Call the cops p.7
The long arm of the law has reached into an investigation of alleged scientific misconduct in Italy, and should perhaps stretch still farther.
The FDA and me p.7
Medical testing firms find it is in their best interests to cooperate with regulators.
Lecture notes p.8
A physics course that hooked a generation reminds us that teachers need support.
Iran hit by drug shortage p.15
Sanctions cause increasing shortfall in medicines and vaccines.
Hominin DNA baffles experts p.16
Analysis of oldest sequence from a human ancestor suggests link to mystery population.
Image search triggers Italian police probe p.18
Method for checking global literature leads to investigation of cancer researcher.
Bacteria evade detection net p.19
Slothful response from regulators and manufacturers means antibiotic resistance is missed.
Museums hunt for relics from genomics’ early days p.20
Collectors band together to salvage cast-off equipment.
Global health: One million deaths p.22
Geology: North America's broken heart p.24
News & Views
Planetary science: Shadows cast on Moon's origin p.90
Stem cells: Dual response to Ras mutation p.91
Astrophysics: Magnetic fields in γ-ray bursts p.92
Structural biology: Ion channel seen by electron microscopy p.93
Nobel 2013: Chemistry: Methods for computational chemistry p.96
ノーベル化学賞は複雑な化学反応系のためのマルチスケールモデルの開発に対して、Martin Karplus、Michael Levitt、 Arieh Warshelの3氏に贈られた。
Nobel 2013: Economics: Predicting asset prices p.97
今年のアルフレッド・ノーベル記念経済学スウェーデン国立銀行賞は、資産価格の実証分析が市場の動向についての理解を進めたことを評価して、Eugene F Fama、Lars Peter Hansen、Robert J Shillerの3氏に贈呈された。
Nobel 2013: Physiology or medicine: Traffic control system within cells p.98
今年のノーベル医学生理学賞はRandy W Schekman、James E Rothman、Thomas C Südhofの3氏が受賞した。受賞理由は、細胞内で産生された大量の分子を適切なタイミングで目的地に間違いなく輸送する仕組みの解明である。
Nobel 2013: Physics: Endowing particles with mass p.99
ノーベル物理学賞は、基本粒子に質量を与える仕組みを理論的に明らかにしたFrançois Englert 、Peter W Higgsの両氏に贈られた。
Activation and allosteric modulation of a muscarinic acetylcholine receptor p.101
Very little is known about how a G-protein-coupled receptor (GPCR) transitions from an inactive to an active state, but this study has solved the X-ray crystal structures of the human M2 muscarinic acetylcholine receptor bound to a high-affinity agonist in an active state and to a high-affinity agonist and a small-molecule allosteric modulator in an active state; the structures provide insights into the activation mechanism and allosteric modulation of muscarinic receptors.
Structure of the TRPV1 ion channel determined by electron cryo-microscopy p.107
A high-resolution electron cryo-microscopy structure of the rat transient receptor potential (TRP) channel TRPV1 in its ‘closed’ state is presented; the overall structure of this ion channel is found to share some common features with voltage-gated ion channels, although several unique, TRP-specific features are also characterized.
TRPV1 structures in distinct conformations reveal activation mechanisms p.113
Using a peptide toxin and small vanilloid agonists as pharmacological probes, high-resolution electron cryo-microscopy structures of rat TRPV1–ligand complexes are solved; these structures highlight conformational differences between TRP and voltage-gated ion channels in their active states, and suggest a dual gating mechanism that may account for the ability of members of the TRP channel superfamily to integrate diverse physiological signals.
Highly polarized light from stable ordered magnetic fields in GRB 120308A p.119
After the initial burst of γ-rays that defines a γ-ray burst (GRB), expanding ejecta collide with the circumburst medium and begin to decelerate at the onset of the afterglow, during which a forward shock travels outwards and a reverse shock propagates backwards into the oncoming collimated flow, or ‘jet’. Light from the reverse shock should be highly polarized if the jet’s magnetic field is globally ordered and advected from the central engine, with a position angle that is predicted to remain stable in magnetized baryonic jet models or vary randomly with time if the field is produced locally by plasma or magnetohydrodynamic instabilities. Degrees of linear polarization of P ≈ 10 per cent in the optical band have previously been detected in the early afterglow, but the lack of temporal measurements prevented definitive tests of competing jet models. Hours to days after the γ-ray burst, polarization levels are low (P < 4 per cent), when emission from the shocked ambient medium dominates. Here we report the detection of P = per cent in the immediate afterglow of Swift γ-ray burst GRB 120308A, four minutes after its discovery in the γ-ray band, decreasing to P = per cent over the subsequent ten minutes. The polarization position angle remains stable, changing by no more than 15 degrees over this time, with a possible trend suggesting gradual rotation and ruling out plasma or magnetohydrodynamic instabilities. Instead, the polarization properties show that GRBs contain magnetized baryonic jets with large-scale uniform fields that can survive long after the initial explosion.
