Serge Rudaz

Spatial and Temporal Dynamics of Jasmonate Synthesis and Accumulation in Arabidopsis in Response to Wounding

A new metabolite profiling approach combined with an ultrarapid sample preparation procedure was used to study the temporal and spatial dynamics of the wound-induced accumulation of jasmonic acid (JA) and its oxygenated derivatives in Arabidopsis thaliana. In addition to well known jasmonates, including hydroxyjasmonates (HOJAs), jasmonoyl-isoleucine (JA-Ile), and its 12-hydroxy derivative (12-HOJA-Ile), a new wound-induced dicarboxyjasmonate, 12-carboxyjasmonoyl-l-isoleucine (12-HOOCJA-Ile) was discovered. HOJAs and 12-HOOCJA-Ile were enriched in the midveins of wounded leaves, strongly differentiating them from the other jasmonate metabolites studied. The polarity of these oxylipins at physiological pH correlated with their appearance in midveins. When the time points of accumulation of different jasmonates were determined, JA levels were found to increase within 2–5 min of wounding. Remarkably, these changes occurred throughout the plant and were not restricted to wounded leaves. The speed of the stimulus leading to JA accumulation in leaves distal to a wound is at least 3 cm/min. The data give new insights into the spatial and temporal accumulation of jasmonates and have implications in the understanding of long-distance wound signaling in plants.

Velocity Estimates for Signal Propagation Leading to Systemic Jasmonic Acid Accumulation in Wounded Arabidopsis

The wound response prohormone jasmonic acid (JA) accumulates rapidly in tissues both proximal and distal to injury sites in plants. Using quantitative liquid chromatography-mass spectrometry after flash freezing of tissues, we found that JA accumulated within 30 s of injury in wounded Arabidopsis leaves (p = 3.5 e−7). JA augmentation distal to wounds was strongest in unwounded leaves with direct vascular connections to wounded leaves wherein JA levels increased significantly within 120 s of wounding (p = 0.00027). This gave conservative and statistically robust temporal boundaries for the average velocity of the long distance signal leading to distal JA accumulation in unwounded leaves of 3.4–4.5 cm min−1. Like JA, transcripts of the JA synthesis gene LIPOXYGENASE2 (LOX2) and the jasmonate response gene JAZ10.3 also accumulated to higher levels in directly interconnected leaves than in indirectly connected leaves. JA accumulation in a lox2-1 mutant plant was initiated rapidly after wounding then slowed progressively compared with the wild type (WT). Despite this, JAZ10.3 expression in the two genotypes was similar. Free cyclopentenone jasmonate levels were similar in both resting WT and lox2-1. In contrast, bound cyclopentenone jasmonates (arabidopsides) were far lower in lox2-1 than in the WT. The major roles of LOX2 are to generate arabidopsides and the large levels of JA that accumulate proximal to the wound. LOX2 is not essential for some of the most rapid events elicited by wounding.

Atmospheric pressure photoionization for coupling liquid-chromatography to mass spectrometry: A review

This review presents the state-of-the-art techniques that couple liquid chromatography (LC) and mass spectrometry (MS) via atmospheric pressure photoionization (APPI). The different ionization mechanisms are discussed as well as the influence of the mobile phase composition, the nature of the dopant, etc. A comparison with other ionization sources, such as electrospray ionization (ESI) and atmospheric pressure chemical ionization (APCI), is reported, and the combination of APPI with these sources is also discussed. Several applications, covering the time period of 2005-2008, for the analysis of drugs, lipids, natural compounds, pesticides, synthetic organics, petroleum derivatives, and other substances are presented.

Intact protein analysis in the biopharmaceutical field

In recent years, a growing number of biopharmaceutical proteins have been produced and are already available, or will be soon available, in the market. These molecules are more complex to analyze than conventional low molecular weight drugs, and thus need powerful analytical approaches for the entire development and delivery process. This review summarizes the analytical techniques available for intact protein determination and the main development steps in which they are applicable. A strong emphasis has been put on separation techniques, liquid chromatography and electrophoretic techniques, but mass spectrometry and spectroscopic approaches are also mentioned. Overall, we highlight how several analytical strategies are necessary to obtain global information.

Knowledge discovery in metabolomics: An overview of MS data handling

While metabolomics attempts to comprehensively analyse the small molecules characterising a biological system, MS has been promoted as the gold standard to study the wide chemical diversity and range of concentrations of the metabolome. On the other hand, extracting the relevant information from the overwhelming amount of data generated by modern analytical platforms has become an important issue for knowledge discovery in this research field. The appropriate treatment of such data is therefore of crucial importance in order, for the data, to provide valuable information. The aim of this review is to provide a broad overview of the methodologies developed to handle and process MS metabolomic data, compare the samples and highlight the relevant metabolites, starting from the raw data to the biomarker discovery. As data handling can be further separated into data processing, data pre-treatment and data analysis, recent advances in each of these steps are detailed separately.

