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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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.

Bioinformatic evidence of widespread priming in type I and II CRISPR-Cas systems
Nicholson, Thomas J. ; Jackson, Simon A. ; Croft, Bradley I. ; Staals, Raymond H.J. ; Fineran, Peter C. ; Brown, Chris M. - \ 2018
RNA Biology (2018). - ISSN 1547-6286
adaptation - adaptive immunity - CRISPR-Cas - primed - priming - spacer acquisition

CRISPR-Cas systems provide bacteria and archaea with adaptive immunity against invading genetic elements, such as plasmids, bacteriophages and archaeal viruses. They consist of cas genes and CRISPR loci, which store genetic memories of previously encountered invaders as short sequences termed spacers. Spacers determine the specificity of CRISPR-Cas defence and immunity can be gained or updated by the addition of new spacers into CRISPR loci. There are two main routes to spacer acquisition, which are known as naïve and primed CRISPR adaptation. Naïve CRISPR adaptation involves the de novo formation of immunity, independent of pre-existing spacers. In contrast, primed CRISPR adaptation (priming) uses existing spacers to enhance the acquisition of new spacers. Priming typically results in spacer acquisition from locations near the site of target recognition by the existing (priming) spacer. Primed CRISPR adaptation has been observed in several type I CRISPR-Cas systems and it is potentially widespread. However, experimental evidence is unavailable for some subtypes, and for most systems, priming has only been shown in a small number of hosts. There is also no current evidence of priming by other CRISPR-Cas types. Here, we used a bioinformatic approach to search for evidence of priming in diverse CRISPR-Cas systems. By analysing the clustering of spacers acquired from phages, prophages and archaeal viruses, including strand and directional biases between subsequently acquired spacers, we demonstrate that two patterns of primed CRISPR adaptation dominate in type I systems. In addition, we find evidence of a priming-like pathway in type II CRISPR-Cas systems.

Chimeric O1K foot-and-mouth disease virus with SAT2 outer capsid as an FMD vaccine candidate
Kotecha, Abhay ; Perez-Martin, Eva ; Harvey, Yongjie ; Zhang, Fuquan ; Ilca, Serban L. ; Fry, Elizabeth E. ; Jackson, Ben ; Maree, Francois ; Scott, Katherine ; Hecksel, Corey W. ; Harmsen, Michiel M. ; Mioulet, Valérie ; Wood, Britta ; Juleff, Nick ; Stuart, David I. ; Charleston, Bryan ; Seago, Julian - \ 2018
Scientific Reports 8 (2018)1. - ISSN 2045-2322

Foot-and-mouth disease virus (FMDV) is highly contagious and infects cloven-hoofed domestic livestock leading to foot-and-mouth disease (FMD). FMD outbreaks have severe economic impact due to production losses and associated control measures. FMDV is found as seven distinct serotypes, but there are numerous subtypes within each serotype, and effective vaccines must match the subtypes circulating in the field. In addition, the O and Southern African Territories (SAT) serotypes, are relatively more thermolabile and their viral capsids readily dissociate into non-immunogenic pentameric subunits, which can compromise the effectiveness of FMD vaccines. Here we report the construction of a chimeric clone between the SAT2 and O serotypes, designed to have SAT2 antigenicity. Characterisation of the chimeric virus showed growth kinetics equal to that of the wild type SAT2 virus with better thermostability, attributable to changes in the VP4 structural protein. Sequence and structural analyses confirmed that no changes from SAT2 were present elsewhere in the capsid as a consequence of the VP4 changes. Following exposure to an elevated temperature the thermostable SAT2-O1K chimera induced higher neutralizing-antibody titres in comparison to wild type SAT2 virus.

