Imperial College London

Dr Jake Bundy

Faculty of MedicineDepartment of Metabolism, Digestion and Reproduction

Senior Lecturer
 
 
 
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Contact

 

+44 (0)20 7594 3039j.bundy Website

 
 
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Location

 

101Sir Alexander Fleming BuildingSouth Kensington Campus

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Summary

 

Publications

Publication Type
Year
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99 results found

Wieder C, Frainay C, Poupin N, Rodríguez-Mier P, Vinson F, Cooke J, Lai RP, Bundy JG, Jourdan F, Ebbels Tet al., 2021, Pathway analysis in metabolomics: Recommendations for the use of over-representation analysis., PLoS Comput Biol, Vol: 17

Over-representation analysis (ORA) is one of the commonest pathway analysis approaches used for the functional interpretation of metabolomics datasets. Despite the widespread use of ORA in metabolomics, the community lacks guidelines detailing its best-practice use. Many factors have a pronounced impact on the results, but to date their effects have received little systematic attention. Using five publicly available datasets, we demonstrated that changes in parameters such as the background set, differential metabolite selection methods, and pathway database used can result in profoundly different ORA results. The use of a non-assay-specific background set, for example, resulted in large numbers of false-positive pathways. Pathway database choice, evaluated using three of the most popular metabolic pathway databases (KEGG, Reactome, and BioCyc), led to vastly different results in both the number and function of significantly enriched pathways. Factors that are specific to metabolomics data, such as the reliability of compound identification and the chemical bias of different analytical platforms also impacted ORA results. Simulated metabolite misidentification rates as low as 4% resulted in both gain of false-positive pathways and loss of truly significant pathways across all datasets. Our results have several practical implications for ORA users, as well as those using alternative pathway analysis methods. We offer a set of recommendations for the use of ORA in metabolomics, alongside a set of minimal reporting guidelines, as a first step towards the standardisation of pathway analysis in metabolomics.

Journal article

Perin G, Fletcher T, Sagi-Kiss V, Gaboriau DCA, Carey MR, Bundy JG, Jones PRet al., 2021, Calm on the surface, dynamic on the inside. Molecular homeostasis of Anabaena sp. PCC 7120 nitrogen metabolism, PLANT CELL AND ENVIRONMENT, Vol: 44, Pages: 1885-1907, ISSN: 0140-7791

Journal article

Geier F, Leroi A, Bundy J, 2019, 13C labelling of nematode worms to improve metabolome coverage by heteronuclear nuclear magnetic resonance experiments, Frontiers in Molecular Biosciences, Vol: 6, ISSN: 2296-889X

Nuclear magnetic resonance (NMR) spectroscopy is widely used as a metabolomics tool, and 1D spectroscopy is overwhelmingly the commonest approach. The use of 2D spectroscopy could offer significant advantages in terms of increased spectral dispersion of peaks, but has a number of disadvantages—in particular, heteronuclear 2D spectroscopy is often much less sensitive than 1D NMR. One factor contributing to this low sensitivity in 13C/1H heteronuclear NMR is the low natural abundance of the 13C stable isotope; as a consequence, where it is possible to label biological material with 13C, there is a potential enhancement of sensitivity of up to around 90fold. However, there are some problems that can reduce the advantages otherwise gained—in particular, the fine structure arising from 13C/13C coupling, which is essentially non-existent at natural abundance, can reduce the possible sensitivity gain and increase the chances of peak overlap. Here, we examined the use of two different heteronuclear single quantum coherence (HSQC) pulse sequences for the analysis of fully 13C-labeled tissue extracts from Caenorhabditis elegans nematodes. The constant time ct-HSQC had improved peak shape, and consequent better peak detection of metabolites from a labeled extract; matching this against reference spectra from the HMDB gave a match to about 300 records (although fewer actual metabolites, as some of these represent false positive matches). This approach gives a rapid and automated initial metabolome assignment, forming an ideal basis for further manual curation.