Fast analysis of doping agents in urine by ultra-high-pressure liquid chromatography–quadrupole time-of-flight mass spectrometry

The general strategy to perform anti-doping analyses of urine samples starts with the screening for a wide range of compounds. This step should be fast, generic and able to detect any sample that may contain a prohibited substance while avoiding false negatives and reducing false positive results. The experiments presented in this work were based on ultra-high-pressure liquid chromatography coupled to hybrid quadrupole time-of-flight mass spectrometry. Thanks to the high sensitivity of the method, urine samples could be diluted 2-fold prior to injection. One hundred and three forbidden substances from various classes (such as stimulants, diuretics, narcotics, anti-estrogens) were analysed on a C(18) reversed-phase column in two gradients of 9min (including two 3min equilibration periods) for positive and negative electrospray ionisation and detected in the MS full scan mode. The automatic identification of analytes was based on retention time and mass accuracy, with an automated tool for peak picking. The method was validated according to the International Standard for Laboratories described in the World Anti-Doping Code and was selective enough to comply with the World Anti-Doping Agency recommendations. In addition, the matrix effect on MS response was measured on all investigated analytes spiked in urine samples. The limits of detection ranged from 1 to 500ng/mL, allowing the identification of all tested compounds in urine. When a sample was reported positive during the screening, a fast additional pre-confirmatory step was performed to reduce the number of confirmatory analyses.

A systematic investigation of the effect of sample diluent on peak shape in hydrophilic interaction liquid chromatography

The aim of this study was to evaluate the importance of sample diluents to improve peak shapes in hydrophilic interaction liquid chromatography (HILIC), using low molecular weight (<1000 Da) analytes as well as peptides (with MW ranging between 1000 and 6000 Da) as model compounds. Various solvents were tested including water, acetonitrile, methanol, ethanol, propan-2-ol, dimethyl sulfoxide, and a number of combinations of them. For the analysis of small MW compounds, best peak shapes were obtained with sample dissolved in pure ACN but, IPA or a mixture of ACN/IPA (50:50, v/v) could represent a viable alternative in the case of solubility issues with pure ACN. For drug discovery applications, DMSO can be employed but in combination with at least 80% of ACN. For peptides analysis, acetonitrile, EtOH and IPA as sample diluents, provided similar chromatographic profiles, but pure EtOH or IPA were recommended to limit denaturation and samples solubility issues. Finally, whatever the nature of the compounds, it is recommended to add the lowest amount of water to the sample diluent, to maintain suitable peak shapes.

Characterization and classification of matrix effects in biological samples analyses

An exhaustive classification of matrix effects occurring when a sample preparation is performed prior to liquid-chromatography coupled to mass spectrometry (LC-MS) analyses was proposed. A total of eight different situations were identified allowing the recognition of the matrix effect typology via the calculation of four recovery values. A set of 198 compounds was used to evaluate matrix effects after solid phase extraction (SPE) from plasma or urine samples prior to LC-ESI-MS analysis. Matrix effect identification was achieved for all compounds and classified through an organization chart. Only 17% of the tested compounds did not present significant matrix effects.

UPLC–TOF-MS for plant metabolomics: A sequential approach for wound marker analysis in Arabidopsis thaliana ☆

The model plant Arabidopsis thaliana was studied for the search of new metabolites involved in wound signalling. Diverse LC approaches were considered in terms of efficiency and analysis time and a 7-min gradient on a UPLC-TOF-MS system with a short column was chosen for metabolite fingerprinting. This screening step was designed to allow the comparison of a high number of samples over a wide range of time points after stress induction in positive and negative ionisation modes. Thanks to data treatment, clear discrimination was obtained, providing lists of potential stress-induced ions. In a second step, the fingerprinting conditions were transferred to longer column, providing a higher peak capacity able to demonstrate the presence of isomers among the highlighted compounds.

Importance of instrumentation for fast liquid chromatography in pharmaceutical analysis

In the last decade, an important technical evolution has occurred in pharmaceutical analysis with numerous innovative supports and advanced instruments that have been proposed to achieve fast or ultra-fast separations in LC with an excellent sensitivity and ease of operation. Among the proposed strategies to increase the throughput, the use of short narrow-bore columns packed with sub-3 μm core-shell and porous sub-2 μm particles have emerged as the gold standards. Nevertheless, to take the full benefits of these modern supports, a suitable chromatographic system has to be employed. This review summarizes the instrumental needs and challenges in terms of extra-column variance, dwell volume, maximum system pressure, detector data acquisition rate, and injection cycle time. In addition, because of their reasonable pressure drop, the use of columns packed with sub-3 μm core-shell particles on a conventional LC instrument is discussed in detail. A methodology is proposed to check the compatibility between stationary phase and instrument, and some solutions are proposed to improve the performance of standard instruments. Finally, because the column technology is evolving faster than instrumentation, it is nowadays possible to purchase short, narrow-bore columns packed with 1.3 μm core-shell particles. Micro columns (1 mm I.D.) packed with 1.7-1.9 μm porous particles are also available from several providers, which limit frictional heating effects and reduce solvent and sample consumption. However, it remains difficult to find instruments compatible with such column geometries and a severe loss of performance may be observed due to the system itself.