EDITORIAL Water, water, every where, but rarely any drop to drink

I would like to give all readers a very warm welcome to 2014 and the first issue of the tenth volume of Metabolomics. As you may be able to work out: the front cover is a celebration of this achievement, and I thank my colleague Dr Steve O’Hagan for his artistry. I am delighted that the journal is in such good shape and this is due to the excellent papers that are submitted and published, and of course the very valuable reviewing that many of you do. Metabolomics has an excellent Editorial board and I am also very grateful to them for their valuable support. You may be pondering over the title, so let me explain. Whilst I have somewhat moderated the quote from ‘‘The Rime of the Ancient Mariner’ ’ by Samuel Taylor Coleridge written in 1797–1798, the water does not refer to any liquid substance per se, nor does the drinking to the ‘dryathlon 1 ’ that I did early last year and will be doing so again to combat any Christmas excesses. Rather the water is an analogy to data—both metabolomics and metadata. Water here is a very apt comparison, as it seems rather ironic that a typical metabolomics experiments generates so much data that it is often referred to in terms of natural disasters—like data floods, data torrents or even data tsunamis. Yet even more ironic that very rarely do we make publicly available the metabolomics data (raw or processed) and the associated metadata with our publications. These metadata are as important as the metabolite data as these refer to the data about the data. We mainly think of these in terms of the important traits or features that we may want to predict, but these also refer to our experimental protocols that ar

Making colourful sense of Raman images of single cells

In order to understand biological systems it is important to gain pertinent information on the spatial localisation of chemicals within cells. With the relatively recent advent of high-resolution chemical imaging this is being realised and one rapidly developing area of research is the Raman mapping of single cells, an approach whose success has vast potential for numerous areas of biomedical research. However, there is a danger of undermining the potential routine use of Raman mapping due to a lack of consistency and transparency in the way false-shaded Raman images are constructed. In this study we demonstrate, through the use of simulated data and real Raman maps of single human keratinocyte (HaCaT) cells, how changes in the application of colour shading can dramatically alter the final Raman images. In order to avoid ambiguity and potential subjectivity in image interpretation we suggest that data distribution plots are used to aid shading approaches and that extreme care is taken to use the most appropriate false-shading for the biomedical question under investigation

Application of surface enhanced Raman scattering to the solution based detection of a popular legal high, 5,6-methylenedioxy-2-aminoindane (MDAI)

The ever increasing numbers and users of designer drugs means that analytical techniques have to evolve constantly to facilitate their identification and detection. We report that surface enhanced Raman scattering (SERS) offers a relatively fast and inexpensive method for the detection of MDAI at low concentrations. Careful optimisation of the silver sol, and salt concentrations was undertaken to ensure the SERS analysis was both reproducible and sensitive. The optimised system demonstrated acceptable peak variations of less than 15% RSD and resulted in a detection limit of just 8 ppm (5.4 × 10-5 M)

Metabolic Fingerprint Analysis of Cytochrome b5-producing E. coli N4830-1 Using FT-IR Spectroscopy

Optimization of recombinant protein expression in bacteria is an important task in order to increase protein yield while maintaining the structural fidelity of the product. In this study, we employ Fourier transform infrared (FT-IR) spectroscopy as a high throughput metabolic fingerprinting approach to optimize and monitor cytochrome b 5 (CYT b 5) production in Escherichia coli N4830-1, as the heterologous host. Cyt b5 was introduced as a plasmid with between 0 and 6 copies under a strong promoter. The FT-IR spectroscopy results combined with multivariate chemometric analysis illustrated discriminations among culture conditions as well as revealing features that correlated to the different cytb 5 gene copy numbers. The second derivative of the FT-IR spectral data allowed for the quantitative detection of Cyt b5 directly inside the intact cells without the need for extraction, and highlighted changes in protein secondary structure that was directly correlated to the cytb 5 gene copy number and protein content, and was in complete agreement with quantitative findings of standard traditional techniques such as SDS-PAGE and western blot analysis

Objective assessment of SERS thin films : Comparison of silver on copper: via galvanic displacement with commercially available fabricated substrates

Many studies report the development of new thin films for surface enhanced Raman scattering (SERS). However, the assessment of these surfaces in terms of their reproducibility for SERS is often subjective and whilst many spectra could and indeed should be reported, very few repeat measurements are typically used. Here, the performance of three SERS thin film substrates is assessed objectively using both univariate and novel multivariate methods. The silver on copper substrate (SoC) was synthesised in-house via galvanic displacement, whilst the other two substrates Klarite and QSERS are commercially available. The reproducibility of these substrates was assessed using rhodamine 6G (R6G) as a probe analyte and seven common vibrational bands that were observed in all R6G spectra were evaluated. In order to be as objective as possible a total of seven different data analysis methods were used to evaluate the surfaces revealing that overall the SoC substrate demonstrates much greater reproducibility when compared to the commercial substrates. Finally, through the collection of large datasets containing 6400 spectra per single substrate we also provide guidelines as to the typical number of spectra that should be collected in order to assess a substrate's performance objectively, and we conclude that this must be a minimum of 180 spectra collected randomly from across the region of interest

Illuminating disease and enlightening biomedicine:Raman spectroscopy as a diagnostic tool

The discovery of the Raman effect in 1928 not only aided fundamental understanding about the quantum nature of light and matter but also opened up a completely novel area of optics and spectroscopic research that is accelerating at a greater rate during the last decade than at any time since its inception. This introductory overview focuses on some of the most recent developments within this exciting field and how this has enabled and enhanced disease diagnosis and biomedical applications. We highlight a small number of stimulating high-impact studies in imaging, endoscopy, stem cell research, and other recent developments such as spatially offset Raman scattering amongst others. We hope this stimulates further interest in this already exciting field, by 'illuminating' some of the current research being undertaken by the latest in a very long line of dedicated experimentalists interested in the properties and potential beneficial applications of light

Dupuytren's: a systems biology disease

Dupuytren's disease (DD) is an ill-defined fibroproliferative disorder of the palm of the hands leading to digital contracture. DD commonly occurs in individuals of northern European extraction. Cellular components and processes associated with DD pathogenesis include altered gene and protein expression of cytokines, growth factors, adhesion molecules, and extracellular matrix components. Histology has shown increased but varying levels of particular types of collagen, myofibroblasts and myoglobin proteins in DD tissue. Free radicals and localised ischaemia have been suggested to trigger the proliferation of DD tissue. Although the existing available biological information on DD may contain potentially valuable (though largely uninterpreted) information, the precise aetiology of DD remains unknown. Systems biology combines mechanistic modelling with quantitative experimentation in studies of networks and better understanding of the interaction of multiple components in disease processes. Adopting systems biology may be the ideal approach for future research in order to improve understanding of complex diseases of multifactorial origin. In this review, we propose that DD is a disease of several networks rather than of a single gene, and show that this accounts for the experimental observations obtained to date from a variety of sources. We outline how DD may be investigated more effectively by employing a systems biology approach that considers the disease network as a whole rather than focusing on any specific single molecule

Rapid discrimination of Enterococcus faecium strains using phenotypic analytical techniques

Clinical isolates of glycopeptide resistant enterococci (GRE) were used to compare three rapid phenotyping and analytical techniques.</p