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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Human Milk Oligosaccharides in Colostrum and Mature Milk of Chinese Mothers : Lewis Positive Secretor Subgroups
Elwakiel, M. ; Hageman, J.A. ; Wang, W. ; Szeto, I.M. ; Goudoever, J.B. van; Hettinga, K.A. ; Schols, H.A. - \ 2018
Journal of Agricultural and Food Chemistry 66 (2018)27. - ISSN 0021-8561 - p. 7036 - 7043.
carbohydrates - genetic polymorphisms - lactation stage - variability

To study the variability in human milk oligosaccharide (HMO) composition of Chinese human milk over a 20-wk lactation period, HMO profiles of 30 mothers were analyzed using CE-LIF. This study showed that total HMO concentrations in Chinese human milk decreased significantly over a 20-wk lactation period, independent of the mother's SeLe status, although with individual variations. In addition, total acidic and neutral HMO concentrations in Chinese human milk decreased over lactation, and levels are driven by their mother's SeLe status. Analysis showed that total neutral fucosylated HMO concentrations in Chinese human milk were higher in the two secretor groups as compared to the nonsecretor group. On the basis of the total neutral fucosylated HMO concentrations in Chinese human milk, HMO profiles within the Se+Le+ group can be divided into two subgroups. HMOs that differed in level between Se+Le+ subgroups were 2′FL, DF-L, LNFP I, and F-LNO. HMO profiles in Dutch human milk also showed Se+Le+ subgroup division, with 2′FL, LNT, and F-LNO as the driving force.

Publisher Correction : Enterotypes in the landscape of gut microbial community composition
Costea, Paul I. ; Hildebrand, Falk ; Arumugam, Manimozhiyan ; Bäckhed, Fredrik ; Blaser, Martin J. ; Bushman, Frederic D. ; Vos, Willem M. de; Ehrlich, S.D. ; Fraser, Claire M. ; Hattori, Masahira ; Huttenhower, Curtis ; Jeffery, Ian B. ; Knights, Dan ; Lewis, James D. ; Ley, Ruth E. ; Ochman, Howard ; O’Toole, Paul W. ; Quince, Christopher ; Relman, David A. ; Shanahan, Fergus ; Sunagawa, Shinichi ; Wang, Jun ; Weinstock, George M. ; Wu, Gary D. ; Zeller, Georg ; Zhao, Liping ; Raes, Jeroen ; Knight, Rob ; Bork, Peer - \ 2018
Nature Microbiology 3 (2018). - ISSN 2058-5276
In the version of this Perspective originally published, the first and last name of co-author Manimozhiyan Arumugam were switched. This has now been corrected in all versions of the Perspective.
Field methods for sampling tree height for tropical forest biomass estimation
Sullivan, Martin J.P. ; Lewis, Simon L. ; Hubau, Wannes ; Qie, Lan ; Baker, Timothy R. ; Banin, Lindsay F. ; Chave, Jerôme ; Cuni-Sanchez, Aida ; Feldpausch, Ted R. ; Lopez-Gonzalez, Gabriela ; Arets, Eric ; Ashton, Peter ; Bastin, Jean François ; Berry, Nicholas J. ; Bogaert, Jan ; Boot, Rene ; Brearley, Francis Q. ; Brienen, Roel ; Burslem, David F.R.P. ; Canniere, Charles de; Chudomelová, Markéta ; Dančák, Martin ; Ewango, Corneille ; Hédl, Radim ; Lloyd, Jon ; Makana, Jean Remy ; Malhi, Yadvinder ; Marimon, Beatriz S. ; Junior, Ben Hur Marimon ; Metali, Faizah ; Moore, Sam ; Nagy, Laszlo ; Vargas, Percy Nuñez ; Pendry, Colin A. ; Ramírez-Angulo, Hirma ; Reitsma, Jan ; Rutishauser, Ervan ; Salim, Kamariah Abu ; Sonké, Bonaventure ; Sukri, Rahayu S. ; Sunderland, Terry ; Svátek, Martin ; Umunay, Peter M. ; Martinez, Rodolfo Vasquez ; Vernimmen, Ronald R.E. ; Torre, Emilio Vilanova ; Vleminckx, Jason ; Vos, Vincent ; Phillips, Oliver L. - \ 2018
Methods in Ecology and Evolution 9 (2018)5. - ISSN 2041-210X - p. 1179 - 1189.
