ELIXIR-UK role in bioinformatics training at the national level and across ELIXIR

ELIXIR-UK is the UK node of ELIXIR, the European infrastructure for life science data. Since its foundation in 2014, ELIXIR-UK has played a leading role in training both within the UK and in the ELIXIR Training Platform, which coordinates and delivers training across all ELIXIR members. ELIXIR-UK contributes to the Training Platform’s coordination and supports the development of training to address key skill gaps amongst UK scientists. As part of this work it acts as a conduit for nationally-important bioinformatics training resources to promote their activities to the ELIXIR community. ELIXIR-UK also leads ELIXIR’s flagship Training Portal, TeSS, which collects information about a diverse range of training and makes it easily accessible to the community. ELIXIR-UK also works with others to provide key digital skills training, partnering with the Software Sustainability Institute to provide Software Carpentry training to the ELIXIR community and to establish the Data Carpentry initiative, and taking a lead role amongst national stakeholders to deliver the StaTS project – a coordinated effort to drive engagement with training in statistics.

Anaerobic metabolism at thermal extremes: a metabolomic test of the oxygen limitation hypothesis in an aquatic insect

Thermal limits in ectotherms may arise through a mismatch between supply and demand of oxygen. At higher temperatures, the ability of their cardiac and ventilatory activities to supply oxygen becomes insufficient to meet their elevated oxygen demand. Consequently, higher levels of oxygen in the environment are predicted to enhance tolerance of heat, whereas reductions in oxygen are expected to reduce thermal limits. Here, we extend previous research on thermal limits and oxygen limitation in aquatic insect larvae and directly test the hypothesis of increased anaerobic metabolism and lower energy status at thermal extremes. We quantified metabolite profiles in stonefly nymphs under varying temperatures and oxygen levels. Under normoxia, the concept of oxygen limitation applies to the insects studied. Shifts in the metabolome of heat-stressed stonefly nymphs clearly indicate the onset of anaerobic metabolism (e.g., accumulation of lactate, acetate, and alanine), a perturbation of the tricarboxylic acid cycle (e.g., accumulation of succinate and malate), and a decrease in energy status (e.g., ATP), with corresponding decreases in their ability to survive heat stress. These shifts were more pronounced under hypoxic conditions, and negated by hyperoxia, which also improved heat tolerance. Perturbations of metabolic pathways in response to either heat stress or hypoxia were found to be somewhat similar but not identical. Under hypoxia, energy status was greatly compromised at thermal extremes, but energy shortage and anaerobic metabolism could not be conclusively identified as the sole cause underlying thermal limits under hyperoxia. Metabolomics proved useful for suggesting a range of possible mechanisms to explore in future investigations, such as the involvement of leaking membranes or free radicals. In doing so, metabolomics provided a more complete picture of changes in metabolism under hypoxia and heat stress.

Fast targeted multidimensional NMR metabolomics of colorectal cancer

The study of small molecules in body fluids has become an important tool to monitor the state of biological organisms. Applications range from model studies using cell lines to applications where human body fluids are used to monitor disease states or drug responses. NMR spectroscopy has been an important tool for metabolomics although severe overlap of signals has limited the number of compounds, which can be unambiguously identified and quantified. Therefore, deconvolution of NMR spectra is one of the greatest challenges for NMR-based metabolomics. This has commonly been achieved by using multidimensional spectra that have the disadvantage of requiring significantly longer acquisition times. Recently, a number of methods have been described to record NMR spectra much faster. Here, we explore the use of Hadamard-encoded TOCSY spectra to simultaneously select multiple lines from crowded NMR spectra of blood serum samples to acquire pseudo-two-dimensional spectra in minutes which would otherwise require many hours. The potential of this approach is demonstrated for the detection of a signature for colorectal cancer from human blood samples.

Metabolomic fingerprint of cryo-stress in a freeze tolerant insect

This study employed H-NMR spectroscopy to assay the metabolome of the high Arctic freeze-tolerant dipteran larvae, Heleomyza borealis, after recovery from exposure to a range of sub-zero temperature treatments. Our data demonstrate the resilience of freeze tolerance in individuals of this permanently freeze-tolerant species that were acclimated to summer temperatures (5 degree C): recovery of homeostasis after 48 h was not significantly disturbed by 2h exposures to -3, -12, or -20 degree C. Evidence of homeostatic perturbation to cryo-stress - both in terms of changes in specific metabolite concentrations as well as systemic changes in metabolism determined using multivariate pattern recognition techniques - was expressed almost entirely at a temperature coincident with the significant onset of mortality (-25 degree C) and considerably below the minimum winter temperatures of its over-wintering habitat (c.-12 degree C).

Liver tumors in wild flatfish: a histopathological, proteomic, and metabolomic study

Fish play host to viral, bacterial, and parasitic diseases in addition to non-infectious conditions such as cancer. The National Marine Monitoring Programme (NMMP) provides information to the U.K. Government on the health status of marine fish stocks. An aspect of this work relates to the presence of tumors and other pathologies in the liver of the offshore sentinel flatfish species, dab (Limanda limanda). Using internationally agreed quality assurance criteria, tumors and pre-tumors are diagnosed using histopathology. The current study has expanded upon this work by integrating these traditional diagnostic approaches with ones utilizing modern technologies for analysis of proteomic and metabolomic profiles of selected lesions. We have applied SELDI and FT-ICR technologies (for proteomic and metabolomic analyses, respectively) to tumor and non-tumor samples resected from the liver of dab. This combined approach has demonstrated how these technologies are able to identify protein and metabolite profiles that are specific to liver tumors. Using histopathology to classify "analysis groups" is key to the success of such an approach since it allows for elimination of spurious samples (e.g., those containing parasite infections) that may confuse interpretation of "omic" data. As such, the pathology laboratory plays a central role in collating information relating to particular specimens and in establishing sampling groups relative to specific diagnostic questions. In this study, we present pilot data, which illustrates that proteomics and metabolomics can be used to discriminate fish liver tumors and suggest future directions for work of this type.

