|Nature - Issue - nature.com science feeds|
The Turkish government must stop university dismissals and commit itself to creating a welcoming research environment if its grand plans for science are to succeed.
A conservative solution to global warming.
Psychologists find that Internet trolls seem impervious to any efforts to change their behaviour.
As people in other nations watch the UK prepare to sever ties, Herman Goossens urges more scientists to stress what the EU does for them.
Gut microbes are important for digestion and immunity in humans— and may also be beneficial to bees.Waldan Kwong at Yale University in New Haven, Connecticut, and his colleagues hand-reared larvae of the honeybee (Apis mellifera; pictured) in the laboratory. They allowed
Helium is a famously inert element, but researchers have made a stable compound from helium and sodium.Artem Oganov at Stony Brook University in New York and his colleagues used an algorithm to look for potentially stable helium compounds and predicted that Na2He
A material can cool surfaces by dissipating heat to outer space as infrared radiation, even when the Sun is at its peak. Similar materials developed previously worked only at night, or were not cost-effective enough to make on a large scale.Xiaobo Yin and Ronggui
High levels of industrial pollution have been found in animals living in the deepest reaches of the Pacific Ocean.The production of polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs)— toxic, non-biodegradable pollutants — was phased out in the 1970s. Alan Jamieson, now at
Endangered African penguins are at risk from overfishing and climate change, which have reduced stocks of prey fish in their juvenile feeding grounds.Richard Sherley and Stephen Votier at the University of Exeter, UK, and their colleagues used satellites to track 54 juvenile African penguins
The first test of a commercial electric train using superconducting cables suggests that the technology could help a typical urban rail network to save an average of 5% in energy.Most electric railways in urban centres suffer from voltage drops because of power losses as
The malaria parasite produces a molecule that affects red blood cells, luring mosquitoes to bite infected people, and may enhance the parasite's spread.Ingrid Faye at Stockholm University and her colleagues found that the parasite Plasmodium falciparum produces a metabolite called HMBPP. This stimulates
The potential increase in air-conditioning use in a warming climate could boost the cost of meeting peak demand for electricity in the United States by up to US$180 billion by the end of the century.Maximilian Auffhammer at the University of California, Berkeley, and his
Mountain climbers tend to acclimatize to high altitudes faster during a second ascent than during the first. Red blood cells have a role in this, 'remembering' how they initially adapted to the low-oxygen conditions.Yang Xia at the University of Texas Health Science Center in
The week in science: 10–16 February 2017.
Agency narrows possible targets for the first-ever sample return from the red planet.
Initiative's first grants will fund a medley of wild ideas from top San Francisco Bay Area biologists, engineers and programmers.
Proposed solution to geometry puzzle allows an object’s structure to be determined from limited information.
International team seeks better picture of wind as it moves over rugged terrain.
Coalition of scientists and research agencies argue for a one-stop shop server.
Unstable molecule couldn’t be made through conventional synthesis, so IBM researchers carried out molecular surgery using a microscope tip.
Political upheaval threatens Turkey’s ambitious plans for research and development.
A newly unearthed article by the great politician reveals that he reasoned like a scientist about the likelihood of extraterrestrials, writes Mario Livio.
Ann Finkbeiner scrutinizes a biography of supremely inventive particle physicist Richard Garwin.
Barbara Kiser reviews five of the week's best science picks.
Roger Kneebone explores how lacemakers, glass artists and percussionists are sharing skills with researchers.
The US Department of Agriculture's sudden removal of thousands of public records relating to animal welfare, supposedly based on a“commitment to being transparent” (see go.nature.com/2ktvzhp), undermines the very purposes of the Animal Welfare Act (see Naturedoi.org/bzg3; 2017). If the department
Dramatic change can suddenly happen when there is a confluence of factors reaching a 'tipping point'— the fall of the Berlin Wall in 1989 is an example. As climate change and societal change both move towards tipping points, the crisis prompted by the election
Early-stage researchers in Denmark are particularly vulnerable to the 'creeping corporate culture' of universities (Nature540, 315;10.1038/540315a2016). Managers are tightening spending after government budget cuts last year ended individual postdoctoral grants from the Danish Council for Independent Research.Furthermore,
We disagree that a 'creeping corporate culture' is harming the University of Copenhagen (Nature540, 315;10.1038/540315a2016). Its continuous rise in the international rankings argues against this suggestion. If the art of science is indeed under corporate pressure, we should
In December 2016, Brazil's government amended its constitution to freeze public spending on biodiversity protection for the next 20 years, along with funding for scientific research, education and health care. As conservation scientists in Brazil, we believe that the country's remarkable biodiversity is an important
A pioneering cancer biologist and Renaissance man.
Creative writing can enrich scientists' research.
A way to help.
A ticket to ride.
The Editorial‘Keep science on track’ (Nature542, 137; 2017) wrongly attributed to Till Sawala and then to Nadine El-Enany the opinion that the proposed boycott of US-based conferences is intended to demonstrate against a ban that hurts everyone. The article also
In the graphic in the Comment 'Journals invite too few women to referee' ( J.Lerback aamp;amp; B.HansonNature541, 455–457; 2017 ), the bar representing the acceptance rate for male first authors in their 70s was mislabelled.
During the last ice age, huge numbers of icebergs were episodically discharged from an ice sheet that covered North America. Numerical modelling suggests that these events resulted from a conceptually simple feedback cycle. See Letter p.332
The enzyme S6K1 phosphorylates the enzyme glutamyl-prolyl tRNA synthetase to modulate metabolic activity and lifespan, revealing an atypical role for this synthetase as a target of a key metabolic signalling pathway. See Letter p.357
Technological advances have allowed scientists to sequence the complex quinoa genome. This highlights the ongoing expansion of genomics beyond major crops to other plants that have relevance for global food security. See Article p.307
One effect of weight-loss surgery is a change in food preferences. An analysis in rats shows that this is caused by altered nutrient signals in the intestine. These activate the vagus nerve to increase signalling in the brain by the neurotransmitter dopamine.
