Identification of a QTL on chromosome 7AS for sodium exclusion in bread wheat

Tese de doutoramento em Engenharia Física (Instrumentação), apresentada à Faculdade de Ciências e Tecnologia da Universidade de CoimbraO número de ciclotrões com capacidade para acelerar protões até cerca de 20 MeV tem vindo a aumentar em todo o mundo. Apesar de o objectivo principal das instalaçõoes que contêm estas máquinas ser a produção de radionuclídeos para tomografia por emissão de positrões (PET, do inglês positron emission tomography), algumas dessas instalações estão equipadas com várias linhas de feixe que podem ser adaptadas para investigação científica. Por exemplo, radiobiologia, radiofisiolgia e outros estudos de dosimetria podem ser realizados utilizando uma destas linhas de feixe devidamente adaptada para o efeito. Neste trabalho, uma das linhas de feixe do ciclotrão PET da Universidade de Coimbra foi complementada e instrumentada por forma a possibilitar a irradiação de um arranjo experimental com um feixe de protões de elevada qualidade. Esta nova linha de feixe foi construída de raíz e sem causar qualquer interferência com as demais linhas do ciclotrão, dedicadas à produção de radionuclídeos. São apresentados resultados tanto experimentais como de simulação, estes últimos obtidos através dos pacotes de simulação SRIM/TRIM e Geant4, tendo como objectivo a medição do pico de Bragg depositado pelo feixe de protões do ciclotrão PET, com uma energia nominal de 18 MeV. Utilizando um bloco de plástico cintilador e uma câmara fotográfica com ligação à internet da marca D-link foi possível medir tanto o alcance como a largura do feixe de protões com uma resolução espacial inferior a 0,1 mm. Os alcances do feixe medidos após este passar pelo meio de um tubo de alumínio com vácuo com 40 cm de comprimento e um segundo tubo com 2,4 m de comprimento permitiram confirmar que a energia efectiva do feixe é de 18 MeV. Mediu-se também o pico de Bragg utilizando um alvo constituído por várias folhas de alumínio intercaladas com lâminas de polietileno. O sinal de corrente foi recolhido das várias folhas de alumínio através de amplificadores de transimpedância fabricados no âmbito desta tese. Verificou-se que o pico de Bragg assim medido é consistente com simulações realizadas utilizando o pacote SRIM/TRIM. Após a instalação da linha de feixe no perímetro exterior do ciclotrão, esta foi caracterizada, calibrada e validada. Para tal, o sinal induzido pela passagem do feixe por uma folha de alumínio com 20 μm de espessura é lido através do amplificador de transimpedância mencionado. Este sinal amplificado providencia informação de dose em tempo real através de um programa desenvolvido em C/C++. Para além da dose, as principais variáveis de monitorização que este programa providencia incluem a corrente do feixe, a carga integrada em conjunto com a taxa de dose. Deste modo a dose e a corrente integrada (carga total) entregue até um dado instante na montagem experimental pode ser controlada por meio de um obturador controlado por computador. Feixes de protões com correntes tão baixas como 10 pA podem deste modo ser aferidas. A folha de alumínio foi escolhida por ser resistente à radiação, possuir baixa densidade e baixa probabilidade de radioactividade induzida pelo feixe e, finalmente, por representar um custo negligenciável. Junta-se a estas vantagens o facto de o método potenciar o cálculo da dose entregue a um alvo durante uma irradiação, com uma perda mínima da energia do feixe de protões, e com dispersão igualmente mínima. Resultados experimentais e simulações com o Geant4 são apresentados que revelam a aplicação, pela primeira vez, de um feixe de 18 MeV proveniente de um ciclotrão para irradiação de uma região seleccionada de um alvo. Fazendo uso do sistema de dosimetria apresentado no parágrafo anterior foi possível irradiar de modo homogéneo uma região circular com 18 mm de diâmetro. Torna-se assim possível irradiar culturas celulares localizadas em placas multi-poços com um diâmetro por poço de 16 mm, como é usual em experiências de radiobiologia. Verificou-se que o controlo do campo magnético aplicado dentro do ciclotrão é crucial para se obter uma irradiação uniforme em todo o campo do alvo. Para tal, efetua-se antes de cada irradiação e com o obturador fechado, um varrimento à corrente que gera o campo magnético dentro do ciclotrão, medindo-se um perfil quase gaussiano e tomando-se o seu valor central para se obter uma irradiação homogénea. As taxas de dose no alvo (entre 500 mGy/s e 5 mGy/s) são obtidas através de um disco em rotação posicionado na trajectória do feixe. O disco, com 150 mm de raio e uma fenda de 0,5 mm na sua extermidade, permite reduzir a taxa de dose por um factor de 