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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    Repositioning of the global epicentre of non-optimal cholesterol
    Taddei, Cristina ; Zhou, Bin ; Bixby, Honor ; Carrillo-Larco, Rodrigo M. ; Danaei, Goodarz ; Jackson, Rod T. ; Farzadfar, Farshad ; Sophiea, Marisa K. ; Cesare, Mariachiara Di; Iurilli, Maria Laura Caminia ; Martinez, Andrea Rodriguez ; Asghari, Golaleh ; Dhana, Klodian ; Gulayin, Pablo ; Kakarmath, Sujay ; Santero, Marilina ; Voortman, Trudy ; Riley, Leanne M. ; Cowan, Melanie J. ; Savin, Stefan ; Bennett, James E. ; Stevens, Gretchen A. ; Paciorek, Christopher J. ; Aekplakorn, Wichai ; Cifkova, Renata ; Giampaoli, Simona ; Kengne, Andre Pascal ; Khang, Young Ho ; Kuulasmaa, Kari ; Laxmaiah, Avula ; Margozzini, Paula ; Mathur, Prashant ; Nordestgaard, Børge G. ; Zhao, Dong ; Aadahl, Mette ; Abarca-Gómez, Leandra ; Rahim, Hanan Abdul ; Abu-Rmeileh, Niveen M. ; Acosta-Cazares, Benjamin ; Adams, Robert J. ; Ferrieres, Jean ; Geleijnse, Johanna M. ; He, Yuna ; Jacobs, Jeremy M. ; Kromhout, Daan ; Ma, Guansheng ; Dam, Rob M. van; Wang, Qian ; Wang, Ya Xing ; Wang, Ying Wei - \ 2020
    Nature 582 (2020)7810. - ISSN 0028-0836 - p. 73 - 77.

    High blood cholesterol is typically considered a feature of wealthy western countries1,2. However, dietary and behavioural determinants of blood cholesterol are changing rapidly throughout the world3 and countries are using lipid-lowering medications at varying rates. These changes can have distinct effects on the levels of high-density lipoprotein (HDL) cholesterol and non-HDL cholesterol, which have different effects on human health4,5. However, the trends of HDL and non-HDL cholesterol levels over time have not been previously reported in a global analysis. Here we pooled 1,127 population-based studies that measured blood lipids in 102.6 million individuals aged 18 years and older to estimate trends from 1980 to 2018 in mean total, non-HDL and HDL cholesterol levels for 200 countries. Globally, there was little change in total or non-HDL cholesterol from 1980 to 2018. This was a net effect of increases in low- and middle-income countries, especially in east and southeast Asia, and decreases in high-income western countries, especially those in northwestern Europe, and in central and eastern Europe. As a result, countries with the highest level of non-HDL cholesterol—which is a marker of cardiovascular risk—changed from those in western Europe such as Belgium, Finland, Greenland, Iceland, Norway, Sweden, Switzerland and Malta in 1980 to those in Asia and the Pacific, such as Tokelau, Malaysia, The Philippines and Thailand. In 2017, high non-HDL cholesterol was responsible for an estimated 3.9 million (95% credible interval 3.7 million–4.2 million) worldwide deaths, half of which occurred in east, southeast and south Asia. The global repositioning of lipid-related risk, with non-optimal cholesterol shifting from a distinct feature of high-income countries in northwestern Europe, north America and Australasia to one that affects countries in east and southeast Asia and Oceania should motivate the use of population-based policies and personal interventions to improve nutrition and enhance access to treatment throughout the world.

    Rising rural body-mass index is the main driver of the global obesity epidemic in adults
    Bixby, Honor ; Bentham, James ; Zhou, Bin ; Cesare, Mariachiara Di; Paciorek, Christopher J. ; Bennett, James E. ; Taddei, Cristina ; Stevens, Gretchen A. ; Rodriguez-Martinez, Andrea ; Carrillo-Larco, Rodrigo M. ; Khang, Young Ho ; Sorić, Maroje ; Gregg, Edward W. ; Miranda, J.J. ; Bhutta, Zulfiqar A. ; Savin, Stefan ; Sophiea, Marisa K. ; Iurilli, Maria L.C. ; Solomon, Bethlehem D. ; Cowan, Melanie J. ; Riley, Leanne M. ; Danaei, Goodarz ; Bovet, Pascal ; Chirita-Emandi, Adela ; Hambleton, Ian R. ; Hayes, Alison J. ; Ikeda, Nayu ; Kengne, Andre P. ; Laxmaiah, Avula ; Li, Yanping ; McGarvey, Stephen T. ; Mostafa, Aya ; Neovius, Martin ; Starc, Gregor ; Zainuddin, Ahmad A. ; Abarca-Gómez, Leandra ; Abdeen, Ziad A. ; Abdrakhmanova, Shynar ; Abdul Ghaffar, Suhaila ; Abdul Hamid, Zargar ; Abubakar Garba, Jamila ; Ferrieres, Jean ; He, Yuna ; Jacobs, Jeremy M. ; Kromhout, Daan ; Ma, Guansheng ; Visser, Marjolein ; Wang, Qian ; Wang, Ya Xing ; Wang, Ying Wei - \ 2019
    Nature 569 (2019)7755. - ISSN 0028-0836 - p. 260 - 264.

