Laboratoire de Mécanique et d’Acoustique

With more than 20 molecules in clinical use, monoclonal antibodies have finally come of age as therapeutics, generating a market value of $11 billion in 2004, expected to reach $26 billion by 2010. While delivering interesting results in the treatment of several major diseases including autoimmune, cardiovascular and infectious diseases, cancer and inflammation, clinical trials and research are generating a wealth of useful information, for instance about associations of clinical responses with Fc receptor polymorphisms and the infiltration and recruitment of effector cells into targeted tissues. Some functional limitations of therapeutic antibodies have come to light such as inadequate pharmacokinetics and tissue accessibility as well as impaired interactions with the immune system, and these deficiencies point to areas where additional research is needed. This review aims at giving an overview of the current state of the art and describes the most promising avenues that are being followed to create the next generation of antibody‐based therapeutic agents. This article is part of a themed section on Vector Design and Drug Delivery. For a list of all articles in this section see the end of this paper, or visit: http://www3.interscience.wiley.com/journal/121548564/issueyear?year=2009

A study of strain localization in triaxial tests on sand, using computed tomography is reported. The inception and the development of the localization are detected and described, both qualitatively and quantitatively. The complex geometrical structures involved in the localization patterns are described and the local void ratio evolution in the localization zone(s) is determined. Dense and loose Hostun RF sand specimens were tested under a confining pressure of 60 kPa. It is shown that strain localization can occur in different localization patterns depending on test conditions; a mechanism involving, simultaneously, a central cone and a set of planes in pairs was found for many of the specimens tested. The comparison of the local void ratio evolution in the shear zones with the global void ratio measurement supports the important conclusion that a limit void ratio is reached in the shear zones. This ratio is significantly different from the final void ratio defined from the global measurements; the lack of physical relevance of the latter is established. Cet article présente les résultats dune étude consacrée à la localisation de la deformation dans Pessai triaxial sur sable, utilisant la tomographie numérisée. On pent ainsi détecter et décrire la naissance de la localisation, depuis ses premières manifestations jusquà la rupture. La description obtenue est à la fois qualitative et quantitative: les structures géométriques complexes qui apparaissent sont caractérisées, et évolution locale de Pindice des vides pent ôtre mesurée. Des échantillons denses et l&cric;ches de sable dHostun RF ont é testés sous une contrainte de confinement de 60 kPa. On montre que la localisation pent sorganiser de fagon assez varée du point de vue géométrique, suivant les conditions dessai; cependant on a observé dans plusieurs cas un mécanisme similaire, qui comprend un c&cric;ne central associé à des paires de plans se coupant suivant une arête située dans le plan dune des extrémités de échantillon. éode de la variation de Pindice des vides dans les zones de cisaillement met en évidence une limite atteinte dans ces zones; par comparaison avec Pindice des vides moyen dans échantillon, on constate que cette limite est sensiblement différente de celle quon pourrait déduire des mesures globales, si Pon ignorait Pexistence de déformations localisées dans échantillon. Ainsi on doit conclure que les mesures globales sont généralement insuffisantes pour caractériser Pindice des vides en grandes déformation dans les échantillons triaxiaux sur les mat6riaux denses.

This paper starts with a brief discussion of so-called wavelet transforms, i.e., decompositions of arbitrary signals into localized contributions labelled by a scale parameter. The main features of the method are first illustrated through simple mathematical examples. Then we present the first applications of the method to the recognition and visualisation of characteristic features of speech and of musical sounds.

This chapter elaborates some closely related methods developed to estimate the effective behavior of nonlinear composites with random microstructures. The constitutive behavior of the individual constituents of the composite is assumed to be governed by a potential, or strain-energy function, in such a way that the strain and stress fields are related by the constitutive relation. The response of the phases is assumed to be linear for purely hydrostatic loadings and nonlinear in shear. The extension of the Hashin–Shtrikman variational principles, which can be used to obtain improved bounds (depending on up to two-point statistical information) for nonlinear composites, is presented. It is possible to obtain nontrivial lower bounds for the effective stress potential by an analogous development taking the polarization field to be piecewise constant. The variational principles are used to generate a general class of bounds for nonlinear composites, by making suitable approximations in the set of admissible linear comparison composites. Various interpretations of the variational procedures are developed, including an interpretation of the resulting bounds in terms of secant moduli. The variational principles for materials with a certain concavity hypothesis are also elaborated.

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Because it drives the compromise between resolution and penetration, the diffraction limit has long represented an unreachable summit to conquer in ultrasound imaging. Within a few years after the introduction of optical localization microscopy, we proposed its acoustic alter ego that exploits the micrometric localization of microbubble contrast agents to reconstruct the finest vessels in the body in-depth. Various groups now working on the subject are optimizing the localization precision, microbubble separation, acquisition time, tracking, and velocimetry to improve the capacity of ultrasound localization microscopy (ULM) to detect and distinguish vessels much smaller than the wavelength. It has since been used in vivo in the brain, the kidney, and tumors. In the clinic, ULM is bound to improve drastically our vision of the microvasculature, which could revolutionize the diagnosis of cancer, arteriosclerosis, stroke, and diabetes.

