CASE REPORT: 17 YEARS SURVIVAL RATE AFTER RADICAL RESECTION OF CEREBELLAR PILOCYTIC ASTROCYTOMA

A case report is presented to approve 17 years survival after Nafziger- Town operation of a boy, aged 5, 5 years, diagnosed with cerebellar pilocytic astrocytoma. Ventriculo- peritoneal (VP) shunt is applied a week before the radical operation. Pre and postoperative (17 years after) computed tomographic scans (CT) as well as histological verification.A case report is presented to approve 17 years survival after Nafziger- Town operation of a boy, aged 5, 5 years, diagnosed with cerebellar pilocytic astrocytoma. Ventriculo- peritoneal (VP) shunt is applied a week before the radical operation. Pre and postoperative (17 years after) computed tomographic scans (CT) as well as histological verification

Adding a New Dimension to DNA Melting Curves.

to be published in Europhysics LettersInternational audienceStandard DNA melting curves record the separation of the two strands versus temperature, but they do not provide any information on the location of the opening. We introduce an experimental method which adds a new dimension to the melting curves of short DNA sequences by allowing us to record the degree of opening in several positions along the molecule all at once. This adds the spatial dimension to the melting curves and allows a precise investigation of the role of the base-pair sequence on the fluctuations and denaturation of the DNA double helix. We illustrate the power of the method by investigating the influence of an AT rich region on the fluctuations of neighboring domains

RSC remodeling of oligo-nucleosomes: an atomic force microscopy study

RSC is an essential chromatin remodeling factor that is required for the control of several processes including transcription, repair and replication. The ability of RSC to relocate centrally positioned mononucleosomes at the end of nucleosomal DNA is firmly established, but the data on RSC action on oligo-nucleosomal templates remains still scarce. By using Atomic Force Microscopy (AFM) imaging, we have quantitatively studied the RSC- induced mobilization of positioned di- and trinucleosomes as well as the directionality of mobilization on mononucleosomal template labeled at one end with streptavidin. AFM imaging showed only a limited set of distinct configurational states for the remodeling products. No stepwise or preferred directionality of the nucleosome motion was observed. Analysis of the corresponding reaction pathways allows deciphering the mechanistic features of RSC-induced nucleosome relocation. The final outcome of RSC remodeling of oligosome templates is the packing of the nucleosomes at the edge of the template, providing large stretches of DNA depleted of nucleosomes. This feature of RSC may be used by the cell to overcome the barrier imposed by the presence of nucleosomes

The dynamics of individual nucleosomes controls the chromatin condensation pathway: direct AFM visualization of variant chromatin

Chromatin organization and dynamics is studied in this work at scales ranging from single nucleosome to nucleosomal array by using a unique combination of biochemical assays, single molecule imaging technique and numerical modeling. We demonstrate that a subtle modification in the nucleosome structure induced by the histone variant H2A.Bbd drastically modifies the higher order organization of the nucleosomal arrays. Importantly, as directly visualized by AFM, conventional H2A nucleosomal arrays exhibit specific local organization, in contrast to H2A.Bbd arrays, which show "beads on a string" structure. The combination of systematic image analysis and theoretical modeling allows a quantitative description relating the observed gross structural changes of the arrays to their local organization. Our results strongly suggest that higher-order organization of H1-free nucleosomal arrays is mainly determined by the fluctuation properties of individual nucleosomes. Moreover, numerical simulations suggest the existence of attractive interactions between nucleosomes to provide the degree of compaction observed for conventional chromatin fibers.Comment: Biophys J. in pres

Interference Mapping in 3D for High-Density Indoor IoT Deployments

Deployment of practical Internet of Things (IoT) in the context of 5G can be hindered by substantial interference and spectrum limitations, especially in the unlicensed frequency bands. Due to the high density of such devices in indoor scenarios, the need for interference characterization which facilitates more effective spectrum utilization is further emphasized. This chapter studies the influence of diverse scenarios for the dense placement of interferers on the spectrum occupancy through the use of 3D interference maps for two popular IoT technologies—LoRa and Wi-Fi. The experiments are performed with software-defined radio (SDR) platforms in real time and an automated positioning tool which provides the measurements to characterize the interference in 3D space. The findings demonstrate a nonuniform character of the interference and the significant impact of fading within the width, height, and length of the examined area. They suggest the role of dynamic relocation for realistic IoT scenarios

Extensive characterization of NF-κB binding uncovers non-canonical motifs and advances the interpretation of genetic functional traits

