FT-ICR/MS and GC-EI/MS Metabolomics Networking Unravels Global Potato Sprout's Responses to Rhizoctonia solani Infection

The complexity of plant-pathogen interactions makes their dissection a challenging task for metabolomics studies. Here we are reporting on an integrated metabolomics networking approach combining gas chromatography/mass spectrometry (GC/MS) with Fourier transform ion cyclotron resonance/mass spectrometry (FT-ICR/MS) and bioinformatics analyses for the study of interactions in the potato sprout-Rhizoctonia solani pathosystem and the fluctuations in the global metabolome of sprouts. The developed bioanalytical and bioinformatics protocols provided a snapshot of the sprout's global metabolic network and its perturbations as a result of pathogen invasion. Mevalonic acid and deoxy-xylulose pathways were substantially up-regulated leading to the biosynthesis of sesquiterpene alkaloids such as the phytoalexins phytuberin, rishitin, and solavetivone, and steroidal alkaloids having solasodine and solanidine as their common aglycons. Additionally, the perturbation of the sprout's metabolism was depicted in fluctuations of the content of their amino acids pool and that of carboxylic and fatty acids. Components of the systemic acquired resistance (SAR) and hypersensitive reaction (HR) such as azelaic and oxalic acids were detected in increased levels in infected sprouts and strategies of the pathogen to overcome plant defense were proposed. Our metabolic approach has not only greatly expanded the multitude of metabolites previously reported in potato in response to pathogen invasion, but also enabled the identification of bioactive plant-derived metabolites providing valuable information that could be exploited in biotechnology, biomarker-assisted plant breeding, and crop protection for the development of new crop protection agents.     

Role of modern chemistry in sustainable arable crop protection

Organic chemistry has been, and for the foreseeable future will remain, vitally important for crop protection. Control of fungal pathogens, insect pests and weeds is crucial to enhanced food provision. As world population continues to grow, it is timely to assess the current situation, anticipate future challenges and consider how new chemistry may help meet those challenges. In future, agriculture will increasingly be expected to provide not only food and feed, but also crops for conversion into renewable fuels and chemical feedstocks. This will further increase the demand for higher crop yields per unit area, requiring chemicals used in crop production to be even more sophisticated. In order to contribute to programmes of integrated crop management, there is a requirement for chemicals to display high specificity, demonstrate benign environmental and toxicological profiles, and be biodegradable. It will also be necessary to improve production of those chemicals, because waste generated by the production process mitigates the overall benefit. Three aspects are considered in this review: advances in the discovery process for new molecules for sustainable crop protection, including tests for environmental and toxicological properties as well as biological activity; advances in synthetic chemistry that may offer efficient and environmentally benign manufacturing processes for modern crop protection chemicals; and issues related to energy use and production through agriculture.     

Standard reporting requirements for biological samples in metabolomics experiments: microbial and in vitro biology experiments

With the increasing use of metabolomics as a means to study a large number of different biological research questions, there is a need for a minimal set of reporting standards that allow the scientific community to evaluate, understand, repeat, compare and re-investigate metabolomics studies. Here we propose, a first draft of minimal requirements to effectively describe the biological context of metabolomics studies that involve microbial or in vitro biological subjects. This recommendation has been produced by the microbiology and in vitro biology working subgroup of the Metabolomics Standards Initiative in collaboration with the yeast systems biology network as part of a wider standardization initiative led by the Metabolomics Society. Microbial and in vitro biology metabolomics is defined by this sub-working group as studies with any cell or organism that require a defined external medium to facilitate growth and propagation. Both a minimal set and a best practice set of reporting standards for metabolomics experiments have been defined. The minimal set of reporting standards for microbial or in vitro biology metabolomics experiments includes those factors that are specific for metabolomics experiments and that critically determine the outcome of the experiments. The best practice set of reporting standards contains both the factors that are specific for metabolomics experiments and general aspects that critically determine the outcome of any microbial or in vitro biological experiment.     

Toxicity testing: creating a revolution based on new technologies

Biotechnology is evolving at a tremendous rate. Although drug discovery is now heavily focused on high throughput and miniaturized screening, the application of these advances to the toxicological assessment of chemicals and chemical products has been slow. Nevertheless, the impending surge in demands for the regulatory toxicity testing of chemicals provides the impetus for the incorporation of novel methodologies into hazard identification and risk assessment. Here, we review the current and likely future value of these new technologies in relation to toxicological evaluation and the protection of human health.     