    Body-mass index (BMI) has increased steadily in most countries in parallel with a rise in the proportion of the population who live in cities 1,2 . This has led to a widely reported view that urbanization is one of the most important drivers of the global rise in obesity 3–6 . Here we use 2,009 population-based studies, with measurements of height and weight in more than 112 million adults, to report national, regional and global trends in mean BMI segregated by place of residence (a rural or urban area) from 1985 to 2017. We show that, contrary to the dominant paradigm, more than 55% of the global rise in mean BMI from 1985 to 2017—and more than 80% in some low- and middle-income regions—was due to increases in BMI in rural areas. This large contribution stems from the fact that, with the exception of women in sub-Saharan Africa, BMI is increasing at the same rate or faster in rural areas than in cities in low- and middle-income regions. These trends have in turn resulted in a closing—and in some countries reversal—of the gap in BMI between urban and rural areas in low- and middle-income countries, especially for women. In high-income and industrialized countries, we noted a persistently higher rural BMI, especially for women. There is an urgent need for an integrated approach to rural nutrition that enhances financial and physical access to healthy foods, to avoid replacing the rural undernutrition disadvantage in poor countries with a more general malnutrition disadvantage that entails excessive consumption of low-quality calories.

    Income growth and climate change effects on global nutrition security to mid-century
    Nelson, Gerald ; Bogard, Jessica ; Lividini, Keith ; Arsenault, Joanne ; Riley, Malcolm ; Sulser, Timothy B. ; Mason-D’Croz, Daniel ; Power, Brendan ; Gustafson, David ; Herrero, Mario ; Wiebe, Keith ; Cooper, Karen ; Remans, Roseline ; Rosegrant, Mark - \ 2018
    Nature Sustainability 1 (2018)12. - ISSN 2398-9629 - p. 773 - 781.

    Twenty-first-century challenges for food and nutrition security include the spread of obesity worldwide and persistent undernutrition in vulnerable populations, along with continued micronutrient deficiencies. Climate change, increasing incomes and evolving diets complicate the search for sustainable solutions. Projecting to the year 2050, we explore future macronutrient and micronutrient adequacy with combined biophysical and socioeconomic scenarios that are country-specific. In all scenarios for 2050, the average benefits of widely shared economic growth, if achieved, are much greater than the modelled negative effects of climate change. Average macronutrient availability in 2050 at the country level appears adequate in all but the poorest countries. Many regions, however, will continue to have critical micronutrient inadequacies. Climate change alters micronutrient availability in some regions more than others. These findings indicate that the greatest food security challenge in 2050 will be providing nutritious diets rather than adequate calories. Research priorities and policies should emphasize nutritional quality by increasing availability and affordability of nutrient-dense foods and improving dietary diversity.

    Contributions of mean and shape of blood pressure distribution to worldwide trends and variations in raised blood pressure : A pooled analysis of 1018 population-based measurement studies with 88.6 million participants
    Ezzati, Majid ; Zhou, Bin ; Bentham, James ; Cesare, Mariachiara di; Bixby, Honor ; Danaei, Goodarz ; Hajifathalian, Kaveh ; Taddei, Cristina ; Carrillo-Larco, Rodrigo M. ; Djalalinia, Shirin ; Khatibzadeh, Shahab ; Lugero, Charles ; Peykari, Niloofar ; Zhang, Wan Zhu ; Bennett, James ; Bilano, Ver ; Stevens, Gretchen A. ; Cowan, Melanie J. ; Riley, Leanne M. ; Chen, Zhengming ; Hambleton, Ian R. ; Jackson, Rod T. ; Kengne, Andre Pascal ; Khang, Young Ho ; Laxmaiah, Avula ; Liu, Jing ; Malekzadeh, Reza ; Neuhauser, Hannelore K. ; Sorić, Maroje ; Starc, Gregor ; Sundström, Johan ; Woodward, Mark ; Abarca-Gómez, Leandra ; Abdeen, Ziad A. ; Abu-Rmeileh, Niveen M. ; Acosta-Cazares, Benjamin ; Adams, Robert J. ; Aekplakorn, Wichai ; Afsana, Kaosar ; Aguilar-Salinas, Carlos A. ; Geleijnse, Johanna M. - \ 2018
    International Journal of Epidemiology 47 (2018)3. - ISSN 0300-5771 - p. 872 - 883i.