Rickettsia conorii is an obligate intracellular bacterium that causes Mediterranean spotted fever in humans. We determined the 1,268,755-nucleotide complete genome sequence of R. conorii, containing 1374 open reading frames. This genome exhibits 804 of the 834 genes of the previously determined R. prowazekii genome plus 552 supplementary open reading frames and a 10-fold increase in the number of repetitive elements. Despite these differences, the two genomes exhibit a nearly perfect colinearity that allowed the clear identification of different stages of gene alterations with gene remnants and 37 genes split in 105 fragments, of which 59 are transcribed. A 38-kilobase sequence inversion was dated shortly after the divergence of the genus.

By the end of 2018, 42 years after the landing of the two Viking seismometers on Mars, InSight will deploy onto Mars' surface the SEIS (Seismic Experiment for Internal Structure) instrument; a six-axes seismometer equipped with both a long-period three-axes Very Broad Band (VBB) instrument and a three-axes short-period (SP) instrument. These six sensors will cover a broad range of the seismic bandwidth, from 0.01 Hz to 50 Hz, with possible extension to longer periods. Data will be transmitted in the form of three continuous VBB components at 2 sample per second (sps), an estimation of the short period energy content from the SP at 1 sps and a continuous compound VBB/SP vertical axis at 10 sps. The continuous streams will be augmented by requested event data with sample rates from 20 to 100 sps. SEIS will improve upon the existing resolution of Viking's Mars seismic monitoring by a factor of 2500 at 1 Hz and 200 000 at 0.1 Hz. An additional major improvement is that, contrary to Viking, the seismometers will be deployed via a robotic arm directly onto Mars' surface and will be protected against temperature and wind by highly efficient thermal and wind shielding. Based on existing knowledge of Mars, it is reasonable to infer a moment magnitude detection threshold of M w 3 at 40 epicentral distance and a potential to detect several tens of quakes and about five impacts per year. In this paper, we first describe the science goals of the experiment and the rationale used to define its requirements. We then provide a detailed description of the hardware, from the sensors to the deployment system and associated performance, including transfer functions of the seismic sensors and temperature sensors. We conclude by describing the experiment ground segment, including data processing services, outreach and education networks and provide a description of the format to be used for future data distribution.

FusionDB (http://igs-server.cnrs-mrs.fr/FusionDB/) constitutes a resource dedicated to in-depth analysis of bacterial and archaeal gene fusion events. Such events can provide the 'Rosetta stone' in the search for potential protein-protein interactions, as well as metabolic and regulatory networks. However, the false positive rate of this approach may be quite high, prompting a detailed scrutiny of putative gene fusion events. FusionDB readily provides much of the information required for that task. Moreover, FusionDB extends the notion of gene fusion from that of a single gene to that of a family of genes by assembling pairs of genes from different genomes that belong to the same Cluster of Orthogonal Groups (COG). Multiple sequence alignments and phylogenetic tree reconstruction for the N- and C-terminal parts of these 'COG fusion' events are provided to distinguish single and multiple fusion events from cases of gene fission, pseudogenes and other false positives. Finally, gene fusion events with matches to known structures of heterodimers in the Protein Data Bank (PDB) are identified and may be visualized. FusionDB is fully searchable with access to sequence and alignment data at all levels. A number of different scores are provided to easily differentiate 'real' from 'questionable' cases, especially when larger database searches are performed. FusionDB is cross-linked with the 'Phylogenomic Display of Bacterial Genes' (PhydBac) online web server. Together, these servers provide the complete set of information required for in-depth analysis of non-homology-based gene function attribution.

Bacteria respond to nutritional stresses by producing an intracellular alarmone, guanosine 5'-(tri)diphosphate, 3'-diphosphate [(p)ppGpp], which triggers the stringent response resulting in growth arrest and expression of resistance genes. In Escherichia coli, upon fatty acid or carbon starvation, SpoT enzyme activity switches from (p)ppGpp degradation to (p)ppGpp synthesis, but the signal and mechanism for this response remain totally unknown. Here, we characterize for the first time a physical interaction between SpoT and acyl carrier protein (ACP) using affinity co-purifications and two-hybrid in E. coli. ACP, as a central cofactor in fatty acid synthesis, may be an ideal candidate as a mediator signalling starvation to SpoT. Accordingly, we show that the ACP/SpoT interaction is specific of SpoT and ACP functions because ACP does not interact with the homologous RelA protein and because SpoT does not interact with a non-functional ACP. Using truncated SpoT fusion proteins, we demonstrate further that ACP binds the central TGS domain of SpoT, consistent with a role in regulation. The behaviours of SpoT point mutants that do not interact with ACP reveal modifications of the balance between the two opposite SpoT catalytic activities thereby changing (p)ppGpp levels. More importantly, these mutants fail to trigger (p)ppGpp accumulation in response to fatty acid synthesis inhibition, supporting the hypothesis that the ACP/SpoT interaction may be involved in SpoT-dependent stress response. This leads us to propose a model in which ACP carries information describing the status of cellular fatty acid metabolism, which in turn can trigger the conformational switch in SpoT leading to (p)ppGpp accumulation.

Biofilm formation by the opportunistic pathogen Pseudomonas aeruginosa requires the expression of a number of surface adhesive components. The expression of surface organelles facilitating biofilm formation is controlled by environmental signals acting through transcriptional regulatory networks. We analysed the expression of a family of P. aeruginosa adhesins encoded by three distinct fimbrial gene clusters (cupA, cupB and cupC). Using transposon mutagenesis, we have identified several regulatory loci that upregulated cupB and cupC transcription. One such locus contains three components, RocS1, RocR and RocA1, which represent a variant of a classical two-component signal transduction pathway. RocS1 is a sensor kinase, RocA1 is a DNA binding response regulator that activates cup genes, and RocR is an antagonist of RocA1 activity. Using a two-hybrid assay, we have shown that RocS1 interacts with receiver domains of both RocA1 and RocR. Expression of the Cup system in response to environmental stimuli is accomplished by a novel mechanism in which the sensor kinase activates its cognate response regulator through a phosphorelay pathway, while an additional repressor protein modulates this interaction.

