Forensics fiasco p.5

doi: 10.1038/500005b

The test for Abenomics p.5

doi: 10.1038/500005a

Labs vie for X-ray source p.13

doi: 10.1038/500013a

NIH mulls rules for validating key results p.14

doi: 10.1038/500014a

Microbiome research goes without a home p.16

doi: 10.1038/500016a

Pilot projects bury carbon dioxide in basalt p.18

doi: 10.1038/500018a

The milk revolution p.20

doi: 10.1038/500020a

On with their heads p.32

doi: 10.1038/nature12458

Unequal equinoxes p.33

doi: 10.1038/nature12456

From big data to mechanism p.34

doi: 10.1038/nature12457

Spot the gorilla p.36

doi: 10.1038/500036a

Tiny thermometers used in living cells p.36

doi: 10.1038/500036b

Angiogenic awakening p.37

doi: 10.1038/nature12459

Myc-driven endogenous cell competition in the early mammalian embryo p.39

doi: 10.1038/nature12389

Integrative genomics identifies APOE ε4 effectors in Alzheimer's disease p.45

doi: 10.1038/nature12415

An age difference of two billion years between a metal-rich and a metal-poor globular cluster p.51

Globular clusters trace the formation history of the spheroidal components of our Galaxy and other galaxies, which represent the bulk of star formation over the history of the Universe. The clusters exhibit a range of metallicities (abundances of elements heavier than helium), with metal-poor clusters dominating the stellar halo of the Galaxy, and higher-metallicity clusters found within the inner Galaxy, associated with the stellar bulge, or the thick disk. Age differences between these clusters can indicate the sequence in which the components of the Galaxy formed, and in particular which clusters were formed outside the Galaxy and were later engulfed along with their original host galaxies, and which were formed within it. Here we report an absolute age of 9.9 ± 0.7 billion years (at 95 per cent confidence) for the metal-rich globular cluster 47 Tucanae, determined by modelling the properties of the cluster’s white-dwarf cooling sequence. This is about two billion years younger than has been inferred for the metal-poor cluster NGC 6397 from the same models, and provides quantitative evidence that metal-rich clusters like 47 Tucanae formed later than metal-poor halo clusters like NGC 6397.

doi: 10.1038/nature12334

Nanometre-scale thermometry in a living cell p.54

Sensitive probing of temperature variations on nanometre scales is an outstanding challenge in many areas of modern science and technology. In particular, a thermometer capable of subdegree temperature resolution over a large range of temperatures as well as integration within a living system could provide a powerful new tool in many areas of biological, physical and chemical research. Possibilities range from the temperature-induced control of gene expression and tumour metabolism to the cell-selective treatment of disease and the study of heat dissipation in integrated circuits. By combining local light-induced heat sources with sensitive nanoscale thermometry, it may also be possible to engineer biological processes at the subcellular level. Here we demonstrate a new approach to nanoscale thermometry that uses coherent manipulation of the electronic spin associated with nitrogen–vacancy colour centres in diamond. Our technique makes it possible to detect temperature variations as small as 1.8 mK (a sensitivity of 9 mK Hz−1/2) in an ultrapure bulk diamond sample. Using nitrogen–vacancy centres in diamond nanocrystals (nanodiamonds), we directly measure the local thermal environment on length scales as short as 200 nanometres. Finally, by introducing both nanodiamonds and gold nanoparticles into a single human embryonic fibroblast, we demonstrate temperature-gradient control and mapping at the subcellular level, enabling unique potential applications in life sciences.

