Imputação de dados em experimentos multiambientais: novos algoritmos utilizando a decomposição por valores singulares

As análises biplot que utilizam os modelos de efeitos principais aditivos com inter- ação multiplicativa (AMMI) requerem matrizes de dados completas, mas, frequentemente os ensaios multiambientais apresentam dados faltantes. Nesta tese são propostas novas metodologias de imputação simples e múltipla que podem ser usadas para analisar da- dos desbalanceados em experimentos com interação genótipo por ambiente (G×E). A primeira, é uma nova extensão do método de validação cruzada por autovetor (Bro et al, 2008). A segunda, corresponde a um novo algoritmo não-paramétrico obtido por meio de modificações no método de imputação simples desenvolvido por Yan (2013). Também é incluído um estudo que considera sistemas de imputação recentemente relatados na literatura e os compara com o procedimento clássico recomendado para imputação em ensaios (G×E), ou seja, a combinação do algoritmo de Esperança-Maximização com os modelos AMMI ou EM-AMMI. Por último, são fornecidas generalizações da imputação simples descrita por Arciniegas-Alarcón et al. (2010) que mistura regressão com aproximação de posto inferior de uma matriz. Todas as metodologias têm como base a decomposição por valores singulares (DVS), portanto, são livres de pressuposições distribucionais ou estruturais. Para determinar o desempenho dos novos esquemas de imputação foram realizadas simulações baseadas em conjuntos de dados reais de diferentes espécies, com valores re- tirados aleatoriamente em diferentes porcentagens e a qualidade das imputações avaliada com distintas estatísticas. Concluiu-se que a DVS constitui uma ferramenta útil e flexível na construção de técnicas eficientes que contornem o problema de perda de informação em matrizes experimentais.

Immunomodulating effects of environmentally realistic copper concentrations in Mytilus edulis adapted to naturally low salinities, link to supplementary material

The monitoring of organisms' health conditions by the assessment of their immunocompetence may serve as an important criterion for the achievement of the Good Environmental Status (GES) as defined in the Marine Strategy Framework Directive (EU). In this context, the complex role of natural environmental stressors, e.g. salinity, and interfering or superimposing effects of anthropogenic chemicals, should be carefully considered, especially in scenarios of low to moderate contamination. Organisms from the Baltic Sea have adapted to the ambient salinity regime, however energetically costly osmoregulating processes may have an impact on the capability to respond to additional stress such as contamination. The assessment of multiple stressors, encompassing natural and anthropogenic factors, influencing an organisms' health was the main aim of the present study. Immune responses of Mytilus edulis, collected and kept at natural salinities of 12 per mil (LS) and 20 per mil (MS), respectively, were compared after short-term exposure (1, 7 and 13 days) to low copper concentrations (5, 9 and 16 µg/L Cu). A significant interaction of salinity and copper exposure was observed in copper accumulation. LS mussels accumulated markedly more copper than MS mussels. No combined effects were detected in cellular responses. Bacterial clearance was mostly achieved by phagocytosis, as revealed by a strong positive correlation between bacterial counts and phagocytic activity, which was particularly pronounced in LS mussels. MS mussels, on the other hand, seemingly accomplished bacterial clearance by employing additional humoral factors (16 µg/L Cu). The greatest separating factor in the PCA biplot between LS and MS mussels was the proportion of granulocytes and hyalinocytes while functional parameters (phagocytic activity and bacterial clearance) were hardly affected by salinity, but rather by copper exposure. In conclusion, immune responses of the blue mussel may be suitable and sensitive biomarkers for the assessment of ecosystem health in brackish waters (10-20 per mil S).

Analysis of line x environment interactions for yield in navy beans. 2. Pattern analysis of lines and environment within years

Seven years of multi-environment yield trials of navy bean (Phaseolus vulgaris L.) grown in Queensland were examined. As is common with plant breeding evaluation trials, test entries and locations varied between years. Grain yield data were analysed for each year using cluster and ordination analyses (pattern analyses). These methods facilitate descriptions of genotype performance across environments and the discrimination among genotypes provided by the environments. The observed trends for genotypic yield performance across environments were partly consistent with agronomic and disease reactions at specific environments and also partly explainable by breeding and selection history. In some cases, similarities in discrimination among environments were related to geographic proximity, in others management practices, and in others similarities occurred between geographically widely separated environments which differed in management practices. One location was identified as having atypical line discrimination. The analysis indicated that the number of test locations was below requirements for adequate representation of line x environment interaction. The pattern analyses methods used were an effective aid in describing the patterns in data for each year and illustrated the variations in adaptive patterns from year to year. The study has implications for assessing the number and location of test sites for plant breeding multi-environment trials, and for the understanding of genetic traits contributing to line x environment interactions.

