Summary To characterize somatic alterations in colorectal carcinoma (CRC), we conducted genome-scale analysis of 276 samples, analyzing exome sequence, DNA copy number, promoter methylation, mRNA and microRNA expression. A subset (97) underwent low-depth-of-coverage whole-genome sequencing. 16% of CRC have hypermutation, three quarters of which have the expected high microsatellite instability (MSI), usually with hypermethylation and MLH1 silencing, but one quarter has somatic mismatch repair gene mutations. Excluding hypermutated cancers, colon and rectum cancers have remarkably similar patterns of genomic alteration. Twenty-four genes are significantly mutated. In addition to the expected APC, TP53, SMAD4, PIK3CA and KRAS mutations, we found frequent mutations in ARID1A, SOX9, and FAM123B/WTX. Recurrent copy number alterations include potentially drug-targetable amplifications of ERBB2 and newly discovered amplification of IGF2. Recurrent chromosomal translocations include fusion of NAV2 and WNT pathway member TCF7L1. Integrative analyses suggest new markers for aggressive CRC and important role for MYC-directed transcriptional activation and repression.

Pancreatic cancer is a highly lethal malignancy with few effective therapies. We performed exome sequencing and copy number analysis to define genomic aberrations in a prospectively accrued clinical cohort (n = 142) of early (stage I and II) sporadic pancreatic ductal adenocarcinoma. Detailed analysis of 99 informative tumours identified substantial heterogeneity with 2,016 non-silent mutations and 1,628 copy-number variations. We define 16 significantly mutated genes, reaffirming known mutations (KRAS, TP53, CDKN2A, SMAD4, MLL3, TGFBR2, ARID1A and SF3B1), and uncover novel mutated genes including additional genes involved in chromatin modification (EPC1 and ARID2), DNA damage repair (ATM) and other mechanisms (ZIM2, MAP2K4, NALCN, SLC16A4 and MAGEA6). Integrative analysis with in vitro functional data and animal models provided supportive evidence for potential roles for these genetic aberrations in carcinogenesis. Pathway-based analysis of recurrently mutated genes recapitulated clustering in core signalling pathways in pancreatic ductal adenocarcinoma, and identified new mutated genes in each pathway. We also identified frequent and diverse somatic aberrations in genes described traditionally as embryonic regulators of axon guidance, particularly SLIT/ROBO signalling, which was also evident in murine Sleeping Beauty transposon-mediated somatic mutagenesis models of pancreatic cancer, providing further supportive evidence for the potential involvement of axon guidance genes in pancreatic carcinogenesis.

A variety of microbial communities and their genes (microbiome) exist throughout the human body, playing fundamental roles in human health and disease. The NIH funded Human Microbiome Project (HMP) Consortium has established a population-scale framework which catalyzed significant development of metagenomic protocols resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomic data available to the scientific community. Here we present resources from a population of 242 healthy adults sampled at 15 to 18 body sites up to three times, which to date, have generated 5,177 microbial taxonomic profiles from 16S rRNA genes and over 3.5 Tb of metagenomic sequence. In parallel, approximately 800 human-associated reference genomes have been sequenced. Collectively, these data represent the largest resource to date describing the abundance and variety of the human microbiome, while providing a platform for current and future studies.

Epistasis-nonlinear genetic interactions between polymorphic loci-is the genetic basis of canalization and speciation, and epistatic interactions can be used to infer genetic networks affecting quantitative traits. However, the role that epistasis plays in the genetic architecture of quantitative traits is controversial. Here, we compared the genetic architecture of three Drosophila life history traits in the sequenced inbred lines of the Drosophila melanogaster Genetic Reference Panel (DGRP) and a large outbred, advanced intercross population derived from 40 DGRP lines (Flyland). We assessed allele frequency changes between pools of individuals at the extremes of the distribution for each trait in the Flyland population by deep DNA sequencing. The genetic architecture of all traits was highly polygenic in both analyses. Surprisingly, none of the SNPs associated with the traits in Flyland replicated in the DGRP and vice versa. However, the majority of these SNPs participated in at least one epistatic interaction in the DGRP. Despite apparent additive effects at largely distinct loci in the two populations, the epistatic interactions perturbed common, biologically plausible, and highly connected genetic networks. Our analysis underscores the importance of epistasis as a principal factor that determines variation for quantitative traits and provides a means to uncover genetic networks affecting these traits. Knowledge of epistatic networks will contribute to our understanding of the genetic basis of evolutionarily and clinically important traits and enhance predictive ability at an individualized level in medicine and agriculture.chill coma recovery | genetic interaction networks | genome-wide association studies | startle response | starvation resistance