    Blood pressure - Global health - Hypertension - Non-communicable disease - Population health

    Background: Change in the prevalence of raised blood pressure could be due to both shifts in the entire distribution of blood pressure (representing the combined effects of public health interventions and secular trends) and changes in its high-blood-pressure tail (representing successful clinical interventions to control blood pressure in the hypertensive population). Our aim was to quantify the contributions of these two phenomena to the worldwide trends in the prevalence of raised blood pressure. Methods: We pooled 1018 population-based studies with blood pressure measurements on 88.6 million participants from 1985 to 2016. We first calculated mean systolic blood pressure (SBP), mean diastolic blood pressure (DBP) and prevalence of raised blood pressure by sex and 10-year age group from 20-29 years to 70-79 years in each study, taking into account complex survey design and survey sample weights, where relevant. We used a linear mixed effect model to quantify the association between (probittransformed) prevalence of raised blood pressure and age-group- and sex-specific mean blood pressure. We calculated the contributions of change in mean SBP and DBP, and of change in the prevalence-mean association, to the change in prevalence of raised blood pressure. Results: In 2005-16, at the same level of population mean SBP and DBP, men and women in South Asia and in Central Asia, the Middle East and North Africa would have the highest prevalence of raised blood pressure, and men and women in the highincome Asia Pacific and high-income Western regions would have the lowest. In most region-sex-age groups where the prevalence of raised blood pressure declined, one half or more of the decline was due to the decline in mean blood pressure. Where prevalence of raised blood pressure has increased, the change was entirely driven by increasing mean blood pressure, offset partly by the change in the prevalence-mean association. Conclusions: Change in mean blood pressure is the main driver of the worldwide change in the prevalence of raised blood pressure, but change in the high-blood-pressure tail of the distribution has also contributed to the change in prevalence, especially in older age groups.

    Worldwide trends in body-mass index, underweight, overweight, and obesity from 1975 to 2016: a pooled analysis of 2416 population-based measurement studies in 128·9 million children, adolescents, and adults
    Bentham, James ; Cesare, Mariachiara Di; Bilano, Ver ; Bixby, Honor ; Zhou, Bin ; Stevens, Gretchen A. ; Riley, Leanne M. ; Taddei, Cristina ; Hajifathalian, Kaveh ; Lu, Yuan ; Savin, Stefan ; Cowan, Melanie J. ; Paciorek, Christopher J. ; Chirita-Emandi, Adela ; Hayes, Alison J. ; Katz, Joanne ; Kelishadi, Roya ; Kengne, Andre Pascal ; Khang, Young Ho ; Laxmaiah, Avula ; Li, Yanping ; Ma, Jun ; Miranda, J.J. ; Mostafa, Aya ; Neovius, Martin ; Padez, Cristina ; Rampal, Lekhraj ; Zhu, Aubrianna ; Bennett, James E. ; Danaei, Goodarz ; Bhutta, Zulfiqar A. ; Ezzati, Majid ; Abarca-Gómez, Leandra ; Abdeen, Ziad A. ; Hamid, Zargar Abdul ; Abu-Rmeileh, Niveen M. ; Acosta-Cazares, Benjamin ; Acuin, Cecilia ; Adams, Robert J. ; Aekplakorn, Wichai ; Afsana, Kaosar ; Aguilar-Salinas, Carlos A. ; Ferrieres, Jean ; Jacobs, Jeremy M. ; Kromhout, Daan ; Ma, Guansheng ; Peeters, Petra H. ; Wang, Qian ; Wang, Ya Xing ; Wang, Ying Wei ; Geleijnse, J.M. - \ 2017
    The Lancet 390 (2017)10113. - ISSN 0140-6736 - p. 2627 - 2642.

    Background Underweight, overweight, and obesity in childhood and adolescence are associated with adverse health consequences throughout the life-course. Our aim was to estimate worldwide trends in mean body-mass index (BMI) and a comprehensive set of BMI categories that cover underweight to obesity in children and adolescents, and to compare trends with those of adults. Methods We pooled 2416 population-based studies with measurements of height and weight on 128·9 million participants aged 5 years and older, including 31·5 million aged 5–19 years. We used a Bayesian hierarchical model to estimate trends from 1975 to 2016 in 200 countries for mean BMI and for prevalence of BMI in the following categories for children and adolescents aged 5–19 years: more than 2 SD below the median of the WHO growth reference for children and adolescents (referred to as moderate and severe underweight hereafter), 2 SD to more than 1 SD below the median (mild underweight), 1 SD below the median to 1 SD above the median (healthy weight), more than 1 SD to 2 SD above the median (overweight but not obese), and more than 2 SD above the median (obesity). Findings Regional change in age-standardised mean BMI in girls from 1975 to 2016 ranged from virtually no change (−0·01 kg/m2 per decade; 95% credible interval −0·42 to 0·39, posterior probability [PP] of the observed decrease being a true decrease=0·5098) in eastern Europe to an increase of 1·00 kg/m2 per decade (0·69–1·35, PP>0·9999) in central Latin America and an increase of 0·95 kg/m2 per decade (0·64–1·25, PP>0·9999) in Polynesia and Micronesia. The range for boys was from a non-significant increase of 0·09 kg/m2 per decade (−0·33 to 0·49, PP=0·6926) in eastern Europe to