ORCID Profile
0000-0002-6482-2615
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Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Plant Cell and Molecular Biology | Plant Physiology | Organic Chemistry | Organic Chemical Synthesis | Crop and Pasture Production | Crop and Pasture Improvement (Selection and Breeding) | Analytical Biochemistry | Characterisation of Biological Macromolecules | Medicinal and Biomolecular Chemistry | Physical organic chemistry | Membrane and Separation Technologies | Genetics | Biotechnology Not Elsewhere Classified | Plant Biochemistry And Physiology | Plant Biology | Plant Growth And Development | Organic chemistry | Gene Expression (incl. Microarray and other genome-wide approaches) | Soil Biology | Crop and Pasture Biochemistry and Physiology | Plant cell and molecular biology | Medical Biochemistry: Lipids |
ANZSRC Socio-Economic Objective (SEO)
Environmentally Sustainable Plant Production not elsewhere classified | Barley | Wheat | Chemical Fertilisers | Management of Greenhouse Gas Emissions from Plant Production | Agricultural and Environmental Standards | Field crops | Higher education | Biological sciences | Production of Biofuels (Biomass) | Farmland, Arable Cropland and Permanent Cropland Soils | Expanding Knowledge in the Chemical Sciences | Expanding Knowledge in the Biological Sciences
Related Links
Publications
LC–MS and GC–MS metabolite profiling of nickel(II) complexes in the latex of the nickel-hyperaccumulating tree Sebertia acuminata and identification of methylated aldaric acid as a new nickel(II) liga
Publisher: Elsevier BV
Date: 2008
DOI: 10.1016/J.PHYTOCHEM.2007.07.001
Abstract: Targeted liquid chromatography-mass spectrometry (LC-MS) technology using size exclusion chromatography and metabolite profiling based on gas chromatography-mass spectrometry (GC-MS) were used to study the nickel-rich latex of the hyperaccumulating tree Sebertia acuminata. More than 120 compounds were detected, 57 of these were subsequently identified. A methylated aldaric acid (2,4,5-trihydroxy-3-methoxy-1,6-hexan-dioic acid) was identified for the first time in biological extracts and its structure was confirmed by 1D and 2D nuclear magnetic resonance (NMR) spectroscopy. After citric acid, it appears to be one of the most abundant small organic molecules present in the latex studied. Nickel(II) complexes of stoichiometry NiII:acid=1:2 were detected for these two acids as well as for malic, itaconic, erythronic, galacturonic, tartaric, aconitic and saccharic acids. These results provide further evidence that organic acids may play an important role in the transport and possibly in the storage of metal ions in hyperaccumulating plants.
Quantitative profiling of polar primary metabolites of two chickpea cultivars with contrasting responses to salinity
Publisher: Elsevier BV
Date: 09-2015
DOI: 10.1016/J.JCHROMB.2015.07.002
Abstract: This study reports a GC-QqQ-MS method for the quantification of forty-eight primary metabolites from four major classes (sugars, sugar acids, sugar phosphates, and organic acids) which can be applied to a number of biological systems. The method was validated in terms of linearity, reproducibility and recovery, using both calibration standards and real s les. Additionally, twenty-eight biogenic amines and amino acids were quantified using an established LC-QqQ-MS method. Both GC-QqQ-MS and LC-QqQ-MS quantitative methods were applied to plant extracts from flower and pod tissue of two chickpea (Cicer arietinum L.) cultivars differing in their ability to tolerate salinity, which were grown under control and salt-treated conditions. Statistical analysis was applied to the data sets using the absolute concentrations of metabolites to investigate the differences in metabolite profiles between the different cultivars, plant tissues, and treatments. The method is a significant improvement of present methodology for quantitative GC-MS metabolite profiling of organic acids and sugars, and provides new insights of chickpea metabolic responses to salinity stress. It is applicable to the analysis of dynamic changes in endogenous concentrations of polar primary metabolites to study metabolic responses to environmental stresses in complex biological tissues.
Metabolomics - The combination of analytical biochemistry, biology, and informatics
Publisher: Elsevier
Date: 2011
The Metabolic Response of Brachypodium Roots to the Interaction with Beneficial Bacteria Is Affected by the Plant Nutritional Status
Publisher: MDPI AG
Date: 03-06-2021
Abstract: The potential of plant growth promoting (PGP) bacteria in improving the performance of plants in suboptimal environments is increasingly acknowledged, but little information is available on the mechanisms underlying this interaction, particularly when plants are subjected to a combination of stresses. In this study, we investigated the effects of the inoculation with the PGP bacteria Azospirillum brasilense (Azospirillum) on the metabolism of the model cereal Brachypodium distachyon (Brachypodium) grown at low temperatures and supplied with insufficient phosphorus. Investigating polar metabolite and lipid fluctuations during early plant development, we found that the bacteria initially elicited a defense response in Brachypodium roots, while at later stages Azospirillum reduced the stress caused by phosphorus deficiency and improved root development of inoculated plants, particularly by stimulating the growth of branch roots. We propose that the interaction of the plant with Azospirillum was influenced by its nutritional status: bacteria were sensed as pathogens while plants were still phosphorus sufficient, but the interaction became increasingly beneficial for the plants as their phosphorus levels decreased. Our results provide new insights on the dynamics of the cereal-PGP bacteria interaction, and contribute to our understanding of the role of beneficial microorganisms in the growth of cereal crops in suboptimal environments.
Epidermal bladder cells confer salinity stress tolerance in the halophyte quinoa and Atriplex species
Publisher: Wiley
Date: 18-07-2017
DOI: 10.1111/PCE.12995
Abstract: Epidermal bladder cells (EBCs) have been postulated to assist halophytes in coping with saline environments. However, little direct supporting evidence is available. Here, Chenopodium quinoa plants were grown under saline conditions for 5 weeks. One day prior to salinity treatment, EBCs from all leaves and petioles were gently removed by using a soft cosmetic brush and physiological, ionic and metabolic changes in brushed and non-brushed leaves were compared. Gentle removal of EBC neither initiated wound metabolism nor affected the physiology and biochemistry of control-grown plants but did have a pronounced effect on salt-grown plants, resulting in a salt-sensitive phenotype. Of 91 detected metabolites, more than half were significantly affected by salinity. Removal of EBC dramatically modified these metabolic changes, with the biggest differences reported for gamma-aminobutyric acid (GABA), proline, sucrose and inositol, affecting ion transport across cellular membranes (as shown in electrophysiological experiments). This work provides the first direct evidence for a role of EBC in salt tolerance in halophytes and attributes this to (1) a key role of EBC as a salt dump for external sequestration of sodium (2) improved K
Characterisation of HvALMT1 function in transgenic barley plants
Publisher: CSIRO Publishing
Date: 2011
DOI: 10.1071/FP10140
Abstract: HvALMT1 from barley (Hordeum vulgare L.) encodes a protein capable of facilitating the transport of malate and other organic anions when expressed in Xenopus oocytes. The HvALMT1 gene is primarily expressed in guard cells of stomata, in regions behind the root apex and at lateral root junctions. We investigated the function of HvALMT1 in planta by overexpressing it in barley under the control of a constitutive promoter. Transgenic plants expressing HvALMT1 at levels four to 9-fold greater than controls showed reduced growth and plants showing the highest expression failed to set seed. Although measurements of conductance indicated that stomatal function was not totally impaired in the transgenic plants the time taken for the stomata to close in response to low light was significantly longer compared with controls. Elemental and metabolomic analyses of the transgenic barley shoots revealed that the concentration of calcium and levels of ascorbate, serine, threonine and pentanoate were consistently greater (2- to 14-fold) in plants that overexpressed HvALMT1, whereas whole-shoot tissue levels of fumarate were significantly lower (60–85% reduction). Transgenic plants also showed significantly greater efflux of malate and succinate from their roots than control plants. Efflux of these organic anions occurred independently of Al3+ and conferred greater Al3+ resistance in solution culture and in acidic soil. These results are consistent with HvALMT1 contributing to anion homeostasis in the cytosol and osmotic adjustment by transporting organic anions out of the cell or by sequestering them into cytosolic vesicles.
Comprehensive metabolic profiling and phenotyping of interspecific introgression lines for tomato improvement
Publisher: Springer Science and Business Media LLC
Date: 12-03-2006
DOI: 10.1038/NBT1192
Abstract: Tomato represents an important source of fiber and nutrients in the human diet and is a central model for the study of fruit biology. To identify components of fruit metabolic composition, here we have phenotyped tomato introgression lines (ILs) containing chromosome segments of a wild species in the genetic background of a cultivated variety. Using this high- ersity population, we identify 889 quantitative fruit metabolic loci and 326 loci that modify yield-associated traits. The mapping analysis indicates that at least 50% of the metabolic loci are associated with quantitative trait loci (QTLs) that modify whole-plant yield-associated traits. We generate a cartographic network based on correlation analysis that reveals whole-plant phenotype associated and independent metabolic associations, including links with metabolites of nutritional and organoleptic importance. The results of our genomic survey illustrate the power of genome-wide metabolic profiling and detailed morphological analysis for uncovering traits with potential for crop breeding.
Feeding the Walls: How Does Nutrient Availability Regulate Cell Wall Composition?
Publisher: MDPI AG
Date: 10-09-2018
DOI: 10.3390/IJMS19092691
Abstract: Nutrients are critical for plants to grow and develop, and nutrient depletion severely affects crop yield. In order to optimize nutrient acquisition, plants adapt their growth and root architecture. Changes in growth are determined by modifications in the cell walls surrounding every plant cell. The plant cell wall, which is largely composed of complex polysaccharides, is essential for plants to attain their shape and to protect cells against the environment. Within the cell wall, cellulose strands form microfibrils that act as a framework for other wall components, including hemicelluloses, pectins, proteins, and, in some cases, callose, lignin, and suberin. Cell wall composition varies, depending on cell and tissue type. It is governed by synthesis, deposition and remodeling of wall components, and determines the physical and structural properties of the cell wall. How nutrient status affects cell wall synthesis and organization, and thus plant growth and morphology, remains poorly understood. In this review, we aim to summarize and synthesize research on the adaptation of root cell walls in response to nutrient availability and the potential role of cell walls in nutrient sensing.
