K genome-wide single nucleotide polymorphism (SNP) data for 2093 pigs, including 1839 domestic pigs representing 122 local and commercial breeds, 215 wild boars, and 39 out-group suids, from Asia, Europe, America, Oceania and Africa. The aim of this study was to infer global patterns in pig domestication and diversity related to demography, migration, and selection. Results: A deep phylogeographic division reflects the dichotomy between early domestication centers. In the core Eastern and Western domestication regions, Chinese pigs show differentiation between breeds due to geographic isolation, whereas this is less pronounced in European pigs. The inferred European origin of pigs in the Americas, Africa, and Australia reflects European expansion during the sixteenth to nineteenth centuries. Human-mediated introgression, which is due, in particular, to importing Chinese pigs into the UK during the eighteenth and nineteenth centuries, played an important role in the formation of modern pig breeds. Inbreeding levels vary markedly between populations, from almost no runs of homozygosity (ROH) in a number of Asian wild boar populations, to up to 20% of the genome covered by ROH in a number of Southern European breeds. Commercial populations show moderate ROH statistics. For domesticated pigs and wild boars in Asia and Europe, we identified highly differentiated loci that include candidate genes related to muscle and body development, central nervous system, reproduction, and energy balance, which are putatively under artificial selection. Conclusions: Key events related to domestication, dispersal, and mixing of pigs from different regions are reflected in the 60K SNP data, including the globalization that has recently become full circle since Chinese pig breeders in the past decades started selecting Western breeds to improve local Chinese pigs. Furthermore, signatures of ongoing and past selection, acting at different times and on different genetic backgrounds, enhance our insight in the mechanism of domestication and selection. The global diversity statistics presented here highlight concerns for maintaining agrodiversity, but also provide a necessary framework for directing genetic conservation.
A validated, transitional and translational porcine model of hepatocellular carcinoma
Schachtschneider, Kyle M. ; Schwind, Regina M. ; Darfour-Oduro, Kwame A. ; De, Arun K. ; Rund, Lauretta A. ; Singh, Kuldeep ; Principe, Daniel R. ; Guzman, Grace ; Ray, Charles E. ; Ozer, Howard ; Gaba, Ron C. ; Schook, Lawrence B. - \ 2017
Oncotarget 8 (2017)38. - ISSN 1949-2553 - p. 63620 - 63634.
Gene expression - Hepatocellular carcinoma - Human - Interventional radiology - Porcine model

Difficult questions are confronting clinicians attempting to improve hepatocellular carcinoma (HCC) outcomes. A large animal model with genetic, anatomical, and physiological similarities to humans is required to transition from mouse models to human clinical trials to address unmet clinical needs. To validate our previously reported inducible porcine cancer model (Oncopig) as a transitional HCC model, Oncopig hepatocyte cultures were transformed using Cre recombinase. The resulting porcine HCC cells (pHCC) expressed oncogenic TP53R167H and KRASG12D, and displayed nuclear pleomorphisms with pale to granular cytoplasm arranged in expanded plates similar to human HCC histopathology. Human HCC transcriptional hallmarks were detected in pHCC cells using RNA-seq, including TERT reactivation, apoptosis evasion, angiogenesis activation, and Wnt signaling activation. Master regulators of gene expression were conserved across Oncopig and 18 human HCC cell lines. pHCC injection into SCID mice resulted in tumors recapitulating human HCC characteristics, including thick trabeculae formation, pseudoacini patterning, and sheets of wellvascularized stroma. Finally, autologous injection of pHCC cells subcutaneously yielded a tumor histologically characterized as Edmondson Steiner (HCC nuclear grade assessment system) grade 2 HCC with trabecular patterning and T-lymphocyte infiltration. These data demonstrate the Oncopig HCC model's utility for improving detection, treatment, and biomarker discovery relevant to human HCC.

Genome-wide SNP data unveils the globalization of domesticated pigs
Yang, Bin ; Cui, Leilei ; Pérez-Enciso, M. ; Traspov, Aleksei ; Crooijmans, Richard P.M.A. ; Zinovieva, Natalia ; Schook, Lawrence B. ; Archibald, Alan ; Gatphayak, Kesinee ; Knorr, Christophe ; Triantafyllidis, Alex ; Alexandri, Panoraia ; Semiadi, Gono ; Hanotte, Olivier ; Dias, Deodália ; Dovč, Peter ; Uimari, Pekka ; Iacolina, Laura ; Scandura, Massimo ; Groenen, Martien A.M. ; Huang, L. ; Megens, Hendrik Jan - \ 2017
Genetics, Selection, Evolution 49 (2017). - ISSN 0999-193X - 15 p.

