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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Association of sleep duration and quality with blood lipids : a systematic review and meta-analysis of prospective studies
Kruisbrink, Marlot ; Robertson, Wendy ; Ji, Chen ; Miller, Michelle A. ; Geleijnse, Johanna M. ; Cappuccio, Francesco P. - \ 2017
BMJ Open 7 (2017)12. - ISSN 2044-6055
blood lipids - cholesterol - meta-analysis - sleep duration - sleep quality - systematic review

OBJECTIVES: To assess the longitudinal evidence of the relationships between sleep disturbances (of quantity and quality) and dyslipidaemia in the general population and to quantify such relationships.

SETTING: Systematic review and meta-analysis following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines.

METHODS: We performed a systematic search of PubMed and Embase (up to 9 September 2017), complemented with manual searches, of prospective population studies describing the association between sleep duration and quality and the incidence of dyslipidaemias. Relative risks (95% CIs) were extracted and pooled using a random effects model. Subgroup analyses by lipid type were performed. Heterogeneity and publication bias were also assessed. Quality was assessed with Downs and Black score.

PARTICIPANTS: Studies were included if they were prospective, had measured sleep quantity and/or quality at baseline and either incident cases of dyslipidaemia or changes in blood lipid fractions assessed prospectively.

PRIMARY OUTCOME MEASURES: Incidence of dyslipidaemia and changes in lipid fractions. Dyslipidaemia was defined as a high total cholesterol, triglycerides, low-density lipoprotein cholesterol or low high-density lipoprotein cholesterol compared with the reference group.

RESULTS: Thirteen studies were identified (eight using sleep duration, four sleep quality and one both). There was heterogeneity in the sleep quality aspects and types of lipids assessed. Classification of sleep duration (per hour/groups) also varied widely. In the pooled analysis of sleep duration (6 studies, 16 cohort samples; 30 033 participants; follow-up 2.6-10 years), short sleep was associated with a risk of 1.01 (95% CI 0.93 to 1.10) of developing dyslipidaemia, with moderate heterogeneity (I2=56%, P=0.003) and publication bias (P=0.035). Long sleep was associated with a risk of 0.98 (95% CI 0.87 to 1.10) for dyslipidaemia, with heterogeneity (I2=63%, P<0.001) and no significant publication bias (P=0.248).

CONCLUSION: The present analysis was unable to find supportive evidence of a significant relationship between sleep duration and the development of dyslipidaemia. However, heterogeneity and small number of studies limit the interpretation.

PROSPERO REGISTRATION NUMBER: CRD42016045242.

