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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    Genomic Regions Associated With Skeletal Type Traits in Beef and Dairy Cattle Are Common to Regions Associated With Carcass Traits, Feed Intake and Calving Difficulty
    Doyle, Jennifer L. ; Berry, Donagh P. ; Veerkamp, Roel F. ; Carthy, Tara R. ; Walsh, Siobhan W. ; Evans, Ross D. ; Purfield, Deirdre C. - \ 2020
    Frontiers in Genetics Livestock Genomics 11 (2020). - ISSN 1664-8021
    cattle - genome-wide association study - linear type traits - sequence - single nucleotide polymorphism - skeletal

    Linear type traits describing the skeletal characteristics of an animal are moderately to strongly genetically correlated with a range of other performance traits in cattle including feed intake, reproduction traits and carcass merit; thus, type traits could also provide useful insights into the morphological differences among animals underpinning phenotypic differences in these complex traits. The objective of the present study was to identify genomic regions associated with five subjectively scored skeletal linear traits, to determine if these associated regions are common in multiple beef and dairy breeds, and also to determine if these regions overlap with those proposed elsewhere to be associated with correlated performance traits. Analyses were carried out using linear mixed models on imputed whole genome sequence data separately in 1,444 Angus, 1,129 Hereford, 6,433 Charolais, 8,745 Limousin, 1,698 Simmental, and 4,494 Holstein-Friesian cattle, all scored for the linear type traits. There was, on average, 18 months difference in age at assessment of the beef versus the dairy animals. While the majority of the identified quantitative trait loci (QTL), and thus genes, were both trait-specific and breed-specific, a large-effect pleiotropic QTL on BTA6 containing the NCAPG and LCORL genes was associated with all skeletal traits in the Limousin population and with wither height in the Angus. Other than that, little overlap existed in detected QTLs for the skeletal type traits in the other breeds. Only two QTLs overlapped the beef and dairy breeds; both QTLs were located on BTA5 and were associated with height in both the Angus and the Holstein-Friesian, despite the difference in age at assessment. Several detected QTLs in the present study overlapped with QTLs documented elsewhere that are associated with carcass traits, feed intake, and calving difficulty. While most breeding programs select for the macro-traits like carcass weight, carcass conformation, and feed intake, the higher degree of granularity with selection on the individual linear type traits in a multi-trait index underpinning the macro-level goal traits, presents an opportunity to help resolve genetic antagonisms among morphological traits in the pursuit of the animal with optimum performance metrics.

    Genomic regions associated with muscularity in beef cattle differ in five contrasting cattle breeds
    Doyle, Jennifer L. ; Berry, Donagh P. ; Veerkamp, Roel F. ; Carthy, Tara R. ; Evans, Ross D. ; Walsh, Siobhán W. ; Purfield, Deirdre C. - \ 2020
    Genetics, Selection, Evolution 52 (2020)1. - ISSN 0999-193X - 1 p.

    BACKGROUND: Linear type traits, which reflect the muscular characteristics of an animal, could provide insight into how, in some cases, morphologically very different animals can yield the same carcass weight. Such variability may contribute to differences in the overall value of the carcass since primal cuts vary greatly in price; such variability may also hinder successful genome-based association studies. Therefore, the objective of our study was to identify genomic regions that are associated with five muscularity linear type traits and to determine if these significant regions are common across five different breeds. Analyses were carried out using linear mixed models on imputed whole-genome sequence data in each of the five breeds, separately. Then, the results of the within-breed analyses were used to conduct an across-breed meta-analysis per trait. RESULTS: We identified many quantitative trait loci (QTL) that are located across the whole genome and associated with each trait in each breed. The only commonality among the breeds and traits was a large-effect pleiotropic QTL on BTA2 that contained the MSTN gene, which was associated with all traits in the Charolais and Limousin breeds. Other plausible candidate genes were identified for muscularity traits including PDE1A, PPP1R1C and multiple collagen and HOXD genes. In addition, associated (gene ontology) GO terms and KEGG pathways tended to differ between breeds and between traits especially in the numerically smaller populations of Angus, Hereford, and Simmental breeds. Most of the SNPs that were associated with any of the traits were intergenic or intronic SNPs located within regulatory regions of the genome. CONCLUSIONS: The commonality between the Charolais and Limousin breeds indicates that the genetic architecture of the muscularity traits may be similar in these breeds due to their similar origins. Conversely, there were vast differences in the QTL associated with muscularity in Angus, Hereford, and Simmental. Knowledge of these differences in genetic architecture between breeds is useful to develop accurate genomic prediction equations that can operate effectively across breeds. Overall, the associated QTL differed according to trait, which suggests that breeding for a morphologically different (e.g. longer and wider versus shorter and smaller) more efficient animal may become possible in the future.

