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.

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A global genetic diversity analysis of Fusarium oxysporum f.sp. cubense : the Panama disease pathogen of banana
Ordóñez R., Nadia - \ 2018
Wageningen University. Promotor(en): Gert Kema, co-promotor(en): Michael Seidl; Harold Meijer. - Wageningen : Wageningen University - ISBN 9789463432986 - 156
Gene expression polymorphism underpins evasion of host immunity in an asexual lineage of the Irish potato famine pathogen
Pais, Marina ; Yoshida, Kentaro ; Giannakopoulou, Artemis ; Pel, Mathieu A. ; Cano, Liliana M. ; Oliva, Ricardo F. ; Witek, Kamil ; Lindqvist-Kreuze, Hannele ; Vleeshouwers, Vivianne G.A.A. ; Kamoun, Sophien - \ 2018
BMC Evolutionary Biology 18 (2018)1. - ISSN 1471-2148
Asexual reproduction - Clonal lineage - Copy number variation - Emergent pathogen - Evolution - Expression polymorphism - Immunity - Loss of heterozygosity - Phenotypic plasticity - Phytophthora infestans - Structural variation

Background: Outbreaks caused by asexual lineages of fungal and oomycete pathogens are a continuing threat to crops, wild animals and natural ecosystems (Fisher MC, Henk DA, Briggs CJ, Brownstein JS, Madoff LC, McCraw SL, Gurr SJ, Nature 484:186-194, 2012; Kupferschmidt K, Science 337:636-638, 2012). However, the mechanisms underlying genome evolution and phenotypic plasticity in asexual eukaryotic microbes remain poorly understood (Seidl MF, Thomma BP, BioEssays 36:335-345, 2014). Ever since the 19th century Irish famine, the oomycete Phytophthora infestans has caused recurrent outbreaks on potato and tomato crops that have been primarily caused by the successive rise and migration of pandemic asexual lineages (Goodwin SB, Cohen BA, Fry WE, Proc Natl Acad Sci USA 91:11591-11595, 1994; Yoshida K, Burbano HA, Krause J, Thines M, Weigel D, Kamoun S, PLoS Pathog 10:e1004028, 2014; Yoshida K, Schuenemann VJ, Cano LM, Pais M, Mishra B, Sharma R, Lanz C, Martin FN, Kamoun S, Krause J, et al. eLife 2:e00731, 2013; Cooke DEL, Cano LM, Raffaele S, Bain RA, Cooke LR, Etherington GJ, Deahl KL, Farrer RA, Gilroy EM, Goss EM, et al. PLoS Pathog 8:e1002940, 2012). However, the dynamics of genome evolution within these clonal lineages have not been determined. The objective of this study was to use a comparative genomics and transcriptomics approach to determine the molecular mechanisms that underpin phenotypic variation within a clonal lineage of P. infestans. Results: Here, we reveal patterns of genomic and gene expression variation within a P. infestans asexual lineage by comparing strains belonging to the South American EC-1 clone that has dominated Andean populations since the 1990s (Yoshida K, Burbano HA, Krause J, Thines M, Weigel D, Kamoun S, PLoS Pathog 10e1004028, 2014; Yoshida K, Schuenemann VJ, Cano LM, Pais M, Mishra B, Sharma R, Lanz C, Martin FN, Kamoun S, Krause J, et al. eLife 2:e00731, 2013; Delgado RA, Monteros-Altamirano AR, Li Y, Visser RGF, van der Lee TAJ, Vosman B, Plant Pathol 62:1081-1088, 2013; Forbes GA, Escobar XC, Ayala CC, Revelo J, Ordonez ME, Fry BA, Doucett K, Fry WE, Phytopathology 87:375-380, 1997; Oyarzun PJ, Pozo A, Ordonez ME, Doucett K, Forbes GA, Phytopathology 88:265-271, 1998). We detected numerous examples of structural variation, nucleotide polymorphisms and loss of heterozygosity within the EC-1 clone. Remarkably, 17 genes are not expressed in one of the two EC-1 isolates despite apparent absence of sequence polymorphisms. Among these, silencing of an effector gene was associated with evasion of disease resistance conferred by a potato immune receptor. Conclusions: Our findings highlight the molecular changes underpinning the exceptional genetic and phenotypic plasticity associated with host adaptation in a pandemic clonal lineage of a eukaryotic plant pathogen. We observed that the asexual P. infestans lineage EC-1 can exhibit phenotypic plasticity in the absence of apparent genetic mutations resulting in virulence on a potato carrying the Rpi-vnt1.1 gene. Such variant alleles may be epialleles that arose through epigenetic changes in the underlying genes.