Report of the Working Group on Marine Benthal and Renewable Energy Developments (WGMBRED) : 6-9 March 2018, Galway, Ireland
Dannheim, Jennifer ; Gill, Andrew B. ; Boon, Arjen ; Brzana, Radoslaw ; Coolen, J.W.P. ; Dauvin, Jean-Claude ; Degraer, Steven ; Jackson, Angus ; Janas, Urszula ; Mesel, I.G. de; O'Beirn, Francis ; Pezy, Jean-Philippe ; Raoux, Aurore ; Sheehan, Emma ; Vanaverbeke, Jan - \ 2018
International Council for the Exploration of the Sea (ICES WGMBRED Report 2018/HAPISG:02) - 68 p.
Quantifying branch architecture of tropical trees using terrestrial LiDAR and 3D modelling
Lau, Alvaro ; Bentley, Lisa Patrick ; Martius, Christopher ; Shenkin, Alexander ; Bartholomeus, Harm ; Raumonen, Pasi ; Malhi, Yadvinder ; Jackson, Tobias ; Herold, Martin - \ 2018
Trees-Structure and Function 32 (2018)5. - ISSN 0931-1890 - p. 1219 - 1231.
Tree architecture is the three-dimensional arrangement of above ground parts of a tree. Ecologists hypothesize that the topology of tree branches represents optimized adaptations to tree’s environment. Thus, an accurate description of tree architecture leads to a better understanding of how form is driven by function. Terrestrial laser scanning (TLS) has demonstrated its potential to characterize woody tree structure. However, most current TLS methods do not describe tree architecture. Here, we examined nine trees from a Guyanese tropical rainforest to evaluate the utility of TLS for measuring tree architecture. First, we scanned the trees and extracted individual tree point clouds. TreeQSM was used to reconstruct woody structure through 3D quantitative structure models (QSMs). From these QSMs, we calculated: (1) length and diameter of branches > 10 cm diameter, (2) branching order and (3) tree volume. To validate our method, we destructively harvested the trees and manually measured all branches over 10 cm (279). TreeQSM found and reconstructed 95% of the branches thicker than 30 cm. Comparing field and QSM data, QSM overestimated branch lengths thicker than 50 cm by 1% and underestimated diameter of branches between 20 and 60 cm by 8%. TreeQSM assigned the correct branching order in 99% of all cases and reconstructed 87% of branch lengths and 97% of tree volume. Although these results are based on nine trees, they validate a method that is an important step forward towards using tree architectural traits based on TLS and open up new possibilities to use QSMs for tree architecture.
Global Carbon Budget 2017
Quéré, Corinne Le; Andrew, Robbie M. ; Friedlingstein, Pierre ; Sitch, Stephen ; Pongratz, Julia ; Manning, Andrew C. ; Ivar Korsbakken, Jan ; Peters, Glen P. ; Canadell, Josep G. ; Jackson, Robert B. ; Boden, Thomas A. ; Tans, Pieter P. ; Andrews, Oliver D. ; Arora, Vivek K. ; Bakker, Dorothee C.E. ; Barbero, Leticia ; Becker, Meike ; Betts, Richard A. ; Bopp, Laurent ; Chevallier, Frédéric ; Chini, Louise P. ; Ciais, Philippe ; Cosca, Catherine E. ; Cross, Jessica ; Currie, Kim ; Gasser, Thomas ; Harris, Ian ; Hauck, Judith ; Haverd, Vanessa ; Houghton, Richard A. ; Hunt, Christopher W. ; Hurtt, George ; Ilyina, Tatiana ; Jain, Atul K. ; Kato, Etsushi ; Kautz, Markus ; Keeling, Ralph F. ; Klein Goldewijk, Kees ; Körtzinger, Arne ; Landschützer, Peter ; Lefèvre, Nathalie ; Lenton, Andrew ; Lienert, Sebastian ; Lima, Ivan ; Lombardozzi, Danica ; Metzl, Nicolas ; Millero, Frank ; Monteiro, Pedro M.S. ; Munro, David R. ; Nabel, Julia E.M.S. ; Nakaoka, Shin Ichiro ; Nojiri, Yukihiro ; Padin, X.A. ; Peregon, Anna ; Pfeil, Benjamin ; Pierrot, Denis ; Poulter, Benjamin ; Rehder, Gregor ; Reimer, Janet ; Rödenbeck, Christian ; Schwinger, Jörg ; Séférian, Roland ; Skjelvan, Ingunn ; Stocker, Benjamin D. ; Tian, Hanqin ; Tilbrook, Bronte ; Tubiello, Francesco N. ; Laan-Luijkx, Ingrid T. van der; Werf, Guido R. van der; Heuven, Steven Van; Viovy, Nicolas ; Vuichard, Nicolas ; Walker, Anthony P. ; Watson, Andrew J. ; Wiltshire, Andrew J. ; Zaehle, Sönke ; Zhu, Dan - \ 2018
Earth System Science Data 10 (2018)1. - ISSN 1866-3508 - p. 405 - 448.
Accurate assessment of anthropogenic carbon dioxide (CO2) emissions and their redistribution among the atmosphere, ocean, and terrestrial biosphere-the "global carbon budget"-is important to better understand the global carbon cycle, support the development of climate policies, and project future climate change. Here we describe data sets and methodology to quantify the five major components of the global carbon budget and their uncertainties. CO2 emissions from fossil fuels and industry (EFF) are based on energy statistics and cement production data, respectively, while emissions from land-use change (ELUC), mainly deforestation, are based on land-cover change data and bookkeeping models. The global atmospheric CO2 concentration is measured directly and its rate of growth (GATM) is computed from the annual changes in concentration. The ocean CO2 sink (SOCEAN) and terrestrial CO2 sink (SLAND) are estimated with global process models constrained by observations. The resulting carbon budget imbalance (BIM), the difference between the estimated total emissions and the estimated changes in the atmosphere, ocean, and terrestrial biosphere, is a measure of imperfect data and understanding of the contemporary carbon cycle. All uncertainties are reported as ±1δ. For the last decade available (2007-2016), EFF was 9.4±0.5 GtC yr-1, ELUC 1.3±0.7 GtC yr-1, GATM 4.7±0.1 GtC yr-1, SOCEAN 2.4±0.5 GtC yr-1, and SLAND 3.0±0.8 GtC yr-1, with a budget imbalance BIM of 0.6 GtC yr-1 indicating overestimated emissions and/or underestimated sinks. For year 2016 alone, the growth in EFF was approximately zero and emissions remained at 9.9±0.5 GtC yr-1. Also for 2016, ELUC was 1.3±0.7 GtC yr-1, GATM was 6.1±0.2 GtC yr-1, SOCEAN was 2.6±0.5 GtC yr-1, and SLAND was 2.7±1.0 GtC yr-1, with a small BIM of-0.3 GtC. GATM continued to be higher in 2016 compared to the past decade (2007-2016), reflecting in part the high fossil emissions and the small SLAND consistent with El Ninõ conditions. The global atmospheric CO2 concentration reached 402.8±0.1 ppm averaged over 2016. For 2017, preliminary data for the first 6-9 months indicate a renewed growth in EFF of C2.0% (range of 0.8 to 3.0 %) based on national emissions projections for China, USA, and India, and projections of gross domestic product (GDP) corrected for recent changes in the carbon intensity of the economy for the rest of the world. This living data update documents changes in the methods and data sets used in this new global carbon budget compared with previous publications of this data set (Le Quéré et al., 2016, 2015b, a, 2014, 2013). All results presented here can be downloaded from https://doi.org/10.18160/GCP-2017 (GCP, 2017).
New perspectives on the ecology of tree structure and tree communities through terrestrial laser scanning
Malhi, Yadvinder ; Jackson, Tobias ; Bentley, Lisa Patrick ; Lau, Alvaro ; Shenkin, Alexander ; Herold, Martin ; Calders, Kim ; Bartholomeus, Harm ; Disney, Mathias I. - \ 2018
Interface Focus 8 (2018)2. - ISSN 2042-8898
Branching - Metabolic scaling theory - Terrestrial laser scanning - Tree architecture - Tree surface area - Wind speed
Terrestrial laser scanning (TLS) opens up the possibility of describing the three-dimensional structures of trees in natural environments with unprecedented detail and accuracy. It is already being extensively applied to describe how ecosystem biomass and structure vary between sites, but can also facilitate major advances in developing and testing mechanistic theories of tree form and forest structure, thereby enabling us to understand why trees and forests have the biomass and three-dimensional structure they do. Here we focus on the ecological challenges and benefits of understanding tree form, and highlight some advances related to capturing and describing tree shape that are becoming possible with the advent of TLS. We present examples of ongoing work that applies, or could potentially apply, new TLS measurements to better understand the constraints on optimization of tree form. Theories of resource distribution networks, such as metabolic scaling theory, can be tested and further refined. TLS can also provide new approaches to the scaling of woody surface area and crown area, and thereby better quantify the metabolism of trees. Finally, we demonstrate how we can develop a more mechanistic understanding of the effects of avoidance of wind risk on tree form and maximum size. Over the next few years, TLS promises to deliver both major empirical and conceptual advances in the quantitative understanding of trees and tree-dominated ecosystems, leading to advances in understanding the ecology of why trees and ecosystems look and grow the way they do.
Contextualising the emergence and impacts of the AIDS epidemic on rural livelihoods and household food security in Masaka, Uganda
Tumwine, Jackson - \ 2018
University. Promotor(en): Cees Leeuwis; Anke Niehof. - Wageningen : Wageningen University - ISBN 9789463432559 - 182