Above-ground biomass estimation - Allometry - Carbon stocks - Forest inventory - Forest structure - Sample size
Quantifying the relationship between tree diameter and height is a key component of efforts to estimate biomass and carbon stocks in tropical forests. Although substantial site-to-site variation in height-diameter allometries has been documented, the time consuming nature of measuring all tree heights in an inventory plot means that most studies do not include height, or else use generic pan-tropical or regional allometric equations to estimate height. Using a pan-tropical dataset of 73 plots where at least 150 trees had in-field ground-based height measurements, we examined how the number of trees sampled affects the performance of locally derived height-diameter allometries, and evaluated the performance of different methods for sampling trees for height measurement. Using cross-validation, we found that allometries constructed with just 20 locally measured values could often predict tree height with lower error than regional or climate-based allometries (mean reduction in prediction error = 0.46 m). The predictive performance of locally derived allometries improved with sample size, but with diminishing returns in performance gains when more than 40 trees were sampled. Estimates of stand-level biomass produced using local allometries to estimate tree height show no over- or under-estimation bias when compared with biomass estimates using field measured heights. We evaluated five strategies to sample trees for height measurement, and found that sampling strategies that included measuring the heights of the ten largest diameter trees in a plot outperformed (in terms of resulting in local height-diameter models with low height prediction error) entirely random or diameter size-class stratified approaches. Our results indicate that even limited sampling of heights can be used to refine height-diameter allometries. We recommend aiming for a conservative threshold of sampling 50 trees per location for height measurement, and including the ten trees with the largest diameter in this sample.
Data from: Recent natural selection causes adaptive evolution of an avian polygenic trait
Bosse, M. ; Spurgin, Lewis G. ; Laine, Veronika N. ; Cole, Ella F. ; Firth, Josh A. ; Gienapp, Phillip ; Gosler, Andrew G. ; McMahon, Keith ; Poissant, Jocelyn ; Verhagen, I.C. ; Groenen, M. ; Oers, C.H.J. ; Sheldon, Ben C. ; Visser, M.E. ; Slate, Jon - \ 2017
adaptation - evolution - genomics - natural selection - bill length - birds - Parus major
We used extensive data from a long-term study of great tits (Parus major) in the United Kingdom and Netherlands to better understand how genetic signatures of selection translate into variation in fitness and phenotypes. We found that genomic regions under differential selection contained candidate genes for bill morphology and used genetic architecture analyses to confirm that these genes, especially the collagen gene COL4A5, explained variation in bill length. COL4A5 variation was associated with reproductive success, which, combined with spatiotemporal patterns of bill length, suggested ongoing selection for longer bills in the United Kingdom. Last, bill length and COL4A5 variation were associated with usage of feeders, suggesting that longer bills may have evolved in the United Kingdom as a response to supplementary feeding.
Enterotypes in the landscape of gut microbial community composition
Costea, Paul I. ; Hildebrand, Falk ; Manimozhiyan, Arumugam ; Bäckhed, Fredrik ; Blaser, Martin J. ; Bushman, Frederic D. ; Vos, Willem M. de; Ehrlich, S.D. ; Fraser, Claire M. ; Hattori, Masahira ; Huttenhower, Curtis ; Jeffery, Ian B. ; Knights, Dan ; Lewis, James D. ; Ley, Ruth E. ; Ochman, Howard ; O'Toole, Paul W. ; Quince, Christopher ; Relman, David A. ; Shanahan, Fergus ; Sunagawa, Shinichi ; Wang, Jun ; Weinstock, George M. ; Wu, Gary D. ; Zeller, Georg ; Zhao, Liping ; Raes, Jeroen ; Knight, Rob ; Bork, Peer - \ 2017
Nature Microbiology 3 (2017)1. - ISSN 2058-5276 - p. 8 - 16.
Population stratification is a useful approach for a better understanding of complex biological problems in human health and wellbeing. The proposal that such stratification applies to the human gut microbiome, in the form of distinct community composition types termed enterotypes, has been met with both excitement and controversy. In view of accumulated data and re-analyses since the original work, we revisit the concept of enterotypes, discuss different methods of dividing up the landscape of possible microbiome configurations, and put these concepts into functional, ecological and medical contexts. As enterotypes are of use in describing the gut microbial community landscape and may become relevant in clinical practice, we aim to reconcile differing views and encourage a balanced application of the concept.
Recent natural selection causes adaptive evolution of an avian polygenic trait
Bosse, Mirte ; Spurgin, Lewis G. ; Laine, Veronika N. ; Cole, Ella F. ; Firth, Josh A. ; Gienapp, Phillip ; Gosler, Andrew G. ; McMahon, Keith ; Poissant, Jocelyn ; Verhagen, Irene ; Groenen, Martien A.M. ; Oers, Kees van; Sheldon, Ben C. ; Visser, Marcel E. ; Slate, Jon - \ 2017
Science 358 (2017)6361. - ISSN 0036-8075 - p. 365 - 368.

