ORCID Profile
0000-0001-6342-9814
Current Organisations
Murdoch University
,
University of Melbourne
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Publisher: Elsevier BV
Date: 06-2010
Publisher: Elsevier BV
Date: 12-2008
DOI: 10.1016/J.BMC.2008.10.026
Abstract: We report the synthesis of (2E,5E)-4-oxoheptadienedioic acid and (2E)-4-oxoheptenedioic acid and evaluation of both diester and diacid analogues as inhibitors of bacterial dihydrodipicolinate synthase. Enzyme kinetic studies allowed the determination of second-order rate constants of inactivation and substrate co-incubation studies have shown the inhibitors act at the active-site. Mass spectrometric analyses have further explored the enzyme-inhibitor interaction and determined the sites of enzyme alkylation.
Publisher: Frontiers Media SA
Date: 28-06-2018
Publisher: Frontiers Media SA
Date: 04-02-2020
Publisher: Frontiers Media SA
Date: 26-02-2019
Publisher: Informa UK Limited
Date: 04-03-2022
DOI: 10.1080/19396368.2022.2027045
Abstract: Endometriosis is a disease defined by the presence of benign lesions of endometrial-like glands and stroma outside the endometrial cavity. Affecting an estimated 11.4% of Australian women, symptoms include chronic pelvic pain, dysmenorrhea and infertility. The current gold standard of diagnosis requires an expensive and invasive laparoscopic surgery, resulting in delayed time to treatment. The identification of a non-invasive endometriosis biomarker - a measurable factor correlating with disease presence or activity - has therefore become a priority in endometriosis research, although no biomarker has yet been validated. As small molecule metabolites and lipids have emerged as a potential focus, this review with systematic approach, aims to summarize studies examining metabolomic biomarkers of endometriosis in order to guide future research. EMBASE, PubMed and Web of Science were searched using keywords:
Publisher: American Chemical Society (ACS)
Date: 16-03-2021
Publisher: Royal Society of Chemistry (RSC)
Date: 2018
DOI: 10.1039/C8CC06405A
Abstract: A covalent, robust, nano-sized tetrahedral cage containing six silicon centres has been synthesised and structurally characterised.
Publisher: Springer Science and Business Media LLC
Date: 13-10-2015
Publisher: Elsevier BV
Date: 04-2012
DOI: 10.1016/J.BMC.2012.01.045
Abstract: Dihydrodipicolinate synthase is a key enzyme in the lysine biosynthesis pathway that catalyzes the condensation of pyruvate and aspartate semi-aldehyde. A series of phenolic ketoacid derivatives that mimic the proposed enzymatic intermediate were designed as potential inhibitors of this enzyme and were synthesized from simple precursors. The ketoacid derivatives were shown to act as slow and slow-tight binding inhibitors. Mass spectrometric experiments provided further evidence to support the proposed model of inhibition, demonstrating either an encounter complex or a condensation product for the slow and slow-tight binding inhibitors, respectively.
Publisher: Elsevier
Date: 2022
Publisher: Cold Spring Harbor Laboratory
Date: 19-10-2020
DOI: 10.1101/2020.10.19.346056
Abstract: Increases in soil salinity impacts growth and yield of agricultural plants by inhibiting plant functions. Soil salinization is increasing because of the pressure of a growing population on food supply. Genetically modified crops and plant breeding techniques are being used to produce plants tolerant to salt stress. However, interactions of fungal endophytes with crop plants can also improve tolerance and is a less expensive approach. Here, the role of Trichoderma harzianum T-22 in alleviating NaCl-induced stress in two barley genotypes (cv. Vlamingh and cv. Gairdner) has been investigated. Metabolomics using GC-MS for polar metabolites and LC-MS for lipids was employed to provide insights into the biochemical changes in barley roots inoculated with fungus during the early stages of interaction. T. harzianum increased the root length of both genotypes under controlled and saline conditions. The fungus reduced the relative concentration of sugars in both genotypes and caused no change in organic acids under saline conditions. Amino acids decreased only in cv. Gairdner in fungus-inoculated roots under saline conditions. Lipid analyses suggest that salt stress causes large changes in the lipid profile of roots but that inoculation with fungus greatly reduces the extent of these changes. By studying a tolerant and a sensitive genotype and their responses to salt and inoculation we have been able to develop hypotheses about what lipid species and metabolites may be involved in the tolerant genotype for its tolerance to salt and how fungal inoculation changes the response of the sensitive genotype to improve its tolerance.