Transdisciplinary understanding of SI in MRAs
Kluvankova, Tatiana ; Gežik, Veronika ; Špaček, Martin ; Brnkalakova, Stanislava ; Slee, Bill ; Polman, N.B.P. ; Valero, Diana ; Bryce, Rosalind ; Alkhaled, Sophie ; Secco, Laura ; Burlando, Catie ; Kozova, Maria ; Miller, David ; Nijnik, Maria ; Perlik, Manfred ; Pisani, Elena ; Price, Martin ; Sarkki, Simo ; Weiss, Gerhard - \ 2017
SIMRA - 53 p.
Set of Methods to Assess SI Implications at Different Levels
Secco, Laura ; Pisani, Elena ; Burlando, Catie ; Re, Riccardo Da; Gatto, Paola ; Pettenella, Davide ; Vassilopoulos, Achilleas ; Akinsete, Ebun ; Koundouri, Phoebe ; Lopolito, Antonio ; Prosperi, Maurizio ; Tuomasiukka, Diana ; Herde, Micheal Den; Lovric, Marko ; Polman, N.B.P. ; Dijkshoorn-Dekker, M.W.C. ; Soma, K. ; Ludvig, Alice ; Weiss, Gerhard ; Zivojinovic, Ivana ; Sarkki, Simo ; Ravazzoli, Elisa ; Torre, Cristina Dalla; Streifeneder, Thomas ; Slee, Bill ; Nijnik, Maria ; Miller, David ; Barlagne, Carla ; Prokofieva, Irina - \ 2017
SIMRA - 203 p.
Diseases of Lily
Chastagner, G.A. ; Tuyl, J.M. van; Verbeek, M. ; Miller, William ; Westerdahl, Becky B. - \ 2017
In: Handbook of Florists' Crops Diseases, Handbook of Plant Disease Management / McGovern, R.J., Elmer, W.H., Springer International Publishing (Handbook of Plant Disease Management ) - ISBN 9783319323749 - 61 p.
Lilies (Lilium spp. and hybrids) are the second largest flower bulb crop in the Netherlands and the most important flower bulb crop in the world. They are grown for bulbs, as cut flowers, as container (potted) plants, or in gardens. Lilies are a vegetatively propagated crop and may be routinely increased by micropropagation (tissue culture) or through scaling (removal of bulb scales from which adventitious bulblets are produced). The propagules are subsequently grown in fields for 2 or 3 y to allow the bulbs to reach sufficient size (generally measured in circumference) for proper flowering and maximum horticultural quality. Although the majority of bulbs produced for worldwide distribution are grown mainly in the Netherlands, bulbs are also grown in other northern European countries, the USA, Asia, Israel, and southern hemisphere locations including Brazil, Australia, New Zealand, Tasmania, and Chile. There are a number of diseases caused by fungi, viruses, bacteria, and nematodes and physiological disorders that affect the production and quality of lily bulb and cut flower crops worldwide. Information on the distribution, epidemiology and management, of the common diseases and disorders is presented in this chapter.
Stakeholder and Citizen Participation in Bioeconomy Strategies : BioSTEP Guidelines for Practitioners
Davies, S. ; Miller, S. ; Bakker, H.C.M. de; Beekman, V. ; Overbeek, M.M.M. - \ 2017
BioSTEP - 12 p.
Primary Charge Separation in the Photosystem II Reaction Center Revealed by a Global Analysis of the Two-dimensional Electronic Spectra
Duan, Hong Guang ; Prokhorenko, Valentyn I. ; Wientjes, I.E. ; Croce, Roberta ; Thorwart, Michael ; Miller, R.J.D. - \ 2017
Scientific Reports 7 (2017). - ISSN 2045-2322 - 9 p.
The transfer of electronic charge in the reaction center of Photosystem II is one of the key building blocks of the conversion of sunlight energy into chemical energy within the cascade of the photosynthetic reactions. Since the charge transfer dynamics is mixed with the energy transfer dynamics, an effective tool for the direct resolution of charge separation in the reaction center is still missing. Here, we use experimental two-dimensional optical photon echo spectroscopy in combination with the theoretical calculation to resolve its signature. A global fitting analysis allows us to clearly and directly identify a decay pathway associated to the primary charge separation. In particular, it can be distinguished from regular energy transfer and occurs on a time scale of 1.5 ps under ambient conditions. This technique provides a general tool to identify charge separation signatures from the energy transport in two-dimensional optical spectroscopy.
Long-term population dynamics in a multi-species assemblage of large herbivores in East Africa
Kiffner, Christian ; Rheault, Helena ; Miller, Elizabeth ; Scheetz, Tanner ; Enriquez, Vivien ; Swafford, Rachelle ; Kioko, John ; Prins, Herbert H.T. - \ 2017
Ecosphere 8 (2017)12. - ISSN 2150-8925
Conservation Effectiveness - Declining Population Paradigm - Ecosystem Dynamics - Lake Manyara National Park - Shrub Encroachment - Ungulates
Wildlife population declines in Africa are widespread. However, species-specific population trends and dynamics in mammal community composition have rarely been described over long time periods. To describe population trends of 13 large herbivore species in Lake Manyara National Park (Tanzania) from 1959 to 2016 and to discover whether the herbivore community structure changed, we used general additive models and additional statistical methods to detect structural changes in the time series. Population dynamics were non-linear and population growth rates were not correlated with precipitation anomalies. Relatively steep population declines of three megaherbivores occurred during the 1980s and early 1990s, resulting in severe reductions in African elephant and buffalo populations and the local extinction of black rhinoceros. These declines coincided with reported peaks of illegal hunting of these species and expansion of agriculture at the periphery of the park. Population densities of elephant and buffalo seem to have stabilized in recent times, yet have not recovered to previous densities. In contrast, eight species (giraffe, zebra, waterbuck, wildebeest, warthog, impala, bushbuck, and baboon) have apparently fared well (similar or higher densities in most recent compared to first decade), despite having undergone substantial fluctuations over the past 58 yr. Population fluctuations in these species were likely caused by disease outbreaks, heavy bush encroachment, and reduced competition with buffalo. Possibly, declines in megaherbivore densities (mainly elephants) facilitated bush encroachment. Albeit grazers are still dominating in the herbivore community, the proportion of browsers is currently increasing, likely encouraged by dense vegetation in the shrub layer in large parts of the park. Overall, herbivore biomass density has declined by ~40% compared to the baseline estimate in the first decade of the time series. Our analyses and ancillary information provide evidence that this overall decline in the herbivore assemblage was triggered by human-induced reductions in megaherbivore population densities during the 1980s, either through excessive poaching, insularization of the park, or both. Likely, this had cascading and interacting effects on the vegetation structure and the herbivore assemblage. Thus, legacy effects of ineffective megaherbivore conservation efforts 30 yr ago are likely still affecting the ecology of this national park.
Evolution and patterns of global health financing 1995-2014 : Development assistance for health, and government, prepaid private, and out-of-pocket health spending in 184 countries
Dieleman, Joseph ; Campbell, Madeline ; Chapin, Abigail ; Eldrenkamp, Erika ; Fan, Victoria Y. ; Haakenstad, Annie ; Kates, Jennifer ; Liu, Yingying ; Matyasz, Taylor ; Micah, Angela ; Reynolds, Alex ; Sadat, Nafis ; Schneider, Matthew T. ; Sorensen, Reed ; Evans, Tim ; Evans, David ; Kurowski, Christoph ; Tandon, Ajay ; Abbas, Kaja M. ; Abera, Semaw Ferede ; Ahmad Kiadaliri, Aliasghar ; Ahmed, Kedir Yimam ; Ahmed, Muktar Beshir ; Alam, Khurshid ; Alizadeh-Navaei, Reza ; Alkerwi, A. ; Amini, Erfan ; Ammar, Walid ; Amrock, Stephen Marc ; Antonio, Carl Abelardo T. ; Atey, Tesfay Mehari ; Avila-Burgos, Leticia ; Awasthi, Ashish ; Barac, Aleksandra ; Bernal, Oscar Alberto ; Beyene, Addisu Shunu ; Beyene, Tariku Jibat ; Birungi, Charles ; Bizuayehu, Habtamu Mellie ; Breitborde, Nicholas J.K. ; Cahuana-Hurtado, Lucero ; Castro, Ruben Estanislao ; Catalá-López, Ferran ; Dalal, Koustuv ; Dandona, Lalit ; Dandona, Rakhi ; Jager, Pieter De; Dharmaratne, Samath D. ; Dubey, Manisha ; Sa Farinha, Carla Sofia E. ; Faro, Andre ; Feigl, Andrea B. ; Fischer, Florian ; Fitchett, Joseph Robert Anderson ; Foigt, Nataliya ; Giref, Ababi Zergaw ; Gupta, Rahul ; Hamidi, Samer ; Harb, Hilda L. ; Hay, Simon I. ; Hendrie, Delia ; Horino, Masako ; Jürisson, Mikk ; Jakovljevic, Mihajlo B. ; Javanbakht, Mehdi ; John, Denny ; Jonas, Jost B. ; Karimi, Seyed M. ; Khang, Young Ho ; Khubchandani, Jagdish ; Kim, Yun Jin ; Kinge, Jonas M. ; Krohn, Kristopher J. ; Kumar, G.A. ; Magdy Abd El Razek, Hassan ; Magdy Abd El Razek, Mohammed ; Majeed, Azeem ; Malekzadeh, Reza ; Masiye, Felix ; Meier, Toni ; Meretoja, Atte ; Miller, Ted R. ; Mirrakhimov, Erkin M. ; Mohammed, Shafiu ; Nangia, Vinay ; Olgiati, Stefano ; Osman, Abdalla Sidahmed ; Owolabi, Mayowa O. ; Patel, Tejas ; Paternina Caicedo, Angel J. ; Pereira, David M. ; Perelman, Julian ; Polinder, Suzanne ; Rafay, Anwar ; Rahimi-Movaghar, Vafa ; Rai, Rajesh Kumar ; Ram, Usha ; Ranabhat, Chhabi Lal ; Roba, Hirbo Shore ; Salama, Joseph ; Savic, Miloje ; Sepanlou, Sadaf G. ; Shrime, Mark G. ; Talongwa, Roberto Tchio ; Ao, Braden J. Te; Tediosi, Fabrizio ; Tesema, Azeb Gebresilassie ; Thomson, Alan J. ; Tobe-Gai, Ruoyan ; Topor-Madry, Roman ; Undurraga, Eduardo A. ; Vasankari, Tommi ; Violante, Francesco S. ; Werdecker, Andrea ; Wijeratne, Tissa ; Xu, Gelin ; Yonemoto, Naohiro ; Younis, Mustafa Z. ; Yu, Chuanhua ; Zaidi, Zoubida ; Sayed Zaki, Maysaa El; Murray, Christopher J.L. - \ 2017
