Characterizing Geo-located Tweets in Brazilian Megacities

This work presents a framework for collecting, processing and mining geo-located tweets in order to extract meaningful and actionable knowledge in the context of smart cities. We collected and characterized more than 9M tweets from the two biggest cities in Brazil, Rio de Janeiro and S\~ao Paulo. We performed topic modeling using the Latent Dirichlet Allocation model to produce an unsupervised distribution of semantic topics over the stream of geo-located tweets as well as a distribution of words over those topics. We manually labeled and aggregated similar topics obtaining a total of 29 different topics across both cities. Results showed similarities in the majority of topics for both cities, reflecting similar interests and concerns among the population of Rio de Janeiro and S\~ao Paulo. Nevertheless, some specific topics are more predominant in one of the cities

Regulation motifs and dynamic of Mitogen Actived Protein Kinase cascade during Xenopus laevis oocytes G2/M transition

Lors de la transition G2/M des ovocytes de Xénope, la voie p39Mos-MEK1-MAPK présente des propriétés dynamiques et physiques particulières telles que l’ultrasensibilité, la bistabilité, l’irréversibilité et un caractère ‘tout-ou-rien’. Ces propriétés sont considérées dans le contexte de la boucle de rétroaction positive qui existe au sein de cette voie. L’objectif de cette thèse s’est focalisé sur le rôle de l’oncoprotéine p39Mos et le recrutement des motifs de régulation qui permettent l’apparition de ces propriétés. Des approches expérimentales et in silico ont été menées pour réaliser une modélisation physiquement et biologiquement réaliste de ce réseau. Le modèle développé tient compte de l’influence du MPF sur l’accumulation de p39Mos et ajuste le rôle de la boucle de rétrocontrôle positif. Par ailleurs, nous avons pu mettre en évidence que p90Rsk, cible des MAPK, est dégradée. La voie MAPK a été activée en absence de p39Mos. Nos résultats montrent que la 1,10 Phénanthroline monohydrate (1,10-PA) active les MAPK suivant une réponse graduelle et ultrasensible. L’action de la 1,10-PA s’exerce en absence de synthèse protéique et de toute boucle de rétrocontrôle, et nous avons émis l’hypothèse que la 1,10 PA agit via l’inactivation d’une MEK-phosphatase. Dans ce contexte, un modèle de pro-action est discuté et des inhibiteurs de phosphatases ont été utilisés pour activer les MAPK en absence de p39Mos. Nos résultats discutent du rôle de la boucle de rétroaction positive dans l’activation des MAPK et montrent que l’ultrasensibilité de réponse des MAPK peut être générée par des motifs de régulation de type pro-action.During G2/M transition in Xenopus oocyte, p39Mos-MEK1-MAPK cascacade harbors specific dynamic and physical properties, such as ultrasensitivity, bistability, irreversibility, and all-or-none responses. These properties are generally considered in the context of the positive feedback loop that embeds the p39Mos-MEK1-MAPK pathway architecture. The objective of this work was focused onto p39Mos oncoprotein and regulation motifs recruitment enabling together the generation of such properties. Both experimental and in silico approaches were undertaken in order to yield a realistic modelisation, physically and biologically relevant for this network. We developed a model that takes into account the influence of MPF onto p39Mos accumulation, and adjusts the role of the positive feedback loop. Also, we were able to show that p90Rsk, target of MAPK, was degraded. This signaling pathway was activated in the absence of p39Mos. Our results show that 1,10 Phénanthroline monohydrate (1,10-PA) is able to induce gradual and ultrasensitive MAPK activation. 1,10-PA action is then exerted in the absence of protein synthesis and positive feedback loop. In this context, a feed forward loop model can be considered, and phosphatase inhibitors were used for MAPK activation in the absence of p39Mos. Our results confront the role attributed to the positive feedback loop in MAPK activation, and show that this ultrasensitive response may be generated in vivo through feed forward regulation motifs

Motifs de régulation et dynamique de la voie Mitogen Activated Protein Kinase lors de la transition G2/M des ovocytes de Xénope