Insights in the epidemiology and diversity of Fusarium oxysporum f. sp. cubense, the causal agent of Panama disease in banana
Kema, G.H.J. ; Garcia Bastidas, F.A. ; Ordonez Roman, N.I. ; Salacinas, Maricar ; Seidl, M.F. ; Thomma, B.P.H.J. ; Meijer, H.J.G. - \ 2018
Gewasbescherming 48 (2018)4/5/6. - ISSN 0166-6495 - p. 123 - 123.
Impact of prediagnostic smoking and smoking cessation on colorectal cancer prognosis : A meta-analysis of individual patient data from cohorts within the CHANCES consortium
Ordóñez-Mena, J.M. ; Walter, V. ; Schöttker, B. ; Jenab, M. ; O'Doherty, M.G. ; Kee, F. ; Bueno-de-Mesquita, B. ; Peeters, P.H.M. ; Stricker, B.H. ; Ruiter, R. ; Hofman, A. ; Söderberg, S. ; Jousilahti, P. ; Kuulasmaa, K. ; Freedman, N.D. ; Wilsgaard, T. ; Wolk, A. ; Nilsson, L.M. ; Tjønneland, A. ; Quirós, J.R. ; Duijnhoven, F.J.B. van; Siersema, P.D. ; Boffetta, P. ; Trichopoulou, A. ; Brenner, H. - \ 2018
Annals of Oncology 29 (2018)2. - ISSN 0923-7534 - p. 472 - 483.
Colorectal neoplasms - Meta-analysis - Smoking - Smoking cessation - Survival
Background: Smoking has been associated with colorectal cancer (CRC) incidence and mortality in previous studies and might also be associated with prognosis after CRC diagnosis. However, current evidence on smoking in association with CRC prognosis is limited. Patients and methods: For this individual patient data meta-analysis, sociodemographic and smoking behavior information of 12 414 incident CRC patients (median age at diagnosis: 64.3 years), recruited within 14 prospective cohort studies among previously cancer-free adults, was collected at baseline and harmonized across studies. Vital status and causes of death were collected for a mean follow-up time of 5.1 years following cancer diagnosis. Associations of smoking behavior with overall and CRC-specific survival were evaluated using Cox regression and standard meta-analysis methodology. Results: A total of 5229 participants died, 3194 from CRC. Cox regression revealed significant associations between former [hazard ratio (HR)=1.12; 95 % confidence interval (CI)=1.04-1.20] and current smoking (HR=1.29; 95% CI=1.04-1.60) and poorer overall survival compared with never smoking. Compared with current smoking, smoking cessation was associated with improved overall (HR<10 years=0.78; 95% CI=0.69-0.88; HR≥10 years=0.78; 95% CI=0.63-0.97) and CRC-specific survival (HR≥10 years=0.76; 95% CI=0.67-0.85). Conclusion: In this large meta-analysis including primary data of incident CRC patients from 14 prospective cohort studies on the association between smoking and CRC prognosis, former and current smoking were associated with poorer CRC prognosis compared with never smoking. Smoking cessation was associated with improved survival when compared with current smokers. Future studies should further quantify the benefits of nonsmoking, both for cancer prevention and for improving survival among CRC patients, in particular also in terms of treatment response.
Nested achetypes of vulnerability in African drylands: where lies potential for sustainable Agricultural intensification?