Elemental and metabolite profiling of nickel hyperaccumulators from New Caledonia
Publisher: Elsevier BV
Date: 09-2012
DOI: 10.1016/J.PHYTOCHEM.2012.06.010
Abstract: Leaf material from nine Ni hyperaccumulating species was collected in New Caledonia: Homalium kanaliense (Vieill.) Briq., Casearia silvana Schltr, Geissois hirsuta Brongn. & Gris, Hybanthus austrocaledonicus Seem, Psychotria douarrei (G. Beauvis.) Däniker, Pycnandra acuminata (Pierre ex Baill.) Swenson & Munzinger (syn Sebertia acuminata Pierre ex Baill.), Geissois pruinosa Brongn. & Gris, Homalium deplanchei (Viell) Warb. and Geissois bradfordii (H.C. Hopkins). The elemental concentration was determined by inductively-coupled plasma optical emission spectrometry (ICP-OES) and from these results it was found that the species contained Ni concentrations from to 250-28,000 mg/kg dry mass. Gas chromatography mass spectrometry (GC-MS)-based metabolite profiling was then used to analyse leaves of each species. The aim of this study was to target Ni-binding ligands through correlation analysis of the metabolite levels and leaf Ni concentration. Approximately 258 compounds were detected in each s le. As has been observed before, a correlation was found between the citric acid and Ni concentrations in the leaves for all species collected. However, the strongest Ni accumulator, P. douarrei, has been found to contain particularly high concentrations of malonic acid, suggesting an additional storage mechanism for Ni. A size exclusion chromatography separation protocol for the separation of Ni-complexes in P. acuminata sap was also applied to aqueous leaf extracts of each species. A number of metabolites were identified in complexes with Ni including Ni-malonate from P. douarrei. Furthermore, the levels for some metabolites were found to correlate with the leaf Ni concentration. These data show that Ni ions can be bound by a range of small molecules in Ni hyperaccumulation in plants.
Facile synthesis, stabilization, and anti-bacterial performance of discrete Ag nanoparticles using Medicago sativa seed exudates
Publisher: Elsevier BV
Date: 2011
DOI: 10.1016/J.JCIS.2010.09.088
Abstract: The biogenic synthesis of metal nanomaterials offers an environmentally benign alternative to the traditional chemical synthesis routes. Colloidal silver (Ag) nanoparticles were synthesized by reacting aqueous AgNO(3) with Medicago sativa seed exudates under non-photomediated conditions. Upon contact, rapid reduction of Ag(+) ions was observed in <1 min with Ag nanoparticle formation reaching 90% completion in <50 min. Effect of Ag concentration, quantity of exudate and pH on the particle size and shape were investigated. At [Ag(+)]=0.01 M and 30°C, largely spherical nanoparticles with diameters in the range of 5-51 nm were generated, while flower-like particle clusters (mean size=104 nm) were observed on treatment at higher Ag concentrations. Pre-dilution of the exudate induced the formation of single-crystalline Ag nanoplates, forming hexagonal particles and nanotriangles with edge lengths of 86-108 nm, while pH adjustment to 11 resulted in monodisperse Ag nanoparticles with an average size of 12 nm. Repeated centrifugation and redispersion enhanced the percentage of nanoplates from 10% to 75% in solution. The kinetics of nanoparticle formation were monitored using ultraviolet-visible spectroscopy and the Ag products were characterized using transmission electron microscopy, selected-area electron diffraction, scanning electron microscopy, X-ray powder diffraction, and atomic force microscopy. X-ray photoelectron spectroscopy was used to investigate the elements and chemical environment in the top layers of the as-synthesized Ag nanoparticles, while the metabolites in the exudate were analyzed using gas chromatography-mass spectroscopy. To our knowledge, this is the first account of M. sativa seed exudate assisted synthesis and stabilization of biogenic Ag nanoparticles the nanoplates are notably smaller and better faceted compared with those synthesized by vascular plant extracts previously reported. Stabilized films of exudate synthesized Ag nanoparticles were effective anti-bacterial agents.
Mitochondrial Complex I activity is inhibited by changes in the abundance of phosphatidylinositol and phosphatidylserine in wheat plants exposed to high temperatures
Publisher: Cold Spring Harbor Laboratory
Date: 06-02-2023
DOI: 10.1101/2023.02.05.527222
Abstract: Identifying the molecular basis of thermotolerance in crops is becoming increasingly important with the changing climatic conditions that challenge future food security. Sustaining cellular energy production under heat stress is vital in maintaining an uninterrupted growth cycle, and thus the mitochondria is instrumental in facilitating the overall heat-tolerance of a crop plant. Using targeted mass spectrometry, the changes in abundance of the lipo-protein network in mitochondrial membranes following a short episode of extremely high temperature were analysed in two wheat cultivars of differing thermotolerance. The results indicated that membrane lipids remodel in favour of shorter fatty acyl tails, and an increase in the abundance of phosphatidylinositol, while specific to the heat-tolerant cultivar was an increase in the abundance of phosphatidylserine. The differences between the lipid profiles of the two cultivars is a likely explanation for the decrease in Complex I NADH dehydrogenase activity in the heat-sensitive cultivar. Further metabolite analysis by LC-MS revealed malate accumulation, indicating that the disruption in Complex I activity impacts the catabolism of reducing equivalents. The measured increase in the total amount of phosphatidylserine in the heat-tolerant cultivar suggests a potential role in conveying thermotolerance for this minor membrane constituent, and highlights that a focus on membrane lipid composition during thermal stress will be essential for the breeding of future heat tolerant crops. We evaluated changes to the lipo-protein network of wheat mitochondria of differing heat tolerance in response to heat shock. Using targeted mass spectrometry, candidate transitions were selected to quantify changes in membrane lipids and the embedded protein components of the electron transport chain, which play a vital role in maintaining respiration. A significant increase in phosphatidylserine was exclusive to the mitochondria of the heat-tolerant wheat cultivar. In the absence of this, the heat-sensitive cultivar displayed a reduced Complex I activity. The minor membrane constituent phosphatidylserine plays a role in conveying thermotolerance, making this membrane lipid a focal point for the breeding of future heat tolerant crops.
Mechanisms associated with Fe ‐deficiency tolerance and signaling in shoots of Pisum sativum
Publisher: Wiley
Date: 17-09-2012
DOI: 10.1111/J.1399-3054.2012.01682.X
Abstract: Mechanisms of Fe-deficiency tolerance and signaling were investigated in shoots of Santi (deficiency tolerant) and Parafield (deficiency intolerant) pea genotypes using metabolomic and physiological approaches. From metabolomic studies, Fe deficiency induced significant increases in N-, S- and tricarboxylic acid cycle metabolites in Santi but not in Parafield. Elevated N metabolites reflect an increase in N-recycling processes. Increased glutathione and S-metabolites suggest better protection of pea plants from Fe-deficiency-induced oxidative stress. Furthermore, Fe-deficiency induced increases in citrate and malate in leaves of Santi suggests long-distance transport of Fe is promoted by better xylem unloading. Supporting a role of citrate in the deficiency tolerance mechanism, physiological experiments showed higher Fe and citrate in the xylem of Santi. Reciprocal-grafting experiments confirm that the Fe-deficiency signal driving root Fe reductase and proton extrusion activity is generated in the shoot. Finally, our studies show that auxin can induce increased Fe-reductase activity and proton extrusion in roots. This article identifies several mechanisms in shoots associated with the differential Fe-deficiency tolerance of genotypes within a species, and provides essential background for future efforts to improve the Fe content and deficiency tolerance in peas.
Water availability moderates N-2 fixation benefit from elevated [CO2]: A 2-year free-air CO2 enrichment study on lentil (Lens culinaris MEDIK.) in a water limited agroecosystem
Publisher: Wiley
Date: 16-07-2018
DOI: 10.1111/PCE.13360
Abstract: Increased biomass and yield of plants grown under elevated [CO
Mass spectrometry imaging for plant biology: a review
Publisher: Springer Science and Business Media LLC
Date: 13-10-2015
Integrative Multi-omics Analyses of Barley Rootzones under Salinity Stress Reveal Two Distinctive Salt Tolerance Mechanisms
Publisher: Elsevier BV
Date: 05-2020
Metabolic Profiling of Transgenic Tomato Plants Overexpressing Hexokinase Reveals That the Influence of Hexose Phosphorylation Diminishes during Fruit Development
Publisher: Oxford University Press (OUP)
Date: 09-2003
Abstract: We have conducted a comprehensive metabolic profiling on tomato (Lycopersicon esculentum) leaf and developing fruit tissue using a recently established gas chromatography-mass spectrometry profiling protocol alongside conventional spectrophotometric and liquid chromatographic methodologies. Applying a combination of these techniques, we were able to identify in excess of 70 small-M r metabolites and to catalogue the metabolite composition of developing tomato fruit. In addition to comparing differences in metabolite content between source and sink tissues of the tomato plant and after the change in metabolite pool sizes through fruit development, we have assessed the influence of hexose phosphorylation through fruit development by analyzing transgenic plants constitutively overexpressing Arabidopsis hexokinase AtHXK1. Analysis of the total hexokinase activity in developing fruits revealed that both wild-type and transgenic fruits exhibit decreasing hexokinase activity with development but that the relative activity of the transgenic lines with respect to wild type increases with development. Conversely, both point-by-point and principal component analyses suggest that the metabolic phenotype of these lines becomes less distinct from wild type during development. In summary, the data presented in this paper demonstrate that the influence of hexose phosphorylation diminishes during fruit development and highlights the importance of greater temporal resolution of metabolism.
Root spatial metabolite profiling of two genotypes of barley(Hordeum vulgareL.) reveals differences in response to short-term salt stress
Publisher: Oxford University Press (OUP)
Date: 05-03-2016
DOI: 10.1093/JXB/ERW059
Current and Emerging Applications of Metabolomics in the Field of Agricultural Biotechnology
Publisher: Wiley
Date: 30-10-2015
Metabolic Profiling of Plants by GC–MS
Publisher: Wiley
Date: 12-04-2013
Investigation of biochemical changes in barley inoculated with Trichoderma harzianum T-22 under salt stress [PREPRINT OR COMPARABLE]
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.
Phenotyping the Chilling and Freezing Responses of Young Microspore Stage Wheat Spikes Using Targeted Metabolome and Lipidome Profiling
Publisher: MDPI AG
Date: 25-05-2020
DOI: 10.3390/CELLS9051309
Abstract: Chilling and frost conditions impose major yield restraints to wheat crops in Australia and other temperate climate regions. Unpredictability and variability of field frost events are major impediments for cold tolerance breeding. Metabolome and lipidome profiling were used to compare the cold response in spikes of cold-tolerant Young and sensitive variety Wyalkatchem at the young microspore (YM) stage of pollen development. We aimed to identify metabolite markers that can reliably distinguish cold-tolerant and sensitive wheat varieties for future cold-tolerance phenotyping applications. We scored changes in spike metabolites and lipids for both varieties during cold acclimation after initial and prolonged exposure to combined chilling and freezing cycles (1 and 4 days, respectively) using controlled environment conditions. The two contrasting wheat varieties showed qualitative and quantitative differences in primary metabolites involved in osmoprotection, but differences in lipid accumulation most distinctively separated the cold response of the two wheat lines. These results resemble what we previously observed in flag leaves of the same two wheat varieties. The fact that this response occurs in tissue types with very different functions indicates that chilling and freezing tolerance in these wheat lines is associated with re-modelling of membrane lipid composition to maintain membrane fluidity.