Journal article

Converso V, Fearn S, ware E, McPhail DS, Flemming A, Bundy JGet al., 2017, Analysis and imaging of biocidal agrochemicals using ToF-SIMS, Scientific Reports, Vol: 7, ISSN: 2045-2322

ToF-SIMS has been increasingly widely used in recent years to look at biological matrices, in particular for biomedical research, although there is still a lot of development needed to maximise the value of this technique in the life sciences. The main issue for biological matrices is the complexity of the mass spectra and therefore the difficulty to specifically and precisely detect analytes in the biological sample. Here we evaluated the use of ToF-SIMS in the agrochemical field, which remains a largely unexplored area for this technique. We profiled a large number of biocidal active ingredients (herbicides, fungicides, and insecticides); we then selected fludioxonil, a halogenated fungicide, as a model compound for more detailed study, including the effect of co-occurring biomolecules on detection limits. There was a wide range of sensitivity of the ToF-SIMS for the different active ingredient compounds, but fludioxonil was readily detected in real-world samples (wheat seeds coated with a commercial formulation). Fludioxonil did not penetrate the seed to any great depth, but was largely restricted to a layer coating the seed surface. ToF-SIMS has clear potential as a tool for not only detecting biocides in biological samples, but also mapping their distribution.

Journal article

Davies SK, Fearn S, Allsopp LP, Harrison F, Ware E, Diggle SP, Filloux A, McPhail DS, Bundy Jet al., 2017, Visualizing Antimicrobials in BacterialBiofilms: Three-Dimensional BiochemicalImaging Using TOF-SIMS, mSphere, Vol: 2, ISSN: 2379-5042

Bacterial biofilms are groups of bacteria that exist within a self-produced extracellular matrix, adhering to each other and usually to a surface. They grow on medical equipment and inserts such as catheters and are responsible for many persistent infections throughout the body, as they can have high resistance to many antimicrobials. Pseudomonas aeruginosa is an opportunistic pathogen that can cause both acute and chronic infections and is used as a model for research into biofilms. Direct biochemical methods of imaging of molecules in bacterial biofilms are of high value in gaining a better understanding of the fundamental biology of biofilms and biochemical gradients within them. Time of flight–secondary-ion mass spectrometry (TOF-SIMS) is one approach, which combines relatively high spatial resolution and sensitivity and can perform depth profiling analysis. It has been used to analyze bacterial biofilms but has not yet been used to study the distribution of antimicrobials (including antibiotics and the antimicrobial metal gallium) within biofilms. Here we compared two methods of imaging of the interior structure of P. aeruginosa in biological samples using TOF-SIMS, looking at both antimicrobials and endogenous biochemicals: cryosectioning of tissue samples and depth profiling to give pseudo-three-dimensional (pseudo-3D) images. The sample types included both simple biofilms grown on glass slides and bacteria growing in tissues in an ex vivo pig lung model. The two techniques for the 3D imaging of biofilms are potentially valuable complementary tools for analyzing bacterial infection.

Journal article

Smith WD, Bardin E, Cameron L, Edmondson CL, Farrant KV, Martin I, Murphy RA, Soren O, Turnbull AR, Wierre-Gore N, Alton EW, Bundy JG, Bush A, Connett GJ, Faust SN, Filloux A, Freemont PS, Jones AL, Takats Z, Webb JS, Williams HD, Davies JCet al., 2017, Current and future therapies for Pseudomonas aeruginosa infection in patients with cystic fibrosis, FEMS Microbiology Letters, Vol: 364, ISSN: 0378-1097

Pseudomonas aeruginosa opportunistically infects the airways of patients with cystic fibrosis and causes significant morbidity and mortality. Initial infection can often be eradicated though requires prompt detection and adequate treatment. Intermittent and then chronic infection occurs in the majority of patients. Better detection of P. aeruginosa infection using biomarkers may enable more successful eradication before chronic infection is established. In chronic infection P. aeruginosa adapts to avoid immune clearance and resist antibiotics via efflux pumps, β-lactamase expression, reduced porins and switching to a biofilm lifestyle. The optimal treatment strategies for P. aeruginosa infection are still being established, and new antibiotic formulations such as liposomal amikacin, fosfomycin in combination with tobramycin and inhaled levofloxacin are being explored. Novel agents such as the alginate oligosaccharide OligoG, cysteamine, bacteriophage, nitric oxide, garlic oil and gallium may be useful as anti-pseudomonal strategies, and immunotherapy to prevent infection may have a role in the future. New treatments that target the primary defect in cystic fibrosis, recently licensed for use, have been associated with a fall in P. aeruginosa infection prevalence. Understanding the mechanisms for this could add further strategies for treating P. aeruginosa in future.