Publisher: Oxford University Press (OUP)
Date: 11-03-2020
DOI: 10.1093/AOB/MCAA038
Abstract: Floral chemical defence strategies remain understudied despite the significance of flowers to plant fitness, and the fact that many flowers contain secondary metabolites that confer resistance to herbivores. Optimal defence and apparency theories predict that the most apparent plant parts and/or those most important to fitness should be most defended. To test whether within-flower distributions of chemical defence are consistent with these theories we used cyanogenic glycosides (CNglycs), which are constitutive defence metabolites that deter herbivores by releasing hydrogen cyanide upon hydrolysis. We used cyanogenic florets of the genus Lomatia to investigate at what scale there may be strategic allocation of CNglycs in flowers, what their localization reveals about function, and whether levels of floral CNglycs differ between eight congeneric species across a climatic gradient. Within-flower distributions of CNglycs during development were quantified, CNglycs were identified and their localization was visualized in cryosectioned florets using matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI). Florets of all congeneric species studied were cyanogenic, and concentrations differed between species. Within florets there was substantial variation in CNglyc concentrations, with extremely high concentrations (up to 14.6 mg CN g−1 d. wt) in pollen and loose, specialized surface cells on the pollen presenter, among the highest concentrations reported in plant tissues. Two tyrosine-derived CNglycs, the monoglycoside dhurrin and diglycoside proteacin, were identified. MALDI-MSI revealed their varying ratios in different floral tissues proteacin was primarily localized to anthers and ovules, and dhurrin to specialized cells on the pollen presenter. The mix of transient specialized cells and pollen of L. fraxinifolia was ~11 % dhurrin and ~1.1 % proteacin by mass. Tissue-specific distributions of two CNglycs and substantial variation in their concentrations within florets suggests their allocation is under strong selection. Localized, high CNglyc concentrations in transient cells challenge the predictions of defence theories, and highlight the importance of fine-scale metabolite visualization, and the need for further investigation into the ecological and metabolic roles of CNglycs in floral tissues.
Publisher: Frontiers Media SA
Date: 15-05-2020
Publisher: Frontiers Media SA
Date: 29-07-2022
DOI: 10.3389/FVETS.2022.905929
Abstract: Firstly, to compare differences in insulin, adiponectin, leptin, and measures of insulin sensitivity between diabetic cats in remission and healthy control cats, and determine whether these are predictors of diabetic relapse. Secondly, to determine if these hormones are associated with serum metabolites known to differ between groups. Thirdly, if any of the hormonal or identified metabolites are associated with measures of insulin sensitivity. Twenty cats in diabetic remission for a median of 101 days, and 21 healthy matched control cats. A casual blood glucose measured on admission to the clinic. Following a 24 h fast, a fasted blood glucose was measured, and blood s le taken for hormone (i.e., insulin, leptin, and adiponectin) and untargeted metabolomic (GC-MS and LC-MS) analysis. A simplified IVGGT (1 g glucose/kg) was performed 3 h later. Cats were monitored for diabetes relapse for at least 9 months (270 days). Cats in diabetic remission had significantly higher serum glucose and insulin concentrations, and decreased insulin sensitivity as indicated by an increase in HOMA and decrease in QUICKI and Bennett indices. Leptin was significantly increased, but there was no difference in adiponectin (or body condition score). Several significant correlations were found between insulin sensitivity indices, leptin, and serum metabolites identified as significantly different between remission and control cats. No metabolites were significantly correlated with adiponectin. No predictors of relapse were identified in this study. Insulin resistance, an underlying factor in diabetic cats, persists in diabetic remission. Cats in remission should be managed to avoid further exacerbating insulin resistance.
Publisher: Cold Spring Harbor Laboratory
Date: 03-09-2022
DOI: 10.1101/2022.08.31.505954
Abstract: Kinetic mass spectrometry imaging (kMSI) integrates imaging-MS with stable isotope labelling to elucidate metabolic fluxes in a spatiotemporal manner. kMSI studies are h ered by high volumes of complex data and a lack of computational workflows for data analysis that additionally address replicated experiments. To meet these challenges, we developed KineticMSI, an open-source R-based tool for processing and analyzing kMSI datasets. KineticMSI includes statistical tools to quantify tracer incorporation across replicated treatment groups spatially in tissues. It allows users to make data-driven decisions by elucidating affected pathways associated with changes in metabolic turnover. We demonstrate a validation of our method by identifying metabolic changes in the hippoc us of a transgenic Huntington’s disease (HD) mouse model as compared to wild-type mice. We discovered significant changes in metabolism of neuronal cell body lipids (phosphatidylinositol and cardiolipins) in HD mice, previously masked by conventional statistical approaches that compare mean tracer incorporation across brain regions.
Publisher: Frontiers Media SA
Date: 30-04-2021
Abstract: Due to their sessile nature, plants rely on root systems to mediate many biotic and abiotic cues. To overcome these challenges, the root proteome is shaped to specific responses. Proteome-wide reprogramming events are magnified in meristems due to their active protein production. Using meristems as a test system, here, we study the major rewiring that plants undergo during cold acclimation. We performed tandem mass tag-based bottom-up quantitative proteomics of two consecutive segments of barley seminal root apexes subjected to suboptimal temperatures. After comparing changes in total and ribosomal protein (RP) fraction-enriched contents with shifts in in idual protein abundances, we report ribosome accumulation accompanied by an intricate translational reprogramming in the distal apex zone. Reprogramming ranges from increases in ribosome biogenesis to protein folding factors and suggests roles for cold-specific RP paralogs. Ribosome biogenesis is the largest cellular investment thus, the vast accumulation of ribosomes and specific translation-related proteins during cold acclimation could imply a ergent ribosomal population that would lead to a proteome shift across the root. Consequently, beyond the translational reprogramming, we report a proteome rewiring. First, triggered protein accumulation includes spliceosome activity in the root tip and a ubiquitous upregulation of glutathione production and S -glutathionylation (S-GSH) assemblage machineries in both root zones. Second, triggered protein depletion includes intrinsically enriched proteins in the tip-adjacent zone, which comprise the plant immune system. In summary, ribosome and translation-related protein accumulation happens concomitantly to a proteome reprogramming in barley root meristems during cold acclimation. The cold-accumulated proteome is functionally implicated in feedbacking transcript to protein translation at both ends and could guide cold acclimation.
