Plasmon scattering from holes: from single hole scattering to Young's experiment

In this article, the scattering of surface plasmon polaritons (SPPs) into photons at holes is investigated. A local, electrically excited source of SPPs using a scanning tunnelling microscope (STM) produces an outgoing circular plasmon wave on a thick (200 nm) gold film on glass containing holes of 250, 500 and 1000 nm diameter. Fourier plane images of the photons from hole-scattered plasmons show that the larger the hole diameter, the more directional the scattered radiation. These results are confirmed by a model where the hole is considered as a distribution of horizontal dipoles whose relative amplitudes, directions, and phases depend linearly on the local SPP electric field. An SPP-Young's experiment is also performed, where the STM-excited SPP-wave is incident on a pair of 1 $\mu$m diameter holes in the thick gold film. The visibility of the resulting fringes in the Fourier plane is analyzed to show that the polarization of the electric field is maintained when SPPs scatter into photons. From this SPP-Young's experiment, an upper bound of $\approx$ 200 nm for the radius of this STM-excited source of surface plasmon polaritons is determined

An in silico approach combined with in vivo experiments enables the identification of a new protein whose overexpression can compensate for specific respiratory defects in Saccharomyces cerevisiae

<p>Abstract</p> <p>Background</p> <p>The mitochondrial inner membrane contains five large complexes that are essential for oxidative phosphorylation. Although the structure and the catalytic mechanisms of the respiratory complexes have been progressively established, their biogenesis is far from being fully understood. Very few complex III assembly factors have been identified so far. It is probable that more factors are needed for the assembly of a functional complex, but that the genetic approaches used to date have not been able to identify them. We have developed a systems biology approach to identify new factors controlling complex III biogenesis.</p> <p>Results</p> <p>We collected all the physical protein-protein interactions (PPI) involving the core subunits, the supernumerary subunits and the assembly factors of complex III and used Cytoscape 2.6.3 and its plugins to construct a network. It was then divided into overlapping and highly interconnected sub-graphs with clusterONE. One sub-graph contained the core and the supernumerary subunits of complex III, it also contained some subunits of complex IV and proteins participating in the assembly of complex IV. This sub-graph was then split with another algorithm into two sub-graphs. The subtraction of these two sub-graphs from the previous sub-graph allowed us to identify a protein of unknown function Usb1p/Ylr132p that interacts with the complex III subunits Qcr2p and Cor1p. We then used genetic and cell biology approaches to investigate the function of Usb1p. Preliminary results indicated that Usb1p is an essential protein with a dual localization in the nucleus and in the mitochondria, and that the over-expression of this protein can compensate for defects in the biogenesis of the respiratory complexes.</p> <p>Conclusions</p> <p>Our systems biology approach has highlighted the multiple associations between subunits and assembly factors of complexes III and IV during their biogenesis. In addition, this approach has allowed the identification of a new factor, Usb1p, involved in the biogenesis of respiratory complexes, which could not have been found using classical genetic screens looking for respiratory deficient mutants. Thus, this systems biology approach appears to be a fruitful new way to study the biogenesis of mitochondrial multi-subunit complexes.</p

The Saccharomyces cerevisiae OXA1 gene is required for the correct assembly of cytochrome c oxidase and oligomycin-sensitive ATP synthase

AbstractThe nuclear gene OXA1 was first isolated in Saccharomyces cerevisiae and found to be required at a post-translational step in cytochrome c oxidase biogenesis, probably at the level of assembly. Mutations in OXA1 lead to a complete respiratory deficiency. The protein Oxa1p is conserved through evolution and a human homolog has been isolated by functional complementation of a yeast oxa1− mutant. In order to further our understanding of the role of Oxa1p, we have constructed two yeast strains in which the OXA1 open reading frame was almost totally deleted. Cytochrome spectra and enzymatic activity measurements show the absence of heme aa3 and of a cytochrome c oxido-reductase activity and dramatic decrease of the oligomycin sensitive ATPase activity. Analysis of the respiratory complexes in non-denaturing gels reveals that Oxa1p is necessary for the correct assembly of the cytochrome c oxidase and the ATP synthase complex

R ES EA R CH Open Access Phenetic and genetic structure of tsetse fly populations (Glossina palpalis palpalis) in southern Ivory Coast

Abstract Background: Sleeping sickness, transmitted by G. p. palpalis, is known to be present in the Ivory Coast. G. p. palpalis has recently been reported to occur in several places within the town of Abidjan, including: (i) the Banco forest, (ii) the Abobo Adjamé University campus and (iii) the zoological park. Could these three places be treated sequentially, as separate tsetse populations, or should they be taken as one area comprising a single, panmictic population? Methods: The amount of gene flow between these places provides strategic information for vector control. It was estimated by the use of both microsatellite DNA and morphometric markers. The idea was to assess the interest of the faster and much less expensive morphometric approach in providing relevant information about population structure. Thus, to detect possible lack of insect exchange between these neighbouring areas of Abidjan, we used both genetic (microsatellite DNA) and phenetic (geometric morphometrics) markers on the same specimens. Using these same markers, we also compared these samples with specimens from a more distant area of south Ivory Coast, the region of Aniassué (186 km north from Abidjan). Results: Neither genetic nor phenetic markers detected significant differentiation between the three Abidjan G. p. palpalis samples. Thus, the null hypothesis of a single panmictic population within the city of Abidjan could not be rejected, suggesting the control strategy should not consider them separately. The markers were also in agreement when comparing G. p. palpalis from Abidjan with those of Aniassué, showing significant divergence between the two sites. Conclusions: Both markers suggested that a successful control of tsetse in Abidjan would require the three Abidjan sites to be considered together, either by deploying control measures simultaneously in all three sites, or by a continuous progression of interventions following for instance the &quot;rolling carpet&quot; principle. To compare the geometry of wing venation of tsetse flies is a cheap and fast technique. Agreement with the microsatellite approach highlights its potential for rapid assessment of population structure

