The effect of ancient population bottlenecks on human phenotypic variation

The origin and patterns of dispersal of anatomically modern humans are the focus of considerable debate. Global genetic analyses have argued for one single origin, placed somewhere in Africa. This scenario implies a rapid expansion, with a series of bottlenecks of small amplitude, which would have led to the observed smooth loss of genetic diversity with increasing distance from Africa. Analyses of cranial data, on the other hand, have given mixed results, and have been argued to support multiple origins of modern humans. Using a large data set of skull measurements and an analytical framework equivalent to that used for genetic data, we show that the loss in genetic diversity has been mirrored by a loss in phenotypic variability. We find evidence for an African origin, placed somewhere in the central/southern part of the continent, which harbours the highest intra-population diversity in phenotypic measurements. We failed to find evidence for a second origin, and we confirm these results on a large genetic data set. Distance from Africa accounts for an average 19-25% of heritable variation in craniometric measurements-a remarkably strong effect for phenotypic measurements known to be under selection.     

Boron and oxygen isotope evidence for recycling of subducted components over the past 2.5 Gyr

Evidence for the deep recycling of surficial materials through the Earth's mantle and their antiquity has long been sought to understand the role of subducting plates and plumes in mantle convection. Radiogenic isotope evidence for such recycling remains equivocal because the age and location of parent-daughter fractionation are not known. Conversely, while stable isotopes can provide irrefutable evidence for low-temperature fractionation, their range in most unaltered oceanic basalts is limited and the age of any variation is unconstrained. Here we show that delta(18)O ratios in basalts from the Azores are often lower than in pristine mantle. This, combined with increased Nb/B ratios and a large range in delta(11)B ratios, provides compelling evidence for the recycling of materials that had undergone fractionation near the Earth's surface. Moreover, delta(11)B is negatively correlated with (187)Os/(188)Os ratios, which extend to subchondritic values, constraining the age of the high Nb/B, (11)B-enriched endmember to be more than 2.5 billion years (Gyr) old. We infer this component to be melt- and fluid-depleted lithospheric mantle from a subducted oceanic plate, whereas other Azores basalts contain a contribution from approximately 3-Gyr-old melt-enriched basalt. We conclude that both components are most probably derived from an Archaean oceanic plate that was subducted, arguably into the deep mantle, where it was stored until thermal buoyancy caused it to rise beneath the Azores islands approximately 3 Gyr later.     

Universal physical responses to stretch in the living cell

With every beat of the heart, inflation of the lung or peristalsis of the gut, cell types of diverse function are subjected to substantial stretch. Stretch is a potent stimulus for growth, differentiation, migration, remodelling and gene expression. Here, we report that in response to transient stretch the cytoskeleton fluidizes in such a way as to define a universal response class. This finding implicates mechanisms mediated not only by specific signalling intermediates, as is usually assumed, but also by non-specific actions of a slowly evolving network of physical forces. These results support the idea that the cell interior is at once a crowded chemical space and a fragile soft material in which the effects of biochemistry, molecular crowding and physical forces are complex and inseparable, yet conspire nonetheless to yield remarkably simple phenomenological laws. These laws seem to be both universal and primitive, and thus comprise a striking intersection between the worlds of cell biology and soft matter physics.     

A human natural killer cell subset provides an innate source of IL-22 for mucosal immunity

Natural killer (NK) cells are classically viewed as lymphocytes that provide innate surveillance against virally infected cells and tumour cells through the release of cytolytic mediators and interferon (IFN)-gamma. In humans, blood CD56(dim) NK cells specialize in the lysis of cell targets. In the lymph nodes, CD56(bright) NK cells secrete IFN-gamma cooperating with dendritic cells and T cells in the generation of adaptive responses. Here we report the characterization of a human NK cell subset located in mucosa-associated lymphoid tissues, such as tonsils and Peyer's patches, which is hard-wired to secrete interleukin (IL)-22, IL-26 and leukaemia inhibitory factor. These NK cells, which we refer to as NK-22 cells, are triggered by acute exposure to IL-23. In vitro, NK-22-secreted cytokines stimulate epithelial cells to secrete IL-10, proliferate and express a variety of mitogenic and anti-apoptotic molecules. NK-22 cells are also found in mouse mucosa-associated lymphoid tissues and appear in the small intestine lamina propria during bacterial infection, suggesting that NK-22 cells provide an innate source of IL-22 that may help constrain inflammation and protect mucosal sites.     

