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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GO-FAANG meeting : a Gathering On Functional Annotation of Animal Genomes
Tuggle, Christopher K. ; Giuffra, Elisabetta ; White, Stephen N. ; Clarke, Laura ; Zhou, Huaijun ; Ross, Pablo J. ; Acloque, Hervé ; Reecy, James M. ; Archibald, Alan ; Bellone, Rebecca R. ; Boichard, Michèle ; Chamberlain, Amanda ; Cheng, Hans ; Crooijmans, Richard P.M.A. ; Delany, Mary E. ; Finno, Carrie J. ; Groenen, Martien A.M. ; Hayes, Ben ; Lunney, Joan K. ; Petersen, Jessica L. ; Plastow, Graham S. ; Schmidt, Carl J. ; Song, Jiuzhou ; Watson, Mick - \ 2016
Animal Genetics 47 (2016)5. - ISSN 0268-9146 - p. 528 - 533.
data coordination centre (DCC) - data sharing - Genomics - metanalysis

The Functional Annotation of Animal Genomes (FAANG) Consortium recently held a Gathering On FAANG (GO-FAANG) Workshop in Washington, DC on October 7–8, 2015. This consortium is a grass-roots organization formed to advance the annotation of newly assembled genomes of domesticated and non-model organisms (www.faang.org). The workshop gathered together from around the world a group of 100+ genome scientists, administrators, representatives of funding agencies and commodity groups to discuss the latest advancements of the consortium, new perspectives, next steps and implementation plans. The workshop was streamed live and recorded, and all talks, along with speaker slide presentations, are available at www.faang.org. In this report, we describe the major activities and outcomes of this meeting. We also provide updates on ongoing efforts to implement discussions and decisions taken at GO-FAANG to guide future FAANG activities. In summary, reference datasets are being established under pilot projects; plans for tissue sets, morphological classification and methods of sample collection for different tissues were organized; and core assays and data and meta-data analysis standards were established.

Fat, fibre and cancer risk in African Americans and rural Africans
O'Keefe, S.J. ; Li, J.V. ; Lahti, Leo ; Ou, J. ; Carbonero, F. ; Khaled, M. ; Postma, J.M. ; Kinross, J. ; Wahl, E. ; Ruder, E. ; Vipperla, K. ; Naidoo, V. ; Mtshali, L. ; Tims, S. ; Puylaert, P.G.B. ; DeLany, J. ; Krasinskas, A. ; Benefiel, A.C. ; Kaseb, H.O. ; Newton, K. ; Nicholson, J.K. ; Vos, W.M. De; Gaskins, H.R. ; Zoetendal, E.G. - \ 2015
microbiota - HITChip - genera
Rates of colon cancer are much higher in African Americans (65:100,000) than in rural South Africans (<5:100,000). The higher rates are associated with higher animal protein and fat, and lower fibre consumption, higher colonic secondary bile acids, lower colonic short-chain fatty acid quantities and higher mucosal proliferative biomarkers of cancer risk in otherwise healthy middle-aged volunteers. Here we investigate further the role of fat and fibre in this association. We performed 2-week food exchanges in subjects from the same populations, where African Americans were fed a high-fibre, low-fat African-style diet and rural Africans a high-fat, low-fibre western-style diet, under close supervision. In comparison with their usual diets, the food changes resulted in remarkable reciprocal changes in mucosal biomarkers of cancer risk and in aspects of the microbiota and metabolome known to affect cancer risk, best illustrated by increased saccharolytic fermentation and butyrogenesis, and suppressed secondary bile acid synthesis in the African Americans.
Fat, fibre and cancer risk in African Americans and rural Africans
O'Keefe, S.J. ; Li, J.V. ; Lahti, L.M. ; Ou, J. ; Carbonero, F. ; Mohammed, K. ; Posma, J.M. ; Kinross, J. ; Wahl, E. ; Ruder, E. ; Vipperla, K. ; Naidoo, V. ; Mtshali, L. ; Tims, S. ; Puylaert, P.G.B. ; DeLany, J. ; Krasinskas, A. ; Benefiel, A.C. ; Kaseb, H.O. ; Newton, K. ; Nicholson, J.K. ; Vos, W.M. de; Gaskins, H.R. ; Zoetendal, E.G. - \ 2015
Nature Communications 6 (2015). - ISSN 2041-1723
butyrate-producing bacteria - resistant starch - colon-cancer - cell-proliferation - phylogenetic microarray - microbial metabolites - intestinal-mucosa - epithelial-cells - gene-expression - human feces
Rates of colon cancer are much higher in African Americans (65:100,000) than in rural South Africans (
Diet, microbiota, and microbial metabolites in colon cancer risk in rural Africans and African Americans
Ou, J. ; Carbonero, F. ; Zoetendal, E.G. ; Delany, J.P. ; Wang, M. ; Newton, K. ; Gaskins, H.R. ; O'Keefe, S.F. - \ 2013
American Journal of Clinical Nutrition 98 (2013)1. - ISSN 0002-9165 - p. 111 - 120.
