MetaCrop 2.0: managing and exploring information about crop plant metabolism

MetaCrop is a manually curated repository of high-quality data about plant metabolism, providing different levels of detail from overview maps of primary metabolism to kinetic data of enzymes. It contains information about seven major crop plants with high agronomical importance and two model plants. MetaCrop is intended to support research aimed at the improvement of crops for both nutrition and industrial use. It can be accessed via web, web services and an add-on to the Vanted software. Here, we present several novel developments of the MetaCrop system and the extended database content. MetaCrop is now available in version 2.0 at http://metacrop.ipk-gatersleben.de

Plant Genetics and Molecular Biology

This book reviews the latest advances in multiple fields of plant biotechnology and the opportunities that plant genetics, genomics and molecular biology have offered for agriculture improvement. Advanced technologies can dramatically enhance our capacity in understanding the molecular basis of traits and utilizing the available resources for accelerated development of high yielding, nutritious, input-use efficient and climate-smart crop varieties. In this book, readers will discover the significant advances in plant genetics, structural and functional genomics, trait and gene discovery, transcriptomics, proteomics, metabolomics, epigenomics, nanotechnology and analytical & decision support tools in breeding. This book appeals to researchers, academics and other stakeholders of global agriculture

Computational tools for large-scale biological network analysis

Tese de doutoramento em InformáticaThe surge of the field of Bioinformatics, among other contributions, provided biological researchers with powerful computational methods for processing and analysing the large amount of data coming from recent biological experimental techniques such as genome sequencing and other omics. Naturally, this led to the opening of new avenues of biological research among which is included the analysis of large-scale biological networks. The analysis of biological networks by itself is not new, but until recently researchers were limited to small-scale networks, due to the complexity inherent to biological systems. Recently, Bioinformatics provided researchers with the tools and methodologies needed to create and study large-scale networks. So, progressively larger networks have been built and more biological complex systems have been represented as networks. Since the study of large-scale biological networks is a relatively recent field, there are still few software tools focused in this research area. The main objective of this work was to contribute to this field, through the development of methodologies and computational tools for the creation and analysis of largescale cellular networks. One of the major contributions was the development of InBiNA, an open-source user-friendly application for the analysis of biological networks. InBiNA is a generic tool that can be used with most kinds of cellular networks, being focused in the analysis of integrated networks potentially representing metabolic, regulatory and/or signalling sub-systems. The usefulness of InBiNA has been shown by a case study including some pathways of Escherichia coli’s metabolism, together with different types of regulatory systems controlling these pathways. Also, TNA4OptFlux, a plug-in for the metabolic engineering software platform OptFlux, was created. Using the methodologies developed during this work, this plug-in is capable of combining the model-based phenotype simulation methods of OptFlux with network-based topological analysis methods, giving the user a new way of analysing the metabolism. One of the major applications is the comparison of the networks corresponding to wild-type and mutant strains, designed by strain optimization algorithms to overproduce interesting compounds. This brings interesting tools for the analyses of the strategies followed by mutant strains, as compared to the original ones. A case study, also using E. coli, for the production of succinate shows the usefulness of the tool. In this thesis the capabilities of InBiNA and TNA4OptFlux are presented, confirming their validity and utility as novel tools in the portfolio of Systems Biology research.O aparecimento do campo da Bioinformática trouxe, entre outras contribuições, ferramentas computacionais poderosas para o processamento e a análise das grandes quantidades de dados provenientes das recentes técnicas experimentais de alto débito em Biologia, tais como a sequenciação de genomas e outra ómicas. Naturalmente, isto conduziu à abertura de novas áreas na investigação biológica, entre as quais se inclui a análise de redes biológicas em larga escala. A análise de redes biológicas, por si só, não é uma novidade, mas até muito recentemente os investigadores da área limitavam-se ao estudo de redes em pequena escala, dada a complexidade inerente aos sistemas biológicos. Recentemente, a Bioinformática veio fornecer as ferramentas e as metodologias necessárias para criar e estudar redes em larga escala. Assim, redes progressivamente maiores têm sido construídas e cada vez mais sistemas biológicos complexos têm sido representados como redes. Dado que a análise de redes biológicas em larga-escala é ainda um campo recente, existem ainda poucas ferramentas focadas nesta área. O principal objetivo deste trabalho é o de contribuir para este campo, através do desenvolvimento de metodologias e ferramentas computacionais que permitam a criação e a análise de redes celulares em larga-escala. Uma das principais contribuições deste trabalho foi o desenvolvimento da aplicação InBiNA, uma aplicação aberta com uma interface amigável e que permite a análise de redes biológicas. Trata-se de uma ferramenta genérica que pode ser usada para analisar diversos tipos de redes celulares, sendo focada na análise de redes integradas, potencialmente representando sub-sistemas metabólicos, regulatórios e/ou de transdução de sinal. A utilidade da aplicação foi demonstrada através de um caso de estudo que envolveu a criação de uma rede incluindo algumas vias metabólicas da bactéria Escherichia coli, em conjunto com diferentes tipos de regulação controlando estas vias. Adicionalmente, o plug-in TNA4OptFlux foi desenvolvido, sendo um plug-in para o OptFlux, uma plataforma de software de Engenharia Metabólica. Usando as metodologias desenvolvidas durante este trabalho, este plug-in é capaz de combinar métodos de simulação de fenótipos baseados em modelos metabólicos com métodos de análise topológica de redes biológicas, fornecendo aos utilizadores uma forma distinta de analisar o metabolismo. Uma das principais aplicações passa pela comparação de redes metabólicas correspondentes a estirpes selvagens e mutantes desenhadas por algoritmos de otimização de estirpes que procuram a sobre-produção de compostos com interesse industrial. Assim, conseguem-se produzir ferramentas com interesse para a análise das estratégias seguidas pelas estirpes mutantes, quando comparadas com as originais. Um caso de estudo usando E. coli para a sobre-produção de succinato demonstra a utilidade das ferramentas. Neste trabalho, as capacidade das aplicações InBiNA e TNA4OptFlux são demonstradas, confirmando a sua validade e utilidade como novas ferramentas no portfólio da investigação na Biologia de Sistemas