Deciphering the Interactions in the Root–Soil Nexus Caused by Urease and Nitrification Inhibitors: A Review
Publisher: MDPI AG
Date: 13-06-2023
Abstract: Optimizing nitrogen (N) availability to plants is crucial for achieving maximum crop yield and quality. However, ensuring the appropriate supply of N to crops is challenging due to the various pathways through which N can be lost, such as ammonia (NH3) volatilization, nitrous oxide emissions, denitrification, nitrate (NO3−) leaching, and runoff. Additionally, N can become immobilized by soil minerals when ammonium (NH4+) gets trapped in the interlayers of clay minerals. Although synchronizing N availability with plant uptake could potentially reduce N loss, this approach is hindered by the fact that N loss from crop fields is typically influenced by a combination of management practices (which can be controlled) and weather dynamics, particularly precipitation, temperature fluctuations, and wind (which are beyond our control). In recent years, the use of urease and nitrification inhibitors has emerged as a strategy to temporarily delay the microbiological transformations of N-based fertilizers, thereby synchronizing N availability with plant uptake and mitigating N loss. Urease inhibitors slow down the hydrolysis of urea to NH4+ and reduce nitrogen loss through NH3 volatilization. Nitrification inhibitors temporarily inhibit soil bacteria (Nitrosomonas spp.) that convert NH4+ to nitrite (NO2−), thereby slowing down the first and rate-determining step of the nitrification process and reducing nitrogen loss as NO3− or through denitrification. This review aims to provide a comprehensive understanding of urease and nitrification inhibitor technologies and their profound implications for plants and root nitrogen uptake. It underscores the critical need to develop design principles for inhibitors with enhanced efficiency, highlighting their potential to revolutionize agricultural practices. Furthermore, this review offers valuable insights into future directions for inhibitor usage and emphasizes the essential traits that superior inhibitors should possess, thereby paving the way for innovative advancements in optimizing nitrogen management and ensuring sustainable crop production.
Characterization of Ion Contents and Metabolic Responses to Salt Stress of Different Arabidopsis AtHKT1;1 Genotypes and Their Parental Strains
Publisher: Elsevier BV
Date: 03-2013
DOI: 10.1093/MP/SSS125
Abstract: Plants employ several strategies to maintain cellular ion homeostasis under salinity stress, including mediating ion fluxes by transmembrane transport proteins and adjusting osmotic pressure by accumulating osmolytes. The HKT (high-affinity potassium transporter) gene family comprises Na(+) and Na(+)/K(+) transporters in erse plant species, with HKT1 as the only member in Arabidopsis thaliana. Cell-type-specific overexpression of AtHKT1 has been shown to prevent shoot Na(+) overaccumulation under salinity stress. Here, we analyzed a broad range of metabolites and elements in shoots and roots of different AtHKT1 genotypes and their parental strains before and after salinity stress, revealing a reciprocal relationship of metabolite differences between an AtHKT1 knockout line (hkt1 ) and the AtHKT1 overexpressing lines (E2586 UAS GAL4 :HKT1 and J2731*UAS GAL4 :HKT1 ). Although levels of root sugars were increased after salt stress in both AtHKT1 overexpressing lines, E2586 UAS GAL4 :HKT1 showed higher accumulation of the osmoprotectants trehalose, gentiobiose, and melibiose, whereas J2731*UAS GAL4 :HKT1 showed higher levels of sucrose and raffinose, compared with their parental lines, respectively. In contrast, the knockout line hkt1 showed strong increases in the levels of the tricarboxylic acid (TCA) cycle intermediates in the shoots after salt treatment. This coincided with a significant depletion of sugars, suggesting that there is an increased rate of carbon influx into the TCA cycle at a constant rate of C-efflux from the cycle, which might be needed to support plant survival during salt stress. Using correlation analysis, we identified associations between the Na(+) content and several sugars, suggesting that regulation of sugar metabolism is important in plant responses to salinity stress.
Edaphic niche characterization of four Proteaceae reveals unique calcicole physiology linked to hyper‐endemism of Grevillea thelemanniana
Publisher: Wiley
Date: 25-08-2020
DOI: 10.1111/NPH.16833
Abstract: Endemism and rarity have long intrigued scientists. We focused on a rare endemic and critically‐endangered species in a global bio ersity hotspot, Grevillea thelemanniana (Proteaceae). We carried out plant and soil analyses of four Proteaceae, including G. thelemanniana , and combined these with glasshouse studies. The analyses related to hydrology and plant water relations as well as soil nutrient concentrations and plant nutrition, with an emphasis on sodium (Na) and calcium (Ca). The local hydrology and matching plant traits related to water relations partially accounted for the distribution of the four Proteaceae. What determined the rarity of G. thelemanniana , however, was its accumulation of Ca. Despite much higher total Ca concentrations in the leaves of the rare G. thelemanniana than in the common Proteaceae, very few Ca crystals were detected in epidermal or mesophyll cells. Instead of crystals, G. thelemanniana epidermal cell vacuoles contained exceptionally high concentrations of noncrystalline Ca. Calcium ameliorated the negative effects of Na on the very salt‐sensitive G. thelemanniana . Most importantly, G. thelemanniana required high concentrations of Ca to balance a massively accumulated feeding‐deterrent carboxylate, trans ‐aconitate. This is the first ex le of a calcicole species accumulating and using Ca to balance accumulation of an antimetabolite.
Low doses of the neonicotinoid insecticide imidacloprid induce ROS triggering neurological and metabolic impairments in Drosophila
Publisher: Proceedings of the National Academy of Sciences
Date: 28-09-2020
Abstract: Intense insecticide usage is suggested to be a significant contributor to the observed decline of insect populations around the world. Beneficial insects play essential roles in food production and ecosystem health. It is therefore vital to understand the mechanisms by which low doses of insecticide impact insect biology in order to understand and assess the threat posed. We investigated the impacts of the neonicotinoid insecticide imidacloprid on Drosophila . The binding of the insecticide to receptors in the brain triggers oxidative stress, reduces energy levels, and induces neurodegeneration as well as vision loss. As the receptors targeted by imidacloprid are conserved among insects, and other insecticides have also been shown to cause oxidative stress, these findings have wider significance.
An investigation of boron toxicity in Barley using metabolomics
Publisher: Oxford University Press (OUP)
Date: 22-09-2006
Abstract: Boron (B) is an essential micronutrient that affects plant growth at either deficient or toxic concentrations in soil. The aim of this work was to investigate the adaptation of barley (Hordeum vulgare) plants to toxic B levels and to increase our understanding of B toxicity tolerance mechanisms. We used a metabolomics approach to compare metabolite profiles in root and leaf tissues of an intolerant, commercial cultivar (cv Clipper) and a B-tolerant Algerian landrace (cv Sahara). After exposure to elevated B (200 and 1,000 μ m), the number and litude of metabolite changes in roots was greater in Clipper than in Sahara. In contrast, leaf metabolites of both cultivars only responded following 1,000 μ m treatment, at which B toxicity symptoms (necrosis) were visible. In addition, metabolite levels were dramatically altered in the tips of leaves of the sensitive cultivar Clipper after growth in 1,000 μ m B compared to those of Sahara. This correlates with a gradual accumulation of B from leaf base to tip in B-intolerant cultivars. Overall, there were always greater differences between tissue types (roots and leaves) than between the two cultivars. This work has provided insights into metabolic differences of two genetically distinct barley cultivars and information about how they respond metabolically to increasing B levels.
Insights into the Efficacy and Binding Mode of 1,4-Disubstituted 1,2,3-Triazoles─A New Class of Agricultural Nitrification Inhibitors
Publisher: American Chemical Society (ACS)
Date: 03-10-2023
Opposite fates of the purine metabolite allantoin under water and nitrogen limitations in bread wheat
Publisher: Springer Science and Business Media LLC
Date: 05-02-2019
DOI: 10.1007/S11103-019-00831-Z
Abstract: Degradation of nitrogen-rich purines is tightly and oppositely regulated under drought and low nitrogen supply in bread wheat. Allantoin is a key target metabolite for improving nitrogen homeostasis under stress. The metabolite allantoin is an intermediate of the catabolism of purines (components of nucleotides) and is known for its housekeeping role in nitrogen (N) recycling and also for its function in N transport and storage in nodulated legumes. Allantoin was also shown to differentially accumulate upon abiotic stress in a range of plant species but little is known about its role in cereals. To address this, purine catabolic pathway genes were identified in hexaploid bread wheat and their chromosomal location was experimentally validated. A comparative study of two Australian bread wheat genotypes revealed a highly significant increase of allantoin (up to 29-fold) under drought. In contrast, allantoin significantly decreased (up to 22-fold) in response to N deficiency. The observed changes were accompanied by transcriptional adjustment of key purine catabolic genes, suggesting that the recycling of purine-derived N is tightly regulated under stress. We propose opposite fates of allantoin in plants under stress: the accumulation of allantoin under drought circumvents its degradation to ammonium (NH
Beta-glucan-depleted, glycopeptide-rich extracts from Brewer’s and Baker’s yeast (Saccharomyces cerevisiae) lower interferon-gamma production by stimulated human blood cells in vitro
Publisher: Elsevier BV
Date: 04-2016
DOI: 10.1016/J.FOODCHEM.2015.11.015
Abstract: Regulation of the human immune system requires controlled pro- and anti-inflammatory responses for host defence against infection and disease states. Yeasts (Saccharomyces cerevisiae), as used in brewing and baking, are mostly known for ability to stimulate the human immune-system predominantly reflecting the pro-inflammatory cell wall β-glucans. However, in this study, using food-compatible processing methods, glycopeptide-enriched and β-glucan-depleted products were each prepared from Brewer's and Baker's yeasts, which suppressed production of interferon-γ (IFN-γ) in human whole blood cell assay, signifying that anti-inflammatory factors are also present in yeast. Anti-inflammatory bioactivities of products prepared from Brewer's and Baker's yeast were compared with the commercial yeast product, Epicor®. While unfractionated Epicor was inactive, the C18 resin-binding fractions of Brewer's and Baker's yeast products and Epicor dose-dependently lowered IFN-γ, demonstrating that Epicor also contained both pro-inflammatory (β-glucans) and anti-inflammatory components. Anti-inflammatory activity was attributed to C18 resin-binding species glyco-peptides in Epicor and experimental yeast products. This study demonstrated that pro- and anti-inflammatory factors could be resolved and enriched in yeasts by suitable processing, with potential to improve specific activities.
Advances in functional genomics for investigating salinity stress tolerance mechanisms in cereals
Publisher: Frontiers Media SA
Date: 2013
Elemental imaging of leaves from the metal hyperaccumulating plant Noccaea caerulescens shows different spatial distribution of Ni, Zn and Cd
Publisher: Royal Society of Chemistry (RSC)
Date: 2015
DOI: 10.1039/C5RA23953B
Abstract: Elemental imaging using laser ablation inductively coupled plasma mass spectrometry was performed on whole leaves of the hyperaccumulating plant Noccaea caerulescens after treatments with either Ni, Zn or Cd.
