Rapid profiling of intact glucosinolates in Arabidopsis leaves by UHPLC-QTOFMS using a charged surface hybrid column.

INTRODUCTION: The analysis of glucosinolates (GS) is traditionally performed by reverse-phase liquid chromatography coupled to ultraviolet detection after a time-consuming desulphation step, which is required for increased retention. Simpler and more efficient alternative methods that can shorten both sample preparation and analysis are much needed. OBJECTIVE: To evaluate the feasibility of using ultrahigh-pressure liquid chromatography coupled to quadrupole time-of-flight mass spectrometry (UHPLC-QTOFMS) for the rapid profiling of intact GS. METHODOLOGY: A simple and short extraction of GS from Arabidopsis thaliana leaves was developed. Four sub-2 µm reverse-phase columns were tested for the rapid separation of these polar compounds using formic acid as the chromatographic additive. High-resolution QTOFMS was used to detect and identify GS. RESULTS: A novel charged surface hybrid (CSH) column was found to provide excellent retention and separation of GS within a total running time of 11 min. Twenty-one GS could be identified based on their accurate mass as well as isotopic and fragmentation patterns. The method was applied to determine the changes in GS content that occur after herbivory in Arabidopsis. In addition, we evaluated its applicability to the profiling of other Brassicaceae species. CONCLUSION: The method developed can profile the full range of GS, including the most polar ones, in a shorter time than previous methods, and is highly compatible with mass spectrometric detection.

CATMA, a comprehensive genome-scale resource for silencing and transcript profiling of Arabidopsis genes.

BACKGROUND: The Complete Arabidopsis Transcript MicroArray (CATMA) initiative combines the efforts of laboratories in eight European countries 1 to deliver gene-specific sequence tags (GSTs) for the Arabidopsis research community. The CATMA initiative offers the power and flexibility to regularly update the GST collection according to evolving knowledge about the gene repertoire. These GST amplicons can easily be reamplified and shared, subsets can be picked at will to print dedicated arrays, and the GSTs can be cloned and used for other functional studies. This ongoing initiative has already produced approximately 24,000 GSTs that have been made publicly available for spotted microarray printing and RNA interference. RESULTS: GSTs from the CATMA version 2 repertoire (CATMAv2, created in 2002) were mapped onto the gene models from two independent Arabidopsis nuclear genome annotation efforts, TIGR5 and PSB-EuGène, to consolidate a list of genes that were targeted by previously designed CATMA tags. A total of 9,027 gene models were not tagged by any amplified CATMAv2 GST, and 2,533 amplified GSTs were no longer predicted to tag an updated gene model. To validate the efficacy of GST mapping criteria and design rules, the predicted and experimentally observed hybridization characteristics associated to GST features were correlated in transcript profiling datasets obtained with the CATMAv2 microarray, confirming the reliability of this platform. To complete the CATMA repertoire, all 9,027 gene models for which no GST had yet been designed were processed with an adjusted version of the Specific Primer and Amplicon Design Software (SPADS). A total of 5,756 novel GSTs were designed and amplified by PCR from genomic DNA. Together with the pre-existing GST collection, this new addition constitutes the CATMAv3 repertoire. It comprises 30,343 unique amplified sequences that tag 24,202 and 23,009 protein-encoding nuclear gene models in the TAIR6 and EuGène genome annotations, respectively. To cover the remaining untagged genes, we identified 543 additional GSTs using less stringent design criteria and designed 990 sequence tags matching multiple members of gene families (Gene Family Tags or GFTs) to cover any remaining untagged genes. These latter 1,533 features constitute the CATMAv4 addition. CONCLUSION: To update the CATMA GST repertoire, we designed 7,289 additional sequence tags, bringing the total number of tagged TAIR6-annotated Arabidopsis nuclear protein-coding genes to 26,173. This resource is used both for the production of spotted microarrays and the large-scale cloning of hairpin RNA silencing vectors. All information about the resulting updated CATMA repertoire is available through the CATMA database http://www.catma.org.

Two waves of recombinase gene expression in developing thymocytes.

