Fruticultura temperada e subtropical

Trabalho de Conclusão de Curso - Universidade Federal de Santa Catarina. Curso de Agronomia

Development of computational tools for the analysis of 2D-nuclear magnetic resonance data

Metabolomics is one of the omics' sciences that has been gaining a lot of interest due to its potential on correlating an organism's biochemical activity and its phenotype. The main techniques that collect data are based on mass spectrometry and nuclear magnetic resonance (NMR) spectroscopy. The last one has the advantage of analysing a sample in vivo without damaging it and while its sensitivity is pointed out as a disadvantage, multidimensional NMR delivers a solution to this issue. It adds layers of information, generating new data that requires advanced bioinformatics methods to extract biological meaning. The need to establish an integrated framework has become imperative due to different approaches that multidimensional NMR has, to tackle reproducibility issues across research groups. In recent work from the host group, specmine, an R package for metabolomics and spectral data analysis/mining, has been developed and improved to wrap and deliver key metabolomic methods that allow a researcher to perform a complete analysis. Tools integrated in specmine were developed to read, visualize, and analyse two-dimensional (2D) NMR. A new specmine structure was created for this type of data, easing interpretation and data visualization. In terms of visualization a novel approach towards three-dimensional environments enables users to interact with their data. The selection of which samples to plot, when the user does not specify an input, is based on a signal-to-noise ratio scale and a method to perform peak detection on 2D NMR based on local maximum search was implemented to obtain a data structure that best benefits from specmine's functionalities. These include pre-processing, univariate, and multivariate analysis as well as machine learning and feature selection methods. The 2D NMR functions were validated using experimental data from two scientific papers, available on metabolomic databases. These data originated two case studies from different NMR sources, Bruker and Varian, which reinforces specmine's flexibility. The case studies were carried out using mainly specmine and other packages for specific processing steps. A pipeline to analyse 2D NMR was added to specmine, in a form of a vignette, to provide a guideline for the newly developed functionalities.info:eu-repo/semantics/publishedVersio

Non-targeted metabolomic profiling of maize landraces (Zea mays l.) combined with chemometric tools

Grain samples of maize landraces were collected and subjected to Fourier Transform Infrared spectroscopy (FTIR) analysis combined with chemometric tools in other to discriminate them regarding the chemical composition. Principal component analysis (PCA) and hierarchical clustering (HCA) were applied on selected peaks of the spectral data. The most important chemical groups found in all maize landrace samples were monoterpenes, sesquiterpenes, tetraterpenes, aminoacids, polysaccharides, lipids and proteins. Trace signals of secondary metabolites were also found in cultivars according to year of harvest.The authors acknowledge CNPq (National Counsel of Technological and Scientific Development) for financial support (Process n 407323/2013-9). The project was also partially funded by the Project PropMine, funded by the agreement between Portuguese FCT and Brazilian CNPq.info:eu-repo/semantics/publishedVersio

Projeto de exportação de software da empresa Altoqi para a Argentina

TCC (graduação) - Universidade Federal de Santa Catarina. Centro Sócio-Econômico. Economia.Este trabalho parte de uma breve revisão literária, voltada essencialmente para a justificativa da entrada de uma empresa brasileira, ligada ao setor de TI no comércio internacional. Com a aproximação de alguns países latino americanos através do MERCOSUL, a empresa AltoQi Tecnologia em Informática S.A. produtora de software voltados para a área de projetos de construção civil no Brasil, procura justificar a decisão de comercialização de seus produtos na Argentina. A justificativa será pautada através das possibilidades proporcionadas pelos 'Daises integrantes desta área preferencial de comércio (MERCOSUL), uma breve análise do segmento, a caracterização do serviço para fins de tributação e a identificação das principais barreiras é entrada dos serviços e soluções encontradas para transposição estas barreiras