Journal article

Gosztolai A, Schumacher J, Behrends V, Bundy JG, Heydenreich F, Bennett MH, Buck M, Barahona Met al., 2017, GlnK facilitates the dynamic regulation of bacterial nitrogen assimilation, Biophysical Journal, Vol: 112, Pages: 2219-2230, ISSN: 1542-0086

Ammonium assimilation in Escherichia coli is regulated by two paralogous proteins (GlnB and GlnK), which orchestrate interactions with regulators of gene expression, transport proteins, and metabolic pathways. Yet how they conjointly modulate the activity of glutamine synthetase, the key enzyme for nitrogen assimilation, is poorly understood. We combine experiments and theory to study the dynamic roles of GlnB and GlnK during nitrogen starvation and upshift. We measure time-resolved in vivo concentrations of metabolites, total and posttranslationally modified proteins, and develop a concise biochemical model of GlnB and GlnK that incorporates competition for active and allosteric sites, as well as functional sequestration of GlnK. The model predicts the responses of glutamine synthetase, GlnB, and GlnK under time-varying external ammonium level in the wild-type and two genetic knock-outs. Our results show that GlnK is tightly regulated under nitrogen-rich conditions, yet it is expressed during ammonium run-out and starvation. This suggests a role for GlnK as a buffer of nitrogen shock after starvation, and provides a further functional link between nitrogen and carbon metabolisms.

Journal article

Nijhuis A, Thompson H, Adam J, Parker A, Gammon L, Lewis A, Bundy JG, Soga T, Jalaly A, Propper D, Jeffery R, Suraweera N, McDonald S, Thaha MA, Feakins R, Lowe R, Bishop CL, Silver Aet al., 2017, Remodelling of microRNAs in colorectal cancer by hypoxia alters metabolism profiles and 5-fluorouracil resistance, Human Molecular Genetics, Vol: 26, Pages: 1552-1564, ISSN: 0964-6906

Solid tumours have oxygen gradients and areas of near and almost total anoxia. Hypoxia reduces sensitivity to 5-fluorouracil (5-FU)-chemotherapy for colorectal cancer (CRC). MicroRNAs (miRNAs) are hypoxia sensors and were altered consistently in six CRC cell lines (colon cancer: DLD-1, HCT116 and HT29; rectal cancer: HT55, SW837 and VACO4S) maintained in hypoxia (1 and 0.2% oxygen) compared with normoxia (20.9%). CRC cell lines also showed altered amino acid metabolism in hypoxia and hypoxia-responsive miRNAs were predicted to target genes in four metabolism pathways: beta-alanine; valine, leucine, iso-leucine; aminoacyl-tRNA; and alanine, aspartate, glutamate. MiR-210 was increased in hypoxic areas of CRC tissues and hypoxia-responsive miR-21 and miR-30d, but not miR-210, were significantly increased in 5-FU resistant CRCs. Treatment with miR-21 and miR-30d antagonists sensitized hypoxic CRC cells to 5-FU. Our data highlight the complexity and tumour heterogeneity caused by hypoxia. MiR-210 as a hypoxic biomarker, and the targeting of miR-21 and miR-30d and/or the amino acid metabolism pathways may offer translational opportunities.