    Whole genome sequence GWAS reveals muscularity in beef cattle differs across five cattle breeds
    Doyle, J.L. ; Berry, D.P. ; Veerkamp, R.F. ; Carthy, Tara R. ; Walsh, S.W. ; Purfield, Deirdre C. - \ 2019
    In: Book of Abstracts of the 70th Annual Meeting of the European Federation of Animal Science. - Wageningen : Wageningen Academic Publishers (Book of Abstracts ) - ISBN 9789086863396 - p. 210 - 210.
    ISSN ISBN 1382-6077
    The cultural politics of climate branding: Project Sunlight, the biopolitics of climate care and the socialisation of the everyday sustainable consumption practices of citizens-consumers
    Doyle, Julie ; Farrell, Nathan ; Goodman, Michael K. - \ 2019
    Climatic Change (2019). - ISSN 0165-0009

    Many corporations are now in the business of bringing climate change ‘home’ in the everyday products that those, in much of the Minority world, can purchase and use, providing opportunities for consumers to literally and figuratively ‘buy in’ to climate mitigation. Yet, what are the implications of this form of highly commoditised, corporate-led, consumer-focused climate branding? In the spaces and practices of the everyday, how and in what ways are corporations framing and socialising responses to climate change and global environmental and social issues? This paper explores these 'questions through a multimodal discourse analysis of Unilever’s ‘Sustainable Living Plan’ (2010) and its ‘Project Sunlight’ campaign (2010–2016). Situating Unilever’s sustainability agenda as indicative of the contemporary climate politics of the corporate sector, that also represents a pivotal moment in the cultural politics of climate change, we critically interrogate Unilever’s mobilisation of the affective and emotional registers of everyday life and human relations in its model of sustainable living. Specifically, we focus on the ways that Unilever encourages acts of branded consumption as a form of—what we call here—climate care, by invoking normative discourses of gender and family through a form of biopolitics, and, at a larger scale, how the corporation is shaping how particular forms of climate capitalism are socialised, normalised and practiced. In doing so, we shift critical attention away from sustainable business analyses of Unilever onto the unexplored socio-cultural dimensions of Unilever’s sustainability model. We argue that Unilever’s socialisation of climate branding and care works to depoliticise climate change actions and actors through a biopolitics that creates a false veneer of democratisation in the form of consumer choice, thereby curtailing more progressive societal action on climate change.

    Soil bacterial community structure and functional responses across a long-term mineral phosphorus (Pi) fertilisation gradient differ in grazed and cut grasslands
    Randall, Kate ; Brennan, Fiona ; Clipson, Nicholas ; Creamer, Rachel ; Griffiths, Bryan ; Storey, Sean ; Doyle, Evelyn - \ 2019
    Applied Soil Ecology 138 (2019). - ISSN 0929-1393 - p. 134 - 143.
    Agricultural management - Bacteria - Grassland - Phosphorus - Soil
    Grasslands form a significant proportion of land used across the globe and future management is important. The objective of this study was to compare the long-term impact of inorganic phosphorus (Pi) fertilisation rates (P0, P15 and P30 ha−1 yr−1) under two grass management trials (grazed vs. cut and removed) on soil physicochemical properties, microbial biomass, phosphomonoesterase activity, bacterial community structure and abundance of a phosphorus (P) mineralising gene (phoD). Under grazing, microbial biomass and soil phosphorus concentrations (total and Pi) generally increased with Pi fertilisation rate, accompanied by significant differences in bacterial community structure between unfertilised (P0) and P30 soil. At the cut and removed site, although Pi was significantly greater in P30 soil, P concentrations (total and Pi) did not increase to the same extent as for grazing, with microbial biomass and bacterial community structures unresponsive to Pi fertilisation. Despite differences in soil P concentrations (total and Pi) and microbial biomass between sites, the abundance of bacterial phoD increased with increasing soil Pi across both sites, while phosphomonoesterase activity decreased. Amplicon sequencing revealed Acidobacteria were the dominant bacterial phylum across both grasslands, but significant differences in relative abundances of bacterial genera were detected at the grazed site only. The bacterial genera Gp6 and Gp16 increased significantly with Pi fertilisation under grazing. Conversely, Bradyrhizobium as well as unclassified genus-type groups belonging to Actinobacteria and Acidimicrobiales significantly decreased with Pi fertilisation, suggesting potential roles in P mobilisation when soil Pi concentrations are low. This study highlights the importance of long-term Pi fertilisation rates and aboveground vegetation removal in shaping soil bacterial community structure and microbial biomass, which in turn may impact soil fertility and plant productivity within agricultural soils.
    A Resurrected Scenario : Single Gain and Massive Loss of Nitrogen-Fixing Nodulation
    Velzen, Robin van; Doyle, Jeff J. ; Geurts, Rene - \ 2019
    Trends in Plant Science 24 (2019)1. - ISSN 1360-1385 - p. 49 - 57.
    evolution - Frankia - nitrogen-fixing root nodules - rhizobia

