New nucleoside-5'-alkylphosphonophosphates and related compounds containing 2'-deoxycytidine, thymidine and adenosine as nucleoside component. Syntheses and their effects on tumor cell growth in vitro

VTwins: inferring causative microbial features from metagenomic data of limited samples

It is difficult to infer causality from high-dimension metagenomic data due to interference from numerous confounders. By imitating the twin studies in genetic research, we develop a straightforward method-virtual twins (VTwins)-to eliminate the confounder effects by transforming the original cohort into a paired cohort of "Twin" samples with distinct phenotypes but matched taxonomic profiles. The results show that VTwins outperforms the conventional approach in the sensitivity of identifying causative features and only requires a 10-fold reduced sample size for recalling disease-associated microbes or pathways, as tested by simulated and empirical data. Benchmark test with other 16 kinds of software further validates the power and applicability of VTwins for handling high-dimension compositional datasets and mining causalities in metagenomic research. In conclusion, VTwins is straightforward and effective in handling high-diversity, high-dimension compositional data, promising applications in mining causalities for metagenomic and potentially other omics data. VTwins is open access and available at https://github.com/mengqingren/VTwins.

Mass spectrometry analysis of nucleosides and nucleotides

Mass spectrometry has been widely utilised in the study of nucleobases, nucleosides and nucleotides as components of nucleic acids and as bioactive metabolites in their own right. In this review, the application of mass spectrometry to such analysis is overviewed in relation to various aspects regarding the analytical mass spectrometric and chromatographic techniques applied and also the various applications of such analysis.

Shotgun lipidomics: electrospray ionization mass spectrometric analysis and quantitation of cellular lipidomes directly from crude extracts of biological samples

Lipidomics, after genomics and proteomics, is a newly and rapidly expanding research field that studies cellular lipidomes and the organizational hierarchy of lipid and protein constituents mediating life processes. Lipidomics is greatly facilitated by recent advances in, and novel applications of, electrospray ionization mass spectrometry (ESI/MS). In this review, we will focus on the advances in ESI/MS, which have facilitated the development of shotgun lipidomics and the utility of intrasource separation as an enabling strategy for utilization of 2D mass spectrometry in shotgun lipidomics of biological samples. The principles and experimental details of the intrasource separation approach will be extensively discussed. Other ESI/MS approaches towards the quantitative analyses of global cellular lipidomes directly from crude lipid extracts of biological samples will also be reviewed and compared. Multiple examples of lipidomic analyses from crude lipid extracts employing these approaches will be given to show the power of ESI/MS techniques in lipidomics. Currently, modern society is plagued by the sequelae of lipid-related diseases. It is our hope that the integration of these advances in multiple disciplines will catalyze the development of lipidomics, and such development will lead to improvements in diagnostics and therapeutics, which will ultimately result in the extended longevity and an improved quality of life for humankind.

Synthesis and antiproliferative potency of 9-beta-D-arabinofuranosyl-2-fluoroadenine phospholipid adducts

Three novel alkylphospholipid and four novel O-alkylglycerophospholipid derivatives of fludarabine (F-ara-AMP), known as a drug for the clinical treatment of chronic lymphocytic leukemia, were synthesized. The antiproliferative activity was determined in comparison to the parent nucleoside fludarabine in an immortalized but nontumorigenic human mammary epithelial cell line (H 184 A1N4), in two human breast tumor cell lines (MaTu and MCF7), and in two leukemic cell lines (HL 60 and Daudi). Fludarabine inhibited the growth of the leucemic cell lines very effectively. The breast tumor cell lines responded with much less sensitivity. The antiproliferative potency of the new compounds strongly depended on the chemical structure of the lipid component, and derivatives with a high effectiveness against one or both of the breast tumor cell lines were described.

Sphingolipid metabolism, apoptosis and resistance to cytotoxic agents: can we interfere?

Sphingolipid metabolism assumes a key role in the complex mechanisms regulating cellular stress responses to environmental stressors, including cytotoxic agents. The sphingolipid metabolic pathways, therefore, are promising sources of anticancer therapeutic strategies. Several sphingolipid metabolites have recently been shown to have bioactivity, and their individual contributions to the regulatory pathways that govern cell growth are currently being established in mammalian cells and yeast. The Sphingomyelin (SM) cycle represents a novel antiproliferative, sphingolipid-mediated signal transduction pathway that regulates cell cycle arrest, differentiation, and apoptosis in response to growth factor deprivation, cytokines, ionizing radiation, heat, and chemotherapy. Ceramide, the putative second messenger of the SM cycle, has been proposed as a molecular sensor of injury and assumes a fundamental role in the cellular stress response. This review will discuss sphingolipid metabolism within the context of the cellular stress response, the contribution of sphingolipids to chemotherapy-mediated apoptosis, and suggest novel sphingolipid-based strategies in the treatment of malignant disease.