Publisher: Oxford University Press (OUP)
Date: 08-03-2017
DOI: 10.1104/PP.16.00055
Publisher: Wiley
Date: 14-02-2018
DOI: 10.1111/TPJ.13822
Publisher: Wiley
Date: 09-2023
DOI: 10.1002/PLD3.528
Publisher: Elsevier BV
Date: 2014
Publisher: Oxford University Press (OUP)
Date: 19-07-2021
DOI: 10.1093/JXB/ERAB335
Abstract: Soil salinity has a serious impact on plant growth and agricultural yield. Inoculation of crop plants with fungal endophytes is a cost-effective way to improve salt tolerance. We used metabolomics to study how Trichoderma harzianum T-22 alleviates NaCl-induced stress in two barley (Hordeum vulgare L.) cultivars, Gairdner and Vlamingh, with contrasting salinity tolerance. GC-MS was used to analyse polar metabolites and LC-MS to analyse lipids in roots during the early stages of interaction with Trichoderma. Inoculation reversed the severe effects of salt on root length in sensitive cv. Gairdner and, to a lesser extent, improved root growth in more tolerance cv. Vlamingh. Biochemical changes showed a similar pattern in inoculated roots after salt treatment. Sugars increased in both cultivars, with ribulose, ribose, and rhamnose specifically increased by inoculation. Salt stress caused large changes in lipids in roots but inoculation with fungus greatly reduced the extent of these changes. Many of the metabolic changes in inoculated cv. Gairdner after salt treatment mirror the response of uninoculated cv. Vlamingh, but there are some metabolites that changed in both cultivars only after fungal inoculation. Further study is required to determine how these metabolic changes are induced by fungal inoculation.
Publisher: Cold Spring Harbor Laboratory
Date: 28-10-2022
DOI: 10.1101/2022.10.27.514128
Abstract: Fungal pathogens pose a major threat to Cannabis sativa production, requiring safe and effective management procedures to control disease. Chitin and chitosan are natural molecules that elicit plant defense responses. Investigation of their effects on C. sativa will advance understanding of plant responses towards elicitors and provide a potential pathway to enhance plant resistance against diseases. Plants were grown in the in vitro Root-TRAPR system and treated with colloidal chitin and chitosan. Plant morphology was monitored, then plant tissues and exudates were collected for enzymatic activity assays, phytohormone quantification, qPCR analysis and proteomics profiling. Chitosan treatments showed increased total chitinase activity and expression of pathogenesis-related (PR) genes by 3-5 times in the root tissues. In the exudates, total peroxidase and chitinase activities and levels of defense proteins such as PR protein 1 and endochitinase 2 were increased. Shoot development was unaffected, but root development was inhibited after chitosan exposure. No significant effects on plant defense were observed upon chitin treatment. These results indicate that colloidal chitosan significantly promoted production and secretion of plant defense proteins in C. sativa root system and could be used as a potential elicitor, particularly in hydroponic scenarios to manage crop diseases. Chitosan induces defense protein productions and secretions in the root tissues and exudates of C. sativa , offering a potential pathway to enhance plant resistance against fungal attack.
Publisher: Wiley
Date: 14-08-2018
DOI: 10.1002/9781119312994.APR0627
Abstract: Plant metabolism is profoundly involved in physiological regulation and defence responses when the environment is adverse and plant growth and development is negatively affected. Metabolomics techniques allow the characterisation of physiological and biochemical responses to different types of environmental stresses in plants, including drought, salinity, and nutrient deficiencies. Metabolomics analyses of plant systems have been mostly carried out on bulked tissues (i.e. whole roots, leaves, or shoots) which can provide important biological information about plant tolerance and avoidance mechanisms to abiotic stresses. However, in idual plant organs and tissues are composed of different kinds of cells which can produce specific metabolic responses to abiotic stress. Thus, recent development and improvement of metabolomics techniques have allowed the analysis of plant metabolic changes in a spatially resolved manner (i.e. in vivo metabolomics, cell‐specific metabolomics, and mass spectrometry imaging (MSI)‐based metabolomics). This article provides a comprehensive overview of the recent findings on plant metabolite changes in response to abiotic stress, recent advancements in metabolomics techniques to study plant metabolism, and prospects of MSI‐based plant metabolomics for the study of plant metabolism.
Publisher: MDPI AG
Date: 20-07-2021
Abstract: Improved methods are required for investigating the systemic metabolic effects of SARS-CoV-2 infection and patient stratification for precision treatment. We aimed to develop an effective method using lipid profiles for discriminating between SARS-CoV-2 infection, healthy controls, and non-SARS-CoV-2 respiratory infections. Targeted liquid chromatography–mass spectrometry lipid profiling was performed on discovery (20 SARS-CoV-2-positive 37 healthy controls 22 COVID-19 symptoms but SARS-CoV-2negative) and validation (312 SARS-CoV-2-positive 100 healthy controls) cohorts. Orthogonal projection to latent structure-discriminant analysis (OPLS-DA) and Kruskal–Wallis tests were applied to establish discriminant lipids, significance, and effect size, followed by logistic regression to evaluate classification performance. OPLS-DA reported separation of SARS-CoV-2 infection from healthy controls in the discovery cohort, with an area under the curve (AUC) of 1.000. A refined panel of discriminant features consisted of six lipids from different subclasses (PE, PC, LPC, HCER, CER, and DCER). Logistic regression in the discovery cohort returned a training ROC AUC of 1.000 (sensitivity = 1.000, specificity = 1.000) and a test ROC AUC of 1.000. The validation cohort produced a training ROC AUC of 0.977 (sensitivity = 0.855, specificity = 0.948) and a test ROC AUC of 0.978 (sensitivity = 0.948, specificity = 0.922). The lipid panel was also able to differentiate SARS-CoV-2-positive in iduals from SARS-CoV-2-negative in iduals with COVID-19-like symptoms (specificity = 0.818). Lipid profiling and multivariate modelling revealed a signature offering mechanistic insights into SARS-CoV-2, with strong predictive power, and the potential to facilitate effective diagnosis and clinical management.