The Lancet 389 (2017)10083. - ISSN 0140-6736 - p. 1981 - 2004.
Background: An adequate amount of prepaid resources for health is important to ensure access to health services and for the pursuit of universal health coverage. Previous studies on global health financing have described the relationship between economic development and health financing. In this study, we further explore global health financing trends and examine how the sources of funds used, types of services purchased, and development assistance for health disbursed change with economic development. We also identify countries that deviate from the trends. Methods: We estimated national health spending by type of care and by source, including development assistance for health, based on a diverse set of data including programme reports, budget data, national estimates, and 964 National Health Accounts. These data represent health spending for 184 countries from 1995 through 2014. We converted these data into a common inflation-adjusted and purchasing power-adjusted currency, and used non-linear regression methods to model the relationship between health financing, time, and economic development. Findings: Between 1995 and 2014, economic development was positively associated with total health spending and a shift away from a reliance on development assistance and out-of-pocket (OOP) towards government spending. The largest absolute increase in spending was in high-income countries, which increased to purchasing power-adjusted $5221 per capita based on an annual growth rate of 3.0%. The largest health spending growth rates were in upper-middle-income (5.9) and lower-middle-income groups (5.0), which both increased spending at more than 5% per year, and spent $914 and $267 per capita in 2014, respectively. Spending in low-income countries grew nearly as fast, at 4.6%, and health spending increased from $51 to $120 per capita. In 2014, 59.2% of all health spending was financed by the government, although in low-income and lower-middle-income countries, 29.1% and 58.0% of spending was OOP spending and 35.7% and 3.0% of spending was development assistance. Recent growth in development assistance for health has been tepid; between 2010 and 2016, it grew annually at 1.8%, and reached US$37.6 billion in 2016. Nonetheless, there is a great deal of variation revolving around these averages. 29 countries spend at least 50% more than expected per capita, based on their level of economic development alone, whereas 11 countries spend less than 50% their expected amount. Interpretation: Health spending remains disparate, with low-income and lower-middle-income countries increasing spending in absolute terms the least, and relying heavily on OOP spending and development assistance. Moreover, tremendous variation shows that neither time nor economic development guarantee adequate prepaid health resources, which are vital for the pursuit of universal health coverage.
Future and potential spending on health 2015-40 : Development assistance for health, and government, prepaid private, and out-of-pocket health spending in 184 countries
Dieleman, Joseph L. ; Campbell, Madeline ; Chapin, Abigail ; Eldrenkamp, Erika ; Fan, Victoria Y. ; Haakenstad, Annie ; Kates, Jennifer ; Li, Zhiyin ; Matyasz, Taylor ; Micah, Angela ; Reynolds, Alex ; Sadat, Nafis ; Schneider, Matthew T. ; Sorensen, Reed ; Abbas, Kaja M. ; Abera, Semaw Ferede ; Ahmad Kiadaliri, Aliasghar ; Ahmed, Muktar Beshir ; Alam, Khurshid ; Alizadeh-Navaei, Reza ; Alkerwi, A. ; Amini, Erfan ; Ammar, Walid ; Antonio, Carl Abelardo T. ; Atey, Tesfay Mehari ; Avila-Burgos, Leticia ; Awasthi, Ashish ; Barac, Aleksandra ; Berheto, Tezera Moshago ; Beyene, Addisu Shunu ; Beyene, Tariku Jibat ; Birungi, Charles ; Bizuayehu, Habtamu Mellie ; Breitborde, Nicholas J.K. ; Cahuana-Hurtado, Lucero ; Castro, Ruben Estanislao ; Catalá-López, Ferran ; Dalal, Koustuv ; Dandona, Lalit ; Dharmaratne, Rakhi Dandona Samath D. ; Dubey, Manisha ; Faro, Andé ; Feigl, Andrea B. ; Fischer, Florian ; Anderson Fitchett, Joseph R. ; Foigt, Nataliya ; Giref, Ababi Zergaw ; Gupta, Rahul ; Hamidi, Samer ; Harb, Hilda L. ; Hay, Simon I. ; Hendrie, Delia ; Horino, Masako ; Jürisson, Mikk ; Jakovljevic, Mihajlo B. ; Javanbakht, Mehdi ; John, Denny ; Jonas, Jost B. ; Karimi, Seyed M. ; Khang, Young Ho ; Khubchandani, Jagdish ; Kim, Yun Jin ; Kinge, Jonas M. ; Krohn, Kristopher J. ; Kumar, G.A. ; Leung, Ricky ; Magdy Abd El Razek, Hassan ; Magdy Abd El Razek, Mohammed ; Majeed, Azeem ; Malekzadeh, Reza ; Malta, Deborah Carvalho ; Meretoja, Atte ; Miller, Ted R. ; Mirrakhimov, Erkin M. ; Mohammed, Shafiu ; Molla, Gedefaw ; Nangia, Vinay ; Olgiati, Stefano ; Owolabi, Mayowa O. ; Patel, Tejas ; Paternina Caicedo, Angel J. ; Pereira, David M. ; Perelman, Julian ; Polinder, Suzanne ; Rafay, Anwar ; Rahimi-Movaghar, Vafa ; Rai, Rajesh Kumar ; Ram, Usha ; Ranabhat, Chhabi Lal ; Roba, Hirbo Shore ; Savic, Miloje ; Sepanlou, Sadaf G. ; Ao, Braden J. Te; Tesema, Azeb Gebresilassie ; Thomson, Alan J. ; Tobe-Gai, Ruoyan ; Topor-Madry, Roman ; Undurraga, Eduardo A. ; Vargas, Veronica ; Vasankari, Tommi ; Violante, Francesco S. ; Wijeratne, Tissa ; Xu, Gelin ; Yonemoto, Naohiro ; Younis, Mustafa Z. ; Yu, Chuanhua ; Zaidi, Zoubida ; Sayed Zaki, Maysaa El; Murray, Christopher J.L. - \ 2017
The Lancet 389 (2017)10083. - ISSN 0140-6736 - p. 2005 - 2030.
Background: The amount of resources, particularly prepaid resources, available for health can affect access to health care and health outcomes. Although health spending tends to increase with economic development, tremendous variation exists among health financing systems. Estimates of future spending can be beneficial for policy makers and planners, and can identify financing gaps. In this study, we estimate future gross domestic product (GDP), all-sector government spending, and health spending disaggregated by source, and we compare expected future spending to potential future spending. Methods: We extracted GDP, government spending in 184 countries from 1980-2015, and health spend data from 1995-2014. We used a series of ensemble models to estimate future GDP, all-sector government spending, development assistance for health, and government, out-of-pocket, and prepaid private health spending through 2040. We used frontier analyses to identify patterns exhibited by the countries that dedicate the most funding to health, and used these frontiers to estimate potential health spending for each low-income or middle-income country. All estimates are inflation and purchasing power adjusted. Findings: We estimated that global spending on health will increase from US$9.21 trillion in 2014 to $24.24 trillion (uncertainty interval [UI] 20.47-29.72) in 2040. We expect per capita health spending to increase fastest in upper-middle-income countries, at 5.3% (UI 4.1-6.8) per year. This growth is driven by continued growth in GDP, government spending, and government health spending. Lower-middle income countries are expected to grow at 4.2% (3.8-4.9). High-income countries are expected to grow at 2.1% (UI 1.8-2.4) and low-income countries are expected to grow at 1.8% (1.0-2.8). Despite this growth, health spending per capita in low-income countries is expected to remain low, at $154 (UI 133-181) per capita in 2030 and $195 (157-258) per capita in 2040. Increases in national health spending to reach the level of the countries who spend the most on health, relative to their level of economic development, would mean $321 (157-258) per capita was available for health in 2040 in low-income countries. Interpretation: Health spending is associated with economic development but past trends and relationships suggest that spending will remain variable, and low in some low-resource settings. Policy change could lead to increased health spending, although for the poorest countries external support might remain essential.
Mode of action based risk assessment of the botanical food-borne alkenylbenzenesapiol and myristicin
Alajlouni, Abdul - \ 2017
Wageningen University. Promotor(en): Ivonne Rietjens, co-promotor(en): Jacques Vervoort; Sebas Wesseling. - Wageningen : Wageningen University - ISBN 9789463434584 - 212