WebSpecmine: a website for metabolomics data analysis and mining

Metabolomics data analysis is an important task in biomedical research. The available tools do not provide a wide variety of methods and data types, nor ways to store and share data and results generated. Thus, we have developed WebSpecmine to overcome the aforementioned limitations. WebSpecmine is a web-based application designed to perform the analysis of metabolomics data based on spectroscopic and chromatographic techniques (NMR, Infrared, UV-visible, and Raman, and LC/GC-MS) and compound concentrations. Users, even those not possessing programming skills, can access several analysis methods including univariate, unsupervised and supervised multivariate statistical analysis, as well as metabolite identification and pathway analysis, also being able to create accounts to store their data and results, either privately or publicly. The tool’s implementation is based in the R project, including its shiny web-based framework. Webspecmine is freely available, supporting all major browsers. We provide abundant documentation, including tutorials and a user guide with case studies.This study was supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2019 unit and BioTecNorte operation (NORTE-01-0145-FEDER-000004) funded by the European Regional Development Fund (ERDF) under the scope of Norte2020—Programa Operacional Regional do Norte. The authors also acknowledge the funding of the project 22231/01/SAICT/2016, “Biodata.pt – Infraestrutura Portuguesa de Dados Biológicos”, funded by FCT and Lisboa 2020/Portugal2020 Partnership Agreement, through the ERDF.info:eu-repo/semantics/publishedVersio

NMRFinder: a novel method for 1D 1H-NMR metabolite annotation

Introduction: Methods for the automated and accurate identification of metabolites in 1D 1H-NMR samples are crucial, but this is still an unsolved problem. Most available tools are mainly focused on metabolite quantification, thus limiting the number of metabolites that can be identified. Also, most only use reference spectra obtained under the same specific conditions of the target sample, limiting the use of available knowledge. Objectives: The main goal of this work was to develop novel methods to perform metabolite annotation from 1D 1H-NMR peaks with enhanced reliability, to aid the users in metabolite identification. An essential step was to construct a vast and up-do-date library of reference 1D 1H-NMR peak lists collected under distinct experimental conditions. Methods: Three different algorithms were evaluated for their capacity to correctly annotate metabolites present in both synthetic and real samples and compared to publicly available tools. The best proposed method was evaluated in a plethora of scenarios, including missing references, missing peaks and peak shifts, to assess its annotation accuracy, precision and recall. Results: We gathered 1816 peak lists for 1387 different metabolites from several sources across different conditions for our reference library. A new method, NMRFinder, is proposed and allows matching 1D 1H-NMR samples with all the reference peak lists in the library, regardless of acquisition conditions. Metabolites are scored according to the number of peaks matching the samples, how unique their peaks are in the library and how close the spectrum acquisition conditions are in relation to those of the samples. Results show a true positive rate of 0.984 when analysing computationally created samples, while 71.8% of the metabolites were annotated when analysing samples from previously identified public datasets. Conclusion NMRFinder performs metabolite annotation reliably and outperforms previous methods, being of great value in helping the user to ultimately identify metabolites. It is implemented in the R package specmine.This study was funded by the PhD scholarship with reference SFRH/BD/138951/2018, awarded by the Portuguese Foundation for Science and Technology (FCT). specifc references. The number of metabolites identifed by the studies’ authors is present at the bottom of each bar. The datasets marked with the red rectangle were acquired with a frequency of 700 MHz for 1D 1 H-NMR spectrainfo:eu-repo/semantics/publishedVersio

Metabolomics-based approaches on wine authentication: a review with case studies

Wine is a natural product with a unique production method, being considered an art due to its unique features. Due to the singularity of its components and the high production cost, wine adulteration events happen frequently, aiming to achieve higher profits, compromising its authenticity. By using analytical techniques, such as nuclear magnetic resonance spectroscopy or mass spectrometry, it is possible to acquire large amounts of metabolomics data related to specific metabolites over distinct samples. A number of multivariate statistical and machine learning methods may be applied, with high discriminative power allowing to achieve information with added-value about important features such as cultivar, age and geographic origin, and also to detect possible adulteration events. Nonetheless, metabolomics data analysis still constitutes a challenge, specially over complex matrices, such as wine. This work entails a comprehensive survey of research work related to metabolomics-based approaches for wine authentication, with particular emphasis on supervised and unsupervised multivariate data analysis. To illustrate the main tasks and steps of metabolomics data analysis, but also to highlight existing challenges in wine authentication issues, two case studies were performed, using the metabolomics data analysis R package specmine. These cases encompass one published dataset, which is re-analyzed here, and a new dataset of Portuguese and Brazilian wines. In both cases, exploratory data analysis in conjunction with multivariate statistical analysis, including principal component analysis and clustering, were performed. It was possible to discriminate the wines according to their cultivar and geographical origin (in the first case) and age (in the second) based on NMR profiles and metabolite identification.info:eu-repo/semantics/publishedVersio

Modelagem e simulação via elementos finitos de uma célula de combustível a etanol direto

