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

Immune response of Pseudosciaena crocea to the injection of Vibrio alginolyticus

For the investigation of anti-infection immune response of Pseudosciaena crocea, 160 healthy fish samples were categorized into infected and control groups. Each individual fish in the infected group was injected intraperitoneally (i.p.) with 0.2 ml bacterial suspension of Vibrio alginolyticus in density of 2 x 10(7) CFU/ml, while each individual in the control group was injected i.p. with 0.2 ml sterile saline solution (0.85%). It was observed that the artificial injection of V. alginolyticus significantly increased the number of erythrocytes, leucocytes, lymphocytes in peripheral blood as well as peripheral serum antibacterial activity and antibody titer of large yellow croaker, and significantly reduced the number of peripheral blood granulocytes as compared with those in the control group. No significant difference in acid phosphytase and superoxide dismutase activity of serum was detected between the two groups. It is suggested that non-specific immune factors including leucocytes and anti-bacteria substance in peripheral blood played important role at the initial stage of infection, and specific immune factors such as antibody then played important role in response to anti-infection at the latter stage

Starvation effects on pathogenic Vibrio alginolyticus in natural seawater

To get a better understanding of the starvation survival strategy of pathogenic Vibrio alginolyticus, log-phase cells were inoculated into sterile natural seawater for starvation studies. The results showed that all of total bacteria number, viable bacteria number and CFU number of V. alginolyticus increased remarkably at the initial starvation stage; after reaching their peaks at 5 d, both total bacteria number and viable bacteria number of V. alginolyticus fell slowly, while the CFU Muni er fell more quickly after reaching its peak at 10 d; V. alginolyticus elongated their cells at the prophase of starvation, and their shrunk their volume and turned their shapes into ovals from rods at the anaphase of starvation; starved cells showed more sensitivity to heating and UV; starved cells showed no significant difference from unstarved ones at the lowest detection limit determined by indirect enzyme-linked immunosorbent assay (ELISA); starved cells' ability to adhere to the skin mucus of large yellow croaker (Pseudosciaena crocea) showed a sharp decline as tire starvation time increases; the cellular protein of V. alginolyticus increased remarkably at the anaphase of starvation. The results indicated that pathogenic 1 alginolyticus could survive in starvation for relatively long periods of time (>= 2 months) in 28 degrees C natural seawater due to the morphological and physiological changes; however, starved 1 alginolyticus cells showed less virulence and higher sensitivity under environmental stresses

Prefabricated construction enabled by the Internet-of-Things

Prefabricated construction has been used for public rental housing in Hong Kong. In order to speed up housing delivery, Hong Kong Housing Authority (HKHA) have employed advanced technologies, including Building Information Modelling (BIM) and Radio Frequency Identification (RFID), in some of their pilot prefabrication-based construction projects. However, the information obtained from BIM and RFID is not well connected and shared among relevant stakeholders. This paper introduces a multi-dimensional Internet of Things (IoT)-enabled BIM platform (MITBIMP) to achieve real-time visibility and traceability in prefabricated construction. Design considerations of a RFID Gateway Operating System, visibility and traceability tools, Data Source Interoperability Services, and decision support services are specified for developing the MITBIMP. A case study from a real-life construction project in Hong Kong is used as a pilot project to demonstrate advanced decision-making by using cutting-edge concepts and technologies within the MITBIMP to providing a basis for real-time visibility and traceability of the whole processes of prefabrication-based construction.Department of Building and Real Estat