We present a general method for estimating the location of small, well-separated scatterers in a randomly inhomogeneous environment using an active sensor array. The main features of this method are (i) an arrival time analysis of the echo received from the scatterers, (ii) a singular value decomposition of the array response matrix in the frequency domain, and (iii) the construction of an objective function in the time domain that is statistically stable and peaks on the scatterers. By statistically stable we mean here that the objective function is self-averaging over individual realizations of the medium. This is a new approach to array imaging that is motivated by time reversal in random media, analyzed in detail previously. It combines features from seismic imaging like arrival time analysis with frequency-domain signal subspace methodology like MUltiple SIgnal Classification (MUSIC). We illustrate the theory with numerical simulations for ultrasound.

While most organisms grow at temperatures ranging between 20 and 50 degrees C, many archaea and a few bacteria have been found capable of withstanding temperatures close to 100 degrees C, or beyond, such as Pyrococcus or Aquifex. Here we report the results of two independent large scale unbiased approaches to identify global protein properties correlating with an extreme thermophile lifestyle. First, we performed a comparative proteome analyses using 30 complete genome sequences from the three kingdoms. A large difference between the proportions of charged versus polar (noncharged) amino acids was found to be a signature of all hyperthermophilic organisms. Second, we analyzed the water accessible surfaces of 189 protein structures belonging to mesophiles or hyperthermophiles. We found that the surfaces of hyperthermophilic proteins exhibited the shift already observed at the genomic level, i.e. a proportion of solvent accessible charged residues strongly increased at the expense of polar residues. The biophysical requirements for the presence of charged residues at the protein surface, allowing protein stabilization through ion bonds, is therefore clearly imprinted and detectable in all genome sequences available to date.

From a set of experimental studies showing how intersegmental coordination develops during childhood in various posturokinetic tasks, we have established a repertoire of equilibrium strategies in the course of ontogenesis. The experimental data demonstrate that the first reference frame used for the organization of balance control during locomotion is the pelvis, especially in young children. Head stabilization during posturokinetic activities, particularly locomotion, constitutes a complex motor skill requiring a long time to develop during childhood. When studying the emergence of postural strategies, it is essential to distinguish between results that can be explained by biomechanical reasons strictly and those reflecting the maturation of the central nervous system (CNS). To address this problem, we have studied our young subjects in situations requiring various types of adaptation. The studies dealing with adaptation of postural strategies aimed at testing short and long-term adaptation capacity of the CNS during imposed transient external biomechanical constraints in healthy children, and during chronic internal constraints in children with skeletal pathologies. In addition to maintenance of balance, another function of posture is to ensure the orientation of a body segment. It appears that the control of orientation and the control of balance both require the trunk as an initial reference frame involving a development from egocentric to exocentric postural control. It is concluded that the first step for children consists in building a repertoire of postural strategies, and the second step consists in learning to select the most appropriate postural strategy, depending on the ability to anticipate the consequence of the movement in order to maintain balance control and the efficiency of the task.

This paper presents Tcoffee@igs, a new server provided to the community by Hewlet Packard computers and the Centre National de la Recherche Scientifique. This server is a web-based tool dedicated to the computation, the evaluation and the combination of multiple sequence alignments. It uses the latest version of the T-Coffee package. Given a set of unaligned sequences, the server returns an evaluated multiple sequence alignment and the associated phylogenetic tree. This server also makes it possible to evaluate the local reliability of an existing alignment and to combine several alternative multiple alignments into a single new one. Tcoffee@igs can be used for aligning protein, RNA or DNA sequences. Datasets of up to 100 sequences (2000 residues long) can be processed. The server and its documentation are available from: http://igs-server.cnrs-mrs.fr/Tcoffee/.

