Global environmental change effects on plant community composition trajectories depend upon management legacies
Perring, Michael P. ; Bernhardt-Römermann, Markus ; Baeten, Lander ; Midolo, Gabriele ; Blondeel, Haben ; Depauw, Leen ; Landuyt, Dries ; Maes, Sybryn L. ; Lombaerde, Emiel De; Carón, Maria Mercedes ; Vellend, Mark ; Brunet, Jörg ; Chudomelová, Markéta ; Decocq, Guillaume ; Diekmann, Martin ; Dirnböck, Thomas ; Dörfler, Inken ; Durak, Tomasz ; Frenne, Pieter De; Gilliam, Frank S. ; Hédl, Radim ; Heinken, Thilo ; Hommel, Patrick ; Jaroszewicz, Bogdan ; Kirby, Keith J. ; Kopecký, Martin ; Lenoir, Jonathan ; Li, Daijiang ; Máliš, František ; Mitchell, Fraser J.G. ; Naaf, Tobias ; Newman, Miles ; Petřík, Petr ; Reczyńska, Kamila ; Schmidt, Wolfgang ; Standovár, Tibor ; Świerkosz, Krzysztof ; Calster, Hans Van; Vild, Ondřej ; Wagner, Eva Rosa ; Wulf, Monika ; Verheyen, Kris - \ 2018
Global Change Biology 24 (2018)4. - ISSN 1354-1013 - p. 1722 - 1740.
Biodiversity change - Climate change - Disturbance regime - ForestREplot - Herbaceous layer - Management intensity - Nitrogen deposition - Plant functional traits - Time lag - Vegetation resurvey
The contemporary state of functional traits and species richness in plant communities depends on legacy effects of past disturbances. Whether temporal responses of community properties to current environmental changes are altered by such legacies is, however, unknown. We expect global environmental changes to interact with land-use legacies given different community trajectories initiated by prior management, and subsequent responses to altered resources and conditions. We tested this expectation for species richness and functional traits using 1814 survey-resurvey plot pairs of understorey communities from 40 European temperate forest datasets, syntheses of management transitions since the year 1800, and a trait database. We also examined how plant community indicators of resources and conditions changed in response to management legacies and environmental change. Community trajectories were clearly influenced by interactions between management legacies from over 200 years ago and environmental change. Importantly, higher rates of nitrogen deposition led to increased species richness and plant height in forests managed less intensively in 1800 (i.e., high forests), and to decreases in forests with a more intensive historical management in 1800 (i.e., coppiced forests). There was evidence that these declines in community variables in formerly coppiced forests were ameliorated by increased rates of temperature change between surveys. Responses were generally apparent regardless of sites' contemporary management classifications, although sometimes the management transition itself, rather than historic or contemporary management types, better explained understorey responses. Main effects of environmental change were rare, although higher rates of precipitation change increased plant height, accompanied by increases in fertility indicator values. Analysis of indicator values suggested the importance of directly characterising resources and conditions to better understand legacy and environmental change effects. Accounting for legacies of past disturbance can reconcile contradictory literature results and appears crucial to anticipating future responses to global environmental change.
Seagrass ecosystem trajectory depends on the relative timescales of resistance, recovery and disturbance
O'Brien, Katherine R. ; Waycott, Michelle ; Maxwell, Paul ; Kendrick, Gary A. ; Udy, James W. ; Ferguson, Angus J.P. ; Kilminster, Kieryn ; Scanes, Peter ; McKenzie, Len J. ; McMahon, Kathryn ; Adams, Matthew P. ; Samper-Villarreal, Jimena ; Collier, Catherine ; Lyons, Mitchell ; Mumby, Peter J. ; Radke, Lynda ; Christianen, Marjolijn J.A. ; Dennison, William C. - \ 2018
Marine Pollution Bulletin 134 (2018). - ISSN 0025-326X - p. 166 - 176.
Colonizing - Opportunistic - Persistent - Recovery - Resilience - Resistance - Seagrass - Trajectory
Seagrass ecosystems are inherently dynamic, responding to environmental change across a range of scales. Habitat requirements of seagrass are well defined, but less is known about their ability to resist disturbance. Specific means of recovery after loss are particularly difficult to quantify. Here we assess the resistance and recovery capacity of 12 seagrass genera. We document four classic trajectories of degradation and recovery for seagrass ecosystems, illustrated with examples from around the world. Recovery can be rapid once conditions improve, but seagrass absence at landscape scales may persist for many decades, perpetuated by feedbacks and/or lack of seed or plant propagules to initiate recovery. It can be difficult to distinguish between slow recovery, recalcitrant degradation, and the need for a window of opportunity to trigger recovery. We propose a framework synthesizing how the spatial and temporal scales of both disturbance and seagrass response affect ecosystem trajectory and hence resilience.
Erratum: Large meta-analysis of genome-wide association studies identifies five loci for lean body mass
Zillikens, M.C. ; Demissie, Serkalem ; Hsu, Yi Hsiang ; Yerges-Armstrong, Laura M. ; Chou, Wen Chi ; Stolk, Lisette ; Livshits, Gregory ; Broer, Linda ; Johnson, Toby ; Koller, Daniel L. ; Kutalik, Zoltán ; Luan, J. ; Malkin, Ida ; Ried, Janina S. ; Smith, Albert V. ; Thorleifsson, Gudmar ; Vandenput, Liesbeth ; Hua Zhao, Jing ; Zhang, Weihua ; Aghdassi, Ali ; Åkesson, Kristina ; Amin, Najaf ; Baier, Leslie J. ; Barroso, Inês ; Bennett, David A. ; Bertram, Lars ; Biffar, Rainer ; Bochud, Murielle ; Boehnke, Michael ; Borecki, Ingrid B. ; Buchman, Aron S. ; Byberg, Liisa ; Campbell, Harry ; Campos Obanda, Natalia ; Cauley, Jane A. ; Cawthon, Peggy M. ; Cederberg, Henna ; Chen, Zhao ; Cho, Nam H. ; Jin Choi, Hyung ; Claussnitzer, Melina ; Collins, Francis ; Cummings, Steven R. ; Jager, Philip L. De; Demuth, Ilja ; Dhonukshe-Rutten, Rosalie A.M. ; Diatchenko, Luda ; Eiriksdottir, Gudny ; Enneman, Anke W. ; Erdos, Mike ; Eriksson, Johan G. ; Eriksson, Joel ; Estrada, Karol ; Evans, Daniel S. ; Feitosa, Mary F. ; Fu, Mao ; Garcia, Melissa ; Gieger, Christian ; Girke, Thomas ; Glazer, Nicole L. ; Grallert, Harald ; Grewal, Jagvir ; Han, Bok Ghee ; Hanson, Robert L. ; Hayward, Caroline ; Hofman, Albert ; Hoffman, Eric P. ; Homuth, Georg ; Hsueh, Wen Chi ; Hubal, Monica J. ; Hubbard, Alan ; Huffman, Kim M. ; Husted, Lise B. ; Illig, Thomas ; Ingelsson, Erik ; Ittermann, Till ; Jansson, John Olov ; Jordan, Joanne M. ; Jula, Antti ; Karlsson, Magnus ; Khaw, Kay Tee ; Kilpeläinen, Tuomas O. ; Klopp, Norman ; Kloth, Jacqueline S.L. ; Koistinen, Heikki A. ; Kraus, William E. ; Kritchevsky, Stephen ; Kuulasmaa, Teemu ; Kuusisto, Johanna ; Laakso, Markku ; Lahti, Jari ; Lang, Thomas ; Langdahl, Bente L. ; Launer, Lenore J. ; Lee, Jong Young ; Lerch, Markus M. ; Lewis, Joshua R. ; Lind, Lars ; Lindgren, Cecilia ; Liu, Yongmei ; Liu, Tian ; Liu, Youfang ; Ljunggren, Östen ; Lorentzon, Mattias ; Luben, Robert N. ; Maixner, William ; McGuigan, Fiona E. ; Medina-Gomez, Carolina ; Meitinger, Thomas ; Melhus, Håkan ; Mellström, Dan ; Melov, Simon ; Michaëlsson, Karl ; Mitchell, Braxton D. ; Morris, Andrew P. ; Mosekilde, Leif ; Newman, Anne ; Nielson, Carrie M. ; O'Connell, Jeffrey R. ; Oostra, Ben A. ; Orwoll, Eric S. ; Palotie, Aarno ; Parker, Stephen C.J. ; Peacock, Munro ; Perola, Markus ; Peters, Annette ; Polasek, Ozren ; Prince, Richard L. ; Räikkönen, Katri ; Ralston, Stuart H. ; Ripatti, Samuli ; Robbins, John A. ; Rotter, Jerome I. ; Rudan, Igor ; Salomaa, Veikko ; Satterfield, Suzanne ; Schadt, Eric E. ; Schipf, Sabine ; Scott, Laura ; Sehmi, Joban ; Shen, Jian ; Soo Shin, Chan ; Sigurdsson, Gunnar ; Smith, Shad ; Soranzo, Nicole ; Stančáková, Alena ; Steinhagen-Thiessen, Elisabeth ; Streeten, Elizabeth A. ; Styrkarsdottir, Unnur ; Swart, Karin M.A. ; Tan, Sian Tsung ; Tarnopolsky, Mark A. ; Thompson, Patricia ; Thomson, Cynthia A. ; Thorsteinsdottir, Unnur ; Tikkanen, Emmi ; Tranah, Gregory J. ; Tuomilehto, Jaakko ; Schoor, Natasja M. van; Verma, Arjun ; Vollenweider, Peter ; Völzke, Henry ; Wactawski-Wende, Jean ; Walker, Mark ; Weedon, Michael N. ; Welch, Ryan ; Wichmann, H.E. ; Widen, Elisabeth ; Williams, Frances M.K. ; Wilson, James F. ; Wright, Nicole C. ; Xie, Weijia ; Yu, Lei ; Zhou, Yanhua ; Chambers, John C. ; Döring, Angela ; Duijn, Cornelia M. van; Econs, Michael J. ; Gudnason, Vilmundur ; Kooner, Jaspal S. ; Psaty, Bruce M. ; Spector, Timothy D. ; Stefansson, Kari ; Rivadeneira, Fernando ; Uitterlinden, André G. ; Wareham, Nicholas J. ; Ossowski, Vicky ; Waterworth, Dawn ; Loos, Ruth J.F. ; Karasik, David ; Harris, Tamara B. ; Ohlsson, Claes ; Kiel, Douglas P. - \ 2017
Nature Communications 8 (2017)1. - ISSN 2041-1723 - 1 p.
A correction to this article has been published and is linked from the HTML version of this article.
Large-scale GWAS identifies multiple loci for hand grip strength providing biological insights into muscular fitness
Willems, Sara M. ; Wright, D.J. ; Day, Felix R. ; Trajanoska, Katerina ; Joshi, P.K. ; Morris, John A. ; Matteini, Amy M. ; Garton, Fleur C. ; Grarup, Niels ; Oskolkov, Nikolay ; Thalamuthu, Anbupalam ; Mangino, Massimo ; Liu, Jun ; Demirkan, Ayse ; Lek, Monkol ; Xu, Liwen ; Wang, Guan ; Oldmeadow, Christopher ; Gaulton, Kyle J. ; Lotta, Luca A. ; Miyamoto-Mikami, Eri ; Rivas, Manuel A. ; White, Tom ; Loh, Po Ru ; Aadahl, Mette ; Amin, Najaf ; Attia, John R. ; Austin, Krista ; Benyamin, Beben ; Brage, Søren ; Cheng, Yu Ching ; Ciȩszczyk, Paweł ; Derave, Wim ; Eriksson, Karl Fredrik ; Eynon, Nir ; Linneberg, Allan ; Lucia, Alejandro ; Massidda, Myosotis ; Mitchell, Braxton D. ; Miyachi, Motohiko ; Murakami, Haruka ; Padmanabhan, Sandosh ; Pandey, Ashutosh ; Papadimitriou, Ioannis ; Rajpal, Deepak K. ; Sale, Craig ; Schnurr, Theresia M. ; Sessa, Francesco ; Shrine, Nick ; Groot, Lisette C.P.G.M. De - \ 2017
Nature Communications 8 (2017). - ISSN 2041-1723
Hand grip strength is a widely used proxy of muscular fitness, a marker of frailty, and predictor of a range of morbidities and all-cause mortality. To investigate the genetic determinants of variation in grip strength, we perform a large-scale genetic discovery analysis in a combined sample of 195,180 individuals and identify 16 loci associated with grip strength (P<5 × 10-8) in combined analyses. A number of these loci contain genes implicated in structure and function of skeletal muscle fibres (ACTG1), neuronal maintenance and signal transduction (PEX14, TGFA, SYT1), or monogenic syndromes with involvement of psychomotor impairment (PEX14, LRPPRC and KANSL1). Mendelian randomization analyses are consistent with a causal effect of higher genetically predicted grip strength on lower fracture risk. In conclusion, our findings provide new biological insight into the mechanistic underpinnings of grip strength and the causal role of muscular strength in age-related morbidities and mortality.
Large meta-analysis of genome-wide association studies identifies five loci for lean body mass
Zillikens, M.C. ; Demissie, Serkalem ; Hsu, Yi Hsiang ; Yerges-Armstrong, Laura M. ; Chou, Wen Chi ; Stolk, Lisette ; Livshits, Gregory ; Broer, Linda ; Johnson, Toby ; Koller, Daniel L. ; Kutalik, Zoltán ; Luan, J.A. ; Malkin, Ida ; Ried, Janina S. ; Smith, Albert V. ; Thorleifsson, Gudmar ; Vandenput, Liesbeth ; Hua Zhao, Jing ; Zhang, Weihua ; Aghdassi, Ali ; Åkesson, Kristina ; Amin, Najaf ; Baier, Leslie J. ; Barroso, Inês ; Bennett, David A. ; Bertram, Lars ; Biffar, Rainer ; Bochud, Murielle ; Boehnke, Michael ; Borecki, Ingrid B. ; Buchman, Aron S. ; Byberg, Liisa ; Campbell, Harry ; Campos Obanda, Natalia ; Cauley, Jane A. ; Cawthon, Peggy M. ; Cederberg, Henna ; Chen, Zhao ; Cho, Nam H. ; Jin Choi, Hyung ; Claussnitzer, Melina ; Collins, Francis ; Cummings, Steven R. ; Jager, Philip L. De; Demuth, Ilja ; Dhonukshe-Rutten, Rosalie A.M. ; DIatchenko, Luda ; Eiriksdottir, Gudny ; Enneman, Anke W. ; Erdos, Mike ; Eriksson, Johan G. ; Eriksson, Joel ; Estrada, Karol ; Evans, Daniel S. ; Feitosa, Mary F. ; Fu, Mao ; Garcia, Melissa ; Gieger, Christian ; Girke, Thomas ; Glazer, Nicole L. ; Grallert, Harald ; Grewal, Jagvir ; Han, Bok Ghee ; Hanson, Robert L. ; Hayward, Caroline ; Hofman, Albert ; Hoffman, Eric P. ; Homuth, Georg ; Hsueh, Wen Chi ; Hubal, Monica J. ; Hubbard, Alan ; Huffman, Kim M. ; Husted, Lise B. ; Illig, Thomas ; Ingelsson, Erik ; Ittermann, Till ; Jansson, John Olov ; Jordan, Joanne