an increase of 0·77 kg/m2 per decade (0·50–1·06, PP>0·9999) in Polynesia and Micronesia. Trends in mean BMI have recently flattened in northwestern Europe and the high-income English-speaking and Asia-Pacific regions for both sexes, southwestern Europe for boys, and central and Andean Latin America for girls. By contrast, the rise in BMI has accelerated in east and south Asia for both sexes, and southeast Asia for boys. Global age-standardised prevalence of obesity increased from 0·7% (0·4–1·2) in 1975 to 5·6% (4·8–6·5) in 2016 in girls, and from 0·9% (0·5–1·3) in 1975 to 7·8% (6·7–9·1) in 2016 in boys; the prevalence of moderate and severe underweight decreased from 9·2% (6·0–12·9) in 1975 to 8·4% (6·8–10·1) in 2016 in girls and from 14·8% (10·4–19·5) in 1975 to 12·4% (10·3–14·5) in 2016 in boys. Prevalence of moderate and severe underweight was highest in India, at 22·7% (16·7–29·6) among girls and 30·7% (23·5–38·0) among boys. Prevalence of obesity was more than 30% in girls in Nauru, the Cook Islands, and Palau; and boys in the Cook Islands, Nauru, Palau, Niue, and American Samoa in 2016. Prevalence of obesity was about 20% or more in several countries in Polynesia and Micronesia, the Middle East and north Africa, the Caribbean, and the USA. In 2016, 75 (44–117) million girls and 117 (70–178) million boys worldwide were moderately or severely underweight. In the same year, 50 (24–89) million girls and 74 (39–125) million boys worldwide were obese. Interpretation The rising trends in children's and adolescents' BMI have plateaued in many high-income countries, albeit at high levels, but have accelerated in parts of Asia, with trends no longer correlated with those of adults. Funding Wellcome Trust, AstraZeneca Young Health Programme.

    Enhanced methane emissions from tropical wetlands during the 2011 la Niña
    Pandey, Sudhanshu ; Houweling, Sander ; Krol, Maarten ; Aben, Ilse ; Monteil, Guillaume ; Nechita-Banda, Narcisa ; Dlugokencky, Edward J. ; Detmers, Rob ; Hasekamp, Otto ; Xu, Xiyan ; Riley, William J. ; Poulter, Benjamin ; Zhang, Zhen ; McDonald, Kyle C. ; White, James W.C. ; Bousquet, Philippe ; Röckmann, Thomas - \ 2017
    Scientific Reports 7 (2017). - ISSN 2045-2322
    Year-to-year variations in the atmospheric methane (CH4) growth rate show significant correlation with climatic drivers. The second half of 2010 and the first half of 2011 experienced the strongest La Niña since the early 1980s, when global surface networks started monitoring atmospheric CH4 mole fractions. We use these surface measurements, retrievals of column-averaged CH4 mole fractions from GOSAT, new wetland inundation estimates, and atmospheric δ13C-CH4 measurements to estimate the impact of this strong La Niña on the global atmospheric CH4 budget. By performing atmospheric inversions, we find evidence of an increase in tropical CH4 emissions of ∼6-9 TgCH4 yr-1 during this event. Stable isotope data suggest that biogenic sources are the cause of this emission increase. We find a simultaneous expansion of wetland area, driven by the excess precipitation over the Tropical continents during the La Niña. Two process-based wetland models predict increases in wetland area consistent with observationally-constrained values, but substantially smaller per-area CH4 emissions, highlighting the need for improvements in such models. Overall, tropical wetland emissions during the strong La Niña were at least by 5% larger than the long-term mean.
    Uncertainties in Predicting Debris Flow Hazards Following Wildfire
    Hyde, K.D. ; Riley, Karin ; Stoof, C.R. - \ 2017
    In: Natural Hazard Uncertainty Assessment: Modeling and Decision Support / Riley, Karin, Webley , Peter, Thompson, Matthew, American Geophysical Union (Geophysical Monograph Series ) - ISBN 9781119027867 - p. 287 - 299.
    Wildfire increases the probability of debris flows posing hazardous conditions where values-at-risk exist downstream of burned areas. Conditions and processes leading to postfire debris flows usually follow a general sequence defined here as the postfire debris flow hazard cascade: biophysical setting, fire processes, fire effects, rainfall, debris flow, and values-at-risk. Prediction of postfire debris flow hazards is a problem of identifying and understanding the spatial and temporal interactions within this cascade. This chapter summarizes present knowledge of the processes involved in this postfire debris flow hazard cascade and identify uncertainties in terms of knowledge gaps, contradictions in current process understanding, stochastic system variables, and limits to data to support hazard prediction. Understanding these uncertainties can improve delineation of areas threatened by postfire debris flows, can guide future research, and, when addressed, contribute to development of comprehensive and robust modeling and prediction systems that may ultimately reduce threats to values-at-risk.
    Balanced phosphorus fertilization on grassland in a mixed grazing and mowing system; results after 18 years
    Curth-van Middelkoop, J.C. ; Ehlert, P.A.I. ; Regelink, I.C. - \ 2016
    In: 26th EGF General Meeting on The Multiple Roles of Grassland in the European Bioeconomy. - Wageningen Academic Publishers - ISBN 9788217016779 - p. 248 - 250.
