J E Thomas-Oates

New University of Lisbon, Caparica, Distrito de Setubal, Portugal

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Publications (183)612.19 Total impact

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    ABSTRACT: The species Neorhizobium galegae comprises two symbiovars that induce nodules on Galega plants. Strains of both symbiovars, orientalis and officinalis, induce nodules on the same plant species, but fix nitrogen only in their own host species. The mechanism behind this strict host specificity is not yet known. In this study, genome sequences of representatives of the two symbiovars were produced, providing new material for studying properties of N. galegae, with a special interest in genomic differences that may play a role in host specificity.
    BMC genomics. 06/2014; 15(1):500.
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    ABSTRACT: Pharmaceuticals present a potential threat to soil organisms, yet our understanding of their fate and uptake in soil systems is limited. This study therefore investigated fate and uptake of 14C labelled carbamazepine, diclofenac, fluoxetine and orlistat in soil-earthworm systems. Sorption coefficients increased in the order of carbamazepine < diclofenac < fluoxetine < orlistat. Dissipation of 14C varied by compound and, for orlistat, there was evidence of formation of non-extractable residues. Uptake of 14C was seen for all compounds. Depuration studies showed complete elimination of 14C for carbamazepine and fluoxetine treatments and partial elimination for orlistat and diclofenac, with >30% of the 14C remaining in the tissue at the end experiment. Pore-water based bioconcentration factors, based on uptake and elimination of 14C, increased in the order carbamazepine < diclofenac < fluoxetine and orlistat. LC-MS/MS and LC-FTMS indicated that the observed uptake in the fluoxetine and carbamazepine treatments was due to the parent compound but that diclofenac was degraded in the test system so uptake was due to unidentifiable transformation products. Comparison of our data with outputs of quantitative structure-activity relationship for estimating BCFs in worms showed that these models tend to overestimate pharmaceutical BCFs so new models are needed.
    Environmental Science & Technology 04/2014; · 5.26 Impact Factor
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    ABSTRACT: We have developed a simple method for the release and isolation of glycoprotein N-glycans from whole cell lysates using less than a million cells, for subsequent implementation with mass spectrometric analysis. Cellular protein extracts prepared using SDS solubilisation were sequentially treated in a membrane filter device to ultimately release glycans enzymatically using PNGase F in the volatile buffer ammonium bicarbonate. The released glycans are recovered in the filtrate following centrifugation, and typically permethylated prior to mass spectrometric analysis. We call our method 'filter-aided N-glycan separation' (FANGS), and have successfully applied it to investigate N-glycan profiles of wild type (WT) and mutant Chinese hamster ovary (CHO) cells. This method is readily multiplexed, and, due to the small numbers of cells needed, is compatible with the analysis of replicate samples to assess the true nature of glycan variability in tissue culture samples.
    Journal of Proteome Research 01/2014; · 5.06 Impact Factor
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    RSC Advances 11/2013; 4:222. · 2.56 Impact Factor
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    ABSTRACT: We have investigated the microstructure and bonding of two biomass-based porous carbon chromatographic stationary phase materials (alginic acid-derived Starbon â and calcium alginate-derived mesoporous carbon spheres (AMCS)) and a commercial porous graphitic carbon (PGC), using high resolution transmission electron microscopy, electron energy loss spectroscopy (EELS), N 2 porosimetry and X-ray photoelectron spectroscopy (XPS). The pla-nar carbon sp 2 -content of all three material types is similar to that of traditional non-graphitizing carbon although, both biomass-based carbon types contain a greater percent-age of fullerene character (i.e. curved graphene sheets) than a non-graphitizing carbon pyrolyzed at the same temperature. This is thought to arise during the pyrolytic breakdown of hexauronic acid residues into C5 intermediates. Energy dispersive X-ray and XPS analy-sis reveals a homogeneous distribution of calcium in the AMCS and a calcium catalysis mechanism is discussed. That both Starbon â and AMCS, with high-fullerene character, show chromatographic properties similar to those of a commercial PGC material with extended graphitic stacks, suggests that, for separations at the molecular level, curved ful-lerene-like and planar graphitic sheets are equivalent in PGC chromatography. In addition, variation in the number of graphitic layers suggests that stack depth has minimal effect on the retention mechanism in PGC chromatography.