    Root nodule endosymbiosis with nitrogen-fixing bacteria provides plants with unlimited access to fixed nitrogen, but at a significant energetic cost. Nodulation is generally considered to have originated in parallel in different lineages, but this hypothesis downplays the genetic complexity of nodulation and requires independent recruitment of many common features across lineages. Recent phylogenomic studies revealed that genes that function in establishing or maintaining nitrogen-fixing nodules are independently lost in non-nodulating relatives of nitrogen-fixing plants. In our opinion, these data are best explained by a scenario of a single gain followed by massively parallel loss of nitrogen-fixing root nodules triggered by events at geological scale.

    Genetic co-variance components within and among muscular, skeletal and functional traits differ among contrasting beef breeds
    Doyle, Jennifer ; Berry, Donagh P. ; Walsh, Siobhan W. ; Veerkamp, R.F. ; Evans, Ross D. ; Carthy, Tara R. - \ 2018
    In: World Congress on Genetics Applied to Livestock Production. - IAVS / Massey University - 8 p.
    Genetic covariance components within and among linear type traits differ among contrasting beef cattle breeds
    Doyle, Jennifer L. ; Berry, Donagh P. ; Walsh, Siobhan W. ; Veerkamp, Roel F. ; Evans, Ross D. ; Carthy, Tara R. - \ 2018
    Journal of Animal Science 96 (2018)5. - ISSN 0021-8812 - p. 1628 - 1639.
    Beef - Breeds - Cattle - Type traits

    Linear type traits describing the skeletal, muscular, and functional characteristics of an animal are routinely scored on live animals in both the dairy and beef cattle industries. Previous studies have demonstrated that genetic parameters for certain performance traits may differ between breeds; no study, however, has attempted to determine if differences exist in genetic parameters of linear type traits among breeds or sexes. Therefore, the objective of the present study was to determine if genetic covariance components for linear type traits differed among five contrasting cattle breeds, and to also investigate if these components differed by sex. A total of 18 linear type traits scored on 3,356 Angus (AA), 31,049 Charolais (CH), 3,004 Hereford (HE), 35,159 Limousin (LM), and 8,632 Simmental (SI) were used in the analysis. Data were analyzed using animal linear mixed models which included the fixed effects of sex of the animal (except in the investigation into the presence of sexual dimorphism), age at scoring, parity of the dam, and contemporary group of herd-date of scoring. Differences (P < 0.05) in heritability estimates, between at least two breeds, existed for 13 out of 18 linear type traits. Differences (P < 0.05) also existed between the pairwise within-breed genetic correlations among the linear type traits. Overall, the linear type traits in the continental breeds (i.e., CH, LM, SI) tended to have similar heritability estimates to each other as well as similar genetic correlations among the same pairwise traits, as did the traits in the British breeds (i.e., AA, HE). The correlation between a linear function of breeding values computed conditional on covariance parameters estimated from the CH breed with a linear function of breeding values computed conditional on covariance parameters estimated from the other breeds was estimated. Replacing the genetic covariance components estimated in the CH breed with those of the LM had least effect but the impact was considerable when the genetic covariance components of the AA were used. Genetic correlations between the same linear type traits in the two sexes were all close to unity (≥0.90) suggesting little advantage in considering these as separate traits for males and females. Results for the present study indicate the potential increase in accuracy of estimated breeding value prediction from considering, at least, the British breed traits separate to continental breed traits.