Journal article

Hastings J, Mains A, Artal-Sanz M, Bergmann S, Braeckman BP, Bundy J, Cabreiro F, Dobson P, Ebert P, Hattwell J, Hefzi H, Houtkooper RH, Jelier R, Joshi C, Kothamachu VB, Lewis N, Lourenço AB, Nie Y, Norvaisas P, Pearce J, Riccio C, Rodriguez N, Santermans T, Scarcia P, Schirra HJ, Sheng M, Smith R, Suriyalaksh M, Towbin B, Tuli MA, van Weeghel M, Weinkove D, Zečić A, Zimmermann J, le Novère N, Kaleta C, Witting M, Casanueva Oet al., 2017, WormJam: A consensusC. elegansMetabolic Reconstruction and Metabolomics Community and Workshop Series, Worm, Vol: 6, Pages: e1373939-e1373939

Journal article

Tredwell GD, Leak DJ, Aw R, Edwards-Jones B, Bundy JGet al., 2017, Rapid screening of cellular stress responses in recombinant Pichiapastoris strains using metabolite profiling, Journal of Industrial Microbiology & Biotechnology, Vol: 44, Pages: 413-417, ISSN: 1476-5535

Heterologous protein production in the yeast Pichia pastoris can be limited by biological responses to high expression levels; the unfolded protein response (UPR) is a key determinant of the success of protein production in this organism. Here, we used untargeted NMR metabolic profiling (metabolomics) of a number of different recombinant strains, carried out in a miniaturized format suitable for screening-level experiments. We identified a number of metabolites (from both cell extracts and supernatants) which correlated well with UPR-relevant gene transcripts, and so could be potential biomarkers for future high-throughput screening of large numbers of P. pastoris clones.

Journal article

Rochfort S, Wyatt MA, Liebeke M, Southam AD, Viant MR, Bundy JGet al., 2016, Aromatic metabolites from the coelomic fluid of Eisenia earthworm species, European Journal of Soil Biology, Vol: 78, Pages: 17-19, ISSN: 1778-3615

Earthworms from the genus Eisenia express coelomic fluid whenunder severe stress. This coelomic fluid contains a complexmixture of small-molecule metabolites, including aromatic metaboliteswhich are known to be species-specific, yet their actual identities remain unknown. We have aimed to characterize selected high-concentration coelomic fluid metabolites. The major aromatic compound in Eisenia venetacoelomic fluid is the rare metabolite α-nicotinamide ribo-side; and the major aromatic compound for Eisenia fetida is closely related to the (already characterized) metabolite of Eisenia andrei, which consists of two aromatic quinazoline-2,4-dionering structures linked by N-acetylspermine. The biological function(s) of these metabolites in earthworms is unknown, but we hypothesize that they represent remnants of larger molecules,possibly bacterial in origin, that are recalcitrant to metabolism by earthworm enzymes.

Journal article

Tredwell GD, Bundy JG, De lorio M, Ebbels TMDet al., 2016, Modelling the acid/base 1H NMR chemical shift limits of metabolites in human urine, Metabolomics, Vol: 12, ISSN: 1573-3890

IntroductionDespite the use of buffering agents the 1H NMR spectra of biofluid samples in metabolic profiling investigations typically suffer from extensive peak frequency shifting between spectra. These chemical shift changes are mainly due to differences in pH and divalent metal ion concentrations between the samples. This frequency shifting results in a correspondence problem: it can be hard to register the same peak as belonging to the same molecule across multiple samples. The problem is especially acute for urine, which can have a wide range of ionic concentrations between different samples.ObjectivesTo investigate the acid, base and metal ion dependent 1H NMR chemical shift variations and limits of the main metabolites in a complex biological mixture.MethodsUrine samples from five different individuals were collected and pooled, and pre-treated with Chelex-100 ion exchange resin. Urine samples were either treated with either HCl or NaOH, or were supplemented with various concentrations of CaCl2, MgCl2, NaCl or KCl, and their 1H NMR spectra were acquired.ResultsNonlinear fitting was used to derive acid dissociation constants and acid and base chemical shift limits for peaks from 33 identified metabolites. Peak pH titration curves for a further 65 unidentified peaks were also obtained for future reference. Furthermore, the peak variations induced by the main metal ions present in urine, Na+, K+, Ca2+ and Mg2+, were also measured.ConclusionThese data will be a valuable resource for 1H NMR metabolite profiling experiments and for the development of automated metabolite alignment and identification algorithms for 1H NMR spectra.