Background: Pigs were domesticated independently in Eastern and Western Eurasia early during the agricultural revolution, and have since been transported and traded across the globe. Here, we present a worldwide survey on 60K genome-wide single nucleotide polymorphism (SNP) data for 2093 pigs, including 1839 domestic pigs representing 122 local and commercial breeds, 215 wild boars, and 39 out-group suids, from Asia, Europe, America, Oceania and Africa. The aim of this study was to infer global patterns in pig domestication and diversity related to demography, migration, and selection. Results: A deep phylogeographic division reflects the dichotomy between early domestication centers. In the core Eastern and Western domestication regions, Chinese pigs show differentiation between breeds due to geographic isolation, whereas this is less pronounced in European pigs. The inferred European origin of pigs in the Americas, Africa, and Australia reflects European expansion during the sixteenth to nineteenth centuries. Human-mediated introgression, which is due, in particular, to importing Chinese pigs into the UK during the eighteenth and nineteenth centuries, played an important role in the formation of modern pig breeds. Inbreeding levels vary markedly between populations, from almost no runs of homozygosity (ROH) in a number of Asian wild boar populations, to up to 20% of the genome covered by ROH in a number of Southern European breeds. Commercial populations show moderate ROH statistics. For domesticated pigs and wild boars in Asia and Europe, we identified highly differentiated loci that include candidate genes related to muscle and body development, central nervous system, reproduction, and energy balance, which are putatively under artificial selection. Conclusions: Key events related to domestication, dispersal, and mixing of pigs from different regions are reflected in the 60K SNP data, including the globalization that has recently become full circle since Chinese pig breeders in the past decades started selecting Western breeds to improve local Chinese pigs. Furthermore, signatures of ongoing and past selection, acting at different times and on different genetic backgrounds, enhance our insight in the mechanism of domestication and selection. The global diversity statistics presented here highlight concerns for maintaining agrodiversity, but also provide a necessary framework for directing genetic conservation.

Human Wellbeing-Sociability, Performance, and Health
Folmer, Britta ; Farah, Adriana ; Jones, Lawrence ; Fogliano, Vincenzo - \ 2017
In: The Craft and Science of Coffee Elsevier Inc. Academic Press - ISBN 9780128035207 - p. 493 - 520.
Coffee - Disease prevention - Health - Historical facts - Performance - Social - Wellbeing
It is well known that coffee is one of the most widely consumed beverages worldwide. Since its discovery, it has played an important role in the life of many people, even though throughout history people have debated the consequences of drinking coffee to the human body and mind. The pleasurable taste and stimulating properties have been worshiped and hated. But along with these love and hate waves science has evolved and revealed that coffee is a complex mixture of substances that may act together to prevent diseases. Today the debate around the stimulating properties of caffeine has moved from "good versus bad" to the quantities needed for a beneficial impact, and amounts corresponding safe consumption. This chapter will explore these aspects bringing an overview of the evolution of coffees role in the well-being of people through history.
Oncopig soft-tissue sarcomas recapitulate key transcriptional features of human sarcomas
Schachtschneider, Kyle M. ; Liu, Yingkai ; Makelainen, Suvi ; Madsen, Ole ; Rund, Laurie A. ; Groenen, Martien A.M. ; Schook, Lawrence B. - \ 2017
Scientific Reports 7 (2017). - ISSN 2045-2322 - 12 p.

Human soft-tissue sarcomas (STS) are rare mesenchymal tumors with a 5-year survival rate of 50%, highlighting the need for further STS research. Research has been hampered by limited human sarcoma cell line availability and the large number of STS subtypes, making development of STS cell lines and animal models representative of the diverse human STS subtypes critical. Pigs represent ideal human disease models due to their similar size, anatomy, metabolism, and genetics compared to humans. The Oncopig encodes inducible KRAS G12D and TP53 R167H transgenes, allowing for STS modeling in a spatial and temporal manner. This study utilized Oncopig STS cell line (fibroblast) and tumor (leiomyosarcoma) RNA-seq data to compare Oncopig and human STS expression profiles. Altered expression of 3,360 and 7,652 genes was identified in Oncopig STS cell lines and leiomyosarcomas, respectively. Transcriptional hallmarks of human STS were observed in Oncopig STS, including altered TP53 signaling, Wnt signaling activation, and evidence of epigenetic reprogramming. Furthermore, master regulators of Oncopig STS expression were identified, including FOSL1, which was previously identified as a potential human STS therapeutic target. These results demonstrate the Oncopig STS model's ability to mimic human STS transcriptional profiles, providing a valuable resource for sarcoma research and cell line development.