Identifying and Predicting Biological Risks Associated With Manufactured Nanoparticles in Aquatic Ecosystems

Nanotechnology has great potential for revolutionizing the treatment of disease, optimizing manufacturing processes and consumer products, and remediating polluted environments. Increased use and disposal of products containing nanoparticles will inevitably result in their accumulation in aquatic ecosystems via direct input and runoff from contaminated soils. Aquatic organisms are particularly susceptible to pollutants due to their large, fragile respiratory epithelium. This potential toxicity can be exacerbated by common stressors, such as changes in water temperature, salinity, pH, and oxygen levels, and must be considered in environmental risk assessments. The unique properties of manufactured nanoparticles present serious problems for risk assessment strategies, and there is a concern in the regulatory community that standard toxicological methods may be inadequate to address these compounds. Our capacity to detect and quantify nanoparticles is extremely limited, especially in complex biological, soil, or water samples. The distinctive chemistry and physical structure of each nanomaterial will determine its bioavailability, and these parameters can be altered over time or with changes in water chemistry. The use of advanced analytical techniques, such as functional genomics, proteomics, and metabolomics, can provide a global assessment of the biological response to a novel chemical and will be important in determining the potential toxicity of nanoparticles. Industry should adopt a proactive approach to identifying potential risks to aquatic ecosystems so that the benefits of nanotechnology can be fully realized.     

Toxicity testing of destruxins and crude extracts from the insect-pathogenic fungus Metarhizium anisopliae

Increasing sensitivity towards secondary metabolites from fungal biological control agents (BCAs) has prompted the toxicological risk assessment of metabolites produced by the insect pathogenic fungus Metarhizium anisopliae. Viability studies on one human and one insect cell line were used to compare the two approaches of testing individual metabolites (destruxins A, B and E) or the complete crude extract from liquid cultures. Furthermore, crude extract was separated into fractions, which did not contain the main destruxins A, B and E. Evaluation of the cytotoxic activity of these different compounds suggested that a wide range of metabolites with synergistic or adverse effects are present in the crude extract. The results indicate that identification and toxicological assessment of each individual metabolite produced by a BCA is not only time and cost-intensive, but also does not convey the whole picture. Testing of the crude extract offers an alternative approach and is recommended when assessing the risks of metabolites for registration purposes.     

Benefits and risks of exotic biological control agents

The use of exotic (=alien) arthropods in classical and augmentative biological control programs has yielded huge economic and ecological benefits. Exotic species of arthropods have contributed to the suppression of key pests in agriculture and forestry or have aided in restoring natural systems affected by adventive species. However, adverse non-target effects of exotic biological control agents have been observed in a number of projects. Non-target effects range from very small effects, e.g. 2% parasitization on a non-target insect on a local level, to massive effects on a large scale. Until now, no consensus on how to judge the magnitude of non-target effects and whether these effects can be tolerated or are unacceptable has emerged. In this paper, we briefly review both the benefits of biological control as well as the associated risks including to human and animal health, plant health and particularly the environment. We also make an attempt at identifying the major challenges for assessing risks and for balancing benefits and risks. There is general agreement that sound risk assessment procedures should precede the release of exotic invertebrate biological control agents and a recent shift??especially for arthropod biological control??from introductions done without meaningful risk assessment studies to projects conducting thorough host range testing can be observed. However, overly stringent regulations that would preclude promising agents from being developed must be avoided.     

Obligatory metabolomic profiling of gene‐edited crops is risk disproportionate

It has been argued that the application of metabolomics to gene‐edited crops would present value in three areas: (i) the detection of gene‐edited crops; (ii) the characterization of unexpected changes that might affect safety; and (iii) building on the track record of rigorous government regulation in supporting consumer acceptance of genetically modified organisms (GMOs). Here, we offer a different perspective, relative to each of these areas: (i) metabolomics is unable to differentiate whether a mutation has resulted from gene editing or from traditional breeding techniques; (ii) it is risk‐disproportionate to apply metabolomics for regulatory purposes to search for possible compositional differences within crops developed using the least likely technique to generate unexpected compositional changes; and (iii) onerous regulations for genetically engineered crops have only contributed to unwarranted public fears, and repeating this approach for gene‐edited crops is unlikely to result in a different outcome. It is also suggested that article proposing the utility of specific analytical techniques to support risk assessment would benefit from the input of scientists with subject matter expertise in risk assessment.     

