Power cuts

doi: 10.1038/490005b

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The price of progress

doi: 10.1038/490005a

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Life sciences

doi: 10.1038/490006a

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Foundation opens TB lab in Africa

doi: 10.1038/490019a

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Misconduct is the main cause of life-sciences retractions

doi: 10.1038/490021a

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Malaria plan under scrutiny

doi: 10.1038/490013a

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The telescopes that came in from the cold

doi: 10.1038/490016a

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SARS veterans tackle coronavirus

doi: 10.1038/490020a

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New cures sought from old drugs

doi: 10.1038/490015a

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News Features


The New Milky Way


doi: 10.1038/490024a

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The chestnut resurrection


doi: 10.1038/490022a

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News & Views


Climate science: The aerosol effect p.40


doi: 10.1038/490040a

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Mucosal immunology: Infection induces friendly fire p.41


doi: 10.1038/490041a

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Quantum physics: Cruise control for a qubit p.43


doi: 10.1038/490043a

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Genomics: Resident risks p.44


doi: 10.1038/490044a

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Astrophysics: Two black holes found in a star cluster p.46


doi: 10.1038/490046a

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Immunology: Tolerating pregnancy p.47


doi: 10.1038/490047a

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The oyster genome reveals stress adaptation and complexity of shell formation p.49

The Pacific oyster Crassostrea gigas belongs to one of the most species-rich but genomically poorly explored phyla, the Mollusca. Here we report the sequencing and assembly of the oyster genome using short reads and a fosmid-pooling strategy, along with transcriptomes of development and stress response and the proteome of the shell. The oyster genome is highly polymorphic and rich in repetitive sequences, with some transposable elements still actively shaping variation. Transcriptome studies reveal an extensive set of genes responding to environmental stress. The expansion of genes coding for heat shock protein 70 and inhibitors of apoptosis is probably central to the oyster’s adaptation to sessile life in the highly stressful intertidal zone. Our analyses also show that shell formation in molluscs is more complex than currently understood and involves extensive participation of cells and their exosomes. The oyster genome sequence fills a void in our understanding of the Lophotrochozoa.

doi: 10.1038/nature11413

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A metagenome-wide association study of gut microbiota in type 2 diabetes p.55

Assessment and characterization of gut microbiota has become a major research area in human disease, including type 2 diabetes, the most prevalent endocrine disease worldwide. To carry out analysis on gut microbial content in patients with type 2 diabetes, we developed a protocol for a metagenome-wide association study (MGWAS) and undertook a two-stage MGWAS based on deep shotgun sequencing of the gut microbial DNA from 345 Chinese individuals. We identified and validated approximately 60,000 type-2-diabetes-associated markers and established the concept of a metagenomic linkage group, enabling taxonomic species-level analyses. MGWAS analysis showed that patients with type 2 diabetes were characterized by a moderate degree of gut microbial dysbiosis, a decrease in the abundance of some universal butyrate-producing bacteria and an increase in various opportunistic pathogens, as well as an enrichment of other microbial functions conferring sulphate reduction and oxidative stress resistance. An analysis of 23 additional individuals demonstrated that these gut microbial markers might be useful for classifying type 2 diabetes.

doi: 10.1038/nature11450

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Comprehensive molecular portraits of human breast tumours p.61

We analysed primary breast cancers by genomic DNA copy number arrays, DNA methylation, exome sequencing, messenger RNA arrays, microRNA sequencing and reverse-phase protein arrays. Our ability to integrate information across platforms provided key insights into previously defined gene expression subtypes and demonstrated the existence of four main breast cancer classes when combining data from five platforms, each of which shows significant molecular heterogeneity. Somatic mutations in only three genes (TP53, PIK3CA and GATA3) occurred at >10% incidence across all breast cancers; however, there were numerous subtype-associated and novel gene mutations including the enrichment of specific mutations in GATA3, PIK3CA and MAP3K1 with the luminal A subtype. We identified two novel protein-expression-defined subgroups, possibly produced by stromal/microenvironmental elements, and integrated analyses identified specific signalling pathways dominant in each molecular subtype including a HER2/phosphorylated HER2/EGFR/phosphorylated EGFR signature within the HER2-enriched expression subtype. Comparison of basal-like breast tumours with high-grade serous ovarian tumours showed many molecular commonalities, indicating a related aetiology and similar therapeutic opportunities. The biological finding of the four main breast cancer subtypes caused by different subsets of genetic and epigenetic abnormalities raises the hypothesis that much of the clinically observable plasticity and heterogeneity occurs within, and not across, these major biological subtypes of breast cancer.

doi: 10.1038/nature11412

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宇宙:球状星団 M22 内の2つの恒星質量ブラックホール

Two stellar-mass black holes in the globular cluster M22 p.71

doi: 10.1038/nature11490

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Comet-like mineralogy of olivine crystals in an extrasolar proto-Kuiper belt p.74

doi: 10.1038/nature11469

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Stabilizing Rabi oscillations in a superconducting qubit using quantum feedback p.77

doi: 10.1038/nature11505

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Sulphate–climate coupling over the past 300,000 years in inland Antarctica p.81

doi: 10.1038/nature11359

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Natural and anthropogenic variations in methane sources during the past two millennia p.85

doi: 10.1038/nature11461

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Dynamical similarity of geomagnetic field reversals p.89

doi: 10.1038/nature11491

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A Silurian armoured aplacophoran and implications for molluscan phylogeny p.94

doi: 10.1038/nature11328

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A transcriptomic hourglass in plant embryogenesis p.98

doi: 10.1038/nature11394

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Pregnancy imprints regulatory memory that sustains anergy to fetal antigen p.102

doi: 10.1038/nature11462

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免疫:インフラマソームによる炎症性脂質メディエーターのin vivoでの迅速な誘導

Rapid induction of inflammatory lipid mediators by the inflammasome in vivo p.107

doi: 10.1038/nature11351

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Paramutation in Drosophila linked to emergence of a piRNA-producing locus p.112

doi: 10.1038/nature11416

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Burkitt lymphoma pathogenesis and therapeutic targets from structural and functional genomics p.116

doi: 10.1038/nature11378

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Structural basis for RNA-duplex recognition and unwinding by the DEAD-box helicase Mss116p p.121

doi: 10.1038/nature11402

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Alternating-access mechanism in conformationally asymmetric trimers of the betaine transporter BetP p.126

doi: 10.1038/nature11403

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