M. ; Jula, Antti ; Karlsson, Magnus ; Khaw, Kay Tee ; Kilpelaïnen, Tuomas O. ; Klopp, Norman ; Kloth, Jacqueline S.L. ; Koistinen, Heikki A. ; Kraus, William E. ; Kritchevsky, Stephen ; Kuulasmaa, Teemu ; Kuusisto, Johanna ; Laakso, Markku ; Lahti, Jari ; Lang, Thomas ; Langdahl, Bente L. ; Launer, Lenore J. ; Lee, Jong Young ; Lerch, Markus M. ; Lewis, Joshua R. ; Lind, Lars ; Lindgren, Cecilia M. ; Liu, Yongmei ; Liu, Tian ; Liu, Youfang ; Ljunggren, Östen ; Lorentzon, Mattias ; Luben, Robert N. ; Maixner, William ; McGuigan, Fiona E. ; Medina-Gomez, Carolina ; Meitinger, Thomas ; Melhus, Håkan ; Mellström, Dan ; Melov, Simon ; Michaëlsson, Karl ; Mitchell, Braxton D. ; Morris, Andrew P. ; Mosekilde, Leif ; Newman, Anne ; Nielson, Carrie M. ; O'Connell, Jeffrey R. ; Oostra, Ben A. ; Orwoll, Eric S. ; Palotie, Aarno ; Parker, Stephan ; Peacock, Munro ; Perola, Markus ; Peters, Annette ; Polasek, Ozren ; Prince, Richard L. ; Raïkkönen, Katri ; Ralston, Stuart H. ; Ripatti, Samuli ; Robbins, John A. ; Rotter, Jerome I. ; Rudan, Igor ; Salomaa, Veikko ; Satterfield, Suzanne ; Schadt, Eric E. ; Schipf, Sabine ; Scott, Laura ; Sehmi, Joban ; Shen, Jian ; Soo Shin, Chan ; Sigurdsson, Gunnar ; Smith, Shad ; Soranzo, Nicole ; Stančáková, Alena ; Steinhagen-Thiessen, Elisabeth ; Streeten, Elizabeth A. ; Styrkarsdottir, Unnur ; Swart, Karin M.A. ; Tan, Sian Tsung ; Tarnopolsky, Mark A. ; Thompson, Patricia ; Thomson, Cynthia A. ; Thorsteinsdottir, Unnur ; Tikkanen, Emmi ; Tranah, Gregory J. ; Tuomilehto, Jaakko ; Schoor, Natasja M. van; Verma, Arjun ; Vollenweider, Peter ; Völzke, Henry ; Wactawski-Wende, Jean ; Walker, Mark ; Weedon, Michael N. ; Welch, Ryan ; Wichman, H.E. ; Widen, Elisabeth ; Williams, Frances M.K. ; Wilson, James F. ; Wright, Nicole C. ; Xie, Weijia ; Yu, Lei ; Zhou, Yanhua ; Chambers, John C. ; Döring, Angela ; Duijn, Cornelia M. Van; Econs, Michael J. ; Gudnason, Vilmundur ; Kooner, Jaspal S. ; Psaty, Bruce M. ; Spector, Timothy D. ; Stefansson, Kari ; Rivadeneira, Fernando ; Uitterlinden, André G. ; Wareham, Nicholas J. ; Ossowski, Vicky ; Waterworth, Dawn M. ; Loos, Ruth J.F. ; Karasik, David ; Harris, Tamara B. ; Ohlsson, Claes ; Kiel, Douglas P. - \ 2017
Nature Communications 8 (2017)1. - ISSN 2041-1723
Lean body mass, consisting mostly of skeletal muscle, is important for healthy aging. We performed a genome-wide association study for whole body (20 cohorts of European ancestry with n = 38,292) and appendicular (arms and legs) lean body mass (n = 28,330) measured using dual energy X-ray absorptiometry or bioelectrical impedance analysis, adjusted for sex, age, height, and fat mass. Twenty-one single-nucleotide polymorphisms were significantly associated with lean body mass either genome wide (p < 5 × 10-8) or suggestively genome wide (p < 2.3 × 10-6). Replication in 63,475 (47,227 of European ancestry) individuals from 33 cohorts for whole body lean body mass and in 45,090 (42,360 of European ancestry) subjects from 25 cohorts for appendicular lean body mass was successful for five single-nucleotide polymorphisms in/near HSD17B11, VCAN, ADAMTSL3, IRS1, and FTO for total lean body mass and for three single-nucleotide polymorphisms in/near VCAN, ADAMTSL3, and IRS1 for appendicular lean body mass. Our findings provide new insight into the genetics of lean body mass.
Low-Frequency Synonymous Coding Variation in CYP2R1 Has Large Effects on Vitamin D Levels and Risk of Multiple Sclerosis
Manousaki, Despoina ; Dudding, Tom ; Haworth, Simon ; Hsu, Yi Hsiang ; Liu, Ching Ti ; Medina-Gómez, Carolina ; Voortman, Trudy ; Velde, Nathalie Van Der; Melhus, Håkan ; Vandenput, Liesbeth ; Noordam, Raymond ; Forgetta, Vincenzo ; Greenwood, Celia M.T. ; Biggs, Mary L. ; Psaty, Bruce M. ; Rotter, Jerome I. ; Zemel, Babette S. ; Mitchell, Jonathan A. ; Taylor, Bruce ; Lorentzon, Mattias ; Karlsson, Magnus ; Jaddoe, Vincent W.V. ; Tiemeier, Henning ; Campos-Obando, Natalia ; Franco, Oscar H. ; Utterlinden, Andre G. ; Broer, Linda ; Schoor, Natasja M. van; Ham, Annelies C. ; Ikram, Arfan M.A. ; Karasik, David ; Mutsert, Renée De; Rosendaal, Frits R. ; Heijer, Martin den; Wang, Thomas J. ; Lind, Lars ; Orwoll, Eric S. ; Mook-Kanamori, Dennis O. ; Michaëlsson, Karl ; Kestenbaum, Bryan ; Ohlsson, Claes ; Mellström, Dan ; Groot, Lisette C.P.G.M. de; Grant, Struan F.A. ; Kiel, Douglas P. ; Zillikens, M.C. ; Rivadeneira, Fernando ; Sawcer, Stephen ; Timpson, Nicholas J. ; Richards, J.B. - \ 2017
American Journal of Human Genetics 101 (2017)2. - ISSN 0002-9297 - p. 227 - 238.
GWAS - Low-frequency genetic variants - Multiple sclerosis - Vitamin D
Vitamin D insufficiency is common, correctable, and influenced by genetic factors, and it has been associated with risk of several diseases. We sought to identify low-frequency genetic variants that strongly increase the risk of vitamin D insufficiency and tested their effect on risk of multiple sclerosis, a disease influenced by low vitamin D concentrations. We used whole-genome sequencing data from 2,619 individuals through the UK10K program and deep-imputation data from 39,655 individuals genotyped genome-wide. Meta-analysis of the summary statistics from 19 cohorts identified in CYP2R1 the low-frequency (minor allele frequency = 2.5%) synonymous coding variant g.14900931G>A (p.Asp120Asp) (rs117913124[A]), which conferred a large effect on 25-hydroxyvitamin D (25OHD) levels (-0.43 SD of standardized natural log-transformed 25OHD per A allele; p value = 1.5 × 10-88). The effect on 25OHD was four times larger and independent of the effect of a previously described common variant near CYP2R1. By analyzing 8,711 individuals, we showed that heterozygote carriers of this low-frequency variant have an increased risk of vitamin D insufficiency (odds ratio [OR] = 2.2, 95% confidence interval [CI] = 1.78-2.78, p = 1.26 × 10-12). Individuals carrying one copy of this variant also had increased odds of multiple sclerosis (OR = 1.4, 95% CI = 1.19-1.64, p = 2.63 × 10-5) in a sample of 5,927 case and 5,599 control subjects. In conclusion, we describe a low-frequency CYP2R1 coding variant that exerts the largest effect upon 25OHD levels identified to date in the general European population and implicates vitamin D in the etiology of multiple sclerosis.