Publisher: Springer Science and Business Media LLC
Date: 2014
Publisher: American Chemical Society (ACS)
Date: 13-11-2022
Abstract: Ultrahigh resolution mass spectrometry (UHR-MS) coupled with direct infusion (DI) electrospray ionization offers a fast solution for accurate untargeted profiling. Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometers have been shown to produce a wealth of insights into complex chemical systems because they enable unambiguous molecular formula assignment even if the vast majority of signals is of unknown identity. Interlaboratory comparisons are required to apply this type of instrumentation in quality control (for food industry or pharmaceuticals), large-scale environmental studies, or clinical diagnostics. Extended comparisons employing different FT-ICR MS instruments with qualitative direct infusion analysis are scarce since the majority of detected compounds cannot be quantified. The extent to which observations can be reproduced by different laboratories remains unknown. We set up a preliminary study which encompassed a set of 17 laboratories around the globe, erse in instrumental characteristics and applications, to analyze the same sets of extracts from commercially available standard human blood plasma and Standard Reference Material (SRM) for blood plasma (SRM1950), which were delivered at different dilutions or spiked with different concentrations of pesticides. The aim of this study was to assess the extent to which the outputs of differently tuned FT-ICR mass spectrometers, with different technical specifications, are comparable for setting the frames of a future DI-FT-ICR MS ring trial. We concluded that a cluster of five laboratories, with erse instrumental characteristics, showed comparable and representative performance across all experiments, setting a reference to be used in a future ring trial on blood plasma.
Publisher: Wiley
Date: 02-04-2023
DOI: 10.1002/PEI3.10106
Abstract: Fungal pathogens pose a major threat to Cannabis sativa production, requiring safe and effective management procedures to control disease. Chitin and chitosan are natural molecules that elicit plant defense responses. Investigation of their effects on C. sativa will advance understanding of plant responses towards elicitors and provide a potential pathway to enhance plant resistance against diseases. Plants were grown in the in vitro Root‐TRAPR system and treated with colloidal chitin and chitosan. Plant morphology was monitored, then plant tissues and exudates were collected for enzymatic activity assays, phytohormone quantification, qPCR analysis and proteomics profiling. Chitosan treatments showed increased total chitinase activity and expression of pathogenesis‐related (PR) genes by 3–5 times in the root tissues. In the exudates, total peroxidase and chitinase activities and levels of defense proteins such as PR protein 1 and endochitinase 2 were increased. Shoot development was unaffected, but root development was inhibited after chitosan exposure. In contrast, chitin treatments had no significant impact on any defense parameters, including enzymatic activities, hormone quantities, gene expression levels and root secreted proteins. These results indicate that colloidal chitosan, significantly enhancing defense responses in C. sativa root system, could be used as a potential elicitor, particularly in hydroponic scenarios to manage crop diseases.
Publisher: American Chemical Society (ACS)
Date: 18-05-2017
DOI: 10.1021/ACS.ANALCHEM.7B00941
Abstract: The use of mass spectrometry coupled with chemical cross-linking of proteins has become a powerful tool for proteins structure and interactions studies. Unlike structural analysis of proteins using chemical reagents specific for lysine or cysteine residues, identification of gas-phase fragmentation patterns of endogenous dityrosine cross-linked peptides have not been investigated. Dityrosine cross-linking in proteins and peptides are clinical markers of oxidative stress, aging, and neurodegenerative diseases including Alzheimer's disease and Parkinson's disease. In this study, we investigated and characterized the fragmentation pattern of a synthetically prepared dityrosine cross-linked dimer of Aβ(1-16) using ESI tandem mass spectrometry. We then detailed the fragmentation pattern of dityrosine cross-linked Aβ(1-16), using collision induced dissociation (CID), higher-energy collision induced dissociation (HCD), electron transfer dissociation (ETD), and electron capture dissociation (ECD). Application of these generic fragmentation rules of dityrosine cross-linked peptides allowed for the identification of dityrosine cross-links in peptides of Aβ and α-synuclein generated in vitro by enzymatic peroxidation. We report, for the first time, the dityrosine cross-linked residues in human hemoglobin and α-synuclein under oxidative conditions. Together these tools open up the potential for automated analysis of this naturally occurring post-translation modification in neurodegenerative diseases as well as other pathological conditions.
