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

Cow embryo culture in vitro

International audienc

PARTITIONING OF TRACE ELEMENTS DURING FLUIDIZED BED COMBUSTION OF HIGH ASH CONTENT LIGNITE FBC2005-78068

ABSTRACT INTRODUCTION The behavior of 20 trace elements (As, B, Ba, Cd, Co, Cr, Cu, Hg, Li, Mn, Mo, Ni, P, Pb, Sb, Se, Sn, Tl, V, Zn) and 8 major and minor elements (Al, Ca, Fe, K, Mg, Na, Si, Ti) during the combustion of high ash content lignite with and without limestone addition have been investigated in the 0.3 MW t Middle East Technical University (METU) Atmospheric Bubbling Fluidized Bed Combustor (ABFBC) Test Rig. Experiments were performed without fines recycle. Inert bed material utilized in the experiments was bed ash obtained previously from the combustion of the same lignite without limestone addition in the same test rig. Concentrations of trace elements in coal, limestone, bottom ash, cyclone ash and filter ash were determined by Inductively Coupled Plasma Optical Emission Spectroscopy (ICP-OES). Measurements show that the distribution of major and minor elements follows the ash split between the bottom ash and fly ash and that the major proportion of most of the trace elements (As, Ba, Cr, Hg, Li, Mo, Ni, Sn, V, Zn) are recovered in fly ash. Comparisons between the trace element partitioning of the runs with and without limestone addition reveal that addition of limestone shifts the partitioning of Ba, Cr, Hg, Mo, Ni, Sn, V, Zn from bottom ash to fly ash. Applications of fluidized bed combustion technology developed for burning coal with high efficiency and within acceptable levels of gaseous pollutant emissions have been steadily increasing in both capacity and number over the past decade. However, gradual introduction of increasingly restrictive legislations on emissions from combustion sources and increasing public concern relating to the emissions of trace elements has been keeping the topic attractive for further research. Extensive research on the trace elements and their partitioning behavior in fluidized bed combustion systems has been carried out previously In an attempt to achieve this objective, a typical Turkish lignite with high ash content was burned in its own ash in the METU 0.3 MW t ABFBC test rig with and without limestone addition and partitioning behavior of major and minor ash components and trace elements were determined

New microsatellite markers for population studies of Phytophthora cinnamomi, an important global pathogen

Abstract Phytophthora cinnamomi is the causal agent of root rot, canker and dieback of thousands of plant species around the globe. This oomycete not only causes severe economic losses but also threatens natural ecosystems. In South Africa, P. cinnamomi affects eucalyptus, avocado, macadamia and indigenous fynbos. Despite being one of the most important plant pathogens with a global distribution, little information is available regarding origin, invasion history and population biology. This is partly due to the limited number of molecular markers available for studying P. cinnamomi. Using available genome sequences for three isolates of P. cinnamomi, sixteen polymorphic microsatellite markers were developed as a set of multiplexable markers for both PCR and Gene Scan assays. The application of these markers on P. cinnamomi populations from avocado production areas in South Africa revealed that they were all polymorphic in these populations. The markers developed in this study represent a valuable resource for studying the population biology and movement of P. cinnamomi and will aid in the understanding of the origin and invasion history of this important species

The enzymatic activities of CD38 enhance CLL growth and trafficking: implications for therapeutic targeting.

The ecto-enzyme CD38 is gaining momentum as a novel therapeutic target for patients with hematological malignancies, with several anti-CD38 monoclonal antibodies in clinical trials with promising results. In chronic lymphocytic leukemia (CLL) CD38 is a marker of unfavorable prognosis and a central factor in the pathogenetic network underlying the disease: activation of CD38 regulates genetic pathways involved in proliferation and movement. Here we show that CD38 is enzymatically active in primary CLL cells and that its forced expression increases disease aggressiveness in a xenograft model. The effect is completely lost when using an enzyme-deficient version of CD38 with a single amino-acid mutation. Through the enzymatic conversion of NAD into ADPR (ADP-ribose) and cADPR (cyclic ADP-ribose), CD38 increases cytoplasmic Ca2+ concentrations, positively influencing proliferation and signaling mediated via chemokine receptors or integrins. Consistently, inhibition of the enzymatic activities of CD38 using the flavonoid kuromanin blocks CLL chemotaxis, adhesion and in vivo homing. In a short-term xenograft model using primary cells, kuromanin treatment traps CLL cells in the blood, thereby increasing responses to chemotherapy. These results suggest that monoclonal antibodies that block the enzymatic activities of CD38 or enzyme inhibitors may prove therapeutically useful