We used extensive data froma long-term study of great tits (Parusmajor) in theUnitedKingdom and Netherlands to better understand how genetic signatures of selection translate into variation in fitness and phenotypes.We found that genomic regions under differential selection contained candidate genes for bill morphology and used genetic architecture analyses to confirmthat these genes, especially the collagen gene COL4A5, explained variation in bill length. COL4A5 variation was associated with reproductive success, which, combined with spatiotemporal patterns of bill length, suggested ongoing selection for longer bills in the United Kingdom. Last, bill length and COL4A5 variation were associated with usage of feeders, suggesting that longer bills may have evolved in the United Kingdom as a response to supplementary feeding.

Use of Repeated Blood Pressure and Cholesterol Measurements to Improve Cardiovascular Disease Risk Prediction : An Individual-Participant-Data Meta-Analysis
Paige, Ellie ; Barrett, Jessica ; Pennells, Lisa ; Sweeting, Michael ; Willeit, Peter ; Angelantonio, Emanuele Di; Gudnason, Vilmundur ; Nordestgaard, Børge G. ; Psaty, Bruce M. ; Goldbourt, Uri ; Best, Lyle G. ; Assmann, Gerd ; Salonen, Jukka T. ; Nietert, Paul J. ; Verschuren, W.M.M. ; Brunner, Eric J. ; Kronmal, Richard A. ; Salomaa, Veikko ; Bakker, Stephan L.J. ; Dagenais, Gilles R. ; Sato, Shinichi ; Jansson, Jan Håkan ; Willeit, Johann ; Onat, Altan ; La Cámara, Agustin Gómez De; Roussel, Ronan ; Völzke, Henry ; Dankner, Rachel ; Tipping, Robert W. ; Meade, Tom W. ; Donfrancesco, Chiara ; Kuller, Lewis H. ; Peters, Annette ; Gallacher, John ; Kromhout, Daan ; Iso, Hiroyasu ; Knuiman, Matthew W. ; Casiglia, Edoardo ; Kavousi, Maryam ; Palmieri, Luigi ; Sundström, Johan ; Davis, Barry R. ; Njølstad, Inger ; Couper, David ; Danesh, John ; Thompson, Simon G. ; Wood, Angela M. - \ 2017
American Journal of Epidemiology 186 (2017)8. - ISSN 0002-9262 - p. 899 - 907.
Cardiovascular disease - Longitudinal measurements - Repeated measurements - Risk factors - Risk prediction
The added value of incorporating information from repeated blood pressure and cholesterol measurements to predict cardiovascular disease (CVD) risk has not been rigorously assessed. We used data on 191,445 adults from the Emerging Risk Factors Collaboration (38 cohorts from 17 countries with data encompassing 1962-2014) with more than 1 million measurements of systolic blood pressure, total cholesterol, and high-density lipoprotein cholesterol. Over a median 12 years of follow-up, 21,170 CVD events occurred. Risk prediction models using cumulative mean values of repeated measurements and summary measures from longitudinal modeling of the repeated measurements were compared with models using measurements from a single time point. Risk discrimination (Cindex) and net reclassification were calculated, and changes in C-indices were meta-analyzed across studies. Compared with the single-time-point model, the cumulative means and longitudinal models increased the C-index by 0.0040 (95% confidence interval (CI): 0.0023, 0.0057) and 0.0023 (95% CI: 0.0005, 0.0042), respectively. Reclassification was also improved in both models; compared with the single-time-point model, overall net reclassification improvements were 0.0369 (95% CI: 0.0303, 0.0436) for the cumulative-means model and 0.0177 (95% CI: 0.0110, 0.0243) for the longitudinal model. In conclusion, incorporating repeated measurements of blood pressure and cholesterol into CVD risk prediction models slightly improves risk prediction.
Characterization of Schistosoma mansoni fucosyltransferases for glyco-engineering of ‘native’ helminth N-glycan structures in planta
Noort, Kim van - \ 2017
Clinical trials with live parasites and mouse model studies have shown the potential of helminths and their excretory/secretory (ES) proteins to dampen allergic reactions and autoimmune disorders. Moreover, glycan-dependent mechanisms of action have been shown to be involved in several cases. To further develop helminth-derived ES glycoproteins as biopharmaceuticals, a large-scale expression system is required for the production of recombinant glycoproteins with defined and tailored glycosylation. The trematode Schistosoma mansoni produces highly fucosylated N-glycan structures on its glycoproteins, which cannot be synthesized in current production systems. Thereto, co-expression of specific fucosyltransferases in the expression host are required to introduce helminth-like N-glycan modifications. In the GeneDB database 20 different S. mansoni fucosyltransferase(SmFucTs) genes for N-glycosylation can be found. To date one α1,3 fucosyltransferase is characterized in vitro using glycan acceptors and shows to synthesize Lewis X. Since in vitro and in vivo characterization may differ, characterization in a biological setting, using the Golgi-system, can be more relevant. Thereto, we examined the function of ten selected SmFucTs by transient co-expression with model proteins in Nicotiana benthamiana plants. With this method we have identified SmFucTs that fucosylate LDN, synthesize Lewis X or are involved in core fucosylation. These functionally characterized fucosyltransferases can immediately be applied to synthesize desired helminth-like N-glycan structures on recombinant glycoproteins in the plant. Therefore characterization of SmFucTs, other glycosyltransferases and combinations of different glycosyltransferases expands our glyco-engineering toolbox and offers perspectives for large scale production of glycoproteins with functional helminth N-glycan structures in plants.