doi: 10.1038/nature12373

Stretchable nanoparticle conductors with self-organized conductive pathways p.59

Research in stretchable conductors is fuelled by diverse technological needs. Flexible electronics, neuroprosthetic and cardiostimulating implants, soft robotics and other curvilinear systems require materials with high conductivity over a tensile strain of 100 per cent (refs 1, 2, 3). Furthermore, implantable devices or stretchable displays need materials with conductivities a thousand times higher while retaining a strain of 100 per cent. However, the molecular mechanisms that operate during material deformation and stiffening make stretchability and conductivity fundamentally difficult properties to combine. The macroscale stretching of solids elongates chemical bonds, leading to the reduced overlap and delocalization of electronic orbitals. This conductivity–stretchability dilemma can be exemplified by liquid metals, in which conduction pathways are retained on large deformation but weak interatomic bonds lead to compromised strength. The best-known stretchable conductors use polymer matrices containing percolated networks of high-aspect-ratio nanometre-scale tubes or nanowires to address this dilemma to some extent. Further improvements have been achieved by using fillers (the conductive component) with increased aspect ratio, of all-metallic composition, or with specific alignment (the way the fillers are arranged in the matrix). However, the synthesis and separation of high-aspect-ratio fillers is challenging, stiffness increases with the volume content of metallic filler, and anisotropy increases with alignment. Pre-strained substrates, buckled microwires and three-dimensional microfluidic polymer networks have also been explored. Here we demonstrate stretchable conductors of polyurethane containing spherical nanoparticles deposited by either layer-by-layer assembly or vacuum-assisted flocculation. High conductivity and stretchability were observed in both composites despite the minimal aspect ratio of the nanoparticles. These materials also demonstrate the electronic tunability of mechanical properties, which arise from the dynamic self-organization of the nanoparticles under stress. A modified percolation theory incorporating the self-assembly behaviour of nanoparticles gave an excellent match with the experimental data.

doi: 10.1038/nature12401

Seasonal sea surface cooling in the equatorial Pacific cold tongue controlled by ocean mixing p.64

Sea surface temperature (SST) is a critical control on the atmosphere, and numerical models of atmosphere–ocean circulation emphasize its accurate prediction. Yet many models demonstrate large, systematic biases in simulated SST in the equatorial ‘cold tongues’ (expansive regions of net heat uptake from the atmosphere) of the Atlantic and Pacific oceans, particularly with regard to a central but little-understood feature of tropical oceans: a strong seasonal cycle. The biases may be related to the inability of models to constrain turbulent mixing realistically, given that turbulent mixing, combined with seasonal variations in atmospheric heating, determines SST. In temperate oceans, the seasonal SST cycle is clearly related to varying solar heating; in the tropics, however, SSTs vary seasonally in the absence of similar variations in solar inputs. Turbulent mixing has long been a likely explanation, but firm, long-term observational evidence has been absent. Here we show the existence of a distinctive seasonal cycle of subsurface cooling via mixing in the equatorial Pacific cold tongue, using multi-year measurements of turbulence in the ocean. In boreal spring, SST rises by 2 kelvin when heating of the upper ocean by the atmosphere exceeds cooling by mixing from below. In boreal summer, SST decreases because cooling from below exceeds heating from above. When the effects of lateral advection are considered, the magnitude of summer cooling via mixing (4 kelvin per month) is equivalent to that required to counter the heating terms. These results provide quantitative assessment of how mixing varies on timescales longer than a few weeks, clearly showing its controlling influence on seasonal cooling of SST in a critical oceanic regime.

doi: 10.1038/nature12363

Feeding andesitic eruptions with a high-speed connection from the mantle p.68

Convergent margin volcanism is ultimately fed by magmas generated in the mantle, but the connection between the mantle and the eruption at the surface is typically obscured by cooling, crystallization and magma mixing within the crust. Geophysical techniques are also not very effective in the lower and middle crust, where seismic events are rare and resolution is generally poor. It has thus been unclear how fast mantle-derived magmas transit the crust and recharge crustal magma chambers. Here we use diffusion modelling of nickel zonation profiles in primitive olivines from diverse primary melts to show how mantle recharge may occur on timescales as short as eruptions themselves. In Irazú volcano in Costa Rica, magmas apparently ascend from their source region in the mantle through crust about 35 kilometres thick in just months to years, recharging hybrid basaltic andesites over the course of the eruption. These results show that large stratovolcanoes with shallow magma chambers may still preserve the deep record of their mantle origin in olivine crystals. This approach—documenting magma ascent timescales from the mantle beneath a convergent margin stratovolcano—can be applied to other eruptions that record magma mixing with recharge melts. Signs of volcanic unrest are typically monitored at the surface or upper crust; new efforts should look deeper, tracking magma movement from the base of the crust to the surface in the months to years before eruptions.