This thesis aims to contribute to current debates on the impact of the AIDS epidemic on the livelihoods and food and nutrition security of rural households in sub-Saharan Africa. Over the last 20 years, numerous studies have been conducted on this subject. Although these studies have generated a relevant line of inquiry that has provided valuable insights into the social and economic impacts of the epidemic, they have tended to extract AIDS from its social, economic, and political context. This has resulted in underexposure of the long-term and diverse patterns and trajectories of the impacts of HIV and AIDS on rural households. This thesis argues that in order to understand the impacts of an epidemic on society, it is necessary to analyse the contextual factors in which an epidemic emerges, spreads, affects society, and either persists, or declines and disappears, as well as the society’s and households’ responses to the epidemic.

The objective of the study was to investigate the contexts (political, economic, cultural, historical and geographical) in which the AIDS epidemic emerged in Uganda in the early 1980s and became a livelihood crisis that caused food and nutrition insecurity. It also sought to understand the ways in which communities and households were affected by the crisis and how they responded to the impacts of the AIDS epidemic over time. The latter was investigated more specifically at the local level of Masaka district. The study utilised the dynamic ecosystem approach developed by Ford (1971) in his work on the ecology of African trypanosomiasis and the work of Stillwaggon (2006) on AIDS and the ecology of poverty. Based on their approaches, four conceptual pillars were formulated that guided the research and analysis: context, diversity, impact, resilience, and their inter­relationships.