Characterization of Schistosoma mansoni fucosyltransferases for glyco-engineering of ‘native’ helminth N-glycan structures in planta
Noort, Kim van - \ 2017
Clinical trials with live parasites and mouse model studies have shown the potential of helminths and their excretory/secretory (ES) proteins to dampen allergic reactions and autoimmune disorders. Moreover, glycan-dependent mechanisms of action have been shown to be involved in several cases. To further develop helminth-derived ES glycoproteins as biopharmaceuticals, a large-scale expression system is required for the production of recombinant glycoproteins with defined and tailored glycosylation. The trematode Schistosoma mansoni produces highly fucosylated N-glycan structures on its glycoproteins, which cannot be synthesized in current production systems. Thereto, co-expression of specific fucosyltransferases in the expression host are required to introduce helminth-like N-glycan modifications. In the GeneDB database 20 different S. mansoni fucosyltransferase(SmFucTs) genes for N-glycosylation can be found. To date one α1,3 fucosyltransferase is characterized in vitro using glycan acceptors and shows to synthesize Lewis X. Since in vitro and in vivo characterization may differ, characterization in a biological setting, using the Golgi-system, can be more relevant. Thereto, we examined the function of ten selected SmFucTs by transient co-expression with model proteins in Nicotiana benthamiana plants. With this method we have identified SmFucTs that fucosylate LDN, synthesize Lewis X or are involved in core fucosylation. These functionally characterized fucosyltransferases can immediately be applied to synthesize desired helminth-like N-glycan structures on recombinant glycoproteins in the plant. Therefore characterization of SmFucTs, other glycosyltransferases and combinations of different glycosyltransferases expands our glyco-engineering toolbox and offers perspectives for large scale production of glycoproteins with functional helminth N-glycan structures in plants.
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.
Significant Correlation Between the Infant Gut Microbiome and Rotavirus Vaccine Response in Rural Ghana
Harris, Vanessa C. ; Armah, George ; Fuentes Enriquez de Salamanca, Susana ; Korpela, Katri E. ; Parashar, Umesh ; Victor, John C. ; Tate, Jacqueline ; Weerth, Carolina de; Giaquinto, Carlo ; Wiersinga, Willem Joost ; Lewis, Kristen D.C. ; Vos, Willem M. de - \ 2017
The Journal of Infectious Diseases 215 (2017)1. - ISSN 0022-1899 - p. 34 - 41.
intestinal microbiome - mucosal immunity - rotavirus vaccine

BACKGROUND:  Rotavirus (RV) is the leading cause of diarrhea-related death in children worldwide and 95% of RV-associated deaths occur in Africa and Asia where RV vaccines (RVVs) have lower efficacy. We hypothesize that differences in intestinal microbiome composition correlate with the decreased RVV efficacy observed in poor settings.

METHODS:  We conducted a nested, case-control study comparing prevaccination, fecal microbiome compositions between 6-week old, matched RVV responders and nonresponders in rural Ghana. These infants' microbiomes were then compared with 154 age-matched, healthy Dutch infants' microbiomes, assumed to be RVV responders. Fecal microbiome analysis was performed in all groups using the Human Intestinal Tract Chip.

RESULTS:  We analyzed findings in 78 Ghanaian infants, including 39 RVV responder and nonresponder pairs. The overall microbiome composition was significantly different between RVV responders and nonresponders (FDR, 0.12), and Ghanaian responders were more similar to Dutch infants than nonresponders (P = .002). RVV response correlated with an increased abundance of Streptococcus bovis and a decreased abundance of the Bacteroidetes phylum in comparisons between both Ghanaian RVV responders and nonresponders (FDR, 0.008 vs 0.003) and Dutch infants and Ghanaian nonresponders (FDR, 0.002 vs 0.009).

CONCLUSIONS:  The intestinal microbiome composition correlates significantly with RVV immunogenicity and may contribute to the diminished RVV immunogenicity observed in developing countries.