5×10−4. Finalmente, vários filmes do tipo Gafchromic EBT2 foram expostos a diferente valores de dose por forma a validar toda a instalação para irradiação de um alvo com feixes de protões. Para tal validação fez-se uso do sistema de dosimetria em filme 2D do Serviço de Radioterapia do Centro Hospitalar Universitário de Coimbra. A dose absoluta nos filmes irradiados com protões foi verificada neste sistema e apresentou uma precisão melhor que 2%.The number of cyclotrons capable of accelerating protons to about 20MeV is increasing throughout the world. Originally aiming at the production of positron emission tomography (PET) radionuclides, some of these facilities are equipped with several beamlines suitable for scientific research. Radiobiology, radiophysiology, and other dosimetric studies can be performed using these beamlines. In this work, a PET cyclotron was fitted with a long beam transport line to irradiate with a good quality proton beam experimental setups. The beamline was configured as a natural extension of one of the cyclotron beam ports, while keeping available the other beam ports for PET radionuclides production. Experimental results are reported, together with SRIM/TRIM and Geant4 simulations, which aim at measuring the Bragg peak of the 18 -MeV proton beam from the PET cyclotron. By using a piece of plastic scintillator and a D-link Ethernet-based camera, the proton beam range and width were measured with a spatial resolution of 0.1mm. The ranges of the proton beam in the plastic scintillator were used to assess its energy after trespassing one or two Havar R windows and either a 40-cm-long or a 2.4-m-long aluminum pipe. The initial energy of the proton beam from the PET cyclotron was found to be 18 MeV. Additionally, the Bragg peak of the protons from the PET cyclotron was assessed using a stacked target consisting of several aluminum foils interleaved with polyethylene sheets, readout by in-house made transimpedance electronics. The measured Bragg peak is consistent with simulations performed using the SRIM/TRIM simulation toolkit. An out-of-yoke irradiation setup using the accelerated proton beam coming from the PET cyclotron was developed, characterized, calibrated, and validated. A 20-μm-thick aluminum transmission foil is readout by in-house made transimpedance electronics, providing online dose information via a C/C++ program. xvii Overview The main monitoring variables include beam current, integrated charge together with dose rate. The beam monitor is able to readout and deliver these variables in real-time. Hence the dose and integrated current (total charge) delivered upto a given instant to an experimental setup may be controlled via a computercontrolled shutter that was installed in the beam path. Proton beam currents down to 10 pA can be assessed using the thin aluminum foil. The aluminum was chosen for this task because it is radiation hard, it has low density and low radiation activity, and finally because it is easily available at negligible cost. In addition, this method allows for calculating the dose delivered to a target during an irradiation with high efficiency, and with minimal proton energy loss and scattering. Experimental results and Geant4 simulations are reported, which aim at using for the first time the 18 -MeV proton beam from a PET cyclotron to irradiate a selected region of a target using the developed dosimetry system. By using this system, a homogeneous beam spot on target with a diameter of 18mm can be controlled. This allows controlled irradiation of cell cultures located in typical biological multi-well dishes with diameters of 16mm each. It was found that the control of the magnetic field applied inside the cyclotron plays a major role for achieving said homogeneity. For that, scanning the magnet current and measuring the corresponding dose rate reveals a quasi-Gaussian shaped curve that must be known before any irradiation procedure (the final shutter is closed during such measurements). The optimum magnet current is taken from the center of the Gaussian-shaped curve, hence producing a homogenous dose on target. The measured dose rate on target ranges from 500mGy/s down to 5mGy/s. This is achieved with a 150mm radius rotating disk with a slit of 0.5mm width, that decreases target dose rates by a factor of 5 × 10−4. Several Gafchromic R EBT2 films were exposed to different values of dose for validating the developed irradiation setup using the 2D film dosimetry system of the Department of Radiotherapy of Coimbra University Hospital Center. The absolute dose in the irradiated films were assessed with a precision better than 2%. It is planned, in the near future, to irradiate small animals, cell cultures, or other materials or samples