The study was structured according to the following research questions: (1) What was the eco­logical context that shaped the AIDS epidemic in Uganda in general and Masaka in particular? (2) What has been the impact of HIV/AIDS on household structure, composition and human capital? (3) What has been the impact of the AIDS epidemic on land ownership, land utilisation and farming practices? (4) What has been the impact of the AIDS epidemic on household food and nutrition security? (5) How have households attempted to cope with the impact of the AIDS epidemic over time? These questions were addressed during the period 2007-2009 in three separate but inter­related stages of data collection. Data was collected using a mixed methods approach. A literature review was done on relevant topics and secondary data were collected. Primary data was gathered through a combination of methods: participant observation, interviews with key informants, a household survey, focus group discussions, and in-depth case studies of selected households. Acknowledging the methodological complexities of determining impacts in a basically cross-sectional study, in the household the survey impact measurement was done by comparing households having members living with HIV and AIDS (AIDS-confirmed households) and households for which this was not the case (non-confirmed households). Additionally, retrospective questioning and documenting historical narratives at the household level were done to capture the historical perspective.

The results show that prior to 1986 Uganda faced a governance crisis and experienced civil and armed conflict. Exacerbated by institutional dysfunctions and environmental deterioration, this crisis caused a decline in the economy, social investments and agricultural production, and an increase of population mobility that led to the expansion of sexual networks. Moreover, it led to the loss of trust in health care institutions and loss of cohesion in the household. The results of this study suggest that the above were accompanied by an ecological crisis resulting in intensification of poverty and migration that increased people’s vulnerability and susceptibility to HIV and AIDS. The results further show that after the country gained relative political stability in the mid-1990s, the context changed; the government restored political stability, and health and other essential infrastructures were put in place. These made it possible to detect HIV/AIDS, provide counselling and treatment of opportunistic infections. Later on antiretroviral (ARV) drugs became available and comprehensive programs for prevention, treatment and care of AIDS could gradually be implemented.

The study yields a mixed picture regarding the demographic impacts of AIDS on the rural households in Masaka. Whereas it is indisputable that AIDS has taken its toll on the households in the study area, the results of this study point to a rather diverse picture. The results show that for all variables analysed in this study to determine the demographic impacts of HIV and AIDS, only household mortality, female headship, in-migration and fostering in of children differed significantly between AIDS-confirmed and non-confirmed households, indicating impacts of the epidemic. The other variables, including household economic status, household dependency ratio and household size, did not show a clear effect of the AIDS epidemic. These results show no evidence of a negative effect of the epidemic on household labour availability. Although it is undeniable that AIDS had caused many deaths before the infected people could start accessing and using antiretroviral treatment (ART), as indicated by significantly higher past household mortality in AIDS-confirmed house­holds, at the time of the study no major demographic impacts of the epidemic were visible at the household level.

Whereas previous studies on HIV and AIDS impacts had predicted and documented that the epidemic would affect household labour, which would result in reduced utilisation of land and affect the farming practices., the results of this study do not show significant differences in agricultural production and the amount of land owned and utilised between AIDS-confirmed and non-confirmed households. The results show that agriculture in the study area has been undergoing several changes, irrespective of household HIV and AIDS status. As the study shows, these changes have been due to a wide range of factors, including pests and diseases, declining soil fertility, falling prices for commercial crops, changes in crop growing and consumption preferences, apart from HIV and AIDS. Another factor that people pointed to in interviews and discussions is climate change, which is affecting the onset and offset of rain periods and causes flooding and drought.

Regarding household food consumption and household food security, this study found no straight­forward relationship with household HIV and AIDS status. Also variables such as household mortality, changes in the area under cultivation, changes in crops and livestock enterprises, and gender of household headship proved to be not significantly related with (self-reported) household food security status. At the same time, the results indicate that household economic status is significantly associated with household food security, which suggests that economically better-off households, apart from owning more land, will often use off-farm income to safeguard their household’s food security. The results from interviews and discussion further show the declining importance of livelihoods solely based on agriculture in rural areas like Masaka, due to the emergence of a vigorous rural off-farm informal economic sector and improved rural infra­structures. These developments enable rural income diversification, in which people living with HIV and AIDS but benefiting from ART can participate as well, and are changing the rural agriculture-based livelihoods. Thus, the results suggest that a wide range of factors other than AIDS influence people’s food and nutrition security. This implies that the impacts of HIV and AIDS on food and nutrition security cannot be addressed in isolation from other factors and drivers affecting the rural live­lihoods and household food security.

The nuanced picture of the impacts of the AIDS epidemic on households in Masaka that this study presents is also evidence of the coping, mitigation and adaptive practices of the affected house­holds, which allowed many of such households to recover from the onslaught of the epidemic. The results from the in-depth household case studies provide a longitudinal picture and highlight the importance of understanding the impacts of the epidemic in the light of the different stages of the household domestic life course, as well as the stage of the epidemic itself and other societal developments like restored political stability and availability of antiretroviral treatment. The results also reveal the importance of the households’ access to and use of different forms of social capital and traditional social support mechanisms for their resilience to AIDS impacts.