Harmonization: Developing Consistent Guidelines for Applying Mode of Action and Dosimetry Information to Cancer and Noncancer Risk Assessment

The 1983 book, Risk Assessment in the Federal Government: Managing the Process, recommended developing consistent inference guidelines for cancer risk assessment. Over the last 15 years, extensive guidance have been provided for hazard assessment for cancer and other endpoints. However, as noted in several recent reports, much less progress has occurred in developing consistent guidelines for quantitative dose response assessment methodologies. This paper proposes an approach for dose response assessment guided by consideration of mode of action (pharmacodynamics) and tissue dosimetry (pharmacokinetics). As articulated here, this systematic process involves eight steps in which available information is integrated, leading first to quantitative analyses of dose response behaviors in the test species followed by quantitative analyses of relevant human exposures. The process should be equally appropriate for both cancer and noncancer endpoints. The eight steps describe the necessary procedures for incorporating mechanistic data and provide multiple options based upon the mode of action by which the chemical causes the toxicity. Given the range of issues involved in developing such a procedure, we have simply sketched the process, focusing on major approaches for using toxicological data and on major options; many details remain to be filled in. However, consistent with the revised carcinogen risk assessment guidance (USEPA, 1996c), we propose a process that would ultimately utilize biologically based or chemical specific pharmacokinetic and pharmacodynamic models as the backbone of these analyses. In the nearer term, these approaches will be combined with analysis of data using more empirical models including options intended for use in the absence of detailed information. A major emphasis in developing any harmonized process is distinguishing policy decisions from those decisions that are affected by the quality and quantity of toxicological data. Identification of data limitations also identifies areas where further study should reduce uncertainty in the final risk evaluations. A flexible dose response assessment procedure is needed to insure that sound toxicological study results are appropriately used to influence risk management decision-making and to encourage the conduct of toxicological studies oriented toward application for dose response assessments.     

Metabolomics: a tool for early detection of toxicological effects and an opportunity for biology based grouping of chemicals-from QSAR to QBAR

BASF has developed a Metabolomics database (MetaMap(?) Tox) containing approximately 500 data rich chemicals, agrochemicals and drugs. This metabolome-database has been built based upon 28-day studies in rats (adapted to OECD 407 guideline) with blood sampling and metabolic profiling after 7, 14 and 28 days of test substance treatment. Numerous metabolome patterns have been established for different toxicological targets (liver, kidney, thyroid, testes, blood, nervous system and endocrine system) which are specific for different toxicological modes of action. With these patterns early detection of toxicological effects and the underlying mechanism can now be obtained from routine studies. Early recognition of toxicological mode of action will help to develop new compounds with a more favourable toxicological profile and will also help to reduce the number of animal studies necessary to do so. Thus this technology contributes to animal welfare by means of reduction through refinement (2R), but also has potential as a replacement method by analyzing samples from in vitro studies. With respect to the REACH legislation for which a large number of animal studies will need to be performed, one of the most promising methods to reduce the number of animal experiments is grouping of chemicals and read-across to those which are data rich. So far mostly chemical similarity or QSAR models are driving the selection process of chemical grouping. However, "omics" technologies such as metabolomics may help to optimize the chemical grouping process by providing biologically based criteria for toxicological equivalence. "From QSAR to QBAR" (quantitative biological activity relationship).     

Recent and potential developments of biofluid analyses in metabolomics

Metabolomics, one of the ‘omic’ sciences in systems biology, is the global assessment and validation of endogenous small-molecule metabolites within a biologic system. Analysis of these key metabolites in body fluids has become an important role to monitor the state of biological organisms and is a widely used diagnostic tool for disease. A majority of these metabolites are being applied to metabolic profiling of the biological samples, for example, plasma and whole blood, serum, urine, saliva, cerebrospinal fluid, synovial fluid, semen, and tissue homogenates. However, the recognition of the need for a holistic approach to metabolism led to the application of metabolomics to biological fluids for disease diagnostics. A recent surge in metabolomic applications which are probably more accurate than routine clinical practice, dedicated to characterizing the biological fluids. While developments in the analysis of biofluid samples encompassing an important impediment, it must be emphasized that these biofluids are complementary. Metabolomics provides potential advantages that classical diagnostic approaches do not, based on following discovery of a suite of clinically relevant biomarkers that are simultaneously affected by the disease. Emerging as a promising biofocus, metabolomics will drive biofluid analyses and offer great benefits for public health in the long-term.     