During T cell development in the thymus, T cell receptor (TCR) alpha, beta, gamma, and delta genes are rearranged and expressed. TCR rearrangement strictly depends upon the coordinate activity of two recombinase activating genes, Rag-1 and Rag-2. In this study we have followed the expression of these genes at different stages of intrathymic development. The results indicate that there are two periods of high Rag-1 and Rag-2 mRNA expression. The first wave peaks early at the CD25+CD4-CD8-CD3- stage of development and coincides with the initial appearance of transcripts derived from fully rearranged TCR beta, gamma, and delta genes, whereas the second wave occurs later at the CD4+CD8+ stage coincident with full-length TCR alpha mRNA expression. Active downregulation of Rag-1 and Rag-2 mRNA expression appears to occur in vivo between the two peaks of recombinase activity. This phenomenon can be mimicked in vitro in response to artificial stimuli such as phorbol myristate acetate and calcium ionophore. Collectively our data suggest that recombinase expression is actively regulated during early thymus development independently of cell surface expression of a mature heterodimeric TCR protein complex.

Interchange of callosal and association projections in the developing visual cortex.

Neurons projecting transitorily into the corpus callosum from area 17 of the cat were retrogradely labeled by the fluorescent tracer Fast Blue (FB) injected into contralateral areas 17 and 18 on postnatal days 1-5. During the second postnatal month these neurons were still labeled by the early injection, although they had eliminated their callosal axon. At this time, 15-20% of these neurons could be retrogradely relabeled by injections of Diamidino Yellow (DY) into ipsilateral areas 17 and 18, but few or none by similar injections in the other areas that receive from area 17 (19, 21a, PMLS, 20a, 20b, DLS). Similarly, area 17 neurons projecting transitorily to contralateral area PMLS during the first postnatal week could be relabeled by DY injections in ipsilateral areas 17 and 18 but not in PMLS. Already around birth, many transitorily callosal neurons in area 17 send bifurcating axons both to contralateral areas 17 and 18 and ipsilateral area 18. It is probable that during postnatal development some of these neurons selectively eliminate their callosal axon collaterals and maintain the projection to ipsilateral area 18. In fact, some transitorily callosal neurons in area 17 can be double-labeled by simultaneous perinatal injections of FB in contralateral areas 17 and 18 and of a new long-lasting retrograde tracer, rhodamine-conjugated latex microspheres, in ipsilateral area 18. The same neurons can then be relabeled by reinjecting ipsilateral area 18 with DY during the second postnatal month. This finding, however, does not exclude the possibility that some transitorily callosal neurons send an axon to ipsilateral area 18 after eliminating their callosal axon. In conclusion, area 17 neurons that project transitorily through the corpus callosum later participate, probably permanently, in ipsilateral corticocortical projections but selectively to areas 17-18. The mechanism responsible for this selectivity is unknown, but it may be related to the differential radial distribution (i.e., to birth date) of area 17 neurons engaged in the various corticocortical projections. The problems raised by the use of long-lasting retrograde fluorescent tracers in neurodevelopmental studies and by the quantification of results of double- and triple-labeling paradigms are also discussed.

Differential distribution of tau proteins in developing cat cerebral cortex and corpus callosum.

During the postnatal development of cat visual cortex and corpus callosum the molecular composition of tau proteins varied with age. In both structures, they changed between postnatal days 19 and 39 from a set of two juvenile forms to a set of at least two adult variants with higher molecular weights. During the first postnatal week, tau proteins were detectable with TAU-1 antibody in axons of corpus callosum and visual cortex, and in some perikarya and dendrites in the visual cortex. At later ages, tau proteins were located exclusively within axons in all cortical layers and in the corpus callosum. Dephosphorylation of postnatal day 11 cortical tissue by alkaline phosphatase strongly increased tau protein immunoreactivity on Western blots and in numerous perikarya and dendrites in all cortical layers, in sections, suggesting that some tau forms had been unmasked. During postnatal development the intensity of this phosphate-dependent somatodendritic staining decreased, but remained in a few neurons in cortical layers II and III. On blots, the immunoreactivity of adult tau to TAU-1 was only marginally increased by dephosphorylation. Other tau antibodies (TAU-2, B19 and BR133) recognized two juvenile and two adult cat tau proteins on blots, and localized tau in axons or perikarya and dendrites in tissue untreated with alkaline phosphatase. Tau proteins in mature tissue were soluble and not associated with detergent-resistant structures. Furthermore, dephosphorylation by alkaline phosphatase resulted in the appearance of more tau proteins in soluble fractions. Therefore tau proteins seem to alter their degree of phosphorylation during development. This could affect microtubule stability as well as influence axonal and dendritic differentiation.