Sietz, D. ; Ordonez, J.C. ; Kok, M.T.J. ; Janssen, P. ; Hilderink, Henk B.M. ; Tittonell, P.A. ; Dijk, J.W.M. van - \ 2017
Environmental Research Letters 12 (2017)9. - ISSN 1748-9326
Food production is key to achieving food security in the drylands of sub-Saharan Africa. Since agricultural productivity is limited, however, due to inherent agro-ecological constraints and land degradation, sustainable agricultural intensification has been widely discussed as an opportunity for improving food security and reducing vulnerability. Yet vulnerability determinants are
distributed heterogeneously in the drylands of sub-Saharan Africa and sustainable intensification cannot be achieved everywhere in cost-effective and efficient ways. To better understand the heterogeneity of farming systems’ vulnerability in order to support decision making at regional scales, we present archetypes, i.e. socio-ecological patterns, of farming systems’ vulnerability in
the drylands of sub-Saharan Africa and reveal their nestedness. We uantitatively indicated the most relevant farming systems’ properties at a sub-national resolution. These factors included water availability, agro-ecological potential, erosion sensitivity, population pressure, urbanisation, remoteness, governance, income and undernourishment. Cluster analysis revealed eight broad
archetypes of vulnerability across all drylands of sub-Saharan Africa. The broad archetype representing better governance and highest remoteness in extremely dry and resource-constrained regions encompassed the largest area share (19%), mainly indicated in western Africa. Moreover, six nested archetypes were identified within those regions with better agropotential and prevalent agricultural livelihoods. Among these patterns, the nested archetype depicting regions with highest erosion sensitivity, severe undernourishment and lower agropotential represented the largest population (30%) and area (28%) share, mainly found in the Sahel region. The nested archetype indicating medium undernourishment, better governance and lowest erosion sensitivity
showed particular potential for sustainable agricultural intensification, mainly in western and some parts of southeastern and eastern Africa. Insights into the nestedness of archetypes allowed a more differentiated discussion of vulnerability and sustainable intensification opportunities, enhancing the evaluation of key interlinkages between land management and food security. The
archetypes may support the transfer of successful intensification strategies based on similarities among the drylands in sub-Saharan Africa.
Importance of Campylobacter jejuni FliS and FliW in flagella biogenesis and flagellin secretion
Radomska, Katarzyna A. ; Wösten, Marc M.S.M. ; Ordoñez, Soledad R. ; Wagenaar, Jaap A. ; Putten, Jos P.M. van - \ 2017
Frontiers in Microbiology 8 (2017). - ISSN 1664-302X - p. 14 - 14.
Campylobacter jejuni - Flagellar chaperone - Flagellar motility - Flagellin - FliS - FliW

Flagella-driven motility enables bacteria to reach their favorable niche within the host. The human foodborne pathogen Campylobacter jejuni produces two heavily glycosylated structural flagellins (FlaA and FlaB) that form the flagellar filament. It also encodes the non-structural FlaC flagellin which is secreted through the flagellum and has been implicated in host cell invasion. The mechanisms that regulate C. jejuni flagellin biogenesis and guide the proteins to the export apparatus are different from those in most other enteropathogens and are not fully understood. This work demonstrates the importance of the putative flagellar protein FliS in C. jejuni flagella assembly. A constructed fliS knockout strain was non-motile, displayed reduced levels of FlaA/B and FlaC flagellin, and carried severely truncated flagella. Pull-down and Far Western blot assays showed direct interaction of FliS with all three C. jejuni flagellins (FlaA, FlaB, and FlaC). This is in contrast to, the sensor and regulator of intracellular flagellin levels, FliW, which bound to FlaA and FlaB but not to FlaC. The FliS protein but not FliW preferred binding to glycosylated C. jejuni flagellins rather than to their non-glycosylated recombinant counterparts. Mapping of the binding region of FliS and FliW using a set of flagellin fragments showed that the C-terminal subdomain of the flagellin was required for FliS binding, whereas the N-terminal subdomain was essential for FliW binding. The separate binding subdomains required for FliS and FliW, the different substrate specificity, and the differential preference for binding of glycosylated flagellins ensure optimal processing and assembly of the C. jejuni flagellins.

Comparison of general obesity and measures of body fat distribution in older adults in relation to cancer risk : Meta-analysis of individual participant data of seven prospective cohorts in Europe
Freisling, Heinz ; Arnold, Melina ; Soerjomataram, Isabelle ; O'Doherty, Mark George ; Ordóñez-Mena, José Manuel ; Bamia, Christina ; Kampman, Ellen ; Leitzmann, Michael ; Romieu, Isabelle ; Kee, Frank - \ 2017
British Journal of Cancer 116 (2017)11. - ISSN 0007-0920 - p. 1486 - 1497.
