Metabolomics: playing piñata with single cells

Serum metabolite profiles of postoperative fatigue syndrome in rat following partial hepatectomy

Postoperative fatigue syndrome is a general complication after surgery. However, there is no ‘‘gold standard’’ for fatigue assessment due to the lack of objective biomarkers. In this study, a rodent model of postoperative fatigue syndrome based on partial hepatectomy was firstly established and serum metabonomic method based on ultra-high performance liquid chromatography coupled with Q-TOF mass spectrometry was applied. Partial least-squares discriminant analysis was used to identify the differential metabolites in 70% partial hepatectomy rats relative to sham rats and 30% partial hepatectomy rats, which showed 70% partial hepatectomy group was significantly distinguishable from 30% partial hepatectomy group and sham group. Eighteen serum metabolites responsible for the discrimination were identified. The levels of hypoxanthine, kynurenine, tryptophan, uric acid, phenylalanine, palmitic acid, arachidonic acid and oleic acid showed progressive elevation from sham group to 30% partial hepatectomy group to 70% partial hepatectomy group, and levels of valine, tyrosine, isoleucine, linoleyl carnitine, palmitoylcarnitine, lysophosphatidylcholine (16:0), lysophosphatidylcholine (20:3), citric acid, succinic acid and hippuric acid showed progressive declining trend from sham group to 30% partial hepatectomy group to 70% partial hepatectomy group. These potential biomarkers help to understand of etiology, pathophysiology and treatment of postoperative fatigue syndrome.

Building biological foundries for next-generation synthetic biology

Synthetic biology is an interdisciplinary field that takes top-down approaches to understand and engineer biological systems through design-build-test cycles. A number of advances in this relatively young field have greatly accelerated such engineering cycles. Specifically, various innovative tools were developed for in silico biosystems design, DNA de novo synthesis and assembly, construct verification, as well as metabolite analysis, which have laid a solid foundation for building biological foundries for rapid prototyping of improved or novel biosystems. This review summarizes the state-of-the-art technologies for synthetic biology and discusses the challenges to establish such biological foundries.

Plant single-cell and single-cell-type metabolomics

In conjunction with genomics, transcriptomics, and proteomics, plant metabolomics is providing large data sets that are paving the way towards a comprehensive and holistic understanding of plant growth, development, defense, and productivity. However, dilution effects from organ- and tissue-based sampling of metabolomes have limited our understanding of the intricate regulation of metabolic pathways and networks at the cellular level. Recent advances in metabolomics methodologies, along with the post-genomic expansion of bioinformatics knowledge and functional genomics tools, have allowed the gathering of enriched information on individual cells and single cell types. Here we review progress, current status, opportunities, and challenges presented by single cell-based metabolomics research in plants.

After the feature presentation: technologies bridging untargeted metabolomics and biology

Liquid chromatography/mass spectrometry-based untargeted metabolomics is now an established experimental approach that is being broadly applied by many laboratories worldwide. Interpreting untargeted metabolomic data, however, remains a challenge and limits the translation of results into biologically relevant conclusions. Here we review emerging technologies that can be applied after untargeted profiling to extend biological interpretation of metabolomic data. These technologies include advances in bioinformatic software that enable identification of isotopes and adducts, comprehensive pathway mapping, deconvolution of MS(2) data, and tracking of isotopically labeled compounds. There are also opportunities to gain additional biological insight by complementing the metabolomic analysis of homogenized samples with recently developed technologies for metabolite imaging of intact tissues. To maximize the value of these emerging technologies, a unified workflow is discussed that builds on the traditional untargeted metabolomic pipeline. Particularly when integrated together, the combination of the advances highlighted in this review helps transform lists of masses and fold changes characteristic of untargeted profiling results into structures, absolute concentrations, pathway fluxes, and localization patterns that are typically needed to understand biology.