Oxygen is essential to most life in the ocean. An analysis shows that oxygen levels have declined by 2% in the global ocean over the past five decades, probably causing habitat loss for many fish and invertebrate species. See Letter p.335
An analysis of more than 2,000 species of bird provides insight into how the animals' diverse beak shapes evolved, and points to a single rare event as a trigger for the rapid initial divergence of avian lineages. See Letter p.344
Chenopodium quinoa (quinoa) is a highly nutritious grain identified as an important crop to improve world food security. Unfortunately, few resources are available to facilitate its genetic improvement. Here we report the assembly of a high-quality, chromosome-scale reference genome sequence for quinoa, which was
During puberty, the mouse mammary gland develops into a highly branched epithelial network. Owing to the absence of exclusive stem cell markers, the location, multiplicity, dynamics and fate of mammary stem cells (MaSCs), which drive branching morphogenesis, are unknown. Here we show that morphogenesis is
Spliceosome rearrangements facilitated by RNA helicase PRP16 before catalytic step two of splicing are poorly understood. Here we report a 3D cryo-electron microscopy structure of the human spliceosomal C complex stalled directly after PRP16 action (C*). The architecture of the catalytic U2–U6 ribonucleoprotein (RNP) core
The detection of infrared radiation enables night vision, health monitoring, optical communications and three-dimensional object recognition. Silicon is widely used in modern electronics, but its electronic bandgap prevents the detection of light at wavelengths longer than about 1,100 nanometres. It is therefore of interest to extend the performance of silicon photodetectors into the infrared spectrum, beyond the bandgap of silicon. Here we demonstrate a photovoltage field-effect transistor that uses silicon for charge transport, but is also sensitive to infrared light owing to the use of a quantum dot light absorber. The photovoltage generated at the interface between the silicon and the quantum dot, combined with the high transconductance provided by the silicon device, leads to high gain (more than 104 electrons per photon at 1,500 nanometres), fast time response (less than 10 microseconds) and a widely tunable spectral response. Our photovoltage field-effect transistor has a responsivity that is five orders of magnitude higher at a wavelength of 1,500 nanometres than that of previous infrared-sensitized silicon detectors. The sensitization is achieved using a room-temperature solution process and does not rely on traditional high-temperature epitaxial growth of semiconductors (such as is used for germanium and III–V semiconductors). Our results show that colloidal quantum dots can be used as an efficient platform for silicon-based infrared detection, competitive with state-of-the-art epitaxial semiconductors.
A colloidal solution is a homogeneous dispersion of particles or droplets of one phase (solute) in a second, typically liquid, phase (solvent). Colloids are ubiquitous in biological, chemical and technological processes, homogenizing highly dissimilar constituents. To stabilize a colloidal system against coalescence and aggregation, the surface of each solute particle is engineered to impose repulsive forces strong enough to overpower van der Waals attraction and keep the particles separated from each other. Electrostatic stabilization of charged solutes works well in solvents with high dielectric constants, such as water (dielectric constant of 80). In contrast, colloidal stabilization in solvents with low polarity, such as hexane (dielectric constant of about 2), can be achieved by decorating the surface of each particle of the solute with molecules (surfactants) containing flexible, brush-like chains. Here we report a class of colloidal systems in which solute particles (including metals, semiconductors and magnetic materials) form stable colloids in various molten inorganic salts. The stability of such colloids cannot be explained by traditional electrostatic and steric mechanisms. Screening of many solute–solvent combinations shows that colloidal stability can be traced to the strength of chemical bonding at the solute–solvent interface. Theoretical analysis and molecular dynamics modelling suggest that a layer of surface-bound solvent ions produces long-ranged charge-density oscillations in the molten salt around solute particles, preventing their aggregation. Colloids composed of inorganic particles in inorganic melts offer opportunities for introducing colloidal techniques to solid-state science and engineering applications.
During the last glacial period, the Laurentide Ice Sheet sporadically discharged huge numbers of icebergs through the Hudson Strait into the North Atlantic Ocean, leaving behind distinct layers of ice-rafted debris in the ocean sediments. Perplexingly, these massive discharge events—Heinrich events—occurred during the cold portion of millennial-scale climate oscillations called Dansgaard–Oeschger cycles. This is in contrast to the expectation that ice sheets expand in colder climates and shrink in warmer climates. Here we use an ice sheet model to show that the magnitude and timing of Heinrich events can be explained by the same processes that drive the retreat of modern marine-terminating glaciers. In our model, subsurface ocean warming associated with variations in the overturning circulation increases underwater melt along the calving face, triggering rapid margin retreat and increased iceberg discharge. On millennial timescales, isostatic adjustment causes the bed to uplift, isolating the terminus from subsurface warming and allowing the ice sheet to advance again until, at its most advanced position, it is poised for another Heinrich event. This mechanism not only explains the timing and magnitude of observed Heinrich events, but also suggests that ice sheets in contact with warming oceans may be vulnerable to catastrophic collapse even with little atmospheric warming.
Ocean models predict a decline in the dissolved oxygen inventory of the global ocean of one to seven per cent by the year 2100, caused by a combination of a warming-induced decline in oxygen solubility and reduced ventilation of the deep ocean. It is thought that such a decline in the oceanic oxygen content could affect ocean nutrient cycles and the marine habitat, with potentially detrimental consequences for fisheries and coastal economies. Regional observational data indicate a continuous decrease in oceanic dissolved oxygen concentrations in most regions of the global ocean, with an increase reported in a few limited areas, varying by study. Prior work attempting to resolve variations in dissolved oxygen concentrations at the global scale reported a global oxygen loss of 550 ± 130 teramoles (1012 mol) per decade between 100 and 1,000 metres depth based on a comparison of data from the 1970s and 1990s. Here we provide a quantitative assessment of the entire ocean oxygen inventory by analysing dissolved oxygen and supporting data for the complete oceanic water column over the past 50 years. We find that the global oceanic oxygen content of 227.4 ± 1.1 petamoles (1015 mol) has decreased by more than two per cent (4.8 ± 2.1 petamoles) since 1960, with large variations in oxygen loss in different ocean basins and at different depths. We suggest that changes in the upper water column are mostly due to a warming-induced decrease in solubility and biological consumption. Changes in the deeper ocean may have their origin in basin-scale multi-decadal variability, oceanic overturning slow-down and a potential increase in biological consumption.