This work investigated the cytotoxicities of three silver nanoparticles (SNPs) SNP-5, SNP-20 and SNP-50 with different sizes ( approximately 5 nm, approximately 20 nm and approximately 50 nm) using four human cell models (A549, SGC-7901, HepG2 and MCF-7). Endpoints included cell morphology, cell viability, cellular membrane integrity, oxidative stress and cell cycle progression. Observable deleterious effects on the cell morphologies and membrane integrity were induced by SNP-5 and SNP-20. SNPs elevated the ROS levels in cells and arrested the cells at S phase. Apoptosis occurred for 4-9% of the exposed cells. All these cellular responses as well as EC50 values were found to be size-dependent for the tested SNPs. Ultrastructural observations confirmed the presence of SNPs inside cells. Elemental analysis of silver in cells by ICP-MS showed that smaller nanoparticles enter cells more easily than larger ones, which may be the cause of higher toxic effects. The findings may assist in the design of SNP applications and provide insights into their toxicity.

Surface-enhanced Raman scattering (SERS) is a powerful fingerprint vibrational spectroscopy with a single-molecule detection limit, but its applications are generally restricted to 'free-electron-like' metal substrates such as Au, Ag and Cu nanostructures. We have invented a shell-isolated nanoparticle-enhanced Raman spectroscopy (SHINERS) technique, using Au-core silica-shell nanoparticles (Au@SiO(2) NPs), which makes SERS universally applicable to surfaces with any composition and any morphology. This protocol describes how to prepare shell-isolated nanoparticles (SHINs) with different well-controlled core sizes (55 and 120 nm), shapes (nanospheres, nanorods and nanocubes) and shell thicknesses (1-20 nm). It then describes how to apply SHINs to Pt and Au single-crystal surfaces with different facets in an electrochemical environment, on Si wafer surfaces adsorbed with hydrogen, on ZnO nanorods, and on living bacteria and fruit. With this method, SHINs can be prepared for use in ~3 h, and each subsequent procedure for SHINERS measurement requires 1-2 h.

Next-generation high-performance structural materials are required for lightweight design strategies and advanced energy applications. Maraging steels, combining a martensite matrix with nanoprecipitates, are a class of high-strength materials with the potential for matching these demands. Their outstanding strength originates from semi-coherent precipitates, which unavoidably exhibit a heterogeneous distribution that creates large coherency strains, which in turn may promote crack initiation under load. Here we report a counterintuitive strategy for the design of ultrastrong steel alloys by high-density nanoprecipitation with minimal lattice misfit. We found that these highly dispersed, fully coherent precipitates (that is, the crystal lattice of the precipitates is almost the same as that of the surrounding matrix), showing very low lattice misfit with the matrix and high anti-phase boundary energy, strengthen alloys without sacrificing ductility. Such low lattice misfit (0.03 ± 0.04 per cent) decreases the nucleation barrier for precipitation, thus enabling and stabilizing nanoprecipitates with an extremely high number density (more than 10 per cubic metre) and small size (about 2.7 ± 0.2 nanometres). The minimized elastic misfit strain around the particles does not contribute much to the dislocation interaction, which is typically needed for strength increase. Instead, our strengthening mechanism exploits the chemical ordering effect that creates backstresses (the forces opposing deformation) when precipitates are cut by dislocations. We create a class of steels, strengthened by Ni(Al,Fe) precipitates, with a strength of up to 2.2 gigapascals and good ductility (about 8.2 per cent). The chemical composition of the precipitates enables a substantial reduction in cost compared to conventional maraging steels owing to the replacement of the essential but high-cost alloying elements cobalt and titanium with inexpensive and lightweight aluminium. Strengthening of this class of steel alloy is based on minimal lattice misfit to achieve maximal precipitate dispersion and high cutting stress (the stress required for dislocations to cut through coherent precipitates and thus produce plastic deformation), and we envisage that this lattice misfit design concept may be applied to many other metallic alloys.

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