Biosynthesis of iron-sulfur clusters (Fe-S) depends on multiprotein systems. Recently, we described the SUF system of Escherichia coli and Erwinia chrysanthemi as being important for Fe-S biogenesis under stressful conditions. The SUF system is made of six proteins: SufC is an atypical cytoplasmic ABC-ATPase, which forms a complex with SufB and SufD; SufA plays the role of a scaffold protein for assembly of iron-sulfur clusters and delivery to target proteins; SufS is a cysteine desulfurase which mobilizes the sulfur atom from cysteine and provides it to the cluster; SufE has no associated function yet. Here we demonstrate that: (i) SufE and SufS are both cystosolic as all members of the SUF system; (ii) SufE is a homodimeric protein; (iii) SufE forms a complex with SufS as shown by the yeast two-hybrid system and by affinity chromatography; (iv) binding of SufE to SufS is responsible for a 50-fold stimulation of the cysteine desulfurase activity of SufS. This is the first example of a two-component cysteine desulfurase enzyme. Biosynthesis of iron-sulfur clusters (Fe-S) depends on multiprotein systems. Recently, we described the SUF system of Escherichia coli and Erwinia chrysanthemi as being important for Fe-S biogenesis under stressful conditions. The SUF system is made of six proteins: SufC is an atypical cytoplasmic ABC-ATPase, which forms a complex with SufB and SufD; SufA plays the role of a scaffold protein for assembly of iron-sulfur clusters and delivery to target proteins; SufS is a cysteine desulfurase which mobilizes the sulfur atom from cysteine and provides it to the cluster; SufE has no associated function yet. Here we demonstrate that: (i) SufE and SufS are both cystosolic as all members of the SUF system; (ii) SufE is a homodimeric protein; (iii) SufE forms a complex with SufS as shown by the yeast two-hybrid system and by affinity chromatography; (iv) binding of SufE to SufS is responsible for a 50-fold stimulation of the cysteine desulfurase activity of SufS. This is the first example of a two-component cysteine desulfurase enzyme. Cysteine is the source of sulfur for biosynthesis of a variety of sulfur-containing biomolecules such as biotin, lipoic acid, molybdopterin, thiamin, thionucleosides in tRNAs as well as iron-sulfur (Fe-S) 1The abbreviations used are: Fe-S, iron-sulfur cluster; PLP, pyridoxal 5-phosphate; c-Myc, cellular myelomonocytar virus; IPTG, isopropyl β-d-thiogalactoside; CSD, cysteine sulfinate desulfinase; NTA, nitrilotriacetic acid; HA, hemagglutinin; HPLC, high performance liquid chromatography.1The abbreviations used are: Fe-S, iron-sulfur cluster; PLP, pyridoxal 5-phosphate; c-Myc, cellular myelomonocytar virus; IPTG, isopropyl β-d-thiogalactoside; CSD, cysteine sulfinate desulfinase; NTA, nitrilotriacetic acid; HA, hemagglutinin; HPLC, high performance liquid chromatography. clusters (1Marquet A. Curr. Opin. Chem. Biol. 2001; 5: 541-549Crossref PubMed Scopus (73) Google Scholar, 2Mihara H. Esaki N. Appl. Microbiol. Biotechnol. 2002; 60: 12-23Crossref PubMed Scopus (222) Google Scholar, 3Parry R.J. Comprehensive Natural Products Chemistry. Elsevier, NY1999: 825Crossref Google Scholar, 4Fontecave M. Ollagnier-de Choudens S. Mulliez E. Chem. Rev. 2003; 103: 2149-2166Crossref PubMed Scopus (165) Google Scholar). Mobilization of sulfur is achieved by a recently discovered class of enzymes, named cysteine desulfurases (2Mihara H. Esaki N. Appl. Microbiol. Biotechnol. 2002; 60: 12-23Crossref PubMed Scopus (222) Google Scholar). The first original observation was made by Dean and co-workers (5Zheng L. White R.H. Cash V.L. Jack R.F. Dean D.R. Proc. Natl. Acad. Sci. U. S. A. 1993; 90: 2754-2758Crossref PubMed Scopus (498) Google Scholar) who identified the product of the nifS gene in Azotobacter vinelandii as a cysteine desulfurase providing inorganic sulfide required for the formation of Fe-S clusters in a component protein of nitrogenase. Since then, homolog genes have been discovered in almost all living organisms and some of the corresponding proteins biochemically and structurally characterized. It is thus now well established that cysteine desulfurases are pyridoxal 5′-phosphate (PLP)-dependent enzymes, which decompose l-cysteine into l-alanine and sulfane-sulfur (Fig. 1) (6Zheng L. White R.H. Cash V.L. Dean D.R. Biochemistry. 1994; 33: 4714-4720Crossref PubMed Scopus (352) Google Scholar). The cysteine desulfuration mechanism has been strongly supported by recent remarkable structural studies of two cysteine desulfurases: the IscS protein from Thermotoga maritima and the SufS protein from Escherichia coli (7Kaiser J.T. Clauser T. Bourenhow G.P. Bartunik H.D. Steinbacher S. Huber R. J. Mol. Biol. 2000; 297: 451-464Crossref PubMed Scopus (125) Google Scholar, 8Mihara H. Fujii T. Kato K. Hata Y. Esaki N. J. Biochem. 2002; 131: 679-685Crossref PubMed Scopus (60) Google Scholar, 9Lima C.D. J. Mol. Biol. 2002; 315: 1199-1208Crossref PubMed Scopus (81) Google Scholar). Even though the three-dimensional structures display significant differences at the active site, they both contain a protein-bound PLP as well as the conserved active cysteine in close proximity (1 in Fig. 1). Furthermore, several postulated intermediates have now been structurally characterized: (i) the enzyme-cysteine complex (2 in Fig. 1), (ii) the enzyme form in which a substrate analogue, propargylglycine, is covalently attached to PLP through an aldimine bond (3 in Fig. 1), and (iii) the enzyme form in which the active cysteine is in the persulfide form (4 in Fig. 1). All cysteine desulfurases thus have a critical cysteine residue in the active site and site-directed mutagenesis of that residue completely abolishes enzyme activity (10Mihara H. Kurihara T. Yoshimura T. Esaki N. J. Biochem. 2000; 127: 559-567Crossref PubMed Scopus (125) Google Scholar). A different situation occurs in the PLP-dependent l-cyst(e)ine C-S-lyase (C-DES) isolated from Synechocystis PCC 6714 which participates to Fe-S cluster assembly in this organism (11Lang T. Kessler D. J. Biol. Chem. 1999; 274: 189-195Abstract Full Text Full Text PDF PubMed Scopus (41) Google Scholar, 12Clausen T. Kaiser J.T. Steegborn C. Huber R. Kessler D. Proc. Natl. Acad. Sci. U. S. A. 2000; 97: 3856-3861Crossref PubMed Scopus (65) Google Scholar). C-DES does not have a conserved functional cysteine residue at the active site and forms pyruvate, rather than alanine, and sulfide from cysteine. It has a strong preference for cystine as a substrate. A cysteine persulfide is also intermediately formed but as a free product during catalysis, further supporting the importance of persulfidic intermediates during Fe-S cluster biosynthesis. Finally, cysteine desulfurases have also the ability to mobilize the selenium atom from selenocysteine, but the mechanism of the reaction is less well understood. Nevertheless it is known that the deselenation process is not dependent on the active site cysteine residue, as shown by site-directed mutagenesis, suggesting different mechanisms for desulfuration and deselenation. E. coli contains three cysteine desulfurases (2Mihara H. Esaki N. Appl. Microbiol. Biotechnol. 2002; 60: 12-23Crossref PubMed Scopus (222) Google Scholar, 10Mihara H. Kurihara T. Yoshimura T. Esaki N. J. Biochem. 2000; 127: 559-567Crossref PubMed Scopus (125) Google Scholar). A first system, named CSD (for cysteine sulfinate desulfinase) and encoded by the csdA gene, has broad substrate specificity since, besides cysteine and selenocysteine, it acts on cysteine sulfinic acid, the best substrate in terms of Km and V m values, cystine and selenocystine (10Mihara H. Kurihara T. Yoshimura T. Esaki N. J. Biochem. 2000; 127: 559-567Crossref PubMed Scopus (125) Google Scholar, 13Mihara H. Kurihara T. Yoshimura T Soda K. Esaki N. J. Biol. Chem. 1997; 272: 22417-22424Abstract Full Text Full Text PDF PubMed Scopus (141) Google Scholar). Its biological function is not identified but it was shown to be the most efficient sulfur donor for the formation of molybdopterin in vitro (14Leimkühler S. Rajagopalan K.V. J. Biol. Chem. 2001; 276: 22024-22031Abstract Full Text Full Text PDF PubMed Scopus (108) Google Scholar). The most extensively studied cysteine desulfurase is the IscS protein because it proved to be essential for biosynthesis of thiamin and most thionucleosides in tRNAs (15Lauhon C.T. Kambampati R. J. Biol. Chem. 2000; 275: 20096-20103Abstract Full Text Full Text PDF PubMed Scopus (157) Google Scholar, 16Lauhon C.T. J. Bacteriol. 2002; 184: 6820-6829Crossref PubMed Scopus (87) Google Scholar, 17Nilsson K. Lundgren H.K. Hagervall T.G. Björk G.R. J. Bacteriol. 2002; 184: 6830-6835Crossref PubMed Scopus (64) Google Scholar). IscS mobilizes sulfur and selenium from cysteine and selenocysteine, respectively, equally well. IscS has been discovered as a component of the ISC system, which plays an important role in the assembly of Fe-S clusters in various iron-sulfur proteins (18Zheng L. Cash V.L. Flint D.H. Dean D.R. J. Biol. Chem. 1998; 273: 13264-13272Abstract Full Text Full Text PDF PubMed Scopus (573) Google Scholar). Several genetic studies in E. coli and yeast clearly demonstrated that deletion of the iscS gene drastically affected the activity of Fe-S containing enzymes (aconitase, biotin synthase, succinate dehydrogenase, ferredoxins) (19Kispal G. Csere P. Prohl C. Lill R. EMBO J. 1999; 18: 3981-3989Crossref PubMed Scopus (585) Google Scholar, J. M. D. A. J. Biol. Chem. 1999; 274: Full Text Full Text PDF PubMed Scopus Google Scholar, P. Proc. Natl. Acad. Sci. U. S. A. 2000; 97: PubMed Scopus Google Scholar, U. Y. J. Biochem. 2001; PubMed Scopus Google Scholar). The cysteine desulfurase is the homodimeric SufS encoded by the It was shown to be for and to display a cysteine desulfurase activity to of the deselenation (10Mihara H. Kurihara T. Yoshimura T. Esaki N. J. Biochem. 2000; 127: 559-567Crossref PubMed Scopus (125) Google Scholar, H. M. Fujii T. Kurihara T. Hata Y. Esaki N. J. Biol. Chem. 1999; 274: Full Text Full Text PDF PubMed Scopus Google Scholar). It was thus rather as a of the conserved residue to completely the cysteine desulfurase activity in in a stimulation of the deselenation activity (10Mihara H. Kurihara T. Yoshimura T. Esaki N. J. Biochem. 2000; 127: 559-567Crossref PubMed Scopus (125) Google Scholar). Even though cysteine desulfurase activity was SufS was to to sulfur SufS to the which was recently shown to be in Fe-S cluster biosynthesis Y. U. J. Biol. Chem. 2002; Full Text Full Text PDF PubMed Scopus Google Scholar, L. M. L. D. Mol. Microbiol. 2001; PubMed Scopus Google Scholar, L. L. D. EMBO J. 2003; PubMed Scopus Google Scholar). Y. U. J. Biol. Chem. 2002; Full Text Full Text PDF PubMed Scopus Google Scholar) that of the both the and the activity of Fe-S proteins in E. coli the was of both the and Y. U. J. Biol. Chem. 2002; Full Text Full Text PDF PubMed Scopus Google Scholar). cysteine desulfurase SufS was to sulfur atom from cysteine to target proteins during assembly of Fe-S the genetic both and important differences the is under both the and the the is L. M. L. D. Mol. Microbiol. 