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The ability to manipulate ROS metabolism in pepper may affect aphid virulence
No full textMyzus persicae has severe economic impact on pepper (Capsicum) cultivation. Previously, we identified two populations of M. persicae, NL and SW, that were avirulent and virulent, respectively on C. baccatum accession PB2013071. The transcriptomics approach used in the current study, which is the first study to explore the pepper−aphid interaction at the whole genome gene expression level, revealed genes whose expression is differentially regulated in pepper accession PB2013071 upon infestation with these M. persicae populations. The NL population induced ROS production genes, while the SW population induced ROS scavenging genes and repressed ROS production genes. We also found that the SW population can induce the removal of ROS which accumulated in response to preinfestion with the NL population, and that preinfestation with the SW population significantly improved the performance of the NL population. This paper supports the hypothesis that M. persicae can overcome the resistance in accession PB2013071 probably because of its ability to manipulate plant defense response especially the ROS metabolism and such ability may benefit avirulent conspecific aphids.</p
Insect pollination is the weakest link in the production of a hybrid seed crop
No full textEcological intensification of farming proposes that more effective use of ecosystem services can, in part, replace external inputs allowing farmers to maintain high crop yields while reducing adverse effects on the environment. However, uptake of ecological intensification among farmers is currently hampered by a lack of realistic studies on the agronomic benefits of enhancing ecosystem services vis-à-vis the benefits of conventional external inputs. Here, we use a full-factorial field experiment to test the relative and interactive effects of fertilisation, irrigation and pollination on crop yield of three parental crop lines of leek (Allium porrum) hybrid seed production. In a commercial leek seed production field, we assessed the agronomic performance of plants receiving conventional or 50 % reduced external inputs and that were either continuously accessible to pollinators or only 50 % of the time. For all crop lines, we found that reducing insect pollination had at least two times stronger effects on crop yield than similar reductions in fertilisation or irrigation. Surprisingly, reducing fertiliser inputs by half did not negatively affect crop yield (one line) or even increased crop yield (two lines), suggesting that in this system fertiliser is an over-applied agricultural input. Reducing irrigation did not affect crop yield in two lines but reduced crop yield in the third line. However, there were strong indications that this negative effect of reduced irrigation was due to reduced attractiveness for pollinators. Effects of fertilisation, irrigation and pollination on crop yield were additive, with the exception of pollination effects being influenced by fertilisation level in one of the lines. Under real-world conditions, reductions in insect pollination consistently reduced hybrid leek crop yield while reductions in external inputs did not. This suggests that in this cropping system insect pollination is the weakest link in the agricultural production process. Our findings help explain why the relation between agricultural intensification and yield growth disappears with the dependence of crops on insect pollination. For insect-depended crops, protection or promotion of pollinators in agricultural landscapes is essential for maintaining high yields.</p
Structural identifiability of large systems biology models
Get PDFA fundamental principle of systems biology is its perpetual need for new technologies that can solve challenging biological questions. This precept will continue to drive the development of novel analytical tools. The virtuous cycle of biological progress can therefore only exist when experts from different disciplines including biology, chemistry, computer science, engineering, mathematics, and medicine collaborate. General opinion is however that one of the challenges facing the systems biology community is the lag in the development of such technologies. The topic of structural identifiability in particular has been of interest to the systems biology community. This is because researchers in this field often face experimental limitations. These limitations, combined with the fact that systems biology models can contain vast numbers of unknown parameters, necessitate an identifiability analysis. In reality, analysing the structural identifiability of systems biology models, even when they contain only a few states and system parameters, may be challenging. As these models increase in size and complexity, this difficulty is exasperated, and one becomes limited to only a few methods capable of analysing large ordinary differential equation models. In this thesis I study the use of a computationally efficient algorithm, well suited to the analysis of large models, in the model development process. The three related objectives of this thesis are: 1) develop an accurate method to asses the structural identifiability of large possibly nonlinear ordinary differential models, 2) implement thismethod in the preliminary design of experiments, and 3) use the method to address the topic of structural unidentifiability. To improve the method’s accuracy, I systematically study the role of individual factors, such as the number of