Source Provenance of Pre-Historic Granitic Grindstones: The Case Study of the Cogotas I Archaeological Site of Arroyo Mucientes/San Lázaro (Castronuño, Valladolid) and a Proposal on the General Methodological Flow Process

The occurrence of hand grindstones at the Cogotas I archaeological sites is considered to be a common feature. Given that a distant-provenance raw material is frequently involved, determination of its source is a basic factor in the search for a better understanding of resource management and for any Political Economy approach. To progress in these directions an overall study should be planned, using selected grindstones with a view to covering diverse sub-zones of the Cogotas I dispersal area, especially because of its considerable distance from the granite basement source. Such a study may today includes diverse analytical procedures combining successive geographic, petrographic, mineralogical and geochemical criteria. To check the plausibility of the proposed methodology, a preliminary test has been carried out on two granite grindstones, obtained at the archaeological excavation at the Castronuño (Valladolid) Cogotian site, which is fifty km away from an inferred source area that was presumably located at Peñausende (Zamora). The result obtained validates the proposed operational process, yielding a generalizable knowledge to other similar situations.

Exploring the joint compositional variability of major components and trace elements in the Tellus soil geochemistry survey (Northern Ireland)

The complexity of modern geochemical data sets is increasing in several aspects (number of available samples, number of elements measured, number of matrices analysed, geological-environmental variability covered, etc), hence it is becoming increasingly necessary to apply statistical methods to elucidate their structure. This paper presents an exploratory analysis of one such complex data set, the Tellus geochemical soil survey of Northern Ireland (NI). This exploratory analysis is based on one of the most fundamental exploratory tools, principal component analysis (PCA) and its graphical representation as a biplot, albeit in several variations: the set of elements included (only major oxides vs. all observed elements), the prior transformation applied to the data (none, a standardization or a logratio transformation) and the way the covariance matrix between components is estimated (classical estimation vs. robust estimation). Results show that a log-ratio PCA (robust or classical) of all available elements is the most powerful exploratory setting, providing the following insights: the first two processes controlling the whole geochemical variation in NI soils are peat coverage and a contrast between “mafic” and “felsic” background lithologies; peat covered areas are detected as outliers by a robust analysis, and can be then filtered out if required for further modelling; and peat coverage intensity can be quantified with the %Br in the subcomposition (Br, Rb, Ni).

Interação genótipo-ambiente na densidade de gemas e comprimento de ramos de pessegueiro

The instability of environment between years in climates of subtropical regions difficult to obtain peach trees genotypes with wide adaptation and stable production, contributing to poor crop. The climate instability can affect development stages as flower bud and vegetative bud formation. The factors understanding that control the bud formation, presents elementary importance for effective solutions search to these problems. The objective this work is verify the temperature effect, relative humidity and rainfall on bud density and length shoot (Brindilas) and identify genotypes with more adaptability and stability for this character. Was used 12 peach trees genotypes growing in experimental orchard in the Technology Federal of Paraná State University, Campus Pato Branco with Cfa Köppen climate according to the classification. Data of rainfall, hourly temperature were collected by the weather station of Simepar. They were used three plants for genotype (rehearsal), identify five shoots per tree, in May of each year. Were carried analyzes of length shoot CR (cm), count number of flower bud (GF) and vegetative bud (GV). Also calculated the relationship between GF/GV and flower bud density and vegetative bud density. Evaluations were performer annual 2007-2014. With these data adaptability and stability analyzes were performed using Biplot methodology and correlations analyzes (Pearson) with climates variables. They used the weather data to calculate the sums of hours with temperatures below 20 °C, temperatures between 20-25 °C, temperature between 25-30 °C and temperature above 30 °C, considering the period of August 1fst of the previous period to February 28 of the following year. Pearson correlation coefficients were used for path analysis, GF and DGF as basic variables. For CR, GV and GF the highest average occurred in 2009/10 period. The genotypes ‘BRS Kampai’ and ‘BRS Libra’ highest CR. They are considered stable and adapted as the CR genotypes ‘Casc. 967’ and ‘BRS Kampai’. There was negative correlation between CR and GV for Σh <20 ° C, Σh> 30 °C and Σh with URA <50% and positive correlation between these variables and Σh 25-30 °C and Σh with URA> 70%. The evaluation of GV ‘Cons. 681’ and ‘Casc. 1055’ can be considered adapted and stable. The lowest average was presented by the genotype ‘Sta. Áurea’ though the genotype is also stable. In GF evaluation genotypes are considered adapted ‘BRS Bonão’, ‘Casc. 1055’, ‘Cons. 681’ with adaptability to all evaluated period. In path analysis was direct effect Σh 25-30 °C on flower bud density. In evaluating DGV and DGF and the variations are due to genetic effect. The most adapted and stable genotypes for DGV were ‘T. Beauty’, ‘T. Snow’, ‘Casc. 1055’ and ‘Cons. 681’. CR and GV variables are strongly affected by environment. GF is strongly affected by genetic conditions and moderately affected by environment. DGV and DGF are affected basically by genetic conditions.