Production and glyco-engineering of immunomodulatory helminth glycoproteins in plants
Wilbers, Ruud H.P. ; Westerhof, Lotte B. ; Noort, Kim Van; Obieglo, Katja ; Driessen, Nicole N. ; Everts, Bart ; Gringhuis, Sonja I. ; Schramm, Gabriele ; Goverse, Aska ; Smant, Geert ; Bakker, Jaap ; Smits, Hermelijn H. ; Yazdanbakhsh, Maria ; Schots, Arjen ; Hokke, Cornelis H. - \ 2017
Scientific Reports 7 (2017). - ISSN 2045-2322
Helminth parasites control host-immune responses by secreting immunomodulatory glycoproteins. Clinical trials and mouse model studies have demonstrated the potential of helminth-derived glycoproteins for the treatment of immune-related diseases, like allergies and autoimmune diseases. Studies are however hampered by the limited availability of native parasite-derived proteins. Moreover, recombinant protein production systems have thus far been unable to reconstitute helminth-like glycosylation essential for the functionality of some helminth glycoproteins. Here we exploited the flexibility of the N-glycosylation machinery of plants to reconstruct the helminth glycoproteins omega-1 and kappa-5, two major constituents of immunomodulatory Schistosoma mansoni soluble egg antigens. Fine-tuning transient co-expression of specific glycosyltransferases in Nicotiana benthamiana enabled the synthesis of Lewis X (LeX) and LDN/LDN-F glycan motifs as found on natural omega-1 and kappa-5, respectively. In vitro and in vivo evaluation of the introduction of native LeX motifs on plant-produced omega-1 confirmed that LeX on omega-1 contributes to the glycoprotein’s Th2-inducing properties. These data indicate that mimicking the complex carbohydrate structures of helminths in plants is a promising strategy to allow targeted evaluation of therapeutic glycoproteins for the treatment of inflammatory disorders. In addition, our results offer perspectives for the development of effective anti-helminthic vaccines by reconstructing native parasite glycoprotein antigens.
Private governance of ocean resources
Groeneveld, R.A. ; Bush, S.R. ; Bailey, M.L. - \ 2017
In: Handbook on the Economics and Management of Sustainable Oceans / Nunes, Paulo A.L.D., Svensson, Lisa E., Markandya, Anil, Edward Elgar Publishing - ISBN 9781786430717 - p. 416 - 428.
The United Nations (UN) post-2015 development agenda (United Nations 2015) calls for the establishment of a global partnership for sustainable development, ‘bringing together Governments, civil society, the private sector, the United Nations system and other actors and mobilizing all available resources’ (Art. 39). The agenda thereby explicitly acknowledges that in addition to governments, private companies and civil society have a pivotal role to play in attaining the new Sustainable Development Goals (SDGs). The natural resource economics literature has traditionally applied a strict dichotomy between public actors (that is, governments) and private institutions, notably markets: markets take care of the allocation of private goods and services, while governments uphold the legal framework within which markets operate and correct market failures such as public goods, monopolies, and limited excludability of natural resources (see, for example, Perman et al. 2011; Tietenberg and Lewis 2012). The task of managing ocean resources has thus in recent history fallen squarely on the shoulders of the nation state. However, we have seen for complex systems, such as fisheries and marine ecosystems, that this dichotomy does not always hold (Ostrom 2010). Rather, the work of Ostrom and others (for example, Folke et al. 2005; Galaz et al. 2012) points to what is referred to as polycentric governance, where private and community institutional structures, sometimes integrated with and sometimes separate from the state, are offering new solutions to global governance challenges. These developments are blurring the strict separation of responsibilities between states, companies and, to an increasing extent, civil society.
Mimicking immunomodulatory helminth glycoproteins in plants to enable treatment of inflammatory diseases
Wilbers, R.H.P. ; Westerhof, L.B. ; Noort, Kim van; Obieglo, K. ; Driessen, N.N. ; Everts, B. ; Goverse, A. ; Smant, G. ; Bakker, J. ; Smits, H.H. ; Yazdanbakhsh, M. ; Schots, A. ; Hokke, C.H. - \ 2017
Helminth parasites control host-immune responses by secreting immunomodulatory glycoproteins. Clinical trials and mouse model studies have demonstrated the potential of helminths and helminth-derived glycoproteins for the treatment of immune-related diseases, like allergies and autoimmune diseases. Studies are however hampered by the limited availability of native parasite-derived proteins. Moreover, recombinant protein production systems have thus far been unable to reconstitute helminth-like glycosylation essential for the functionality of helminth glycoproteins. Here we exploited the flexibility of the N-glycosylation machinery of plants to reconstruct two helminth glycoproteins, omega-1 and kappa-5, major constituents of immunomodulatory Schistosoma mansoni soluble egg antigens. Fine-tuning transient co-expression of specific glycosyltransferases in Nicotiana benthamiana enabled the synthesis of Lewis X (LeX) and LDN/LDN-F glycan motifs as found on natural omega-1 and kappa-5, respectively. In vitro and in vivo evaluation of the introduction of native LeX motifs on plant-produced omega-1 confirmed that LeX on omega-1 contributes to the glycoprotein’s Th2-inducing properties. These data indicate that mimicking the complex carbohydrate structures of helminths in plants is a promising strategy to allow targeted evaluation of therapeutic glycoproteins for the treatment of inflammatory disorders. In addition, our results offer perspectives for the development of effective anti-helminthic vaccines by reconstructing native parasite glycoprotein antigens.