Ageing - Body fat distribution - Cancer - CHANCES consortium - Cohort - Obesity - Prevention

Background:We evaluated the associations of anthropometric indicators of general obesity (body mass index, BMI), an established risk factor of various cancer, and body fat distribution (waist circumference, WC; hip circumference, HC; and waist-to-hip ratio, WHR), which may better reflect metabolic complications of obesity, with total obesity-related and site-specific (colorectal and postmenopausal breast) cancer incidence.Methods:This is a meta-analysis of seven prospective cohort studies participating in the CHANCES consortium including 18 668 men and 24 751 women with a mean age of 62 and 63 years, respectively. Harmonised individual participant data from all seven cohorts were analysed separately and alternatively for each anthropometric indicator using multivariable Cox proportional hazards models.Results:After a median follow-up period of 12 years, 1656 first-incident obesity-related cancers (defined as postmenopausal female breast, colorectum, lower oesophagus, cardia stomach, liver, gallbladder, pancreas, endometrium, ovary, and kidney) had occurred in men and women. In the meta-analysis of all studies, associations between indicators of adiposity, per s.d. increment, and risk for all obesity-related cancers combined yielded the following summary hazard ratios: 1.11 (95% CI 1.02-1.21) for BMI, 1.13 (95% CI 1.04-1.23) for WC, 1.09 (95% CI 0.98-1.21) for HC, and 1.15 (95% CI 1.00-1.32) for WHR. Increases in risk for colorectal cancer were 16%, 21%, 15%, and 20%, respectively per s.d. of BMI, WC, HC, and WHR. Effect modification by hormone therapy (HT) use was observed for postmenopausal breast cancer (Pinteraction <0.001), where never HT users showed an ∼20% increased risk per s.d. of BMI, WC, and HC compared to ever users.Conclusions:BMI, WC, HC, and WHR show comparable positive associations with obesity-related cancers combined and with colorectal cancer in older adults. For postmenopausal breast cancer we report evidence for effect modification by HT use.

Nested archetypes of vulnerability in African drylands : where lies potential for sustainable agricultural intensification?
Sietz, D. ; Ordoñez, J. ; Kok, M. ; Janssen, P. ; Hilderink, H. ; Tittonell, P.A. ; Dijk, H. - \ 2017
Environmental Research Letters (2017). - ISSN 1748-9326
Food production is key to achieving food security in the drylands of sub-Saharan Africa. Since agricultural productivity is limited, however, due to inherent agro-ecological constraints and land degradation, sustainable agricultural intensification has been widely discussed as an opportunity for improving food security and reducing vulnerability. Yet, vulnerability determinants are heterogeneously distributed in the drylands of sub-Saharan Africa and sustainable intensification cannot be achieved everywhere in cost-effective and efficient ways. To better understand the heterogeneity in farming systems' vulnerability in support of decision making at regional scales, we present archetypes, that is to say socio-ecological patterns, of farming systems' vulnerability in the drylands of sub-Saharan Africa and reveal their nestedness. We quantitatively indicated the most relevant farming systems' properties at a sub-national resolution. These factors included water availability, agro-ecological potential, erosion sensitivity, population pressure, urbanisation, remoteness, governance, income and undernourishment. Cluster analysis revealed eight broad archetypes of vulnerability across all drylands of sub-Saharan Africa. The broad archetype representing better governance and highest remoteness encompassed the largest area share (19%), mainly indicated in western Africa. Moreover, six nested archetypes were identified within those regions with better agropotential and prevalent agricultural livelihoods. Among these patterns, the nested archetype depicting regions with highest erosion sensitivity, severe undernourishment and lower agropotential represented the largest population (30%) and area share (28%), mainly found in the Sahel region. The nested archetype indicating medium undernourishment, better governance and lowest erosion sensitivity showed particular potential for sustainable agricultural intensification, mainly in western and some parts of southeastern and eastern Africa. Insights into the nesting of archetypes allowed a more differentiated discussion of vulnerability and sustainable intensification opportunities, enhancing the evaluation of key interlinkages between land management and food security. The archetypes can support the transfer of successful intensification strategies based on similarities among the drylands in sub-Saharan Africa.
Latest insights in the epidemiology and diversity of Fusarium oxysporum f.sp. cubense, the causal agent of Panama disease in banana
Kema, G.H.J. ; Garcia Bastidas, F.A. ; Ordonez Roman, N.I. ; Salacinas, Maricar ; Seidl, M.F. ; Thomma, B.P.H.J. ; Meijer, H.J.G. - \ 2017
In: Abstract Book 29th Fungal Genetics Conference Asilomar 17, Pacific Grove, CA, USA 14-19 March 2017. - Genetics Society of America - p. 88 - 88.
