植物代谢组学的研究方法及其应用

代谢组是指某一生物或细胞在一特定生理时期内所有的低分子量代谢产物。植物代谢组学是指对植物抽提物中代谢组进行高通量、无偏差全面分析的技术。近年来, 植物代谢组学研究取得了很大进展。本文介绍了其含义、历史沿革及研究方法, 并用典型实例阐释了它的应用方向。     

植物代谢组学的研究方法及其应用

代谢组是指某一生物或细胞在一特定生理时期内所有的低分子量代谢产物.植物代谢组学是指对植物抽提物中代谢组进行高通量、无偏差全面分析的技术.近年来,植物代谢组学研究取得了很大进展.本文介绍了其含义、历史沿革及研究方法,并用典型实例阐释了它的应用方向.     

植物应答非生物胁迫的代谢组学研究进展

代谢组学技术是研究植物代谢的理想平台, 通过现代检测分析技术对胁迫环境下植物中代谢产物进行定性和定量分析, 可以监测其随时间变化的规律。而各种组学平台包括基因组学、转录组学及代谢组学的整合, 更是一个强有力的工具箱, 将所获得的不同组学的信息联系起来, 有利于从整体研究生物系统对基因或环境变化的响应, 如可判断代谢物的变化是从哪一个层面开始发生的, 帮助人们揭开复杂的植物胁迫应答机制。该文对近期代谢组学技术及其与蛋白质组学、基因组学技术相结合探索植物应答非生物胁迫的研究进行了综述。代谢组学的应用, 拓展了对植物耐受非生物胁迫分子机制的认识, 开展更多这方面的研究, 再通过植物代谢组学、转录组学、蛋白质组学和基因组学整合, 有助于从整体水平上把握植物胁迫应答机制。     

Microbial metabolomics

Microbial metabolomics constitutes an integrated component of systems biology. By studying the complete set of metabolites within a microorganism and monitoring the global outcome of interactions between its development processes and the environment, metabolomics can potentially provide a more accurate snap shot of the actual physiological state of the cell. Recent advancement of technologies and post-genomic developments enable the study and analysis of metabolome. This unique contribution resulted in many scientific disciplines incorporating metabolomics as one of their "omics" platforms. This review focuses on metabolomics in microorganisms and utilizes selected topics to illustrate its impact on the understanding of systems microbiology.     

Proteomics and metabolomics in cancer drug development

In this review article, the main recent advancements in the field of proteomics and metabolomics and their application in cancer research are described. In the second part of the review the main metabolic alterations observed in cancer cells are thoroughly dissected, especially those involving anabolic pathways and NADPH-generating pathways, which indirectly affect anabolic reactions, other than the maintenance of the redox poise. Alterations to mitochondrial pathways and thereby deriving oncometabolites are also detailed. The third section of the review is a discussion of how and to what extent (mutations to) tumor suppressors and oncogenes end up influencing cancer cell metabolism and cell fate, either promoting survival and proliferation or autophagy and apoptosis. In the last section of the review, an overview is provided of therapeutic strategies that make use of metabolic reprogramming approaches.     

The potential of metabolomics tools in bioremediation studies

As a post-genomics tool, metabolomics is a young and vibrant field of science in its exponential growth phase. Metabolome analysis has become very popular recently, and novel techniques for acquiring and analyzing metabolomics data continue to emerge that are useful for a variety of biological studies. The bioremediation field has a lot to gain from the advances in this emerging area. Thus, this review article focuses on the potential of various experimental and conceptual approaches developed for metabolomics to be applied in bioremediation research, such as strategies for elucidation of biodegradation pathways using isotope distribution analysis and molecular connectivity analysis, the assessment of mineralization process using metabolic footprinting analysis, and the improvement of the biodegradation process via metabolic engineering. We demonstrate how the use of metabolomics tools can significantly extend and enhance the power of existing bioremediation approaches by providing a better overview of the biodegradation process.     

The utility of metabolomics in natural product and biomarker characterization

BackgroundMetabolomics is a well-established rapidly developing research field involving quantitative and qualitative metabolite assessment within biological systems. Recent improvements in metabolomics technologies reveal the unequivocal value of metabolomics tools in natural products discovery, gene-function analysis, systems biology and diagnostic platforms.Scope of reviewWe review here some of the prominent metabolomics methodologies employed in data acquisition and analysis of natural products and disease-related biomarkers.Major conclusionsThis review demonstrates that metabolomics represents a highly adaptable technology with diverse applications ranging from environmental toxicology to disease diagnosis. Metabolomic analysis is shown to provide a unique snapshot of the functional genetic status of an organism by examining its biochemical profile, with relevance toward resolving phylogenetic associations involving horizontal gene transfer and distinguishing subgroups of genera possessing high genetic homology, as well as an increasing role in both elucidating biosynthetic transformations of natural products and detecting preclinical biomarkers of numerous disease states.General significanceThis review expands the interest in multiplatform combinatorial metabolomic analysis. The applications reviewed range from phylogenetic assignment, biosynthetic transformations of natural products, and the detection of preclinical biomarkers.     