Comprehensive analysis of Arabidopsis expression level polymorphisms with simple inheritance.

In Arabidopsis thaliana, gene expression level polymorphisms (ELPs) between natural accessions that exhibit simple, single locus inheritance are promising quantitative trait locus (QTL) candidates to explain phenotypic variability. It is assumed that such ELPs overwhelmingly represent regulatory element polymorphisms. However, comprehensive genome-wide analyses linking expression level, regulatory sequence and gene structure variation are missing, preventing definite verification of this assumption. Here, we analyzed ELPs observed between the Eil-0 and Lc-0 accessions. Compared with non-variable controls, 5' regulatory sequence variation in the corresponding genes is indeed increased. However, approximately 42% of all the ELP genes also carry major transcription unit deletions in one parent as revealed by genome tiling arrays, representing a >4-fold enrichment over controls. Within the subset of ELPs with simple inheritance, this proportion is even higher and deletions are generally more severe. Similar results were obtained from analyses of the Bay-0 and Sha accessions, using alternative technical approaches. Collectively, our results suggest that drastic structural changes are a major cause for ELPs with simple inheritance, corroborating experimentally observed indel preponderance in cloned Arabidopsis QTL.

The Role of AtPHO1 in the Guard Cell Movements of Arabidopsis thaliana

In plants, stomatal opening and closing are driven by ion fluxes that cause changes in guard cell turgor and volume, a process that is in turn regulated by complex environ¬mental and hormonal signals such as light and the phytohormone abscisic acid (ABA). With this study, we present genetic evidence that stomatal movements in response to ABA are influenced by PHOl expression in guard cells of Arabidopsis thaliana. PHOl is a phosphate exporter involved in phosphate loading into the root xylem ves¬sels and, as a result, the phol mutant is characterized by low shoot phosphate lev¬els. In leaves, PHOl was found expressed at higher level in guard cells, and was quickly up-regulated following treatment with ABA. The phol mutant was unaffected in ROS production following ABA treatment, and in stomatal movements in response to different light cues, high extracellular calcium, auxin, and fusicoccin. However, stomatal movements in response to ABA treatment were severely impaired, both in terms of induction of closure and inhibition of opening. Stomatal movements in re¬sponse to hydrogen peroxide and reduced CO2 was altered as well. Micro-grafting a phol shoot scion onto wild-type root stock resulted in plants with normal shoot growth and Pi content, but failed to restore normal stomatal response to ABA treat-ment, showing that the impairment was not a simple pleiotropic consequence of phos¬phate deficiency. PHOl knockdown using RNAi specifically in guard cells of wild-type plants caused a reduced stomatal response to ABA. In agreement, specific expression of PHOl in guard cells of phol plants complemented the mutant guard cell phenotype and re-established ABA sensitivity, although full functional complementation was co- dependent on shoot Pi sufficiency. Down-regulation of PHOl in guard cells did not alter the expression of ABA marker genes, indicating that PHOl does not affect the ABA signal transduction cascade at the transcriptional level. Together, these data reveal an important role for phosphate and PHOl action in the stomatal response to ABA. Résumé L'ouverture et la fermeture des stomates des plantes sont des mouvements contrôlés par des flux d'ions causant des fluctuations de la turgescence des cellules de garde. Ce procédé est en retour régulé par des signaux environnementaux et hormonaux complexes, comme la lumière et l'hormone végétale acide abscissique (ABA). Nous présentons ici des preuves génétiques montrant que les mouvements stomatiques en réponse à l'ABA sont influencés par l'expression de PHOl dans les cellules de garde d'Arabidopsis thaliana. PHOl est un exporteur de phosphate, impliqué dans l'efflux de phosphate des cellules corticales racinaires vers les vaisseaux de xylème. En con¬séquence, le mutant phol est caractérisé par de faibles niveaux de phosphate dans les parties aériennes. Dans les feuilles, PHOl est exprimé préférentiellement dans les cellules de garde, comparé au mésophylle, et est rapidement induit par le traitement à l'ABA. Le mutant phol n'est pas affecté dans la perception de l'ABA, dans la pro¬duction de ROS en réponse à l'ABA, et dans la réponse des stomates aux traitements de lumière, à l'auxine, à la fusiccocine, et la forte concentration extracellulaire de cal¬cium. En revanche, les mouvements de stomates en réponse aux traitements à l'ABA sont fortement affectés, dans l'induction de la fermeture des stomates comme dans l'inhibition de leur ouverture. De plus, les mouvements de stomates en réponse au péroxyde d'hydrogène et à la diminution du CO2 sont aussi compromis. La création de micro-greffes composées d'une partie aérienne phol greffés sur un système racinaire sauvage génère des plantes avec une croissance et une teneur en phosphate normale, mais ne permet pas de restaurer la réponse des stomates à l'ABA, ce qui démontre que le défaut de réponse à l'ABA n'est pas une simple conséquence pléiotropique de la carence en phosphate. La répression par RNAi de l'expression de PHOl dans les stomates de plantes sauvages provoque une réduction de la réponse des stomates à l'ABA, mais n'affecte pas la réponse de gènes marqueurs à l'ABA, ce qui suggère que PHOl n'agit pas au niveau transcriptionnel. Parallèlement, l'expression de PHOl dans les cellules de gardes de mutants phol complémente le phénotype stomatique mutant et rétablit la réponse à l'ABA, bien que la totale complémentation nécessite l'apport normal de phosphate aux parties aériennes. Ensemble, ces résultats révè¬lent l'influence importante de PHOl et du phosphate dans la réponse des stomates à l'ABA.

