Quantifying the free living energy exchanges of Arctic ungulates with stable isotopes

When natural diets meet an animal's requirement for energy, other essential nutrients will usually be supplied in amounts at least sufficient for survival. Knowledge of the energy requirements of free ranging species under typical conditions are important in assessing both their nutritional needs and their ecological impact. The doubly labelled water (DLW) method is currently the most promising objective field methodology for estimating free living energy expenditure but expenditure is only equal to the energy requirement when an animal is in energy balance. Reproduction and seasonal cycles of fat deposition and utilization represent significant components of the energy budget of arctic ungulates but the information gained in the course of a typical DLW study may be used to estimate processes such as milk output and fat storage and mobilization in order to predict requirements from expenditure. The DLW method has been exhaustively validated under highly controlled conditions and the introduction of innovations such as faecal sampling for the estimation of body water isotopic enrichment, the availability of appropriate correction factors and stoichiometrics for known sources of error, and iterative calculation of unknown parameters, have produced a methodology suitable for use in truly free ranging species. The few studies carried out so far in arctic ungulates indicate that previous predictions have generally underestimated the true level of expenditure, that there is considerable between animal variation in the level of expenditure and that this is largely determined by physical activity. The disadvantages of the DLW methodology are that it remains expensive and the isotope analysis is technically demanding. Furthermore, although DLW can provide an accurate value for free living energy expenditure, it is often important to have information on the individual components of expenditure, for example the relative contribution of physical activity and thermoregulatory thermogenesis, in order to interpret the values for overall expenditure. For these reasons the most valuable use of the DLW method in the field may be to validate factorial models and other approaches so that they may be used with confidence. Additional important information on the energy exchanges of free ranging animals may be obtained from other stable isotope methodologies. In addition to the use of the isotopes 2H and lsO in the DLW method, natural variations in the abundance of "C and 15N in the arctic environment may be exploited to study diet selection in truly free living arctic ungulates

Global agricultural, food and energy price spikes : Impacts on low income households in the United Kingdom and policy options

The authors acknowledge the support of Scottish Government ClimateXChange Centre and the Rural and Environment Science and Analytical Services Division.Peer reviewedPublisher PD

DNA methyltransferase candidate polymorphisms, imprinting methylation, and birth outcome

Peer reviewedPublisher PD

Breast cancer risk and imprinting methylation in blood

Date of Acceptance: 17/08/2015 Acknowledgements This study was supported by the Breast Cancer Campaign (2008MayPR46) and Fraserburgh Moonlight Prowl Breast Cancer Charity. PH, GH and GWH acknowledge the support of the Scottish Government. We would like to thank Val Bain and Michela Donnarumma for help with the data and sample collection.Peer reviewedPublisher PD

SpectralNET – an application for spectral graph analysis and visualization

BACKGROUND: Graph theory provides a computational framework for modeling a variety of datasets including those emerging from genomics, proteomics, and chemical genetics. Networks of genes, proteins, small molecules, or other objects of study can be represented as graphs of nodes (vertices) and interactions (edges) that can carry different weights. SpectralNET is a flexible application for analyzing and visualizing these biological and chemical networks. RESULTS: Available both as a standalone .NET executable and as an ASP.NET web application, SpectralNET was designed specifically with the analysis of graph-theoretic metrics in mind, a computational task not easily accessible using currently available applications. Users can choose either to upload a network for analysis using a variety of input formats, or to have SpectralNET generate an idealized random network for comparison to a real-world dataset. Whichever graph-generation method is used, SpectralNET displays detailed information about each connected component of the graph, including graphs of degree distribution, clustering coefficient by degree, and average distance by degree. In addition, extensive information about the selected vertex is shown, including degree, clustering coefficient, various distance metrics, and the corresponding components of the adjacency, Laplacian, and normalized Laplacian eigenvectors. SpectralNET also displays several graph visualizations, including a linear dimensionality reduction for uploaded datasets (Principal Components Analysis) and a non-linear dimensionality reduction that provides an elegant view of global graph structure (Laplacian eigenvectors). CONCLUSION: SpectralNET provides an easily accessible means of analyzing graph-theoretic metrics for data modeling and dimensionality reduction. SpectralNET is publicly available as both a .NET application and an ASP.NET web application from . Source code is available upon request

A novel targeted/untargeted GC-Orbitrap metabolomics methodology applied to Candida albicans and Staphylococcus aureus biofilms