The ABRF Metabolomics Research Group 2013 Study: Investigation of Spiked Compound Differences in a Human Plasma Matrix

Metabolomics is an emerging field that involves qualitative and quantitative measurements of small molecule metabolites in a biological system. These measurements can be useful for developing biomarkers for diagnosis, prognosis, or predicting response to therapy. Currently, a wide variety of metabolomics approaches, including nontargeted and targeted profiling, are used across laboratories on a routine basis. A diverse set of analytical platforms, such as NMR, gas chromatography-mass spectrometry, Orbitrap mass spectrometry, and time-of-flight-mass spectrometry, which use various chromatographic and ionization techniques, are used for resolution, detection, identification, and quantitation of metabolites from various biological matrices. However, few attempts have been made to standardize experimental methodologies or comparative analyses across different laboratories. The Metabolomics Research Group of the Association of Biomolecular Resource Facilities organized a “round-robin” experiment type of interlaboratory study, wherein human plasma samples were spiked with different amounts of metabolite standards in 2 groups of biologic samples (A and B). The goal was a study that resembles a typical metabolomics analysis. Here, we report our efforts and discuss challenges that create bottlenecks for the field. Finally, we discuss benchmarks that could be used by laboratories to compare their methodologies.     

Miniature bioreactors: current practices and future opportunities

This review focuses on the emerging field of miniature bioreactors (MBRs), and examines the way in which they are used to speed up many areas of bioprocessing. MBRs aim to achieve this acceleration as a result of their inherent high-throughput capability, which results from their ability to perform many cell cultivations in parallel. There are several applications for MBRs, ranging from media development and strain improvement to process optimisation. The potential of MBRs for use in these applications will be explained in detail in this review. MBRs are currently based on several existing bioreactor platforms such as shaken devices, stirred-tank reactors and bubble columns. This review will present the advantages and disadvantages of each design together with an appraisal of prototype and commercialised devices developed for parallel operation. Finally we will discuss how MBRs can be used in conjunction with automated robotic systems and other miniature process units to deliver a fully-integrated, high-throughput (HT) solution for cell cultivation process development.     

Environmental metabolomics: a SWOT analysis (strengths, weaknesses, opportunities, and threats)

Metabolomic approaches have the potential to make an exceptional contribution to understanding how chemicals and other environmental stressors can affect both human and environmental health. However, the application of metabolomics to environmental exposures, although getting underway, has not yet been extensively explored. This review will use a SWOT analysis model to discuss some of the strengths, weaknesses, opportunities, and threats that are apparent to an investigator venturing into this relatively new field. SWOT has been used extensively in business settings to uncover new outlooks and identify problems that would impede progress. The field of environmental metabolomics provides great opportunities for discovery, and this is recognized by a high level of interest in potential applications. However, understanding the biological consequence of environmental exposures can be confounded by inter- and intra-individual differences. Metabolomic profiles can yield a plethora of data, the interpretation of which is complex and still being evaluated and researched. The development of the field will depend on the availability of technologies for data handling and that permit ready access metabolomic databases. Understanding the relevance of metabolomic endpoints to organism health vs adaptation vs variation is an important step in understanding what constitutes a substantive environmental threat. Metabolomic applications in reproductive research are discussed. Overall, the development of a comprehensive mechanistic-based interpretation of metabolomic changes offers the possibility of providing information that will significantly contribute to the protection of human health and the environment.     

Environmental metabolomics: a critical review and future perspectives

Environmental metabolomics is the application of metabolomics to characterise the interactions of organisms with their environment. This approach has many advantages for studying organism–environment interactions and for assessing organism function and health at the molecular level. As such, metabolomics is finding an increasing number of applications in the environmental sciences, ranging from understanding organismal responses to abiotic pressures, to investigating the responses of organisms to other biota. These interactions can be studied from individuals to populations, which can be related to the traditional fields of ecophysiology and ecology, and from instantaneous effects to those over evolutionary time scales, the latter enabling studies of genetic adaptation. This review provides a comprehensive and current overview of environmental metabolomics research. We begin with an overview of metabolomic studies into the effects of abiotic pressures on organisms. In the field of ecophysiology, studies on the metabolic responses to temperature, water, food availability, light and circadian rhythms, atmospheric gases and season are reviewed. A section on ecotoxicogenomics discusses research in aquatic and terrestrial ecotoxicology, assessing organismal responses to anthropogenic pollutants in both the laboratory and field. We then discuss environmental metabolomic studies of diseases and biotic–biotic interactions, in particular herbivory. Finally, we critically evaluate the contribution that metabolomics has made to the environmental sciences, and highlight and discuss recommendations to advance our understanding of the environment, ecology and evolution using a metabolomics approach.