Flicker Light-Induced Retinal Vasodilation Is Unaffected by Inhibition of Epoxyeicosatrienoic Acids and Prostaglandins in Humans
Publisher: Association for Research in Vision and Ophthalmology (ARVO)
Date: 08-10-2014
Abstract: To investigate the role of epoxyeicosatrienoic acids (EETs) and prostaglandins (PGs) in retinal blood vessel calibers and vasodilation during flicker light stimulation in humans. Twelve healthy nonsmokers participated in a balanced crossover study. Oral fluconazole 400 mg and dispersible aspirin 600 mg were used to inhibit production of EETs and PGs, respectively. Retinal imaging was performed 1 hour after drug ingestion with the Dynamic Vessel Analyzer. Resting calibers of selected vessel segments were recorded in measurement units (MU). Maximum percentage dilations during flicker stimulation were calculated from baseline calibers. We then studied six participants each after fluconazole and aspirin ingestions at 30-minute intervals for 2 hours. Within-subject differences were assessed by ANOVA and Dunnett-adjusted pairwise comparisons with significance taken at P < 0.05. In crossover study participants, mean (SD) arteriole and venule dilations without drug administration were 4.4% (2.0%) and 4.6% (1.7%), respectively. Neither drug affected vasodilation during flicker stimulation. Mean (SD) resting arteriole and venule calibers on no-drug visits were 119.6 (10.6) MU and 145.7 (17.0) MU, respectively. Fluconazole reduced mean (±95% CI) resting venule calibers by 5.1 (4.3) MU. In repeated measures participants, neither drug affected vasodilations, but fluconazole reduced resting venule calibers over 2 hours (P < 0.001). Epoxyeicosatrienoic acids and prostaglandins are unlikely to be primary mediators of flicker light-induced retinal vasodilation in humans. However, EETs may play a role in the regulation of retinal vascular tone and blood flow under resting physiological conditions.
Optimal nutrient exchange and immune responses operate in partner specificity in the cnidarian-dinoflagellate symbiosis
Publisher: Proceedings of the National Academy of Sciences
Date: 20-11-2017
Abstract: Flexibility in the endosymbiotic Symbiodinium community could provide reef-building corals with the capacity to survive environmental change, but this may be restricted to compatible host-symbiont combinations. Therefore, determining the underlying molecular, cellular, and physiological processes of symbiont compatibility is of critical importance for elucidating the resilience and adaptability of coral reefs. We coupled gene expression data with high-throughput metabolite profiling to compare the effects on the sea anemone Aiptasia when colonized by the thermally tolerant, opportunistic, but comparatively unproductive Symbiodinium trenchii vs. the regular symbiont species, Symbiodinium minutum . This powerful approach revealed strong evidence that optimal nutritional exchange and the response to intracellular oxidative stress are important determinants in the success of novel cnidarian-dinoflagellate symbioses.
Partner switching and metabolic flux in a model cnidarian–dinoflagellate symbiosis
Publisher: The Royal Society
Date: 28-11-2018
Abstract: Metabolite exchange is fundamental to the viability of the cnidarian–Symbiodiniaceae symbiosis and survival of coral reefs. Coral holobiont tolerance to environmental change might be achieved through changes in Symbiodiniaceae species composition, but differences in the metabolites supplied by different Symbiodiniaceae species could influence holobiont fitness. Using 13 C stable-isotope labelling coupled to gas chromatography–mass spectrometry, we characterized newly fixed carbon fate in the model cnidarian Exaiptasia pallida (Aiptasia) when experimentally colonized with either native Breviolum minutum or non-native Durusdinium trenchii . Relative to anemones containing B. minutum , D. trenchii -colonized hosts exhibited a 4.5-fold reduction in 13 C-labelled glucose and reduced abundance and ersity of 13 C-labelled carbohydrates and lipogenesis precursors, indicating symbiont species-specific modifications to carbohydrate availability and lipid storage. Mapping carbon fate also revealed significant alterations to host molecular signalling pathways. In particular, D. trenchii- colonized hosts exhibited a 40-fold reduction in 13 C-labelled scyllo -inositol, a potential interpartner signalling molecule in symbiosis specificity. 13 C-labelling also highlighted differential antioxidant- and ammonium-producing pathway activities, suggesting physiological responses to different symbiont species. Such differences in symbiont metabolite contribution and host utilization may limit the proliferation of stress-driven symbioses this contributes valuable information towards future scenarios that select in favour of less-competent symbionts in response to environmental change.
13C metabolomics reveals widespread change in carbon fate during coral bleaching
Publisher: Springer Science and Business Media LLC
Date: 12-12-2018
DOI: 10.1007/S11306-017-1306-8
Abstract: Rising seawater temperatures are threatening the persistence of coral reefs where above critical thresholds, thermal stress results in a breakdown of the coral-dinoflagellate symbiosis and the loss of algal symbionts (coral bleaching). As symbiont-derived organic products typically form a major portion of host energy budgets, this has major implications for the fitness and persistence of symbiotic corals. We aimed to determine change in autotrophic carbon fate within in idual compounds and downstream metabolic pathways in a coral symbiosis exposed to varying degrees of thermal stress and bleaching. We applied gas chromatography-mass spectrometry coupled to a stable isotope tracer ( Thermal stress resulted in partner-specific changes in carbon fate, which progressed with heat stress duration. We detected modifications to carbohydrate and fatty acid metabolism, lipogenesis, and homeostatic responses to thermal, oxidative and osmotic stress. Despite pronounced photodamage, remaining in hospite symbionts continued to produce organic products de novo and translocate to the coral host. However as bleaching progressed, we observed minimal These data have major implications for our understanding of coral symbiosis function during bleaching. Our findings suggest that during early stage bleaching, remaining symbionts continue to effectively translocate a variety of organic products to the host, however under prolonged thermal stress there is likely a reduction in the quality of these products.
Metabolomic study reveals a selective accumulation of l-arginine in the d-ornithine treated tobacco cell suspension culture
Publisher: Elsevier BV
Date: 2014
Cell-Type-Specific H+-ATPase Activity in Root Tissues Enables K+ Retention and Mediates Acclimation of Barley (Hordeum vulgare) to Salinity Stress
Publisher: Oxford University Press (OUP)
Date: 21-10-2016
DOI: 10.1104/PP.16.01347
Metabolomics of capsicum ripening reveals modification of the ethylene related-pathway and carbon metabolism
Publisher: Elsevier BV
Date: 03-2014
Comparative metabolomics implicates threitol as a fungal signal supporting colonization of Armillaria luteobubalina on eucalypt roots
Publisher: Wiley
Date: 03-12-2020
DOI: 10.1111/PCE.13672
Abstract: Armillaria root rot is a fungal disease that affects a wide range of trees and crops around the world. Despite being a widespread disease, little is known about the plant molecular responses towards the pathogenic fungi at the early phase of their interaction. With recent research highlighting the vital roles of metabolites in plant root-microbe interactions, we sought to explore the presymbiotic metabolite responses of Eucalyptus grandis seedlings towards Armillaria luteobuablina, a necrotrophic pathogen native to Australia. Using a metabolite profiling approach, we have identified threitol as one of the key metabolite responses in E. grandis root tips specific to A. luteobubalina that were not induced by three other species of soil-borne microbes of different lifestyle strategies (a mutualist, a commensalist, and a hemi-biotrophic pathogen). Using isotope labelling, threitol detected in the Armillaria-treated root tips was found to be largely derived from the fungal pathogen. Exogenous application of d-threitol promoted microbial colonization of E. grandis and triggered hormonal responses in root cells. Together, our results support a role of threitol as an important metabolite signal during eucalypt-Armillaria interaction prior to infection thus advancing our mechanistic understanding on the earliest stage of Armillaria disease development. Comparative metabolomics of eucalypt roots interacting with a range of fungal lifestyles identified threitol enrichment as a specific characteristic of Armillaria pathogenesis. Our findings suggest that threitol acts as one of the earliest fungal signals promoting Armillaria colonization of roots.
Single cell-type analysis of cellular lipid remodelling in response to salinity in the epidermal bladder cells of the model halophyte Mesembryanthemum crystallinum
Publisher: Wiley
Date: 03-07-2018
DOI: 10.1111/PCE.13352
Abstract: Salt stress causes dramatic changes in the organization and dynamic properties of membranes, however, little is known about the underlying mechanisms involved. Modified trichomes, known as epidermal bladder cells (EBC), on the leaves and stems of the halophyte Mesembryanthemum crystallinum can be successfully exploited as a single-cell-type system to investigate salt-induced changes to cellular lipid composition. In this study, alterations in key molecular species from different lipid classes highlighted an increase in phospholipid species, particularly those from phosphatidylcholine and phosphatidic acid (PA), where the latter is central to the synthesis of membrane lipids. Triacylglycerol (TG) species decreased during salinity, while there was little change in plastidic galactolipids. EBC transcriptomic and proteomic data mining revealed changes in genes and proteins involved in lipid metabolism and the upregulation of transcripts for PIPKIB, PI5PII, PIPKIII, and phospholipase D delta suggested the induction of signalling processes mediated by phosphoinositides and PA. TEM and flow cytometry showed the dynamic nature of lipid droplets in these cells under salt stress. Altogether, this work indicates that the metabolism of TG might play an important role in EBC response to salinity as either an energy reserve for sodium accumulation and/or driving membrane biosynthesis for EBC expansion.
Time-resolution of the shoot and root growth of the model cereal Brachypodium in response to inoculation with Azospirillum bacteria at low phosphorus and temperature
Publisher: Springer Science and Business Media LLC
Date: 11-2021
DOI: 10.1007/S10725-020-00675-4
Abstract: A non-invasive plant phenotyping platform, GrowScreen-PaGe , was used to resolve the dynamics of shoot and root growth of the model cereal Brachypodium ( Brachypodium distachyon Bd21-3) in response to the plant growth promoting (PGP) bacteria Azospirillum ( Azospirillum brasilense Sp245). Inoculated Brachypodium plants had greater early vigor and higher P use efficiency than non-inoculated Brachypodium at low P and low temperature conditions. Root systems were imaged non-invasively at eight time points and data combined with leaf area, shoot biomass and nutrient content from destructive subs les at 7, 14 and 21 days after inoculation (DAI). Azospirillum colonisation of roots improved Brachypodium shoot and, to a greater degree, root growth in three independent experiments. Inoculation promoted P use efficiency in shoots but not P concentration or uptake, despite increased total root length. Longer roots in inoculated plants arose from twofold faster branch root growth but slower axile root growth, detected at 11 DAI. Analysis of the spatio-temporal phenotypes indicated that the effects of Azospirillum inoculation increased as shoot P concentration declined, but the magnitude depended on the time after inoculation and growth rate of branch roots compared to axile roots. High throughput plant phenotyping platforms allow the details of plant-microorganism symbioses to be resolved, offering insights into the timing of changes in different tissues to allow molecular mechanisms to be determined.
Inoculation of barley with Trichoderma harzianum T-22 modifies lipids and metabolites to improve salt tolerance
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.