Lors de la transition G2/M des ovocytes de Xénope, la voie p39Mos-MEK1-MAPK présente des propriétés dynamiques et physiques particulières telles que l ultrasensibilité, la bistabilité, l irréversibilité et un caractère tout-ou-rien . Ces propriétés sont considérées dans le contexte de la boucle de rétroaction positive qui existe au sein de cette voie. L objectif de cette thèse s est focalisé sur le rôle de l oncoprotéine p39Mos et le recrutement des motifs de régulation qui permettent l apparition de ces propriétés. Des approches expérimentales et in silico ont été menées pour réaliser une modélisation physiquement et biologiquement réaliste de ce réseau. Le modèle développé tient compte de l influence du MPF sur l accumulation de p39Mos et ajuste le rôle de la boucle de rétrocontrôle positif. Par ailleurs, nous avons pu mettre en évidence que p90Rsk, cible des MAPK, est dégradée. La voie MAPK a été activée en absence de p39Mos. Nos résultats montrent que la 1,10 Phénanthroline monohydrate (1,10-PA) active les MAPK suivant une réponse graduelle et ultrasensible. L action de la 1,10-PA s exerce en absence de synthèse protéique et de toute boucle de rétrocontrôle, et nous avons émis l hypothèse que la 1,10 PA agit via l inactivation d une MEK-phosphatase. Dans ce contexte, un modèle de pro-action est discuté et des inhibiteurs de phosphatases ont été utilisés pour activer les MAPK en absence de p39Mos. Nos résultats discutent du rôle de la boucle de rétroaction positive dans l activation des MAPK et montrent que l ultrasensibilité de réponse des MAPK peut être générée par des motifs de régulation de type pro-action.During G2/M transition in Xenopus oocyte, p39Mos-MEK1-MAPK cascacade harbors specific dynamic and physical properties, such as ultrasensitivity, bistability, irreversibility, and all-or-none responses. These properties are generally considered in the context of the positive feedback loop that embeds the p39Mos-MEK1-MAPK pathway architecture. The objective of this work was focused onto p39Mos oncoprotein and regulation motifs recruitment enabling together the generation of such properties. Both experimental and in silico approaches were undertaken in order to yield a realistic modelisation, physically and biologically relevant for this network. We developed a model that takes into account the influence of MPF onto p39Mos accumulation, and adjusts the role of the positive feedback loop. Also, we were able to show that p90Rsk, target of MAPK, was degraded. This signaling pathway was activated in the absence of p39Mos. Our results show that 1,10 Phénanthroline monohydrate (1,10-PA) is able to induce gradual and ultrasensitive MAPK activation. 1,10-PA action is then exerted in the absence of protein synthesis and positive feedback loop. In this context, a feed forward loop model can be considered, and phosphatase inhibitors were used for MAPK activation in the absence of p39Mos. Our results confront the role attributed to the positive feedback loop in MAPK activation, and show that this ultrasensitive response may be generated in vivo through feed forward regulation motifs.LILLE1-Bib. Electronique (590099901) / SudocSudocFranceF

The M-phase specific hyperphosphorylation of Staufen2 involved the cyclin-dependent kinase CDK1

International audienceBackground: Staufen2 (STAU2) is an RNA-binding protein involved in the post-transcriptional regulation of gene expression. This protein was shown to be required for organ formation and cell differentiation. Although STAU2 functions have been reported in neuronal cells, its role in dividing cells remains deeply uncharacterized. Especially, its regulation during the cell cycle is completely unknown.Results: In this study, we showed that STAU2 isoforms display a mitosis-specific slow migration pattern on SDS-gels in all tested transformed and untransformed cell lines. Deeper analyses in hTert-RPE1 and HeLa cells further indicated that the slow migration pattern of STAU2 isoforms is due to phosphorylation. Time course studies showed that STAU2 phosphorylation occurs before prometaphase and terminates as cells exit mitosis. Interestingly, STAU2 isoforms were phosphorylated on several amino acid residues in the C-terminal half via the cyclin-dependent kinase 1 (Cdk1), an enzyme known to play crucial roles during mitosis. Introduction of phospho-mimetic or phospho-null mutations in STAU2 did not impair its RNA-binding capacity, its stability, its interaction with protein co-factors or its sub-cellular localization, suggesting that STAU2 phosphorylation in mitosis does not regulate these functions. Similarly, STAU2 phosphorylation is not likely to be crucial for cell cycle progression since expression of phosphorylation mutants in hTert-RPE1 cells did not impair cell proliferation.Conclusions: Altogether, these results indicate that STAU2 isoforms are phosphorylated during mitosis and that the phosphorylation process involves Cdk1. The meaning of this post-translational modification is still elusive

Correction to: The M-phase specific hyperphosphorylation of Staufen2 involved the cyclin-dependent kinase CDK1

Following publication of the original article [1], the authors reported a change to one of the author names

Nitric oxide-donor SNAP induces Xenopus eggs activation.