Olivine in an unexpected location on Vesta’s surface p.122
Olivine is a major component of the mantle of differentiated bodies, including Earth. Howardite, eucrite and diogenite (HED) meteorites represent regolith, basaltic-crust, lower-crust and possibly ultramafic-mantle samples of asteroid Vesta, which is the lone surviving, large, differentiated, basaltic rocky protoplanet in the Solar System. Only a few of these meteorites, the orthopyroxene-rich diogenites, contain olivine, typically with a concentration of less than 25 per cent by volume. Olivine was tentatively identified on Vesta, on the basis of spectral and colour data, but other observations did not confirm its presence. Here we report that olivine is indeed present locally on Vesta’s surface but that, unexpectedly, it has not been found within the deep, south-pole basins, which are thought to be excavated mantle rocks. Instead, it occurs as near-surface materials in the northern hemisphere. Unlike the meteorites, the olivine-rich (more than 50 per cent by volume) material is not associated with diogenite but seems to be mixed with howardite, the most common surface material. Olivine is exposed in crater walls and in ejecta scattered diffusely over a broad area. The size of the olivine exposures and the absence of associated diogenite favour a mantle source, but the exposures are located far from the deep impact basins. The amount and distribution of observed olivine-rich material suggest a complex evolutionary history for Vesta.
Late-twentieth-century emergence of the El Niño propagation asymmetry and future projections p.126
The El Niño/Southern Oscillation (ENSO) is the Earth’s most prominent source of interannual climate variability, exerting profound worldwide effects. Despite decades of research, its behaviour continues to challenge scientists. In the eastern equatorial Pacific Ocean, the anomalously cool sea surface temperatures (SSTs) found during La Niña events and the warm waters of modest El Niño events both propagate westwards, as in the seasonal cycle. In contrast, SST anomalies propagate eastwards during extreme El Niño events, prominently in the post-1976 period, spurring unusual weather events worldwide with costly consequences. The cause of this propagation asymmetry is currently unknown. Here we trace the cause of the asymmetry to the variations in upper ocean currents in the equatorial Pacific, whereby the westward-flowing currents are enhanced during La Niña events but reversed during extreme El Niño events. Our results highlight that propagation asymmetry is favoured when the westward mean equatorial currents weaken, as is projected to be the case under global warming. By analysing past and future climate simulations of an ensemble of models with more realistic propagation, we find a doubling in the occurrences of El Niño events that feature prominent eastward propagation characteristics in a warmer world. Our analysis thus suggests that more frequent emergence of propagation asymmetry will be an indication of the Earth’s warming climate.
Foundering of lower island-arc crust as an explanation for the origin of the continental Moho p.131
A long-standing theory for the genesis of continental crust is that it is formed in subduction zones. However, the observed seismic properties of lower crust and upper mantle in oceanic island arcs differ significantly from those in the continental crust. Accordingly, significant modifications of lower arc crust must occur, if continental crust is indeed formed from island arcs. Here we investigate how the seismic characteristics of arc crust are transformed into those of the continental crust by calculating the density and seismic structure of two exposed sections of island arc (Kohistan and Talkeetna). The Kohistan crustal section is negatively buoyant with respect to the underlying depleted upper mantle at depths exceeding 40 kilometres and is characterized by a steady increase in seismic velocity similar to that observed in active arcs. In contrast, the lower Talkeetna crust is density sorted, preserving only relicts (about ten to a hundred metres thick) of rock with density exceeding that of the underlying mantle. Specifically, the foundering of the lower Talkeetna crust resulted in the replacement of dense mafic and ultramafic cumulates by residual upper mantle, producing a sharp seismic discontinuity at depths of around 38 to 42 kilometres, characteristic of the continental Mohorovičić discontinuity (the Moho). Dynamic calculations indicate that foundering is an episodic process that occurs in most arcs with a periodicity of half a million to five million years. Moreover, because foundering will continue after arc magmatism ceases, this process ultimately results in the formation of the continental Moho.