    In the Netherlands the P application standard including animal manure and P fertilizer has decreased to
    balanced P fertilization since 2015. Moving towards balanced P fertilization might affect grassland yield
    and quality, because soil processes might influence the P availability for plant uptake. In the short term,
    balanced P fertilization is not expected to limit dry matter (DM) production of grass on soils with a
    sufficient to high soil P. Decreases in P content and P offtake of grass are, however, expected directly after
    decreasing P fertilization. In the longer term decreases of herbage yield can be foreseen. With balanced P
    fertilization, annual DM yield and P content of alternately grazed and mown grassland were lower than
    at a surplus of 9 or 18 kg P ha-1 yr-1 on sand and peat. However, differences between P treatments in DM
    yield and P content remained constant over the whole period. On the marine clay soil, no differences in
    DM yield were found between P treatments, but P content in the herbage were lower with balanced P
    fertilization than with surplus P fertilization. The risk of yield reduction seems to be related to uneven
    distribution of dung patches and the P buffering capacity of the soil.
    High turnover drives prolonged persistence of influenza in managed pig herds
    Pitzer, Virginia E. ; Aguas, Ricardo ; Riley, Steven ; Loeffen, Willie L.A. ; Wood, James L.N. ; Grenfell, Bryan T. - \ 2016
    Journal of the Royal Society, Interface 13 (2016)119. - ISSN 1742-5689
    Influenza - Mathematical modelling - Surveillance - Swine - Transmission dynamics

    Pigs have long been hypothesized to play a central role in the emergence of novel human influenza A virus (IAV) strains, by serving as mixing vessels for mammalian and avian variants. However, the key issue of viral persistence in swine populations at different scales is ill understood. We address this gap using epidemiological models calibrated against seroprevalence data from Dutch finishing pigs to estimate the 'critical herd size' (CHS) for IAV persistence. We then examine the viral phylogenetic evidence for persistence by comparing human and swine IAV. Models suggest a CHS of approximately 3000 pigs above which influenza was likely to persist, i.e. orders of magnitude lower than persistence thresholds for IAV and other acute viruses in humans. At national and regional scales, we found much stronger empirical signatures of prolonged persistence of IAV in swine compared with human populations. These striking levels of persistence in small populations are driven by the high recruitment rate of susceptible piglets, and have significant implications for management of swine and for overall patterns of genetic diversity of IAV.

    Monitoring vegetation change and dynamics on U.S. Army training lands using satellite image time series analysis
    Hutchinson, J.M.S. ; Jacquin, A. ; Hutchinson, S.L. ; Verbesselt, J. - \ 2015
    Journal of Environmental Management 150 (2015). - ISSN 0301-4797 - p. 355 - 366.
    locally weighted regression - structural-change models - plant community - trend analysis - modis ndvi - phenology - wildlife - gimms
    Given the significant land holdings of the U.S. Department of Defense, and the importance of those lands to support a variety of inherently damaging activities, application of sound natural resource conservation principles and proactive monitoring practices are necessary to manage military training lands in a sustainable manner. This study explores a method for, and the utility of, analyzing vegetation condition and trends as sustainability indicators for use by military commanders and land managers, at both the national and local levels, in identifying when and where vegetation-related environmental impacts might exist. The BFAST time series decomposition method was applied to a ten-year MODIS NDVI time series dataset for the Fort Riley military installation and Konza Prairie Biological Station (KPBS) in northeastern Kansas. Imagery selected for time-series analysis were 16-day MODIS NDVI (MOD13Q1 Collection 5) composites capable of characterizing vegetation change induced by human activities and climate variability. Three indicators related to gradual interannual or abrupt intraannual vegetation change for each pixel were calculated from the trend component resulting from the BFAST decomposition. Assessment of gradual interannual NDVI trends showed the majority of Fort Riley experienced browning between 2001 and 2010. This result is supported by validation using high spatial resolution imagery. The observed versus expected frequency of linear trends detected at Fort Riley and KPBS were significantly different and suggest a causal link between military training activities and/or land management practices. While both sites were similar with regards to overall disturbance frequency and the relative spatial extents of monotonic or interrupted trends, vegetation trajectories after disturbance were significantly different. This suggests that the type and magnitude of disturbances characteristic of each location result in distinct post-disturbance vegetation responses. Using a remotely-sensed vegetation index time series with BFAST and the indicators outlined here provides a consistent and relatively rapid assessment of military training lands with applicability outside of grassland biomes. Characterizing overall trends and disturbance responses of vegetation can promote sustainable use of military lands and assist land managers in targeting specific areas for various rehabilitation activities.
    Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche
    Morin, E. ; Kohler, A. ; Baker, A.R. ; Foulongne-Oriol, M. ; Lombard, V. ; Nagy, L.G. ; Ohm, R.A. ; Patyshakuliyeva, A. ; Brun, A. ; Aerts, A.L. ; Bailey, A.M. ; Billette, C. ; Coutinho, P.M. ; Deakin, G. ; Doddapaneni, H. ; Floudas, D. ; Grimwood, J. ; Hildén, K. ; Kües, U. ; LaButti, K.M. ; Lapidus, A. ; Lindquist, E.A. ; Lucas, S.M. ; Murat, C. ; Riley, R.W. ; Salamov, A.A. ; Schmutz, J. ; Subramanian, V. ; Wösten, H.A.B. ; Xu, J. ; Eastwood, D.C. ; Foster, G.D. ; Sonnenberg, A.S.M. ; Cullen, D. ; Vries, R.P. de; Lundell, T. ; Hibbett, D.S. ; Henrissat, B. ; Burton, K.S. ; Kerrigan, R.W. ; Challen, M.P. ; Grigorievf, I.V. ; Martin, M. - \ 2012
    Proceedings of the National Academy of Sciences of the United States of America 109 (2012)43. - ISSN 0027-8424 - p. 17501 - 17506.
    cultivated mushroom - coprinus-cinereus - schizophyllum-commune - coprinopsis-cinerea - fungi - gene - decomposition - chromosomes - degradation - substances
    Agaricus bisporus is the model fungus for the adaptation, persistence, and growth in the humic-rich leaf-litter environment. Aside from its ecological role, A. bisporus has been an important component of the human diet for over 200 y and worldwide cultivation of the “button mushroom” forms a multibillion dollar industry. We present two A. bisporus genomes, their gene repertoires and transcript profiles on compost and during mushroom formation. The genomes encode a full repertoire of polysaccharide-degrading enzymes similar to that of wood-decayers. Comparative transcriptomics of mycelium grown on defined medium, casing-soil, and compost revealed genes encoding enzymes involved in xylan, cellulose, pectin, and protein degradation are more highly expressed in compost. The striking expansion of heme-thiolate peroxidases and ß-etherases is distinctive from Agaricomycotina wood-decayers and suggests a broad attack on decaying lignin and related metabolites found in humic acid-rich environment. Similarly, up-regulation of these genes together with a lignolytic manganese peroxidase, multiple copper radical oxidases, and cytochrome P450s is consistent with challenges posed by complex humic-rich substrates. The gene repertoire and expression of hydrolytic enzymes in A. bisporus is substantially different from the taxonomically related ectomycorrhizal symbiont Laccaria bicolor. A common promoter motif was also identified in genes very highly expressed in humic-rich substrates. These observations reveal genetic and enzymatic mechanisms governing adaptation to the humic-rich ecological niche formed during plant degradation, further defining the critical role such fungi contribute to soil structure and carbon sequestration in terrestrial ecosystems. Genome sequence will expedite mushroom breeding for improved agronomic characteristics.
    Clostridium difficile infections in the community: a zoonotic disease?
    Hensgens, M.P.M. ; Keessen, A.M. ; Squire, M.M. ; Riley, T.V. ; Koene, M.G.J. ; Boer, E. de; Lipman, L.J. ; Kuijper, E.J. - \ 2012
    Clinical Microbiology and Infection 18 (2012)7. - ISSN 1198-743X - p. 635 - 645.
    retail ground meat - general-practice - food animals - antimicrobial susceptibility - fatal enterocolitis - neonatal diarrhea - intestinal flora - north-america - pcr ribotypes - prevalence
    Clostridium difficile infections (CDIs) are traditionally seen in elderly and hospitalized patients who have used antibiotic therapy. In the community, CDIs requiring a visit to a general practitioner are increasingly occurring among young and relatively healthy individuals without known predisposing factors. C. difficile is also found as a commensal or pathogen in the intestinal tracts of most mammals, and various birds and reptiles. In the environment, including soil and water, C. difficile may be ubiquitous; however, this is based on limited evidence. Food products such as (processed) meat, fish and vegetables can also contain C. difficile, but studies conducted in Europe report lower prevalence rates than in North America. Absolute counts of toxigenic C. difficile in the environment and food are low, however the exact infectious dose is unknown. To date, direct transmission of C. difficile from animals, food or the environment to humans has not been proven, although similar PCR ribotypes are found. We therefore believe that the overall epidemiology of human CDI is not driven by amplification in animals or other sources. As no outbreaks of CDI have been reported among humans in the community, host factors that increase vulnerability to CDI might be of more importance than increased exposure to C. difficile. Conversely, emerging C. difficile ribotype 078 is found in high numbers in piglets, calves, and their immediate environment. Although there is no direct evidence proving transmission to humans, circumstantial evidence points towards a zoonotic potential of this type. In future emerging PCR ribotypes, zoonotic potential needs to be considered
    A two-locus DNA sequence database for typing plant and human pathogens within the Fusarium oxysporum species complex
    O'Donnell, K. ; Gueidan, C. ; Sink, S. ; Johnston, P.R. ; Crous, P.W. ; Glenn, A. ; Riley, R. ; Zitomer, N.C. ; Colyer, P. ; Waalwijk, C. ; Lee, T. van der; Moretti, A. ; Kang, S. ; Kim, H.S. ; Geiser, D.M. ; Juba, J.H. ; Baayen, R.P. ; Cromey, M.G. ; Bithel, S. ; Sutton, D.A. ; Skovgaard, K. ; Ploetz, R. ; Kistler, H.C. ; Elliot, M. ; Davis, M. ; Sarver, B.A.J. - \ 2009
    Fungal Genetics and Biology 46 (2009)12. - ISSN 1087-1845 - p. 936 - 948.