Publisher: Georg Thieme Verlag KG
Date: 14-12-2016
Publisher: Frontiers Media SA
Date: 25-09-2019
Publisher: American Chemical Society (ACS)
Date: 22-01-2014
DOI: 10.1021/IC402860R
Abstract: The trianion Z(3-) obtained from 9-phenyl 2,3,7-trihydroxyfluor-6-one, ZH3, affords dioxomolybdenum and dioxotungsten derivatives which contain [4 + 4] metallocycles of composition [(MO2)4Z4](4-) (M = Mo, W) in combination with a variety of counter cations. The syntheses, structures and ESMS of the following compounds are presented: compound 1, (MePPh3)3(NBu4)[(MoO2)4Z4] compound 2, (MePPh3)3(NBu4)[(WO2)4Z4] compound 3, (MePPh3)4[(WO2)4Z4] compound 4, (PPh4)2(NBu4)2[(MoO2)4Z4] compound 5, (AsPh4)3(NBu4)[(MoO2)4Z4] compound 6, (AsPh4)2(NBu4)2[(WO2)4Z4] compound 7, (Ph3PNPPh3)(NBu4)3[(MoO2)4Z4] compound 8, (Ph3PNPPh3)(NBu4)3[(WO2)4Z4] compound 9, (NEt4)(NBu4)3[(MoO2)4Z4]. The metallocycles in all of these compounds have similar structures, with the four metal centers located at the corners of a square slightly distorted, to varying degrees, toward a rhombus and also toward a tetrahedron. Various cations are bound inside the anionic metallocycles. ESI mass spectrometry shows that the metallocycles remain intact in the gas phase, forming [(MO2)4Z4](4-), {X-[(MO2)4Z4]}(3-) and in some cases {X2-[(MO2)4Z4]}(2-) where X(+) is an organic cation.
Publisher: Cold Spring Harbor Laboratory
Date: 08-05-2023
DOI: 10.1101/2023.05.08.23289637
Abstract: We present compelling evidence for the existence of an extended innate viperin dependent pathway which provides crucial evidence for an adaptive response to viral agents like SARS-CoV-2. We show the in vivo biosynthesis of a family of endogenous cytosine metabolites with potential antiviral activity. Two dimensional Nuclear magnetic resonance (NMR) spectroscopy revealed a characteristic spin-system motif indicating the presence of an extended panel of urinary metabolites during the acute viral replication phase. Mass spectrometry additionally allowed the characterization and quantification of the most abundant serum metabolites showing potential diagnostic value of the compounds for viral infections. In total, we unveiled ten nucleoside (cytosine and uracil based) analogue structures, eight of which were previously unknown in humans. The molecular structures of the nucleoside analogues and their correlation with an array of serum cytokines, including IFN-α2, IFN-γ and IL-10, suggest an association with the viperin enzyme contributing to an endogenous innate immune defence mechanism against viral infection.
Publisher: Springer Science and Business Media LLC
Date: 14-08-2018
DOI: 10.1007/S00018-018-2897-6
Abstract: Sea anemone venoms have long been recognized as a rich source of peptides with interesting pharmacological and structural properties, but they still contain many uncharacterized bioactive compounds. Here we report the discovery, three-dimensional structure, activity, tissue localization, and putative function of a novel sea anemone peptide toxin that constitutes a new, sixth type of voltage-gated potassium channel (K
Publisher: Oxford University Press (OUP)
Date: 22-04-2010
Abstract: Low-molecular-weight borate complexes were isolated from canola (Brassica napus) and wheat (Triticum aestivum) phloem exudates, as well as the cytoplasm of the fresh-water alga Chara corallina, and identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Phloem exudate was collected from field-grown canola inflorescence stalks by shallow incision, while wheat phloem exudate was collected by aphid stylectomy. Chara cytoplasm was collected by careful manual separation of the cell wall, vacuole, and cytosolic compartments. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry showed the presence of isotopic borate complexes, at mass-to-charge ratio of 690.22/691.22 in the canola and wheat phloem and at 300.11/301.11 in canola phloem and Chara cytoplasm. Using reference compounds, the borate complexes with mass-to-charge ratio 690.22/691.22 was identified as a bis-sucrose (Suc) borate complex in which the 4,6-hydroxyl pairs from the two α-glucopyranoside moieties formed an [L2B]−1 complex. Further investigation using liquid chromatography electrospray ionization triple quadrupole mass spectrometry analysis confirmed the presence of the bis-Suc borate complex in wheat phloem with a concentration up to 220 μ m. The 300.11/301.11 complex was putatively identified as a bis-N-acetyl-serine borate complex but its concentration was below the detection limits of the liquid chromatography electrospray ionization triple quadrupole mass spectrometer so could not be quantified. The presence of borate complexes in the phloem provides a mechanistic explanation for the observed phloem boron mobility in canola and wheat and other species that transport Suc as their primary photoassimilate.
Publisher: Springer Science and Business Media LLC
Date: 14-10-2021
DOI: 10.1038/S41531-021-00239-X
Abstract: Characterisation and diagnosis of idiopathic Parkinson’s disease (iPD) is a current challenge that h ers both clinical assessment and clinical trial development with the potential inclusion of non-PD cases. Here, we used a targeted mass spectrometry approach to quantify 38 metabolites extracted from the serum of 231 in iduals. This cohort is currently one of the largest metabolomic studies including iPD patients, drug-naïve iPD, healthy controls and patients with Alzheimer’s disease as a disease-specific control group. We identified six metabolites (3-hydroxykynurenine, aspartate, beta-alanine, homoserine, ornithine (Orn) and tyrosine) that are significantly altered between iPD patients and control participants. A multivariate model to predict iPD from controls had an area under the curve (AUC) of 0.905, with an accuracy of 86.2%. This panel of metabolites may serve as a potential prognostic or diagnostic assay for clinical trial prescreening, or for aiding in diagnosing pathological disease in the clinic.