Anticorps antineuronaux: un domaine en plein développement [Anti-neuronal antibodies: a rapidly developing field].

Anti-neuronal antibodies are implicated in various neurological syndromes that are sometimes associated with tumors. Depending on the antigenic target (nuclear, cytoplasmic or extracellular cell-surface or synaptic) the clinical presentation is different. In neurological syndromes associated with antibodies specific for intracellular antigens, the T-cell mediated immunological response predominates as pathogenic effector and the response to treatment is typically poor. In contrast, in syndromes related to antibodies against extracellular targets, the role of the antibodies is pathogenic and the neurological syndrome often responds better to immunomodulatory treatment, associated or not with an anti-tumoral treatment. We review the spectrum of anti-neuronal antibodies and their corresponding clinical and therapeutic characteristics.

Study of the SRR1-gene family in Arabidopsis, yeast and mouse cells

Abstract: Light is a very important environmental cue for plants. In addition to the energy for photosynthesis, it also provides information that is essential for many processes including seed germination, seedlings development, neighbours detection or transition from the vegetative to the reproductive state. Plants evolved different photoreceptors, among which the phytochromes (PHY), which are red/far-red photoreceptors. This family is composed of 5 members in Arabidopsis thaliana, among which phyB plays the major role for detection of red light. Phytochromes are also able to reset the phase of the circadian clock, which is composed of a complicated network of genes able to produce rhythms of about 24 hours, even in constant conditions. SRR1 (Sensitivity to Red light Reduced) is a gene that was shown to act in the phyB pathway as well as in the circadian clock. It was proposed to play a role in the maintenance of rhythms of the core oscillator because of the circadian phenotype of the srr1 mutant in constant light and in constant darkness. In the present study, we present data confirming the role of SRR1 in the core oscillator. Moreover, we show that SRR1 levels are not limiting for circadian rhythms nor for light perception. We show that the protein levels, the sub-cellular localisation or the complex in which SRR1 is found are not regulated in a circadian manner. Orthologues of SRR1 exist in numerous eukaryotes, forming a new gene family. None of the members of this family have been described. Here, we present data suggesting that the mouse orthologue of SRR1 may not be required for oscillation of the circadian clock of mouse cells in culture. The yeast gene (called BER1 for Benomyl REsistant) was studied to understand the biochemical function of this gene family. Based on synthetic genetic screens, a role of Ber1 was inferred in microtubules dynamics, N-terminal acetylation of protein and proteasome biogenesis. The effect of Ber1 on microtubules was confirmed by the observation that the ber1Δ mutant is more resistant to microtubule-depolymerising drugs and microscopic examination of microtubules in ber 1 Δ mutants. Complementation assays of ber1 Δ mutants and srrl mutants failed to reveal any obvious functional conservation of the mouse, yeast and Arabidopsis orthologues. In conclusion, the SRR1 family might encode genes that either plays different roles in different organisms, or have similar biochemical function but are involved in diverse pathway. Résumé: La lumière est un des facteurs abiotiques les plus important pour les plantes. En plus de l'énergie fournie pour la photosynthèse, elle fourni également de l'information nécessaire pour différents processus comme la germination, le développement des jeunes plantules, la détection de plantes avoisinantes ou encore la transition entre le développement végétatif et reproductif. Plusieurs types de photorécepteurs sont apparus chez les plantes au cours de l'évolution, notamment les