Panama disease or Fusarium wilt of banana draws global attention. The currently developing epidemic of the so-called Tropical Race 4 (TR4) is caused by a single clone of Fusarium oxysporum f.sp. cubense (Foc); vegetative compatibility group 01213. It is reminiscent of the previous epidemic that wiped out “Gros Michel” bananas in Central America, which pushed the banana industry into bankruptcy. The epidemic was eventually quenched by cultivating “Cavendish” bananas, which are resistant to the so-called Foc Race 1 strains that caused the epidemic in “Gros Michel”. The industry revived and thrives by the success of “Cavendish” that has developed into a global monoculture. The emergence of TR4 caused havoc and wipes out “Cavendish” plantations in South East Asia, from where the disease now has spread into the Near and Middle East and Africaa. Banana production in many regions is at stake and there are no sustainable solutions available. Our research focuses on the international complexity and addresses mostly genetic diversity in host and pathogen as well as epidemiological aspects embedded in multidisciplinary programs. We have used genotyping by sequencing technologies to describe global and regional diversity in the causal agent Foc and have phenotyped hundreds of banana accessions with various Foc genotypes. Methods to rapidly detect - particularly TR4 - and manage the disease have been developed to slow down the epidemic. This provides the necessary time for developing durable solutions that also contribute to break the hegemony of the global “Cavendish” monoculture by introducing a diversified panel of banana cultivars. The latest developments will be presented and discussed.
Feedback control of Campylobacter jejuni flagellin levels through reciprocal binding of FliW to flagellin and the global regulator CsrA
Radomska, Katarzyna A. ; Ordoñez, Soledad R. ; Wösten, Marc M.S.M. ; Wagenaar, Jaap A. ; Putten, Jos P.M. van - \ 2016
Molecular Microbiology 102 (2016)2. - ISSN 0950-382X - p. 207 - 220.

Bacterial flagella assembly is tightly regulated to ensure a timely and sequential production of the various flagellum constituents. In the pathogen Campylobacter jejuni the hierarchy in flagella biosynthesis is largely determined at the transcriptional level through the activity of the alternative sigma factors sigma54 and sigma28. Here, we report that C. jejuni flagellin levels are also controlled at the post-transcriptional level via the thus far poorly-characterized flagellar assembly factor FliW. Analysis of flagellin synthesis in C. jejuni 81116 and a ΔfliW knock-out mutant showed reduced flagellin protein levels in the mutant strain while ectopic expression of FliW resulted in enhanced levels. Real-time RT-PCR revealed relatively minor changes in flaA and flaB mRNA levels for the recombinant and parent strain consistent with post-transcriptional regulation. Purified FliW was found to bind to FlaA and FlaB flagellin as well as to the global post-transcriptional regulator CsrA. Inactivation of CsrA resulted in increased levels of flagellin translation. An in vitro translation assay confirmed the regulatory role of CsrA in flagellin biosynthesis. We propose that competitive reciprocal binding of FliW to flagellins and the RNA binding protein CsrA serves as a feedback mechanism to control the number of cytosolic flagellin copies at the protein level.

First report of fusarium oxysporum f. sp. cubense tropical race 4 causing panama disease in cavendish bananas in Pakistan and Lebanon
Ordoñez, N. ; García-Bastidas, F. ; Laghari, H.B. ; Akkary, M.Y. ; Harfouche, E.N. ; Awar, B.N. al; Kema, G.H.J. - \ 2016
Plant Disease 100 (2016)1. - ISSN 0191-2917 - p. 209 - 209.
Panama disease of banana, caused byFusarium oxysporumf. sp.cubense(Foc), poses a great risk to global banana production. Tropical race 4 (TR4) of Foc, which affects Cavendish bananas as well as many other banana cultivars (Ploetz 2006), was confirmed for the first time outside Southeast Asia in Jordan in 2013 (García-Bastidas et al. 2014). In Pakistan, bananas are produced in the Sindh and Balochistan provinces (91% [31,000 ha] and 9% of the country’s production, respectively). Symptoms ofFusariumwilt, including wilting of leaves and vascular discoloration in rhizomes and pseudostems, were first observed in 2012 in a 2-ha Cavendish plantation in Baoo Pooran (ca. 24°N, 68°E), Sindh Province. By January 2014, approximately 121 ha were affected. In Lebanon, bananas are produced for local consumption and regional export, especially to Syria. Yellowing of leaves and internal vascular discoloration in the pseudostems was first observed in Cavendish plants in October 2013 in the Mansouri and Berghliyeh regions. Thus far, 1 ha has been affected. Infected pseudostem tissue samples from Pakistan and Lebanon were processed for Foc isolation and characterization as described byGarcía-Bastidas et al. (2014). White colonies