Mass-balance ecosystem model of the East China Sea

Using the Ecopath mass-balance trophodynamic model, this paper analyzed the trophic levels, flows, food web structure and ecosystem maturity of the East China Sea, and identified ecologically important functional groups in the ecosystem. The model is based on fishery resource surveys of the East China Sea in 2000, studies on diet composition and global databases such as FishBase and the Sea Around Us Project Database. The results showed that trophic levels of the functional groups are between 2.86 and 4.37, with an average of 3.32. Anchocy (Engraulis japonicus), small fishes and benthic crustaceans such as shrimps and crabs are important groups in terms of the trophic structure and flow dynamics in the East China Sea. Energy flows of most groups are between specific trophic levels, except file fish (Thamnaconus spp.), pomfret (Pampus spp.) and cephalopods. Trophic transfer efficiency of levels II, III, IV and more than V are 11.8%, 21.1%, 17.4% and 22.1–22.5%, respectively. Effects of fishery – the largest ‘consumer’ of the ecosystem – are much stronger than those exerted by biological groups in the system. The model suggests that the current fishery can further reduce the complexity of the ecosystem. Evaluations of the system indices suggest that maturity of the ecosystem is low. The conclusion of this model indicates that it was the overfishing that caused the ecosystem of the East China Sea declined, which should be taken into account as a critical reference for fisheries management in the future.     

Reductive carboxylation supports growth in tumour cells with defective mitochondria

Mitochondrial metabolism provides precursors to build macromolecules in growing cancer cells. In normally functioning tumour cell mitochondria, oxidative metabolism of glucose- and glutamine-derived carbon produces citrate and acetyl-coenzyme A for lipid synthesis, which is required for tumorigenesis. Yet some tumours harbour mutations in the citric acid cycle (CAC) or electron transport chain (ETC) that disable normal oxidative mitochondrial function, and it is unknown how cells from such tumours generate precursors for macromolecular synthesis. Here we show that tumour cells with defective mitochondria use glutamine-dependent reductive carboxylation rather than oxidative metabolism as the major pathway of citrate formation. This pathway uses mitochondrial and cytosolic isoforms of NADP(+)/NADPH-dependent isocitrate dehydrogenase, and subsequent metabolism of glutamine-derived citrate provides both the acetyl-coenzyme A for lipid synthesis and the four-carbon intermediates needed to produce the remaining CAC metabolites and related macromolecular precursors. This reductive, glutamine-dependent pathway is the dominant mode of metabolism in rapidly growing malignant cells containing mutations in complex I or complex III of the ETC, in patient-derived renal carcinoma cells with mutations in fumarate hydratase, and in cells with normal mitochondria subjected to acute pharmacological ETC inhibition. Our findings reveal the novel induction of a versatile glutamine-dependent pathway that reverses many of the reactions of the canonical CAC, supports tumour cell growth, and explains how cells generate pools of CAC intermediates in the face of impaired mitochondrial metabolism.     

Whole-genome analysis informs breast cancer response to aromatase inhibition

To correlate the variable clinical features of oestrogen-receptor-positive breast cancer with somatic alterations, we studied pretreatment tumour biopsies accrued from patients in two studies of neoadjuvant aromatase inhibitor therapy by massively parallel sequencing and analysis. Eighteen significantly mutated genes were identified, including five genes (RUNX1, CBFB, MYH9, MLL3 and SF3B1) previously linked to haematopoietic disorders. Mutant MAP3K1 was associated with luminal A status, low-grade histology and low proliferation rates, whereas mutant TP53 was associated with the opposite pattern. Moreover, mutant GATA3 correlated with suppression of proliferation upon aromatase inhibitor treatment. Pathway analysis demonstrated that mutations in MAP2K4, a MAP3K1 substrate, produced similar perturbations as MAP3K1 loss. Distinct phenotypes in oestrogen-receptor-positive breast cancer are associated with specific patterns of somatic mutations that map into cellular pathways linked to tumour biology, but most recurrent mutations are relatively infrequent. Prospective clinical trials based on these findings will require comprehensive genome sequencing.