The main conclusions about the contextuality of the emergence and course of the AIDS epidemic, the impact of general and location-specific factors other than HIV and AIDS on people’s lives and livelihoods, and the changes in the context that have occurred during the last two decades, indicate the need to move beyond HIV/AIDS-specific policies to broad development approaches, including policies aiming at social protection and addressing social inequalities in society. The need for an integrative approach also applies to agricultural policy and the need to address the challenges that this sector is facing. In doing so, contextual diversity has to be taken into account and local narratives should inform policy and practice. The kind of integrative approach used in this study, which could be referred to as political ecology, has yielded results that underscore the wider implications of the interrelations between HIV and AIDS impacts, rural livelihood, food and nutrition security, societal change and the advance of antiretroviral therapy, in Uganda and elsewhere. It is observed here that to understand and respond effectively to the negative impacts of AIDS and the problem of food and nutrition insecurity, it is necessary to pay attention to the diverse and interconnected causalities and drivers responsible for social change.

Recent progress in understanding climate thresholds : Ice sheets, the Atlantic meridional overturning circulation, tropical forests and responses to ocean acidification
Good, Peter ; Bamber, Jonathan ; Halladay, Kate ; Harper, Anna B. ; Jackson, Laura C. ; Kay, Gillian ; Kruijt, Bart ; Lowe, Jason A. ; Phillips, Oliver L. ; Ridley, Jeff ; Srokosz, Meric ; Turley, Carol ; Williamson, Phillip - \ 2018
Progress in Physical Geography 42 (2018)1. - ISSN 0309-1333 - p. 24 - 60.
Atlantic meridional overturning circulation - climate change - ice sheets - ocean acidification - thresholds - tropical forests
This article reviews recent scientific progress, relating to four major systems that could exhibit threshold behaviour: ice sheets, the Atlantic meridional overturning circulation (AMOC), tropical forests and ecosystem responses to ocean acidification. The focus is on advances since the Intergovernmental Panel on Climate Change Fifth Assessment Report (IPCC AR5). The most significant developments in each component are identified by synthesizing input from multiple experts from each field. For ice sheets, some degree of irreversible loss (timescales of millennia) of part of the West Antarctic Ice Sheet (WAIS) may have already begun, but the rate and eventual magnitude of this irreversible loss is uncertain. The observed AMOC overturning has decreased from 2004–2014, but it is unclear at this stage whether this is forced or is internal variability. New evidence from experimental and natural droughts has given greater confidence that tropical forests are adversely affected by drought. The ecological and socio-economic impacts of ocean acidification are expected to greatly increase over the range from today’s annual value of around 400, up to 650 ppm CO2 in the atmosphere (reached around 2070 under RCP8.5), with the rapid development of aragonite undersaturation at high latitudes affecting calcifying organisms. Tropical coral reefs are vulnerable to the interaction of ocean acidification and temperature rise, and the rapidity of those changes, with severe losses and risks to survival at 2 °C warming above pre-industrial levels. Across the four systems studied, however, quantitative evidence for a difference in risk between 1.5 and 2 °C warming above pre-industrial levels is limited.
The Sphagnome Project : enabling ecological and evolutionary insights through a genus-level sequencing project
Weston, David J. ; Turetsky, Merritt R. ; Johnson, Matthew G. ; Granath, Gustaf ; Lindo, Zoë ; Belyea, Lisa R. ; Rice, Steven K. ; Hanson, David T. ; Engelhardt, Katharina A.M. ; Schmutz, Jeremy ; Dorrepaal, Ellen ; Euskirchen, Eugénie S. ; Stenøien, Hans K. ; Szövényi, Péter ; Jackson, Michelle ; Piatkowski, Bryan T. ; Muchero, Wellington ; Norby, Richard J. ; Kostka, Joel E. ; Glass, Jennifer B. ; Rydin, Håkan ; Limpens, Juul ; Tuittila, Eeva Stiina ; Ullrich, Kristian K. ; Carrell, Alyssa ; Benscoter, Brian W. ; Chen, Jin Gui ; Oke, Tobi A. ; Nilsson, Mats B. ; Ranjan, Priya ; Jacobson, Daniel ; Lilleskov, Erik A. ; Clymo, R.S. ; Shaw, A.J. - \ 2018
New Phytologist 217 (2018)1. - ISSN 0028-646X - p. 16 - 25.
ecological genomics - ecosystem engineering - evolutionary genetics - genome sequencing - niche construction - peatlands - Sphagnome - Sphagnum
Considerable progress has been made in ecological and evolutionary genetics with studies demonstrating how genes underlying plant and microbial traits can influence adaptation and even ‘extend’ to influence community structure and ecosystem level processes. Progress in this area is limited to model systems with deep genetic and genomic resources that often have negligible ecological impact or interest. Thus, important linkages between genetic adaptations and their consequences at organismal and ecological scales are often lacking. Here we introduce the Sphagnome Project, which incorporates genomics into a long-running history of Sphagnum research that has documented unparalleled contributions to peatland ecology, carbon sequestration, biogeochemistry, microbiome research, niche construction, and ecosystem engineering. The Sphagnome Project encompasses a genus-level sequencing effort that represents a new type of model system driven not only by genetic tractability, but by ecologically relevant questions and hypotheses.
Biochemical proxies indicate differences in soil C cycling induced by long-term tillage and residue management in a tropical agroecosystem
Margenot, Andrew J. ; Pulleman, Mirjam M. ; Sommer, Rolf ; Paul, Birthe K. ; Parikh, Sanjai J. ; Jackson, Louise E. ; Fonte, Steven J. - \ 2017
Plant and Soil 420 (2017)1-2. - ISSN 0032-079X - p. 315 - 329.
Conservation agriculture - Enzyme activities - Glucosidase - Kenya - Residue - Soil organic carbon - Tillage

