Some thoughts about food-borne diseases

The food-borne diseases - FBD (defined as any syndrome - signs and symptoms - caused by ingestion of food or foodingredients, spices, beverages or water containing etiologic agents in such quantities that affect consumer health, individually or group of people) constitute a serious global problem in public health.Unhealthy foods ill each year at least two billion people, and can cause death. Although some countries have made greatstrides in controlling, the disease burden associated with food globally that number is growing. Threats of pollutionaffecting the food consumed may come from the places where crops are growing or animals are raised and ascend alongthe chain to the manner in which they are produced, plus the fact many people lack clean water for consumption, whichrepresents a high risk factor for the presentation of gastroenteric diseases

Prediction and analysis of JET fusion performance based on reduced first principle transport models

The design of a Tokamak device is carried out initially with a 0D approach aiming at defining the plasma engineering parameters estimated with the help of empirical scaling laws, and the technological limits of the device components. The assessment of local parameters (1D) is then required to define the optimal plasma performance during the entire time evolution of the discharge. In this contest, the transport of energy and particles in fusion plasmas is one of the main actor in determining the evolution of a plasma scenario both in present experiments and in future reactors. The Joint European Torus (JET) experiment has operated in deuterium (D) and tritium (T) main ion plasma composition in 1997 (DTE1) and in 2021 (DTE2). The most important differences between the two experimental campaigns are related to the plasma facing components, carbon (C) in DTE1 and Be/W in DTE2, the increased additional heating power, and the presence of improved diagnostics, especially at the plasma edge which is determinant in the global plasma performance. After DTE1 the high levels of T retention in the C-wall have been considered unacceptable for a reactor, leading to the substitution of the C-wall with a metallic wall in the design of the International Tokamak Experimental Reactor (ITER). DTE2 campaign at JET aimed at studying D-T plasmas in the closest conditions to ITER operations. Differently from DTE1, the recent campaign focused on the stationarity of the performance and on addressing ITER-relevant aspects such as α-particles physics, plasma wall interactions and plasma heating schemes. In preparation to D-T operations, a wide experimental and modelling activity has been performed at JET in order to optimise the plasma scenarios. The focus of this thesis is the extrapolation in D-T main ion plasma composition of the JET baseline scenario. The latter is a high confinement mode (H-mode) plasma, characterized by the presence of Edge Localized Modes (ELMs), where the confinement relies on high plasma current. In ITER D-T operations, the baseline scenario is envisaged to achieve a gain factor, defined as the ratio between the fusion power and the input power, Q = Pfus/Pin ≈ 10. The objective of the thesis has been achieved through extensive integrated modelling, based on the reduced first principles transport models QuaLiKiz and TGLF employing different assumptions, and in a wide range of plasma operating conditions. QuaLiKiz and TGLF transport models have been validated in reference D plasmas, and their extrapolation capability with different plasma parameters has been tested by performing blind predictions. The results of the predictive modelling have been compared with the experimental data and analysed in order to address the sensitivity of the plasma scenario to the experimental boundary conditions. The QuaLiKiz transport model has also been validated against the experimental results produced at JET in DTE1. Before the start of the DTE2 campaign, an estimate of the particle sources required to sustain a 50-50 D-T baseline plasma has been obtained. This result has provided inputs to the JET control team in the preparation phase of the baseline fuelling scheme. This contribution boosted JET D-T operations without spending experimental time, neutron and T budget. The results of the predictive modelling performed in preparation to DTE2 are presented and discussed. The sensitivity of the predictions to plasma parameters v vi such as current, toroidal magnetic field, pedestal confinement and impurity content are analysed together with the sensitivity to the available amount of auxiliary heating power. The experimental results obtained in DTE2 by the baseline scenario are also presented and discussed. In the last part of this thesis, the implications of the modelling assumptions performed on D pulses will be compared with the assumptions done on D-T discharges with the experimental boundary conditions. The key parameters needed for reliable predictions of future experiments are discussed both in D and D-T main ion plasma composition. The estimate of particle sources obtained before the DTE2 campaign are adjusted to reproduce the experimental conditions, leading to an estimate of the different fuelling channels and an evaluation of the wall sources. The thesis is organised as follows: • In Chapter 1 we introduce fusion as a potential energy source. • In Chapter 2 we describe the Tokamak configuration and the JET experi- mental device, and we present a first comparison between the different D-T experimental campaign, and between the different scenarios prepared for DTE2. • In Chapter 3 we introduce the issue of energy and particle transport in Tokamaks, we present the theoretical background and the state of the art of transport analysis. The models used in this work are presented together with the different assumptions implemented in JINTRAC. • In Chapter 4 we present and discuss the validation of the reduced first principle transport models performed on D pulses. The extrapolations in D-T plasma mixture are presented with their sensitivity to the operating conditions. • In Chapter 5 we present and discuss the baseline results obtained in DTE2. The predictive simulations are improved by adopting the actual boundary conditions of the D-T experiments, and we discuss the impact of the different assumptions on the modelling of D plasmas extrapolated to D-T plasma mixture. We show the limits of predictive simulations in integrated modelling, and we use the predictive simulations to obtain an estimate of the different fuelling sources in the D-T experiments