doi: 10.1038/nature12342

The molecular logic for planarian regeneration along the anterior–posterior axis p.73

The planarian Dugesia japonica can regenerate a complete individual from a head, trunk or tail fragment via activation of somatic pluripotent stem cells. About a century ago, Thomas Hunt Morgan attempted to explain the extraordinary regenerative ability of planarians by positing two opposing morphogenetic gradients of formative “head stuff” and “tail stuff” along the anterior–posterior axis. However, Morgan’s hypothesis remains open to debate. Here we show that extracellular signal-related kinase (ERK) and Wnt/β-catenin signalling pathways establish a solid framework for planarian regeneration. Our data suggest that ERK signalling forms a spatial gradient in the anterior region during regeneration. The fibroblast growth factor receptor-like gene nou-darake (which serves as an output of ERK signalling in the differentiating head) and posteriorly biased β-catenin activity negatively regulate ERK signalling along the anterior–posterior axis in distinct manners, and thereby posteriorize regenerating tissues outside the head region to reconstruct a complete head-to-tail axis. On the basis of this knowledge about D. japonica, we proposed that β-catenin signalling is responsible for the lack of head-regenerative ability of tail fragments in the planarian Phagocata kawakatsui, and our confirmation thereof supports the notion that posterior β-catenin signalling negatively modulates the ERK signalling involved in anteriorization across planarian species. These findings suggest that ERK signalling has a pivotal role in triggering globally dynamic differentiation of stem cells in a head-to-tail sequence through a default program that promotes head tissue specification in the absence of posteriorizing signals. Thus, we have confirmed the broad outline of Morgan’s hypothesis, and refined it on the basis of our proposed default property of planarian stem cells.

doi: 10.1038/nature12359

Restoration of anterior regeneration in a planarian with limited regenerative ability p.77

Variability of regenerative potential among animals has long perplexed biologists. On the basis of their exceptional regenerative abilities, planarians have become important models for understanding the molecular basis of regeneration. However, planarian species with limited regenerative abilities are also found. Despite the importance of understanding the differences between closely related, regenerating and non-regenerating organisms, few studies have focused on the evolutionary loss of regeneration, and the molecular mechanisms leading to such regenerative loss remain obscure. Here we examine Procotyla fluviatilis, a planarian with restricted ability to replace missing tissues, using next-generation sequencing to define the gene expression programs active in regeneration-permissive and regeneration-deficient tissues. We found that Wnt signalling is aberrantly activated in regeneration-deficient tissues. Notably, downregulation of canonical Wnt signalling in regeneration-deficient regions restores regenerative abilities: blastemas form and new heads regenerate in tissues that normally never regenerate. This work reveals that manipulating a single signalling pathway can reverse the evolutionary loss of regenerative potential.

doi: 10.1038/nature12403

Reactivating head regrowth in a regeneration-deficient planarian species p.81

Species capable of regenerating lost body parts occur throughout the animal kingdom, yet close relatives are often regeneration incompetent. Why in the face of ‘survival of the fittest’ some animals regenerate but others do not remains a fascinating question. Planarian flatworms are well known and studied for their ability to regenerate from minute tissue pieces, yet species with limited regeneration abilities have been described even amongst planarians. Here we report the characterization of the regeneration defect in the planarian Dendrocoelum lacteum and its successful rescue. Tissue fragments cut from the posterior half of the body of this species are unable to regenerate a head and ultimately die. We find that this defect originates during the early stages of head specification, which require inhibition of canonical Wnt signalling in other planarian species. Notably, RNA interference (RNAi)-mediated knockdown of Dlac-β-catenin-1, the Wnt signal transducer, restored the regeneration of fully functional heads on tail pieces, rescuing D. lacteum’s regeneration defect. Our results demonstrate the utility of comparative studies towards the reactivation of regenerative abilities in regeneration-deficient animals. Furthermore, the availability of D. lacteum as a regeneration-impaired planarian model species provides a first step towards elucidating the evolutionary mechanisms that ultimately determine why some animals regenerate and others do not.