Helium isotopes provide an important tool for tracing early-Earth, primordial reservoirs that have survived in the planet’s interior. Volcanic hotspot lavas, like those erupted at Hawaii and Iceland, can host rare, high 3He/4He isotopic ratios (up to 50 times the present atmospheric ratio, Ra) compared to the lower 3He/4He ratios identified in mid-ocean-ridge basalts that form by melting the upper mantle (about 8Ra; ref. 5). A long-standing hypothesis maintains that the high-3He/4He domain resides in the deep mantle, beneath the upper mantle sampled by mid-ocean-ridge basalts, and that buoyantly upwelling plumes from the deep mantle transport high-3He/4He material to the shallow mantle beneath plume-fed hotspots. One problem with this hypothesis is that, while some hotspots have 3He/4He values ranging from low to high, other hotspots exhibit only low 3He/4He ratios. Here we show that, among hotspots suggested to overlie mantle plumes, those with the highest maximum 3He/4He ratios have high hotspot buoyancy fluxes and overlie regions with seismic low-velocity anomalies in the upper mantle, unlike plume-fed hotspots with only low maximum 3He/4He ratios. We interpret the relationships between 3He/4He values, hotspot buoyancy flux, and upper-mantle shear wave velocity to mean that hot plumes—which exhibit seismic low-velocity anomalies at depths of 200 kilometres—are more buoyant and entrain both high-3He/4He and low-3He/4He material. In contrast, cooler, less buoyant plumes do not entrain this high-3He/4He material. This can be explained if the high-3He/4He domain is denser than low-3He/4Hemantle components hosted in plumes, and if high-3He/4He material is entrained from the deep mantle only by the hottest, most buoyant plumes. Such a dense, deep-mantle high-3He/4He domain could remain isolated from the convecting mantle, which may help to explain the preservation of early Hadean (ggt;4.5 billion years ago) geochemical anomalies in lavas sampling this reservoir.
The origin and expansion of biological diversity is regulated by both developmental trajectories and limits on available ecological niches. As lineages diversify, an early and often rapid phase of species and trait proliferation gives way to evolutionary slow-downs as new species pack into ever more densely occupied regions of ecological niche space. Small clades such as Darwin’s finches demonstrate that natural selection is the driving force of adaptive radiations, but how microevolutionary processes scale up to shape the expansion of phenotypic diversity over much longer evolutionary timescales is unclear. Here we address this problem on a global scale by analysing acrowdsourced dataset of three-dimensional scanned bill morphology from more than 2,000 species. We find that bill diversity expanded early in extant avian evolutionary history, before transitioning to a phase dominated by packing of morphological space. However, this early phenotypic diversification is decoupled from temporal variation in evolutionary rate: rates of bill evolution vary among lineages but are comparatively stable through time. We find that rare, but major, discontinuities in phenotype emerge from rapid increases in rate along single branches, sometimes leading to depauperate clades with unusual bill morphologies. Despite these jumps between groups, the major axes of within-group bill-shape evolution are remarkably consistent across birds. We reveal that macroevolutionary processes underlying global-scale adaptive radiations support Darwinian and Simpsonian ideas of microevolution within adaptive zones and accelerated evolution between distinct adaptive peaks.
Brain enlargement has been observed in children with autism spectrum disorder (ASD), but the timing of this phenomenon, and the relationship between ASD and the appearance of behavioural symptoms, are unknown. Retrospective head circumference and longitudinal brain volume studies of two-year olds followed up at four years of age have provided evidence that increased brain volume may emerge early in development. Studies of infants at high familial risk of autism can provide insight into the early development of autism and have shown that characteristic social deficits in ASD emerge during the latter part of the first and in the second year of life. These observations suggest that prospective brain-imaging studies of infants at high familial risk of ASD might identify early postnatal changes in brain volume that occur before an ASD diagnosis. In this prospective neuroimaging study of 106 infants at high familial risk of ASD and 42 low-risk infants, we show that hyperexpansion of the cortical surface area between 6 and 12 months of age precedes brain volume overgrowth observed between 12 and 24 months in 15 high-risk infants who were diagnosed with autism at 24 months. Brain volume overgrowth was linked to the emergence and severity of autistic social deficits. A deep-learning algorithm that primarily uses surface area information from magnetic resonance imaging of the brain of 6–12-month-old individuals predicted the diagnosis of autism in individual high-risk children at 24 months (with a positive predictive value of 81% and a sensitivity of 88%). These findings demonstrate that early brain changes occur during the period in which autistic behaviours are first emerging.
The mammalian liver consists of hexagon-shaped lobules that are radially polarized by blood flow and morphogens. Key liver genes have been shown to be differentially expressed along the lobule axis, a phenomenon termed zonation, but a detailed genome-wide reconstruction of this spatial division of labour has not been achieved. Here we measure the entire transcriptome of thousands of mouse liver cells and infer their lobule coordinates on the basis of a panel of zonated landmark genes, characterized with single-molecule fluorescence in situ hybridization. Using this approach, we obtain the zonation profiles of all liver genes with high spatial resolution. We find that around 50% of liver genes are significantly zonated and uncover abundant non-monotonic profiles that peak at the mid-lobule layers. These include a spatial order of bile acid biosynthesis enzymes that matches their position in the enzymatic cascade. Our approach can facilitate the reconstruction of similar spatial genomic blueprints for other mammalian organs.