Genetic incompatibilities are widespread within species p.135
The importance of epistasis—non-additive interactions between alleles—in shaping population fitness has long been a controversial topic, hampered in part by lack of empirical evidence. Traditionally, epistasis is inferred on the basis of non-independence of genotypic values between loci for a given trait. However, epistasis for fitness should also have a genomic footprint. To capture this signal, we have developed a simple approach that relies on detecting genotype ratio distortion as a sign of epistasis, and we apply this method to a large panel of Drosophila melanogaster recombinant inbred lines. Here we confirm experimentally that instances of genotype ratio distortion represent loci with epistatic fitness effects; we conservatively estimate that any two haploid genomes in this study are expected to harbour 1.15 pairs of epistatically interacting alleles. This observation has important implications for speciation genetics, as it indicates that the raw material to drive reproductive isolation is segregating contemporaneously within species and does not necessarily require, as proposed by the Dobzhansky–Muller model, the emergence of incompatible mutations independently derived and fixed in allopatry. The relevance of our result extends beyond speciation, as it demonstrates that epistasis is widespread but that it may often go undetected owing to lack of statistical power or lack of genome-wide scope of the experiments.
A melanocyte lineage program confers resistance to MAP kinase pathway inhibition p.138
Malignant melanomas harbouring point mutations (Val600Glu) in the serine/threonine-protein kinase BRAF (BRAF(V600E)) depend on RAF–MEK–ERK signalling for tumour cell growth. RAF and MEK inhibitors show remarkable clinical efficacy in BRAF(V600E) melanoma; however, resistance to these agents remains a formidable challenge. Global characterization of resistance mechanisms may inform the development of more effective therapeutic combinations. Here we carried out systematic gain-of-function resistance studies by expressing more than 15,500 genes individually in a BRAF(V600E) melanoma cell line treated with RAF, MEK, ERK or combined RAF–MEK inhibitors. These studies revealed a cyclic-AMP-dependent melanocytic signalling network not previously associated with drug resistance, including G-protein-coupled receptors, adenyl cyclase, protein kinase A and cAMP response element binding protein (CREB). Preliminary analysis of biopsies from BRAF(V600E) melanoma patients revealed that phosphorylated (active) CREB was suppressed by RAF–MEK inhibition but restored in relapsing tumours. Expression of transcription factors activated downstream of MAP kinase and cAMP pathways also conferred resistance, including c-FOS, NR4A1, NR4A2 and MITF. Combined treatment with MAPK-pathway and histone-deacetylase inhibitors suppressed MITF expression and cAMP-mediated resistance. Collectively, these data suggest that oncogenic dysregulation of a melanocyte lineage dependency can cause resistance to RAF–MEK–ERK inhibition, which may be overcome by combining signalling- and chromatin-directed therapeutics.
Oncogenic Nras has bimodal effects on stem cells that sustainably increase competitiveness p.143
‘Pre-leukaemic’ mutations are thought to promote clonal expansion of haematopoietic stem cells (HSCs) by increasing self-renewal and competitiveness; however, mutations that increase HSC proliferation tend to reduce competitiveness and self-renewal potential, raising the question of how a mutant HSC can sustainably outcompete wild-type HSCs. Activating mutations in NRAS are prevalent in human myeloproliferative neoplasms and leukaemia. Here we show that a single allele of oncogenic NrasG12D increases HSC proliferation but also increases reconstituting and self-renewal potential upon serial transplantation in irradiated mice, all prior to leukaemia initiation. NrasG12D also confers long-term self-renewal potential to multipotent progenitors. To explore the mechanism by which NrasG12D promotes HSC proliferation and self-renewal, we assessed cell-cycle kinetics using H2B–GFP label retention and 5-bromodeoxyuridine (BrdU) incorporation. NrasG12D had a bimodal effect on HSCs, increasing the frequency with which some HSCs divide and reducing the frequency with which others divide. This mirrored bimodal effects on reconstituting potential, as rarely dividing NrasG12D HSCs outcompeted wild-type HSCs, whereas frequently dividing NrasG12D HSCs did not. NrasG12D caused these effects by promoting STAT5 signalling, inducing different transcriptional responses in different subsets of HSCs. One signal can therefore increase HSC proliferation, competitiveness and self-renewal through bimodal effects on HSC gene expression, cycling and reconstituting potential.