phytochromes (PHI, qui perçoivent la lumière rouge et rouge lointaine. Cette famille est composé de 5 membres chez Arabidopsis thaliana, parmi lesquels phyB est le principal récepteur pour la lumière rouge. Les phytochromes sont aussi utiles pour la synchronisation entre les cycles jour-nuit dus à la rotation de la terre et l'horloge circadienne. Cette dernière est composée d'un réseau compliqué qui permet la production de rythmes capables de perdurer même en conditions constantes. SRRI (Sensitivity to Red light Reduced) est un gène qui agit dans la voie de signalisation de phyB ainsi que dans l'horloge circadienne. Il a été proposé que SRRI joue un rôle dans la maintenance des rythmes de l'oscillateur principal à cause des phénotypes circadiens du mutant srrl observés en lumière et en obscurité continue. Dans ce travail, nous présentons des données confirmant le rôle de SRR1 dans l'oscillateur principal. Nous montrons que les niveaux d'expression de SRRI ne sont pas limitants pour les rythmes circadiens ou la perception de la lumière. Enfin, nous montrons que le niveau d'accumulation de la protéine, sa localisation subcellulaire ou encore la taille du complexe dans lequel SRRl est trouvé ne sont pas régulés de façon circadiennes. Des orthologues de SRRI existent chez de nombreux eucaryotes, formant une nouvelle famille de gènes. Aucun des membres de cette famille n'a été étudié avant ce travail. Nous présentons des données suggérant que l'orthologue de la souris n'est peut-être pas requis pour les oscillations de l'horloge circadienne de cellules de souris en culture. Le gène de la levure (appelé SERI pour Benomyl REsistant) a été étudié afin de mieux comprendre la fonction biochimique de cette famille de gène. Une analyse par crible synthétique léthal a révélé un rôle de Ber1 dans la dynamique des microtubules, l'acétylation des protéines en N-terminal et la biogenèse du protéasome. L'effet de Ber1 sur les microtubules a été confirmé par l'observation du mutant ber1 en présence de drogue capable de dépolymériser les microtubules. Celui-ci est plus résistant à ces drogues que le type sauvage. Des expériences de complémentation n'ont pas montré de conservation de la fonction entre SRRI et ses homologues de souris ou de levure. En conclusion, la famille SRRI code pour des gènes qui pourraient avoir soit des rôles différents selon les organismes, soit la même fonction biochimique mais qui serait utile pour des voies de signalisation différentes.

Natural genetic variation of root system architecture from Arabidopsis to Brachypodium: towards adaptive value.

Root system architecture is a trait that displays considerable plasticity because of its sensitivity to environmental stimuli. Nevertheless, to a significant degree it is genetically constrained as suggested by surveys of its natural genetic variation. A few regulators of root system architecture have been isolated as quantitative trait loci through the natural variation approach in the dicotyledon model, Arabidopsis. This provides proof of principle that allelic variation for root system architecture traits exists, is genetically tractable, and might be exploited for crop breeding. Beyond Arabidopsis, Brachypodium could serve as both a credible and experimentally accessible model for root system architecture variation in monocotyledons, as suggested by first glimpses of the different root morphologies of Brachypodium accessions. Whether a direct knowledge transfer gained from molecular model system studies will work in practice remains unclear however, because of a lack of comprehensive understanding of root system physiology in the native context. For instance, apart from a few notable exceptions, the adaptive value of genetic variation in root system modulators is unknown. Future studies should thus aim at comprehensive characterization of the role of genetic players in root system architecture variation by taking into account the native environmental conditions, in particular soil characteristics.