Comparative Genomics Points to Tandem Duplications ofSADGene Clusters as Drivers of Increased ω-3 Content inS. hispanicaSeeds
Publisher: Cold Spring Harbor Laboratory
Date: 28-08-2023
DOI: 10.1101/2023.08.27.555029
Abstract: A high-quality chromosome-level reference genome of S. hispanica was assembled and analysed. Ancestral whole-genome duplication events have not promoted the high α-linolenic acid content in S. hispanica seeds Tandem duplication of six stearoyl-ACP desaturase genes is a plausible cause for high ω-3 content in chia seeds. Salvia hispanica L. (chia) is an abundant source of ω-3 polyunsaturated fatty acids (PUFAs) that are highly beneficial to human health. The genomic basis for this accrued PUFA content in this emerging crop was investigated through the assembly and comparative analysis of a chromosome-level reference genome for S. hispanica (321.5 Mbp). The highly contiguous 321.5Mbp genome assembly, which covers all six chromosomes enabled the identification of 32,922 protein coding genes. Two whole-genome duplications (WGD) events were identified in the S. hispanica lineage. However, these WGD events could not be linked to the high α-linolenic acid (ALA, ω-3) accumulation in S. hispanica seeds based on phylogenomics. Instead, our analysis supports the hypothesis that evolutionary expansion through tandem duplications of specific lipid gene families, particularly the stearoyl-acyl carrier protein (ACP) desaturase ( ShSAD ) gene family, is the main driver of the abundance of ω-3 PUFAs in S. hispanica seeds. The insights gained from the genomic analysis of S. hispanica will help leveraging advanced genome editing techniques and will greatly support breeding efforts for improving ω-3 content in other oil crops.
Metabolite profiling of wheat (Triticum aestivum L.) phloem exudate
Publisher: Springer Science and Business Media LLC
Date: 2014
Whole-genome mapping of agronomic and metabolic traits to identify novel quantitative trait loci in bread wheat grown in a water-limited environment
Publisher: Oxford University Press (OUP)
Date: 09-05-2013
Comparative metabolic and ionomic profiling of two cultivars of Stevia rebaudiana Bert. (Bertoni) grown under salinity stress
Publisher: Elsevier BV
Date: 08-2018
DOI: 10.1016/J.PLAPHY.2018.05.001
Abstract: This study provides a comprehensive investigation on the impact of increasing NaCl concentrations on hydroponically grown Stevia rebaudiana cultivars (Shoutian-2 and Fengtian). Growth parameters including plant height, biomass and physiological responses including osmotic potential were measured. In addition, the levels of steviol glycosides, elements and primary metabolites were measured and statistically evaluated. The cultivar Fengtian grew faster, accumulated less Na
Integrative Multi-Omics Analysis of Barley Genotypes Shows Differential Salt-Induced Osmotic Barriers and Response Phases Among Rootzones
Publisher: Cold Spring Harbor Laboratory
Date: 31-10-2019
DOI: 10.1101/825059
Abstract: The mechanisms underlying rootzone-localised responses to salinity stress during early stage of barley development remains fragmentary and elusive. Here, we performed a comprehensive detection of the multi-root-omes (transcriptomes, metabolomes, lipidomes) of a domesticated barley cultivar (Clipper) and a landrace (Sahara) with seedling root growth maintained and restricted in response to salt stress, respectively. Novel generalized linear models were designed to determine differentially expressed genes (DEG) or abundant metabolites (DAM) specific to salt treatments, genotypes, or rootzones (meristematic Z1, elongation Z2, maturation Z3). Based on pathway over-representation of the DEG and DAM, phenylpropanoid biosynthesis is the most statistically over-represented biological pathways among all salinity responses observed. Together with the histological evidence, an intense salt-induced lignin impregnation was found only at the stelic cell wall of Clipper Z2, comparing to a unique elevation of suberin deposition across Sahara Z2. This suggests two differential salt-induced modulations of apoplastic flow between the genotypes. Based on global correlation network construction of the DEG and DAM, callose deposition that potentially adjusted the symplastic flow in roots was almost independent of salinity in rootzones of Clipper, but was markedly decreased in that of Sahara. Through closer examinations of molecular and hormonal clues, we further demonstrate that the salinity response in rootzones of Clipper were mostly at recovery phase, comparing to Sahara with rootzones retained at quiescence. Taken together, we propose that two distinctive salt tolerance mechanisms could exist in Clipper (growth-sustaining) and Sahara (salt-shielding), providing important clues for improving crop plasticity to cope with the deteriorating global salinization of soil.
Plant Growth Promotion and Heat Stress Amelioration in Arabidopsis Inoculated with Paraburkholderia phytofirmans PsJN Rhizobacteria Quantified with the GrowScreen-Agar II Phenotyping Platform
Publisher: MDPI AG
Date: 30-10-2022
Abstract: High temperatures inhibit plant growth. A proposed strategy for improving plant productivity under elevated temperatures is the use of plant growth-promoting rhizobacteria (PGPR). While the effects of PGPR on plant shoots have been extensively explored, roots—particularly their spatial and temporal dynamics—have been hard to study, due to their below-ground nature. Here, we characterized the time- and tissue-specific morphological changes in bacterized plants using a novel non-invasive high-resolution plant phenotyping and imaging platform—GrowScreen-Agar II. The platform uses custom-made agar plates, which allow air exchange to occur with the agar medium and enable the shoot to grow outside the compartment. The platform provides light protection to the roots, the exposure of it to the shoots, and the non-invasive phenotyping of both organs. Arabidopsis thaliana, co-cultivated with Paraburkholderia phytofirmans PsJN at elevated and ambient temperatures, showed increased lengths, growth rates, and numbers of roots. However, the magnitude and direction of the growth promotion varied depending on root type, timing, and temperature. The root length and distribution per depth and according to time was also influenced by bacterization and the temperature. The shoot biomass increased at the later stages under ambient temperature in the bacterized plants. The study offers insights into the timing of the tissue-specific, PsJN-induced morphological changes and should facilitate future molecular and biochemical studies on plant–microbe–environment interactions.
Metabolomics, Standards, and Metabolic Modeling for Synthetic Biology in Plants
Publisher: Frontiers Media SA
Date: 21-10-2015
LC-MS Profiling to Link Metabolic and Phenotypic Diversity in Plant Mapping Populations
Publisher: Springer New York
Date: 2014
DOI: 10.1007/978-1-4939-1258-2_3
Abstract: Numerous studies have revealed the extent of genetic, phenotypic, and metabolic variation between different plant cultivars/varieties. We present a specialized protocol for large-scale targeted and untargeted metabolite profiling for s les from large plant mapping populations using both reversed-phase and aqueous normal-phase LC-MS. This methodology provides a fast and combined targeted/nontargeted workflow as a powerful tool to discriminate related plant phenotypes and describes methods to combine mass features and agronomic traits to link phenotypic to metabolic traits independent of putative metabolite identities. This easily reproducible analytical strategy, in combination with a sophisticated data processing and analysis workflow, can be applicable to a wide range of plant mapping populations.
Profiling of polar metabolites in biological extracts using diamond hydride‐based aqueous normal phase chromatography
Publisher: Wiley
Date: 30-06-2009
Abstract: Highly polar metabolites, such as sugars and most amino acids are not retained by conventional RP LC columns. Without sufficient retention low concentration compounds are not detected due ion suppression and structural isomers are not resolved. In contrast, hydrophilic interaction chromatography (HILIC) and aqueous normal phase chromatography (ANP) retain compounds based on their hydrophilicity and therefore provides a means of separating highly polar compounds. Here, an ANP method based on the diamond hydride stationary phase is presented for profiling biological small molecules by LC. A rapid separation system based upon a fast gradient that delivers reproducible chromatography is presented. Approximately 1000 compounds were reproducibly detected in human urine s les and clear differences between these s les were identified. This chromatography was also applied to xylem fluid from soyabean (Glycine max) plants to which 400 compounds were detected. This method greatly increases the metabolite coverage over RP-only metabolite profiling in biological s les. We show that both forms of chromatography are necessary for untargeted comprehensive metabolite profiling and that the diamond hydride stationary phase provides a good option for polar metabolite analysis.
Plant Tissue Extraction for Metabolomics
Publisher: Humana Press
Date: 2013
DOI: 10.1007/978-1-62703-577-4_2
Abstract: Plants are not only important producers of foods and energy storages (e.g., sugars, carbohydrates, proteins, and fats) in the form of grains, fruits, and vegetables, they also provide many valuable products to human existence including wood, fibers, oils, resins, pigments, antioxidants, and sources of medicine. Most importantly in light of this book, plants have been a source of therapeutic and health promoting compounds throughout history. This chapter describes several essential considerations for the extraction process when aiming to study plant metabolism or to characterize the chemical composition of plant originated s les using metabolomics technologies.
Salt-stress induced alterations in the root lipidome of two barley genotypes with contrasting responses to salinity
Publisher: CSIRO Publishing
Date: 2016
DOI: 10.1071/FP15253
Abstract: Changes in lipid metabolism and composition as well as in distinct lipid species have been linked with altered plant growth, development and responses to environmental stresses including salinity. However, there is little information available in the literature focusing on lipids in roots under soil-related stresses such as salinity. Barley (Hordeum vulgare L.) is a major cereal grain and, as a glycophyte, suffers substantial yield loss when grown under saline conditions. Relatively little is understood of adaptation and tolerance mechanisms involving lipids and lipid metabolism in barley roots during development and under exposure to salinity stress. In this study we investigated the lipid composition of barley roots of Clipper and Sahara – two genotypes with contrasting responses to salinity – before and after salinity stress using a combination of three lipidomics techniques: Fatty acid compositional analysis, untargeted lipid profiling, and targeted analysis to profile quantitatively the in idual molecular species of key plant lipid classes. Our results provide new insight into the effect of salinity on fatty acid profiles and key lipid classes within barley roots of two different genotypes, which is discussed in the context of current knowledge of the root metabolic responses of cereal crops to salinity stress.
Author Correction: Germline mutations in mitochondrial complex I reveal genetic and targetable vulnerability in IDH1-mutant acute myeloid leukaemia
Publisher: Springer Science and Business Media LLC
Date: 15-07-2022
Metabolic responses to salt stress of barley (Hordeum vulgare L.) cultivars, Sahara and Clipper, which differ in salinity tolerance
Publisher: Oxford University Press (OUP)
Date: 10-08-2009
DOI: 10.1093/JXB/ERP243
Metabolite profiling of symbiont and host during thermal stress and bleaching in the coral Acropora aspera
Publisher: Springer Science and Business Media LLC
Date: 18-10-2017
Spatially Enriched Paralog Rearrangements Argue Functionally Diverse Ribosomes Arise during Cold Acclimation in Arabidopsis
Publisher: MDPI AG
Date: 07-06-2021
DOI: 10.3390/IJMS22116160
Abstract: Ribosome biogenesis is essential for plants to successfully acclimate to low temperature. Without dedicated steps supervising the 60S large subunits (LSUs) maturation in the cytosol, e.g., Rei-like (REIL) factors, plants fail to accumulate dry weight and fail to grow at suboptimal low temperatures. Around REIL, the final 60S cytosolic maturation steps include proofreading and assembly of functional ribosomal centers such as the polypeptide exit tunnel and the P-Stalk, respectively. In consequence, these ribosomal substructures and their assembly, especially during low temperatures, might be changed and provoke the need for dedicated quality controls. To test this, we blocked ribosome maturation during cold acclimation using two independent reil double mutant genotypes and tested changes in their ribosomal proteomes. Additionally, we normalized our mutant datasets using as a blank the cold responsiveness of a wild-type Arabidopsis genotype. This allowed us to neglect any reil-specific effects that may happen due to the presence or absence of the factor during LSU cytosolic maturation, thus allowing us to test for cold-induced changes that happen in the early nucleolar biogenesis. As a result, we report that cold acclimation triggers a reprogramming in the structural ribosomal proteome. The reprogramming alters the abundance of specific RP families and/or paralogs in non-translational LSU and translational polysome fractions, a phenomenon known as substoichiometry. Next, we tested whether the cold-substoichiometry was spatially confined to specific regions of the complex. In terms of RP proteoforms, we report that remodeling of ribosomes after a cold stimulus is significantly constrained to the polypeptide exit tunnel (PET), i.e., REIL factor binding and functional site. In terms of RP transcripts, cold acclimation induces changes in RP families or paralogs that are significantly constrained to the P-Stalk and the ribosomal head. The three modulated substructures represent possible targets of mechanisms that may constrain translation by controlled ribosome heterogeneity. We propose that non-random ribosome heterogeneity controlled by specialized biogenesis mechanisms may contribute to a preferential or ultimately even rigorous selection of transcripts needed for rapid proteome shifts and successful acclimation.
