DNA loops and semicatenated DNA junctions

BACKGROUND: Alternative DNA conformations are of particular interest as potential signals to mark important sites on the genome. The structural variability of CA microsatellites is particularly pronounced; these are repetitive poly(CA) · poly(TG) DNA sequences spread in all eukaryotic genomes as tracts of up to 60 base pairs long. Many in vitro studies have shown that the structure of poly(CA) · poly(TG) can vary markedly from the classical right handed DNA double helix and adopt diverse alternative conformations. Here we have studied the mechanism of formation and the structure of an alternative DNA structure, named Form X, which was observed previously by polyacrylamide gel electrophoresis of DNA fragments containing a tract of the CA microsatellite poly(CA) · poly(TG) but had not yet been characterized. RESULTS: Formation of Form X was found to occur upon reassociation of the strands of a DNA fragment containing a tract of poly(CA) · poly(TG), in a process strongly stimulated by the nuclear proteins HMG1 and HMG2. By inserting Form X into DNA minicircles, we show that the DNA strands do not run fully side by side but instead form a DNA knot. When present in a closed DNA molecule, Form X becomes resistant to heating to 100°C and to alkaline pH. CONCLUSIONS: Our data strongly support a model of Form X consisting in a DNA loop at the base of which the two DNA duplexes cross, with one of the strands of one duplex passing between the strands of the other duplex, and reciprocally, to form a semicatenated DNA junction also called a DNA hemicatenane

Avoiding adsorption of DNA to polypropylene tubes and denaturation of short DNA fragments.

Two problems can arise when working with small quantities of DNA in polypropylene tubes: first, significant amounts of DNA can become lost by sticking to the tube walls; second, short DNA fragments tend to denature when binding to polypropylene. In addition, DNA also tends to denature upon dehydration. We have found that a simple way to solve these problems is by using polyallomer tubes instead of polypropylene and by avoiding certain salts, such as sodium acetate, when drying DNA

High affinity binding of proteins HMG1 and HMG2 to semicatenated DNA loops

BACKGROUND: Proteins HMG1 and HMG2 are two of the most abundant non histone proteins in the nucleus of mammalian cells, and contain a domain of homology with many proteins implicated in the control of development, such as the sex-determination factor Sry and the Sox family of proteins. In vitro studies of interactions of HMG1/2 with DNA have shown that these proteins can bind to many unusual DNA structures, in particular to four-way junctions, with binding affinities of 10(7) to 10(9) M(-1). RESULTS: Here we show that HMG1 and HMG2 bind with a much higher affinity, at least 4 orders of magnitude higher, to a new structure, Form X, which consists of a DNA loop closed at its base by a semicatenated DNA junction, forming a DNA hemicatenane. The binding constant of HMG1 to Form X is higher than 5 × 10(12) M(-1), and the half-life of the complex is longer than one hour in vitro. CONCLUSIONS: Of all DNA structures described so far with which HMG1 and HMG2 interact, we have found that Form X, a DNA loop with a semicatenated DNA junction at its base, is the structure with the highest affinity by more than 4 orders of magnitude. This suggests that, if similar structures exist in the cell nucleus, one of the functions of these proteins might be linked to the remarkable property of DNA hemicatenanes to associate two distant regions of the genome in a stable but reversible manner

Improved Image Partitioning for Compression and Representation using the Lab Color Space in the LAR Image Codec

International audienceThe LAR codec is an advanced image compression method relying on a quadtree partitioning of the image. The partitioning strongly impacts the LAR codec efficiency and enables both compression and representation efficiency. In order to increase the perceptual representation abilities without penalizing the compression efficiency we introduce and evaluate two partitioning criteria working in the Lab color space. These criteria are confronted to the original criterion and their compression and robustness performances are analyzed