Study of tRNA modifying enzymes and codon usage bias in cancer

Recent evidences indicate that tRNA modifications and tRNA modifying enzymes may play important roles in complex human diseases such as cancer, neurological disorders and mitochondrial-linked diseases. We postulate that expression deregulation of tRNA modifying enzymes affects the level of tRNA modifications and, consequently, their function and the translation efficiency of their tRNA corresponding codons. Due to the degeneracy of the genetic code, most amino acids are encoded by two to six synonymous codons. This degeneracy and the biased usage of synonymous codons cause alterations that can span from protein folding to enhanced translation efficiency of a select gene group. In this work, we focused on cancer and performed a meta-analysis study to compare microarray gene expression profiles, reported by previous studies and evaluate the codon usage of different types of cancer where tRNA modifying enzymes were found de-regulated. A total of 36 different tRNA modifying enzymes were found de-regulated in most cancer datasets analyzed. The codon usage analysis revealed a preference for codons ending in AU for the up-regulated genes, while the down-regulated genes show a preference for GC ending codons. Furthermore, a PCA biplot analysis showed this same tendency. We also analyzed the codon usage of the datasets where the CTU2 tRNA modifying enzyme was found deregulated as this enzyme affects the wobble position (position 34) of specific tRNAs. Our data points to a distinct codon usage pattern between up and downregulated genes in cancer, which might be caused by the deregulation of specific tRNA modifying enzymes. This codon usage bias may augment the transcription and translation efficiency of some genes that otherwise, in a normal situation, would be translated less efficiently.

ADAPTATION OF INTRODUCED MUNGBEAN GENOTYPES IN UGANDA

Mungbean ( Vigna radiata (L.) Wilczek) is an important source of nutrients and income for smallholder farmers in East Africa. Mungbean production in countries like Uganda largely depends on landraces, in the absence of improved varieties. In order to enhance productivity, efforts have been underway to develop and evaluate mungbean varieties that meet farmers’ needs in various parts of the country. This study was conducted at six locations in Uganda, to determine the adaptability of introduced mungbean genotypes, and identify mungbean production mega-environments in Uganda. Eleven genotypes (Filsan, Sunshine, Blackgram, Mauritius1, VC6148 (50-12), VC6173 (B-10),Yellowmungo, KPS1, VC6137(B-14),VC6372(45-60),VC6153(B-20P) and one local check were evaluated in six locations during 2013 and 2014. The locations were; National Semi Arid Resources Research Institute (NaSARRI), Abi Zonal Agricultural Research and Development Institute (AbiZARDI),Kaberamaido variety trial center, Kumi variety trial center, Nabuin Zonal Agricultural Research and Development Institute (NabuinZARDI), and Ngetta Zonal Agricultural Research and Development Institute (NgettaZARDI). G × E interactions were significant for grain yield. Through GGEBiplot analysis, three introduced genotypes (Filsan, Blackgram and Sunshine) were found to be stable and high yielding, and therefore, were recommended for release. The six test multi-locations were grouped into two candidate mega-environments for mungbean production (one comprising of AbiZARDI and Kaberamaido and the other comprising of NaSARRI, NabuinZARDI, Kumi, and NgettaZARDI). National Semi Arid Resources Research Institute (NaSARRI) was the most suitable environment in terms of both discriminative ability and representativeness and therefore can be used for selection of widely adaptable genotypes.