Modulators or facilitators? Roles of lipids in plant root–microbe interactions
Publisher: Elsevier BV
Date: 02-2022
DOI: 10.1016/J.TPLANTS.2021.08.004
Abstract: Lipids have erse functions in regulating the plasma membrane's cellular processes and signaling mediation. Plasma membrane lipids are also involved in the plant's complex interactions with the surrounding microorganisms, with which plants are in various forms of symbiosis. The roles of lipids influence the whole microbial colonization process, thus shaping the rhizomicrobiome. As chemical signals, lipids facilitate the stages of rhizospheric interactions - from plant root to microbe, microbe to microbe, and microbe to plant root - and modulate the plant's defense responses upon perception or contact with either beneficial or phytopathogenic microorganisms. Although studies have come a long way, further investigation is needed to discover more lipid species and elucidate novel lipid functions and profiles under various stages of plant root-microbe interactions.
The Effect of Cold Stress on the Root-Specific Lipidome of Two Wheat Varieties with Contrasting Cold Tolerance
Publisher: MDPI AG
Date: 20-05-2022
Abstract: Complex glycerolipidome analysis of wheat upon low temperature stress has been reported for above-ground tissues only. There are no reports on the effects of cold stress on the root lipidome nor on tissue-specific responses of cold stress wheat roots. This study aims to investigate the changes of lipid profiles in the different developmental zones of the seedling roots of two wheat varieties with contrasting cold tolerance exposed to chilling and freezing temperatures. We analyzed 273 lipid species derived from 21 lipid classes using a targeted profiling approach based on MS/MS data acquired from schedule parallel reaction monitoring assays. For both the tolerant Young and sensitive Wyalkatchem species, cold stress increased the phosphatidylcholine and phosphatidylethanolamine compositions, but decreased the monohexosyl ceramide compositions in the root zones. We show that the difference between the two varieties with contrasting cold tolerance could be attributed to the change in the in idual lipid species, rather than the fluctuation of the whole lipid classes. The outcomes gained from this study may advance our understanding of the mechanisms of wheat adaptation to cold and contribute to wheat breeding for the improvement of cold-tolerance.
A Quantitative Profiling Method of Phytohormones and Other Metabolites Applied to Barley Roots Subjected to Salinity Stress
Publisher: Frontiers Media SA
Date: 10-01-2017
Reproductive Stage Drought Tolerance in Wheat: Importance of Stomatal Conductance and Plant Growth Regulators
Publisher: MDPI AG
Date: 29-10-2021
Abstract: Drought stress requires plants to adjust their water balance to maintain tissue water levels. Isohydric plants (‘water-savers’) typically achieve this through stomatal closure, while anisohydric plants (‘water-wasters’) use osmotic adjustment and maintain stomatal conductance. Isohydry or anisohydry allows plant species to adapt to different environments. In this paper we show that both mechanisms occur in bread wheat (Triticum aestivum L.). Wheat lines with reproductive drought-tolerance delay stomatal closure and are temporarily anisohydric, before closing stomata and become isohydric at higher threshold levels of drought stress. Drought-sensitive wheat is isohydric from the start of the drought treatment. The capacity of the drought-tolerant line to maintain stomatal conductance correlates with repression of ABA synthesis in spikes and flag leaves. Gene expression profiling revealed major differences in the drought response in spikes and flag leaves of both wheat lines. While the isohydric drought-sensitive line enters a passive growth mode (arrest of photosynthesis, protein translation), the tolerant line mounts a stronger stress defence response (ROS protection, LEA proteins, cuticle synthesis). The drought response of the tolerant line is characterised by a strong response in the spike, displaying enrichment of genes involved in auxin, cytokinin and ethylene metabolism/signalling. While isohydry may offer advantages for longer term drought stress, anisohydry may be more beneficial when drought stress occurs during the critical stages of wheat spike development, ultimately improving grain yield.
An Arabidopsis lipid map reveals differences between tissues and dynamic changes throughout development
Publisher: Wiley
Date: 24-05-2021
DOI: 10.1111/TPJ.15278
Abstract: Mass spectrometry is the predominant analytical tool used in the field of plant lipidomics. However, there are many challenges associated with the mass spectrometric detection and identification of lipids because of the highly complex nature of plant lipids. Studies into lipid biosynthetic pathways, gene functions in lipid metabolism, lipid changes during plant growth and development, and the holistic examination of the role of plant lipids in environmental stress responses are often hindered. Here, we leveraged a robust pipeline that we previously established to extract and analyze lipid profiles of different tissues and developmental stages from the model plant Arabidopsis thaliana . We analyzed seven tissues at several different developmental stages and identified more than 200 lipids from each tissue analyzed. The data were used to create a web‐accessible in silico lipid map that has been integrated into an electronic Fluorescent Pictograph (eFP) browser. This in silico library of Arabidopsis lipids allows the visualization and exploration of the distribution and changes of lipid levels across selected developmental stages. Furthermore, it provides information on the characteristic fragments of lipids and adducts observed in the mass spectrometer and their retention times, which can be used for lipid identification. The Arabidopsis tissue lipid map can be accessed at bar.utoronto.ca/efp_arabidopsis_lipid/cgi‐bin/efpWeb.cgi .
Hyperaccumulation of zinc by Noccaea caerulescens results in a cascade of stress responses and changes in the elemental profile
Publisher: Oxford University Press (OUP)
Date: 2014
DOI: 10.1039/C4MT00132J
Abstract: Noccaea caerulescens can accumulate more than 2% Zn in the leaves without showing any outwards signs of toxicity however a myriad of elemental and metabolite changes occur at these concentrations.
High-mass-resolution MALDI mass spectrometry imaging reveals detailed spatial distribution of metabolites and lipids in roots of barley seedlings in response to salinity stress
Publisher: Springer Science and Business Media LLC
Date: 19-04-2018
Systems-based approaches enable identification of gene targets which improve the flavour profile of low-ethanol wine yeast strains
Publisher: Elsevier BV
Date: 09-2018
DOI: 10.1016/J.YMBEN.2018.08.006
Abstract: Metabolic engineering has been vital to the development of industrial microbes such as the yeast Saccharomyces cerevisiae. However, sequential rounds of modification are often needed to achieve particular industrial design targets. Systems biology approaches can aid in identifying genetic targets for modification through providing an integrated view of cellular physiology. Recently, research into the generation of commercial yeasts that can produce reduced-ethanol wines has resulted in metabolically-engineered strains of S. cerevisiae that are less efficient at producing ethanol from sugar. However, these modifications led to the concomitant production of off-flavour by-products. A combination of transcriptomics, proteomics and metabolomics was therefore used to investigate the physiological changes occurring in an engineered low-ethanol yeast strain during alcoholic fermentation. Integration of 'omics data identified several metabolic reactions, including those related to the pyruvate node and redox homeostasis, as being significantly affected by the low-ethanol engineering methodology, and highlighted acetaldehyde and 2,4,5-trimethyl-1,3-dioxolane as the main off-flavour compounds. Gene remediation strategies were then successfully applied to decrease the formation of these by-products, while maintaining the 'low-alcohol' phenotype. The data generated from this comprehensive systems-based study will inform wine yeast strain development programmes, which, in turn, could potentially play an important role in assisting winemakers in their endeavour to produce low-alcohol wines with desirable flavour profiles.
A new peak detection algorithm for MALDI mass spectrometry data based on a modified Asymmetric Pseudo-Voigt model
Publisher: Springer Science and Business Media LLC
Date: 12-2015
Mapping carbon fate during bleaching in a model cnidarian symbiosis: the application of 13C metabolomics
Publisher: Wiley
Date: 08-03-2017
DOI: 10.1111/NPH.14515
Abstract: Coral bleaching is a major threat to the persistence of coral reefs. Yet we lack detailed knowledge of the metabolic interactions that determine symbiosis function and bleaching‐induced change. We mapped autotrophic carbon fate within the free metabolite pools of both partners of a model cnidarian–dinoflagellate symbiosis ( Aiptasia–Symbiodinium ) during exposure to thermal stress via the stable isotope tracer ( 13 C bicarbonate), coupled to GC‐MS. Symbiont photodamage and pronounced bleaching coincided with substantial increases in the turnover of non 13 C‐labelled pools in the dinoflagellate (lipid and starch store catabolism). However, 13 C enrichment of multiple compounds associated with ongoing carbon fixation and de novo biosynthesis pathways was maintained (glucose, fatty acid and lipogenesis intermediates). Minimal change was also observed in host pools of 13 C‐enriched glucose (a major symbiont‐derived mobile product). However, host pathways downstream showed altered carbon fate and/or pool composition, with accumulation of compatible solutes and nonenzymic antioxidant precursors. In hospite symbionts continue to provide mobile products to the host, but at a significant cost to themselves, necessitating the mobilization of energy stores. These data highlight the need to further elucidate the role of metabolic interactions between symbiotic partners, during the process of thermal acclimation and coral bleaching.
Transition from a maternal to external nitrogen source in maize seedlings.
Publisher: Wiley
Date: 04-2017
DOI: 10.1111/JIPB.12525
Detection of QTL for metabolic and agronomic traits in wheat with adjustments for variation at genetic loci that affect plant phenology
Publisher: Elsevier BV
Date: 04-2015
DOI: 10.1016/J.PLANTSCI.2015.01.008
Abstract: Mapping of quantitative trait loci associated with levels of in idual metabolites (mQTL) was combined with the mapping of agronomic traits to investigate the genetic basis of variation and co-variation in metabolites, agronomic traits, and plant phenology in a field-grown bread wheat population. Metabolome analysis was performed using liquid chromatography-mass spectrometry resulting in identification of mainly polar compounds, including secondary metabolites. A total of 558 metabolic features were obtained from the flag leaves of 179 doubled haploid lines, of which 197 features were putatively identified, mostly as alkaloids, flavonoids and phenylpropanoids. Coordinated genetic control was observed for several groups of metabolites, such as organic acids influenced by two loci on chromosome 7A. Five major phenology-related loci, which were introduced as cofactors in the analyses, differed in their impact upon metabolic and agronomic traits with QZad-aww-7A having more impact on the expression of both metabolite and agronomic QTL than Ppd-B1, Vrn-A1, Eps, and QZad-aww-7D. This QTL study validates the utility of combining agronomic and metabolomic traits as an approach to identify potential trait enhancement targets for breeding selection and reinforces previous results that demonstrate the importance of including plant phenology in the assessment of useful traits in this wheat mapping population.