Diversity and carbon storage across the tropical forest biome
Sullivan, Martin J.P. ; Talbot, Joey ; Lewis, Simon L. ; Phillips, Oliver L. ; Qie, Lan ; Begne, Serge K. ; Chave, Jerôme ; Cuni-Sanchez, Aida ; Hubau, Wannes ; Lopez-Gonzalez, Gabriela ; Bongers, Frans ; Peña-Claros, Marielos ; Sheil, Douglas - \ 2017
Scientific Reports 7 (2017). - ISSN 2045-2322

Tropical forests are global centres of biodiversity and carbon storage. Many tropical countries aspire to protect forest to fulfil biodiversity and climate mitigation policy targets, but the conservation strategies needed to achieve these two functions depend critically on the tropical forest tree diversity-carbon storage relationship. Assessing this relationship is challenging due to the scarcity of inventories where carbon stocks in aboveground biomass and species identifications have been simultaneously and robustly quantified. Here, we compile a unique pan-Tropical dataset of 360 plots located in structurally intact old-growth closed-canopy forest, surveyed using standardised methods, allowing a multi-scale evaluation of diversity-carbon relationships in tropical forests. Diversity-carbon relationships among all plots at 1 ha scale across the tropics are absent, and within continents are either weak (Asia) or absent (Amazonia, Africa). A weak positive relationship is detectable within 1 ha plots, indicating that diversity effects in tropical forests may be scale dependent. The absence of clear diversity-carbon relationships at scales relevant to conservation planning means that carbon-centred conservation strategies will inevitably miss many high diversity ecosystems. As tropical forests can have any combination of tree diversity and carbon stocks both require explicit consideration when optimising policies to manage tropical carbon and biodiversity.

Seasonal drought limits tree species across the Neotropics
Esquivel-Muelbert, Adriane ; Baker, Timothy R. ; Dexter, Kyle G. ; Lewis, Simon L. ; Steege, Hans ter; Lopez-Gonzalez, Gabriela ; Monteagudo Mendoza, Abel ; Brienen, Roel ; Feldpausch, Ted R. ; Pitman, Nigel ; Alonso, Alfonso ; Heijden, Geertje van der; Peña-Claros, Marielos ; Ahuite, Manuel ; Alexiaides, Miguel ; Álvarez Dávila, Esteban ; Murakami, Alejandro Araujo ; Arroyo, Luzmila ; Aulestia, Milton ; Balslev, Henrik ; Barroso, Jorcely ; Boot, Rene ; Cano, Angela ; Chama Moscoso, Victor ; Comiskey, James A. ; Cornejo, Fernando ; Dallmeier, Francisco ; Daly, Douglas C. ; Dávila, Nallarett ; Duivenvoorden, Joost F. ; Duque Montoya, Alvaro Javier ; Erwin, Terry ; Fiore, Anthony Di; Fredericksen, Todd ; Fuentes, Alfredo ; García-Villacorta, Roosevelt ; Gonzales, Therany ; Guevara Andino, Juan Ernesto ; Honorio Coronado, Euridice N. ; Huamantupa-Chuquimaco, Isau ; Killeen, Timothy J. ; Malhi, Yadvinder ; Mendoza, Casimiro ; Mogollón, Hugo ; Jørgensen, Peter Møller ; Montero, Juan Carlos ; Mostacedo, Bonifacio ; Nauray, William ; Neill, David ; Vargas, Percy Núñez ; Palacios, Sonia ; Palacios Cuenca, Walter ; Pallqui Camacho, Nadir Carolina ; Peacock, Julie ; Phillips, Juan Fernando ; Pickavance, Georgia ; Quesada, Carlos Alberto ; Ramírez-Angulo, Hirma ; Restrepo, Zorayda ; Reynel Rodriguez, Carlos ; Paredes, Marcos Ríos ; Sierra, Rodrigo ; Silveira, Marcos ; Stevenson, Pablo ; Stropp, Juliana ; Terborgh, John ; Tirado, Milton ; Toledo, Marisol ; Torres-Lezama, Armando ; Umaña, María Natalia ; Urrego, Ligia Estela ; Vasquez Martinez, Rodolfo ; Gamarra, Luis Valenzuela ; Vela, César I.A. ; Vilanova Torre, Emilio ; Vos, Vincent ; Hildebrand, Patricio von; Vriesendorp, Corine ; Wang, Ophelia ; Young, Kenneth R. ; Zartman, Charles Eugene ; Phillips, Oliver L. - \ 2017
Ecography 40 (2017)5. - ISSN 0906-7590 - p. 618 - 629.