Publisher: Frontiers Media SA
Date: 28-08-2019
Publisher: Informa UK Limited
Date: 22-11-2014
DOI: 10.4161/EPI.27248
Publisher: American Chemical Society (ACS)
Date: 27-09-2021
Publisher: Springer Science and Business Media LLC
Date: 19-04-2018
Publisher: American Society for Microbiology
Date: 27-04-2021
Abstract: Many microbial pathogens switch between different growth and physiological states in vivo in order to adapt to local nutrient levels and host microbicidal responses. Heterogeneity in microbial growth and metabolism may also contribute to nongenetic mechanisms of drug resistance and drug failure.
Publisher: Springer New York
Date: 2018
DOI: 10.1007/978-1-4939-7819-9_17
Abstract: Mass spectrometry imaging (MSI) is a developing technique to measure the spatiotemporal distribution of many biomolecules in tissues. Over the preceding decade MSI has been adopted by plant biologists and applied in a broad range of areas including: primary metabolism, natural products, plant defense, plant responses to abiotic and biotic stress, plant lipids, and the developing field of spatial metabolomics. This methods chapter covers preparation of plant tissues for matrix-assisted laser desorption ionization (MALDI)-MSI, including s le embedding and freezing, sectioning, mounting, and matrix deposition using both sublimation and spray deposition prior to MSI analysis.
Publisher: Springer Science and Business Media LLC
Date: 12-2015
Publisher: Wiley
Date: 04-2017
DOI: 10.1111/JIPB.12525
Publisher: Springer Science and Business Media LLC
Date: 11-2018
DOI: 10.1007/S11306-018-1449-2
Abstract: Metabolomics aims to identify the changes in endogenous metabolites of biological systems in response to intrinsic and extrinsic factors. This is accomplished through untargeted, semi-targeted and targeted based approaches. Untargeted and semi-targeted methods are typically applied in hypothesis-generating investigations (aimed at measuring as many metabolites as possible), while targeted approaches analyze a relatively smaller subset of biochemically important and relevant metabolites. Regardless of approach, it is well recognized amongst the metabolomics community that gas chromatography-mass spectrometry (GC-MS) is one of the most efficient, reproducible and well used analytical platforms for metabolomics research. This is due to the robust, reproducible and selective nature of the technique, as well as the large number of well-established libraries of both commercial and 'in house' metabolite databases available. This review provides an overview of developments in GC-MS based metabolomics applications, with a focus on s le preparation and preservation techniques. A number of chemical derivatization (in-time, in-liner, offline and microwave assisted) techniques are also discussed. Electron impact ionization and a summary of alternate mass analyzers are highlighted, along with a number of recently reported new GC columns suited for metabolomics. Lastly, multidimensional GC-MS and its application in environmental and biomedical research is presented, along with the importance of bioinformatics. The purpose of this review is to both highlight and provide an update on GC-MS analytical techniques that are common in metabolomics studies. Specific emphasis is given to the key steps within the GC-MS workflow that those new to this field need to be aware of and the common pitfalls that should be looked out for when starting in this area.
Publisher: Wiley
Date: 04-06-2012
DOI: 10.1002/PROT.24106
Abstract: The crystal structure of Escherichia coli dihydrodipicolinate synthase with pyruvate and substrate analogue succinic acid semialdehyde condensed with the active site lysine-161 was solved to a resolution of 2.3 Å. Comparative analysis to a previously reported structure both resolves the configuration at the aldol addition center, where the final addition product clearly displays the (S)-configuration, and the final conformation of the adduct within the active site. Direct comparison to two other crystal structures found in the Protein Data Bank, 1YXC, and 3DU0, demonstrates significant similarity between the active site residues of these structures.
Publisher: Springer International Publishing
Date: 2017
DOI: 10.1007/978-3-319-47656-8_12
Abstract: Mass spectrometry imaging (MSI) is rapidly maturing as an advanced method for spatial metabolite profiling. Herein, we provide an introduction to MSI including types of instrumentation, detailed s le preparation, data collection, overview of data analysis steps, software, common standards, and new developments. Further, we provide an overview of MSI in the clinical space over the past 3 years where MSI has been deployed in erse research areas including cancer, neurobiology, lipidomics, and metabolite profiling and mapping to name only a few. We provide several ex les demonstrating the applicability of MSI to spatially profile metabolites in unique systems requiring special considerations outside of the norm.
Publisher: Wiley
Date: 31-05-2016
DOI: 10.1111/JVIM.13952
Publisher: Oxford University Press (OUP)
Date: 08-10-2018
DOI: 10.1104/PP.18.00998
Publisher: CSIRO Publishing
Date: 2019
DOI: 10.1071/FP19122
Abstract: Plant nutrition can affect the allocation of resources to plant chemical defences, yet little is known about how phosphorus (P) supply, and relative nitrogen (N) and P supply, affect chemical defences, especially in species with intrinsically conservative nutrient use adapted to P-impoverished soils. Waratah (Telopea speciosissima (Sm.) R.Br.), like other Proteaceae, is adapted nutrient-poor soils. It was identified as having cyanogenic glycosides (CNglycs) throughout the plant. T. speciosissima seedlings were grown for 15 weeks under two N and P concentrations. CNglycs (N-based defence) and nutrients were quantified in above- and below-ground organs foliar carbon (C)-based phenolics and tannins were also quantified. CNglyc concentrations in roots were on average 51-fold higher than in above-ground tissues and were affected by both N and P supply, whereas foliar CNglyc concentrations only responded to N supply. Leaves had high concentrations of C-based defences, which increased under low N, and were not correlated with N-based defences. Greater root chemical defence against herbivores and pathogens may be important in a non-mycorrhizal species that relies on basal resprouting following disturbance. The differing responses of secondary chemistry in above- and below-ground organs to P and N demonstrate the importance of broadening the predominantly foliar focus of plant defence studies.