Global gridded crop model evaluation : Benchmarking, skills, deficiencies and implications
Müller, Christoph ; Elliott, Joshua ; Chryssanthacopoulos, James ; Arneth, Almut ; Balkovic, Juraj ; Ciais, Philippe ; Deryng, Delphine ; Folberth, Christian ; Glotter, Michael ; Hoek, Steven ; Iizumi, Toshichika ; Izaurralde, Roberto C. ; Jones, Curtis ; Khabarov, Nikolay ; Lawrence, Peter ; Liu, Wenfeng ; Olin, Stefan ; Pugh, Thomas A.M. ; Ray, Deepak K. ; Reddy, Ashwan ; Rosenzweig, Cynthia ; Ruane, Alex C. ; Sakurai, Gen ; Schmid, Erwin ; Skalsky, Rastislav ; Song, Carol X. ; Wang, Xuhui ; Wit, Allard De; Yang, Hong - \ 2017
Geoscientific Model Development 10 (2017)4. - ISSN 1991-959X - p. 1403 - 1422.
Crop models are increasingly used to simulate crop yields at the global scale, but so far there is no general framework on how to assess model performance. Here we evaluate the simulation results of 14 global gridded crop modeling groups that have contributed historic crop yield simulations for maize, wheat, rice and soybean to the Global Gridded Crop Model Intercomparison (GGCMI) of the Agricultural Model Intercomparison and Improvement Project (AgMIP). Simulation results are compared to reference data at global, national and grid cell scales and we evaluate model performance with respect to time series correlation, spatial correlation and mean bias. We find that global gridded crop models (GGCMs) show mixed skill in reproducing time series correlations or spatial patterns at the different spatial scales. Generally, maize, wheat and soybean simulations of many GGCMs are capable of reproducing larger parts of observed temporal variability (time series correlation coefficients (r) of up to 0.888 for maize, 0.673 for wheat and 0.643 for soybean at the global scale) but rice yield variability cannot be well reproduced by most models. Yield variability can be well reproduced for most major producing countries by many GGCMs and for all countries by at least some. A comparison with gridded yield data and a statistical analysis of the effects of weather variability on yield variability shows that the ensemble of GGCMs can explain more of the yield variability than an ensemble of regression models for maize and soybean, but not for wheat and rice. We identify future research needs in global gridded crop modeling and for all individual crop modeling groups. In the absence of a purely observation-based benchmark for model evaluation, we propose that the best performing crop model per crop and region establishes the benchmark for all others, and modelers are encouraged to investigate how crop model performance can be increased. We make our evaluation system accessible to all crop modelers so that other modeling groups can also test their model performance against the reference data and the GGCMI benchmark.
Local Ion Signatures (LIS) for the examination of comprehensive two-dimensional gas chromatography applied to fire debris analysis
Lopatka, Martin ; Sampat, Andjoe A. ; Jonkers, Steffan ; Adutwum, Lawrence A. ; Mol, Hans G.J. ; Weg, Guido van der; Harynuk, James J. ; Schoenmakers, Peter J. ; Asten, Arian van; Sjerps, Marjan J. ; Vivó-Truyols, Gabriel - \ 2017
Forensic Chemistry 3 (2017). - ISSN 2468-1709 - p. 1 - 13.
Chemometrics - Comprehensive two-dimensional gas chromatography (GC × GC–MS) - Fire Debris Analysis (FDA) - Likelihood ratio (LR) - Local Ion Signature (LIS)