    vegetative compatibility groups - f-sp cubense - fragment-length-polymorphisms - intergenic spacer region - genetic diversity - ribosomal dna - fungus fusarium - discontinuous distribution - phylogenetic diversity - nectria-haematococca
    We constructed a two-locus database, comprising partial translation elongation factor (EF-1a) gene sequences and nearly full-length sequences of the nuclear ribosomal intergenic spacer region (IGS rDNA) for 850 isolates spanning the phylogenetic breadth of the Fusarium oxysporum species complex (FOSC). Of the 850 isolates typed, 101 EF-1a, 203 IGS rDNA, and 256 two-locus sequence types (STs) were differentiated. Analysis of the combined dataset suggests that two-thirds of the STs might be associated with a single host plant. This analysis also revealed that the 26 STs associated with human mycoses were genetically diverse, including several which appear to be nosocomial in origin. A congruence analysis, comparing partial EF-1a and IGS rDNA bootstrap consensus, identified a significant number of conflicting relationships dispersed throughout the bipartitions, suggesting that some of the IGS rDNA sequences may be non-orthologous. We also evaluated enniatin, fumonisin and moniliformin mycotoxin production in vitro within a phylogenetic framework.
    Multiple pathways guide oxygen diffusion into flavoenzyme active sites
    Baron, R. ; Riley, C. ; Chenprakhon, P. ; Thotsaporn, K. ; Winter, R.T. ; Alfieri, A. ; Forneris, F. ; Berkel, W.J.H. van; Chaiyen, P. ; Fraaije, M.W. ; Mattevi, A. ; McCammon, J.A. - \ 2009
    Proceedings of the National Academy of Sciences of the United States of America 106 (2009)26. - ISSN 0027-8424 - p. 10603 - 10608.
    x-ray crystallography - molecular-dynamics - streptomyces-coelicolor - cholesterol oxidase - alditol oxidase - protein - o-2 - enzyme - fluorescence - simulations
    Dioxygen (O2) and other gas molecules have a fundamental role in a variety of enzymatic reactions. However, it is only poorly understood which O2 uptake mechanism enzymes employ to promote efficient catalysis and how general this is. We investigated O2 diffusion pathways into monooxygenase and oxidase flavoenzymes, using an integrated computational and experimental approach. Enhanced-statistics molecular dynamics simulations reveal spontaneous protein-guided O2 diffusion from the bulk solvent to preorganized protein cavities. The predicted protein-guided diffusion paths and the importance of key cavity residues for oxygen diffusion were verified by combining site-directed mutagenesis, rapid kinetics experiments, and high-resolution X-ray structures. This study indicates that monooxygenase and oxidase flavoenzymes employ multiple funnel-shaped diffusion pathways to absorb O2 from the solvent and direct it to the reacting C4a atom of the flavin cofactor. The difference in O2 reactivity among dehydrogenases, monooxygenases, and oxidases ultimately resides in the fine modulation of the local environment embedding the reactive locus of the flavin
    Detailed Analysis of the Expression of an Alpha-gliadin Promoter and the Deposition of Alpha-gliadin Protein During Wheat Grain Development
    Herpen, T.W.J.M. van; Riley, M. ; Sparks, C. ; Jones, H.D. ; Gritsch, C. ; Dekking, E.H. ; Hamer, R.J. ; Bosch, H.J. ; Salentijn, E.M.J. ; Smulders, M.J.M. ; Shewry, P.R. ; Gilissen, L.J.W.J. - \ 2008
    Annals of Botany 102 (2008)3. - ISSN 0305-7364 - p. 331 - 342.