Spatio-Temporal Dynamics of Yeast Mitochondrial Biogenesis: Transcriptional and Post-Transcriptional mRNA Oscillatory Modules

Examples of metabolic rhythms have recently emerged from studies of budding yeast. High density microarray analyses have produced a remarkably detailed picture of cycling gene expression that could be clustered according to metabolic functions. We developed a model-based approach for the decomposition of expression to analyze these data and to identify functional modules which, expressed sequentially and periodically, contribute to the complex and intricate mitochondrial architecture. This approach revealed that mitochondrial spatio-temporal modules are expressed during periodic spikes and specific cellular localizations, which cover the entire oscillatory period. For instance, assembly factors (32 genes) and translation regulators (47 genes) are expressed earlier than the components of the amino-acid synthesis pathways (31 genes). In addition, we could correlate the expression modules identified with particular post-transcriptional properties. Thus, mRNAs of modules expressed “early” are mostly translated in the vicinity of mitochondria under the control of the Puf3p mRNA-binding protein. This last spatio-temporal module concerns mostly mRNAs coding for basic elements of mitochondrial construction: assembly and regulatory factors. Prediction that unknown genes from this module code for important elements of mitochondrial biogenesis is supported by experimental evidence. More generally, these observations underscore the importance of post-transcriptional processes in mitochondrial biogenesis, highlighting close connections between nuclear transcription and cytoplasmic site-specific translation

Biogenesis of mitochondrial respiratory complexes in budding yeast saccharomyces cerevisiae

La biogenèse des complexes respiratoires mitochondriaux est un processus compliqué nécessitant l intervention de nombreux facteurs extrinsèques. Au cours de ma thèse, j ai étudié trois d entre eux chez S. cerevisiae. (1) Oxa1p est un facteur général intervenant dans l assemblage des complexes respiratoires III, IV et V. Nous avons étudié le rôle de ses domaines fonctionnels, mis en évidence des interactions entre eux et proposons un modèle de son organisation structurale dans la membrane interne. (2) Nous avons identifié l un de ses partenaires, Man1p, de fonction jusqu alors inconnue. Il est essentiel à la viabilité cellulaire, doublement localisé dans le noyau et les mitochondries et présent sous deux isoformes. (3) Nous avons mis en évidence Bca1p comme nouveau facteur d assemblage du complexe III. Nous avons montré qu il est ancré dans la membrane interne, expose un large domaine dans l espace intermembranaire et agirait tardivement dans l insertion de sous-unités III.The biogenesis of mitochondrial respiratory complexes is a sophisticated process and requires many extrinsic factors. During my PhD I focused on three of them in S. cerevisiae. (1) Oxa1p is a general factor which plays a role in the assembly of the respiratory complexes III, IV and V. We have studied the role of its functional domains, highlighted the interactions between these domains and propose a model for its structural organization in the inner membrane. (2) We have identified a new partner, Man1p, whose function is still not known. It is essential for cellular viability, has a dual localization in the nucleus and in the mitochondria and two isoforms. (3) We have highlighted a new assembly factor of complex III, Bca1p. We have shown that it is embedded within the inner membrane, exposes a big domain into the intermembrane space and could act late during the insertion of subunits III.VERSAILLES-BU Sciences et IUT (786462101) / SudocPARIS-BIUP (751062107) / SudocSudocFranceF

Contrôle de la biogenèse des complexes OXPHOS et de leurs interactions chez Saccharomyces cerevisiae