Journal article

Davies SK, Leroi A, Burt A, Bundy JG, Baer CFet al., 2016, The mutational structure of metabolism in Caenorhabditis elegans., Evolution, Vol: 70, Pages: 2239-2246, ISSN: 0014-3820

A properly functioning organism must maintain metabolic homeostasis. Deleterious mutations degrade organismal function, presumably at least in part via effects on metabolic function. Here we present an initial investigation into the mutational structure of the Caenorhabditis elegans metabolome by means of a mutation accumulation experiment. We find that pool sizes of 29 metabolites vary greatly in their vulnerability to mutation, both in terms of the rate of accumulation of genetic variance (the mutational variance, VM) and the rate of change of the trait mean (the mutational bias, ΔM). Strikingly, some metabolites are much more vulnerable to mutation than any other trait previously studied in the same way. Although we cannot statistically assess the strength of mutational correlations between individual metabolites, principal component analysis provides strong evidence that some metabolite pools are genetically correlated, but also that there is substantial scope for independent evolution of different groups of metabolites. Averaged over MA lines, PC3 is positively correlated with relative fitness, but a model in which metabolites are uncorrelated with fitness is nearly as good by Akaike's Information Criterion (AIC). This article is protected by copyright. All rights reserved.

Journal article

Spurgeon DJ, Liebeke M, Anderson C, Kille P, Lawlor A, Bundy JG, Lahive Eet al., 2016, Ecological drivers influence the distributions of two cryptic lineages in an earthworm morphospecies, APPLIED SOIL ECOLOGY, Vol: 108, Pages: 8-15, ISSN: 0929-1393

Journal article

Luyten W, Antal P, Braeckman BP, Bundy J, Cirulli F, Fang-Yen C, Fuellen G, Leroi A, Liu Q, Martorell P, Metspalu A, Perola M, Ristow M, Saul N, Schoofs L, Siems K, Temmerman L, Smets T, Wolk A, Rattan SISet al., 2016, Ageing with elegans: a research proposal to map healthspan pathways, BIOGERONTOLOGY, Vol: 17, Pages: 771-782, ISSN: 1389-5729

Journal article

Goncalves SF, Davies SK, Bennett M, Raab A, Feldmann J, Kille P, Loureiro S, Spurgeon DJ, Bundy JGet al., 2016, Sub-lethal cadmium exposure increases phytochelatin concentrations in the aquatic snail Lymnaea stagnalis, Science of the Total Environment, Vol: 568, Pages: 1054-1058, ISSN: 0048-9697

Phytochelatins are metal-binding metabolites found in almostall plant species and some animal groups, including nematodes andannelids, where they can play an important role in detoxifying metalssuch as cadmium. Species from several other taxa contain a phytochelatinsynthase (PCS) gene orthologue, including molluscs, indicating they mayhave the potential to synthesize phytochelatins. However, the presence ofa gene alone does not demonstrate that it plays a functional role inmetal detoxification. In the present study, we show that the aquaticsnail Lymnaea stagnalis produced both penta- and heptapeptidephytochelatins (i.e. phytochelatin-2 and phytochelatin-3), and theirlevels increased in response to sub-lethal levels of cadmium.

Journal article

Lund-Palau H, Turnbull AR, Bush A, Bardin E, Cameron L, Soren O, Wierre-Gore N, Alton EW, Bundy JG, Connett G, Faust SN, Filloux A, Freemont P, Jones A, Khoo V, Morales S, Murphy R, Pabary R, Simbo A, Schelenz S, Takats Z, Webb J, Williams HD, Davies JCet al., 2016, Pseudomonas aeruginosa infection in cystic fibrosis: pathophysiological mechanisms and therapeutic approaches, Expert Review of Respiratory Medicine, Vol: 10, Pages: 685-697, ISSN: 1747-6348

Pseudomonas aeruginosa is a remarkably versatile environmental bacterium with an extraordinary capacity to infect the cystic fibrosis (CF) lung. Infection with P. aeruginosa occurs early, and although eradication can be achieved following early detection, chronic infection occurs in over 60% of adults with CF. Chronic infection is associated with accelerated disease progression and increased mortality. Extensive research has revealed complex mechanisms by which P. aeruginosa adapts to and persists within the CF airway. Yet knowledge gaps remain, and prevention and treatment strategies are limited by the lack of sensitive detection methods and by a narrow armoury of antibiotics. Further developments in this field are urgently needed in order to improve morbidity and mortality in people with CF. Here, we summarize current knowledge of pathophysiological mechanisms underlying P. aeruginosa infection in CF. Established treatments are discussed, and an overview is offered of novel detection methods and therapeutic strategies in development.