Nitric oxide (NO) is identified as a signaling molecule involved in many cellular or physiological functions including meiotic maturation and parthenogenetic activation of mammalian oocytes. We observed that nitric oxide donor SNAP was potent to induce parthenogenetic activation in Xenopus eggs. NO-scavenger CPTIO impaired the effects of SNAP, providing evidence for the effects of the latter to be specific upon NO release. In Xenopus eggs, SNAP treatment induced pigment rearrangement, pronucleus formation and exocytosis of cortical granules. At a biochemical level, SNAP exposure lead to MAPK and Rsk inactivation within 30 minutes whereas MPF remained active, in contrast to calcium ionophore control where MPF activity dropped rapidly. MAPK inactivation could be correlated to pronuclear envelope reformation observed. In SNAP-treated eggs, a strong increase in intracellular calcium level was observed. NO effects were impaired in calcium-free or calcium limited medium, suggesting that that parthenogenetic activation of Xenopus oocytes with a NO donor was mainly calcium-dependent

Ultrasensitive MAPK/Erk activation in absence of protein synthesis in Xenopus oocytes

The mitogen-activated protein kinase (MAPK) cascade in <em>Xenopus</em> oocytes exhibits an all-or-none, ultrasensitive response, which is believed to result from a positive feed-back loop. Here we describe a context where 1,10-phenanthroline slowly, but strongly, activates MAPK while it impairs protein synthesis in a zincdependent manner, abolishing any feed-back loop. The induced-MAPK response was found to be strongly ultrasensitive. We argue that underlying this behaviour is a regulation motif akin to a feed-forward loop acting <em>in vivo</em>

Optimization of ERK Activity Biosensors for both Ratiometric and Lifetime FRET Measurements

Among biosensors, genetically-encoded FRET-based biosensors are widely used to localize and measure enzymatic activities. Kinases activities are of particular interest as their spatiotemporal regulation has become crucial for the deep understanding of cell fate decisions. This is especially the case for ERK, whose activity is a key node in signal transduction pathways and can direct the cell into various processes. There is a constant need for better tools to analyze kinases in vivo, and to detect even the slightest variations of their activities. Here we report the optimization of the previous ERK activity reporters, EKAR and EKAREV. Those tools are constituted by two fluorophores adapted for FRET experiments, which are flanking a specific substrate of ERK, and a domain able to recognize and bind this substrate when phosphorylated. The latter phosphorylation allows a conformational change of the biosensor and thus a FRET signal. We improved those biosensors with modifications of: (i) fluorophores and (ii) linkers between substrate and binding domain, resulting in new versions that exhibit broader dynamic ranges upon EGF stimulation when FRET experiments are carried out by fluorescence lifetime and ratiometric measurements. Herein, we characterize those new biosensors and discuss their observed differences that depend on their fluorescence properties

NO scavenger CPTIO does not impair maturation by, progesterone but suppresses SNAP effects on metaphase-II arrested eggs.

<p>(A) Effect of CPTIO on meiotic maturation. Histogram showing percentages of matured oocytes (with white spot) after overnight treatment with progesterone (10 µM) either in medium ND96 supplemented 10 mM CPTIO (CPTIO) or oocyte in pure ND96 injected 40 mM CPTIO (injCPTIO). Groups PG + (only progesterone), PG − (without progesterone) and inj water (progesterone and injection 15nl water) was a control of maturation and effect of microinjection. Error bands represent ± SEM values. Different superscripts indicate significant differences (P<0.05). (B) Histogram showing percentages of parthenogenetic activated oocytes after 2 hours treatment with 5 mM SNAP, 10 mM CPTIO or 10 µM A23187 injected or non-injected 40 mM NO scavenger CPTIO or water. Error bands represent ±SEM values. Different superscripts indicate significant differences (P<0.05). Data are shown as mean percentage of activation of five independent experiments. (C) Western blot analysis. After 2 hours ocytes were taken off, homogenized in lysis buffer, and immunoblotted with antibodies against Xp42^Mpk1 and p90^Rsk. (D) Control oocyte in metaphase II arrested oocytes exhibits typical bipolar spindle with chromosomes and the first polar body (nuclear red/picro-indigo carmine staining). (E) Activation after A23187 treatment: typical pronucleus. (F) Oocyte activated by SNAP with pronucleus. (G) Oocyte after SNAP&CPTIO treatment in metaphase II. Scale bars represent 10 µm (D,G) and 40 µm (E,F).</p