The elevated Curie temperature and half-metallicity in the ferromagnetic semiconductor Lax_{x}Eu1−x_{1-x}O

Here we study the effect of La doping in EuO thin films using SQUID magnetometry, muon spin rotation ($\mu$SR), polarized neutron reflectivity (PNR), and density functional theory (DFT). The $\mu$SR data shows that the La$_{0.15}$Eu$_{0.85}$O is homogeneously magnetically ordered up to its elevated $T_{\rm C}$. It is concluded that bound magnetic polaron behavior does not explain the increase in $T_{\rm C}$ and an RKKY-like interaction is consistent with the $\mu$SR data. The estimation of the magnetic moment by DFT simulations concurs with the results obtained by PNR, showing a reduction of the magnetic moment per La$_{x}$Eu$_{1-x}$O for increasing lanthanum doping. This reduction of the magnetic moment is explained by the reduction of the number of Eu-4$f$ electrons present in all the magnetic interactions in EuO films. Finally, we show that an upwards shift of the Fermi energy with La or Gd doping gives rise to half-metallicity for doping levels as high as 3.2 %.Comment: 7 pages, 11 figure

Physical mapping of chromosomes 3HS and 3DS

Relatório de estágio do mestrado em Ensino da Educação Física nos Ensinos Básico e Secundário, apresentado à Faculdade de Ciências do Desporto e Educação Física da Universidade de CoimbraO presente documento divide-se em duas partes: a reflexão dos aspetos relacionados com o estágio pedagógico e o desenvolvimento do tema-problema. Numa primeira fase será dado enfoque à prática da docência, desenvolvida na escola E.B.2,3 Dr. Daniel de Matos. Serão apresentadas as expectativas iniciais em relação à prática, serão apresentadas e justificadas as opções metodológicas tomadas ao longo do estágio, serão relatadas as atividades desenvolvidas durante o estágio e será realçada a componente ética e profissional da profissão. De seguida será realizada uma justificação das opções tomadas. Para finalizar a primeira parte do presente trabalho será feita uma análise reflexiva sobre a prática pedagógica. Na segunda parte temos o tema-problema e seu desenvolvimento, num documento que se pretende orientador da prática docente e auxiliar de como resolver comportamentos de desvio da tarefa por parte dos alunos. Servirá também para analisar e mostrar conclusões sobre o problema que a escola atual, enquanto organização enfrenta, a indisciplina. Será efetuada uma pequena investigação, em que o objetivo é analisar a perceção dos docentes de uma escola pública sobre a gravidade dos comportamentos de indisciplina praticados. O objetivo é chegar a alguma conclusão que possa ajudar/beneficiar os professores da escola na procura de estratégias e metodologias que possam minimizar o impacto deste tipo de comportamentos no normal funcionamento da aula. This document is divided into two parts: a reflection of aspects related to teaching practice and development of the “theme-issue”. Initially focus will be given to the practice of teaching, developed in E.B.2, 3 Dr. Daniel de Matos school. Initial expectations will be presented, as well as the methodological choices made along the stage and its reasons. The activities made during the internship will be reported and I will emphasize ethics and professional component of the teacher’s profession. Then I will do a justification of the choices made. To finish the first part of this work I will make a reflective analysis of teaching practice. In the second part we have the “theme-issue” and its development, a document intended to be the guiding teaching practice and assist in solving the task behaviors of misuse by students. Will also serve to analyze and display conclusions about the problem that the current school, as an organization, faces, the indiscipline. Will be performed a little investigation, in which the objective is to analyze the perceptions of teachers in a public school on the severity of disruptive behaviors committed. The goal is to achieve some conclusion that can help / benefit school teachers in finding strategies and methodologies that can minimize the impact of such behaviors on normal class

Evaluating biases in filter-based aerosol absorption measurements using photoacoustic spectroscopy