生态代谢组学研究进展

代谢组学指某一生物系统中产生的或已存在的代谢物组的研究,以质谱和核磁共振技术为分析平台,以信息建模与系统整合为目标。随着代谢组学中的研究方法与技术成为生态学研究的有力工具,生态代谢组学概念应运而生,即研究某一个生物体对环境变化的代谢物组水平的响应。理清代谢组学与生态代谢组学学科发展的脉络,综述代谢组学研究中的常用技术及其优势与局限性,论述代谢组学技术在生态学研究中的应用现状,展望代谢组学技术与其他系统生物学组学技术的结合在生态学中的应用前景,提出生态代谢组学研究者未来要完成的任务和面对的挑战。     

稀有人参皂苷IH901在体内外的生物转化及其生物活性

人参皂苷IH901是近年人参代谢组学研究中新发现的一种稀有人参皂苷。IH901在天然人参中并不存在,系口服人参后通过系列肠道微生物在体内代谢转化,最终入血的主要代谢产物之一。最新药理学研究表明,IH901在抗肿瘤、抗炎、抗糖尿病和抗衰老等方面均表现出良好的生物活性,是人参在体内发挥活性作用的主要物质。近年来,在体内转化IH901的理论指导下,国内外学者通过体外酶转化和微生物转化等生物工程技术在大规模提取制备IH901等研究方面均取得突破性的进展。以下综述了稀有人参皂苷IH901在体内外的生物转化及其生物活性等研究进展。     

Answering biological questions by analysis of the strawberry metabolome

Background

The qualitative and quantitative analysis of all low molecular weight metabolites within a biological sample, known as the metabolome, provides powerful insights into their roles in biological systems and processes. The study of all the chemical structures, concentrations, and interactions of the thousands of metabolites is called metabolomics. However present state of the art methods and equipment can only analyse a small portion of the numerous, structurally diverse groups of chemical substances found in biological samples, especially with respect to samples of plant origin with their huge diversity of secondary metabolites. Nevertheless, metabolite profiling and fingerprinting techniques have been applied to the analysis of the strawberry metabolome since their early beginnings.

Aim

The application of metabolomics and metabolite profiling approaches within strawberry research was last reviewed in 2011. Here, we aim to summarize the latest results from research of the strawberry metabolome since its last review with a special emphasis on studies that address specific biological questions.

Key scientific concepts

Analysis of strawberry, and other fruits, requires a plethora of analytical methods and approaches encompassing the analysis of primary and secondary metabolites, as well as capturing and quantifying volatile compounds that are related to aroma as well as fruit development, function and plant-to-plant communication. The success and longevity of metabolite and volatile profiling approaches in fruit breeding relies upon the ability of the approach to uncover biologically meaningful insights. The key concepts that must be addressed and are reviewed include: gene function analysis and genotype comparison, analysis of environmental effects and plant protection, screening for bioactive compounds for food and non-food uses, fruit development and physiology as well as fruit sensorial quality. In future, the results will facilitate fruit breeding due to the identification of metabolic QTLs and candidate genes for fruit quality and consumer preference.

     

Plan for an Integrated Human and Environmental Risk Assessment in the S. Domingos Mine Area (Portugal)

The need for the integration of the assessment of human and ecological risks in contaminated areas, such as derelict mines, widely increases. The risk assessment process is becoming a powerful tool to provide sound scientific bases for decision-making processes. In Portugal, the risk assessment process is in its early years and the lack of multidisciplinary teams of experts is frequently mentioned as the main obstacle to its implementation. Therefore, the majority of the reclamation actions are based on impact assessment studies that usually are characterized by few biological and toxicological considerations. In order to account for some of these constraints, the ecological risk assessment framework proposed by the U.S. Environmental Protection Agency was used to plan the assessment of human and ecological risks posed by the high concentrations of metals scattered in the vicinity of S. Domingos mine, a cuprous pyrite mine located in the Southeast Alentejo (Portugal). This study presents the problem formulation phase of the assessment. It includes all the scientific information available for the area, a conceptual model, and an analysis plan for the risk assessment process. Following a tiered approach, several tasks were planned in order to acquire chemical, toxicological, and ecological information, in order to compensate for the lack of toxicity data for site-specific species.     

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.     

Risk analysis and management decisions for weed biological control agents: Ecological theory and modeling results

Biologically based control methods offer many advantages for the control of invasive plant species; however, these methods are not without risks to native species. Thus, there is a need for more effective and efficient methods of risk analysis for biological control agents. We show how the process of ecological risk assessment established by the United States’ Environmental Protection Agency may be adapted to improve assessment of the risks of proposed biological control agents. We discuss the risks posed by weed biological control agents, and present a simple individual-based model of herbivorous insect movement and oviposition on two species of host plant, a target invasive plant species and a non-target native species, in simulated landscapes. The model shows that risks of non-target impacts may be influenced by the details of the movement behavior of biological control agents in heterogeneous landscapes. The specific details of insect movement that appear to be relevant are readily measured in field trials and the general modeling approach is readily adapted to real landscapes. Current biological control risk assessments typically emphasize effects analysis at the expense of exposure analysis; the modeling approach presented here provides a simple and feasible way to incorporate exposure analyses. We conclude that models such as ours should be given serious consideration as part of a comprehensive strategy of risk assessment for proposed weed biological control agents.