experimentally measured sensors, on the sharpness of results. Based on the findings, I propose measures that can improve numerical accuracy. To address the second objective, I introduce an iterative identifiability algorithm that can determine minimal sets of outputs that need to be measured to ensure a model’s local structural identifiability. I also illustrate how one could potentially reduce the computational demand of the algorithm, enabling a user to detect minimal output sets of large ordinary differential equation models within minutes. For the last objective, I investigate the role of initial conditions in a model’s structural unidentifiability. I show that the method can detect problematic values for large ordinary differential equation models. I illustrate its role in reinstating the local structural identifiability of a model by identifying problematic initial conditions. I also show that the method can provide theoretical suggestions for the reparameterization of structurally unidentifiable models. The novelty of this work is that the algorithm allows for unknown initial conditions to be parameterised and accordingly, repameterisations requiring the transformation of states, associated with unidentifiable initial conditions, can easily be obtained. The computational efficiency of the method allows for the reparameterisation of large ordinary differential equation models in particular. To conclude, in this thesis I introduce an method that can be used during the model development process in an array of useful applications. These include: 1) determining minimal output sets, 2) reparameterising structurally unidentifiable models and 3) detecting problematic initial conditions. Each of these application can be implemented before any experiments are conducted and can play a potential role in the optimisation of the modelling process
Breeding top genotypes and accelerating response to recurrent selection by selecting parents with greater gametic variance
No full textBecause of variation in linkage phase and heterozygosity among individuals, some individuals produce genetically more variable gametes than others. With the availability of genomic EBVs (GEBVs) or estimates of SNP-effects together with phased genotypes, differences in gametic variability can be quantified by simulating a set of virtual gametes of each selection candidate. Previous results in dairy cattle show that gametic variance can be large. Here, we show that breeders can increase the probability of breeding a top-ranking genotype and response to recurrent selection by selecting parents that produce more variable gametes, using ffiffiffi the index I ¼ GEBV þ p2xpSDgGEBV; where xp is the standardized normal truncation point belonging to selected proportion p, and SDgGEBV is the SD of the GEBV of an individual’s gametes. Benefits of the index were considerably larger in an ongoing selection program with equilibrium genetic parameters than in an initially unselected population. Superiority of the index over selection on GEBV increased strongly with the magnitude of the SDgGEBV; indicating that benefits of the index may vary considerably among populations. Compared to selection on ordinary GEBV, the probability of breeding a top-ranking individual can be increased by ~36%, and response to selection by ~3.6% when selection is strong (P = 0.001) based on values for the Holstein-Friesian dairy cattle population. Two-stage selection, with a preselection on GEBV and a final selection on the index, considerably reduced computational requirements with little loss of benefits. Response to multiple generations of selection and inheritance of the SDgEBV require further study.</p
Dynamic path-dependent landslide susceptibility modelling
No full textThis contribution tests the added value of including landslide path dependency in statistically based landslide susceptibility modelling. A conventional pixel-based landslide susceptibility model was compared with a model that includes landslide path dependency and with a purely path-dependent landslide susceptibility model. To quantify path dependency among landslides, we used a space–time clustering (STC) measure derived from Ripley's space–time K function implemented on a point-based multi-temporal landslide inventory from the Collazzone study area in central Italy. We found that the values of STC obey an exponential-decay curve with a characteristic timescale of 17 years and characteristic spatial scale of 60 m. This exponential space–time decay of the effect of a previous landslide on landslide susceptibility was used as the landslide path-dependency component of susceptibility models. We found that the performance of the conventional landslide susceptibility model improved considerably when adding the effect of landslide path dependency. In fact, even the purely path-dependent landslide susceptibility model turned out to perform better than the conventional landslide susceptibility model. The conventional plus path-dependent and path-dependent landslide susceptibility model and their resulting maps are dynamic and change over time, unlike conventional landslide susceptibility maps
How the neurotoxin β-N-Methylamino-L-Alanine accumulates in bivalves: distribution of the different accumulation fractions among organs
