Structural basis for the initiation of eukaryotic transcription-coupled DNA repair

Eukaryotic transcription-coupled repair (TCR) is an important and well-conserved sub-pathway of nucleotide excision repair that preferentially removes DNA lesions from the template strand that block translocation of RNA polymerase II (Pol II). Cockayne syndrome group B (CSB, also known as ERCC6) protein in humans (or its yeast orthologues, Rad26 in Saccharomyces cerevisiae and Rhp26 in Schizosaccharomyces pombe) is among the first proteins to be recruited to the lesion-arrested Pol II during the initiation of eukaryotic TCR. Mutations in CSB are associated with the autosomal-recessive neurological disorder Cockayne syndrome, which is characterized by progeriod features, growth failure and photosensitivity1. The molecular mechanism of eukaryotic TCR initiation remains unclear, with several long-standing unanswered questions. How cells distinguish DNA lesion-arrested Pol II from other forms of arrested Pol II, the role of CSB in TCR initiation, and how CSB interacts with the arrested Pol II complex are all unknown. The lack of structures of CSB or the Pol II–CSB complex has hindered our ability to address these questions. Here we report the structure of the S. cerevisiae Pol II–Rad26 complex solved by cryo-electron microscopy. The structure reveals that Rad26 binds to the DNA upstream of Pol II, where it markedly alters its path. Our structural and functional data suggest that the conserved Swi2/Snf2-family core ATPase domain promotes the forward movement of Pol II, and elucidate key roles for Rad26 in both TCR and transcription elongation

Enhancement of Localization Systems in NLOS Urban Scenario with Multipath Ray Tracing Fingerprints and Machine Learning

A hybrid technique is proposed to enhance the localization performance of a time difference of arrival (TDOA) deployed in non-line-of-sight (NLOS) suburban scenario. The idea was to use Machine Learning framework on the dataset, produced by the ray tracing simulation, and the Channel Impulse Response estimation from the real signal received by each sensor. Conventional localization techniques mitigate errors trying to avoid NLOS measurements in processing emitter position, while the proposed method uses the multipath fingerprint information produced by ray tracing (RT) simulation together with calibration emitters to refine a Machine Learning engine, which gives an extra layer of information to improve the emitter position estimation. The ray-tracing fingerprints perform the target localization embedding all the reflection and diffraction in the propagation scenario. A validation campaign was performed and showed the feasibility of the proposed method, provided that the buildings can be appropriately included in the scenario description

J. Biol. Chem.

Rab geranylgeranyltransferase (RabGGTase) catalyzes the prenylation of Rab proteins. Despite possessing a single active site, RabGGTase is able to add geranylgeranyl moieties onto each of the two C-terminal cysteine residues of Rab. We have studied the kinetics of Rab double prenylation employing a combination of a novel high pressure liquid chromatography (HPLC)-based in vitro prenylation assay and fluorescence spectroscopy. Transfer of the first geranylgeranyl group proceeds with a k(1) = 0.16 s(-1), while the conversion from singly to double prenylated Rab is 4-fold slower (k(2) = 0.039 s(-1)). We found that following the first transfer reaction, the conjugated lipid is removed from the active site of RabGGTase but mono-prenylated Rab.REP complex remains bound to RabGGTase with a K-d < 1nM. In contrast to the doubly prenylated Rab7.REP dissociation of the mono-prenylated species from RabGGTase was only weakly stimulated by phosphoisoprenoid. Based on the obtained rate constants we calculated that at least 72% of mono-prenylated Rab molecules proceed to double prenylation without dissociating from RabGGTase. The obtained data provides an explanation of how RabGGTase discriminates between mono-prenylated intermediate and double prenylated reaction product. It also indicates that the phosphoisoprenoid acts both as a substrate and as a sensor governing the kinetics of protein-protein interactions in the double prenylation reaction

Epitaxies Si/SiGe(C) pour transistors bipolaires avancés

L objectif de cette thèse est d étudier les épitaxies SiGeC sélectives par rapport au nitrure de silicium afin d améliorer les performances en fréquence des transistors bipolaires à hétérojonction à structure complètement auto alignée. Pour répondre à cette attente, le système SiH4/GeH4/SiH3CH3/HCl/B2H6/H2 est utilisé pour élaborer nos épitaxies sélectives. Cette chimie à base de silane permet d augmenter significativement la vitesse de croissance par rapport au système SiCl2H2/GeH4/HCl/H2 utilisé classiquement, aussi bien pour un dépôt silicium sélectif que pour un film SiGe sélectif. Par exemple, pour un film Si0,75Ge0,25 la vitesse de croissance est multipliée par un facteur 8. L incorporation des atomes de carbone dans les sites substitutionnels est facilitée par cette hausse du taux de croissance. En effet, la teneur en carbone substitutionnel est plus élevée en utilisant le silane comme précurseur de silicium (jusqu à un facteur 4). L effet bloquant du carbone sur la diffusion du bore est alors meilleur et le dopant est mieux contenu dans la base Si/SiGeC:B. Cette meilleure incorporation du carbone se reflète dans les résultats électriques. Le courant IB n augmente pas aux fortes concentrations de carbone, ce qui signifie qu il n y a pas de centres recombinants dans la base. Le courant IC et la fréquence fT augmentent aussi, ce qui suggère que la largeur de la base neutre est plus fine et donc que la diffusion du bore est ralentie. Nous avons également mis en évidence l existence d une corrélation entre le courant IB et l intensité du signal de photoluminescence à température ambiante. En effet, considérant que leurs mécanismes de recombinaison sont similaires, nous avons noté que la hausse de IB correspond à la chute de la photoluminescence.The objective of this thesis is to study SiGe(C) epitaxial growth selective towards silicon nitride. Selective Epitaxial Growth (SEG) allows to improve frequence performances of heterojunction bipolar transistors, with fully self aligned structure. With this purpose, the SiH4/GeH4/SiH3CH3/HCl/B2H6/H2 system is used to elaborate selective epitaxial growth layer. Si SEG and SiGe SEG growth rates are significantly increased with silane-based chemistry, as compared to the standard SiCl2H2/GeH4/HCl/H2 one. For instance, Si0,75Ge0,25 layer growth rate can be increased by a factor 8. Carbon incorporation in substitutional sites is also improved by this growth rate increase. Indeed, using silane, the substitutional carbon content hugely increased (up to a factor 4). We found better carbon blocking effect on boron diffusion. Better carbon atoms incorporation improves electrical results. There is no IB current degradation with higher carbon concentrations, which means that there is no recombination centers in base electrode. IC current and fT frequence increase too, which suggest neutral base width is narrower and boron out-diffusion is lower. We noted that recombination mechanisms of IB current and photoluminescence at room temperature are similar and that base current can be correlated with photoluminescence intensity. Indeed, we show that IB current increases when photoluminescence signal decreases.GRENOBLE1-BU Sciences (384212103) / SudocSudocFranceF