The protein quality control system manages plant defence compound synthesis p.148
Jasmonates are ubiquitous oxylipin-derived phytohormones that are essential in the regulation of many development, growth and defence processes. Across the plant kingdom, jasmonates act as elicitors of the production of bioactive secondary metabolites that serve in defence against attackers. Knowledge of the conserved jasmonate perception and early signalling machineries is increasing, but the downstream mechanisms that regulate defence metabolism remain largely unknown. Here we show that, in the legume Medicago truncatula, jasmonate recruits the endoplasmic-reticulum-associated degradation (ERAD) quality control system to manage the production of triterpene saponins, widespread bioactive compounds that share a biogenic origin with sterols. An ERAD-type RING membrane-anchor E3 ubiquitin ligase is co-expressed with saponin synthesis enzymes to control the activity of 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR), the rate-limiting enzyme in the supply of the ubiquitous terpene precursor isopentenyl diphosphate. Thus, unrestrained bioactive saponin accumulation is prevented and plant development and integrity secured. This control apparatus is equivalent to the ERAD system that regulates sterol synthesis in yeasts and mammals but that uses distinct E3 ubiquitin ligases, of the HMGR degradation 1 (HRD1) type, to direct destruction of HMGR. Hence, the general principles for the management of sterol and triterpene saponin biosynthesis are conserved across eukaryotes but can be controlled by divergent regulatory cues.
Histone deacetylase 3 coordinates commensal-bacteria-dependent intestinal homeostasis p.153
The development and severity of inflammatory bowel diseases and other chronic inflammatory conditions can be influenced by host genetic and environmental factors, including signals derived from commensal bacteria. However, the mechanisms that integrate these diverse cues remain undefined. Here we demonstrate that mice with an intestinal epithelial cell (IEC)-specific deletion of the epigenome-modifying enzyme histone deacetylase 3 (HDAC3ΔIEC mice) exhibited extensive dysregulation of IEC-intrinsic gene expression, including decreased basal expression of genes associated with antimicrobial defence. Critically, conventionally housed HDAC3ΔIEC mice demonstrated loss of Paneth cells, impaired IEC function and alterations in the composition of intestinal commensal bacteria. In addition, HDAC3ΔIEC mice showed significantly increased susceptibility to intestinal damage and inflammation, indicating that epithelial expression of HDAC3 has a central role in maintaining intestinal homeostasis. Re-derivation of HDAC3ΔIEC mice into germ-free conditions revealed that dysregulated IEC gene expression, Paneth cell homeostasis and intestinal barrier function were largely restored in the absence of commensal bacteria. Although the specific mechanisms through which IEC-intrinsic HDAC3 expression regulates these complex phenotypes remain to be determined, these data indicate that HDAC3 is a critical factor that integrates commensal-bacteria-derived signals to calibrate epithelial cell responses required to establish normal host–commensal relationships and maintain intestinal homeostasis.
Immunosuppressive CD71+ erythroid cells compromise neonatal host defence against infection p.158
Newborn infants are highly susceptible to infection. This defect in host defence has generally been ascribed to the immaturity of neonatal immune cells; however, the degree of hyporesponsiveness is highly variable and depends on the stimulation conditions. These discordant responses illustrate the need for a more unified explanation for why immunity is compromised in neonates. Here we show that physiologically enriched CD71+ erythroid cells in neonatal mice and human cord blood have distinctive immunosuppressive properties. The production of innate immune protective cytokines by adult cells is diminished after transfer to neonatal mice or after co-culture with neonatal splenocytes. Neonatal CD71+ cells express the enzyme arginase-2, and arginase activity is essential for the immunosuppressive properties of these cells because molecular inhibition of this enzyme or supplementation with l-arginine overrides immunosuppression. In addition, the ablation of CD71+ cells in neonatal mice, or the decline in number of these cells as postnatal development progresses parallels the loss of suppression, and restored resistance to the perinatal pathogens Listeria monocytogenes and Escherichia coli. However, CD71+ cell-mediated susceptibility to infection is counterbalanced by CD71+ cell-mediated protection against aberrant immune cell activation in the intestine, where colonization with commensal microorganisms occurs swiftly after parturition. Conversely, circumventing such colonization by using antimicrobials or gnotobiotic germ-free mice overrides these protective benefits. Thus, CD71+ cells quench the excessive inflammation induced by abrupt colonization with commensal microorganisms after parturition. This finding challenges the idea that the susceptibility of neonates to infection reflects immune-cell-intrinsic defects and instead highlights processes that are developmentally more essential and inadvertently mitigate innate immune protection. We anticipate that these results will spark renewed investigation into the need for immunosuppression in neonates, as well as improved strategies for augmenting host defence in this vulnerable population.