Assessing the Efficacy, Acute Toxicity, and Binding Modes of the Agricultural Nitrification Inhibitors 3,4-Dimethyl-1H-pyrazole (DMP) and Dicyandiamide (DCD) with Nitrosomonas europaea
Publisher: American Chemical Society (ACS)
Date: 25-01-2023
Structural and functional measures of marine microbial communities: An experiment to assess implications for oil spill management
Publisher: Elsevier BV
Date: 06-2018
DOI: 10.1016/J.MARPOLBUL.2018.04.054
Abstract: Microbial communities are ecologically important in aquatic environments and impacts on microbes have the potential to affect a number of functional processes. We have amended seawater with a crude oil and assessed changes in species composition as well as a measure of functional ersity (the ability of the community to utilise different carbon sources) and the community level metabolic signature. We found that there was a degree of functional redundancy in the community we tested. Oiled assemblages became less erse and more dominated by specialist hydrocarbon degraders, carbon source utilisation increased initially but there was no change in metabolic signature in this small scale laboratory experiment. This study supports the decision framework around management of oil spills. This package of methods has the potential to be used in the testing and selection of new dispersants for use in oil spill response.
A SIEVE-RAFT HYPOTHESIS FOR THE REGULATION OF ENDOTHELIAL FENESTRATIONS
Publisher: Elsevier BV
Date: 08-2013
Rapid and Inexpensive Assay for Testing the Efficiency of Potential New Synthetic Nitrification Inhibitors
Publisher: American Chemical Society (ACS)
Date: 20-02-2023
Germline mutations in mitochondrial complex I reveal genetic and targetable vulnerability in IDH1-mutant acute myeloid leukaemia
Publisher: Springer Science and Business Media LLC
Date: 12-05-2022
DOI: 10.1038/S41467-022-30223-9
Abstract: The interaction of germline variation and somatic cancer driver mutations is under-investigated. Here we describe the genomic mitochondrial landscape in adult acute myeloid leukaemia (AML) and show that rare variants affecting the nuclear- and mitochondrially-encoded complex I genes show near-mutual exclusivity with somatic driver mutations affecting isocitrate dehydrogenase 1 ( IDH1 ), but not IDH2 suggesting a unique epistatic relationship. Whereas AML cells with rare complex I variants or mutations in IDH1 or IDH2 all display attenuated mitochondrial respiration, heightened sensitivity to complex I inhibitors including the clinical-grade inhibitor, IACS-010759, is observed only for IDH1 -mutant AML. Furthermore, IDH1 mutant blasts that are resistant to the IDH1-mutant inhibitor, ivosidenib, retain sensitivity to complex I inhibition. We propose that the IDH1 mutation limits the flexibility for citrate utilization in the presence of impaired complex I activity to a degree that is not apparent in IDH2 mutant cells, exposing a mutation-specific metabolic vulnerability. This reduced metabolic plasticity explains the epistatic relationship between the germline complex I variants and oncogenic IDH1 mutation underscoring the utility of genomic data in revealing metabolic vulnerabilities with implications for therapy.
Changes in the Sugarcane Metabolome with Stem Development. Are They Related to Sucrose Accumulation?
Publisher: Oxford University Press (OUP)
Date: 04-2007
DOI: 10.1093/PCP/PCM027
Abstract: Sucrose content increases with internode development down the stem of sugarcane. In an attempt to determine which other changes in metabolites may be linked to sucrose accumulation gas chromatography-mass spectrometry was used to obtain metabolic profiles from methanol/water extracts of four s les of different age down the stem of cultivar Q117. Extracts were derivatized with either N-methyl-N-(trimethylsilyl) trifluoracetamide (TMS) or N-methyl N-(tert-butyldimethylsilyl) trifluoroacetamide (TBS) separately in order to increase the number of metabolites that could be detected. This resulted in the measurement of 121 and 71 metabolites from the TMS and TBS derivatization, respectively. Fifty-five metabolites were identified using commercial and publicly available libraries. Statistical analysis of the metabolite profiles resulted in clustering of tissue types. Particular metabolites were correlated with the level of sucrose accumulation, which as expected increased down the stem. Metabolites, such as tricarboxylic acid cycle intermediates and amino acids, were more abundant in the M2 s le (meristem to internode 2) that was actively growing and decreased in an apparently coordinated developmentally programmed manner in more mature internodes down the stem. However, other metabolites such as trehalose and raffinose showed positive correlations with sucrose concentration. Here we discuss the technique used to measure metabolites in sugarcane and the changes in metabolite abundance down the sugarcane stem.
Molecular Mechanisms of Pseudomonas-Assisted Plant Nitrogen Uptake: Opportunities for Modern Agriculture
Publisher: Scientific Societies
Date: 09-2023
DOI: 10.1094/MPMI-10-22-0223-CR
Abstract: Pseudomonas spp. make up 1.6% of the bacteria in the soil and are found throughout the world. More than 140 species of this genus have been identified, some beneficial to the plant. Several species in the family Pseudomonadaceae, including Azotobacter vinelandii AvOP, Pseudomonas stutzeri A1501, Pseudomonas stutzeri DSM4166, Pseudomonas szotifigens 6HT33bT and Pseudomonas sp. K1 can fix nitrogen from the air. The genes required for these reactions are organized in a nitrogen fixation island, obtained via horizontal gene transfer from Klebsiella pneumoniae, Pseudomonas stutzeri and Azotobacter vinelandii. Today, this island is conserved in Pseudomonas spp. from different geographical locations, which in turn have evolved to deal with different geo-climatic conditions. Here, we summarize the molecular mechanisms behind Pseudomonas driven plant growth promotion, with particular focus on improving plant performance at limiting nitrogen (N), and improving plant N content. We describe Pseudomonas-plant interaction strategies in the soil, noting that the mechanisms of denitrification, ammonification, and secondary metabolite signalling are only marginally explored. Plant growth promotion is dependent on the abiotic conditions, and differs at sufficient and deficient N. The molecular controls behind different plant response are not fully elucidated. We suggest that superposition of transcriptome, proteome, and metabolome data and their integration with plant phenotype development through time will help fill these gaps. The aim of this review is to summarize the knowledge behind Pseudomonas driven nitrogen fixation and to point to possible agricultural solutions
Low doses of the organic insecticide spinosad trigger lysosomal defects, ROS driven lipid dysregulation and neurodegeneration in flies
Publisher: Cold Spring Harbor Laboratory
Date: 04-02-2021
DOI: 10.1101/2021.02.03.429672
Abstract: The plight of insect populations around the world and the threats it poses to agriculture and ecosystems has thrown insecticide use into the spotlight. Spinosad is an organic insecticide, considered less harmful to beneficial insects than synthetic insecticides, but its mode of action remains unclear. Using Drosophila, we show that low doses of spinosad reduce cholinergic response in neurons by antagonizing Dα6 nAChRs. Dα6 nAChRs are transported to lysosomes that become enlarged and accumulate upon spinosad treatment. Oxidative stress is initiated in the central nervous system, and spreads to midgut and disturbs lipid storage in metabolic tissues in a Dα6-dependent manner. Spinosad toxicity was ameliorated with the antioxidant N-Acetylcysteine amide (NACA). Chronic exposures lead to mitochondrial defects, severe neurodegeneration and blindness in adult animals. The many deleterious effects of low doses of this insecticide reported here point to an urgent need for rigorous investigation of its impacts on beneficial insects.
Nitrogen assimilation system in maize is regulated by developmental and tissue-specific mechanisms
Publisher: Springer Science and Business Media LLC
Date: 10-08-2016
DOI: 10.1007/S11103-016-0512-5
Abstract: We found metabolites, enzyme activities and enzyme transcript abundances vary significantly across the maize lifecycle, but weak correlation exists between the three groups. We identified putative genes regulating nitrate assimilation. Progress in improving nitrogen (N) use efficiency (NUE) of crop plants has been h ered by the complexity of the N uptake and utilisation systems. To understand this complexity we measured the activities of seven enzymes and ten metabolites related to N metabolism in the leaf and root tissues of Gaspe Flint maize plants grown in 0.5 or 2.5 mM NO3 (-) throughout the lifecycle. The amino acids had remarkably similar profiles across the lifecycle except for transient responses, which only appeared in the leaves for aspartate or in the roots for asparagine, serine and glycine. The activities of the enzymes for N assimilation were also coordinated to a certain degree, most noticeably with a peak in root activity late in the lifecycle, but with wide variation in the activity levels over the course of development. We analysed the transcriptional data for gene sets encoding the measured enzymes and found that, unlike the enzyme activities, transcript levels of the corresponding genes did not exhibit the same coordination across the lifecycle and were only weakly correlated with the levels of various amino acids or in idual enzyme activities. We identified gene sets which were correlated with the enzyme activity profiles, including seven genes located within previously known quantitative trait loci for enzyme activities and hypothesise that these genes are important for the regulation of enzyme activities. This work provides insights into the complexity of the N assimilation system throughout development and identifies candidate regulatory genes, which warrant further investigation in efforts to improve NUE in crop plants.
Inactivation of Mitochondrial Complex I Induces the Expression of a Twin Cysteine Protein that Targets and Affects Cytosolic, Chloroplastidic and Mitochondrial Function
Publisher: Elsevier BV
Date: 05-2016
DOI: 10.1016/J.MOLP.2016.01.009
Abstract: At12Cys-1 (At5g64400) and At12Cys-2 (At5g09570) are two closely related isogenes that encode small, twin cysteine proteins, typically located in mitochondria. At12Cys-2 transcript is induced in a variety of mutants with disrupted mitochondrial proteins, but an increase in At12Cys protein is only detected in mutants with reduced mitochondrial complex I abundance. Induction of At12Cys protein in mutants that lack mitochondrial complex I is accompanied by At12Cys protein located in mitochondria, chloroplasts, and the cytosol. Biochemical analyses revealed that even single gene deletions, i.e., At12cys-1 or At12cys-2, have an effect on mitochondrial and chloroplast functions. However, only double mutants, i.e., At12cys-1:At12cys-2, affect the abundance of protein and mRNA transcripts encoding translation elongation factors as well as rRNA abundance. Blue native PAGE showed that At12Cys co-migrated with mitochondrial supercomplex I + III. Likewise, deletion of both At12cys-1 and At12cys-2 genes, but not single gene deletions, results in enhanced tolerance to drought and light stress and increased anti-oxidant capacity. The induction and multiple localization of At12Cys upon a reduction in complex I abundance provides a mechanism to specifically signal mitochondrial dysfunction to the cytosol and then beyond to other organelles in the cell.
The genome of Chenopodium quinoa
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.