Alkenylbenzenes including estragole, methyleugenol, safrole, elemicin, apiol, and myristicin are naturally occurring in many herbs such as parsley, dill, basil, tarragon, fennel and nutmeg (Kreydiyyeh and Usta, 2002, Smith et al., 2002, Semenov et al., 2007). Estragole, methyleugenol and safrole are genotoxic and carcinogenic in rodent bioassays inducing liver tumors (Boberg et al., 1986, Boberg et al., 1983, Drinkwater et al., 1976, Miller et al., 1983, Swanson et al., 1981, Wiseman et al., 1985, Wiseman et al., 1987, Wislocki et al., 1977). Because of that, the use of methyleugenol, safrole and estragole as pure substances in foodstuff has been prohibited in the EU from September 2008 onwards (European Commission (EC), 2008). For apiol and myristicin data for their risk assessment are limited and more research is needed to support the evaluation of the risk resulting from consumption of products containing these compounds (WHO, 2009). The aim of the current thesis was to perform a mode of action based risk assessment of exposure to low doses of apiol and myristicin by using physiologically based kinetic (PBK) modelling based read-across from other alkenylbenzenes and to use the results obtained for risk assessment of consumption of plant food supplements (PFS) and other botanical products containing parsley and dill.

Chapter 1 provides general background information to alkenylbenzenes especially apiol and myristicin, a description of the chemical, metabolic and toxicity characteristics of apiol and myristicin and other structurally related alkenylbenzenes, a brief outline of the method used for their risk assessment and a short introduction to PBK modelling. Besides that, Chapter 1 include the aim of the current thesis. In Chapter 2 and Chapter 3, PBK models for respectively apiol and myristicin in male rat and human were defined, enabling prediction of dose-dependent effects in bioactivation and detoxification of these alkenylbenzenes. The PBK model based predictions were subsequently compared to those for safrole enabling estimation of a BMDL10 for apiol and myristicin from read-across from the BMDL10 available for safrole, thereby enabling risk assessment of current dietary exposure to apiol. In Chapter 4 and 5, the risk assessment of exposure to apiol and related alkenylbenzenes through drinking of parsley and dill based herbal teas and consumption of parsley and dill containing PFS was performed using the BMDL10 values derived in Chapter 2 and 3. The results showed that consumption of parsley and dill based herbal teas and PFS would be a priority for risk management if consumed for longer periods of time. Chapter 6 includes a general discussion of the thesis results obtained and the future perspectives that describe the needs to further research, based on alternatives for animals testing, to improve the risk assessment approaches for different botanical preparations.

Altogether, the results obtained through different thesis chapters show that integration of different approaches provides the basis for a mode of action and PBK modelling based read-across from compounds for which tumor data are available to related compounds for which such data are lacking. This can contribute to the development of alternatives for animal testing and will facilitate the risk assessment of compounds for which in vivo toxicity studies on tumor formation data are unavailable.

