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Climate scienceThe aerosol effect p.40

Anthropogenic aerosols in the atmosphere undoubtedly influence climate. But do the approaches taken in climate models to account for the effects of aerosols provide meaningful estimates of those effects? Two climate scientists offer their opinions.

Bjorn Stevens & Olivier Boucher

doi: 10.1038/490040a

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Mucosal immunologyInfection induces friendly fire p.41

Our immune system usually ignores 'friendly' gut bacteria. But when infection with a pathogen damages the intestine's mucosal lining, the resident microbes can invade the body, inducing immune responses directed at themselves.

doi: 10.1038/490041a

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Quantum physicsCruise control for a qubit p.43

Continuous feedback control — monitoring a system and adjusting its dynamics — is widely used to keep systems 'on track'. This approach has now been used to maintain the cycling of a quantum bit almost indefinitely. See Letter p.77

Howard M. Wiseman

doi: 10.1038/490043a

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GenomicsResident risks p.44

An innovative method for probing the genomes of the vast community of microorganisms that inhabit the human gut provides an alternative approach to identifying risk factors for type 2 diabetes. See Letter p.55

Julia Oh & Julia A. Segre

doi: 10.1038/490044a

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ImmunologyTolerating pregnancy p.47

The activity of specific suppressive immune cells, some of which persist to aid subsequent pregnancies, helps to explain how a pregnant female's immune system tolerates fetal antigens inherited from the father. See Letter p.102

Alexander G. Betz

doi: 10.1038/490047a

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Articles

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.

Guofan Zhang, Xiaodong Fang, Ximing Guo, Li Li, Ruibang Luo, Fei Xu, Pengcheng Yang, Linlin Zhang, Xiaotong Wang, Haigang Qi + et al.

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.

Junjie Qin, Yingrui Li, Zhiming Cai, Shenghui Li, Jianfeng Zhu, Fan Zhang, Suisha Liang, Wenwei Zhang, Yuanlin Guan, Dongqian Shen + et al.

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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Letters

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

Roland Schmitz, Ryan M. Young, Michele Ceribelli, Sameer Jhavar, Wenming Xiao, Meili Zhang, George Wright, Arthur L. Shaffer, Daniel J. Hodson, Eric Buras + et al.

doi: 10.1038/nature11378

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