AntiSMASH 4.0 - improvements in chemistry prediction and gene cluster boundary identification
Blin, Kai ; Wolf, Thomas ; Chevrette, Marc G. ; Lu, Xiaowen ; Schwalen, Christopher J. ; Kautsar, Satria A. ; Suarez Duran, Hernando G. ; Los Santos, Emmanuel L.C. De; Kim, Hyun Uk ; Nave, Mariana ; Dickschat, Jeroen S. ; Mitchell, Douglas A. ; Shelest, Ekaterina ; Breitling, Rainer ; Takano, Eriko ; Lee, Sang Yup ; Weber, Tilmann ; Medema, Marnix H. - \ 2017
Nucleic acids research 45 (2017)W1. - ISSN 0305-1048 - p. W36 - W41.
Many antibiotics, chemotherapeutics, crop protection agents and food preservatives originate from molecules produced by bacteria, fungi or plants. In recent years, genome mining methodologies have been widely adopted to identify and characterize the biosynthetic gene clusters encoding the production of such compounds. Since 2011, the â € antibiotics and secondary metabolite analysis shell - antiSMASH' has assisted researchers in efficiently performing this, both as a web server and a standalone tool. Here, we present the thoroughly updated antiSMASH version 4, which adds several novel features, including prediction of gene cluster boundaries using the ClusterFinder method or the newly integrated CASSIS algorithm, improved substrate specificity prediction for non-ribosomal peptide synthetase adenylation domains based on the new SANDPUMA algorithm, improved predictions for terpene and ribosomally synthesized and post-translationally modified peptides cluster products, reporting of sequence similarity to proteins encoded in experimentally characterized gene clusters on a per-protein basis and a domain-level alignment tool for comparative analysis of trans-AT polyketide synthase assembly line architectures. Additionally, several usability features have been updated and improved. Together, these improvements make antiSMASH up-to-date with the latest developments in natural product research and will further facilitate computational genome mining for the discovery of novel bioactive molecules.
Stadium Coltan : artisanal mining, reforms and social change in eastern Democratic Republic of Congo
Wakenge, Claude Iguma - \ 2017
Wageningen University. Promotor(en): D.J.M. Hilhorst, co-promotor(en): K. Vlassenroot; J.G.R. Cuvelier. - Wageningen : Wageningen University - ISBN 9789463434560 - 210
mining - conflict - economic sociology - cooperatives - reconstruction - poverty - rural sociology - workers - feedstocks - minerals - congo democratic republic - central africa - mijnbouw - conflict - economische sociologie - coöperaties - reconstructie - armoede - rurale sociologie - werkers - industriële grondstoffen - mineralen - democratische republiek kongo - centraal-afrika
In the Democratic Republic of Congo (DRC), the mining sector has the potential to play a pivotal role in post-conflict reconstruction (World Bank, 2008), and artisanal mining sustains the livelihoods of millions people in the country (PACT, 2010). However, in the last 15 years, minerals from this artisanal mining have been ill-reputed. Eastern DRC has often been characterised by chronic instability and violent conflicts (Autesserre, 2010; Stearns, 2011) because it is widely believed that minerals in this region have attracted the greed of national and foreign armed groups, who benefit from the mining business.
Although this ‘greed hypothesis’ has been criticised for its inconsistent performance in explaining resource-related conflicts (Le Billon, 2010; Ross, 2006), various national and international reform initiatives have gained momentum (Verbruggen et al., 2011). These initiatives aim to make the Congolese artisanal mining sector more transparent and to prevent ‘conflict minerals’ from entering the international market. In 2014, 13 reform initiatives—10 focusing on 3T (tantalum, tin and tungsten) and three on gold—were operational in eastern DRC (Cuvelier et al. 2014: 5). The implicit assumptions are that mining reforms will fully ‘clean’ artisanal mining of violence and corruption and that this will contribute to sustaining people’s livelihoods (Garrett and Mitchell, 2009: 12).
This study investigated initiatives intended to ‘formalise’ artisanal mining in DRC—in other words, they aimed to bring mining under state control. The study especially focuses on the effects of one among these initiatives—the ITRI Tin Supply Chain Initiative (iTSCi)—on two groups of actors: miners (creuseurs) and middlemen (négociants). This thesis thus presents a fine-grained case study of the iTSCi. Designed by the International Tin Research Institute in 2009, iTSCi provides a means of determining the origin of 3T and documenting the trading chain for these minerals by ‘tagging and bagging’ the loads of 3T near miners’ shafts (at postes d’achat/selling points or buying stations), at counting offices (comptoirs) and in mineral depots, before the minerals are exported through the international market.
This is a qualitative study undertaken at three coltan mining sites of northern Katanga: Kahendwa, Kisengo and Mai-Baridi. Coltan has been extracted at these sites since 2007. From March 2013 to September 2014, data were collected using participant observation of people’s practices (extraction/sale of coltan and various types of interactions between trading houses, cooperatives, mineworkers (creuseurs) and middlemen (négociants), as well as detailed in-depth interviews with creuseurs, négociants and their households. Data were also collected from the staff of mining cooperatives, trading houses, state authorities and civil servants—predominantly of the Service d’Assistance et d’Encadrement du Small-Scale Mining (SAESSCAM) and the Division des Mines. The last group of informants were a group of clandestine coltan négociants (known as hiboux—literally, ‘owls’), who were followed in the study.
The purpose of this research is to study the micro-dynamics of changes after the reforms following the implementation of iTSCi. The study thus provides insights into how iTSCi is concretely implemented and how it has altered the organisation of mining and the trade of coltan. The study also aims to examine how this organisation affected creuseurs and négociants. The main research question of this study is as follows:
How have initiatives to reform artisanal mining (iTSCi in particular) affected institutional change, how does this relate to changes in patterns of coltan production and trade, how were creuseurs and négociants affected by these changes, and how did these groups respond in the coltan mining areas of Kahendwa, Kisengo and Mai Baridi (northern Katanga) from 2009 to 2014?
Analytically, the study adopted three main theoretical perspectives. First, an actor-oriented approach was taken, building on the premise that individual actors have the agency, knowledge and experience to reflect upon their situation and to respond to changes in their surrounding context (Giddens, 1984). Although the examined mining reforms consist predominantly of ‘ready-made’ techniques such as iTSCi’s ‘tagging and bagging’, analysing reforms with an actor orientation helps to highlight people’s reactions and responses. This includes how reform policies are applied in institutions (e.g. mining cooperatives), how they interact, how they are assigned meaning and how they are negotiated by social actors (Christoplos and Hilhorst, 2009).
Second, the study builds on the sociology of economic life, which holds that economic action is a form of social action that is socially ‘embedded’, meaning that it is linked with or dependent on actions and institutions (such as social networks) that are noneconomic in content, goals and processes (Granovetter, 2005). This perspective facilitates the analysis of the livelihoods of négociants, including mechanisms of smuggling minerals into and beyond the mining areas where iTSCi is in force.
Third, this thesis introduced the original concept of ‘enclaves of regulations’. These enclaves refer to the mining areas where iTSCi or other reforms are in force. This thesis has shown that, although these ‘enclaves’ appear to be ‘closed’ and insulated from the environment in terms of the locally applied rules for the mining and trading of minerals (e.g. ‘tagging and bagging’), in reality, such closure is not complete. This thesis has demonstrated that it would therefore be more appropriate to consider these ‘enclaves’ as semi-autonomous fields with porous boundaries.
Apart from the introduction and the concluding chapters, this thesis is composed of five chapters. Chapter 2 explores the evolution of the mineral sector in the Katanga province. It analyses the history of mining, the initiation of artisanal mining and how the ongoing reforms have been informed by this history. In this chapter, it is shown that there is a long history of the organisation of mining in the Katangese province. The reforms therefore did not enter into a stage of anarchy, or an institutional void, but they added a layer to already existing forms of organisation.