Novel Developments of the MetaCrop Information System for Facilitating Systems Biological Approaches

Crop plants play a major role in human and animal nutrition and increasingly contribute to chemical or pharmaceutical industry and renewable resources. In order to achieve important goals, such as the improvement of growth or yield, it is indispensable to understand biological processes on a detailed level. Therefore, the well-structured management of fine-grained information about metabolic pathways is of high interest. Thus, we developed the MetaCrop information system, a manually curated repository of high quality information concerning the metabolism of crop plants. However, the data access to and flexible export of information of MetaCrop in standard exchange formats had to be improved. To automate and accelerate the data access we designed a set of web services to be integrated into external software. These web services have already been used by an add-on for the visualisation toolkit VANTED. Furthermore, we developed an export feature for the MetaCrop web interface, thus enabling the user to compose individual metabolic models using SBML

Novel developments of the MetaCrop information system for facilitating systems biological approaches

Hippe K, Colmsee C, Czauderna T, et al. Novel developments of the MetaCrop information system for facilitating systems biological approaches. J Integr Bioinform. 2010;7(3):347-352.Crop plants play a major role in human and animal nutrition and increasingly contribute to chemical or pharmaceutical industry and renewable resources. In order to achieve important goals, such as the improvement of growth or yield, it is indispensable to understand biological processes on a detailed level. Therefore, the well-structured management of fine-grained information about metabolic pathways is of high interest. Thus, we developed the MetaCrop information system, a manually curated repository of high quality information concerning the metabolism of crop plants. However, the data access to and flexible export of information of MetaCrop in standard exchange formats had to be improved. To automate and accelerate the data access we designed a set of web services to be integrated into external software. These web services have already been used by an add-on for the visualisation toolkit VANTED. Furthermore, we developed an export feature for the MetaCrop web interface, thus enabling the user to compose individual metabolic models using SBML