Le complexe III de la chaine respiratoire mitochondriale (OXPHOS III) chez S. cerevisiae est assemblé à partir de dix sous-unités structurales codées par le génome soit nucléaire, soit mitochondrial et fait intervenir une douzaine de protéines extrinsèques au complexe. Nous avons étudié l une d entre elle, Bcs1, une ATPase oligomérique conservée de la famille des protéines AAA (ATPases Associated with diverse cellular Activities), qui contrôle la dernière étape de l assemblage du complexe III. Chez l Homme, des mutations dans l orthologue de BCS1, BCS1L, sont associées à différentes maladies. Nous avons montré que des mutations dans les résidus conservés du domaine AAA de Bcs1 peuvent être compensées par des mutations dans les sous-unités de l ATP synthase mitochondriale (OXPHOS V). Ces mutations compensatrices diminuent toutes l activité d hydrolyse de l ATP de l enzyme et nous avons proposé que la biogenèse du complexe III puisse être modulée selon l état énergétique mitochondrial par Bcs1 via sa dépendance à l ATP. Nous avons aussi identifié des mutations compensatrices dans d autres gènes et le cas particulier de la délétion du RRF1, facteur général du recyclage des ribosomes mitochondriaux, a été étudié. Nous avons montré que l absence de Rrf1 a un effet différent sur la stabilité et la traduction des divers ARNm mitochondriaux. Nos résultats suggèrent une coopération entre les facteurs généraux et les facteurs spécifiques de la traduction mitochondriale dans le contrôle de l expression des sous-unités des complexes OXPHOS traduites dans la mitochondrie.OXPHOS complexes are multi-subunit complexes embedded in the inner mitochondrial membrane. We have studied the assembly factor Bcs1 that is a membrane-bound AAA-ATPase, required for the assembly of complex III. Mutations in the human gene BCS1L are responsible for various mild to lethal pathologies. Extragenic compensatory mutations able to restore the assembly of complex III in yeast bcs1 mutants were found in different genes not directly connected to the complex, revealing new networks of protein interactions. Mutations in catalytic subunits of ATP synthase were identified and thoroughly characterized. This work has allowed us to propose a novel regulatory loop via the ATP-dependent activity of Bcs1 protein, connecting the production of mitochondrial complex III and the activity of the ATP synthase. Moreover, these results hold promise for the development of therapies, targeting the mitochondrial adenine nucleotide pool, in treatment of BCS1-based disorders. We also show that the absence of RRF1, a mitochondrial ribosome recycling factor, is able to compensate defects of bcs1 mutants. Deletion of RRF1 has a differential impact on the stability and translation of mitochondrial mRNAs. Our results suggest cooperation between general and specific translation factors in controlling the expression of mtDNA-encoded subunits of the OXPHOS complexes.EVRY-Bib. électronique (912289901) / SudocSudocFranceF

Biogenèse des complexes respiratoires mitochondriaux chez la levure S. cerevisiae et les cellules humaines

La chaîne respiratoire mitochondriale est composée de complexes multimériques, constitués de sous-unités codées par l ADN nucléaire et l ADN mitochondrial (ADNmit) et sa biogenèse nécessite donc une coordination étroite entre la mitochondrie et le noyau. De nombreux facteurs nucléaires sont impliqués dans l expression de l ADNmit et l assemblage des différentes sous-unités. Durant ma thèse, je me suis intéressée à trois des facteurs jouant un rôle dans la biogenèse des complexes respiratoires chez S. cerevisiae et l homme. La protéine Oxa1 est impliquée dans l insertion co-traductionnelle de sous-unités membranaires de plusieurs complexes respiratoires chez S. cerevisiae. J ai étudié le rôle de la protéine Oxa1L chez l homme en réalisant l extinction du gène OXA1L par interférence ARN dans des fibroblastes. Mes travaux et ceux publiés récemment chez l homme et la levure apportent une éclairage nouveau sur le rôle d Oxa1. A partir d un mutant ponctuel d OXA1 chez S. cerevisiae, j ai isolé un suppresseur en copies multiples, le gène RMD9 et montré que Rmd9p contrôle la stabilité/maturation de tous les ARNm mitochondriaux codant des sous-unités des complexes respiratoires. Enfin, Bcs1, une ATPase de la famille AAA, est requise pour l assemblage du complexe respiratoire III. Chez l homme, des mutations dans le gène BCS1L sont responsables de pathologies assez diverses. J ai mené une étude structure-fonction de Bcs1p chez S. cerevisiae et mis en évidence dans le domaine AAA trois régions cruciales pour la fonction. J ai aussi isolé des suppresseurs extragéniques dont l identification devrait permettre de mieux comprendre les rôles de cette protéineThe mitochondrial respiratory chain consists of multimeric complexes composed of subunits encoded by the nuclear and mitochondrial genomes. Its biogenesis requires a fine tuning between nucleus and mitochondria. Several nuclear encoded factors are involved in mitochondrial gene expression and the following assembly of subunits. During my thesis I got interested in three factors involved in respiratory complex biogenesis in the yeast S. cerevisiae and in human. The Oxa1 protein is involved in co-translational insertion of membrane subunits belonging to several complexes. I studied the role of Oxa1 in human by silencing its expression using RNA interference in fibroblasts. This work and other published data on yeast and human provide a new insight into the role of Oxa1. In addition I isolated the RMD9 gene as a high copy suppressor of an oxa1 mutant in S. cerevisiae. I showed that Rmd9p controls the stability/maturation of all mitochondrial mRNA encoding respiratory complex subunits. Finally Bcs1, an ATPase belonging to the AAA family is required for assembly of respiratory complex III. In human, mutations in the BCS1L gene are responsible for various pathologies. I performed a structure-function analysis of Bcs1p in S. cerevisiae. This study reveals three critical regions in the AAA domain. Besides I isolated extragenic suppressors which identification should contribute to a better understanding of Bcs1 function.VERSAILLES-BU Sciences et IUT (786462101) / SudocSudocFranceF