    Phylogenomics reveals multiple losses of nitrogen-fixing root nodule symbiosis
    Griesmann, Maximilian ; Chang, Yue ; Liu, Xin ; Song, Yue ; Haberer, Georg ; Crook, Matthew B. ; Billault-Penneteau, Benjamin ; Lauressergues, Dominique ; Keller, Jean ; Imanishi, Leandro ; Roswanjaya, Yuda Purwana ; Kohlen, Wouter ; Pujic, Petar ; Battenberg, Kai ; Alloisio, Nicole ; Liang, Yuhu ; Hilhorst, Henk ; Salgado, Marco G. ; Hocher, Valerie ; Gherbi, Hassen ; Svistoonoff, Sergio ; Doyle, Jeff J. ; He, Shixu ; Xu, Yan ; Xu, Shanyun ; Qu, Jing ; Gao, Qiang ; Fang, Xiaodong ; Fu, Yuan ; Normand, Philippe ; Berry, Alison M. ; Wall, Luis G. ; Ané, Jean Michel ; Pawlowski, Katharina ; Xu, Xun ; Yang, Huanming ; Spannagl, Manuel ; Mayer, Klaus F.X. ; Wong, Gane Ka Shu ; Parniske, Martin ; Delaux, Pierre Marc ; Cheng, Shifeng - \ 2018
    Science 361 (2018)6398. - ISSN 0036-8075 - 18 p.

    The root nodule symbiosis of plants with nitrogen-fixing bacteria impacts global nitrogen cycles and food production but is restricted to a subset of genera within a single clade of flowering plants. To explore the genetic basis for this scattered occurrence, we sequenced the genomes of ten plant species covering the diversity of nodule morphotypes, bacterial symbionts and infection strategies. In a genome-wide comparative analysis of a total of 37 plant species, we discovered signatures of multiple independent loss-of-function events in the indispensable symbiotic regulator NODULE INCEPTION (NIN) in ten out of 13 genomes of non-nodulating species within this clade. The discovery that multiple independent losses shaped the present day distribution of nitrogen-fixing root nodule symbiosis in plants reveals a phylogenetically wider distribution in evolutionary history and a so far underestimated selection pressure against this symbiosis.

    Linking diagnostic features to soil microbial biomass and respiration in agricultural grassland soil : A large-scale study in Ireland
    Richter, A. ; Huallacháin, D.O. ; Doyle, E. ; Clipson, N. ; Leeuwen, J.P. van; Heuvelink, G.B. ; Creamer, R.E. - \ 2018
    European Journal of Soil Science 69 (2018)3. - ISSN 1351-0754 - p. 414 - 428.
    The functional potential of soil ecosystems can be predicted from the activity and abundance of the microbial community in relation to key soil properties. When describing microbial community dynamics, soil physicochemical properties have traditionally been used. The extent of correlations between properties, however, differs between studies, especially across larger spatial scales. In this research we analysed soil microbial biomass and substrate-induced respiration of 156 samples from Irish grasslands. In addition to the standard physicochemical, soil type and land management variables, soil diagnostic properties were included to identify if these important soil-landscape genesis classes affected microbial biomass and respiration dynamics in Irish soil. Apart from physicochemical properties, soil drainage class was identified as having an important effect on microbial properties. In particular, biomass-specific basal (qCO2) and substrate-induced respiration (SIR:CFE) were explained best by the soil drainage. Poorly drained soil had smaller values of these respiration measures than well-drained soil. We concluded that this resulted from different groups within the microbial community that could use readily available carbon sources, which suggests a change in microbial community dynamics associated with soil texture and periods of water stress. Overall, our results indicate that soil quality assessments should include both physicochemical properties and diagnostic classes, to provide a better understanding of the behaviour of soil microbial communities. Highlights: Assessing the effect of soil diagnostic features and properties on microbial biomass and respiration A soil biological survey from 156 grassland sites in Ireland Soil drainage class has an important effect on microbial properties Soil quality assessments should include both physicochemical properties and diagnostic classes
    Comparative analysis of spatial genetic structure in an ant-plant symbiosis reveals a tension zone and highlights speciation processes in tropical Africa
    Blatrix, Rumsaïs ; Peccoud, Jean ; Born, Céline ; Piatscheck, Finn ; Benoit, Laure ; Sauve, Mathieu ; Djiéto-Lordon, Champlain ; Atteke, Christiane ; Wieringa, Jan J. ; Harris, David J. ; Mckey, Doyle - \ 2017
    Journal of Biogeography 44 (2017)8. - ISSN 0305-0270 - p. 1856 - 1868.
    Africa - Barteria - Climatic oscillations - Guinea-Congolian rainforest - Incipient speciation - Phylogeography - Pleistocene - Symbiosis - Tension zone - Tetraponera