2001; PubMed Scopus Google Scholar, K. J. Bacteriol. 1999; PubMed Google Scholar, M. D.R. G. J. Bacteriol. 2001; PubMed Scopus Google Scholar, K. J. Mol. Microbiol. Biotechnol. 2002; Google Scholar, T. C. H. Proc. Natl. Acad. Sci. U. S. A. 2001; PubMed Scopus Google Scholar). this to the that the SUF system under such as and L. M. L. D. Mol. Microbiol. 2001; PubMed Scopus Google Scholar, L. L. D. EMBO J. 2003; PubMed Scopus Google Scholar, M. D.R. G. J. Bacteriol. 2001; PubMed Scopus Google Scholar). The genes in this genetic and E. coli and Erwinia a have recently on the function of the corresponding both SufC to be the most critical protein during biosynthesis of Fe-S clusters of in E. chrysanthemi E. coli in a of all to and L. M. L. D. Mol. Microbiol. 2001; PubMed Scopus Google Scholar, L. L. D. EMBO J. 2003; PubMed Scopus Google Scholar). Furthermore, in of E. chrysanthemi L. M. L. D. Mol. Microbiol. 2001; PubMed Scopus Google Scholar, L. L. D. EMBO J. 2003; PubMed Scopus Google Scholar). SufC is an in the it with SufB and L. L. D. EMBO J. 2003; PubMed Scopus Google Scholar). have recently that SufA is to iron-sulfur clusters and to in vitro to target such as biotin Choudens S. L. Y. L. M. J. Biol. 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The proteins in by the of SufS and was into into by and of proteins was by isopropyl at an of at by in containing and by of two through a two was with a under the by the the was extensively with a containing and the proteins from the a containing for Cysteine of SufS and activity was from the of formed from cysteine was of a with The reaction in a of of m of of and of of and cysteine. The reaction was at to an was and the reaction by the of m the was for that was on a and the residue into of a A was and at by on a with an with to a T. J. Mol. Biol. 2001; PubMed Scopus Google Scholar). The cysteine desulfurase activity is in of was by the of with Biochem. PubMed Scopus Google Scholar). of SufS and chrysanthemi protein was in E. coli with the a of be from a in a than form as by not for a cysteine desulfurase a in with the of protein-bound E. chrysanthemi SufE was in the form of a that was in E. coli with the protein was with a as by was a that SufE was in corresponding to a of of be from an SufE is and no in of SufS and to the cellular of SufS and was to the E. chrysanthemi This an deletion in the gene to a of the E. M. Mol. Microbiol. 1994; PubMed Scopus Google Scholar). The and of be by an protein of the and a E. chrysanthemi and genes into a such that SufS protein was to an and SufE protein was to a shown in Fig. and to be SufS and SufE are in the cellular as and L. L. D. EMBO J. 2003; PubMed Scopus Google Scholar). for the of a SufS protein with SufE by the yeast two-hybrid The E. chrysanthemi and genes with the with the to and a first of of the gene was used as a of on containing activity on yeast The and (Fig. a of in liquid was used as of efficient two-hybrid and (Fig. was also SufE from E. chrysanthemi and SufS from E. coli the yeast two-hybrid system not the SufS and SufE proteins was further of E. coli both SufS and proteins an affinity of the with of of the two proteins (Fig. 1). with containing high of two which identified by as being and SufS (Fig. a SufS was not to to not both genetic and demonstrated that SufS with SufE an of SufS Cysteine of SufS to of from cysteine was all the the of was Fig. the of both in the in the of of and in with SufS a strong preference for as a substrate and was active cysteine. deselenation of was by the of cysteine desulfurase activity was drastically in the of The of formed from cysteine was to that from The of SufE required for activity was to be close to the with to SufS as shown in Fig. suggesting a SufE not display cysteine desulfurase activity not of the cysteine desulfurase activity of SufS by SufS was with different of SufE in the of and cysteine. a reaction the was as under The of the of the desulfuration and deselenation by SufS are shown in Fig. A and be the the V V and the enzyme are shown in Km for was in with the by (10Mihara H. Kurihara T. Yoshimura T. Esaki N. J. Biochem. 2000; 127: 559-567Crossref PubMed Scopus (125) Google Scholar) for SufS from E. and was by the of V in the of SufE was to that in the of cysteine as a a V was in the of SufE as with that in the of SufE corresponding to a 50-fold SufE not on the Km for cysteine in both m m in a E. chrysanthemi SufE was also to the cysteine desulfurase activity of E. coli but not that of E. coli CSD and IscS proteins the of a function of SufE not of SufS for Cysteine the SufS active site cysteine residue was required for the SufS Cysteine of E. coli SufS has been to be essential for the cysteine desulfuration activity but not for deselenation (10Mihara H. Kurihara T. Yoshimura T. Esaki N. J. Biochem. 2000; 127: 559-567Crossref PubMed Scopus (125) Google Scholar). we the corresponding cysteine residue in E. chrysanthemi SufS to a The E. chrysanthemi SufS protein was and for cysteine shown in the both in the and in the of SufE that this cysteine is essential for the reaction by the The of SufS to form a complex with SufE was by the of the yeast two-hybrid system that SufE with of SufS. deselenation was not affected by the not desulfurase activity of m in a It is now well established that biosynthesis of iron-sulfur (Fe-S) clusters is the of the of several protein conserved all living organisms (2Mihara H. Esaki N. Appl. Microbiol. Biotechnol. 2002; 60: 12-23Crossref PubMed Scopus (222) Google Scholar, J. Dean D. Curr. Opin. Chem. Biol. 2003; PubMed Scopus Google Scholar, U. Lill R. 2000; PubMed Scopus Google Scholar, R. K. A. H. Prohl C. G. Biol. Chem. 1999; PubMed Scopus Google Scholar). have recently an of of such the SUF system, from E. coli and E. chrysanthemi L. M. L. D. Mol. Microbiol. 2001; PubMed Scopus Google Scholar, L. L. D. EMBO J. 2003; PubMed Scopus Google Scholar, Choudens S. L. Y. L. M. J. Biol. Chem. 2003; Full Text Full Text PDF Scopus Google Scholar). This system is it is of the for Fe-S cluster assembly known It thus provides a for at the the mechanism of this important biological process and for the for an efficient the has been shown to an important role under under under for example it is an important for L. M. L. D. Mol. Microbiol. 2001; PubMed Scopus Google Scholar, L. L. D. EMBO J. 2003; PubMed Scopus Google Scholar, K. J. Bacteriol. 1999; PubMed Google Scholar, M. D.R. G. J. Bacteriol. 2001; PubMed Scopus Google Scholar, K. J. Mol. Microbiol. Biotechnol. 2002; Google Scholar). The contains of the cysteine desulfurases of E. coli and E. SufS was to for the sulfur atom of cysteine as a source for sulfide in Fe-S we by the cysteine desulfurase activity of which with the SufS was rather as a because of ability to the of selenium from (10Mihara H. Kurihara T. Yoshimura T. Esaki N. J. Biochem. 2000; 127: 559-567Crossref PubMed Scopus (125) Google Scholar). The cysteine desulfurase activity of SufS been in the of the protein from E. coli and it is with the enzyme from E. not this but also a the component encoded by the the SufE we that SufE and SufS to form a This in a of the cysteine desulfurase activity of SufS. The activity was of of SufE and almost a 50-fold with the activity of SufS This strongly that the active complex is made by of both a of this stimulation by SufS as a cysteine with to of the cysteine IscS and This activity is now with the that SufS provides the to mobilize sulfur required for Fe-S cluster assembly from free cysteine. It is important to that cysteine desulfuration by the complex occurs the active site of SufS of the conserved active cysteine in E. chrysanthemi in this site abolishes the activity it does not complex SufE has a on the cysteine desulfurase activity of SufS though the mechanism of the reaction is This is the activity of a reaction that does not the cysteine residue of the active site, was not affected of this it is that and genes to the it is that in SufS does not but is associated with the SUF system the with a system both cysteine desulfurase and we the first example of a cysteine desulfurase enzyme containing two different but we that be discovered in the a close homolog of SufE in E. coli is the protein encoded by the gene, which is in the CSD, of the cysteine desulfurases L. M. L. D. Mol. Microbiol. 2001; PubMed Scopus Google Scholar, Mol. Microbiol. 2001; PubMed Scopus (87) Google Scholar). It is thus to that CSD forms a complex with the This is under in and structural studies are also required for the for the of SufE on SufS have shown that binding of SufE to SufS no on the Km for cysteine but a on the V m This was because SufS from E. in complex with a cysteine as a substrate. (10Mihara H. Kurihara T. Yoshimura T. Esaki N. J. Biochem. 2000; 127: 559-567Crossref PubMed Scopus (125) Google Scholar) that this was not the with the SufS protein from E. Since is known on the and the of the of the reaction as well as the for the does not the for the of The three-dimensional of SufS from E. coli has been H. Fujii T. Kato K. Hata Y. Esaki N. J. Biochem. 2002; 131: 679-685Crossref PubMed Scopus (60) Google Scholar). it does not a for the activity of SufS It has been that the critical active site cysteine residue in E. from the and that the be by because of the of the to which Since SufE the reaction cysteine as the substrate it is to the that binding of SufE to SufS in structural of the active site, a of the cysteine residue with to the The of a three-dimensional of the complex into the of this class of cysteine recent from with the a function for of the six of the as well as L. L. D. EMBO J. 2003; PubMed Scopus Google Scholar, Choudens S. L. Y. L. M. J. Biol. Chem. 2003; Full Text Full Text PDF Scopus Google Scholar). to into three of are to form a first complex with activity L. L. D. EMBO J. 2003; PubMed Scopus Google Scholar). complex is made with SufS and SufE and strong cysteine desulfurase Finally, SufA has been identified as a protein scaffold for assembly of and sulfur Fe-S clusters which be to Choudens S. L. Y. L. M. J. Biol. Chem. 2003; Full Text Full Text PDF Scopus Google Scholar). is that under that of Fe-S clusters a for to the SUF system contains the to this (i) the cysteine desulfurase mobilizes sulfur from (ii) and the scaffold protein to Fe-S (iii) the are to the target proteins; (iv) the function of the be to the required for the formation of Fe-S several of (Fig. It is that the source of we that the SUF system participates to the of from L. L. D. EMBO J. 2003; PubMed Scopus Google Scholar). the for and D. and J. for with J. and J. P. for