doi: 10.1038/nature12414

Dual-mode operation of neuronal networks involved in left–right alternation p.85

All forms of locomotion are repetitive motor activities that require coordinated bilateral activation of muscles. The executive elements of locomotor control are networks of spinal neurons that determine gait pattern through the sequential activation of motor-neuron pools on either side of the body axis. However, little is known about the constraints that link left–right coordination to locomotor speed. Recent advances have indicated that both excitatory and inhibitory commissural neurons may be involved in left–right coordination. But the neural underpinnings of this, and a possible causal link between these different groups of commissural neurons and left–right alternation, are lacking. Here we show, using intersectional mouse genetics, that ablation of a group of transcriptionally defined commissural neurons—the V0 population—leads to a quadrupedal hopping at all frequencies of locomotion. The selective ablation of inhibitory V0 neurons leads to a lack of left–right pattern at low frequencies, mixed coordination at medium frequencies, and alternation at high locomotor frequencies. When ablation is targeted to excitatory V0 neurons, left–right alternation is present at low frequencies, and hopping is restricted to medium and high locomotor frequencies. Therefore, the intrinsic logic of the central control of locomotion incorporates a modular organization, with two subgroups of V0 neurons required for the existence of left–right alternating modes at different speeds of locomotion. The two molecularly distinct sets of commissural neurons may constrain species-related naturally occurring frequency-dependent coordination and be involved in the evolution of different gaits.

doi: 10.1038/nature12286

AID stabilizes stem-cell phenotype by removing epigenetic memory of pluripotency genes p.89

The activation-induced cytidine deaminase (AID; also known as AICDA) enzyme is required for somatic hypermutation and class switch recombination at the immunoglobulin locus. In germinal-centre B cells, AID is highly expressed, and has an inherent mutator activity that helps generate antibody diversity. However, AID may also regulate gene expression epigenetically by directly deaminating 5-methylcytosine in concert with base-excision repair to exchange cytosine. This pathway promotes gene demethylation, thereby removing epigenetic memory. For example, AID promotes active demethylation of the genome in primordial germ cells. However, different studies have suggested either a requirement or a lack of function for AID in promoting pluripotency in somatic nuclei after fusion with embryonic stem cells. Here we tested directly whether AID regulates epigenetic memory by comparing the relative ability of cells lacking AID to reprogram from a differentiated murine cell type to an induced pluripotent stem cell. We show that Aid-null cells are transiently hyper-responsive to the reprogramming process. Although they initiate expression of pluripotency genes, they fail to stabilize in the pluripotent state. The genome of Aid-null cells remains hypermethylated in reprogramming cells, and hypermethylated genes associated with pluripotency fail to be stably upregulated, including many MYC target genes. Recent studies identified a late step of reprogramming associated with methylation status, and implicated a secondary set of pluripotency network components. AID regulates this late step, removing epigenetic memory to stabilize the pluripotent state.

doi: 10.1038/nature12299

A stable transcription factor complex nucleated by oligomeric AML1–ETO controls leukaemogenesis p.93

Transcription factors are frequently altered in leukaemia through chromosomal translocation, mutation or aberrant expression. AML1–ETO, a fusion protein generated by the t(8;21) translocation in acute myeloid leukaemia, is a transcription factor implicated in both gene repression and activation. AML1–ETO oligomerization, mediated by the NHR2 domain, is critical for leukaemogenesis, making it important to identify co-regulatory factors that ‘read’ the NHR2 oligomerization and contribute to leukaemogenesis. Here we show that, in human leukaemic cells, AML1–ETO resides in and functions through a stable AML1–ETO-containing transcription factor complex (AETFC) that contains several haematopoietic transcription (co)factors. These AETFC components stabilize the complex through multivalent interactions, provide multiple DNA-binding domains for diverse target genes, co-localize genome wide, cooperatively regulate gene expression, and contribute to leukaemogenesis. Within the AETFC complex, AML1–ETO oligomerization is required for a specific interaction between the oligomerized NHR2 domain and a novel NHR2-binding (N2B) motif in E proteins. Crystallographic analysis of the NHR2–N2B complex reveals a unique interaction pattern in which an N2B peptide makes direct contact with side chains of two NHR2 domains as a dimer, providing a novel model of how dimeric/oligomeric transcription factors create a new protein-binding interface through dimerization/oligomerization. Intriguingly, disruption of this interaction by point mutations abrogates AML1–ETO-induced haematopoietic stem/progenitor cell self-renewal and leukaemogenesis. These results reveal new mechanisms of action of AML1–ETO, and provide a potential therapeutic target in t(8;21)-positive acute myeloid leukaemia.