    Carbon 10/2013; 67:514. · 5.87 Impact Factor
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    ABSTRACT: The facile racemization of protein-bound amino acids plays an important role in the ageing and pathologies of living tissues, and can be exploited for protein geochronological studies in sub-fossil biominerals. However, the in-chain degradation pathways of amino acids are complex and difficult to elucidate. Serine has proven to be particularly elusive and its ability to racemize as a peptide-bound residue (like asparagine and aspartic acid) has not been demonstrated. This study investigates the patterns of degradation of a model peptide (WNSVWAW) at elevated temperatures, quantifying the extent of racemization and peptide bond hydrolysis using RP-HPLC and tracking the presence of degradation products by MALDI-MS. We provide direct evidence that under these experimental conditions both serine and asparagine are able to undergo racemization as internally-bound residues, which shows their potential for initiating protein breakdown and provides an explanation for the presence of d-enantiomers in living mammalian tissues.
    Analytical Chemistry 05/2013; · 5.70 Impact Factor
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    ABSTRACT: The nod(ulation) genes of Rhizobium tropici CIAT899 can be induced by very low concentrations (nM -microM range) of several flavonoid molecules secreted by the roots of leguminous plants under a number of different conditions. Some of these conditions have been investigated and appear to have a great influence on the concentration and the number of different Nod(ulation) factors, which can induce root nodule primordia and pseudo-nodules in several leguminous plant roots. In one such condition, we added up to 300 mM NaCl to the induction medium of R. tropici CIAT899 containing the nod gene inducer apigenin (Estévez et al., 2009). At the higher concentrations of NaCl, larger amounts and more different Nod factors were produced than in the absence of extra NaCl. To our surprise, under control conditions (300 mM NaCl without apigenin) some Nod factor-like spots were also observed on the thin layer plates used to detect incorporation of radiolabelled glucosamine into newly synthesised Nod factors. This phenomenon was further investigated with thin layer plates, fusions of nod genes to the lacZ gene, HPLC, mass spectrometry and the formation of pseudo-nodules on bean roots. Here we report that in the absence of flavonoid inducers, high concentrations of NaCl induced nod genes and the production of Nod factors.
    Molecular Plant-Microbe Interactions 12/2012; · 4.31 Impact Factor
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    Dataset: CMLS online
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    ABSTRACT: Haberlea rhodopensis is a resurrection plant with remarkable tolerance to desiccation. Haberlea exposed to drought stress, desiccation, and subsequent rehydration showed no signs of damage or severe oxidative stress compared to untreated control plants. Transcriptome analysis by next-generation sequencing revealed a drought-induced reprogramming, which redirected resources from growth towards cell protection. Repression of photosynthetic and growth-related genes during water deficiency was concomitant with induction of transcription factors (members of the NAC, NF-YA, MADS box, HSF, GRAS, and WRKY families) presumably acting as master switches of the genetic reprogramming, as well as with an upregulation of genes related to sugar metabolism, signaling, and genes encoding early light-inducible (ELIP), late embryogenesis abundant (LEA), and heat shock (HSP) proteins. At the same time, genes encoding other LEA, HSP, and stress protective proteins were constitutively expressed at high levels even in unstressed controls. Genes normally involved in tolerance to salinity, chilling, and pathogens were also highly induced, suggesting a possible cross-tolerance against a number of abiotic and biotic stress factors. A notable percentage of the genes highly regulated in dehydration and subsequent rehydration were novel, with no sequence homology to genes from other plant genomes. Additionally, an extensive antioxidant gene network was identified with several gene families possessing a greater number of antioxidant genes than most other species with sequenced genomes. Two of the transcripts most abundant during all conditions encoded catalases and five more catalases were induced in water-deficient samples. Using the pharmacological inhibitor 3-aminotriazole (AT) to compromise catalase activity resulted in increased sensitivity to desiccation. Metabolome analysis by GC or LC-MS revealed accumulation of sucrose, verbascose, spermidine, and γ-aminobutyric acid during drought, as well as particular secondary metabolites accumulating during rehydration. This observation, together with the complex antioxidant system and the constitutive expression of stress protective genes suggests that both constitutive and inducible mechanisms contribute to the extreme desiccation tolerance of H. rhodopensis.
    Cellular and Molecular Life Sciences CMLS 09/2012; · 5.62 Impact Factor
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    ABSTRACT: Genes for mannitol-metabolizing enzymes, mannitol phosphate dehydrogenase (MPDH) and mannitol dehydrogenase (MDH), have been recently identified in the genome of Acanthamoeba castellanii and their potential role in stress tolerance was proposed. Using qRT-PCR, comparison has been made of mRNA levels of the enzymes for mannitol metabolism at various time intervals during the stress defence reactions of encystation and pseudocyst formation. Gradual decrease of both enzymes during encystation and slight increases at the beginning of pseudocyst formation were observed. Detailed analysis of mRNA sequences of the two genes revealed similarities with various alcohol dehydrogenases rather than mannitol dehydrogenases. Our results indicate there is probably no protective role for mannitol in Acanthamoeba as no mannitol was detected using HILIC ESI MS, in any Acanthamoeba life cycle stage. Possible misinterpretation of previously published sequences as encoding enzymes of the mannitol metabolic pathway is discussed.