developed from the surface sterilized (70% ethanol) tissue on Komada’s medium (Leslie and Summerell 2006) and nine single microconidia isolates were generated, four from the Pakistan sample and five from the Lebanon samples and transferred to quarter-strength PDA. All isolates phenotypically resembledF. oxysporum(Leslie and Summerell 2006) and were diagnosed as vegetative compatibility group (VCG) 01213, which was confirmed by PCR, thereby corroborating that VCG01213 only represents TR4 strains (Ploetz 2006). Subsequently, one of the isolates from Pakistan (Pak1.1A) and one isolate each from Mansouri (Leb1.1A) and Berghliyeh (Leb1.2C) in Lebanon were analyzed for pathogenicity. Inoculum production and inoculation were according toDita et al. (2010)by dipping (30 min, 106spores/ml) root-wounded 10-week-old Cavendish cv. Grand Naine plants, which were then placed in sand in 3-liter pots under 28°C, 70% relative humidity, and a 16-h diurnal light periods for 6 weeks. Sets of three plants were each treated with either Pak1.1A, Leb1.1A, Leb1.2C, or TR4 (reference isolate II-5, which was diagnosed as TR4 by PCR and pathogenicity analyses, seeDita et al. 2010). Control sets were each treated with either Foc Race1 (Cruz das Almas, Brazil, seeDita et al. 2010) or water. After 4 weeks, all plants inoculated with the isolates from Pakistan, Lebanon, and TR4 (II-5) produced typical symptoms of Fusarium wilt. After 6 weeks, internal symptoms were recorded and tissue was collected from all plants and plated on Komada’s medium. TR4 was confirmed by PCR from isolates that were recovered from all symptomatic plants. No isolates were recovered from plants infected with Race 1 or the water controls, all of which remained asymptomatic. Thus, we confirm the presence of TR4 in Pakistan and Lebanon and its continued expansion and distribution in Western Asia. Although comparatively limited production areas have been affected to date, increasing damage will undoubtedly occur in these countries in the near future.
Quantification of the smoking-associated cancer risk with rate advancement periods : Meta-analysis of individual participant data from cohorts of the CHANCES consortium
Ordóñez-Mena, José Manuel ; Schöttker, Ben ; Mons, Ute ; Jenab, Mazda ; Freisling, Heinz ; Bueno-de-Mesquita, Bas ; O'Doherty, Mark G. ; Scott, Angela ; Kee, Frank ; Stricker, Bruno H. ; Hofman, Albert ; Keyser, Catherine E. de; Ruiter, Rikje ; Söderberg, Stefan ; Jousilahti, Pekka ; Kuulasmaa, Kari ; Freedman, Neal D. ; Wilsgaard, Tom ; Groot, Lisette C.P.G.M. de; Kampman, Ellen ; Håkansson, Niclas ; Orsini, Nicola ; Wolk, Alicja ; Nilsson, Lena Maria ; Tjønneland, Anne ; Pajak, Andrzej ; Malyutina, Sofia ; Kubínová, Růžena ; Tamosiunas, Abdonas ; Bobak, Martin ; Katsoulis, Michail ; Orfanos, Philippos ; Boffetta, Paolo ; Trichopoulou, Antonia ; Brenner, Hermann - \ 2016
BMC Medicine 14 (2016)1. - ISSN 1741-7015
Cancer - Cohort - Incidence - Meta-analysis - Mortality - Smoking

Background: Smoking is the most important individual risk factor for many cancer sites but its association with breast and prostate cancer is not entirely clear. Rate advancement periods (RAPs) may enhance communication of smoking related risk to the general population. Thus, we estimated RAPs for the association of smoking exposure (smoking status, time since smoking cessation, smoking intensity, and duration) with total and site-specific (lung, breast, colorectal, prostate, gastric, head and neck, and pancreatic) cancer incidence and mortality. Methods: This is a meta-analysis of 19 population-based prospective cohort studies with individual participant data for 897,021 European and American adults. For each cohort we calculated hazard ratios (HRs) for the association of smoking exposure with cancer outcomes using Cox regression adjusted for a common set of the most important potential confounding variables. RAPs (in years) were calculated as the ratio of the logarithms of the HRs for a given smoking exposure variable and age. Meta-analyses were employed to summarize cohort-specific HRs and RAPs. Results: Overall, 140,205 subjects had a first incident cancer, and 53,164 died from cancer, during an average follow-up of 12 years. Current smoking advanced the overall risk of developing and dying from cancer by eight and ten years, respectively, compared with never smokers. The greatest advancements in cancer risk and mortality were seen for lung cancer and the least for breast cancer. Smoking cessation was statistically significantly associated with delays in the risk of cancer development and mortality compared with continued smoking. Conclusions: This investigation shows that smoking, even among older adults, considerably advances, and cessation delays, the risk of developing and dying from cancer. These findings may be helpful in more effectively communicating the harmful effects of smoking and the beneficial effect of smoking cessation.