Metabolic pathways that contribute to adiposity and ageing are activated by the mammalian target of rapamycin complex 1 (mTORC1) and p70 ribosomal protein S6 kinase 1 (S6K1) axis. However, known mTORC1–S6K1 targets do not account for observed loss-of-function phenotypes, suggesting that there are additional downstream effectors of this pathway. Here we identify glutamyl-prolyl-tRNA synthetase (EPRS) as an mTORC1–S6K1 target that contributes to adiposity and ageing. Phosphorylation of EPRS atSer999 by mTORC1–S6K1 induces its release from the aminoacyl tRNA multisynthetase complex, which is required for execution of noncanonical functions of EPRS beyond protein synthesis. To investigate the physiological function of EPRS phosphorylation, we generated Eprs knock-in mice bearing phospho-deficient Ser999-to-Ala (S999A) and phospho-mimetic (S999D) mutations. Homozygous S999A mice exhibited low body weight, reduced adipose tissue mass, and increased lifespan, similar to S6K1-deficient mice and mice with adipocyte-specific deficiency of raptor, an mTORC1 constituent. Substitution of the EprsS999D allele in S6K1-deficient mice normalized body mass and adiposity, indicating that EPRS phosphorylation mediates S6K1-dependent metabolic responses. In adipocytes, insulin stimulated S6K1-dependent EPRS phosphorylation and release from the multisynthetase complex. Interaction screening revealed that phospho-EPRS binds SLC27A1 (that is, fatty acid transport protein 1, FATP1), inducing its translocation to the plasma membrane and long-chain fatty acid uptake. Thus, EPRS and FATP1 are terminal mTORC1–S6K1 axis effectors that are critical for metabolic phenotypes.
Malignant neoplasms evolve in response to changes in oncogenic signalling. Cancer cell plasticity in response to evolutionary pressures is fundamental to tumour progression and the development of therapeutic resistance. Here we determine the molecular and cellular mechanisms of cancer cell plasticity in a conditional oncogenic Kras mouse model of pancreatic ductal adenocarcinoma (PDAC), a malignancy that displays considerable phenotypic diversity and morphological heterogeneity. In this model, stochastic extinction of oncogenic Kras signalling and emergence of Kras-independent escaper populations (cells that acquire oncogenic properties) are associated with de-differentiation and aggressive biological behaviour. Transcriptomic and functional analyses of Kras-independent escapers reveal the presence of Smarcb1–Myc-network-driven mesenchymal reprogramming and independence from MAPK signalling. A somatic mosaic model of PDAC, which allows time-restricted perturbation of cell fate, shows that depletion of Smarcb1 activates the Myc network, driving an anabolic switch that increases protein metabolism and adaptive activation of endoplasmic-reticulum-stress-induced survival pathways. Increased protein turnover renders mesenchymal sub-populations highly susceptible to pharmacological and genetic perturbation of the cellular proteostatic machinery and the IRE1-α–MKK4 arm of the endoplasmic-reticulum-stress-response pathway. Specifically, combination regimens that impair the unfolded protein responses block the emergence of aggressive mesenchymal subpopulations in mouse and patient-derived PDAC models. These molecular and biological insights inform a potential therapeutic strategy for targeting aggressive mesenchymal features of PDAC.
The toxicity of misfolded proteins and mitochondrial dysfunction are pivotal factors that promote age-associated functional neuronal decline and neurodegenerative disease. Accordingly, neurons invest considerable cellular resources in chaperones, protein degradation, autophagy and mitophagy to maintain proteostasis and mitochondrial quality. Complicating the challenges of neuroprotection, misfolded human disease proteins and mitochondria can move into neighbouring cells via unknown mechanisms, which may promote pathological spread. Here we show that adult neurons from Caenorhabditis elegans extrude large (approximately 4 μm) membrane-surrounded vesicles called exophers that can contain protein aggregates and organelles. Inhibition of chaperone expression, autophagy or the proteasome, in addition to compromising mitochondrial quality, enhances the production of exophers. Proteotoxically stressed neurons that generate exophers subsequently function better than similarly stressed neurons that did not produce exophers. The extruded exopher transits through surrounding tissue in which some contents appear degraded, but some non-degradable materials can subsequently be found in more remote cells, suggesting secondary release. Our observations suggest that exopher-genesis is a potential response to rid cells of neurotoxic components when proteostasis and organelle function are challenged. We propose that exophers are components of a conserved mechanism that constitutes a fundamental, but formerly unrecognized, branch of neuronal proteostasis and mitochondrial quality control, which, when dysfunctional or diminished with age, might actively contribute to pathogenesis in human neurodegenerative disease and brain ageing.
Mitochondria are double-membraned organelles with variable shapes influenced by metabolic conditions, developmental stage, and environmental stimuli. Their dynamic morphology is a result of regulated and balanced fusion and fission processes. Fusion is crucial for the health and physiological functions of mitochondria, including complementation of damaged mitochondrial DNAs and the maintenance of membrane potential. Mitofusins are dynamin-related GTPases that are essential for mitochondrial fusion. They are embedded in the mitochondrial outer membrane and thought to fuse adjacent mitochondria via combined oligomerization and GTP hydrolysis. However, the molecular mechanisms of this process remain unknown. Here we present crystal structures of engineered human MFN1 containing the GTPase domain and a helical domain during different stages of GTP hydrolysis. The helical domain is composed of elements from widely dispersed sequence regions of MFN1 and resembles the‘neck’ of the bacterial dynamin-like protein. The structures reveal unique features of its catalytic machinery and explain how GTP binding induces conformational changes to promote GTPase domain dimerization in the transition state. Disruption of GTPase domain dimerization abolishes the fusogenic activity of MFN1. Moreover, a conserved aspartate residue trigger was found to affect mitochondrial elongation in MFN1, probably through a GTP-loading-dependent domain rearrangement. Thus, we propose a mechanistic model for MFN1-mediated mitochondrial tethering, and our results shed light on the molecular basis of mitochondrial fusion and mitofusin-related human neuromuscular disorders.