    Molecular and Biochemical Parasitology 04/2012; 184(2):118-21. · 2.73 Impact Factor
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    ABSTRACT: We have explored two divinylbenzene cross-linked polystyrene supports for use in a solid-supported N-terminal peptide tagging strategy. Resin-bound tags designed to be cleaved in a single step at the N-terminus of peptides have been devised and explored as peptide N-terminal tagging reagents (constructs) for subsequent mass spectrometric analysis. While the brominated tagging approach shows promise, the use of these specific solid supports has drawbacks, in terms of tagging reaction scale, for real applications in proteomics.
    ACS combinatorial science. 02/2012; 14(2):97-100.
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    ABSTRACT: N-linked glycans play key roles in protein folding, stability, and function. Biosynthetic modification of N-linked glycans, within the endoplasmic reticulum, features sequential trimming and readornment steps. One unusual enzyme, endo-α-mannosidase, cleaves mannoside linkages internally within an N-linked glycan chain, short circuiting the classical N-glycan biosynthetic pathway. Here, using two bacterial orthologs, we present the first structural and mechanistic dissection of endo-α-mannosidase. Structures solved at resolutions 1.7-2.1 Å reveal a (β/α)(8) barrel fold in which the catalytic center is present in a long substrate-binding groove, consistent with cleavage within the N-glycan chain. Enzymatic cleavage of authentic Glc(1/3)Man(9)GlcNAc(2) yields Glc(1/3)-Man. Using the bespoke substrate α-Glc-1,3-α-Man fluoride, the enzyme was shown to act with retention of anomeric configuration. Complexes with the established endo-α-mannosidase inhibitor α-Glc-1,3-deoxymannonojirimycin and a newly developed inhibitor, α-Glc-1,3-isofagomine, and with the reducing-end product α-1,2-mannobiose structurally define the -2 to +2 subsites of the enzyme. These structural and mechanistic data provide a foundation upon which to develop new enzyme inhibitors targeting the hijacking of N-glycan synthesis in viral disease and cancer.
    Proceedings of the National Academy of Sciences 01/2012; 109(3):781-6. · 9.74 Impact Factor
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    ABSTRACT: The early (2-4 d) effects of slowly imposed soil water deficit on Lupinus albus photosynthetic performance, carbon metabolism, and hormonal balance in different organs (leaf blade, stem stele, stem cortex, and root) were evaluated on 23-d-old plants (growth chamber assay). Our work shows that several metabolic adjustments occurred prior to alteration of the plant water status, implying that water deficit is perceived before the change in plant water status. The slow, progressive decline in soil water content started to be visible 3 d after withholding water (3 DAW). The earliest plant changes were associated with organ-specific metabolic responses (particularly in the leaves) and with leaf conductance and only later with plant water status and photosynthetic rate (4 DAW) or photosynthetic capacity (according to the Farquhar model; 6 DAW). Principal component analysis (PCA) of the physiological parameters, the carbohydrate and the hormone levels and their relative values, as well as leaf water-soluble metabolites full scan data (LC-MS/MS), showed separation of the different sampling dates. At 6 DAW classically described stress responses are observed, with plant water status, ABA level, and root hormonal balance contributing to the separation of these samples. Discrimination of earlier stress stages (3 and 4 DAW) is only achieved when the relative levels of indole-3-acetic acid (IAA), cytokinins (Cks), and carbon metabolism (glucose, sucrose, raffinose, and starch levels) are taken into account. Our working hypothesis is that, in addition to single responses (e.g. ABA increase), the combined alterations in hormone and carbohydrate levels play an important role in the stress response mechanism. Response to more advanced stress appears to be associated with a combination of cumulative changes, occurring in several plant organs. The carbohydrate and hormonal balance in the leaf (IAA to bioactive-Cks; soluble sugars to IAA and starch to IAA; relative abundances of the different soluble sugars) flag the initial responses to the slight decrease in soil water availability (10-15% decrease). Further alterations in sucrose to ABA and in raffinose to ABA relative values (in all organs) indicate that soil water availability continues to decrease. Such alterations when associated with changes in the root hormone balance indicate that the stress response is initiated. It is concluded that metabolic balance (e.g. IAA/bioactive Cks, carbohydrates/IAA, sucrose/ABA, raffinose/ABA, ABA/IAA) is relevant in triggering adjustment mechanisms.