Journal article

Hao J, Liebeke M, Sommer U, Viant MR, Bundy JG, Ebbels TMDet al., 2016, Statistical correlations between NMR spectroscopy and direct infusion FT-ICR mass spectrometry aid annotation of unknowns in metabolomics, Analytical Chemistry, Vol: 88, Pages: 2583-2589, ISSN: 1520-6882

NMR spectroscopy and mass spectrometry are the two major analytical platforms for metabolomics, and both generatesubstantial data with hundreds to thousands of observed peaks for a single sample. Many of these are unknown, and peak assignmentis generally complex and time-consuming. Statistical correlations between data types have proven useful in expediting this process,for example in prioritizing candidate assignments. However, this approach has not been formally assessed for the comparison ofdirect-infusion mass spectrometry (DIMS) and NMR data. Here, we present a systematic analysis of a sample set (tissue extracts),and the utility of a simple correlation threshold to aid metabolite identification. The correlations were surprisingly successful inlinking structurally related signals, with 15 of 26 NMR-detectable metabolites having their highest correlation to a cognate MS ion.However, we found that the distribution of the correlations was highly dependent on the nature of the MS ion, such as the adducttype. This approach should help to alleviate this important bottleneck where both 1D NMR and DIMS datasets have been collected.

Journal article

La Rosa R, Behrends V, Williams HD, Bundy JG, Rojo Fet al., 2015, Influence of the Crc regulator on the hierarchical use of carbon sources from a complete medium in Pseudomonas, Environmental Microbiology, Vol: 18, Pages: 807-818, ISSN: 1462-2920

The Crc protein, together with the Hfq protein, participates in catabolite repression in pseudomonads, helping to coordinate metabolism. Little is known about how Crc affects the hierarchy of metabolite assimilation from complex mixtures. Using proton NMR spectroscopy, we carried out comprehensive metabolite profiling of culture supernatants (metabolic footprinting) over the course of growth of both Pseudomonas putida and P. aeruginosa, and compared the wild-type strains to deletion mutants for crc. A complex metabolite consumption hierarchy was observed, which was broadly similar between the two species, although with some important differences, for example in sugar utilisation. The order of metabolite utilisation changed upon inactivation of the crc gene, but even in the Crc-null strains some compounds were completely consumed before late metabolites were taken up. This suggests the presence of additional regulatory elements that determine the time and order of consumption of compounds. Unexpectedly, the loss of Crc led both species to excrete acetate and pyruvate as a result of unbalanced growth during exponential phase, compounds that were later consumed in stationary phase. This loss of carbon during growth helps to explain the contribution of the Crc/Hfq regulatory system to evolutionary fitness of pseudomonads.

Journal article

Burgess SJ, Hussein T, Yeoman JA, Iamshanova O, Chan KX, Boehm M, Bundy J, Bialek W, Murray JW, Nixon PJet al., 2015, Identification of the elusive pyruvate reductase of Chlamydomonas reinhardtii chloroplasts, Plant and Cell Physiology, Vol: 57, Pages: 82-94, ISSN: 1471-9053

Under anoxic conditions the green alga Chlamydomonas reinhardtii activates various 67 fermentation pathways leading to the creation of formate, acetate, ethanol and small 68 amounts of other metabolites including D-lactate and hydrogen. Progress has been 69 made in identifying the enzymes involved in these pathways and their sub-cellular 70 locations; however, the identity of the enzyme involved in reducing pyruvate to D-71 lactate has remained unclear. Based on sequence comparisons, enzyme activity 72 measurements, X-ray crystallography, biochemical fractionation and analysis of 73 knock-down mutants we conclude that pyruvate reduction in the chloroplast is 74 catalysed by a tetrameric NAD⁺-dependent D-lactate dehydrogenase encoded by 75 Cre07.g324550. Its expression during aerobic growth supports a possible function as a 76 ‘lactate valve’ for the export of lactate to the mitochondrion for oxidation by 77 cytochrome-dependent D-lactate dehydrogenases and by glycolate dehydrogenase. 78 We also present a revised spatial model of fermentation based on our 79 immunochemical detection of the likely pyruvate decarboxylase, PDC3, in the 80 cytoplasm.