Pacing redistributes glycogen within the developing myocardium.

Electrical pacing at physiological rate induces myocardial remodeling associated with regional changes in workload, blood flow and oxygen consumption. However, to what extent energy-producing pathways are also modified within the paced heart remains to be investigated. Pacing could particularly affect glycogen metabolism since hypertrophy stimulates glycolysis and increased workload favors glucose over fat oxidation. In order to test this hypothesis, we used the embryonic chick heart model in which ventricular pacing rapidly resulted in thinning of the ventricle wall and thickening of the atrial wall. Hearts of stage 22HH chick embryos were submitted in ovo to asynchronous and intermittent ventricular pacing delivered at physiological rate during 24 h. The resulting alterations of glycogen content were determined in atrium, ventricle and conotruncus of paced and sham-operated hearts. Hemodynamic parameters of the paced and spontaneously beating hearts were derived from computerized image analysis of video recordings. With respect to sham, paced hearts showed a significant decrease in glycogen content (nmoles glucose units/microg protein; mean+/-S.D.) only in atrium (1.48+/-0.40 v 0.84+/-0.34, n=8) and conotruncus (0.75+/-0.28 v 0.42+/-0.23, n=8). Pacing decreased the end diastolic and stroke volumes by 34 and 44%, respectively. Thus, the rapid glycogen depletion in regions remote from the stimulation site appears to be associated with regional changes in workload and remodeling. These findings underscore the importance of the coupling mechanisms between metabolic pathways and myocardial remodeling in the ectopically paced heart.

Jasmonate controls polypeptide patterning in undamaged tissue in wounded Arabidopsis leaves.

Wounding initiates a strong and largely jasmonate-dependent remodelling of the transcriptome in the leaf blades of Arabidopsis (Arabidopsis thaliana). How much control do jasmonates exert on wound-induced protein repatterning in leaves? Replicated shotgun proteomic analyses of 2.5-mm-wide leaf strips adjacent to wounds revealed 106 differentially regulated proteins. Many of these gene products have not emerged as being wound regulated in transcriptomic studies. From experiments using the jasmonic acid (JA)-deficient allene oxide synthase mutant we estimated that approximately 95% of wound-stimulated changes in protein levels were deregulated in the absence of JA. The levels of two tonoplast proteins already implicated in defense response regulation, TWO-PORE CHANNEL1 and the calcium-V-ATPase ACA4 increased on wounding, but their transcripts were not wound inducible. The data suggest new roles for jasmonate in controlling the levels of calcium-regulated pumps and transporters, proteins involved in targeted proteolysis, a putative bacterial virulence factor target, a light-dependent catalyst, and a key redox-controlled enzyme in glutathione synthesis. Extending the latter observation we found that wounding increased the proportion of oxidized glutathione in leaves, but only in plants able to synthesize JA. The oxidizing conditions generated through JA signaling near wounds help to define the cellular environment in which proteome remodelling occurs.

Oviposition by pierid butterflies triggers defense responses in Arabidopsis.

Insect eggs represent a threat for the plant as hatching larvae rapidly start with their feeding activity. Using a whole-genome microarray, we studied the expression profile of Arabidopsis (Arabidopsis thaliana) leaves after oviposition by two pierid butterflies. For Pieris brassicae, the deposition of egg batches changed the expression of hundreds of genes over a period of 3 d after oviposition. The transcript signature was similar to that observed during a hypersensitive response or in lesion-mimic mutants, including the induction of defense and stress-related genes and the repression of genes involved in growth and photosynthesis. Deposition of single eggs by Pieris rapae caused a similar although much weaker transcriptional response. Analysis of the jasmonic acid and salicylic acid mutants coi1-1 and sid2-1 indicated that the response to egg deposition is mostly independent of these signaling pathways. Histochemical analyses showed that egg deposition is causing a localized cell death, accompanied by the accumulation of callose, and the production of reactive oxygen species. In addition, activation of the pathogenesis-related1::beta-glucuronidase reporter gene correlated precisely with the site of egg deposition and was also triggered by crude egg extract. This study provides molecular evidence for the detection of egg deposition by Arabidopsis plants and suggests that oviposition causes a localized response with strong similarity to a hypersensitive response.