Chapter 3 focuses on mining cooperatives as newly introduced institutions aimed at governing the artisanal mining sites. Through a single case study, the chapter analyses how these cooperatives —especially the Coopérative des Artisanaux Miniers du Congo, CDMC—were introduced into the mining areas and how they interacted and blended with pre-existing miners’ organisations. This chapter demonstrates that cooperatives have been an emergent—rather than durable—solution in terms of representing the interests of artisanal miners.
In Chapter 4, I provide a different perspective on ‘conflict minerals’. I thus introduce the notion of ‘reform conflicts’ to emphasise that, although ongoing reforms aim to sever the supposed linkages between the artisanal mining business and violent conflicts, these reforms have become a driving force behind the emergence of new conflicts over property rights and access to minerals.
Chapter 5 is about livelihoods. It analyses how the reforms have influenced the livelihoods and socioeconomic position of négociants. This chapter also explores what kind of opportunities the reforms have offered to this group of mineral brokers often considered powerful in the mineral supply chain and explains what kind of constraints the négociants have confronted and why they have opted to diversify their livelihood portfolios. The chapter has shown that the reforms have affected this group of mineral brokers in different ways. Some négociants were well off, whereas others have been excluded from the mineral commodity chain. These findings contradict the widespread opinion that négociants are always abusive brokers in the mineral production and commodity chain.
Chapter 6 analyses the responses of creuseurs and négociants to iTSCi. Although the mining sites where iTSCi is in force appear to be ‘enclaves of regulations’, I explore the strategies of creuseurs and négociants to bypass iTSCi and the reforms, especially around the coltan trade. This chapter demonstrates that coltan smuggling is a deeply rooted practice. Despite the reforms, smuggling continues in different forms.
All of the elements highlighted above suggest that mining reforms have undergone a major shift, from addressing the initial problems associated with ‘conflict minerals’ to creating or reinforcing various types of problems, such as the influence of ‘big men’ in the mining business, coltan smuggling and the emergence of new conflicts over accessing minerals. This means that reform initiatives such as iTSCi should be based on knowledge about the actual situation. Thus, understanding and addressing these new types of problems calls for a comprehensive approach at both local and broader levels.
Current remote sensing approaches to monitoring forest degradation in support of countries measurement, reporting and verification (MRV) systems for REDD+
Mitchell, Anthea L. ; Rosenqvist, Ake ; Mora, Brice - \ 2017
Carbon Balance and Management 12 (2017)1. - ISSN 1750-0680
Above-ground biomass - Carbon emissions - Degradation - Disturbance - Forests - Measurement reporting and verification - Monitoring - REDD+ - Time-series
Forest degradation is a global phenomenon and while being an important indicator and precursor to further forest loss, carbon emissions due to degradation should also be accounted for in national reporting within the frame of UN REDD+. At regional to country scales, methods have been progressively developed to detect and map forest degradation, with these based on multi-resolution optical, synthetic aperture radar (SAR) and/or LiDAR data. However, there is no one single method that can be applied to monitor forest degradation, largely due to the specific nature of the degradation type or process and the timeframe over which it is observed. The review assesses two main approaches to monitoring forest degradation: first, where detection is indicated by a change in canopy cover or proxies, and second, the quantification of loss (or gain) in above ground biomass (AGB). The discussion only considers degradation that has a visible impact on the forest canopy and is thus detectable by remote sensing. The first approach encompasses methods that characterise the type of degradation and track disturbance, detect gaps in, and fragmentation of, the forest canopy, and proxies that provide evidence of forestry activity. Progress in these topics has seen the extension of methods to higher resolution (both spatial and temporal) data to better capture the disturbance signal, distinguish degraded and intact forest, and monitor regrowth. Improvements in the reliability of mapping methods are anticipated by SAR-optical data fusion and use of very high resolution data. The second approach exploits EO sensors with known sensitivity to forest structure and biomass and discusses monitoring efforts using repeat LiDAR and SAR data. There has been progress in the capacity to discriminate forest age and growth stage using data fusion methods and LiDAR height metrics. Interferometric SAR and LiDAR have found new application in linking forest structure change to degradation in tropical forests. Estimates of AGB change have been demonstrated at national level using SAR and LiDAR-assisted approaches. Future improvements are anticipated with the availability of next generation LiDAR sensors. Improved access to relevant satellite data and best available methods are key to operational forest degradation monitoring. Countries will need to prioritise their monitoring efforts depending on the significance of the degradation, balanced against available resources. A better understanding of the drivers and impacts of degradation will help guide monitoring and restoration efforts. Ultimately we want to restore ecosystem service and function in degraded forests before the change is irreversible.
Soil protistology rebooted: 30 fundamental questions to start with
Geisen, Stefan ; Mitchell, Edward A.D. ; Wilkinson, David M. ; Adl, Sina ; Bonkowski, Michael ; Brown, Matthew W. ; Fiore-Donno, Anna Maria ; Heger, Thierry J. ; Jassey, Vincent E.J. ; Krashevska, Valentyna ; Lahr, Daniel J.G. ; Marcisz, Katarzyna ; Mulot, Matthieu ; Payne, Richard ; Singer, David ; Anderson, O.R. ; Charman, Dan J. ; Ekelund, Flemming ; Griffiths, Bryan S. ; Rønn, Regin ; Smirnov, Alexey ; Bass, David ; Belbahri, Lassaâd ; Berney, Cédric ; Blandenier, Quentin ; Chatzinotas, Antonis ; Clarholm, Marianne ; Dunthorn, Micah ; Feest, Alan ; Fernández, Leonardo D. ; Foissner, Wilhelm ; Fournier, Bertrand ; Gentekaki, Eleni ; Hájek, Michal ; Helder, Hans ; Jousset, Alexandre ; Koller, Robert ; Kumar, Santosh ; Terza, Antonietta La; Lamentowicz, Mariusz ; Mazei, Yuri ; Santos, Susana S. ; Seppey, Christophe V.W. ; Spiegel, Frederick W. ; Walochnik, Julia ; Winding, Anne ; Lara, Enrique - \ 2017
Soil Biology and Biochemistry 111 (2017). - ISSN 0038-0717 - p. 94 - 103.
Protists are the most diverse eukaryotes. These microbes are keystone organisms of soil ecosystems and
regulate essential processes of soil fertility such as nutrient cycling and plant growth. Despite this,
protists have received little scientific attention, especially compared to bacteria, fungi and nematodes in
soil studies. Recent methodological advances, particularly in molecular biology techniques, have made
the study of soil protists more accessible, and have created a resurgence of interest in soil protistology.
This ongoing revolution now enables comprehensive investigations of the structure and functioning of
soil protist communities, paving the way to a new era in soil biology. Instead of providing an exhaustive
review, we provide a synthesis of research gaps that should be prioritized in future studies of soil
protistology to guide this rapidly developing research area. Based on a synthesis of expert opinion we
propose 30 key questions covering a broad range of topics including evolution, phylogenetics, functional
ecology, macroecology, paleoecology, and methodologies. These questions highlight a diversity of topics
that will establish soil protistology as a hub discipline connecting different fundamental and applied
fields such as ecology, biogeography, evolution, plant-microbe interactions, agronomy, and conservation
biology. We are convinced that soil protistology has the potential to be one of the most exciting frontiers
The genome of Chenopodium quinoa
Jarvis, D.E. ; Shwen Ho, Yung ; Lightfoot, Damien J. ; Schmöckel, Sandra M. ; Li, Bo ; Borm, T.J.A. ; Ohyanagi, Hajime ; Mineta, Katsuhiko ; Mitchell, Craig T. ; Saber, Noha ; Kharbatia, Najeh M. ; Rupper, Ryan R. ; Sharp, Aaron R. ; Dally, Nadine ; Boughton, Berin A. ; Woo, Yong H. ; Gao, Ge ; Schijlen, E.G.W.M. ; Guo, Xiujie ; Momin, Afaque A. ; Negräo, Sónia ; Al-Babili, Salim ; Gehring, Christoph ; Roessner, Ute ; Jung, Christian ; Murphy, Kevin ; Arold, Stefan T. ; Gojobori, Takashi ; Linden, C.G. van der; Loo, E.N. van; Jellen, Eric N. ; Maughan, Peter J. ; Tester, Mark - \ 2017
Nature 542 (2017)7641. - ISSN 0028-0836 - p. 307 - 312.