Within the tropics, the species richness of tree communities is strongly and positively associated with precipitation. Previous research has suggested that this macroecological pattern is driven by the negative effect of water-stress on the physiological processes of most tree species. This implies that the range limits of inventory plots of closed canopy forest distributed across the western Neotropics taxa are defined by their ability to occur under dry conditions, and thus in terms of species distributions predicts a nested pattern of taxa distribution from wet to dry areas. However, this 'dry-tolerance' hypothesis has yet to be adequately tested at large spatial and taxonomic scales. Here, using a dataset of 531 we investigated how precipitation, evaluated both as mean annual precipitation and as the maximum climatological water deficit, influences the distribution of tropical tree species, genera and families. We find that the distributions of tree taxa are indeed nested along precipitation gradients in the western Neotropics. Taxa tolerant to seasonal drought are disproportionally widespread across the precipitation gradient, with most reaching even the wettest climates sampled; however, most taxa analysed are restricted to wet areas. Our results suggest that the 'dry tolerance' hypothesis has broad applicability in the world's most species-rich forests. In addition, the large number of species restricted to wetter conditions strongly indicates that an increased frequency of drought could severely threaten biodiversity in this region. Overall, this study establishes a baseline for exploring how tropical forest tree composition may change in response to current and future environmental changes in this region.
Data from: "African savanna-forest boundary dynamics: a 20-year study"
Cuni-sanchez, Aida ; White, Lee J.T. ; Calders, K. ; Jeffery, Kathryn J. ; Abernethy, Katharine ; Burt, Andrew ; Disney, Mathias ; Gilpin, Martin ; Gomez-dans, Jose L. ; Lewis, Simon L. - \ 2016
Recent studies show widespread encroachment of forest into savannas with important consequences for the global carbon cycle and land-atmosphere interactions. However, little research has focused on in situ measurements of forest-savanna boundary change over time. Using long-term inventory plots we quantify changes in above-ground biomass (AGB), vegetation structure and biodiversity over 20 years for five vegetation types (savanna, colonising forest or F1, successional monodominant forest or F2, Marantaceae forest or F3 and mixed forest or F4) along a savanna-forest transition of central Gabon, all occurring on similar soils. Additionally, we use novel 3D terrestrial laser scanning (TLS) measurements to assess forest structure differences across the transition. Overall, F1 and F2 forests increased in AGB, mainly as a result of adding stems (recruitment in F1) or increased Basal Area (F2). Some plots of F3 and F4 increased in AGB while some decreased. Changes in biodiversity and species’ dominance were small. After 20 years no plot could be classified as having moved to the next stage in the succession. TLS vertical plant profiles showed very distinctive differences amongst the vegetation types. We highlight two relevant points: (i) as forest colonises, changes in biodiversity are much slower than changes in forest structure or AGB; and (ii) all forest types store important quantities of Carbon. Decades long-term monitoring is likely to be required to assess the speed of transition between vegetation types, ideally with TLS, as this provides more objective forest classifications than inventory monitoring.
3D Measurements of Tropical Forest Structure for BIOMASS, Morphology and Calibration and Validation of Satellite Observations
Disney, Mathias ; Burt, Andrew ; Calders, K. ; Raumonen, P. ; Herold, M. ; Lewis, P. ; Lewis, S. ; Boni Vicari, M. ; Rowland, L. ; Meir, P. ; Mitchard, Edward - \ 2016
Engineering of plants for the expression of helminth glycoproteins with their native N-glycan structures
Wilbers, R.H.P. ; Westerhof, L.B. ; Noort, Kim van; Nguyen, D.L. ; Smant, G. ; Bakker, J. ; Hokke, C.H. ; Schots, A. - \ 2016
- 1 p.
Schistosoma mansoni is a parasitic trematode that, like other helminths, secretes immunomodulatory proteins. These secreted proteins are main topics of research as they are possible vaccine candidates or may have therapeutic potential to treat inflammatory disorders. Many helminth secretory proteins carry complex N-glycans, but the exact role of these N-glycans on immunomodulatory properties remains to be elucidated. As the purification of a single glycoprotein from S. mansoni is inefficient and unsustainable, a platform is required that enables production of such glycoproteins. Here we show that S. mansoni-derived glycoproteins can be efficiently produced in plants. Furthermore, we have engineered the plant glycosylation machinery to synthesise N-glycans carrying structures like Lewis X or LDNF. Altogether, our results demonstrate that plants are an excellent platform for the expression of helminth glycoproteins with their native N-glycans. This opens up a new field of research and might lead to the identification of novel therapeutic targets.