EHMT1 controls brown adipose cell fate and thermogenesis through the PRDM16 complex p.163
Brown adipose tissue (BAT) dissipates chemical energy in the form of heat as a defence against hypothermia and obesity. Current evidence indicates that brown adipocytes arise from Myf5+ dermotomal precursors through the action of PR domain containing protein 16 (PRDM16) transcriptional complex. However, the enzymatic component of the molecular switch that determines lineage specification of brown adipocytes remains unknown. Here we show that euchromatic histone-lysine N-methyltransferase 1 (EHMT1) is an essential BAT-enriched lysine methyltransferase in the PRDM16 transcriptional complex and controls brown adipose cell fate. Loss of EHMT1 in brown adipocytes causes a severe loss of brown fat characteristics and induces muscle differentiation in vivo through demethylation of histone 3 lysine 9 (H3K9me2 and 3) of the muscle-selective gene promoters. Conversely, EHMT1 expression positively regulates the BAT-selective thermogenic program by stabilizing the PRDM16 protein. Notably, adipose-specific deletion of EHMT1 leads to a marked reduction of BAT-mediated adaptive thermogenesis, obesity and systemic insulin resistance. These data indicate that EHMT1 is an essential enzymatic switch that controls brown adipose cell fate and energy homeostasis.
Structural basis for the modular recognition of single-stranded RNA by PPR proteins p.168
Pentatricopeptide repeat (PPR) proteins represent a large family of sequence-specific RNA-binding proteins that are involved in multiple aspects of RNA metabolism. PPR proteins, which are found in exceptionally large numbers in the mitochondria and chloroplasts of terrestrial plants, recognize single-stranded RNA (ssRNA) in a modular fashion. The maize chloroplast protein PPR10 binds to two similar RNA sequences from the ATPI–ATPH and PSAJ–RPL33 intergenic regions, referred to as ATPH and PSAJ, respectively. By protecting the target RNA elements from 5′ or 3′ exonucleases, PPR10 defines the corresponding 5′ and 3′ messenger RNA termini. Despite rigorous functional characterizations, the structural basis of sequence-specific ssRNA recognition by PPR proteins remains to be elucidated. Here we report the crystal structures of PPR10 in RNA-free and RNA-bound states at resolutions of 2.85 and 2.45 Å, respectively. In the absence of RNA binding, the nineteen repeats of PPR10 are assembled into a right-handed superhelical spiral. PPR10 forms an antiparallel, intertwined homodimer and exhibits considerable conformational changes upon binding to its target ssRNA, an 18-nucleotide PSAJ element. Six nucleotides of PSAJ are specifically recognized by six corresponding PPR10 repeats following the predicted code. The molecular basis for the specific and modular recognition of RNA bases A, G and U is revealed. The structural elucidation of RNA recognition by PPR proteins provides an important framework for potential biotechnological applications of PPR proteins in RNA-related research areas.
Structure of LIMP-2 provides functional insights with implications for SR-BI and CD36 p.172
Members of the CD36 superfamily of scavenger receptor proteins are important regulators of lipid metabolism and innate immunity. They recognize normal and modified lipoproteins, as well as pathogen-associated molecular patterns. The family consists of three members: SR-BI (which delivers cholesterol to the liver and steroidogenic organs and is a co-receptor for hepatitis C virus), LIMP-2/LGP85 (which mediates lysosomal delivery of β-glucocerebrosidase and serves as a receptor for enterovirus 71 and coxsackieviruses) and CD36 (a fatty-acid transporter and receptor for phagocytosis of effete cells and Plasmodium-infected erythrocytes). Notably, CD36 is also a receptor for modified lipoproteins and β-amyloid, and has been implicated in the pathogenesis of atherosclerosis and of Alzheimer’s disease. Despite their prominent roles in health and disease, understanding the function and abnormalities of the CD36 family members has been hampered by the paucity of information about their structure. Here we determine the crystal structure of LIMP-2 and infer, by homology modelling, the structure of SR-BI and CD36. LIMP-2 shows a helical bundle where β-glucocerebrosidase binds, and where ligands are most likely to bind to SR-BI and CD36. Remarkably, the crystal structure also shows the existence of a large cavity that traverses the entire length of the molecule. Mutagenesis of SR-BI indicates that the cavity serves as a tunnel through which cholesterol(esters) are delivered from the bound lipoprotein to the outer leaflet of the plasma membrane. We provide evidence supporting a model whereby lipidic constituents of the ligands attached to the receptor surface are handed off to the membrane through the tunnel, accounting for the selective lipid transfer characteristic of SR-BI and CD36.