Background & aim: A potential benefit of conservation agriculture (CA) is soil organic carbon (SOC) accrual, yet recent studies indicate limited or no impact of CA on total SOC in tropical agroecosystems. We evaluated biochemical indicators of soil C cycling after 9 years (18 seasons) of contrasting tillage with and without maize residue retention in western Kenya. Methods: Potential activities of C-cycling enzymes (β-glucosidase, GLU; β-galactosidase, GAL; glucosaminidase, GLM; cellobiohydrolase, CEL), permanganate-oxidizable C (POXC), and soil organic matter (SOM) composition (by infrared spectroscopy) were measured. Results: POXC tended to be greater under reduced tillage and residue retention, but did not significantly differ among treatments (≤ 2% of SOC). Despite no significant differences in SOC concentrations or stocks, activities of all 4 C-cycling enzymes responded strongly to tillage, and to a lesser extent to residue management. Activities of GLU, GAL, and GLM were greatest under the combination of reduced tillage and residue retention relative to other treatments. Reduced tillage produced an enrichment in carboxyl C = O (+6%) and decreased polysaccharide C-O (−3.5%) relative to conventional tillage irrespective of residue management. Conclusions: Though enzyme activities and POXC are typically associated with SOC accrual, changes in soil C cycling at this site have not translated into significant differences in SOC after 9 years. Elevated enzyme activities may have offset potential SOC accumulation under CA. However, the ratio of C-cycling enzyme activities to SOC was higher under reduced tillage and residue retention relative to other treatments, indicating that stoichiometric scaling of SOC and enzyme activities does not explain absence of significant differences in SOC among tillage and residue managements. Potential factors that may explain the low SOC accrual rates in this tropical agroecosystem included the low, albeit realistic, levels of residue retention, nutrient limitations, and high temperatures favoring decomposition.