real-time pcr - chain fatty-acids - butyrate-producing bacteria - sulfate-reducing bacteria - bile-acids - liquid-chromatography - quantitative-analysis - sodium-butyrate - human gut - diversity
BACKGROUND: Epidemiologic studies have suggested that most cases of sporadic colon cancer can be attributed to diet. The recognition that colonic microbiota have a major influence on colonic health suggests that they might mediate colonic carcinogenesis. OBJECTIVE: To examine the hypothesis that the influence of diet on colon cancer risk is mediated by the microbiota through their metabolites, we measured differences in colonic microbes and their metabolites in African Americans with a high risk and in rural native Africans with a low risk of colon cancer. DESIGN: Fresh fecal samples were collected from 12 healthy African Americans aged 50-65 y and from 12 age- and sex-matched native Africans. Microbiomes were analyzed with 16S ribosomal RNA gene pyrosequencing together with quantitative polymerase chain reaction of the major fermentative, butyrate-producing, and bile acid-deconjugating bacteria. Fecal short-chain fatty acids were measured by gas chromatography and bile acids by liquid chromatography-mass spectrometry. RESULTS: Microbial composition was fundamentally different, with a predominance of Prevotella in native Africans (enterotype 2) and of Bacteroides in African Americans (enterotype 1). Total bacteria and major butyrate-producing groups were significantly more abundant in fecal samples from native Africans. Microbial genes encoding for secondary bile acid production were more abundant in African Americans, whereas those encoding for methanogenesis and hydrogen sulfide production were higher in native Africans. Fecal secondary bile acid concentrations were higher in African Americans, whereas short-chain fatty acids were higher in native Africans. CONCLUSION: Our results support the hypothesis that colon cancer risk is influenced by the balance between microbial production of health-promoting metabolites such as butyrate and potentially carcinogenic metabolites such as secondary bile acids
African winter population trends of European waterbirds : the identification of critical sites and the effectiveness of Ramsar and IBA site designation for the conservation of migratory waterbirds
Kleijn, D. ; Nagy, S. ; Delany, S. ; Nasirwa, O. ; Dodman, T. ; Goedhart, P.W. - \ 2011
Wageningen : Alterra (Alterra-report 2148) - 30
watervogels - winter - vogeltrek - wildbescherming - populatiedynamica - afrika - europa - vogels - monitoring - waterfowl - bird migration - wildlife conservation - population dynamics - africa - europe - birds
IBA = important bird area
An Atlas of Wader Populations in Africa and Western Eurasia
Delany, S. ; Scott, D. ; Helmink, A.T.F. ; Dodman, T. ; Flink, S. ; Stroud, D. ; Haanstra, L. - \ 2009
London : Wetlands International - ISBN 9789058820471 - 524
populatie-ecologie - conservering - zoögeografie - afrika - europa - waadvogels - vogeltrek - population ecology - conservation - zoogeography - africa - europe - waders - bird migration
This publication is a compilation of current knowledge of the numbers, distribution and movements of one of the most remarkable groups of birds in the region covered by the African-Eurasian Migratory Waterbird Agreement (AEWA). Long-term waterbird count data have been combined with an extensive literature review, especially published results of bird ringing and national bird atlases, to produce maps showing the population boundaries that are used as a basis of the conservation of these species. The maps are supported by informative species accounts that highlight the movements, population status and conservation of waders in the AEWA region.