Introduction: Combined infections from Candida albicans and Staphylococcus aureus are a leading cause of death in the developed world. Evidence suggests that Candida enhances the virulence of Staphylococcus—hyphae penetrate through tissue barriers, while S. aureus tightly associates with the hyphae to obtain entry to the host organism. Indeed, in a biofilm state, C. albicans enhances the antimicrobial resistance characteristics of S. aureus. The association of these microorganisms is also associated with significantly increased morbidity and mortality. Due to this tight association we hypothesised that metabolic effects were also in evidence. Objectives: To explore the interaction, we used a novel GC-Orbitrap-based mass spectrometer, the Q Exactive GC, which combines the high peak capacity and chromatographic resolution of gas chromatography with the sub-ppm mass accuracy of an Orbitrap system. This allows the capability to leverage the widely available electron ionisation libraries for untargeted applications, along with expanding accurate mass libraries and targeted matches based around authentic standards. Methods: Optimised C. albicans and S. aureus mono- and co-cultured biofilms were analysed using the new instrument in addition to the fresh and spent bacterial growth media. Results: The targeted analysis experiment was based around 36 sugars and sugar phosphates, 22 amino acids and five organic acids. Untargeted analysis resulted in the detection of 465 features from fresh and spent medium and 405 from biofilm samples. Three significantly changing compounds that matched to high scoring library fragment patterns were chosen for validation. Conclusion: Evaluation of the results demonstrates that the Q Exactive GC is suitable for metabolomics analysis using a targeted/untargeted methodology. Many of the results were as expected: e.g. rapid consumption of glucose and fructose from the medium regardless of the cell type. Modulation of sugar-phosphate levels also suggest that the pentose phosphate pathway could be enhanced in the cells from co-cultured biofilms. Untargeted metabolomics results suggested significant production of cell-wall biosynthesis components and the consumption of non-proteinaceous amino-acids

Epigenetic studies in children at risk of stunting and their parents in India, Indonesia and Senegal : A UKRI GCRF Action Against Stunting Hub protocol paper

ASR provided research and organisational support within the Action Against Stunting Hub (AASH) epigenetics theme and drafted and revised the manuscript. MN led the AASH epigenetic theme in Senegal and oversees the implementation of the epigenetic protocol and contributed to the development of the protocol and critically revised the manuscript. RRK led the AASH epigenetic theme in India and oversaw the implementation of the epigenetic protocol, contributed to the development of the protocol and critically revised the manuscript. MKH led the AASH epigenetic theme in Indonesia and oversaw the implementation of the epigenetic protocol, contributed to the development of the protocol and critically revised the manuscript. DYD was responsible for monitoring evaluation and learning on the hub, critically reviewed the protocol and revised the manuscript. LFA managed the implementation of the study in India, critically reviewed the protocol and revised the manuscript. NLZ managed the implementation of the study in Indonesia, critically reviewed the protocol and revised the manuscript. AD managed the implementation of the study in Senegal, critically reviewed the protocol and revised the manuscript. DY, TCA and MN are epigenetic researchers in Indonesia, critically reviewed the protocol and reviewed the manuscript. MG, DS, SSV and MM are epigenetic researchers in India, critically reviewed the protocol and reviewed the manuscript. GWH advised on the statistical aspects of the protocol and the power calculation and reviewed the manuscript. UF is the AASH project lead in Indonesia, contributed to study design and coordination of the study and thematic linkages; supervised drafting of the manuscript. BF is the AASH project lead in Senegal, contributed to study design and coordination of the study and thematic linkages and supervised drafting of the manuscript. BK is the AASH project lead in India, contributed to study design and coordination of the study and thematic linkages and supervised drafting of the manuscript. PH is the AASH project deputy lead and epigenetic theme lead who designed the study, drafted and revised the manuscript, carried out the statistical calculations.Peer reviewe

Eggs for Improving Nutrition, cognitive development and reducing linear growth retardation among Infants and young Children (ENRICH) : Protocol of an egg supplementation trial among children aged 9-18 months in Hyderabad, India

SKB, SRC and BK: conceptualised, designed the study and wrote first draft. LFA, TD, DPP, MC, KS and PA: developed detailed protocols, planned data collection, critical input to manuscript. RM, HD-K, CH, SFR, RPullakhandam, RPalika, RRK, RNK, MLJ and PH: concept, design, critical inputs to manuscript.Peer reviewe