doi: 10.1038/nature12287

Reshaping of the conformational search of a protein by the chaperone trigger factor p.98

Protein folding is often described as a search process, in which polypeptides explore different conformations to find their native structure. Molecular chaperones are known to improve folding yields by suppressing aggregation between polypeptides before this conformational search starts, as well as by rescuing misfolds after it ends. Although chaperones have long been speculated to also affect the conformational search itself—by reshaping the underlying folding landscape along the folding trajectory—direct experimental evidence has been scarce so far. In Escherichia coli, the general chaperone trigger factor (TF) could play such a role. TF has been shown to interact with nascent chains at the ribosome, with polypeptides released from the ribosome into the cytosol, and with fully folded proteins before their assembly into larger complexes. To investigate the effect of TF from E. coli on the conformational search of polypeptides to their native state, we investigated individual maltose binding protein (MBP) molecules using optical tweezers. Here we show that TF binds folded structures smaller than one domain, which are then stable for seconds and ultimately convert to the native state. Moreover, TF stimulates native folding in constructs of repeated MBP domains. The results indicate that TF promotes correct folding by protecting partially folded states from distant interactions that produce stable misfolded states. As TF interacts with most newly synthesized proteins in E. coli, we expect these findings to be of general importance in understanding protein folding pathways.

doi: 10.1038/nature12293

Structural basis for the inhibition of bacterial multidrug exporters p.102

The multidrug efflux transporter AcrB and its homologues are important in the multidrug resistance of Gram-negative pathogens. However, despite efforts to develop efflux inhibitors, clinically useful inhibitors are not available at present. Pyridopyrimidine derivatives are AcrB- and MexB-specific inhibitors that do not inhibit MexY; MexB and MexY are principal multidrug exporters in Pseudomonas aeruginosa. We have previously determined the crystal structure of AcrB in the absence and presence of antibiotics. Drugs were shown to be exported by a functionally rotating mechanism through tandem proximal and distal multisite drug-binding pockets. Here we describe the first inhibitor-bound structures of AcrB and MexB, in which these proteins are bound by a pyridopyrimidine derivative. The pyridopyrimidine derivative binds tightly to a narrow pit composed of a phenylalanine cluster located in the distal pocket and sterically hinders the functional rotation. This pit is a hydrophobic trap that branches off from the substrate-translocation channel. Phe 178 is located at the edge of this trap in AcrB and MexB and contributes to the tight binding of the inhibitor molecule through a π–π interaction with the pyridopyrimidine ring. The voluminous side chain of Trp 177 located at the corresponding position in MexY prevents inhibitor binding. The structure of the hydrophobic trap described in this study will contribute to the development of universal inhibitors of MexB and MexY in P. aeruginosa.

doi: 10.1038/nature12300

Unusual base pairing during the decoding of a stop codon by the ribosome p.107

During normal translation, the binding of a release factor to one of the three stop codons (UGA, UAA or UAG) results in the termination of protein synthesis. However, modification of the initial uridine to a pseudouridine (Ψ) allows efficient recognition and read-through of these stop codons by a transfer RNA (tRNA), although it requires the formation of two normally forbidden purine–purine base pairs. Here we determined the crystal structure at 3.1 Å resolution of the 30S ribosomal subunit in complex with the anticodon stem loop of tRNASer bound to the ΨAG stop codon in the A site. The ΨA base pair at the first position is accompanied by the formation of purine–purine base pairs at the second and third positions of the codon, which show an unusual Watson–Crick/Hoogsteen geometry. The structure shows a previously unsuspected ability of the ribosomal decoding centre to accommodate non-canonical base pairs.

doi: 10.1038/nature12302