Pre-diagnostic vitamin D concentrations and cancer risks in older individuals: an analysis of cohorts participating in the CHANCES consortium
Ordonez-Mena, J.M. ; Schöttker, B. ; Fedirko, V. ; Jenab, M. ; Olsen, A. ; Halkjaer, J. ; Kampman, E. ; Groot, C.P.G.M. de; Jansen, E. ; Bueno-de-Mesquita, H.B. ; Peeters, P.H. - \ 2016
European Journal of Epidemiology 31 (2016)3. - ISSN 0393-2990 - p. 311 - 323.
The associations of circulating 25-hydroxyvitamin D [25(OH)D] concentrations with total and site-specific cancer incidence have been examined in several epidemiological studies with overall inconclusive findings. Very little is known about the association of vitamin D with cancer incidence in older populations. We assessed the association of pre-diagnostic serum 25(OH)D levels with incidence of all cancers combined and incidence of lung, colorectal, breast, prostate and lymphoid malignancies among older adults. Pre-diagnostic 25(OH)D concentrations and cancer incidence were available in total for 15,486 older adults (mean age 63, range 50–84 years) participating in two cohort studies: ESTHER (Germany) and TROMSØ (Norway); and a subset of previously published nested-case control data from a another cohort study: EPIC-Elderly (Greece, Denmark, Netherlands, Spain and Sweden) from the CHANCES consortium on health and aging. Cox proportional hazards or logistic regression were used to derive multivariable adjusted hazard and odds ratios, respectively, and their 95 % confidence intervals across 25(OH)D categories. Meta-analyses with random effects models were used to pool study-specific risk estimates. Overall, lower 25(OH)D concentrations were not significantly associated with increased incidence of most of the cancers assessed. However, there was some evidence of increased breast cancer and decreased lymphoma risk with higher 25(OH)D concentrations. Our meta-analyses with individual participant data from three large European population-based cohort studies provide at best limited support for the hypothesis that vitamin D may have a major role in cancer development and prevention among European older adults.
Global effects of soil and climate on leaf photosynthetic traits and rates
Maire, V. ; Wright, I.J. ; Prentice, I.C. ; Batjes, N.H. ; Bhaskar, R. ; Bodegom, P.M. van; Cornwell, W.K. ; Ellsworth, D. ; Niinemets, Ü. ; Ordonez, A. ; Reich, P.B. ; Santiago, L.S. - \ 2015
Global Ecology and Biogeography 24 (2015)6. - ISSN 1466-822X - p. 706 - 717.
Aim
The influence of soil properties on photosynthetic traits in higher plants is poorly quantified in comparison with that of climate. We address this situation by quantifying the unique and joint contributions to global leaf-trait variation from soils and climate.
Location
Terrestrial ecosystems world-wide.
Methods
Using a trait dataset comprising 1509 species from 288 sites, with climate and soil data derived from global datasets, we quantified the effects of 20 soil and 26 climate variables on light-saturated photosynthetic rate (Aarea), stomatal conductance (gs), leaf nitrogen and phosphorus (Narea and Parea) and specific leaf area (SLA) using mixed regression models and multivariate analyses.
Results
Soil variables were stronger predictors of leaf traits than climatic variables, except for SLA. On average, Narea, Parea and Aarea increased and SLA decreased with increasing soil pH and with increasing site aridity. gs declined and Parea increased with soil available P (Pavail). Narea was unrelated to total soil N. Joint effects of soil and climate dominated over their unique effects on Narea and Parea, while unique effects of soils dominated for Aarea and gs. Path analysis indicated that variation in Aarea reflected the combined independent influences of Narea and gs, the former promoted by high pH and aridity and the latter by low Pavail.
Main conclusions
Three environmental variables were key for explaining variation in leaf traits: soil pH and Pavail, and the climatic moisture index (the ratio of precipitation to potential evapotranspiration). Although the reliability of global soil datasets lags behind that of climate datasets, our results nonetheless provide compelling evidence that both can be jointly used in broad-scale analyses, and that effects uniquely attributable to soil properties are important determinants of leaf photosynthetic traits and rates. A significant future challenge is to better disentangle the covarying physiological, ecological and evolutionary mechanisms that underpin trait–environment relationships.