Optimized method for the determination of phosphoarginine in abalone tissue by high-performance liquid chromatography

A rapid high-performance liquid chromatography method for the determination of phosphoarginine (PArg) in invertebrate tissue has been redeveloped and validated. The method employs a reversed-phase amino column and a KH2PO4-acetonitrile mobile phase. PArg peak identity was confirmed by comparison with a known standard and via enzymatic conversion. Additionally linear calibration data, low intra-assay variability (<4%), and a detection limit of 5 pmol were determined. The method was demonstrated using PArg extracted from red abalone (Haliotis rufescens) adductor muscle. Validation of the extraction procedure was also completed, including the measurement of a 100.2+/-0.9% extraction efficiency.

Hydrogen bond breaking dynamics of the water trimer in the translational and librational band region of liquid water

The effect of exciting each of the three classes of intermolecular vibrations on the hydrogen bond lifetime (tau(H)) of the isolated water trimer is investigated by far-infrared laser spectroscopy. Single excitation of a librational vibration decreases tau(H) by 3 orders of magnitude to tau(H) = 1-6 ps, comparable to the time scale of a number of important bulk water dynamical relaxation processes. In contrast, excitation of translational or torsional vibrations has no significant effect (tau(H) = 1-2 ns). Although such a dependence of tau(H) on intermolecular motions has also been proposed for liquid water via computer simulations, these are the first experiments that provide a detailed molecular picture of the respective motions without extensive interpretation.

Regulation of brain-derived neurotrophic factor messenger RNA levels in avian hypothalamic slice cultures

Mechanisms regulating the expression of brain-derived neurotrophic factor, a member of the neurotrophin family, have been extensively studied in the rat cerebral cortex, hippocampus and cerebellum. In contrast, little is known regarding the regulation of this growth factor in the hypothalamus. Here we present an analysis of the regulation of brain-derived neurotrophic factor messenger RNA levels in chick embryo hypothalamic slice cultures following exposure to potassium chloride, glutamate agonists and sex steroids. Following a week in chemically-defined media the tissue was depolarized by exposure to 50 mM potassium chloride for 6h, resulting in a significant 4.2-fold increase in the level of brain-derived neurotrophic factor messenger RNA. This result is consistent with studies of other brain regions. Similar 6-h acute exposures of the hypothalamic cultures to 25 microM N-methyl-D-aspartic acid, 25 microM kainic acid and 25 microM alpha-amino-3-hydroxy-5-methyl-isoxazole-4-propionic acid also significantly increased messenger RNA levels 2.5-, 2.1- and 1.4-fold, respectively. It was previously reported that brain-derived neurotrophic factor levels within the rat cerebral cortex, olfactory bulb and hippocampus are altered by exposure to 17beta-estradiol. Here we show that in hypothalamic slice cultures neither acute nor chronic treatments with 10 and 100 nM 17beta-estradiol and 10nM testosterone significantly altered the steady-state level of this growth factor. These findings show that neuronal activity, induced by glutamate agonists and potassium chloride, can regulate brain-derived neurotrophic factor messenger RNA levels within embryonic hypothalamic slice cultures. This regulation could play a critical role in the modulation of programmed cell death and synaptic maturation during development of the hypothalamus.

Far-infrared VRT spectroscopy of two water trimer isotopomers: vibrationally averaged structures and rearrangement dynamics

We report the measurement of far-infrared vibration-rotation tunnelling parallel bands of two partially deuterated water trimer isotopomers: (D2O)2DOH and (H2O)2DOH at 97.2607 cm-1 and approximately 86 cm-1, respectively. The hydrogen bond rearrangement dynamics of the two mixed trimers can be described by the simplified molecular symmetry G8, which accounts for both the flipping and bifurcation tunnelling motions previously established for (H2O)3 and (D2O)3. The observed donor tunnelling quartet, rather than triplet, splitting indicates that the two homogeneous monomers (D2O or H2O) in each mixed trimer experience slightly different environments. Vibrationally averaged structures of (H2O)3, (D2O)3, and (D2O)2DOH were examined in a Monte Carlo simulation of the out-of-plane flipping motions of the free atoms. The simulation addresses both the symmetric top behaviour and the negative zero-point inertial defect for (H2O)3 and (D2O)3, which were insufficiently counted in all previous structure models. The average ground state O--O separations, which are correlated to other angular coordinates, were determined to be 2.84 +/- 0.01 angstroms for all three species. The simulated difference in hydrogen bond nonlinearity also supports the inequivalency of the two homogeneous monomers. The structural simulation shows that the unique H in (D2O)2DOH is free, while a torsional analysis suggests the unique D in (H2O)2DOH is bound within the cyclic ring. Both bands can be assigned to the pseudorotational transitions which correlate to those found in the pure trimers.