Type I interferon is required for T helper (Th) 2 induction by dendritic cells
Webb, Lauren M. ; Lundie, Rachel J. ; Borger, Jessica G. ; Brown, Sheila L. ; Connor, Lisa M. ; Cartwright, Adam N.R. ; Dougall, Annette M. ; Wilbers, Ruud H.P. ; Cook, Peter C. ; Jackson-Jones, Lucy H. ; Phythian-Adams, Alexander T. ; Johansson, Cecilia ; Davis, Daniel M. ; Dewals, Benjamin G. ; Ronchese, Franca ; Macdonald, Andrew S. - \ 2017
The EMBO Journal 36 (2017)16. - ISSN 0261-4189 - p. 2311 - 2465.
Dendritic cell - Interferon - Priming - Th2
Type 2 inflammation is a defining feature of infection with parasitic worms (helminths), as well as being responsible for widespread suffering in allergies. However, the precise mechanisms involved in T helper (Th) 2 polarization by dendritic cells (DCs) are currently unclear. We have identified a previously unrecognized role for type I IFN (IFN-I) in enabling this process. An IFN-I signature was evident in DCs responding to the helminth Schistosoma mansoni or the allergen house dust mite (HDM). Further, IFN-I signaling was required for optimal DC phenotypic activation in response to helminth antigen (Ag), and efficient migration to, and localization with, T cells in the draining lymph node (dLN). Importantly, DCs generated from Ifnar1-/- mice were incapable of initiating Th2 responses in vivo. These data demonstrate for the first time that the influence of IFN-I is not limited to antiviral or bacterial settings but also has a central role to play in DC initiation of Th2 responses.
Coral reefs in the Anthropocene
Hughes, Terry P. ; Barnes, Michele L. ; Bellwood, David R. ; Cinner, Joshua E. ; Cumming, Graeme S. ; Jackson, Jeremy B.C. ; Kleypas, Joanie ; De Leemput, Ingrid A. Van; Lough, Janice M. ; Morrison, Tiffany H. ; Palumbi, Stephen R. ; Nes, Egbert H. Van; Scheffer, Marten - \ 2017
Nature 546 (2017)7656. - ISSN 0028-0836 - p. 82 - 90.
Coral reefs support immense biodiversity and provide important ecosystem services to many millions of people. Yet reefs are degrading rapidly in response to numerous anthropogenic drivers. In the coming centuries, reefs will run the gauntlet of climate change, and rising temperatures will transform them into new configurations, unlike anything observed previously by humans. Returning reefs to past configurations is no longer an option. Instead, the global challenge is to steer reefs through the Anthropocene era in a way that maintains their biological functions. Successful navigation of this transition will require radical changes in the science, management and governance of coral reefs.
Maximum Plant Uptakes for Water, Nutrients, and Oxygen Are Not Always Met by Irrigation Rate and Distribution in Water-based Cultivation Systems
Blok, Chris ; Jackson, Brian E. ; Guo, Xianfeng ; Visser, Pieter H.B. De; Marcelis, Leo F.M. - \ 2017
Frontiers in Plant Science 8 (2017). - ISSN 1664-462X
Growing on rooting media other than soils in situ -i.e., substrate-based growing- allows for higher yields than soil-based growing as transport rates of water, nutrients, and oxygen in substrate surpass those in soil. Possibly water-based growing allows for even higher yields as transport rates of water and nutrients in water surpass those in substrate, even though the transport of oxygen may be more complex. Transport rates can only limit growth when they are below a rate corresponding to maximum plant uptake. Our first objective was to compare Chrysanthemum growth performance for three water-based growing systems with different irrigation. We compared; multi-point irrigation into a pond (DeepFlow); one-point irrigation resulting in a thin film of running water (NutrientFlow) and multi-point irrigation as droplets through air (Aeroponic). Second objective was to compare press pots as propagation medium with nutrient solution as propagation medium. The comparison included DeepFlow water-rooted cuttings with either the stem 1 cm into the nutrient solution or with the stem 1 cm above the nutrient solution. Measurements included fresh weight, dry weight, length, water supply, nutrient supply, and oxygen levels. To account for differences in radiation sum received, crop performance was evaluated with Radiation Use Efficiency (RUE) expressed as dry weight over sum of Photosynthetically Active Radiation. The reference, DeepFlow with substrate-based propagation, showed the highest RUE, even while the oxygen supply provided by irrigation was potentially growth limiting. DeepFlow with water-based propagation showed 15–17% lower RUEs than the reference. NutrientFlow showed 8% lower RUE than the reference, in combination with potentially limiting irrigation supply of nutrients and oxygen. Aeroponic showed RUE levels similar to the reference and Aeroponic had non-limiting irrigation supply of water, nutrients, and oxygen. Water-based propagation affected the subsequent cultivation in the DeepFlow negatively compared to substrate-based propagation. Water-based propagation resulted in frequent transient discolorations after transplanting in all cultivation systems, indicating a factor, other than irrigation supply of water, nutrients, and oxygen, influencing plant uptake. Plant uptake rates for water, nutrients, and oxygen are offered as a more fundamental way to compare and improve growing systems.
CRISPR-Cas : Adapting to change
Jackson, Simon A. ; McKenzie, Rebecca E. ; Fagerlund, Robert D. ; Kieper, Sebastian N. ; Fineran, Peter C. ; Brouns, Stan J.J. - \ 2017
Science 356 (2017)6333. - ISSN 0036-8075
Bacteria and archaea are engaged in a constant arms race to defend against the ever-present threats of viruses and invasion by mobile genetic elements. The most flexible weapons in the prokaryotic defense arsenal are the CRISPR-Cas adaptive immune systems. These systems are capable of selective identification and neutralization of foreign DNA and/or RNA. CRISPR-Cas systems rely on stored genetic memories to facilitate target recognition. Thus, to keep pace with a changing pool of hostile invaders, the CRISPR memory banks must be regularly updated with new information through a process termed CRISPR adaptation. In this Review, we outline the recent advances in our understanding of the molecular mechanisms governing CRISPR adaptation. Specifically, the conserved protein machinery Cas1-Cas2 is the cornerstone of adaptive immunity in a range of diverse CRISPR-Cas systems.
Ottawa Statement from the Sparking Solutions Summit on Population Health Intervention Research : Déclaration d’Ottawa issue du sommet Provoquer des solutions sur la recherche interventionnelle en santé des populations
Ruggiero, Erica Di; Potvin, Louise ; Allegrante, John P. ; Dawson, Angus ; Verweij, Marcel ; Leeuw, Evelyn De; Dunn, James R. ; Franco, Eduardo ; Frohlich, Katherine L. ; Geneau, Robert ; Jackson, Suzanne ; Kaufman, Jay S. ; Morabia, Alfredo ; Mcleroy, Kenneth R. ; Ridde, Valéry - \ 2016
Canadian Journal of Public Health 107 (2016)6. - ISSN 1920-7476 - p. e492 - e496.
Synthetic biology and the prospects for responsible innovation
Macnaghten, Philip ; Owen, Richard ; Jackson, Roland - \ 2016
Essays in Biochemistry 60 (2016)4. - ISSN 0071-1365 - p. 347 - 355.
In this article we provide a short review of the debate on responsible innovation and its intersection with synthetic biology, focusing on initiatives we have witnessed and been involved with in the UK. First, we describe the ways in which responsibility in science has been reconfigured institutionally, from an internal focus on the provision of objective and reliable knowledge, to a more external view that embraces the ways in which it has an impact on society. Secondly, we introduce a framework for responsible innovation as a (partial) response to this shift, highlighting its constituent dimensions and the capacities and competencies that are needed to put it into practice. Thirdly, we chart the development of social science research on synthetic biology, addressing its evolution from an 'ethical, legal and social implications' (ELSI) frame to a responsible innovation frame. Fourthly, we review findings from UK social science research with the synthetic biology community setting out challenges for productive collaboration. And finally, we conclude with suggestions on the need for changes in institutional governance.
The Politics and Consequences of Virtual Water Export
Vos, J.M.C. ; Boelens, R.A. - \ 2016
In: Eating, Drinking: Surviving / Jackson, Peter, Spiess, Walter E.L., Sultana, Farhana, Springer International Publishing (SpringerBriefs in Global Understanding ) - ISBN 9783319424675 - p. 31 - 41.
Virtual water is the water used or contaminated to produce a good or a service. With the large increase of export of agricultural produce during the last decades the amount of virtual water export has grown as well. Increased water contamination and water extraction for export from relative dry areas affects local ecosystems and communities. Simultaneously, the increased virtual water trade has weakened the local control over water resources by local communities, to the expense of multinational agribusiness and retailer companies. This repatterning of water control is fomented by numerous national governments, and at the same time contested by local communities. Partly as reaction to the critics on water depletion, agribusiness and retailers have created a number of water stewardship standards. Notwithstanding the possibilities for local communities to articulate their demands with these standards, until now most water stewardship standards have had little – or even negative – effects.
Interference-driven spacer acquisition is dominant over naive and primed adaptation in a native CRISPR-Cas system
Staals, Raymond H.J. ; Jackson, Simon A. ; Biswas, Ambarish ; Brouns, Stan J.J. ; Brown, Chris M. ; Fineran, Peter C. - \ 2016
Nature Communications 7 (2016). - ISSN 2041-1723