Biotransformation and bioactivation reactions–2016 literature highlights
Khojasteh, S.C. ; Rietjens, Ivonne M.C.M. ; Dalvie, Deepak ; Miller, Grover - \ 2017
Drug Metabolism Reviews 49 (2017)3. - ISSN 0360-2532 - p. 285 - 317.
aldehyde oxidase - bioactivation - Biotransformation - cytochrome P450 - UGT
We are pleased to present a second annual issue highlighting a previous year’s literature on biotransformation and bioactivation. Each contributor to this issue worked independently to review the articles published in 2016 and proposed three to four articles, which he or she believed would be of interest to the broader research community. In each synopsis, the contributing author summarized the procedures, analyses and conclusions as described in the original manuscripts. In the commentary sections, our authors offer feedback and highlight aspects of the work that may not be apparent from an initial reading of the article. To be fair, one should still read the original article to gain a more complete understanding of the work conducted. Most of the articles included in this review were published in Drug Metabolism and Disposition or Chemical Research in Toxicology, but attempts were made to seek articles in 25 other journals. Importantly, these articles are not intended to represent a consensus of the best papers of the year, as we did not want to make any arbitrary standards for this purpose, but rather they were chosen by each author for their notable findings and descriptions of novel metabolic pathways or biotransformations. I am pleased that Drs. Rietjens and Dalvie have again contributed to this annual review. We would like to welcome Grover P Miller as an author for this year’s issue, and we thank Tom Baillie for his contributions to last year’s edition. We have intentionally maintained a balance of authors such that two come from an academic setting and two come from industry. Finally, please drop us a note if you find this review helpful. We would be pleased to hear your opinions of our commentary, and we extend an invitation to anyone who would like to contribute to a future edition of this review. This article is dedicated to Professor Thomas Baillie for his exceptional contributions to the field of drug metabolism.
Campylobacter pinnipediorum sp. Nov., isolated from pinnipeds, comprising Campylobacter pinnipediorum subsp. pinnipediorum subsp. nov. and Campylobacter pinnipediorum subsp. caledonicus subsp. nov
Gilbert, Maarten J. ; Miller, William G. ; St. Leger, Judy ; Chapman, Mary H. ; Timmerman, Arjen J. ; Duim, Birgitta ; Foster, Geoffrey ; Wagenaar, Jaap A. - \ 2017
International Journal of Systematic and Evolutionary Microbiology 67 (2017)6. - ISSN 1466-5026 - p. 1961 - 1968.
Average nucleotide identity - Campylobacter - Novel species - Pinnipeds - Urease - Whole genome sequencing

During independent diagnostic screenings of otariid seals in California (USA) and phocid seals in Scotland (UK), Campylobacter-like isolates, which differed from the established taxa of the genus Campylobacter, were cultured from abscesses and internal organs of different seal species. A polyphasic study was undertaken to determine the taxonomic position of these six isolates. The isolates were characterized by 16S rRNA gene and AtpA sequence analysis and by conventional phenotypic testing. The whole-genome sequences were determined for all isolates, and the average nucleotide identity (ANI) was determined. The isolates formed a separate phylogenetic clade, divergent from all other taxa of the genus Campylobacter and most closely related to Campylobactermucosalis. Although all isolates showed 100 % 16S rRNA gene sequence homology, AtpA and ANI analyses indicated divergence between the otariid isolates from California and the phocid isolates from Scotland, which warrants subspecies status for each clade. The two subspecies could also be distinguished phenotypically on the basis of catalase activity. This study shows clearly that the isolates obtained from pinnipeds represent a novel species within the genus Campylobacter, for which the name Campylobacter pinnipediorum sp. nov. is proposed. Within this novel species, the Californian isolates represent a separate subspecies, for which the name C. pinnipediorum subsp. pinnipediorum subsp. nov. is proposed. The type strain for both this novel species and subspecies is RM17260T (=LMG 29472T=CCUG 69570T). The Scottish isolates represent another subspecies, for which the name C. pinnipediorum subsp. caledonicus subsp. nov. is proposed. The type strain of this subspecies is M302/10/6T (=LMG 29473T=CCUG 68650T).

Indicators of the ‘wild seafood’ provisioning ecosystem service based on the surplus production of commercial fish stocks
Piet, G.J. ; Overzee, H.M.J. van; Miller, D.C.M. ; Gelabert, E.R. - \ 2017
Ecological Indicators 72 (2017). - ISSN 1470-160X - p. 194 - 202.
Ecosystem services - Fisheries management - Fishing mortality - Seafood provisioning - Spawning stock biomass - Sustainable exploitation

The ‘Wild Seafood’ Provisioning Service (WSPS), on which commercial fisheries rely, is probably one of the best studied marine ecosystem services due to its economic relevance and because extensive information sources exist for assessment purposes. Yet, the indicators often proposed are not suitable to describe the capacity of the ecosystem to deliver the WSPS. Therefore this study proposes surplus production (SP), a well-established concept in fisheries science, as the basis to calculate the capacity of marine ecosystems to provide the WSPS. SP is defined as the difference between stock production (through recruitment and body growth) and losses through natural mortality. This is, therefore, the production of the stock that could be harvested sustainably without decreasing the biomass. To assess the sustainability of the exploitation of the WSPS we also developed an indicator for this based on SP and compared it to existing fisheries management indicators. When both SP-based indicators showed a decreasing trend, contrasting with an increasing trend in the existing fisheries management indicators, the calculation of the SP-based indicators was scrutinized revealing that the weighting of the stocks into an aggregated indicator, strongly determines the indicator values, even up to the point that the trend is reversed. The aggregated indicators based on SP-weighted stocks can be considered complementary to existing fisheries management indicators as the former accurately reflect the capacity of the commercial fish to provide the WSPS and the sustainability of the exploitation of this service. In contrast the existing fisheries management indicators primarily reflect the performance of management towards achieving fisheries-specific policy goals.