Background Genetic studies have provided ample evidence of the influence of non-coding DNA polymorphisms on trait variance, particularly those occurring within transcription factor binding sites. Protein binding microarrays and other platforms that can map these sites with great precision have enhanced our understanding of how a single nucleotide polymorphism can alter binding potential within an in vitro setting, allowing for greater predictive capability of its effect on a transcription factor binding site. Results We have used protein binding microarrays and electrophoretic mobility shift assay-sequencing (EMSA-Seq), a deep sequencing based method we developed to analyze nine distinct human NF-κB dimers. This family of transcription factors is one of the most extensively studied, but our understanding of its DNA binding preferences has been limited to the originally described consensus motif, GGRRNNYYCC. We highlight differences between NF-κB family members and also put under the spotlight non-canonical motifs that have so far received little attention. We utilize our data to interpret the binding of transcription factors between individuals across 1,405 genomic regions laden with single nucleotide polymorphisms. We also associated binding correlations made using our data with risk alleles of disease and demonstrate its utility as a tool for functional studies of single nucleotide polymorphisms in regulatory regions. Conclusions NF-κB dimers bind specifically to non-canonical motifs and these can be found within genomic regions in which a canonical motif is not evident. Binding affinity data generated with these different motifs can be used in conjunction with data from chromatin immunoprecipitation-sequencing (ChIP-Seq) to enable allele-specific analyses of expression and transcription factor-DNA interactions on a genome-wide scale.Wellcome Trust (London, England) (grant 075491/Z/04)European Commission (Seventh Framework Programme FP7/2007-2013: Model-In (222008))European Commission (Seventh Framework Programme FP7 ITN Network INTEGER (214902))Medical Research Council (Canada) (MRC project grant G0700818

Kinky DNA in solution: Small-angle-scattering study of a nucleosome positioning sequence

DNA is a flexible molecule, but the degree of its flexibility is subject to debate. The commonly-accepted persistence length of lp ≈ 500Å is inconsistent with recent studies on short-chain DNA that show much greater flexibility but do not probe its origin. We have performed x-ray and neutron small-angle scattering on a short DNA sequence containing a strong nucleosome positioning element and analyzed the results using a modified Kratky-Porod model to determine possible conformations. Our results support a hypothesis from Crick and Klug in 1975 that some DNA sequences in solution can have sharp kinks, potentially resolving the discrepancy. Our conclusions are supported by measurements on a radiation-damaged sample, where single-strand breaks lead to increased flexibility and by an analysis of data from another sequence, which does not have kinks, but where our method can detect a locally enhanced flexibility due to an AT domain.Spanish Ministry of Economy, Industry and Competitiveness (BES-2013-065453, EEBB-I-2015-09973, FIS2012-38827). S.C.L. and UC-154 are grateful for the support of Junta de Castilla y Leon (Spain) Nanofibersafe BU079U16. D.A. acknowledges funding from the Agence Nationale de la Recherche through ANR-12-BSV5-0017-01 “Chrome” and ANR-17-CE11-0019-03 “Chrom3D” grants. N.T. acknowledges support by the project Advanced Materials and Devices (MIS 5002409, Competitiveness, Entrepreneurship and Innovation, NSRF 2014-2020) cofinanced by Greece and the European Regional Development Fund

The incorporation of the novel histone variant H2AL2 confers unusual structural and functional properties of the nucleosome

In this work we have studied the properties of the novel mouse histone variant H2AL2. H2AL2 was used to reconstitute nucleosomes and the structural and functional properties of these particles were studied by a combination of biochemical approaches, atomic force microscopy (AFM) and electron cryo-microscopy. DNase I and hydroxyl radical footprinting as well as micrococcal and exonuclease III digestion demonstrated an altered structure of the H2AL2 nucleosomes all over the nucleosomal DNA length. Restriction nuclease accessibility experiments revealed that the interactions of the H2AL2 histone octamer with the ends of the nucleosomal DNA are highly perturbed. AFM imaging showed that the H2AL2 histone octamer was complexed with only ∼130 bp of DNA. H2AL2 reconstituted trinucleosomes exhibited a type of a ‘beads on a string’ structure, which was quite different from the equilateral triangle 3D organization of conventional H2A trinucleosomes. The presence of H2AL2 affected both the RSC and SWI/SNF remodeling and mobilization of the variant particles. These unusual properties of the H2AL2 nucleosomes suggest a specific role of H2AL2 during mouse spermiogenesis