Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

Application of neodymium isotope ratio measurements for the origin assessment of uranium ore concentrates

A novel procedure has been developed for the measurement of 143Nd/144Nd isotope ratio in various uranium-bearing materials, such as uranium ores and ore concentrates (UOC) in order to evaluate the usefulness and applicability of variations of 143Nd/144Nd isotope ratio for provenance assessment in nuclear forensics. Neodymium was separated and pre-concentrated by extraction chromatography and then the isotope ratios were measured by multi-collector inductively coupled plasma mass spectrometry (MC-ICP-MS). The method was validated by the measurement of standard reference materials (La Jolla, JB-2 and BCR-2) and the applicability of the procedure was demonstrated by the analysis of uranium samples of world-wide origin. The investigated samples show distinct 143Nd/144Nd ratio depending on the ore type, deposit age and Sm/Nd ratio. Together with other characteristics of the material in question, the Nd isotope ratio is a promising signature for nuclear forensics and suggests being indicative of the source material, the uranium ore.RST/Radiation, Science and TechnologyApplied Science

Molecular architecture control in synthesis of spherical Ln-containing nanoparticles

Among the procedures to prepare lanthanide-containing nanoparticles a gap exists in the range between 5 and 40 nm. The miniemulsion technique presented here is intended to fill this discontinuity and offers a facile method that can be applied for the preparation of nanoparticles for various applications, e.g. medical imaging, optics and catalysis. We demonstrate that formation of nanodroplets under emulsion conditions is the key step in the size control of the nanoparticles. The type of surfactant and the nature of the dispersed and continuous phases strongly influence the interfacial activity and, consequently, the size of the final solid particles that result from the subsequent thermal decomposition. Moreover, the choice of the surfactant determines the final elemental composition of the particles, leading to either lanthanide oxides or oxysulfates when using Brij® 35 or sodium dodecyl sulfate, respectively. Nanoparticles of holmium and gadolinium were prepared and their applicability as magnetic resonance imaging contrast agents is shown.BiotechnologyApplied Science

Direct observation of Hsp90-induced compaction in a protein chain

The chaperone heat shock protein 90 (Hsp90) is well known to undergo important conformational changes, which depend on nucleotide and substrate interactions. Conversely, how the conformations of its unstable and disordered substrates are affected by Hsp90 is difficult to address experimentally yet is central to its function. Here, using optical tweezers, we find that Hsp90 promotes local contractions in unfolded chains that drive their global compaction down to dimensions of folded states. This compaction has a gradual nature while showing small steps, is stimulated by ATP, and performs mechanical work against counteracting forces that expand the chain dimensions. The Hsp90 interactions suppress the formation of larger-scale folded, misfolded, and aggregated structures. The observations support a model in which Hsp90 alters client conformations directly by promoting local intra-chain interactions while suppressing distant ones. We conjecture that chain compaction may be central to how Hsp90 protects unstable clients and cooperates with Hsp70.BN/Sander Tans La