No full textThe environmental neurotoxin β-methylamino-l-alanine (BMAA) may represent a risk for human health. BMAA accumulates in freshwater and marine organisms consumed by humans. However, few data are available about the kinetics of BMAA accumulation and detoxification in exposed organisms, as well as the organ distribution and the fractions in which BMAA is present in tissues (free, soluble bound or precipitated bound cellular fractions). Here, we exposed the bivalve mussel Dreissena polymorpha to 7.5 µg of dissolved BMAA/mussel/3 days for 21 days, followed by 21 days of depuration in clear water. At 1, 3, 8, 14 and 21 days of exposure and depuration, the hemolymph and organs (digestive gland, the gills, the mantle, the gonad and muscles/foot) were sampled. Total BMAA as well as free BMAA, soluble bound and precipitated bound BMAA were quantified by tandem mass spectrometry. Free and soluble bound BMAA spread throughout all tissues from the first day of exposure to the last day of depuration, without a specific target organ. However, precipitated bound BMAA was detected only in muscles and foot from the last day of exposure to day 8 of depuration, at a lower concentration compared to free and soluble bound BMAA. In soft tissues (digestive gland, gonad, gills, mantle and muscles/foot), BMAA mostly accumulated as a free molecule and in the soluble bound fraction, with variations occurring between the two fractions among tissues and over time. The results suggest that the assessment of bivalve contamination by BMAA may require the quantification of total BMAA in whole individuals when possible
On continuities and discontinuities : The making of technology-driven interventions and the encounter with the MasAgro Programme in Mexico
No full textMost of our work and knowledge as researchers in agriculture is taken to farmers in the form of technology-driven interventions. The central assumption behind these projects is that farmers can improve their livelihoods by increasing their crop yields and crop productivity. Over time, due to the criticisms on how these modern technologies failed to include the most marginalised people and the negative environmental impacts of their use, a call for participatory approaches to development, addressing the environmental agenda, human rights and social justice and the role of a socially responsible civil society and industry has emerged. Yet there remains a need for using modern technologies to increase crop productivity to lift farmers out from poverty. For example, the World Bank indicates that to achieve the Sustainable Development goal of “Zero hunger”, the small-holder farmers will play a crucial role by increasing their yield and productivity while also using sustainable food systems. Hence, researchers have a role as key actors in developing modern technologies that fit the new challenges. In Mexico researchers have played a central role in designing of technology-driven interventions that seek to increase agricultural productivity. Researchers have offered silver bullets, i.e. technologies that promise to serve as simple solutions to complex problems, to politicians. Mexican agricultural policy historically has promoted agricultural production based on modern technologies to increase yields through several interventions, from the Mexican Agricultural Programme in the 1940’s to the Sustainable Modernisation of the Traditional Agriculture (MasAgro) Programme launched in 2010. Some authors argue that this model has subsidised inequality because the winners of these policies have historically been the same group of well-endowed farmers. Most of the small farmers, subsistence farmers and landless agricultural labourers have historically been excluded from programmes to engage them as producers. Yet, the effectiveness of these interventions is often unclear, which leads us to wonder why some technologies and paradigms are dominant over others and therefore continue to be promoted and implemented, despite the uncertainty about their effectiveness? and why some other technologies and approaches are discontinued or considered irrelevant in global narrative and agendas? Thus, we need to look at our work critically through the lens of political agronomy to explain how agendas are negotiated and what the underlying assumptions are. My research focus on understanding how mechanisms are shaping processes of continuity and discontinuity in technology-driven interventions like MasAgro Programme in Mexico – reinforcing the prevalence of particular technologies and groups of beneficiaries and excluding others. In doing so, I used the case of MasAgro Programme, led by the International Maize and Wheat Improvement Centre and the Mexican Ministry of Agriculture and Rural Development, to analyse processes of processes of continuity and discontinuity and social inclusion and exclusion. My first case study (Chapter 2) is contextual and focuses on the social life of MasAgro Programme in Mexico. Here I explore the mechanisms that allowed the emergence of MasAgro Programme and how it gave continuity to the agricultural production paradigm as MasAgro Programme was initially portrayed as a second Green Revolution. MasAgro Programme found continuity over three different government periods, which is unusual for programmes in Mexico depending on government funds. Thus, I investigate how MasAgro Programme and other technologies and linked interventions encountered causing continuity of some of their processes but discontinuity of others. In the end, I show how there is an interdependence among actors, specifically among the government and researchers and how they converge at one point to negotiate agendas causing processes of continuity, discontinuity, social inclusion and exclusion. The second case study (Chapter 3) focuses on Conservation Agriculture (CA) practices in the region of Bajío Mexico. I study what mechanisms