The spliceosome excises introns from pre-mRNAs in two sequential transesterifications—branching and exon ligation—catalysed at a single catalytic metal site in U6 small nuclear RNA (snRNA). Recently reported structures of the spliceosomal C complex with the cleaved 5′ exon and lariat–3′-exon bound to the catalytic centre revealed that branching-specific factors such as Cwc25 lock the branch helix into position for nucleophilic attack of the branch adenosine at the 5′ splice site. Furthermore, the ATPase Prp16 is positioned to bind and translocate the intron downstream of the branch point to destabilize branching-specific factors and release the branch helix from the active site. Here we present, at 3.8 Å resolution, the cryo-electron microscopy structure of a Saccharomyces cerevisiae spliceosome stalled after Prp16-mediated remodelling but before exon ligation. While the U6 snRNA catalytic core remains firmly held in the active site cavity of Prp8 by proteins common to both steps, the branch helix has rotated by 75° compared to the C complex and is stabilized in a new position by Prp17, Cef1 and the reoriented Prp8 RNase H-like domain. This rotation of the branch helix removes the branch adenosine from the catalytic core, creates a space for 3′ exon docking, and restructures the pairing of the 5′ splice site with the U6 snRNA ACAGAGA region. Slu7 and Prp18, which promote exon ligation, bind together to the Prp8 RNase H-like domain. The ATPase Prp22, bound to Prp8 in place of Prp16, could interact with the 3′ exon, suggesting a possible basis for mRNA release after exon ligation. Together with the structure of the C complex, our structure of the C* complex reveals the two major conformations of the spliceosome during the catalytic stages of splicing.
|Nature - AOP - nature.com science feeds|
Chemists have long aspired to synthesize two-dimensional polymers that are fully conjugated— an attribute that imparts potentially useful properties. Just such a material has been prepared using a solid-state polymerization reaction.
It emerges that blood-cancer-targeting drugs that block a tumour-survival pathway also activate a mutation-causing enzyme in mice and in human cells. This might have implications for the clinical use of these drugs.
Many organ surfaces are covered by a protective epithelial-cell layer. It emerges that such layers are maintained by cell stretching that triggers cell division mediated by the force-sensitive ion-channel protein Piezo1.
The genomes of 102 primary pancreatic neuroendocrine tumours have been sequenced, revealing mutations in genes with functions such as chromatin remodelling, DNA damage repair, mTOR activation and telomere maintenance, and a greater-than-expected contribution from germ line mutations.
Adipose tissue is a major source of circulating exosomal miRNAs, which contribute to the regulation of gene expression in distant tissues and organs.
Activation-induced cytidine deaminase (AID) is a B-cell-specific enzyme that targets immunoglobulin genes to initiate class switch recombination and somatic hypermutation. In addition, through off-target activity, AID has a much broader effect on genomic instability by initiating oncogenic chromosomal translocations and mutations involved in the development and progression of lymphoma. AID expression is tightly regulated in B cells and its overexpression leads to enhanced genomic instability and lymphoma formation. The phosphatidylinositol 3-kinaseδ (PI3Kδ) pathway regulates AID by suppressing its expression in B cells. Drugs for leukaemia or lymphoma therapy such as idelalisib, duvelisib and ibrutinib block PI3Kδ activity directly or indirectly, potentially affecting AID expression and, consequently, genomic stability in B cells. Here weshow that treatment of primary mouse B cells with idelalisib or duvelisib, and to a lesser extent ibrutinib, enhanced the expression of AID and increased somatic hypermutation and chromosomal translocation frequency to the Igh locus and to several AID off-target sites. Both of these effects were completely abrogated in AID-deficient B cells. PI3Kδ inhibitors or ibrutinib increased the formation of AID-dependent tumours in pristane-treated mice. Consistently, PI3Kδ inhibitors enhanced AID expression and translocation frequency to IGH and AID off-target sites in human chronic lymphocytic leukaemia and mantle cell lymphoma cell lines, and patients treated with idelalisib, but not ibrutinib, showed increased somatic hypermutation in AID off-targets. In summary, we show that PI3Kδ or Bruton’s tyrosine kinase inhibitors increase genomic instability in normal and neoplastic B cells by an AID-dependent mechanism. This effect should be carefully considered, as such inhibitors can be administered to patients for years.
Uniparental disomy (UPD), in which an individual contains a pair of homologous chromosomes originating from only one parent, is a frequent phenomenon that is linked to congenital disorders and various cancers. UPD is thought to result mostly from pre- or post-zygotic chromosome missegregation. However, the factors that drive UPD remain unknown. Here we use the fission yeast Schizosaccharomyces pombe as a model to investigate UPD, and show that defects in the RNA interference (RNAi) machinery or in the YTH domain-containing RNA elimination factor Mmi1 cause high levels of UPD in vegetative diploid cells. This phenomenon is not due to defects in heterochromatin assembly at centromeres. Notably, in cells lacking RNAi components or Mmi1, UPD is associated with the untimely expression of gametogenic genes. Deletion of the upregulated gene encoding the meiotic cohesin Rec8 or the cyclin Crs1 suppresses UPD in both RNAi and mmi1 mutants. Moreover, overexpression of Rec8 is sufficient to trigger UPD in wild-type cells. Rec8 expressed in vegetative cells localizes to chromosomal arms and to the centromere core, where it is required for localization of the cohesin subunit Psc3. The centromeric localization of Rec8 and Psc3 promotes UPD by uniquely affecting chromosome segregation, causing a reductional segregation of one homologue. Together, these findings establish the untimely vegetative expression of gametogenic genes as a causative factor of UPD, and provide a solid foundation for understanding this phenomenon, which is linked to diverse human diseases.