    Aim: Pleistocene climatic oscillations induced range fluctuations in African rain forest organisms and may have shaped species diversification through allopatric speciation events. We compared the spatial genetic structure of two forest species that live in obligate symbiosis and thus must have experienced the same range fluctuations, as a means to discriminate incipient speciation from transient differentiation simply resulting from past divergence. Location: Western central Africa. Methods: We genotyped 765 individuals of the tree Barteria fistulosa and 605 colonies of its symbiotic ant Tetraponera aethiops at 12 and 13 microsatellite loci, respectively. We compared the spatial genetic structure of the two symbionts by using Bayesian clustering algorithms, isolation-by-distance analyses and clines of synthetic alleles. We used species niche modelling (climatic and soil variables) to investigate ecological variables associated with genetic discontinuities in tree populations. Results: The trees and the ants showed congruent patterns of spatial genetic structure. However, the trees showed a very steep genetic discontinuity between groups north and south of latitude 1° N, which was much weaker in the ants. There was no evidence for effective gene flow between the two tree lineages in contact at the transition zone, despite the presence of a few hybrids. Niche modelling did not predict the occurrence of northern trees south of this genetic transition, and vice versa. Main conclusions: The genetic discontinuity near latitude 1° N is inferred to be a tension zone resulting from reproductive incompatibilities between previously allopatric tree lineages. This tension zone may have stabilized at a climatic transition (between boreal and austral seasonal regimes), and matches patterns of genetic structure previously observed in other forest plant species. Our results illustrate independent speciation between two species that live in specific and obligate symbiosis and suggest that a tension zone may separate lineages of several central African forest plants near the thermal equator.