D3.3: Good practice guidelines for stakeholder and citizen participation in bioeconomy strategies
Davies, Sara ; Ribeiro, Barbara ; Millar, Kate ; Miller, Stephen ; Vironen, Heidi ; Charles, David ; Griestop, Laura ; Hasenheit, Marius ; Kiresiewa, Zoritza ; Hoes, A.C. ; Overbeek, M.M.M. ; Bianchini, Chiara - \ 2016
EU - 35 p.
biobased economy - government policy - public participation - case studies - decision making - multi-stakeholder processes - overheidsbeleid - publieke participatie - gevalsanalyse - besluitvorming - multi-stakeholder processen
This document has been developed as part of Work Package 3 of the BioSTEP project, which has examined current participatory practices, involving both stakeholders and citizens, in bioeconomy strategies in six case studies, namely: Two case studies at national level (Finland and Germany); Four case studies at regional level (Bio-based Delta in the Netherlands, Saxony-Anhalt in Germany, Scotland in the United Kingdom, and the Veneto in Italy). Key documentary sources include international and national practice-based literature on stakeholder and public engagement, as well as other BioSTEP publications. Two earlier reports (Charles et al., 2016; Davies et al., 2016) provide a detailed overview of participation in these six case studies of national and regional bioeconomy strategies. Building on this work, as well as on a review of existing research on stakeholder and citizen engagement in the bioeconomy, this document sets out guidance and suggestions for designing and undertaking engagement with stakeholders and citizens in relation to national and regional bioeconomy strategies.
International Advances in Pesticide Application : at the School of Agriculture, Universitat Politècnica de Catalunya, Barcelona, Spain, on 13-15 January 2016
Balsari, P. ; Cooper, S.E. ; Gill, E. ; Glass, C.R. ; Jones, W. ; Magri, B. ; Miller, P.C.H. ; Mountford-Smith, D. ; Nuyttens, D. ; Robinson, T.H. ; Stock, D. ; Taylor, J.C. ; Zande, J.C. van de - \ 2016
The Association of Applied Biologists (Aspects of Applied Biology 132) - 430 p.
This international event marked the 14th occasion of this biennial conference and provided an opportunity to discuss pesticide (and bio-pesticide) application issues in an informal setting with platform and poster presentations. Key workers from research institutes, industry and regulatory authorities provided a unique mix of biological and engineering sciences.

Many governments of late have realised the importance of agricultural technologies with renewed emphasis on funding strategies aimed at developing new ideas and bringing developments to market. All this, in an effort to provide sustained development of their agricultural industry and food security while globally offering sustenance for an ever growing population. While much of these efforts gravitate towards the informatics and precision control technologies we should not forget the expanse that is crop protection and application technology’s part. The adoption of the holistic approaches of Integrated Pest Management offer growers’ avenues for control as the registration pressure on traditional chemistry continues to erode the farmers’ armoury. The diversion of attention towards the development of bio-pesticides by many major companies reinforces this shift in attitude and expectations, but may also encourage accepted application methods to be re-examined. While the use of larger more sophisticated machines in the application of pesticides and bio pesticides offer opportunities in maximising production on an industrial scale it must be remembered that assistance on a small scale can also offer considerable benefits. The papers presented here contribute to the wealth of knowledge needed to support a safe, sustainable and efficient industry.
Feed intake, growth, and body and carcass attributes of feedlot steers supplemented with two levels of calcium nitrate or urea
Hegarty, R.S. ; Miller, J. ; Oelbrandt, N. ; Li, L. ; Luijben, J.P.M. ; Robinson, D.L. ; Nolan, J.V. ; Perdok, H.B. - \ 2016
Journal of Animal Science 94 (2016)12. - ISSN 0021-8812 - p. 5372 - 5381.
Beef cattle - Body composition - Carcass - Feedlot - Nitrate - Urea

Nitrate supplementation has been shown to be effective in reducing enteric methane emission from ruminants, but there have been few large-scale studies assessing the effects of level of nitrate supplementation on feed intake, animal growth, or carcass and meat quality attributes of beef cattle. A feedlot study was conducted to assess the effects of supplementing 0.25 or 0.45% NPN in dietary DM as either urea (Ur) or calcium nitrate (CaN) on DMI, ADG, G:F, and carcass attributes of feedlot steers (n = 383). The levels of NPN inclusion were selected as those at which nitrate has previously achieved measurable mitigation of enteric methane. The higher level of NPN inclusion reduced ADG as did replacement of Ur with CaN (P <0.01). A combined analysis of DMI for 139 steers with individual animal intake data and pen-average intakes for 244 bunk-fed steers showed a significant interaction between NPN source and level (P = 0.02) with steers on the high-CaN diet eating less than those on the other 3 diets (P <0.001). Neither level nor NPN source significantly affected cattle G:F. There was a tendency (P = 0.05) for nitratesupplemented cattle to have a slower rate of eating (g DMI/min) than Ur-supplemented cattle. When adjusted for BW, neither NPN source nor inclusion level affected cross-sectional area of the LM or fatness measured on the live animal. Similarly, there were no significant main effects of treatments on dressing percentage or fat depth or muscling attributes of the carcass after adjustment for HCW (P > 0.05). Analysis of composited meat samples showed no detectable nitrates or nitrosamines in raw or cooked meat, and the level of nitrate detected in meat from nitrate-supplemented cattle was no higher than for Ur-fed cattle (P > 0.05). We conclude that increasing NPN inclusion from 0.25 to 0.45% NPN in dietary DM and replacing Ur with CaN decreased ADG in feedlot cattle without improving G:F.