    Journal of Experimental Botany 07/2011; 62(14):4965-74. · 5.24 Impact Factor
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    ABSTRACT: Archaeological work in advance of construction at a site on the edge of York, UK, yielded human remains of prehistoric to Romano-British date. Amongst these was a mandible and cranium, the intra-cranial space of which contained shrunken but macroscopically recognizable remains of a brain. Although the distinctive surface morphology of the organ is preserved, little recognizable brain histology survives. Though rare, the survival of brain tissue in otherwise skeletalised human remains from wet burial environments is not unique. A survey of the literature shows that similar brain masses have been previously reported in diverse circumstances. We argue for a greater awareness of these brain masses and for more attention to be paid to their detection and identification in order to improve the reporting rate and to allow a more comprehensive study of this rare archaeological survival.
    Journal of Archaeological Science 07/2011; 38(7):1641–1654. · 1.89 Impact Factor
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    ABSTRACT: Burkholderia cenocepacia is an important opportunistic pathogen, and one of the most striking features of the Burkholderia genus is the collection of polar lipids present in its membrane, including phosphatidylethanolamine (PE) and ornithine-containing lipids (OLs), as well as the 2-hydroxylated derivatives of PE and OLs (2-OH-PE and 2-OH-OLs, respectively), which differ from the standard versions by virtue of the presence of a hydroxyl group at C2 (2-OH) of an esterified fatty acyl residue. Similarly, a lipid A-esterified myristoyl group from Salmonella typhimurium can have a 2-hydroxy modification that is due to the LpxO enzyme. We thus postulated that 2-hydroxylation of 2-OH-OLs might be catalyzed by a novel dioxygenase homologue of LpxO. In B. cenocepacia, we have now identified two open reading frames (BCAM1214 and BCAM2401) homologous to LpxO from S. typhimurium. The introduction of bcam2401 (designated olsD) into Sinorhizobium meliloti leads to the formation of one new lipid and in B. cenocepacia of two new lipids. Surprisingly, the lipid modifications on OLs due to OlsD occur on the amide-linked fatty acyl chain. This is the first report of a hydroxyl modification of OLs on the amide-linked fatty acyl moiety. Formation of hydroxylated OLs occurs only when the biosynthesis pathway for nonmodified standard OLs is intact. The hydroxyl modification of OLs on the amide-linked fatty acyl moiety occurs only under acid stress conditions. An assay has been developed for the OlsD dioxygenase, and an initial characterization of the enzyme is presented.
    Biochemistry 06/2011; 50(29):6396-408. · 3.38 Impact Factor
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    ABSTRACT: The schistosome tegument provides a major interface with the host blood stream in which it resides. Our recent proteomic studies have identified a range of proteins present in the complex tegument structure, and two models of protective immunity have implicated surface proteins as mediating antigens. We have used the QconCAT technique to evaluate the relative and absolute amounts of tegument proteins identified previously. A concatamer comprising R- or K-terminated peptides was generated with [(13)C(6)] lysine/arginine amino acids. Two tegument surface preparations were each spiked with the purified SmQconCAT as a standard, trypsin digested, and subjected to MALDI ToF-MS. The absolute amounts of protein in the biological samples were determined by comparing the areas under the pairs of peaks, separated by 6m/z units, representing the light and heavy peptides derived from the biological sample and SmQconCAT, respectively. We report that aquaporin is the most abundant transmembrane protein, followed by two phosphohydrolases. Tetraspanin Tsp-2 and Annexin-2 are also abundant but transporters are scarce. Sm200 surface protein comprised the bulk of the GPI-anchored fraction and likely resides in the secreted membranocalyx. Two host IgGs were identified but in amounts much lower than their targets. The findings are interpreted in relation to the models of protective immunity.