Determinación de análisis bromatológico proximal y calidad culinaria de Phaseolus vulgaris L. (frijol común) grano negro criollo cultivado en la zona occidental de El Salvador

Esta investigación apuesta a la utilización del Phaseolus vulgaris L. (frijol común) grano negro criollo como un recurso que aumente el acceso alimenticio de las familias salvadoreñas. Para ello se estudió la calidad culinaria y bromatológica de tres variedades de Phaseolus vulgaris L. (frijol común) grano negro criollo que respalde el fomento del consumo de esta leguminosa. Los análisis realizados comprende la calidad culinaria que consiste en la determinación del coeficiente de hidratación, tiempo de cocción, densidad del caldo y las dimensiones del grano; y el análisis bromatológico proximal que consiste en la determinación de cenizas, humedad, proteína cruda, fibra cruda, extracto étereo, extracto libre de nitrógeno y minerales de importancia tales como: hierro, calcio, magnesio y zinc. Las muestras son variedades de Phaseolus vulgaris L. (frijol común) grano negro criollo (Cuarentín, Tamazulapa y El Porvenir) cultivadas en la zona occidental de El Salvador. Los resultados se compararon con los valores de referencia de frijol grano negro seco presentados en las tablas de composición de alimentos del Instituto de Nutrición de Centroamérica y Panamá (INCAP), y se evaluaron estadísticamente a través del análisis de varianza de un factor, análisis de diferencia significativa honesta de Tukey y representación gráfica Biplot. La variedad de frijol común grano negro criollo con mejores resultados en cuanto a calidad culinaria fue la variedad Cuarentín, en cambio en calidad bromatológica y cuantificación de micronutrientes los mejores resultados fueron para las variedades Cuarentín y Tamazulapa; sin embargo, la variedad con mayor cantidad proteica fue la variedad El Porvenir.

Análise AMMI em caracteres vegetativos de genótipos de bananeiras no Amapá.

A bananicultura representa importante cadeia econômica no Estado, mas quase a totalidade dos frutos é proveniente de outras localidades, tornando-se necessário o desenvolvimento regional. Desta forma o objetivo deste trabalho foi avaliar, em Porto Grande-AP, o desempenho produtivo de cinco cultivares de bananeira, resistentes à Sigatoka-negra que tem inviabilizado a produção regional. O delineamento experimental foi em blocos casualizados com cinco tratamentos e quatro repetições. Foram avaliados: número da folha mais jovem infectada (FMJI); altura da planta do nível do solo à inserção da inflorescência (APL), circunferência do pseudocaule a 30 cm de altura do solo (CPL); número de folhas viáveis (NFV) e; número total de folhas na planta (NFP). Como principais resultados, obteve-se na análise de variância a dominância de anos nas fontes de variação em NFV, ALT e CPL, sendo que para FMJI e NEP foram os ruídos. Na análise AMMI os eixos IPCA1 e IPCA2 explicaram a totalidade da SQGxE. Os genótipos mais estáveis no biplot AMMI foramG3 e G5 para FMJI; G1 para CPL e; G2 para NFV e os com especificidade adaptativa a determinados ambientes foram G1 e G4 para FMJI; G2 e G3 para CPL e; G1, G3, G4 e G5 para NFV. Os ambientes avaliados individualmente tiveram maior contribuição na interação GxE do que os genótipos e também foram contrastantes em AMMI2, indicativo de que fatores relativos às diferenças entre os anos agrícolas foram determinantes na interação associada ao IPCA1.

Adaptability and phenotypic stability of soybean cultivars for grain yield and oil content.

ABSTRACT. The aim of this study was to verify the adaptability and stability of soybean cultivars with regards to yield and oil content. Data of soybean yield and oil content were used from experiments set up in six environments in the 2011/12 and 2012/13 crop seasons in the municipalities of Patos de Minas, Uberaba, Lavras, and São Gotardo, Minas Gerais, Brazil, testing 36 commercial soybean cultivars of both conventional and transgenic varieties. The Wricke method and GGE biplot analysis were used to evaluate adaptability and stability of these cultivars. Large variations were observed in grain yield in relation to the different environments studied, showing that these materials are adaptable. The cultivars exhibited significant differences in oil content. The cultivars BRSGO204 (Goiânia) and BRSMG (Garantia) exhibited the greatest average grain yield in the different environments studied, and the cultivar BRSMG 760 SRR had the greatest oil content among the cultivars evaluated. Ecovalence was adopted to identify the most stable cultivars, and the estimates were nearly uniform both for grain yield and oil content, showing a variation of 0.07 and 0.01%, respectively. The GGE biplot was efficient at identifying cultivars with high adaptability and phenotype stability.