This is the final version. Available from Copernicus Publications via the DOI in this record.Biases in absorption coefficients measured using a filter-based absorption photometer (Tricolor Absorption Photometer, or TAP) at wavelengths of 467, 528 and 652 nm are evaluated by comparing to measurements made using photoacoustic spectroscopy (PAS). We report comparisons for ambient sampling covering a range of aerosol types including urban, fresh biomass burning and aged biomass burning. Data are also used to evaluate the performance of three different TAP correction schemes. We found that photoacoustic and filter-based measurements were well correlated, but filter-based measurements generally overestimated absorption by up to 45 %. Biases varied with wavelength and depended on the correction scheme applied. Optimal agreement to PAS data was achieved by processing the filterbased measurements using the recently developed correction scheme of Müller et al. (2014), which consistently reduced biases to 0 %–18% at all wavelengths. The biases were found to be a function of the ratio of organic aerosol mass to light-absorbing carbon mass, although applying the Müller et al. (2014) correction scheme to filter-based absorption measurements reduced the biases and the strength of this correlation significantly. Filter-based absorption measurement biases led to aerosol single-scattering albedos that were biased low by values in the range 0.00–0.07 and absorption Ångström exponents (AAEs) that were in error by (0.03–0.54). The discrepancy between the filter-based and PAS absorption measurements is lower than reported in some earlier studies and points to a strong dependence of filterbased measurement accuracy on aerosol source type.Natural Environment Research CouncilNatural Environment Research Council/Met OfficeResearch Council of Norway (ACBC and NetBC grants)Royal Society of Chemistry (Analytical Chemistry Trust Fund, Tom West Fellowship

Molecular interaction of the gamma-clade homeodomain-leucine zipper class I transcription factors during the wheat response to water deficit

The ᵧ-clade of class I homeodomain-leucine zipper (HD-Zip I) transcription factors (TFs) constitute members which play a role in adapting plant growth to conditions of water deficit. Given the importance of wheat (Triticum aestivum L.) as a global food crop and the impact of water deficit upon grain yield, we focused on functional aspects of wheat drought responsive HD-Zip I TFs. While the wheat ᵧ-clade HD-Zip I TFs share significant sequence similarities with homologous genes from other plants, the clade-specific features in transcriptional response to abiotic stress were detected. We demonstrate that wheat TaHDZipI- 3, TaHDZipI-4, and TaHDZipI-5 genes respond differentially to a variety of abiotic stresses, and that proteins encoded by these genes exhibit pronounced differences in oligomerisation, strength of DNA binding, and trans-activation of an artificial promoter. Three-dimensional molecular modelling of the protein-DNA interface was conducted to address the ambiguity at the central nucleotide in the pseudo-palindromic cis-element CAATNATTG that is recognised by all three HD-Zip I proteins. The coexpression of these genes in the same plant tissues together with the ability of HD-Zip I TFs of the ᵧ -clade to heterodimerise suggests a role in the regulatory mechanisms of HD-Zip I dependent transcription. Our findings highlight the complexity of TF networks involved in plant responses to water deficit. A better understanding of the molecular complexity at the protein level during crop responses to drought will enable adoption of efficient strategies for production of cereal plants with enhanced drought tolerance.John C. Harris, Pradeep Sornaraj, Mathew Taylor, Natalia Bazanova, Ute Baumann, Ben Lovell, Peter Langridge, Sergiy Lopato, Maria Hrmov

Quantitative trait loci for yield and grain plumpness relative to maturity in three populations of barley (Hordeum vulgare L.) grown in a low rain-fall environment

Identifying yield and grain plumpness QTL that are independent of developmental variation or phenology is of paramount importance for developing widely adapted and stable varieties through the application of marker assisted selection. The current study was designed to dissect the genetic basis of yield performance and grain plumpness in southern Australia using three doubled haploid (DH) populations developed from crosses between adapted parents that are similar in maturity and overall plant development. Three interconnected genetic populations, Commander x Fleet (CF), Commander x WI4304 (CW), and Fleet x WI4304 (FW) developed from crossing of Australian elite barley genotypes, were used to map QTL controlling yield and grain plumpness. QTL for grain plumpness and yield were analysed using genetic linkage maps made of genotyping-by-sequencing markers and major phenology genes, and field trials at three drought prone environments for two growing seasons. Seventeen QTL were detected for grain plumpness. Eighteen yield QTL explaining from 1.2% to 25.0% of the phenotypic variation were found across populations and environments. Significant QTL x environment interaction was observed for all grain plumpness and yield QTL, except QPlum.FW-4H.1 and QYld.FW-2H.1. Unlike previous yield QTL studies in barley, none of the major developmental genes, including Ppd-H1, Vrn-H1, Vrn-H2 and Vrn-H3, that drive barley adaption significantly affected grain plumpness and yield here. Twenty-two QTL controlled yield or grain plumpness independently of known maturity QTL or genes. Adjustment for maturity effects through co-variance analysis had no major effect on these yield QTL indicating that they control yield per se.Bulti Tesso Obsa, Jason Eglinton, Stewart Coventry, Timothy March, Maxime Guillaume, Thanh Phuoc Le, Matthew Hayden, Peter Langridge, Delphine Fleur