A geração de energia é um tema em constante debate, seja referente a sua eficiência e renovabilidade, ou a emissão de poluentes. Além disso, o consumo de energia tem crescido cada vez mais ao longo dos anos e, em contrapartida, combustíveis fósseis, que são responsáveis por cerca de 80% da geração de energia do mundo, correm risco de escassez. Uma tecnologia com características renováveis que tem se mostrado promissora e, ainda, mais eficiente que os geradores de energia tradicionais é a célula de combustível, que alimentada por etanol torna o processo limpo e eficiente. Neste trabalho, desenvolve-se um modelo numérico bi-dimensional para células de combustível com membrana trocadora de prótons alimentada por etanol produzido a partir de biomassa. O modelo leva em consideração o escoamento, a variação da concentração das espécies químicas, a variação da temperatura, a taxa de passagem de etanol através da membrana e as perdas sobrepotenciais no ânodo e no cátodo. As simulações numéricas são feitas utilizando o método de elementos finitos para discretização no espaço e o método de Crank-Nicolson para discretização no tempo. colorredAs perdas sobrepotenciais da célula são calculadas utilizando parâmetros (velocidade, concentração e temperatura) calculados com o modelo numérico. Resultados de escoamento, variação da concentração das espécies e temperatura, passagem de etanol através da membrana, densidade de corrente limitante, comparação de vazões e porosidades são exibidos. Apresenta-se resultados de tensão da célula comparando catalisadores, temperaturas iniciais e concentrações iniciais com dados experimentais encontrados na literatura.The generation of energy is a subject in constant debate, be it referring to its efficiency and renewability or the emission of pollutants. In addition, energy consumption has grown over the years, and fossil fuels, which account for about 80% of the world’s energy generation, run the risk of becoming scarce. A technology with renewable characteristics that has proven to be promising and even more efficient than traditional power generators is the fuel cell, which fueled by ethanol makes the process clean and efficient. In this work, a two-dimensional numerical model is developed for fuel cells with proton exchange membrane fed by ethanol produced from biomass. The model takes into account the flow, the variation of the chemical species concentration, the temperature variation, the rate of passage of the ethanol through the membrane and the overpotential losses in the anode and the cathode. Numerical simulations are done using the finite element method for discretizations in space and the Crank-Nicolson method for discretizations in time. The overpotential losses of the cell are calculated using parameters (velocity, concentration and temperature) obtained with the numerical model. Results of flow, variation of species concentration and temperature, passage of ethanol through the membrane, limiting current density, flow rate and porosity comparison are shown. Results of cell voltage are presented comparing catalysts, starting temperatures and concentrations with experimental data found in the literature

Specmine: an R package for metabolomics and spectral data analysis and mining

Book of Abstracts of CEB Annual Meeting 2017info:eu-repo/semantics/publishedVersio

A chemometrics approach for nuclear magnetic resonance data to characterize the partial metabolome banana peels from southern Brazil

Banana peels are well recognized as a source of important bioactive compounds, such as phenolics, carotenoids, biogenic amines, among others. As such, they have recently started to be used for industrial purposes. However, its composition seems to be strongly affected by biotic or abiotic ecological factors. Thus, this study aimed to investigate banana peels chemical composition, not only to get insights on eventual metabolic changes caused by the seasons, in southern Brazil, but also to identify the most relevant metabolites for these processes. To achieve this, a Nuclear magnetic resonance (NMR)-based metabolic profiling strategy was adopted, followed by chemometrics analysis, using the specmine package for the R environment, and metabolite identification. The results showed that the metabolomic approach adopted allowed identifying a series of primary and secondary metabolites in the aqueous extracts investigated. Besides, over the seasons the metabolic profiles of the banana peels showed to contain biologically active compounds relevant to the skin wound healing process, indicating the biotechnological potential of that raw material.To CNPq (National Counsel of Technological and Scientific Development) for financial support (Process n 407323/2013-9), to CAPES (Coordination for the Improvement of Higher Education Personnel), and EPAGRI (Agricultural Research and Rural Extension Company of Santa Catarina). The research fellowship from CNPq on behalf of M. Maraschin is acknowledged. The work is partially funded by Project PropMine, funded by the agreement between Portuguese FCT and Brazilian CNPq. This study was also partially supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2013 unit and COMPETE 2020 (POCI-01-0145FEDER-006684) and BioTecNorte operation (NORTE-01-0145-FEDER-000004) funded by European Regional Development Fund under the scope of Norte2020 – Programa Operacional Regional do Norte.info:eu-repo/semantics/publishedVersio