Journal article

Davies SK, Bundy JG, Leroi AM, 2015, Metabolic Youth in Middle Age: Predicting Aging in Caenorhabditis elegans Using Metabolomics, Journal of Proteome Research, Vol: 14, Pages: 4603-4609, ISSN: 1535-3907

Many mutations and allelic variants are known that influence the rate at which animals age. But when in life do such variants diverge from normal patterns of ageing? And is this divergence visible in their physiologies? To investigate these questions we have used 1H NMR spectroscopy to study how the metabolome of the nematode Caenorhabditis elegans changes as it grows older. We identify a series of metabolic changes that, collectively, predict the age of wild-type worms. We then show that long-lived mutant daf-2(m41) worms are metabolically youthful compared to wild-type worms - but that this relative youth only appears in middle age. Finally, we show that metabolic age predicts the timing and magnitude of differences in age-specific mortality between these strains. Thus the future mortality of these two genotypes can be predicted long before most of the worms die.

Journal article

Bundy JG, Liebeke M, Strittmatter N, Fearn S, Morgan AJ, Kille P, Fuchser J, Wallis D, Palchykov V, Robertson J, Lahive E, Spurgeon DJ, McPhail DS, Takats Zet al., 2015, Unique metabolites protect earthworms against plant polyphenols, Nature Communications, Vol: 6, Pages: 1-7, ISSN: 2041-1723

All higher plants produce polyphenols, for defence against above-ground herbivory. These polyphenols also influence the soil micro- and macrofauna that break down plant leaf litter. Polyphenols therefore indirectly affect the fluxes of soil nutrients and, ultimately, carbon turnover and ecosystem functioning in soils. It is unknown how earthworms, the major component of animal biomass in many soils, cope with high-polyphenol diets. Here, we show that earthworms possess a class of unique surface-active metabolites in their gut, which we term ‘drilodefensins’. These compounds counteract the inhibitory effects of polyphenols on earthworm gut enzymes, and high polyphenol diets increase drilodefensin concentrations in both laboratory and field populations. This shows that drilodefensins protect earthworms from the harmful effects of ingested polyphenols. We have identified the key mechanism for adaptation to a dietary challenge in an animal group that has a major role in organic matter recycling in soils worldwide.

Journal article

Lewis A, Mehta S, Hanna LN, Rogalski LA, Jeffery R, Nijhuis A, Kumagai T, Biancheri P, Bundy JG, Bishop CL, Feakins R, Di Sabatino A, Lee JC, Lindsay JO, Silver Aet al., 2015, Low Serum Levels of MicroRNA-19 Are Associated with a Stricturing Crohn's Disease Phenotype, INFLAMMATORY BOWEL DISEASES, Vol: 21, Pages: 1926-1934, ISSN: 1078-0998

Journal article

Thompson RB, Reffatto V, Bundy JG, Kortvely E, Flinn JM, Lanzirotti A, Jones EA, McPhail DS, Fearn S, Boldt K, Ueffing M, Ratu SGS, Pauleikhoff L, Bird AC, Lengyel Iet al., 2015, Correction: Identification of hydroxyapatite spherules provides new insight into subretinal pigment epithelial deposit formation in the aging eye (Proceedings of the National Academy of Sciences of the United States of America (2015) 112, 5, (1565-1570) DOI: 10.1073/pnas.1413347112), Proceedings of the National Academy of Sciences, Vol: 112, Pages: E3971-E3971, ISSN: 0027-8424