Comparative Genomics of Campylobacter fetus from Reptilesand Mammals Reveals Divergent Evolution in Host-Associated Lineages
Gilbert, Maarten J. ; Miller, William G. ; Yee, Emma ; Zomer, Aldert ; Graaf-Van Bloois, Linda Van Der; Fitzgerald, C. ; Forbes, Ken J. ; Méric, Guillaume ; Sheppard, S. ; Wagenaar, J.A. ; Duim, Birgitta - \ 2016
Genome Biology and Evolution 8 (2016)6. - ISSN 1759-6653 - p. 2006 - 2019.
Campylobacter fetus currently comprises three recognized subspecies, which display distinct host association. Campylobacter fetus subsp. fetus and C. fetus subsp. venerealis are both associated with endothermic mammals, primarily ruminants, whereas C. fetus subsp. testudinum is primarily associated with ectothermic reptiles. Both C. fetus subsp. testudinum and C. fetus subsp. fetus have been associated with severe infections, often with a systemic component, in immunocompromised humans. To study the genetic factors associated with the distinct host dichotomy in C. fetus, whole-genome sequencing and comparison of mammal- and reptile-associated C. fetus was performed. The genomes of C. fetus subsp. testudinum isolated from either reptiles or humans were compared with elucidate the genetic factors associated with pathogenicity in humans. Genomic comparisons showed conservation of gene content and organization among C. fetus subspecies, but a clear distinction between mammal- and reptile-associated C. fetus was observed. Several genomic regions appeared to be subspecies specific, including a putative tricarballylate catabolism pathway, exclusively present in C. fetus subsp. testudinum strains. Within C. fetus subsp. testudinum, sapA, sapB, and sapAB type strains were observed. The recombinant locus iamABC (mlaFED) was exclusively associated with invasive C. fetus subsp. testudinum strains isolated from humans. A phylogenetic reconstruction was consistent with divergent evolution in host-associated strains and the existence of a barrier to lateral gene transfer between mammal- and reptile-associated C. fetus. Overall, this study shows that reptile-associated C. fetus subsp. testudinum is genetically divergent from mammal-associated C. fetus subspecies.
Studying the Mammalian Intestinal Microbiome Using Animal Models
Hugenholtz, F. ; Zhang, J. ; O'Toole, P.W. ; Smidt, H. - \ 2016
In: Manual of Environmental Microbiology / Yates, Marylyn V., Nakatsu, Cindy H., Miller, Robert V., Pillai, Suresh D., Washington DC : ASM Press - ISBN 9781555816025 - p. 4.4.2 - 1-4.4.2-10.
The gastrointestinal (GI) tract of humans and animals is colonized by microorganisms immediately after birth. The composition of the GI tract microbiota undergoes remarkable alterations during early age, reaches a relative stable status in adulthood, and is driven by external factors such as habitual diet, location along the intestine, antibiotic therapy and maternal microbiota, and intrinsic factors such as host species and genotype. Whereas usually faecal samples are used for assessing the impact on the microbiota in human intervention studies, in vitro and animal models provide an easier way to collect many (invasive) samples, have multiple comparisons and regulating the genotype background. Animal models, and in particular mammalian models, provide an alternative way to study the in vivo responses to beneficial, commensal and pathogenic microorganisms in the GI tract, including studies that aim to see the impact of the host system as well. The main animals used to study the mammalian GI tract are rodents (mainly mice and rats) and pigs. Rodent and pig models, including gnotobiotic and humanized rodents and pigs and minipigs, have been extensively employed in gut microbiota studies, and especially the piglet model has been suggested as an appropriate model for human infant studies. With pig models, several intestinal sampling techniques can be applied in kinetic microbiota studies, including small intestinal segment perfusion and cannulation. In many cases, to test a certain treatment, a tiered approach consisting of complementary methods is employed, comprising in vitro, in vivo animal models, eventually leading towards human intervention studies.
Genome-wide analysis identifies 12 loci influencing human reproductive behavior
Barban, Nicola ; Jansen, Rick ; Vlaming, Ronald de; Vaez, Ahmad ; Mandemakers, Jornt J. ; Tropf, Felix C. ; Shen, Xia ; Wilson, James F. ; Chasman, Daniel I. ; Nolte, Ilja M. ; Tragante, Vinicius ; Laan, Sander W. van der; Perry, John R.B. ; Kong, Augustine ; Ahluwalia, Tarunveer S. ; Albrecht, Eva ; Yerges-Armstrong, Laura ; Atzmon, Gil ; Auro, Kirsi ; Ayers, Kristin ; Bakshi, Andrew ; Ben-Avraham, Danny ; Berger, Klaus ; Bergman, Aviv ; Bertram, Lars ; Bielak, Lawrence F. ; Bjornsdottir, Gyda ; Bonder, Marc Jan ; Broer, Linda ; Bui, Minh ; Barbieri, Caterina ; Cavadino, Alana ; Chavarro, Jorge E. ; Turman, Constance ; Concas, Maria Pina ; Cordell, Heather J. ; Davies, Gail ; Eibich, Peter ; Eriksson, Nicholas ; Esko, Tõnu ; Eriksson, Joel ; Falahi, Fahimeh ; Felix, Janine F. ; Fontana, Mark Alan ; Franke, Lude ; Gandin, Ilaria ; Gaskins, Audrey J. ; Gieger, Christian ; Gunderson, Erica P. ; Guo, Xiuqing ; Hayward, Caroline ; He, Chunyan ; Hofer, Edith ; Huang, Hongyan ; Joshi, Peter K. ; Kanoni, Stavroula ; Karlsson, Robert ; Kiechl, Stefan ; Kifley, Annette ; Kluttig, Alexander ; Kraft, Peter ; Lagou, Vasiliki ; Lecoeur, Cecile ; Lahti, Jari ; Li-Gao, Ruifang ; Lind, Penelope A. ; Liu, Tian ; Makalic, Enes ; Mamasoula, Crysovalanto ; Matteson, Lindsay ; Mbarek, Hamdi ; McArdle, Patrick F. ; McMahon, George ; Meddens, S.F.W. ; Mihailov, Evelin ; Miller, Mike ; Missmer, Stacey A. ; Monnereau, Claire ; Most, Peter J. van der; Myhre, Ronny ; Nalls, Mike A. ; Nutile, Teresa ; Kalafati, Ioanna Panagiota ; Porcu, Eleonora ; Prokopenko, Inga ; Rajan, Kumar B. ; Rich-Edwards, Janet ; Rietveld, Cornelius A. ; Robino, Antonietta ; Rose, Lynda M. ; Rueedi, Rico ; Ryan, Kathleen A. ; Saba, Yasaman ; Schmidt, Daniel ; Smith, Jennifer A. ; Stolk, Lisette ; Streeten, Elizabeth ; Tönjes, Anke ; Thorleifsson, Gudmar ; Ulivi, Sheila ; Wedenoja, Juho ; Wellmann, Juergen ; Willeit, Peter ; Yao, Jie ; Yengo, Loic ; Zhao, Jing Hua ; Zhao, Wei ; Zhernakova, Daria V. ; Amin, Najaf ; Andrews, Howard ; Balkau, Beverley ; Barzilai, Nir ; Bergmann, Sven ; Biino, Ginevra ; Bisgaard, Hans ; Bønnelykke, Klaus ; Boomsma, Dorret I. ; Buring, Julie E. ; Campbell, Harry ; Cappellani, Stefania ; Ciullo, Marina ; Cox, Simon R. ; Cucca, Francesco ; Toniolo, Daniela ; Davey-Smith, George ; Deary, Ian J. ; Dedoussis, George ; Deloukas, Panos ; Duijn, Cornelia M. van; Geus, Eco J.C. de; Eriksson, Johan G. ; Evans, Denis A. ; Faul, Jessica D. ; Sala, Cinzia Felicita ; Froguel, Philippe ; Gasparini, Paolo ; Girotto, Giorgia ; Grabe, Hans-Jörgen ; Greiser, Karin Halina ; Groenen, Patrick J.F. ; Haan, Hugoline G. de; Haerting, Johannes ; Harris, Tamara B. ; Heath, Andrew C. ; Heikkilä, Kauko ; Hofman, Albert ; Homuth, Georg ; Holliday, Elizabeth G. ; Hopper, John ; Hyppönen, Elina ; Jacobsson, Bo ; Jaddoe, Vincent W.V. ; Johannesson, Magnus ; Jugessur, Astanand ; Kähönen, Mika ; Kajantie, Eero ; Kardia, Sharon L.R. ; Keavney, Bernard ; Kolcic, Ivana ; Koponen, Päivikki ; Kovacs, Peter ; Kronenberg, Florian ; Kutalik, Zoltan ; Bianca, Martina la; Lachance, Genevieve ; Iacono, William G. ; Lai, Sandra ; Lehtimäki, Terho ; Liewald, David C. ; Lindgren, Cecilia M. ; Liu, Yongmei ; Luben, Robert ; Lucht, Michael ; Luoto, Riitta ; Magnus, Per ; Magnusson, Patrik K.E. ; Martin, Nicholas G. ; McGue, Matt ; McQuillan, Ruth ; Medland, Sarah E. ; Meisinger, Christa ; Mellström, Dan ; Metspalu, Andres ; Traglia, Michela ; Milani, Lili ; Mitchell, Paul ; Montgomery, Grant W. ; Mook-Kanamori, Dennis ; Mutsert, Renée de; Nohr, Ellen A. ; Ohlsson, Claes ; Olsen, Jørn ; Ong, Ken K. ; Paternoster, Lavinia ; Pattie, Alison ; Penninx, Brenda W.J.H. ; Perola, Markus ; Peyser, Patricia A. ; Pirastu, Mario ; Polasek, Ozren ; Power, Chris ; Kaprio, Jaakko ; Raffel, Leslie J. ; Räikkönen, Katri ; Raitakari, Olli ; Ridker, Paul M. ; Ring, Susan M. ; Roll, Kathryn ; Rudan, Igor ; Ruggiero, Daniela ; Rujescu, Dan ; Salomaa, Veikko ; Schlessinger, David ; Schmidt, Helena ; Schmidt, Reinhold ; Schupf, Nicole ; Smit, Johannes ; Sorice, Rossella ; Spector, Tim D. ; Starr, John M. ; Stöckl, Doris ; Strauch, Konstantin ; Stumvoll, Michael ; Swertz, Morris A. ; Thorsteinsdottir, Unnur ; Thurik, A.R. ; Timpson, Nicholas J. ; Tung, Joyce Y. ; Uitterlinden, André G. ; Vaccargiu, Simona ; Viikari, Jorma ; Vitart, Veronique ; Völzke, Henry ; Vollenweider, Peter ; Vuckovic, Dragana ; Waage, Johannes ; Wagner, Gert G. ; Wang, Jie Jin ; Wareham, Nicholas J. ; Weir, David R. ; Willemsen, Gonneke ; Willeit, Johann ; Wright, Alan F. ; Zondervan, Krina T. ; Stefansson, Kari ; Krueger, Robert F. ; Lee, James J. ; Benjamin, Daniel J. ; Cesarini, David ; Koellinger, Philipp D. ; Hoed, Marcel den; Snieder, Harold ; Mills, Melinda C. - \ 2016
Nature Genetics 48 (2016)12. - ISSN 1061-4036 - p. 1462 - 1472.
The genetic architecture of human reproductive behavior—age at first birth (AFB) and number of children ever born (NEB)—has a strong relationship with fitness, human development, infertility and risk of neuropsychiatric disorders. However, very few genetic loci have been identified, and the underlying mechanisms of AFB and NEB are poorly understood. We report a large genome-wide association study of both sexes including 251,151 individuals for AFB and 343,072 individuals for NEB. We identified 12 independent loci that are significantly associated with AFB and/or NEB in a SNP-based genome-wide association study and 4 additional loci associated in a gene-based effort. These loci harbor genes that are likely to have a role, either directly or by affecting non-local gene expression, in human reproduction and infertility, thereby increasing understanding of these complex traits.
Teaching and learning reflexivity in problem-oriented inter- and transdisciplinary research
Fortuin, K.P.J. ; Koppen, C.S.A. van - \ 2016
In: Conference Proceedings. - Wageningen : Wageningen University & Research - p. 209 - 213.
A crucial skill for researchers involved in inter- and transdisciplinary projects is the ability to reflect not only on the problem and its solutions but also on the process of knowledge production itself. In other words, these researchers require reflexive skills. Reflexive skills refer to the ability of researchers to question the different sorts of knowledge used, to recognize the epistemological and normative aspects involved, and to reflect on their own and others' roles in these knowledge processes (Fortuin and van Koppen 2015). Literature shows that reflexivity in interdisciplinary and transdisciplinary research is important, yet difficult to learn (Miller et al. 2008, Godemann 2008, Kueffer et al. 2012). Reflexive skills need to be trained. Existing literature provides, however, little specific guidance on how to do so. The research presented in this paper aimed at developing and evaluating a teaching and learning strategy for reflexive skills in interdisciplinarity and transdisciplinarity specifically.
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