Despite acting as a barrier for the organs they encase, epithelial cells turn over at some of the fastest rates in the body. However, epithelial cell division must be tightly linked to cell death to preserve barrier function and prevent tumour formation. How does the number of dying cells match those dividing to maintain constant numbers? When epithelial cells become too crowded, they activate the stretch-activated channel Piezo1 to trigger extrusion of cells that later die. However, it is unclear how epithelial cell division is controlled to balance cell death at the steady state. Here we show that mammalian epithelial cell division occurs in regions of low cell density where cells are stretched. By experimentally stretching epithelia, we find that mechanical stretch itself rapidly stimulates cell division through activation of the Piezo1 channel. To stimulate cell division, stretch triggers cells that are paused in early G2 phase to activate calcium-dependent phosphorylation of ERK1/2, thereby activating the cyclin B transcription that is necessary to drive cells into mitosis. Although both epithelial cell division and cell extrusion require Piezo1 at the steady state, the type of mechanical force controls the outcome: stretch induces cell division, whereas crowding induces extrusion. How Piezo1-dependent calcium transients activate two opposing processes may depend on where and how Piezo1 is activated, as it accumulates in different subcellular sites with increasing cell density. In sparse epithelial regions in which cells divide, Piezo1 localizes to the plasma membrane and cytoplasm, whereas in dense regions in which cells extrude, it forms large cytoplasmic aggregates. Because Piezo1 senses both mechanical crowding and stretch, it may act as a homeostatic sensor to control epithelial cell numbers, triggering extrusion and apoptosis in crowded regions and cell division in sparse regions.
A highly protective malaria vaccine would greatly facilitate the prevention and elimination of malaria and containment of drug-resistant parasites. A high level (more than 90%) of protection against malaria in humans has previously been achieved only by immunization with radiation-attenuated Plasmodium falciparum (Pf) sporozoites (PfSPZ) inoculated by mosquitoes; by intravenous injection of aseptic, purified, radiation-attenuated, cryopreserved PfSPZ (‘PfSPZ Vaccine’); or by infectious PfSPZ inoculated by mosquitoes to volunteers taking chloroquine or mefloquine (chemoprophylaxis with sporozoites). We assessed immunization by direct venous inoculation of aseptic, purified, cryopreserved, non-irradiated PfSPZ (‘PfSPZ Challenge’) to malaria-naive, healthy adult volunteers taking chloroquine for antimalarial chemoprophylaxis (vaccine approach denoted as PfSPZ-CVac). Three doses of 5.12 × 104 PfSPZ of PfSPZ Challenge at 28-day intervals were well tolerated and safe, and prevented infection in 9 out of 9 (100%) volunteers who underwent controlled human malaria infection ten weeks after the last dose (group III). Protective efficacy was dependent on dose and regimen. Immunization with 3.2 × 103 (group I) or 1.28 × 104 (group II) PfSPZ protected 3 out of 9 (33%) or 6 out of 9 (67%) volunteers, respectively. Three doses of 5.12 × 104 PfSPZ at five-day intervals protected 5 out of 8 (63%) volunteers. The frequency of Pf-specific polyfunctional CD4 memory T cells was associated with protection. On a 7,455 peptide Pf proteome array, immune sera from at least 5 out of 9 group III vaccinees recognized each of 22 proteins. PfSPZ-CVac is a highly efficacious vaccine candidate; when we are able to optimize the immunization regimen (dose, interval between doses, and drug partner), this vaccine could be used for combination mass drug administration and a mass vaccination program approach to eliminate malaria from geographically defined areas.
Mechanistic target of rapamycin complex 1 (TORC1) integrates nutrient signals to control cell growth and organismal homeostasis across eukaryotes. The evolutionarily conserved GATOR complex regulates mTORC1 signalling through Rag GTPases, and GATOR1 displays GTPase activating protein (GAP) activity for RAGA and RAGB (RAGA/B) and GATOR2 has been proposed to be an inhibitor of GATOR1. Furthermore, the metazoan-specific SESN proteins function as guanine nucleotide dissociation inhibitors (GDIs) for RAGA/B, and interact with GATOR2 with unknown effects. Here we show that SZT2 (seizure threshold 2), a metazoan-specific protein mutated in epilepsy, recruits a fraction of mammalian GATOR1 and GATOR2 to form a SZT2-orchestrated GATOR (SOG) complex with an essential role in GATOR- and SESN-dependent nutrient sensing and mTORC1 regulation. The interaction of SZT2 with GATOR1 and GATOR2 was synergistic, and an intact SOG complex was required for its localization at the lysosome. SZT2 deficiency resulted in constitutive mTORC1 signalling in cells under nutrient-deprived conditions and neonatal lethality in mice, which was associated with failure to inactivate mTORC1 during fasting. Hyperactivation of mTORC1 in SZT2-deficient cells could be partially corrected by overexpression of the GATOR1 component DEPDC5, and by the lysosome-targeted GATOR2 component WDR59 or lysosome-targeted SESN2. These findings demonstrate that SZT2 has a central role in dictating GATOR-dependent nutrient sensing by promoting lysosomal localization of SOG, and reveal an unexpected function of lysosome-located GATOR2 in suppressing mTORC1 signalling through SESN recruitment.