The phylogenetic diversity of prokaryotic communities exposed to arid conditions in the hot desert of Tataouine (south Tunisia) was estimated with a combination of a culture and - molecular-based analysis. Thirty-one isolates, representative of each dominant morphotypes, were affiliated to Actinobacteria, Firmicutes, Proteobacteria and the CFB group while none related to Archaea. Analysis of 16S rRNA gene libraries revealed the presence of species related to Bacteria and Archaea. Sequences related to Archaea were all affiliated to the non-thermophilic Crenarchaeota subgroup. Bacterial sequences were dominated by Proteobacteria, Actinobacteria and Acidobacteria; a few sequences were distributed among eight others phyla, including Thermus/Deinococcus relatives. A correlation between tolerance to desiccation and to radiation has been demonstrated for the radiotolerant bacteria Deinococcus radiodurans. Because bacteria living in the hot desert of Tataouine are one way or another tolerant to desiccation, we investigate whether they could also be tolerant to radiation. Exposition of soil samples to intense gamma radiation yields Bacillus, Thermus/Deinococcus and alpha-Proteobacteria relatives. Four of these strains correspond to radiotolerant species as revealed by evaluation of the resistance levels of the individual cultures. A detailed analysis of the resistance levels for two Thermus/Deinococcus and two alpha-Proteobacteria relatives revealed that they correspond to new radiotolerant species.