Chenopodium quinoa (quinoa) is a highly nutritious grain identified as an important crop to improve world food security. Unfortunately, few resources are available to facilitate its genetic improvement. Here we report the assembly of a high-quality, chromosome-scale reference genome sequence for quinoa, which was produced using single-molecule real-time sequencing in combination with optical, chromosome-contact and genetic maps. We also report the sequencing of two diploids from the ancestral gene pools of quinoa, which enables the identification of sub-genomes in quinoa, and reduced-coverage genome sequences for 22 other samples of the allotetraploid goosefoot complex. The genome sequence facilitated the identification of the transcription factor likely to control the production of anti-nutritional triterpenoid saponins found in quinoa seeds, including a mutation that appears to cause alternative splicing and a premature stop codon in sweet quinoa strains. These genomic resources are an important first step towards the genetic improvement of quinoa.
Nutrition for the ageing brain: Towards evidence for an optimal diet
Vauzour, David ; Camprubi-Robles, Maria ; Miquel-Kergoat, Sophie ; Andres-Lacueva, Cristina ; Bánáti, Diána ; Barberger-Gateau, Pascale ; Bowman, Gene L. ; Caberlotto, Laura ; Clarke, Robert ; Hogervorst, Eef ; Kiliaan, Amanda J. ; Lucca, Ugo ; Manach, Claudine ; Minihane, Anne-Marie ; Mitchell, Ellen Siobhan ; Perneczky, Robert ; Perry, Hugh ; Roussel, Anne-Marie ; Schuermans, Jeroen ; Sijben, John ; Spencer, Jeremy P.E. ; Thuret, Sandrine ; De Rest, Ondine Van; Vandewoude, Maurits ; Wesnes, Keith ; Williams, Robert J. ; Williams, Robin S.B. ; Ramirez, Maria - \ 2017
Ageing Research Reviews 35 (2017). - ISSN 1568-1637 - p. 222 - 240.
As people age they become increasingly susceptible to chronic and extremely debilitating brain diseases. The precise cause of the neuronal degeneration underlying these disorders, and indeed normal brain ageing remains however elusive. Considering the limits of existing preventive methods, there is a desire to develop effective and safe strategies. Growing preclinical and clinical research in healthy individuals or at the early stage of cognitive decline has demonstrated the beneficial impact of nutrition on cognitive functions. The present review is the most recent in a series produced by the Nutrition and Mental Performance Task Force under the auspice of the International Life Sciences Institute Europe (ILSI Europe). The latest scientific advances specific to how dietary nutrients and non-nutrient may affect cognitive ageing are presented. Furthermore, several key points related to mechanisms contributing to brain ageing, pathological conditions affecting brain function, and brain biomarkers are also discussed. Overall, findings are inconsistent and fragmented and more research is warranted to determine the underlying mechanisms and to establish dose-response relationships for optimal brain maintenance in different population subgroups. Such approaches are likely to provide the necessary evidence to develop research portfolios that will inform about new dietary recommendations on how to prevent cognitive decline.
Genome-wide analysis identifies 12 loci influencing human reproductive behavior
Barban, Nicola ; Jansen, Rick ; Vlaming, Ronald de; Vaez, Ahmad ; Mandemakers, Jornt J. ; Tropf, Felix C. ; Shen, Xia ; Wilson, James F. ; Chasman, Daniel I. ; Nolte, Ilja M. ; Tragante, Vinicius ; Laan, Sander W. van der; Perry, John R.B. ; Kong, Augustine ; Ahluwalia, Tarunveer S. ; Albrecht, Eva ; Yerges-Armstrong, Laura ; Atzmon, Gil ; Auro, Kirsi ; Ayers, Kristin ; Bakshi, Andrew ; Ben-Avraham, Danny ; Berger, Klaus ; Bergman, Aviv ; Bertram, Lars ; Bielak, Lawrence F. ; Bjornsdottir, Gyda ; Bonder, Marc Jan ; Broer, Linda ; Bui, Minh ; Barbieri, Caterina ; Cavadino, Alana ; Chavarro, Jorge E. ; Turman, Constance ; Concas, Maria Pina ; Cordell, Heather J. ; Davies, Gail ; Eibich, Peter ; Eriksson, Nicholas ; Esko, Tõnu ; Eriksson, Joel ; Falahi, Fahimeh ; Felix, Janine F. ; Fontana, Mark Alan ; Franke, Lude ; Gandin, Ilaria ; Gaskins, Audrey J. ; Gieger, Christian ; Gunderson, Erica P. ; Guo, Xiuqing ; Hayward, Caroline ; He, Chunyan ; Hofer, Edith ; Huang, Hongyan ; Joshi, Peter K. ; Kanoni, Stavroula ; Karlsson, Robert ; Kiechl, Stefan ; Kifley, Annette ; Kluttig, Alexander ; Kraft, Peter ; Lagou, Vasiliki ; Lecoeur, Cecile ; Lahti, Jari ; Li-Gao, Ruifang ; Lind, Penelope A. ; Liu, Tian ; Makalic, Enes ; Mamasoula, Crysovalanto ; Matteson, Lindsay ; Mbarek, Hamdi ; McArdle, Patrick F. ; McMahon, George ; Meddens, S.F.W. ; Mihailov, Evelin ; Miller, Mike ; Missmer, Stacey A. ; Monnereau, Claire ; Most, Peter J. van der; Myhre, Ronny ; Nalls, Mike A. ; Nutile, Teresa ; Kalafati, Ioanna Panagiota ; Porcu, Eleonora ; Prokopenko, Inga ; Rajan, Kumar B. ; Rich-Edwards, Janet ; Rietveld, Cornelius A. ; Robino, Antonietta ; Rose, Lynda M. ; Rueedi, Rico ; Ryan, Kathleen A. ; Saba, Yasaman ; Schmidt, Daniel ; Smith, Jennifer A. ; Stolk, Lisette ; Streeten, Elizabeth ; Tönjes, Anke ; Thorleifsson, Gudmar ; Ulivi, Sheila ; Wedenoja, Juho ; Wellmann, Juergen ; Willeit, Peter ; Yao, Jie ; Yengo, Loic ; Zhao, Jing Hua ; Zhao, Wei ; Zhernakova, Daria V. ; Amin, Najaf ; Andrews, Howard ; Balkau, Beverley ; Barzilai, Nir ; Bergmann, Sven ; Biino, Ginevra ; Bisgaard, Hans ; Bønnelykke, Klaus ; Boomsma, Dorret I. ; Buring, Julie E. ; Campbell, Harry ; Cappellani, Stefania ; Ciullo, Marina ; Cox, Simon R. ; Cucca, Francesco ; Toniolo, Daniela ; Davey-Smith, George ; Deary, Ian J. ; Dedoussis, George ; Deloukas, Panos ; Duijn, Cornelia M. van; Geus, Eco J.C. de; Eriksson, Johan G. ; Evans, Denis A. ; Faul, Jessica D. ; Sala, Cinzia Felicita ; Froguel, Philippe ; Gasparini, Paolo ; Girotto, Giorgia ; Grabe, Hans-Jörgen ; Greiser, Karin Halina ; Groenen, Patrick J.F. ; Haan, Hugoline G. de; Haerting, Johannes ; Harris, Tamara B. ; Heath, Andrew C. ; Heikkilä, Kauko ; Hofman, Albert ; Homuth, Georg ; Holliday, Elizabeth G. ; Hopper, John ; Hyppönen, Elina ; Jacobsson, Bo ; Jaddoe, Vincent W.V. ; Johannesson, Magnus ; Jugessur, Astanand ; Kähönen, Mika ; Kajantie, Eero ; Kardia, Sharon L.R. ; Keavney, Bernard ; Kolcic, Ivana ; Koponen, Päivikki ; Kovacs, Peter ; Kronenberg, Florian ; Kutalik, Zoltan ; Bianca, Martina la; Lachance, Genevieve ; Iacono, William G. ; Lai, Sandra ; Lehtimäki, Terho ; Liewald, David C. ; Lindgren, Cecilia M. ; Liu, Yongmei ; Luben, Robert ; Lucht, Michael ; Luoto, Riitta ; Magnus, Per ; Magnusson, Patrik K.E. ; Martin, Nicholas G. ; McGue, Matt ; McQuillan, Ruth ; Medland, Sarah E. ; Meisinger, Christa ; Mellström, Dan ; Metspalu, Andres ; Traglia, Michela ; Milani, Lili ; Mitchell, Paul ; Montgomery, Grant W. ; Mook-Kanamori, Dennis ; Mutsert, Renée de; Nohr, Ellen A. ; Ohlsson, Claes ; Olsen, Jørn ; Ong, Ken K. ; Paternoster, Lavinia ; Pattie, Alison ; Penninx, Brenda W.J.H. ; Perola, Markus ; Peyser, Patricia A. ; Pirastu, Mario ; Polasek, Ozren ; Power, Chris ; Kaprio, Jaakko ; Raffel, Leslie J. ; Räikkönen, Katri ; Raitakari, Olli ; Ridker, Paul M. ; Ring, Susan M. ; Roll, Kathryn ; Rudan, Igor ; Ruggiero, Daniela ; Rujescu, Dan ; Salomaa, Veikko ; Schlessinger, David ; Schmidt, Helena ; Schmidt, Reinhold ; Schupf, Nicole ; Smit, Johannes ; Sorice, Rossella ; Spector, Tim D. ; Starr, John M. ; Stöckl, Doris ; Strauch, Konstantin ; Stumvoll, Michael ; Swertz, Morris A. ; Thorsteinsdottir, Unnur ; Thurik, A.R. ; Timpson, Nicholas J. ; Tung, Joyce Y. ; Uitterlinden, André G. ; Vaccargiu, Simona ; Viikari, Jorma ; Vitart, Veronique ; Völzke, Henry ; Vollenweider, Peter ; Vuckovic, Dragana ; Waage, Johannes ; Wagner, Gert G. ; Wang, Jie Jin ; Wareham, Nicholas J. ; Weir, David R. ; Willemsen, Gonneke ; Willeit, Johann ; Wright, Alan F. ; Zondervan, Krina T. ; Stefansson, Kari ; Krueger, Robert F. ; Lee, James J. ; Benjamin, Daniel J. ; Cesarini, David ; Koellinger, Philipp D. ; Hoed, Marcel den; Snieder, Harold ; Mills, Melinda C. - \ 2016
Nature Genetics 48 (2016)12. - ISSN 1061-4036 - p. 1462 - 1472.
The genetic architecture of human reproductive behavior—age at first birth (AFB) and number of children ever born (NEB)—has a strong relationship with fitness, human development, infertility and risk of neuropsychiatric disorders. However, very few genetic loci have been identified, and the underlying mechanisms of AFB and NEB are poorly understood. We report a large genome-wide association study of both sexes including 251,151 individuals for AFB and 343,072 individuals for NEB. We identified 12 independent loci that are significantly associated with AFB and/or NEB in a SNP-based genome-wide association study and 4 additional loci associated in a gene-based effort. These loci harbor genes that are likely to have a role, either directly or by affecting non-local gene expression, in human reproduction and infertility, thereby increasing understanding of these complex traits.
|Results of a desk study on best practices for animal transport
Mitchell, M.A. ; Spoolder, H.A.M. - \ 2016
In: Book of Abstracts of the 67th Annual Meeting of the European Association for Animal Production. - EAAP scientific committee - ISBN 9789086868308 - p. 531 - 531.
The EU has provides a harmonised legal framework for animal transport. Part of that framework is the EU adopted Regulation (EC) 1/2005. The content and impact of the Regulation has been the subject of a Scientific Opinion by EFSA in 2011 followed in 2012 by an impact report from the Commission to the European
Parliament and the Council. Three key recommendations were formulated the latter of which stated ‘As regards the gap between the requirements of the legislation and available scientific evidence the Commission sees that this is best addressed by the adoption of guides to good practice’. It is expected that the development of Guides to Good and Best Practice can improve the welfare of animals during transportation, particularly by reducing national and regional differences in interpretation of the requirements of the Regulation. The
Transport Guides project was commissioned by DG SANTE to produce Guides to Good Practice for cattle, sheep, pigs, horses and poultry in the European Union (http://www.animaltransportguides.eu). The project has been undertaken by a research consortium comprised of 16 representative organisations from 9 Member States and a stakeholder platform with 10 member organisations. The first phase of this project involved the examination of a wide range of information sources and literature to identify and evaluate available recommendations for good and best practices during all stages of transport. Good practices are those that reflect the requirements in the legislation. Best Practices are defined as providing additional guidance on how to exceed legally defined minimum welfare requirements. The first results of this project include analyses of the collected information for each of the species: each species section includes analyses of the practices identified, followed by an overview of all available practices presented in tabulated form. These findings are
the basis for the development of Guides to Good and Best Practices in the next steps of the project, and will be presented at the meeting.
Impact of the shedding level on transmission of persistent infections in Mycobacterium avium subspecies paratuberculosis (MAP)
Slater, Noa ; Mitchell, Rebecca Mans ; Whitlock, Robert H. ; Fyock, Terry ; Pradhan, Abani Kumar ; Knupfer, Elena ; Schukken, Ynte Hein ; Louzoun, Yoram - \ 2016
Veterinary Research 47 (2016)1. - ISSN 0928-4249
Super-shedders are infectious individuals that contribute a disproportionate amount of infectious pathogen load to the environment. A super-shedder host may produce up to 10 000 times more pathogens than other infectious hosts. Super-shedders have been reported for multiple human and animal diseases. If their contribution to infection dynamics was linear to the pathogen load, they would dominate infection dynamics. We here focus on quantifying the effect of super-shedders on the spread of infection in natural environments to test if such an effect actually occurs in Mycobacterium avium subspecies paratuberculosis (MAP). We study a case where the infection dynamics and the bacterial load shed by each host at every point in time are known. Using a maximum likelihood approach, we estimate the parameters of a model with multiple transmission routes, including direct contact, indirect contact and a background infection risk. We use longitudinal data from persistent infections (MAP), where infectious individuals have a wide distribution of infectious loads, ranging upward of three orders of magnitude. We show based on these parameters that the effect of super-shedders for MAP is limited and that the effect of the individual bacterial load is limited and the relationship between bacterial load and the infectiousness is highly concave. A 1000-fold increase in the bacterial contribution is equivalent to up to a 2-3 fold increase in infectiousness.