Urgent preliminary assessment of ornithological data relevant to the spread of Avian Influenze in Europe
Atkinson, P.W. ; Clark, J.A. ; Delany, S. ; Diagana, Ch.H. ; Feu, Ch. du; Fiedler, W. ; Fransson, Th. ; Gaulthier-Clerc, M. ; Grantham, M. ; Gschweng, M. ; Hagemeijer, W. ; Helmink, A.T.F. ; Johnson, A. ; Khomenko, S. ; Martakis, G.F.P. ; Overdijk, O. ; Robinson, R.A. ; Solokha, A. ; Spina, F. ; Sylla, S.I. ; Veen, J. ; Visser, D. - \ 2006
Wageningen : Wetlands International - 342
wilde vogels - migratie - aviaire influenzavirussen - epidemiologie - gegevens verzamelen - landen van de europese unie - aviaire influenza A-virussen - ornitologie - wild birds - migration - avian influenza viruses - epidemiology - data collection - european union countries - avian influenza A viruses - ornithology
In the course of 2005 the highly pathogenic Avian Influenza Asian lineage HPAI H5N1 virus spread from Southeast Asia to SW Siberia, Kazakhstan and the Southern Urals. Migratory birds were suspected of playing a role in the spread of the disease. This meant that the EU could be under direct threat as a number of waterbirds (geese, ducks and shorebirds in particular) were known to migrate through the infected areas to the EU in winter. The European Commission (DG Environment) therefore asked Wetlands International and EURING to undertake the present study. The aims of the project were: (1) to identify species which pose a relatively high risk of spreading H5N1 along their migration routes to the European Union, (2) to analyse the migration routes of these socalled Higher Risk Species on the basis of recoveries of ringed birds, (3) to identify wetland sites where Higher Risk Species concentrate in large numbers during migration and wintering and (4) to develop and test a format for the rapid assessment of ornithological data at the level of wetland sites, in order to prepare wetland managers for an outbreak of H5N1.
Waterbird Population Estimates - Fourth Edition
Delany, S. ; Scott, D. ; Helmink, A.T.F. - \ 2006
Wageningen : Wetlands International - ISBN 9058820319 - 239
watervogels - vogels - schattingen - populatiebiologie - waterfowl - birds - estimates - population biology
Second report on chicken genes and chromosomes 2005
Schmid, M. ; Nanda, I. ; Hoehn, H. ; Schartl, M. ; Haaf, T. ; Buerstedde, J.M. ; Arakawa, H. ; Caldwell, R.B. ; Weigend, S. ; Burt, D.W. ; Smith, J. ; Griffin, D.K. ; Masabanda, J.S. ; Groenen, M.A.M. ; Crooijmans, R.P.M.A. ; Vignal, A. ; Fillon, V. ; Morisson, M. ; Pitel, F. ; Vignoles, M. ; Garrigues, A. ; Gellin, J. ; Rodionov, A.V. ; Galkina, S.A. ; Lukina, N.A. ; Ben-Ari, G. ; Blum, S. ; Hillel, J. ; Twito, T. ; Lavi, U. ; David, L. ; Feldman, M.W. ; Delany, M.E. ; Conley, C.C. ; Fowler, V.M. ; Hedges, S.B. ; Godbout, R. ; Katyal, S. ; Smith, C. ; Hudson, Q. ; Sinclair, A. ; Mizuno, S. - \ 2005
Cytogenetic and Genome Research 109 (2005)4. - ISSN 1424-8581 - p. 415 - 479.
single-nucleotide polymorphisms - expressed sequence tags - dt40 cell-line - in-situ hybridization - telomerase rna gene - 5s ribosomal-rna - mhc class-i - major histocompatibility complex - translation initiation factor-4a - nucleolar-size polymorphisms
Numbers and distribution of wintering waterbirds in the Western Palearctic and Southwest Asia in 1997, 1998 and 1999; results from the international waterbird census
Gilissen, N. ; Haanstra, L. ; Delany, S. ; Boere, G. ; Hagemeijer, W. - \ 2002
Wageningen : Wetlands International - ISBN 9789058820112 - 182
vogels - watervogels - monitoring - inventarisaties - overwintering - zuidwest-azië - ecologie - fauna - ornithologie - trekvogels - Europa - Azië - Noord-Afrika - birds - waterfowl - inventories - south west asia
Using population trend analyses to debug the wader database
Ens, B.J. ; Haanstra, L. ; Delany, S. - \ 2001
Bulletin / Wader Study Group 96 (2001). - ISSN 0260-3799 - p. 28 - 28.
database - fauna - ecologie - ornithologie - steltlopers - vogels
Remote sensing of soils in a eucalypt forest environment.
Skidmore, A.K. ; Varekamp, C. ; Wilson, L. ; Knowles, E. ; Delany, J. - \ 1997
International Journal of Remote Sensing 18 (1997)1. - ISSN 0143-1161 - p. 39 - 56.
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