    Animals and us: history, exciting developments, cross-pollination and new directions for applied ethology research
    Brown, J. ; Seddon, Y. ; Rault, J.L. ; Doyle, R. ; Jensen, P. ; Rodenburg, T.B. ; Marchant-Forde, J. - \ 2016
    In: Proceedings of the 50th congress of the International Society for Applied Ethology. - Wageningen : Wageningen Academic Publishers - ISBN 9789086862870 - p. 112 - 112.
    Applied ethology is a relatively new eld, which has grown rapidly in scope, geographical distribution and in€uence since the inception of the SVE/ISAE in 1966. There has been limited historical documentation of the eld, and students new to the area have little information available to understand the history of this science beyond what is found in journal publications.
    To address this gap, several ISAE members and a‚liated researchers have compiled a book, ‘Animals and us: 50 years and more of applied ethology’ which documents and celebrates the rst 50 years of the ISAE. The book is written in four parts, including: (1) the history of the society and early pioneers; (2) research advances in behaviour; (3) global perspectives;
    and (4) future directions for applied ethology research. Contributing authors include many leading researchers in the field- too numerous to mention here. This presentation will explore highlights from the text related to achievements, trends in research, collaborative studies with other elds, and new directions for both basic and applied research, all in an attempt to explain why ethologists are so passionate about their work, and why this eld remains more exciting now than ever before. �emes include human-animal interaction, personality, play
    behaviour, cognition, multi-level selection, polyvagal theory, and the relationship between applied ethology and animal welfare science. We conclude that other animals, with their amazing and various forms and habits, may be the perfect human enrichment.
    PLASTOX: Direct and indirect ecotoxicological impacts of microplastics on marine organisms
    Booth, Andy ; Sakaguchi-Soder, Kaori ; Sobral, Paula ; Airoldi, Laura ; Sempere, Richard ; Franeker, J.A. van; Magnusson, Kerstin ; Doyle, Thomas ; Morrison, Liam ; Salaverria, Iurgi ; Colen, Carl van; Herzke, Dorte ; Orbea, Amaia ; Gabrielsen, Geir Wing ; Nies, Hartmut ; Galloway, Tamara ; Oyen, Albert Van - \ 2016
    Potential food hazards from organic greenhouse horticulture
    Alsanius, B.W. ; Dorais, M. ; Doyle, O. ; Oancea, F. ; Spadaro, D. ; Meijer, R.J.M. - \ 2016
    BioGreenhouse (Fact sheet BioGreenhouse ) - 3
    organic farming - horticulture - greenhouse horticulture - plant protection - plant diseases - food safety - agricultural research - biologische landbouw - tuinbouw - glastuinbouw - gewasbescherming - plantenziekten - voedselveiligheid - landbouwkundig onderzoek
    This factsheet describes the critical hazards in organic greenhouse horticulture (OGH) crop production and identifies the crucial knowledge gaps.
    Minimum Information about a Biosynthetic Gene cluster
    Medema, M.H. ; Kottmann, Renzo ; Yilmaz, Pelin ; Cummings, Matthew ; Biggins, J.B. ; Blin, Kai ; Bruijn, Irene De; Chooi, Yit Heng ; Claesen, Jan ; Coates, R.C. ; Cruz-Morales, Pablo ; Duddela, Srikanth ; Düsterhus, Stephanie ; Edwards, Daniel J. ; Fewer, David P. ; Garg, Neha ; Geiger, Christoph ; Gomez-Escribano, Juan Pablo ; Greule, Anja ; Hadjithomas, Michalis ; Haines, Anthony S. ; Helfrich, Eric J.N. ; Hillwig, Matthew L. ; Ishida, Keishi ; Jones, Adam C. ; Jones, Carla S. ; Jungmann, Katrin ; Kegler, Carsten ; Kim, Hyun Uk ; Kötter, Peter ; Krug, Daniel ; Masschelein, Joleen ; Melnik, Alexey V. ; Mantovani, Simone M. ; Monroe, Emily A. ; Moore, Marcus ; Moss, Nathan ; Nützmann, Hans Wilhelm ; Pan, Guohui ; Pati, Amrita ; Petras, Daniel ; Reen, F.J. ; Rosconi, Federico ; Rui, Zhe ; Tian, Zhenhua ; Tobias, Nicholas J. ; Tsunematsu, Yuta ; Wiemann, Philipp ; Wyckoff, Elizabeth ; Yan, Xiaohui ; Yim, Grace ; Yu, Fengan ; Xie, Yunchang ; Aigle, Bertrand ; Apel, Alexander K. ; Balibar, Carl J. ; Balskus, Emily P. ; Barona-Gómez, Francisco ; Bechthold, Andreas ; Bode, Helge B. ; Borriss, Rainer ; Brady, Sean F. ; Brakhage, Axel A. ; Caffrey, Patrick ; Cheng, Yi Qiang ; Clardy, Jon ; Cox, Russell J. ; Mot, René De; Donadio, Stefano ; Donia, Mohamed S. ; Donk, Wilfred A. Van Der; Dorrestein, Pieter C. ; Doyle, Sean ; Driessen, Arnold J.M. ; Ehling-Schulz, Monika ; Entian, Karl Dieter ; Fischbach, Michael A. ; Gerwick, Lena ; Gerwick, William H. ; Gross, Harald ; Gust, Bertolt ; Hertweck, Christian ; Höfte, Monica ; Jensen, Susan E. ; Ju, Jianhua ; Katz, Leonard ; Kaysser, Leonard ; Klassen, Jonathan L. ; Keller, Nancy P. ; Kormanec, Jan ; Kuipers, Oscar P. ; Kuzuyama, Tomohisa ; Kyrpides, Nikos C. ; Kwon, Hyung Jin ; Lautru, Sylvie ; Lavigne, Rob ; Lee, Chia Y. ; Linquan, Bai ; Liu, Xinyu ; Liu, Wen ; Luzhetskyy, Andriy ; Mahmud, Taifo ; Mast, Yvonne ; Méndez, Carmen ; Metsä-Ketelä, Mikko ; Micklefield, Jason ; Mitchell, Douglas A. ; Moore, Bradley S. ; Moreira, Leonilde M. ; Müller, Rolf ; Neilan, Brett A. ; Nett, Markus ; Nielsen, Jens ; O'Gara, Fergal ; Oikawa, Hideaki ; Osbourn, Anne ; Osburne, Marcia S. ; Ostash, Bohdan ; Payne, Shelley M. ; Pernodet, Jean Luc ; Petricek, Miroslav ; Piel, Jörn ; Ploux, Olivier ; Raaijmakers, Jos M. ; Salas, José A. ; Schmitt, Esther K. ; Scott, Barry ; Seipke, Ryan F. ; Shen, Ben ; Sherman, David H. ; Sivonen, Kaarina ; Smanski, Michael J. ; Sosio, Margherita ; Stegmann, Evi ; Süssmuth, Roderich D. ; Tahlan, Kapil ; Thomas, Christopher M. ; Tang, Yi ; Truman, Andrew W. ; Viaud, Muriel ; Walton, Jonathan D. ; Walsh, Christopher T. ; Weber, Tilmann ; Wezel, Gilles P. Van; Wilkinson, Barrie ; Willey, Joanne M. ; Wohlleben, Wolfgang ; Wright, Gerard D. ; Ziemert, Nadine ; Zhang, Changsheng ; Zotchev, Sergey B. ; Breitling, Rainer ; Takano, Eriko ; Glöckner, Frank Oliver - \ 2015
    Nature Chemical Biology 11 (2015)9. - ISSN 1552-4450 - p. 625 - 631.