The mechanistic target of rapamycin complex 1 (mTORC1) is a central regulator of cell growth that responds to diverse environmental signals and is deregulated in many human diseases, including cancer and epilepsy. Amino acids are a key input to this system, and act through the Rag GTPases to promote the translocation of mTORC1 to the lysosomal surface, its site of activation. Multiple protein complexes regulate the Rag GTPases in response to amino acids, including GATOR1, a GTPase activating protein for RAGA, and GATOR2, a positive regulator of unknown molecular function. Here we identify a protein complex (KICSTOR) that is composed of four proteins, KPTN, ITFG2, C12orf66 and SZT2, and that is required for amino acid or glucose deprivation to inhibit mTORC1 in cultured human cells. In mice that lack SZT2, mTORC1 signalling is increased in several tissues, including in neurons in the brain. KICSTOR localizes to lysosomes; binds and recruits GATOR1, but not GATOR2, to the lysosomal surface; and is necessary for the interaction of GATOR1 with its substrates, the Rag GTPases, and with GATOR2. Notably, several KICSTOR components are mutated in neurological diseases associated with mutations that lead to hyperactive mTORC1 signalling. Thus, KICSTOR is a lysosome-associated negative regulator of mTORC1 signalling, which, like GATOR1, is mutated in human disease.
The semiconductor industry is increasingly of the view that Moore’s law—which predicts the biennial doubling of the number of transistors per microprocessor chip—is nearing its end. Consequently, the pursuit of alternative semiconducting materials for nanoelectronic devices, including single-walled carbon nanotubes (SWNTs), continues. Arrays of horizontal nanotubes are particularly appealing for technological applications because they optimize current output. However, the direct growth of horizontal SWNT arrays with controlled chirality, that would enable the arrays to be adapted for a wider range of applications and ensure the uniformity of the fabricated devices, has not yet been achieved. Here we show that horizontal SWNT arrays with predicted chirality can be grown from the surfaces of solid carbide catalysts by controlling the symmetries of the active catalyst surface. We obtained horizontally aligned metallic SWNT arrays with an average density of more than 20 tubes per micrometre in which 90 per cent of the tubes had chiral indices of (12, 6), and semiconducting SWNT arrays with an average density of more than 10 tubes per micrometre in which 80 per cent of the nanotubes had chiral indices of (8, 4). The nanotubes were grown using uniform size Mo2C and WC solid catalysts. Thermodynamically, the SWNT was selectively nucleated by matching its structural symmetry and diameter with those of the catalyst. We grew nanotubes with chiral indices of (2m, m) (where m is a positive integer), the yield of which could be increased by raising the concentration of carbon to maximize the kinetic growth rate in the chemical vapour deposition process. Compared to previously reported methods, such as cloning, seeding and specific-structure-matching growth, our strategy of controlling the thermodynamics and kinetics offers more degrees of freedom, enabling the chirality of as-grown SWNTs in an array to be tuned, and can also be used to predict the growth conditions required to achieve the desired chiralities.
B-lymphoid transcription factors, such as PAX5 and IKZF1, are critical for early B-cell development, yet lesions of the genes encoding these transcription factors occur in over 80% of cases of pre-B-cell acute lymphoblastic leukaemia (ALL). The importance of these lesions in ALL has, until now, remained unclear. Here, by combining studies using chromatin immunoprecipitation with sequencing and RNA sequencing, we identify a novel B-lymphoid program for transcriptional repression of glucose and energy supply. Our metabolic analyses revealed that PAX5 and IKZF1 enforce a state of chronic energy deprivation, resulting in constitutive activation of the energy-stress sensor AMPK. Dominant-negative mutants of PAX5 and IKZF1, however, relieved this glucose and energy restriction. In a transgenic pre-B ALL mouse model, the heterozygous deletion of Pax5 increased glucose uptake and ATP levels by more than 25-fold. Reconstitution of PAX5 and IKZF1 in samples from patients with pre-B ALL restored a non-permissive state and induced energy crisis and cell death. A CRISPR/Cas9-based screen of PAX5 and IKZF1 transcriptional targets identified the products of NR3C1 (encoding the glucocorticoid receptor), TXNIP (encoding a glucose-feedback sensor) and CNR2 (encoding a cannabinoid receptor) as central effectors of B-lymphoid restriction of glucose and energy supply. Notably, transport-independent lipophilic methyl-conjugates of pyruvate and tricarboxylic acid cycle metabolites bypassed the gatekeeper function of PAX5 and IKZF1 and readily enabled leukaemic transformation. Conversely, pharmacological TXNIP and CNR2 agonists and a small-molecule AMPK inhibitor strongly synergized with glucocorticoids, identifying TXNIP, CNR2 and AMPK as potential therapeutic targets. Furthermore, our results provide a mechanistic explanation for the empirical finding that glucocorticoids are effective in the treatment of B-lymphoid but not myeloid malignancies. Thus, B-lymphoid transcription factors function as metabolic gatekeepers by limiting the amount of cellular ATP to levels that are insufficient for malignant transformation.
Reciprocity is a general, fundamental principle governing various physical systems, which ensures that the transfer function—the transmission of a physical quantity, say light intensity—between any two points in space is identical, regardless of geometrical or material asymmetries. Breaking this transmission symmetry offers enhanced control over signal transport, isolation and source protection. So far, devices thatbreak reciprocity (and therefore show non-reciprocity) have been mostly considered in dynamic systems involving electromagnetic, acoustic and mechanical wave propagation associated with fields varying in space and time. Here we show that it is possible to break reciprocity in static systems, realizing mechanical metamaterials that exhibit vastly different output displacements under excitation from different sides, as well as one-way displacement amplification. This is achieved by combining large nonlinearities with suitable geometrical asymmetries and/or topological features. In addition to extending non-reciprocity and isolation to statics, our work sheds light on energy propagation in nonlinear materials with asymmetric crystalline structures and topological properties. We anticipate that breaking reciprocity will open avenues for energy absorption, conversion and harvesting, soft robotics, prosthetics and optomechanics.