Locally Adaptive Resolution (LAR) codec

The JPEG committee has initiated a study of potential technologies dedicated to future generation image compression systems. The idea is to design a new norm of image compression, named JPEG AIC (Advanced Image Coding), together with advanced evaluation methodologies, closely matching to human vision system characteristics. JPEG AIC thus aimed at defining a complete coding system able to address advanced functionalities such as lossy to lossless compression, scalability (spatial, temporal, depth, quality, complexity, component, granularity...), robustness, embed-ability, content description for image handling at object level... The chosen compression method would have to fit perceptual metrics defined by the JPEG community within the JPEG AIC project. In this context, we propose the Locally Adaptive Resolution (LAR) codec as a contribution to the relative call for technologies, tending to fit all of previous functionalities. This method is a coding solution that simultaneously proposes a relevant representation of the image. This property is exploited through various complementary coding schemes in order to design a highly scalable encoder. The LAR method has been initially introduced for lossy image coding. This efficient image compression solution relies on a content-based system driven by a specific quadtree representation, based on the assumption that an image can be represented as layers of basic information and local texture. Multiresolution versions of this codec have shown their efficiency, from low bit rates up to lossless compressed images. An original hierarchical self-extracting region representation has also been elaborated: a segmentation process is realized at both coder and decoder, leading to a free segmentation map. This later can be further exploited for color region encoding, image handling at region level. Moreover, the inherent structure of the LAR codec can be used for advanced functionalities such as content securization purposes. In particular, dedicated Unequal Error Protection systems have been produced and tested for transmission over the Internet or wireless channels. Hierarchical selective encryption techniques have been adapted to our coding scheme. Data hiding system based on the LAR multiresolution description allows efficient content protection. Thanks to the modularity of our coding scheme, complexity can be adjusted to address various embedded systems. For example, basic version of the LAR coder has been implemented onto FPGA platform while respecting real-time constraints. Pyramidal LAR solution and hierarchical segmentation process have also been prototyped on DSPs heterogeneous architectures. This chapter first introduces JPEG AIC scope and details associated requirements. Then we develop the technical features, of the LAR system, and show the originality of the proposed scheme, both in terms of functionalities and services. In particular, we show that the LAR coder remains efficient for natural images, medical images, and art images

WG1N5327 - Medical image database for lossless codec evaluation

This document presents the CAIMAN Project medical image database for JPEG commitee evaluation works purposes.This document describes the CAIMAN ANR project contribution on medical images to be considered for AIC. In order to evaluate the medical image codec, we have compiled a list of medical image (X-ray, CT, MRI) for the development and analysis of medical image compression scheme. All images can be found on a secure FTP server, and can be use freely for research purpose

WG1N5315 - Response to Call for AIC evaluation methodologies and compression technologies for medical images: LAR Codec

This document presents the LAR image codec as a response to Call for AIC evaluation methodologies and compression technologies for medical images.This document describes the IETR response to the specific call for contributions of medical imaging technologies to be considered for AIC. The philosophy behind our coder is not to outperform JPEG2000 in compression; our goal is to propose an open source, royalty free, alternative image coder with integrated services. While keeping the compression performances in the same range as JPEG2000 but with lower complexity, our coder also provides services such as scalability, cryptography, data hiding, lossy to lossless compression, region of interest, free region representation and coding

Gaussianity of Cosmic Velocity Fields and Linearity of the Velocity-Gravity Relation

We present a numerical study of the relation between the cosmic peculiar velocity field and the gravitational acceleration field. We show that on mildly non-linear scales (4-10 Mpc Gaussian smoothing), the distribution of the Cartesian coordinates of each of these fields is well approximated by a Gaussian. In particular, their kurtoses and negentropies are small compared to those of the velocity divergence and density fields. We find that at these scales the relation between the velocity and gravity field follows linear theory to good accuracy. Specifically, the systematic errors in velocity-velocity comparisons due to assuming the linear model do not exceed 6% in beta. To correct for them, we test various nonlinear estimators of velocity from density. We show that a slight modification of the alpha-formula proposed by Kudlicki et al. yields an estimator which is essentially unbiased and has a small variance.Comment: 11 pages, 15 figures; matches the version accepted for publication in MNRA

HMGB1 interacts with human topoisomerase IIα and stimulates its catalytic activity

DNA topoisomerase IIα (topo IIα) is an essential nuclear enzyme and its unique decatenation activity has been implicated in many aspects of chromosome dynamics such as chromosome replication and segregation during mitosis. Here we show that chromatin-associated protein HMGB1 (a member of the large family of HMG-box proteins with possible functions in DNA replication, transcription, recombination and DNA repair) promotes topo IIα-mediated catenation of circular DNA, relaxation of negatively supercoiled DNA and decatenation of kinetoplast DNA. HMGB1 interacts with topo IIα and this interaction, like the stimulation of the catalytic activity of the enzyme, requires both HMG-box domains of HMGB1. A mutant of HMGB1, which cannot change DNA topology stimulates DNA decatenation by topo IIα indistinguishably from the wild-type protein. Although HMGB1 stimulates ATP hydrolysis by topo IIα, the DNA cleavage is much more enhanced. The observed abilities of HMGB1 to interact with topo IIα and promote topo IIα binding to DNA suggest a mechanism by which HMGB1 stimulates the catalytic activity of the enzyme via enhancement of DNA cleavage

OMNIBOT - De la Division Omnidirectionnelle à la Commande de Robot Mobile

National audienceLe projet Omnibot a pour principaux objectifs, la conception et l'optimisation d'une boucle perception-commande, en partant du composant (imageur) jusqu'à la navigation du robot. Cette approche originale permet ainsi la création d'une nouvelle génération de capteurs pour la vision omnidirectionnelle tout en gardant une interaction constante avec des applications réelles. L'objectif final de ce projet est de proposer un démonstrateur mettant en œuvre un robot mobile command par un asservissement visuel omndirectionnel. Ce projet fait actuellement l'objet des quatre parties qui sont développées ci après