    A wide variety of enzymatic pathways that produce specialized metabolites in bacteria, fungi and plants are known to be encoded in biosynthetic gene clusters. Information about these clusters, pathways and metabolites is currently dispersed throughout the literature, making it difficult to exploit. To facilitate consistent and systematic deposition and retrieval of data on biosynthetic gene clusters, we propose the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard.

    Amplified stretch of bottlebrush-coated DNA in nanofluidic channels
    Zhang, C. ; Hernandez Garcia, A. ; Jiang, K. ; Gong, Z.Y. ; Guttula, D. ; Ng, S.Y. ; Malar, P.P. ; Kan, J.A. van; Dai, L. ; Doyle, P.S. ; Vries, R.J. de; Maarel, J.R.C. van der - \ 2013
    Nucleic acids research 41 (2013)20. - ISSN 0305-1048
    single-molecule - force microscopy - nanochannel - length - confinement - compaction - polymers - protein - device
    The effect of a cationic-neutral diblock polypeptide on the conformation of single DNA molecules confined in rectangular nanochannels is investigated with fluorescence microscopy. An enhanced stretch along the channel is observed with increased binding of the cationic block of the polypeptide to DNA. A maximum stretch of 85% of the contour length can be achieved inside a channel with a cross-sectional diameter of 200 nm and at a 2-fold excess of polypeptide with respect to DNA charge. With site-specific fluorescence labelling, it is demonstrated that this maximum stretch is sufficient to map large-scale genomic organization. Monte Carlo computer simulation shows that the amplification of the stretch inside the nanochannels is owing to an increase in bending rigidity and thickness of bottlebrush-coated DNA. The persistence lengths and widths deduced from the nanochannel data agree with what has been estimated from the analysis of atomic force microscopy images of dried complexes on silica.
    Towards a new classification system for legumes: Progress report from the 6th International Legume Conference
    Pontes Coelho Borges, L.M. ; Bruneau, A. ; Cardoso, D. ; Crisp, M. ; Delgado-Salinas, A. ; Doyle, J.J. ; Egan, A. ; Herendeen, P.S. ; Hughes, C. ; Kenicer, G. ; Klitgaard, B. ; Koenen, E. ; Lavin, M. ; Lewis, G. ; Luckow, M. ; Mackinder, B. ; Malecot, V. ; Miller, J.T. ; Pennington, R.T. ; Queiroz, L.P. de; Schrire, B. ; Simon, M.F. ; Steele, K. ; Torke, B. ; Wieringa, J.J. ; Wojciechowski, M.F. ; Boatwright, S. ; Estrella, M. de la; Mansano, V.D. ; Prado, D.E. ; Stirton, C. ; Wink, M. - \ 2013
    South African Journal of Botany 89 (2013). - ISSN 0254-6299 - p. 3 - 9.
    caesalpinioid legumes - phylogeny - leguminosae - evolution - diversification - dipsacales - sequences - lineages - gene - rbcl
    Legume systematists have been making great progress in understanding evolutionary relationships within the Leguminosae (Fabaceae), the third largest family of flowering plants. As the phylogenetic picture has become clearer, so too has the need for a revised classification of the family. The organization of the family into three subfamilies and 42 tribes is outdated and evolutionarily misleading. The three traditionally recognized subfamilies, Caesalpinioideae, Mimosoideae, and Papilionoideae, do not adequately represent relationships within the family. The occasion of the Sixth International Legume Conference in Johannesburg, South Africa in January 2013, with its theme "Towards a new classification system for legumes," provided the impetus to move forward with developing a new classification. A draft classification, based on current phylogenetic results and a set of principles and guidelines, was prepared in advance of the conference as the basis for discussion. The principles, guidelines, and draft classification were presented and debated at the conference. The objectives of the discussion were to develop consensus on the principles that should guide the development of the classification, to discuss the draft classification's strengths and weaknesses and make proposals for its revision, and identify and prioritize phylogenetic deficiencies that must be resolved before the classification could be published. This paper describes the collaborative process by a large group of legume systematists, publishing under the name Legume Phylogeny Working Group, to develop a new phylogenetic classification system for the Leguminosae. The goals of this paper are to inform the broader legume community, and others, of the need for a revised classification, and spell out clearly what the alternatives and challenges are for a new classification system for the family. (C) 2013 SAAB. Published by Elsevier B.V. All rights reserved.