Publisher: Wiley
Date: 25-11-2019
DOI: 10.1002/JMS.4460
Abstract: The eye is an elegant organ consisting of a number of tissues and fluids with specialised functions that together allow it to effectively transmit and transduce light input to the brain for visual perception. One key determinant of this integrated function is the spatial relationship of ocular tissues. Biomolecular distributions within the main ocular tissues cornea, lens, and retina have been studied extensively in isolation, yet the potential for metabolic communication between ocular tissues via the ocular humours has been difficult to visualise. To address this limitation, the current study presents a method to map spatial distributions of metabolites and small molecules in whole eyes, including ocular humours. Using a tape-transfer system and freeze-drying, the spatial distribution of ocular small molecules was investigated in mouse, rat, fish (black bream), and rabbit eyes using negative ion mode MALDI imaging mass spectrometry. Full-scan imaging was used for discovery experiments, while MS/MS imaging for identification and localisation was also demonstrated. In all eyes, metabolites such as glutathione and phospholipids were localised in the main ocular tissues. In addition, in rodent eyes, major metabolites were distributed relatively uniformly in ocular humours. In contrast, both uniform and spatially defined ocular metabolite distributions were observed in the black bream eye. Tissue and ocular humour distributions were reproducible, as demonstrated by the three-dimensional analysis of a mouse eye, and able to be captured with high spatial resolution analysis. The presented method could be used to further investigate the role of inter-tissue metabolism in ocular health, and to support the development of therapeutics to treat major ocular diseases.
Publisher: American Chemical Society (ACS)
Date: 19-05-2021
Publisher: Springer Science and Business Media LLC
Date: 05-2017
DOI: 10.1038/NATURE22384
Abstract: This corrects the article DOI: 10.1038/nature21370.
Publisher: Springer Science and Business Media LLC
Date: 08-02-2017
DOI: 10.1038/NATURE21370
Abstract: Chenopodium quinoa (quinoa) is a highly nutritious grain identified as an important crop to improve world food security. Unfortunately, few resources are available to facilitate its genetic improvement. Here we report the assembly of a high-quality, chromosome-scale reference genome sequence for quinoa, which was produced using single-molecule real-time sequencing in combination with optical, chromosome-contact and genetic maps. We also report the sequencing of two diploids from the ancestral gene pools of quinoa, which enables the identification of sub-genomes in quinoa, and reduced-coverage genome sequences for 22 other s les of the allotetraploid goosefoot complex. The genome sequence facilitated the identification of the transcription factor likely to control the production of anti-nutritional triterpenoid saponins found in quinoa seeds, including a mutation that appears to cause alternative splicing and a premature stop codon in sweet quinoa strains. These genomic resources are an important first step towards the genetic improvement of quinoa.
Publisher: American Chemical Society (ACS)
Date: 10-2008
DOI: 10.1021/IC800544J
Abstract: The rigid, angular ligand 3,3,3',3'-tetramethyl-1,1'spirobisindane-5,5',6,6'-tetrol, LH4, in the form of its tetra-anion, L(4-), affords crystalline compounds containing the triangular macrocyclic boron derivative [B3L3](3-) with the counter cations, triethylammonium, imidazolium, tetraethylammonium, and protonated dabco (dabco = 1,4-diazabicyclo[2,2,2]octane). Within a triangular unit all three chiral L(4-) ligands have the same hand although the crystal does contain a racemic mixture of macrocycles. In all four compounds, one out of the three counter-cations per macrocycle is bound inside the macrocycle.
Publisher: Springer Science and Business Media LLC
Date: 20-04-2017
Publisher: Elsevier BV
Date: 12-2019
DOI: 10.1016/J.FOODRES.2019.108665
Abstract: Despite recent studies on health benefits of chia seed owing to its high content of ω-3 fatty acids, little work has been conducted on extractability of its nutrients. We examined the effect of soaking chia seed in water on the extractability of its omega fatty acids and lipids. State-of-the-art mass spectrometry techniques including GC-MS, LC-MS, and MALDI-MSI were utilized to identify and determine the spatial distribution of omega fatty acids and lipids in chia seed. Results showed that 24 h soaking in water improves the extractability of omega fatty acids and the ω-6:ω-3 ratio. Increase in the release levels of triacylglycerols and diacylglycerols and reduction in the release levels of phosphatidylcholines are envisaged to be the result of cell wall weakening and consequently availability of lipids for extraction. Results of MALDI-MSI show that highly abundant lipid species are mainly localised in the chia seed endosperm rather than its mucilage.