Worse comes to worst: bananas and Panama disease—when plant and pathogen clones meet
Ordonez Roman, N.I. ; Seidl, M.F. ; Waalwijk, C. ; Drenth, A. ; Kilian, A. ; Thomma, B.P.H.J. ; Ploetz, R.C. ; Kema, G.H.J. - \ 2015
PLoS Pathogens 11 (2015)11. - ISSN 1553-7366 - 7
bananas - tropical small fruits - agricultural research - fungal diseases - fusarium oxysporum f.sp. cubense - soil fungi - pathogenicity - food production - genetic diversity - plant protection - bananen - tropisch kleinfruit - landbouwkundig onderzoek - schimmelziekten - bodemschimmels - pathogeniteit - voedselproductie - genetische diversiteit - gewasbescherming
This article deals with: Bananas: their origin and global rollout; genetic diversity of Fusarium oxysporum f.sp. cubense, the causal agent of Panama Disease; Panama Disease: history repeats itself; tropical race 4, a single pathogen clone, threatens global banana production; strategies for sustainable Panama Disease management.
Food security in African dryland: learning from socio-ecological patterns of smallholder agriculture
Sietz, D. ; Ordonez, J.C. ; Kok, M. ; Janssen, P. ; Hilderink, H. ; Dijk, H. - \ 2015
Indirect interactions among tropical tree species through shared rodent seed predators: a novel mechanism of tree species coexistence
Garzon-Lopez, C.X. ; Ballesteros-Mejia, L. ; Ordonez, A. ; Bohlman, S.A. ; Olff, H. ; Jansen, P.A. - \ 2015
Ecology Letters 18 (2015)8. - ISSN 1461-023X - p. 752 - 760.
rain-forest tree - apparent competition - density-dependence - spatial autocorrelation - plant recruitment - dispersal - palm - herbivores - diversity - survival
The coexistence of numerous tree species in tropical forests is commonly explained by negative dependence of recruitment on the conspecific seed and tree density due to specialist natural enemies that attack seeds and seedlings (‘Janzen–Connell’ effects). Less known is whether guilds of shared seed predators can induce a negative dependence of recruitment on the density of different species of the same plant functional group. We studied 54 plots in tropical forest on Barro Colorado Island, Panama, with contrasting mature tree densities of three coexisting large seeded tree species with shared seed predators. Levels of seed predation were far better explained by incorporating seed densities of all three focal species than by conspecific seed density alone. Both positive and negative density dependencies were observed for different species combinations. Thus, indirect interactions via shared seed predators can either promote or reduce the coexistence of different plant functional groups in tropical forest.
Farmers' vulnerability in African drylands, a quantitative and spatially-explicit typology based on clustering
Sietz, D. ; Ordonez, J.C. ; Kok, M. ; Janssen, P. ; Hilderink, H. ; Lüdeke, M. ; Walther, C. ; Sterzel, T. ; Dijk, H. van - \ 2014
First Report of Fusarium oxysporum f sp cubense Tropical Race 4 associated with Panama Disease of banana outside Southeast Asia
Garcia-Bastidas, F. ; Ordonez, N. ; Konkol, J. ; Al-Quasim, M. ; Naser, Z. ; Abdelwali, M. ; Salem, N.M. ; Waalwijk, C. ; Ploetz, R.C. ; Kema, G.H.J. - \ 2014
Plant Disease 98 (2014)5. - ISSN 0191-2917 - p. 694 - 694.
graminicola - maize - wilt
Constraints and opportunities for tree diversity management along the forest transition curve to achieve multifunctional agriculture
Ordonez, J.C. ; Luedeling, E. ; Kindt, R. ; Tata, H.L. ; Harja, D. ; Jamnadass, R. ; Noordwijk, M. van - \ 2014
Current Opinion in Environmental Sustainability 6 (2014). - ISSN 1877-3435 - p. 54 - 60.
ecosystem services - functional diversity - biodiversity - agroforestry - tropics - systems
On-farm tree diversity patterns result from a social-ecological process shaped by different actors. Farmer preferences, tree-site matching, seed dispersal, tree domestication and delivery via nurseries all play important roles in forming these patterns. As part of a wider interest in tree cover transition curves that link agroforestation stages of landscapes to a preceding deforestation process, we here focus on ‘tree diversity transition curves’ i. as a conceptual framework to understand current processes and how shifts in drivers affect tree diversity and ii. to help identify constraints and opportunities for interventions. We provide some examples of current research efforts and make suggestions for databases and analyzes that are required to improve our understanding of tree diversity transitions. We explore drivers, consequences and entry points for tree diversity management to achieve multifunctional agriculture.
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