    Journal of proteomics 06/2011; 74(9):1519-33. · 5.07 Impact Factor
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    ABSTRACT: The membrane-associated and membrane-spanning constituents of the Schistosoma mansoni tegument surface, the parasite's principal interface with the host bloodstream, have recently been characterized using proteomic techniques. Biotinylation of live worms using membrane-impermeant probes revealed that only a small subset of the proteins was accessible to the reagents. Their position within the multilayered architecture of the surface has not been ascertained. An enzymatic shaving approach on live worms has now been used to release the most accessible components, for analysis by MS/MS. Treatment with trypsin, or phosphatidylinositol-specific phospholipase C (PiPLC), only minimally impaired membrane integrity. PiPLC-enriched proteins were distinguished from those released in parasite vomitus or by handling damage, using isobaric tagging. Trypsin released five membrane proteins, Sm200, Sm25 and three annexins, plus host CD44 and the complement factors C3 and C4. Nutrient transporters and ion channels were absent from the trypsin fraction, suggesting a deeper location in the surface complex; surprisingly, two BAR-domain containing proteins were released. Seven parasite and two host proteins were enriched by PiPLC treatment, the vaccine candidate Sm29 being the most prominent along with two orthologues of human CD59, potentially inhibitors of complement fixation. The enzymes carbonic anhydrase and APD-ribosyl cyclase were also enriched, plus Sm200 and alkaline phosphatase. Host GPI-anchored proteins CD48 and CD90, suggest 'surface painting' during worm peregrination in the portal system. Our findings suggest that the membranocalyx secreted over the tegument surface is not the inert barrier previously proposed, some tegument proteins being externally accessible to enzymes and thus potentially located within it. Furthermore, the detection of C3 and C4 indicates that the complement cascade is initiated, while two CD59 orthologues suggest a potential mechanism for its inhibition. The detection of several host proteins is a testimonial to the acquisitive properties of the tegument surface. The exposed parasite proteins could represent novel vaccine candidates for combating this neglected disease.
    PLoS Neglected Tropical Diseases 01/2011; 5(3):e993. · 4.57 Impact Factor
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    ABSTRACT: The minerals involved in the formation of metazoan skeletons principally comprise glassy silica, calcium phosphate or carbonate. Because of their ancient heritage, glass sponges (Hexactinellida) may shed light on fundamental questions such as molecular evolution, the unique chemistry and formation of the first skeletal silica-based structures, and the origin of multicellular animals. We have studied anchoring spicules from the metre-long stalk of the glass rope sponge (Hyalonema sieboldi; Porifera, Class Hexactinellida), which are remarkable for their size, durability, flexibility and optical properties. Using slow-alkali etching of biosilica, we isolated the organic fraction, which was revealed to be dominated by a hydroxylated fibrillar collagen that contains an unusual [Gly-3Hyp-4Hyp] motif. We speculate that this motif is predisposed for silica precipitation, and provides a novel template for biosilicification in nature.
    Nature Chemistry 12/2010; 2(12):1084-8. · 21.76 Impact Factor
  • Rapid Communications in Mass Spectrometry 11/2010; 24(22):3372. · 2.51 Impact Factor

Publication Stats

3k Citations
612.19 Total Impact Points

Institutions

  • 2011
    • New University of Lisbon
      • Institute of Chemical and Biological Technology (ITQB)
      Caparica, Distrito de Setubal, Portugal
  • 1997–2011
    • Universidad Nacional Autónoma de México
      • • Centre for Genomic Sciences
      • • Institute of Biotechnology
      Mexico City, The Federal District, Mexico
    • Karl-Franzens-Universität Graz
      • Department of Analytical Chemistry
      Gratz, Styria, Austria
  • 2010
    • Technische Universität Dresden
      Dresden, Saxony, Germany
  • 2003–2010
    • The University of York
      • • Department of Biology
      • • Department of Chemistry
      York, ENG, United Kingdom
  • 2004–2009
    • University of Aberdeen
      • Department of Chemistry
      Aberdeen, SCT, United Kingdom
  • 2003–2006
    • Universidad de Sevilla
      • Departamento de Química Orgánica
      Sevilla, Andalusia, Spain
  • 1994–2006
    • Leiden University
      • Institute of Biology Leiden
      Leiden, South Holland, Netherlands
  • 1992–2006
    • Utrecht University
      • • Division of Biomolecular Mass Spectrometry
      • • Division of Biomolecular Mass Spectrometry and Proteomics
      • • Bijvoet Institute for Biomolecular Research
      • • Division of Organic Chemistry and Catalysis
      Utrecht, Utrecht, Netherlands
  • 2005
    • Max Planck Institute for Evolutionary Anthropology
      • Department of Human Evolution
      Leipzig, Saxony, Germany
  • 2002
    • The University of Manchester
      • Michael Barber Centre for Mass Spectrometry (MBCMS)
      Manchester, ENG, United Kingdom
  • 2000
    • University of London
      Londinium, England, United Kingdom
  • 1999–2000
    • University of Oslo
      • Department of Pharmacy
      Kristiania (historical), Oslo County, Norway
    • Technische Universität Berlin
      • Institut für Biotechnologie
      Berlin, Land Berlin, Germany
  • 1997–1999
    • Research Center Borstel
      Borstel, Lower Saxony, Germany
  • 1993–1995
    • University of Turku
      • Department of Medical Biochemistry and Genetics
      Turku, Western Finland, Finland