Erratum: Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range
Henderson, Gemma ; Cox, Faith ; Ganesh, Siva ; Jonker, Arjan ; Young, Wayne ; Abecia, Leticia ; Angarita, Erika ; Aravena, Paula ; Nora Arenas, Graciela ; Ariza, Claudia ; Attwood, Graeme T. ; Mauricio Avila, Jose ; Avila-stagno, Jorge ; Bannink, André ; Barahona, Rolando ; Batistotti, Mariano ; Bertelsen, Mads F. ; Brown-Kav, Aya ; Carvajal, Andres M. ; Cersosimo, Laura ; Vieira Chaves, Alexandre ; Church, John ; Clipson, Nicholas ; Cobos-peralta, Mario A. ; Cookson, Adrian L. ; Cravero, Silvio ; Cristobal Carballo, Omar ; Crosley, Katie ; Cruz, Gustavo ; Cerón Cucchi, María ; Barra, Rodrigo de la; Menezes, Alexandre B. de; Detmann, Edenio ; Dieho, Kasper ; Dijkstra, Jan ; Reis, William L.S. Dos; Dugan, Mike E.R. ; Hadi Ebrahimi, Seyed ; Eythórsdóttir, Emma ; Nde Fon, Fabian ; Fraga, Martín ; Franco, Francisco ; Friedeman, Chris ; Fukuma, Naoki ; Gagić, Dragana ; Gangnat, Isabelle ; Javier Grilli, Diego ; Guan, Le Luo ; Heidarian Miri, Vahideh ; Hernandez-Sanabria, Emma ; Gomez, Alma Ximena Ibarra ; Isah, Olubukola A. ; Ishaq, Suzanne ; Jami, Elie ; Jelincic, Juan ; Kantanen, Juha ; Kelly, William J. ; Kim, Seon-Ho ; Klieve, Athol ; Kobayashi, Yasuo ; Koike, Satoshi ; Kopecny, Jan ; Nygaard Kristensen, Torsten ; Julie Krizsan, Sophie ; Lachance, Hannah ; Lachman, Medora ; Lamberson, William R. ; Lambie, Suzanne ; Lassen, Jan ; Leahy, Sinead C. ; Lee, Sang-Suk ; Leiber, Florian ; Lewis, Eva ; Lin, Bo ; Lira, Raúl ; Lund, Peter ; Macipe, Edgar ; Mamuad, Lovelia L. ; Cuquetto Mantovani, Hilário ; Marcoppido, Gisela Ariana ; Márquez, Cristian ; Martin, Cécile ; Martinez, Gonzalo ; Eugenia Martinez, Maria ; Lucía Mayorga, Olga ; McAllister, Tim A. ; McSweeney, Chris ; Mestre, Lorena ; Minnee, Elena ; Mitsumori, Makoto ; Mizrahi, Itzhak ; Molina, Isabel ; Muenger, Andreas ; Muñoz, Camila ; Murovec, Bostjan ; Newbold, John ; Nsereko, Victor ; O’donovan, Michael ; Okunade, Sunday ; O’neill, Brendan ; Ospina, Sonia ; Ouwerkerk, Diane ; Parra, Diana ; Pereira, Luiz Gustavo Ribeiro ; Pinares-patiño, Cesar ; Pope, Phil B. ; Poulsen, Morten ; Rodehutscord, Markus ; Rodriguez, Tatiana ; Saito, Kunihiko ; Sales, Francisco ; Sauer, Catherine ; Shingfield, Kevin ; Shoji, Noriaki ; Simunek, Jiri ; Stojanović-Radić, Zorica ; Stres, Blaz ; Sun, Xuezhao ; Swartz, Jeffery ; Liang Tan, Zhi ; Tapio, Ilma ; Taxis, Tasia M. ; Tomkins, Nigel ; Ungerfeld, Emilio ; Valizadeh, Reza ; Adrichem, Peter van; Hamme, Jonathan van; Hoven, Woulter van; Waghorn, Garry ; Wallace, John R. ; Wang, Min ; Waters, Sinéad M. ; Keogh, Kate ; Witzig, Maren ; Wright, Andre-Denis G. ; Yamano, Hidehisa ; Yan, Tianhai ; Yáñez-ruiz, David R. ; Yeoman, Carl J. ; Zambrano, Ricardo ; Zeitz, Johanna ; Zhou, Mi ; Wei Zhou, Hua ; Xia Zou, Cai ; Zunino, Pablo ; Janssen, Peter H. - \ 2016
Scientific Reports 6 (2016). - ISSN 2045-2322 - 2 p.
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