Under nano- to femtosecond pulsed illumination at their plasmonic resonance wavelength, metal nanoparticles efficiently absorb the incident light energy that is subsequently converted into heat. In a liquid environment, with sufficiently high pulse fluences (light energy per unit area), this heat generation may result in the local formation of a transient nanobubble. This phenomenon has been the subject of a decade of investigations and is at the basis of numerous applications from cancer therapy to photoacoustic imaging. The aim of this article is to clarify the question of the fluence threshold required for bubble formation. Using a Runge-Kutta-4 numerical algorithm modeling the heat diffusion around a spherical gold nanoparticle, we numerically investigate the influence of the nanoparticle diameter, pulse duration (from the femto- to the nanosecond range), wavelength, and Kapitza resistivity in order to explain the observations reported in the literature.

Pseudomonas aeruginosa controls the production of many exoproteins and secondary metabolites via a hierarchical quorum sensing (QS) regulatory cascade involving the LuxR-like proteins LasR, RhlR and their cognate signal molecules N-(3-oxododecanoyl)-l-homoserine lactone (3O-C12-HSL) and N-(butanoyl)-l-homoserine lactone (C4-HSL). The finding of a third LuxR-type protein in P. aeruginosa, QscR, adds further complexity to this regulatory network. It has been shown previously that QscR represses transcription of three QS-controlled gene clusters, phz (phenazine), hcn (hydrogen cyanide) and qsc105 (Chugani, Whiteley, Lee, D'Argenio, Manoil, and Greenberg, 2001, Proc Natl Acad Sci USA 98: 2752-2757). In this study, we identify two novel QscR targets these are lasB, encoding the extracellular elastase, and the second phenazine gene cluster, both of which are downregulated by QscR. In addition, we show that QscR synthesis is regulated by the two-component response regulator GacA. Taking advantage of the in vivo fluorescence anisotropy technology that we have developed, we show that QscR can be found in several different types of association. Indeed, we identify QscR multimers in the absence of any acyl-HSL, lower order QscR oligomers associated either with C4-HSL or 3O-C12-HSL and QscR-containing heterodimers with LasR or RhlR. The formation of heterodimers between QscR and LasR or RhlR, in the absence of acyl-HSLs, is a very exciting, new result that should improve our understanding of the QscR network and its relationship to the production of P. aeruginosa virulence factors.