Assessing convergence processes at the intersection of the food and pharmaceutical industries in functional food innovation using different perspectives
Bornkessel, S. - \ 2016
Wageningen University. Promotor(en): Onno Omta; Stefanie Broring. - Wageningen : Wageningen University - ISBN 9789462576599 - 129
functional foods - innovations - food industry - non-food industries - pharmacology - functionele voedingsmiddelen - innovaties - voedselindustrie - non-food industrieën - farmacologie
Assessing convergence processes at the intersection of the food and pharmaceutical industries in functional food innovation using different perspectives
The worldwide growing functional food market (e.g. Menrad, 2003, Ding et al., 2015) is based on the convergence of the food and pharmaceutical sectors (Omta, 2004, Bröring, 2005), since functional foods incorporate a nutritional as well as a health benefit (Spence, 2006, Hasler, 2002). Several studies provide a comprehensive overview of convergence definitions and their different emphases (Bröring, 2005, Curran, 2010, Hacklin, 2008, Preschitschek, 2014), mainly following the common idea summarised by the Organisation for Economic Co‐operation and Development as follows: ‘the blurring of technical and regulatory boundaries between sectors of the economy’ (OECD, 1992). On the one hand, this emerging segment offers a plethora of innovation opportunities. On the other hand, companies focusing on this emerging segment have to employ knowledge and technologies outside of their traditional expertise. The importance of innovation increases, since the emergence of the functional food market implies an intensification of competitive pressure. Due to high failure rates, there is an urgent need to improve the food innovation process (Stewart-Knox and Mitchell, 2003).
The convergence process is considered to follow the consecutive steps of science, technology and market convergence, leading to a complete industry convergence in which companies or whole industry segments fuse (Curran et al., 2010, Hacklin, 2008). Linking these steps to the simplified innovation process, the comparative perspective on the innovation and convergence processes delivers a framework with which to analyse innovation processes in converging industries using different perspectives. Therefore, the present thesis aims
Ø to evaluate convergence processes using different perspectives in order to derive an assessment framework of the innovation process in converging industries.
This study deals with the functional food sector emerging between the food and pharmaceutical industries while using certain functional ingredients as units of analysis.
The present thesis comprises two parts. It first focuses on the procedural perspective of convergence processes in order to deliver a comprehensive analysis of the complete convergence process. This is then complemented in the second part by a focus on the later steps of market and industry convergence.
In the first part, this study delivers quantitative (Chapter 2 – life cycle approach) and qualitative (Chapter 3 – perspective of innovation value chain) measures for the comprehensive analysis of the complete convergence process. While the life cycle approach focuses on the development showing the movement of complete industry sectors, the innovation value chain perspective delivers insights into the underlying strategic cross-industry activities on a company level. Next to the comprehensive analysis of the convergence process, this study delivers two levels with which to analyse the later phases in converging industries: first, the analysis of cross-industry collaborations on a company level (Chapter 4), and second, the analysis of ingredient awareness on a consumer level (Chapter 5). While the analysis on a company level delivers an approach to analyse cross-industry innovation using the resource-based view, the consumer perspective sheds light upon the consumers’ perception of the products delivered in the convergence areas.
In summary, convergence implies a changing competitive environment. The evaluation of this phenomenon is therefore of high importance for researchers and practitioners alike. This thesis enhances the research field of convergence by delivering an overall assessment framework that integrates different perspectives to screen convergence processes and to analyse converging competences. The scope and the unit of analysis, along with the adaptation of theoretical concepts, extend already existing convergence assessment approaches. Besides the analysis of the early phases of convergence processes used to anticipate industrial developments (e.g. Curran et al., 2010), the elaboration of the complete convergence process delivers an approach to face the multifaceted challenges during the innovation process in converging industries. The practical implications of this study is that it provides companies in convergence areas different measures to evaluate convergence processes in order to identify relevant convergence areas. Depending on the phase of the convergence process, the appropriate method or mixture of methods can be used to substantiate strategic corporate decisions such as for instance product positioning.
CCoAOMT down-regulation activates anthocyanin biosynthesis in petunia
Shaipulah, N.F.M. ; Muhlemann, Joëlle K. ; Woodworth, Benjamin D. ; Moerkercke, Alex Van; Verdonk, J.C. ; Ramirez, A.A. ; Haring, Michel A. ; Dudareva, Natalia ; Schuurink, Robert C. - \ 2016
Plant Physiology 170 (2016)2. - ISSN 0032-0889 - p. 717 - 731.
Anthocyanins and volatile phenylpropenes (isoeugenol and eugenol) in petunia (Petunia hybrida) flowers have the precursor 4-coumaryl coenzyme A (CoA) in common. These phenolics are produced at different stages during flower development. Anthocyanins are synthesized during early stages of flower development and sequestered in vacuoles during the lifespan of the flowers. The production of isoeugenol and eugenol starts when flowers open and peaks after anthesis. To elucidate additional biochemical steps toward (iso)eugenol production, we cloned and characterized a caffeoyl-coenzyme A O-methyltransferase (PhCCoAOMT1) from the petals of the fragrant petunia ‘Mitchell’. Recombinant PhCCoAOMT1 indeed catalyzed the methylation of caffeoyl-CoA to produce feruloyl CoA. Silencing of PhCCoAOMT1 resulted in a reduction of eugenol production but not of isoeugenol. Unexpectedly, the transgenic plants had purple-colored leaves and pink flowers, despite the fact that cv Mitchell lacks the functional R2R3-MYB master regulator ANTHOCYANIN2 and has normally white flowers. Our results indicate that down-regulation of PhCCoAOMT1 activated the anthocyanin pathway through the R2R3-MYBs PURPLE HAZE (PHZ) and DEEP PURPLE, with predominantly petunidin accumulating. Feeding cv Mitchell flowers with caffeic acid induced PHZ expression, suggesting that the metabolic perturbation of the phenylpropanoid pathway underlies the activation of the anthocyanin pathway. Our results demonstrate a role for PhCCoAOMT1 in phenylpropene production and reveal a link between PhCCoAOMT1 and anthocyanin production.
Combining satellite data for better tropical forest monitoring
Reiche, Johannes ; Lucas, Richard ; Mitchell, A.L. ; Verbesselt, Jan ; Hoekman, D.H. ; Haarpaintner, Jörg ; Kellndorfer, J.M. ; Rosenqvist, Ake ; Lehmann, E.A. ; Woodcock, C.E. ; Seifert, Frank Martin ; Herold, Martin - \ 2016
Nature Climate Change 6 (2016)2. - ISSN 1758-678X - p. 120 - 122.
Implementation of policies to reduce forest loss challenges the Earth observation community to improve forest monitoring. An important avenue for progress is the use of new satellite missions and the combining of optical and synthetic aperture radar sensor data.
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.
Differences in intermittent and continuous fecal shedding patterns between natural and experimental Mycobacterium avium subspecies paratuberculosis infections in cattle
Mitchell, R.M. ; Schukken, Ynte ; Koets, A.P. ; Weber, Maarten ; Bakker, D. ; Stabel, Judy ; Whitlock, R.H. ; Louzoun, Yoram - \ 2015
Veterinary Research 46 (2015). - ISSN 0928-4249 - 10 p.
The objective of this paper is to study shedding patterns of cows infected with Mycobacterium avium subsp. paratuberculosis (MAP). While multiple single farm studies of MAP dynamics were reported, there is not large scale meta-analysis of both natural and experimental infections. Large difference in shedding patterns between experimentally and naturally infected cows were observed. Experimental infections are thus probably driven by different pathological mechanisms. For further evaluations of shedding patterns only natural infections were used. Within such infections, the transition to high shedding was studied as a proxy to the development of a clinical disease. The majority of studied cows never developed high shedding levels. Those that do, typically never reduced their shedding level to low or no shedding. Cows that eventually became high shedders showed a pattern of continuous shedding. In contrast, cows with an intermittent shedding pattern had a low probability to ever become high shedders. In addition, cows that start shedding at a younger age (less than three years of age) have a lower hazard of becoming high shedders compared to cows starting to shed at an older age. These data suggest the presence of three categories of immune control. Cows that are intermittent shedders have the infection process under control (no progressive infection). Cows that start shedding persistently at a young age partially control the infection, but eventually will be high shedders (slow progressive infection), while cows that start shedding persistently at an older age cannot effectively control the infection and become high shedders rapidly.