De novo transcriptome assembly and analysis of differentially expressed genes of two barley genotypes reveal root-zone-specific responses to salt exposure
Publisher: Springer Science and Business Media LLC
Date: 16-08-2016
DOI: 10.1038/SREP31558
Abstract: Plant roots are the first organs sensing and responding to salinity stress, manifested differentially between different root types, and also at the in idual tissue and cellular level. High genetic ersity and the current lack of an assembled map-based sequence of the barley genome severely limit barley research potential. We used over 580 and 600 million paired-end reads, respectively, to create two de novo assemblies of a barley landrace (Sahara) and a malting cultivar (Clipper) with known contrasting responses to salinity. Generalized linear models were used to statistically access spatial, treatment-related, and genotype-specific responses. This revealed a spatial gene expression gradient along the barley root, with more differentially expressed transcripts detected between different root zones than between treatments. The root transcriptome also showed a gradual transition from transcripts related to sugar-mediated signaling at the root meristematic zone to those involved in cell wall metabolism in the elongation zone, and defense response-related pathways toward the maturation zone, with significant differences between the two genotypes. The availability of these additional transcriptome reference sets will serve as a valuable resource to the cereal research community, and may identify valuable traits to assist in breeding programmes.
Identification of physiological changes and key metabolites coincident with postharvest internal browning of pineapple ( Ananas comosus L.) fruit
Publisher: Elsevier BV
Date: 03-2018
Diurnal Changes in Transcript and Metabolite Levels during the Iron Deficiency Response of Rice.
Publisher: Springer Science and Business Media LLC
Date: 20-04-2017
Genetic variation in the root growth response of barley genotypes to salinity stress
Publisher: CSIRO Publishing
Date: 2013
DOI: 10.1071/FP12290
Abstract: We aimed to identify genetic variation in root growth in the cereal crop barley (Hordeum vulgare L.) in response to the early phase of salinity stress. Seminal root elongation was examined at various concentrations of salinity in seedlings of eight barley genotypes consisting of a landrace, wild barley and cultivars. Salinity inhibited seminal root elongation in all genotypes, with considerable variation observed between genotypes. Relative root elongation rates were 60–90% and 30–70% of the control rates at 100 and 150 mM NaCl, respectively. The screen identified the wild barley genotype CPI71284–48 as the most tolerant, maintaining root elongation and biomass in response to salinity. Root elongation was most significantly inhibited in the landrace Sahara. Root and shoot Na+ concentrations increased and K+ concentrations decreased in all genotypes in response to salinity. However, the root and shoot ion concentrations did not correlate with root elongation rates, suggesting that the Na+ and K+ concentrations were not directly influencing root growth, at least during the early phase of salt stress. The identification of genetic ersity in root growth responses to salt stress in barley provides important information for future genetic, physiological and biochemical characterisation of mechanisms of salinity tolerance.
Metabolic profiling of a transgenic Caenorhabditis elegans Alzheimer model
Publisher: Springer Science and Business Media LLC
Date: 30-07-2015
A Golgi UDP-GlcNAc transporter delivers substrates for N-linked glycans and sphingolipids
Publisher: Springer Science and Business Media LLC
Date: 17-09-2018
DOI: 10.1038/S41477-018-0235-5
Abstract: Glycosylation requires activated glycosyl donors in the form of nucleotide sugars to drive processes such as post-translational protein modifications and glycolipid and polysaccharide biosynthesis. Most of these reactions occur in the Golgi, requiring cytosolic-derived nucleotide sugars, which need to be actively transferred into the Golgi lumen by nucleotide sugar transporters. We identified a Golgi-localized nucleotide sugar transporter from Arabidopsis thaliana with affinity for UDP-N-acetyl-D-glucosamine (UDP-GlcNAc) and assigned it UDP-GlcNAc transporter 1 (UGNT1). Profiles of N-glycopeptides revealed that plants carrying the ugnt1 loss-of-function allele are virtually devoid of complex and hybrid N-glycans. Instead, the N-glycopeptide population from these alleles exhibited high-mannose structures, representing structures prior to the addition of the first GlcNAc in the Golgi. Concomitantly, sphingolipid profiling revealed that the biosynthesis of GlcNAc-containing glycosyl inositol phosphorylceramides (GIPCs) is also reliant on this transporter. By contrast, plants carrying the loss-of-function alleles affecting ROCK1, which has been reported to transport UDP-GlcNAc and UDP-N-acetylgalactosamine, exhibit no changes in N-glycan or GIPC profiles. Our findings reveal that plants contain a single UDP-GlcNAc transporter that delivers an essential substrate for the maturation of N-glycans and the GIPC class of sphingolipids.
RNA Catabolites Contribute to the Nitrogen Pool and Support Growth Recovery of Wheat
Publisher: Frontiers Media SA
Date: 02-11-2018
Cellulose biosynthesis inhibitor isoxaben causes nutrient-dependent and tissue-specific Arabidopsis phenotypes
Publisher: Oxford University Press (OUP)
Date: 12-10-2023
A Historical overview of natural products in drug discovery
Publisher: MDPI AG
Date: 16-04-2012
Dietary intervention rescues myopathy associated with neurofibromatosis type 1
Publisher: Oxford University Press (OUP)
Date: 08-12-2017
DOI: 10.1093/HMG/DDX423
Abstract: Neurofibromatosis type 1 (NF1) is an autosomal dominant genetic disorder with complex symptomology. In addition to a predisposition to tumors, children with NF1 can present with reduced muscle mass, global muscle weakness, and impaired motor skills, which can have a significant impact on quality of life. Genetic mouse models have shown a lipid storage disease phenotype may underlie muscle weakness in NF1. Herein we confirm that biopsy specimens from six in iduals with NF1 similarly manifest features of a lipid storage myopathy, with marked accumulation of intramyocellular lipid, fibrosis, and mononuclear cell infiltrates. Intramyocellular lipid was also correlated with reductions in neurofibromin protein expression by western analysis. An RNASeq profile of Nf1null muscle from a muscle-specific Nf1 knockout mouse (Nf1MyoD-/-) revealed alterations in genes associated with glucose regulation and cell signaling. Comparison by lipid mass spectrometry demonstrated that Nf1null muscle specimens were enriched for long chain fatty acid (LCFA) containing neutral lipids, such as cholesterol esters and triacylglycerides, suggesting fundamentally impaired LCFA metabolism. The subsequent generation of a limb-specific Nf1 knockout mouse (Nf1Prx1-/-) recapitulated all observed features of human NF1 myopathy, including lipid storage, fibrosis, and muscle weakness. Collectively, these insights led to the evaluation of a dietary intervention of reduced LCFAs, and enrichment of medium-chain fatty acids (MCFAs) with L-carnitine. Following 8-weeks of dietary treatment, Nf1Prx1-/- mice showed a 45% increase in maximal grip strength, and a 71% reduction in intramyocellular lipid staining compared with littermates fed standard chow. These data link NF1 deficiency to fundamental shifts in muscle metabolism, and provide strong proof of principal that a dietary intervention can ameliorate symptoms.
Salt stress alters membrane lipid content and lipid biosynthesis pathways in the plasma membrane and tonoplast
Publisher: Oxford University Press (OUP)
Date: 15-03-2022
Abstract: Plant cell membranes are the sites of sensing and initiation of rapid responses to changing environmental factors including salinity stress. Understanding the mechanisms involved in membrane remodeling is important for studying salt tolerance in plants. This task remains challenging in complex tissue due to suboptimal subcellular membrane isolation techniques. Here, we capitalized on the use of a surface charge-based separation method, free flow electrophoresis, to isolate the tonoplast (TP) and plasma membrane (PM) from leaf tissue of the halophyte ice plant (Mesembryanthemum crystallinum L.). Results demonstrated a membrane-specific lipidomic remodeling in this plant under salt conditions, including an increased proportion of bilayer forming lipid phosphatidylcholine in the TP and an increase in nonbilayer forming and negatively charged lipids (phosphatidylethanolamine and phosphatidylserine) in the PM. Quantitative proteomics showed salt-induced changes in proteins involved in fatty acid synthesis and desaturation, glycerolipid, and sterol synthesis, as well as proteins involved in lipid signaling, binding, and trafficking. These results reveal an essential plant mechanism for membrane homeostasis wherein lipidome remodeling in response to salt stress contributes to maintaining the physiological function of in idual subcellular compartments.
Plant metabolomics reveals conserved and divergent metabolic responses to salinity
Publisher: Wiley
Date: 08-11-2007
DOI: 10.1111/J.1399-3054.2007.00993.X
Abstract: New metabolic profiling technologies provide data on a wider range of metabolites than traditional targeted approaches. Metabolomic technologies currently facilitate acquisition of multivariate metabolic data using erse, mostly hyphenated, chromatographic detection systems, such as GC-MS or liquid chromatography coupled to mass spectrometry, Fourier-transformed infrared spectroscopy or NMR-based methods. Analysis of the resulting data can be performed through a combination of non-supervised and supervised statistical methods, such as independent component analysis and analysis of variance, respectively. These methods reduce the complex data sets to information, which is relevant for the discovery of metabolic markers or for hypothesis-driven, pathway-based analysis. Plant responses to salinity involve changes in the activity of genes and proteins, which invariably lead to changes in plant metabolism. Here, we highlight a selection of recent publications in the salt stress field, and use gas chromatography time-of-flight mass spectrometry profiles of polar fractions from the plant models, Arabidopsis thaliana, Lotus japonicus and Oryza sativa to demonstrate the power of metabolite profiling. We present evidence for conserved and ergent metabolic responses among these three species and conclude that a change in the balance between amino acids and organic acids may be a conserved metabolic response of plants to salt stress.
Effect of Spirotetramat Application on Salicylic Acid, Antioxidative Enzymes, Amino Acids, Mineral Elements, and Soluble Carbohydrates in Cucumber (Cucumis sativus L.)
Publisher: MDPI
Date: 29-11-2021
Non-protein amino acids in Australian acacia seed: Implications for food security and recommended processing methods to reduce djenkolic acid
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.
A high-resolution HPLC-QqTOF platform using parallel reaction monitoring for in-depth lipid discovery and rapid profiling.
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.
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Linkage Projects - Grant ID: LP140100239
Start Date: 04-2015
End Date: 12-2018
Amount: $524,000.00
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View Funded ActivityARC Future Fellowships - Grant ID: FT130100326
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Amount: $872,240.00
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View Funded ActivityDiscovery Projects - Grant ID: DP200101162
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Amount: $375,000.00
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View Funded ActivityDiscovery Projects - Grant ID: DP230100296
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End Date: 02-2026
Amount: $389,000.00
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View Funded ActivityIndustrial Transformation Research Hubs - Grant ID: IH200100023
Start Date: 08-2021
End Date: 08-2026
Amount: $4,950,000.00
Funder: Australian Research Council
View Funded ActivityLinkage Projects - Grant ID: LP130101055
Start Date: 06-2014
End Date: 06-2018
Amount: $524,718.00
Funder: Australian Research Council
View Funded ActivityLinkage Infrastructure, Equipment And Facilities - Grant ID: LE0775534
Start Date: 2007
End Date: 12-2007
Amount: $300,000.00
Funder: Australian Research Council
View Funded ActivityLinkage Infrastructure, Equipment And Facilities - Grant ID: LE160100015
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End Date: 12-2016
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