Publisher: Wiley
Date: 29-11-2020
DOI: 10.1111/PCE.13653
Publisher: Springer Science and Business Media LLC
Date: 30-07-2015
Publisher: Oxford University Press (OUP)
Date: 14-08-2018
Publisher: Springer Science and Business Media LLC
Date: 20-03-2020
Publisher: Springer Science and Business Media LLC
Date: 09-04-2022
DOI: 10.1186/S13007-022-00875-1
Abstract: Plant growth devices, for ex le, rhizoponics, rhizoboxes, and ecosystem fabrication (EcoFAB), have been developed to facilitate studies of plant root morphology and plant-microbe interactions in controlled laboratory settings. However, several of these designs are suitable only for studying small model plants such as Arabidopsis thaliana and Brachypodium distachyon and therefore require modification to be extended to larger plant species like crop plants. In addition, specific tools and technical skills needed for fabricating these devices may not be available to researchers. Hence, this study aimed to establish an alternative protocol to generate a larger, modular and reusable plant growth device based on different available resources. Root-TRAPR (Root-Transparent, Reusable, Affordable three-dimensional Printed Rhizo-hydroponic) system was successfully developed. It consists of two main parts, an internal root growth chamber and an external structural frame. The internal root growth chamber comprises a polydimethylsiloxane (PDMS) gasket, microscope slide and acrylic sheet, while the external frame is printed from a three-dimensional (3D) printer and secured with nylon screws. To test the efficiency and applicability of the system, industrial hemp ( Cannabis sativa ) was grown with or without exposure to chitosan, a well-known plant elicitor used for stimulating plant defense. Plant root morphology was detected in the system, and plant tissues were easily collected and processed to examine plant biological responses. Upon chitosan treatment, chitinase and peroxidase activities increased in root tissues (1.7- and 2.3-fold, respectively) and exudates (7.2- and 21.6-fold, respectively). In addition, root to shoot ratio of phytohormone contents were increased in response to chitosan. Within 2 weeks of observation, hemp plants exhibited dwarf growth in the Root-TRAPR system, easing plant handling and allowing increased replication under limited growing space. The Root-TRAPR system facilitates the exploration of root morphology and root exudate of C. sativa under controlled conditions and at a smaller scale. The device is easy to fabricate and applicable for investigating plant responses toward elicitor challenge. In addition, this fabrication protocol is adaptable to study other plants and can be applied to investigate plant physiology in different biological contexts, such as plant responses against biotic and abiotic stresses.
Publisher: Elsevier BV
Date: 07-2015
DOI: 10.1016/J.FOODCHEM.2015.01.072
Abstract: Seed of Australian acacia species, Acacia colei, Acacia elecantha, Acacia torulosa, Acacia turmida and Acacia saligna, were analysed for the presence of toxic non-protein amino acids and the levels of essential amino acids. Amines were derivatised with 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate before analysis using liquid chromatography electrospray ionisation triple quadrupole mass spectrometry (LC-ESI-QQQ-MS). Multiple reaction monitoring (MRM) with optimised transitions and collision energies for each analyte were employed. The known nephrotoxic compound djenkolic acid was found to be present at elevated levels in all species tested. The lowest levels were in A. colei (0.49% w/w) and the highest in A. saligna (1.85% w/w). Observed levels of djenkolic acid are comparable to measured and reported levels found in the djenkol bean. Subsequent testing of seed processing methods showed djenkolic acid levels can be significantly reduced by over 90% by dry roasting at 180 °C rendering the seed safe for human consumption.
Publisher: American Chemical Society (ACS)
Date: 03-2022
DOI: 10.1021/ACS.ANALCHEM.1C05389
Abstract: SARS-CoV-2 infection causes a significant reduction in lipoprotein-bound serum phospholipids give rise to supramolecular phospholipid composite (SPC) signals observed in diffusion and relaxation edited
Publisher: Elsevier BV
Date: 10-2018
DOI: 10.1016/J.ACA.2018.03.062
Abstract: Here, we developed a robust lipidomics workflow merging both targeted and untargeted approaches on a single liquid chromatography coupled to quadrupole-time of flight (LC-QqTOF) mass spectrometry platform with parallel reaction monitoring (PRM). PRM assays integrate both untargeted profiling from MS1 scans and targeted profiling obtained from MS/MS data. This workflow enabled the discovery of more than 2300 unidentified features and identification of more than 600 lipid species from 23 lipid classes at the level of fatty acid/long chain base/sterol composition in a barley root extracts. We detected the presence of 142 glycosyl inositol phosphorylceramides (GIPC) with HN(Ac)-HA as the core structure of the polar head, 12 cardiolipins and 17 glucuronosyl diacylglycerols (GlcADG) which have been rarely reported previously for cereal crops. Using a scheduled algorithm with up to 100 precursors multiplexed per duty cycle, the PRM assay was able to achieve a rapid profiling of 291 species based on MS/MS data by a single injection. We used this novel approach to demonstrate the applicability and efficiency of the workflow to study salt stress induced changes in the barley root lipidome. Results show that 221 targeted lipids and 888 unknown features were found to have changed significantly in response to salt stress. This combined targeted and untargeted single workflow approach provides novel applications of lipidomics addressing biological questions.
Publisher: Elsevier BV
Date: 2008
DOI: 10.1016/J.BMCL.2007.11.108
Abstract: Dihydrodipicolinate synthase (DHDPS) is a key enzyme in lysine biosynthesis and a potential antibiotic target. The enzyme catalyses the condensation of (S)-aspartate semi-aldehyde (ASA) and pyruvate to form dihydrodipicolinate. Constrained diketopimelic acid derivatives have been designed as mimics of the acyclic enzyme-bound condensation product of ASA and pyruvate. Several of the compounds are shown to be active, slow-binding inhibitors with improved inhibition of DHDPS.
No related grants have been discovered for Berin Boughton.