    Ecosystem services and ethics
    Jax, K. ; Barton, D.N. ; Chan, K.M.A. ; Groot, R.S. de; Doyle, U. ; Eser, U. ; Goerg, C. ; Gomez-Baggethun, E. ; Griewald, Y. ; Haber, W. ; Haines-Young, R. ; Heink, U. ; Jahn, T. ; Joosten, H. ; Kerschbaumer, L. ; Korn, H. ; Luck, G.W. ; Matzdorf, B. ; Muraca, B. ; Nesshover, C. ; Norton, B. ; Ott, K. ; Potschin, M. ; Rauschmayer, F. ; Haaren, C. von; Wichmann, S. - \ 2013
    Ecological Economics 93 (2013). - ISSN 0921-8009 - p. 260 - 268.
    environmental ethics - conservation - biodiversity - valuation - values - economics - ecology - science
    A major strength of the ecosystem services (ESS) concept is that it allows a succinct description of how human well-being depends on nature, showing that the neglect of such dependencies has negative consequences on human well-being and the economy. As ESS refer to human needs and interests, values are to be considered when dealing with the concept in practice. As a result we argue that in using the concept there is a need to be clear about what different dimensions of value are involved, and be aware of ethical issues that might be associated with the concept. A systematic analysis of the ethical implications associated to the ESS concept is still lacking. We address this deficiency by scrutinising value dimensions associated with the concept, and use this to explore the associated ethical implications. We then highlight how improved transparency in the use of the ESS concept can contribute to using its strengths without succumbing to possible drawbacks arising from ethical problems. These problems concern the dangers that some uses of the concept have in obscuring certain types of value, and in masking unevenness in the distribution of costs and benefits that can arise in the management of ESS.
    Legume phylogeny and classification in the 21st century: Progress, prospects and lessons for other species-rich clades
    Bruneau, A. ; Doyle, J.J. ; Herendeen, P. ; Hughes, C. ; Kenicer, G. ; Lewis, G. ; Mackinder, B.A. ; Pennington, R.T. ; Sanderson, M.J. ; Wojciechowski, M.F. ; Boatwright, S. ; Brown, G. ; Cardoso, D. ; Crips, M. ; Egan, A. ; Fortunato, R. ; Hawkins, J. ; Kajita, T. ; Klitgaard, B.B. ; Koenen, E. ; Lavin, M. ; Luckow, M. ; Marazzi, B. ; McMahon, M.M. ; Miller, J.T. ; Murphy, D.J. ; Ohashi, H. ; Queiroz, L.P. de; Rico, L. ; Särkinen, T. ; Schrire, B. ; Simon, M.F. ; Souza, E.R. ; Steele, K. ; Torke, B.M. ; Wieringa, J.J. ; Wijk, B.E. - \ 2013
    Taxon 62 (2013)2. - ISSN 0040-0262 - p. 217 - 248.
    swartzia leguminosae-papilionoideae - tribe millettieae leguminosae - chloroplast dna regions - southern south-america - intron spacer regions - matk coding sequence - plastid trnl-f - molecular phylogenetics - divergence times - s.l. leguminosae
    The Leguminosae, the third-largest angiosperm family, has a global distribution and high ecological and economic importance. We examine how the legume systematic research community might join forces to produce a comprehensive phylogenetic estimate for the ca. 751 genera and ca. 19,500 species of legumes and then translate it into a phylogeny-based classification. We review the current state of knowledge of legume phylogeny and highlight where problems lie, for example in taxon sampling and phylogenetic resolution. We review approaches from bioinformatics and next-generation sequencing, which can facilitate the production of better phylogenetic estimates. Finally, we examine how morphology can be incorporated into legume phylogeny to address issues in comparative biology and classification. Our goal is to stimulate the research needed to improve our knowledge of legume phylogeny and evolution; the approaches that we discuss may also be relevant to other species-rich angiosperm clades
    Discourse communities as catalysts for science and technology communication
    Molder, H. te - \ 2012
    In: Citizen Voices. Performing Public Participation in Science and Environment Communication / Phillips, L., Carvalho, A., Doyle, J., Bristol UK/Chicago USA : Intellect/The University of Chicago Press - ISBN 9781841506210 - p. 97 - 118.
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