    endosperm-specific expression - celiac-disease - activates transcription - transgenic wheat - gene-expression - functional-analysis - barley endosperm - seed development - gcn4-like motif - bzip protein
    Background and Aims: Alpha-gliadin proteins are important for the industrial quality of bread wheat flour, but they also contain many epitopes that can trigger celiac (c¿liac) disease (CD). The B-genome-encoded -gliadin genes, however, contain very few epitopes. Controlling -gliadin gene expression in wheat requires knowledge on the processes of expression and deposition of -gliadin protein during wheat grain development. Methods: A 592-bp fragment of the promotor of a B-genome-encoded -gliadin gene driving the expression of a GUS reporter gene was transformed into wheat. A large number of transgenic lines were used for data collection. GUS staining was used to determine GUS expression during wheat kernel development, and immunogold labelling and tissue printing followed by staining with an -gliadin-specific antibody was used to detect -gliadin protein deposited in developing wheat kernels. The promoter sequence was screened for regulatory motifs and compared to other available -gliadin promoter sequences. Key Results: GUS expression was detected primarily in the cells of the starchy endosperm, notably in the subaleurone layer but also in the aleurone layer. The -gliadin promoter was active from 11 days after anthesis (DAA) until maturity, with an expression similar to that of a 326-bp low molecular weight (LMW) subunit gene promoter reported previously. An -gliadin-specific antibody detected -gliadin protein in protein bodies in the starchy endosperm and in the subaleurone layer but, in contrast to the promoter activity, no -gliadin was detected in the aleurone cell layer. Sequence comparison showed differences in regulatory elements between the promoters of -gliadin genes originating from different genomes (A and B) of bread wheat both in the region used here and upstream. Conclusions: The results suggest that additional regulator elements upstream of the promoter region used may specifically repress expression in the aleurone cell layer. Observed differences in expression regulator motifs between the -gliadin genes on the different genomes (A and B) of bread wheat leads to a better understanding how -gliadin expression can be controlled
    Alpha-gliadin genes from the A, B, and D genomes of wheat contain different sets of celiac disease epitopes
    Herpen, T.W.J.M. van; Goryunova, S.V. ; Salentijn, E.M.J. ; Riley, M. ; Sparks, C. ; Veelen, P. van; Bosch, H.J. ; Gilissen, L.J.W.J. ; Smulders, M.J.M. ; Jones, H.D. ; Shewry, P.R. ; Hamer, R.J. - \ 2007
    In: Gluten Proteins 2006 / Lookhart, G.L., St. Paul, Minnesota : AAAC International - ISBN 9781891127571 - p. 321 - 325.
    Summary Response options and strategies
    Brown, K. ; Chambers, B.J. ; Chopra, K. ; Cropper, A. ; Duriappah, A.K. ; Faith, D. ; Gupta, J. ; Kumar, P. ; Leemans, R. ; Mackensen, J. ; Mooney, H.A. ; Reid, W.V. ; Riley, J. ; Simons, H. ; Spierenburg, M. ; Watson, R.T. - \ 2005
    In: Ecosystems and human well-being. Policy responses / Chopra, K., Leemans, R., Kumar, P., Simons, H., Washington DC : Island Press (The millennium ecosystem assessment series Vol. 3) - ISBN 9781559632690 - p. 1 - 21.
    Partial cytochrome oxidase II sequences distinguish the sibling species Trichogramma minutum Riley and Trichogramma platneri Nagarkatti
    Borghuis, A. ; Pinto, J.D. ; Platner, G.R. ; Stouthamer, R. - \ 2004
    Biological Control 30 (2004). - ISSN 1049-9644 - p. 90 - 94.
    complex hymenoptera - biological-control - t-platneri - utility - gene - dna
    The egg parasitoids Trichogramma minutum Riley and Trichogramma platneri Nagarkatti are commonly used in North America for the control of Lepidoptera in orchards, These species are morphologically indistinguishable, but reproductively incompatible. An easy identification technique is highly desirable, because release of the wrong species in the native area of the other species may result in a depression of intended biological control. Here we show that the DNA sequences of the mitochondrial cytochrome oxidase II (COII) gene differ between the species. These differences can be visualized by restricting the COII PCR product with the restriction enzyme; VspI. This method makes a rapid identification of these economically important sibling species possible. (C) 2003 Elsevier Inc. All rights reserved.
    Precise sex allocation, local mate competition, and sex ratio shifts in the parasitoid wasp Trichogramma pretiosum
    Luck, R.F. ; Janssen, J.A.M. ; Pinto, J.D. ; Oatman, E.R. - \ 2001
    Behavioral Ecology and Sociobiology 49 (2001). - ISSN 0340-5443 - p. 311 - 321.
    We determined the sex, order, and clutch size of eggs laid by the parasitoid wasp, Trichogramma pretiosum Riley, in the eggs of one of its natural hosts, Trichoplusia ni (Hübner). The parasitoid allocated sex non-randomly to hosts in the laboratory with a variance significantly less than that of a binomial (random) distribution, our null model. More clutches of two or more eggs contained a single male egg as the second or third egg laid than would be expected by chance and none contained two or more male eggs. T. pretiosum also increased the sex ratio ( ale) of its offspring with increasing foundress numbers by increasing the frequency of male offspring as the second egg in a two-egg clutch allocated to unparasitized hosts and as the single egg allocated to previously parasitized hosts. These results indicate that T. pretiosum allocates the sex of its offspring precisely. Precise sex allocation is favored under local mate competition because it reduces variation in the number of sons per patch thus maximizing the number of inseminated daughters emigrating from the patch. Similar combinations of female and male offspring emerged from T. ni eggs parasitized by T. pretiosum in the field, again with a sex ratio variance less than that expected for a binomial distribution. These results strongly suggest that this parasitoid species manifests local mate competition
    Issues of scale for environmental indicators
    Stein, A. ; Riley, J. ; Halberg, N. - \ 2001
    Agriculture, Ecosystems and Environment 87 (2001). - ISSN 0167-8809 - p. 215 - 232.
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