A study of molecular responses to abiotic and biotic stresses in Arachis

Em seu ambiente natural, as plantas são expostas a uma série de estresses abióticos e bióticos. Entre eles, a seca é um grande obstáculo à agricultura e, em associação com patógenos e pragas, pode causar prejuízos de até US$38 bilhões de 2005 a 2015, e comprometer a segurança alimentar. Com as mudanças climáticas e aquecimento global, esse cenário tende a agravar-se, aumentando a ocorrência de secas, a amplitude da gama de hospedeiros e virulência de agentes patogênicos. O estudo da resposta molecular à estresses individuais em diferentes plantas assim como a resposta a estresses combinados, constitui um grande avanço, para a compreensão de possíveis trade-offs entre tolerância e suscetibilidade à estresses abióticos e bióticos, quanto o desenvolvimento de cultivares mais resistentes. Visando um melhor entendimento da resposta moleculares de plantas, o presente estudo empregou diferentes ferramentas, como genômica comparativa e transcritomas. O uso dessas ferramentas visou a identificação de genes comumente regulados por diferentes estresses. No capítulo I, o transcritoma de quatro diferentes espécies de plantas (Arachis stenosperma, Coffea arabica, Glycine max e Oryza glaberrima) inoculadas com nematoides das galhas (Meloidogyne spp.) foram analisados e combinados com dados de genômica comparativa gerados a partir do proteoma de 22 espécies de plantas. No total, 17 famílias de proteínas ortólogas são comumente reguladas pela inoculação de nematoides das galhas, representando ao todo 364 proteínas. A anotação funcional desses ortogrupos indicou que a maioria dessas proteínas está associada à parede celular, receptores quinases e a estresse, e tendo uma única família de fatores de transcrição representada, ERF a qual desempenha um papel fundamental na resposta de defesa da planta. No Capítulo II, a análise do transcritoma de Arachis stenosperma submetido à combinação de dois estresses, seca e inoculação por nematoides das galhas, foi realizada. Diversos genes de resistência a estresses combinados foram identificados sendo que uma resposta transcricional distinta foi observada quando da imposição de estresses combinados, quando comparada a estresses individuais. Apenas 14 genes foram encontrados em comum entre a seca, inoculação por nematoides e estresses combinados e 209 genes foram exclusivamente regulados no tratamento combinado. Este resultado demonstra que uma reprogramação molecular única é empregada pela planta sob múltiplos estresses, o que não pode ser previsto pela análise de cada estresse aplicado individualmente. A análise de genômica comparativa e a análise de estresse combinado realizadas no presente estudo permitiram a identificação de famílias de genes essenciais à resistência / tolerância de plantas. A família das expansinas, a qual foi modulada durante a seca, infecção por RKN e UV, revelando uma importante família de genes em resposta a múltiplos estresses e em espécies distintas; e um gene de desidrina, cuja superexpressão em Arabidopsis revelou um importante trade-off entre estresses abióticos e bióticos.In their natural environment plants are exposed to a range of abiotic and biotic stresses. Among them, drought is a major constraint to agriculture and, in association with pathogen and pests, can cause losses of up to$38 billion from 2005 to 2015 and compromise food security. With the advent of climate change and global warming, this scenario tends to become worse, with an increase in drought occurrence and pathogen`s host range and virulence. Breeding programs are doing great efforts to find solutions to improve multiple stress resistance in plants, however, the trade-offs between abiotic stress tolerance and biotic stress susceptibility have hardly been investigated. Here, a comparative genomics study was conducted, which has the potential to identify putative evolutionarily conserved genes involved in universal defense mechanisms, to identify genes regulated in common by Meloidogyne spp infection in four plant species (Arachis stenosperma, Coffea arabica, Glycine max, and Oryza glaberrima). In total, 17 orthologs protein families which respond to the inoculation of RKN in the four species, comprising a total of 364 proteins. The functional annotation of these orthogroups indicated that the majority of these genes are associated with the cell wall, receptor kinases and stress related, with the transcription factor ERF playing a pivotal role in these defense responses. A number of multiple-stress resistant genes was identified by analyzing the transcriptome of a resistant wild Arachis species, A. stenosperma, under the combination of RKN and drought imposition. An overall distinct transcriptional response was observed for the combinatory stress imposition when compared to each individual stress, with only 14 genes found in common among drought, nematode infection and combined stresses and 209 exclusively regulated genes within the combined treatment. This result demonstrates that a unique molecular reprogramming is employed by the plant under multiple stresses, which cannot be predicted by the analysis of each individual stress alone. The comparative genomics and the cross-stress analysis conducted in this study enabled the identification of genes families which are essential to plant resistance/tolerance. The gene family of the expansins which was modulated during drought, RKN infection and UV, disclosing an important gene family in response to multiple stresses and across species; and a dehydrin gene, 13 which overexpression in Arabidopsis revealed an important trade-off between abiotic and biotic stresses