The early light-induced proteins (ELIPs) belong to the multigenic family of pigment-binding light-harvesting complexes. ELIPs accumulate transiently and are believed to play a protective role in plants exposed to high levels of light. Constitutive expression of the ELIP2 gene in Arabidopsis resulted in a marked reduction of the pigment content of the chloroplasts, both in mature leaves and during greening of etiolated seedlings. The chlorophyll loss was associated with a decrease in the number of photosystems in the thylakoid membranes, but the photosystems present were fully assembled and functional. A detailed analysis of the chlorophyll-synthesizing pathway indicated that ELIP2 accumulation downregulated the level and activity of two important regulatory steps: 5-aminolevulinate synthesis and Mg-protoporphyrin IX (Mg-Proto IX) chelatase activity. The contents of glutamyl tRNA reductase and Mg chelatase subunits CHLH and CHLI were lowered in response to ELIP2 accumulation. In contrast, ferrochelatase activity was not affected and the inhibition of Heme synthesis was null or very moderate. As a result of reduced metabolic flow from 5-aminolevulinic acid, the steady state levels of various chlorophyll precursors (from protoporphyrin IX to protochlorophyllide) were strongly reduced in the ELIP2 overexpressors. Taken together, our results indicate that the physiological function of ELIPs could be related to the regulation of chlorophyll concentration in thylakoids. This seems to occur through an inhibition of the entire chlorophyll biosynthesis pathway from the initial precursor of tetrapyrroles, 5-aminolevulinic acid. We suggest that ELIPs work as chlorophyll sensors that modulate chlorophyll synthesis to prevent accumulation of free chlorophyll, and hence prevent photooxidative stress.