enabled CA technology to find continuity through several interventions for a period of 30 years. At the same time, I look at how processes of discontinuity interacted with that apparent continuity in CA technology research. I apply the boundary concept to analyse who contributed to the making of those CA-like technology interventions, what their interests and agendas were and therefore who was included and excluded. I show how research and politics are mutually dependent and how they generate a discontinuity of project interventions which, paradoxically, represent a continuity of agendas and research processes. In my third case study (Chapter 4), I explore how native maize cultivation continues to persist in Yavesía, an indigenous village in Oaxaca, despite agricultural policy in Mexico having been designed to force discontinuity on native maize cultivation. I situate this case study in the broader debate of agricultural production and traditionality paradigms for maize cultivation in Mexico. I show how, for the farmers of Yavesía, the encounter with MasAgro Programme is one of many that represent opportunities to give continuity to their ‘comunalidad’ linked to maize cultivation” as a mode of making a living. With this chapter I also show some of the intangible meanings of maize cultivation that cannot be captured in a productivity oriented rational but at the same time how the meaning of traditionality changes over time around maize cultivation in an attempt by farmers to adapt to a changing world. The fourth case study (Chapter 5) focuses on a mobile phone-based SMS system called MasAgro Mobile (MVV), which provides farmers with farming information to empower them in their practice as farmers. MVV found continuity over different government periods as did the larger MasAgro Programme, but also by different institutions. Thus, I explore how it found continuity but also how learning was driven by processes of continuity and discontinuity and what mechanisms allowed or prevented that lessons were learned. With this case study I show the political dimensions shaping how learning occurs and why some lessons are taken on board whereas others do not. Finally, in the discussion (Chapter 6), I summarise the answer to my research question on how processes of continuity and discontinuity take place based on my empirical cases and lead to processes of inclusion and exclusion. I also present a final reflection on the practical implications of my findings and how to move forward
Phylogenomics changes our understanding about earwig evolution
No full textEarwigs are one of the comparatively species‐poor insect orders. Although various aspects of the phylogeny of this lineage are poorly understood, before the present study, there was a general consensus that Dermaptera comprises two major lineages: the paraphyletic Protodermaptera or ‘lower earwigs’ and the monophyletic Epidermaptera or ‘higher earwigs’, which are nested within the former. Our phylogenomic study based on the analysis of 3247 nuclear single‐copy genes reverses these relationships by placing monophyletic Protodermaptera within paraphyletic Epidermaptera. This phylogenetic reversal among the major earwig lineages is not contradicted by morphological arguments but results in far‐reaching reinterpretations of the dermapteran ground plan. Within Dermaptera, Apachyidae form the sister group to the remaining earwigs which might imply that social behaviour is not part of the earwig ground plan. Our results corroborate the monophyly of Eudermaptera within Epidermaptera and the paraphyly of several traditional families. The monophyly of Protodermaptera is supported by molecular and morphological evidence, although the exact position of Karschiellidae which were not included in the molecular dataset cannot be determined.<br/
N2Africa Podcaster no. 58 : Putting nitrogen fixation to work for smallholder farmers in Africa: January 2020
No full textPhD Student specia
When climate change is not blamed: the politics of disaster attribution in international perspective
No full textAnalyzing the politics and policy implications in Brazil of attributing extreme weather events to climate change, we argue for greater place-based sensitivity in recommendations for how to frame extreme weather events relative to climate change. Identifying geographical limits of current recommendations to emphasize the climate role in such events, we explore Brazilian framings of the two tragic national disasters, as apparent in newspaper coverage of climate change. We find that a variety of contextual factors compel environmental leaders and scientists in Brazil to avoid and discourage highlighting the role of climate change in national extreme events. Against analysts’ general deficit-finding assumptions, we argue that the Brazilian framing tendency reflects sound strategic, socio-environmental reasoning, and discuss circumstances in which attributing such events to climate change—and, by extension, attribution science—can be ineffective for policy action on climate change and other socio-environmental issues in need of public pressure and preventive action. The case study has implications beyond Brazil by begging greater attention to policies and politics in particular places before assuming that attribution science and discursive emphasis on the climate role in extreme events are the most strategic means of achieving climate mitigation and disaster preparedness. Factors at play in Brazil might also structure extreme events attribution politics in other countries, not least some other countries of the global South.</p