Journal article

Thompson RB, Reffatto V, Bundy JG, Kortvely E, Flinne JM, Lanzirotti A, Jones EA, McPhail DS, Fearn S, Bold K, Ueffing M, Singh SG, Pauleikhoff L, Bird AC, Lengyel Iet al., 2015, Identification of hydroxyapatite spherules provides new insight into subretinal pigment epithelial deposit formation in the aging eye, Proceedings of the National Academy of Sciences of the United States of America, Vol: 112, Pages: 1565-1570, ISSN: 1091-6490

Accumulation of protein- and lipid-containing deposits external to the retinal pigment epithelium (RPE) is common in the aging eye, and has long been viewed as the hallmark of age-related macular degeneration (AMD). The cause for the accumulation and retention of molecules in the sub-RPE space, however, remains an enigma. Here, we present fluorescence microscopy and X-ray diffraction evidence for the formation of small (0.5–20 μm in diameter), hollow, hydroxyapatite (HAP) spherules in Bruch’s membrane in human eyes. These spherules are distinct in form, placement, and staining from the well-known calcification of the elastin layer of the aging Bruch’s membrane. Secondary ion mass spectrometry (SIMS) imaging confirmed the presence of calcium phosphate in the spherules and identified cholesterol enrichment in their core. Using HAP-selective fluorescent dyes, we show that all types of sub-RPE deposits in the macula, as well as in the periphery, contain numerous HAP spherules. Immunohistochemical labeling for proteins characteristic of sub-RPE deposits, such as complement factor H, vitronectin, and amyloid beta, revealed that HAP spherules were coated with these proteins. HAP spherules were also found outside the sub-RPE deposits, ready to bind proteins at the RPE/choroid interface. Based on these results, we propose a novel mechanism for the growth, and possibly even the formation, of sub-RPE deposits, namely, that the deposit growth and formation begin with the deposition of insoluble HAP shells around naturally occurring, cholesterol-containing extracellular lipid droplets at the RPE/choroid interface; proteins and lipids then attach to these shells, initiating or supporting the growth of sub-RPE deposits.

Journal article

Behrends V, Maharjan RP, Ryall B, Feng L, Liu B, Wang L, Bundy JG, Ferenci Tet al., 2014, A metabolic trade-off between phosphate and glucose utilization in Escherichia coli, MOLECULAR BIOSYSTEMS, Vol: 10, Pages: 2820-2822, ISSN: 1742-206X

Journal article

Liebeke M, Bruford MW, Donnelly RK, Ebbels TM, Hao J, Kille P, Lahive E, Madison RM, Morgan AJ, Pinto-Juma GA, Spurgeon DJ, Svendsen C, Bundy JGet al., 2014, Identifying biochemical phenotypic differences between cryptic species., Biology Letters, Vol: 10, ISSN: 1744-9561

Molecular genetic methods can distinguish divergent evolutionary lineages in what previously appeared to be single species, but it is not always clear what functional differences exist between such cryptic species. We used a metabolomic approach to profile biochemical phenotype (metabotype) differences between two putative cryptic species of the earthworm Lumbricus rubellus. There were no straightforward metabolite biomarkers of lineage, i.e. no metabolites that were always at higher concentration in one lineage. Multivariate methods, however, identified a small number of metabolites that together helped distinguish the lineages, including uncommon metabolites such as Nε-trimethyllysine, which is not usually found at high concentrations. This approach could be useful for characterizing functional trait differences, especially as it is applicable to essentially any species group, irrespective of its genome sequencing status.

Journal article

Hao J, Liebeke M, Astle W, De Iorio M, Bundy JG, Ebbels TMDet al., 2014, Bayesian deconvolution and quantification of metabolites in complex 1D NMR spectra using BATMAN, NATURE PROTOCOLS, Vol: 9, Pages: 1416-1427, ISSN: 1754-2189

Journal article

Bundy JG, Kille P, Liebeke M, Spurgeon DJet al., 2014, Metallothioneins May Not Be Enough-The Role of Phytochelatins in Invertebrate Metal Detoxification, ENVIRONMENTAL SCIENCE & TECHNOLOGY, Vol: 48, Pages: 885-886, ISSN: 0013-936X

Journal article

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