CRISPR-Cas systems provide bacteria with adaptive immunity against foreign nucleic acids by acquiring short, invader-derived sequences called spacers. Here, we use high-throughput sequencing to analyse millions of spacer acquisition events in wild-type populations of Pectobacterium atrosepticum. Plasmids not previously encountered, or plasmids that had escaped CRISPR-Cas targeting via point mutation, are used to provoke naive or primed spacer acquisition, respectively. The origin, location and order of spacer acquisition show that spacer selection through priming initiates near the site of CRISPR-Cas recognition (the protospacer), but on the displaced strand, and is consistent with 3′-5′ translocation of the Cas1:Cas2-3 acquisition machinery. Newly acquired spacers determine the location and strand specificity of subsequent spacers and demonstrate that interference-driven spacer acquisition ( € targeted acquisition') is a major contributor to adaptation in type I-F CRISPR-Cas systems. Finally, we show that acquisition of self-targeting spacers is occurring at a constant rate in wild-type cells and can be triggered by foreign DNA with similarity to the bacterial chromosome.

The role of digital data entry in participatory environmental monitoring
Brammer, Jeremy R. ; Brunet, Nicolas D. ; Burton, A.C. ; Cuerrier, Alain ; Danielsen, Finn ; Dewan, Kanwaljeet ; Herrmann, Thora Martina ; Jackson, Micha V. ; Kennett, Rod ; Larocque, Guillaume ; Mulrennan, Monica ; Pratihast, Arun Kumar ; Saint-Arnaud, Marie ; Scott, Colin ; Humphries, Murray M. - \ 2016
Conservation Biology 30 (2016)6. - ISSN 0888-8892 - p. 1277 - 1287.
Ciencia ciudadana - Citizen science - Community-based monitoring - Conocimiento ecológico tradicional - Monitoreo basado en comunidades - Monitoreo y manejo participativo - Participación de público en la investigación científica - Participatory monitoring and management - Public participation in scientific research - Traditional ecological knowledge

Many argue that monitoring conducted exclusively by scientists is insufficient to address ongoing environmental challenges. One solution entails the use of mobile digital devices in participatory monitoring (PM) programs. But how digital data entry affects programs with varying levels of stakeholder participation, from nonscientists collecting field data to nonscientists administering every step of a monitoring program, remains unclear. We reviewed the successes, in terms of management interventions and sustainability, of 107 monitoring programs described in the literature (hereafter programs) and compared these with case studies from our PM experiences in Australia, Canada, Ethiopia, Ghana, Greenland, and Vietnam (hereafter cases). Our literature review showed that participatory programs were less likely to use digital devices, and 2 of our 3 more participatory cases were also slow to adopt digital data entry. Programs that were participatory and used digital devices were more likely to report management actions, which was consistent with cases in Ethiopia, Greenland, and Australia. Programs engaging volunteers were more frequently reported as ongoing, but those involving digital data entry were less often sustained when data collectors were volunteers. For the Vietnamese and Canadian cases, sustainability was undermined by a mismatch in stakeholder objectives. In the Ghanaian case, complex field protocols diminished monitoring sustainability. Innovative technologies attract interest, but the foundation of effective participatory adaptive monitoring depends more on collaboratively defined questions, objectives, conceptual models, and monitoring approaches. When this foundation is built through effective partnerships, digital data entry can enable the collection of more data of higher quality. Without this foundation, or when implemented ineffectively or unnecessarily, digital data entry can be an additional expense that distracts from core monitoring objectives and undermines project sustainability. The appropriate role of digital data entry in PM likely depends more on the context in which it is used and less on the technology itself.

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