Forensic examination of fire debris evidence is a notoriously difficult analytical task due to the complexity and variability of sample composition. The use of comprehensive two-dimensional gas chromatography with mass spectrometry detection (GC × GC–MS) allows the coupling of orthogonal retention mechanisms and therefore a high peak capacity. We demonstrate recent innovations in combining chemometric techniques for data reduction and feature selection, with evaluation of the evidence for forensic questions pertaining to the detection and subsequent classification of ignitable liquid residue (ILR) in fire debris samples. Chromatograms are divided into non-overlapping spatially delimited regions; for each of these regions a Local Ion Signature (LIS) is computed by summing the intensities, per nominal mass/charge over all points contained within each region. This yields a reduced feature space representing the original data as a set of consolidated ion traces. Subsequent feature selection is performed by evaluating the individual efficacy of each feature using a univariate score-based likelihood ratio (LR) approach for discriminating between pairs of same or different type samples. The retained features are used to model each ILR class using linear discriminant analysis (LDA). Results are demonstrated for 155 arson samples containing a diversity of substrate compounds and several known ignitable liquids. ILR detection is performed at 84% accuracy with fewer than 1% false positives followed by subsequent classification. Likelihood ratio distributions are presented referring to both detection and classification tasks.

The science, policy and practice of nature-based solutions : An interdisciplinary perspective
Nesshöver, Carsten ; Assmuth, Timo ; Irvine, Katherine N. ; Rusch, Graciela M. ; Waylen, Kerry A. ; Delbaere, Ben ; Haase, Dagmar ; Jones-Walters, Lawrence ; Keune, Hans ; Kovacs, Eszter ; Krauze, Kinga ; Külvik, Mart ; Rey, Freddy ; Dijk, Jiska van; Vistad, Odd Inge ; Wilkinson, Mark E. ; Wittmer, Heidi - \ 2017
Science of the Total Environment 579 (2017). - ISSN 0048-9697 - p. 1215 - 1227.
Ecosystem management - Ecosystem services - Environmental governance - Sustainability
In this paper, we reflect on the implications for science, policy and practice of the recently introduced concept of Nature-Based Solutions (NBS), with a focus on the European context. First, we analyse NBS in relation to similar concepts, and reflect on its relationship to sustainability as an overarching framework. From this, we derive a set of questions to be addressed and propose a general framework for how these might be addressed in NBS projects by funders, researchers, policy-makers and practitioners. We conclude that: (1) NBS need to be developed and discussed in relation to existing concepts to clarify their added value;(2) When considering and implementing NBS, the ‘relabelling’ of related concepts and the misuse of the concept have to be prevented in order to avoid misunderstanding, duplication and unintended consequences;(3) NBS as currently framed by the European Commission provides an opportunity for: a) transdisciplinary research into the design and implementation of solutions based on nature; and b) overcoming a bias towards development alternatives with narrow perspectives that focus on short-term economic gains and effectiveness;(4) The strength of the NBS concept is its integrative, systemic approach which prevents it from becoming just another “green communication tool” that provides justification for a classical model of natural resource exploitation and management measures.To realise their full potential, NBS must be developed by including the experience of all relevant stakeholders such that ‘solutions’ contribute to achieving all dimensions of sustainability. As NBS are developed, we must also moderate the expectations placed on them since the precedent provided by other initiatives whose aim was to manage nature sustainably demonstrates that we should not expect NBS to be cheap and easy, at least not in the short-term.
The database of the PREDICTS (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems) project
Hudson, Lawrence N. ; Newbold, Tim ; Contu, Sara ; Hill, Samantha L.L. ; Lysenko, Igor ; Palma, Adriana De; Phillips, Helen R.P. ; Alhusseini, Tamera I. ; Bedford, Felicity E. ; Bennett, Dominic J. ; Bugter, R.J.F. - \ 2017
Ecology and Evolution 7 (2017)1. - ISSN 2045-7758 - p. 145 - 188.
The PREDICTS project—Projecting Responses of Ecological Diversity In Changing Terrestrial Systems (www.predicts.org.uk)—has collated from published studies a large, reasonably representative database of comparable samples of biodiversity from multiple sites that differ in the nature or intensity of human impacts relating to land use. We have used this evidence base to develop global and regional statistical models of how local biodiversity responds to these measures. We describe and make freely available this 2016 release of the database, containing more than 3.2 million records sampled at over 26,000 locations and representing over 47,000 species. We outline how the database can help in answering a range of questions in ecology and conservation biology. To our knowledge, this is the largest and most geographically and taxonomically representative database of spatial comparisons of biodiversity that has been collated to date; it will be useful to researchers and international efforts wishing to model and understand the global status of biodiversity.
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