The maternal-to-zygotic transition (MZT) is one of the most profound and tightly orchestrated processes during the early life of embryos, yet factors that shape the temporal pattern of vertebrate MZT are largely unknown. Here we show that over one-third of zebrafish maternal messenger RNAs (mRNAs) can be N6-methyladenosine (m6A) modified, and the clearance of these maternal mRNAs is facilitated by an m6A-binding protein, Ythdf2. Removal of Ythdf2 in zebrafish embryos decelerates the decay of m6A-modified maternal mRNAs and impedes zygotic genome activation. These embryos fail to initiate timely MZT, undergo cell-cycle pause, and remain developmentally delayed throughout larval life. Our study reveals m6A-dependent RNA decay as a previously unidentified maternally driven mechanism that regulates maternal mRNA clearance during zebrafish MZT, highlighting the critical role of m6A mRNA methylation in transcriptome switching and animal development.
A systematic analysis of bipolar cells, which act as a central signalling conduit in the retina, reveals that the neurons' diverse responses to light are generated largely by feedback from neighbouring amacrine cells.
The functional diversity of bipolar cells, which split visual inputs into different excitatory channels within the retina, arises from centre–surround interactions in their receptive fields that tune both spatial and temporal signalling.
Human cells have twenty-three pairs of chromosomes. In cancer, however, genes can be amplified in chromosomes or in circular extrachromosomal DNA (ecDNA), although the frequency and functional importance of ecDNA are not understood. We performed whole-genome sequencing, structural modelling and cytogenetic analyses of 17 different cancer types, including analysis of the structure and function of chromosomes during metaphase of 2,572 dividing cells, and developed a software package called ECdetect to conduct unbiased, integrated ecDNA detection and analysis. Here we show that ecDNA was found in nearly half of human cancers; its frequency varied by tumour type, but it was almost never found in normal cells. Driver oncogenes were amplified most commonly in ecDNA, thereby increasing transcript level. Mathematical modelling predicted that ecDNA amplification would increase oncogene copy number and intratumoural heterogeneity more effectively than chromosomal amplification. We validated these predictions by quantitative analyses of cancer samples. The results presented here suggest that ecDNA contributes to accelerated evolution in cancer.
Exceptionally preserved fossils provide crucial insights into extinct body plans and organismal evolution. Molluscs, one of the most disparate animal phyla, radiated rapidly during the early Cambrian period (approximately 535–520 million years ago (Ma)). The problematic fossil taxa Halkieria and Orthrozanclus (grouped in Sachitida) have been assigned variously to stem-group annelids, brachiopods, stem-group molluscs or stem-group aculiferans (Polyplacophora and Aplacophora), but their affinities have remained controversial owing to a lack of preserved diagnostic characters. Here we describe a new early sachitid, Calvapilosa kroegeri gen. et sp. nov. from the Fezouata biota of Morocco (Early Ordovician epoch, around 478 Ma). The new taxon is characterized by the presence of a single large anterior shell plate and polystichous radula bearing a median tooth and several lateral and uncinal teeth in more than 125 rows. Its flattened body is covered by hollow spinose sclerites, and a smooth, ventral girdle flanks an extensive mantle cavity. Phylogenetic analyses resolve C. kroegeri as a stem-group aculiferan together with other single-plated forms such as Maikhanella (Siphogonuchites) and Orthrozanclus; Halkieria is recovered closer to the aculiferan crown. These genera document the stepwise evolution of the aculiferan body plan from forms with a single, almost conchiferan-like shell through two-plated taxa such as Halkieria, to the eight-plated crown-group aculiferans. C. kroegeri therefore provides key evidence concerning the long debate about the crown molluscan affinities of sachitids. This new discovery strongly suggests that the possession of only a single calcareous shell plate and the presence of unmineralised sclerites are plesiomorphic (an ancestral trait) for the molluscan crown.
The rise of oxygen on the early Earth (about 2.4 billion years ago) caused a reorganization of marine nutrient cycles, including that of nitrogen, which is important for controlling global primary productivity. However, current geochemical records lack the temporal resolution to address the nature and timing of the biogeochemical response to oxygenation directly. Here we couple records of ocean redox chemistry with nitrogen isotope (15N/14N) values from approximately 2.31-billion-year-old shales of the Rooihoogte and Timeball Hill formations in South Africa, deposited during the early stages of the first rise in atmospheric oxygen on the Earth (the Great Oxidation Event). Our data fill a gap of about 400 million years in the temporal 15N/14N record and provide evidence for the emergence of a pervasive aerobic marine nitrogen cycle. The interpretation of our nitrogen isotope data in the context of iron speciation and carbon isotope data suggests biogeochemical cycling across a dynamic redox boundary, with primary productivity fuelled by chemoautotrophic production and a nitrogen cycle dominated by nitrogen loss processes using newly available marine oxidants. This chemostratigraphic trend constrains the onset of widespread nitrate availability associated with ocean oxygenation. The rise of marine nitrate could have allowed for the rapid diversification and proliferation of nitrate-using cyanobacteria and, potentially, eukaryotic phytoplankton.
Synthetic lethality and collateral lethality are two well-validated conceptual strategies for identifying therapeutic targets in cancers with tumour-suppressor gene deletions. Here, we explore an approach to identify potential synthetic-lethal interactions by screening mutually exclusive deletion patterns in cancer genomes. We sought to identify‘synthetic-essential’ genes: those that are occasionally deleted in some cancers but are almost always retained in the context of a specific tumour-suppressor deficiency. We also posited that such synthetic-essential genes would be therapeutic targets in cancers that harbour specific tumour-suppressor deficiencies. In addition to known synthetic-lethal interactions, this approach uncovered the chromatin helicase DNA-binding factor CHD1 as a putative synthetic-essential gene in PTEN-deficient cancers. In PTEN-deficient prostate and breast cancers, CHD1 depletion profoundly and specificallysuppressed cell proliferation, cell survival and tumorigenic potential. Mechanistically, functional PTEN stimulates the GSK3β-mediated phosphorylation of CHD1 degron domains, which promotes CHD1 degradation via the β-TrCP-mediated ubiquitination–proteasome pathway. Conversely, PTEN deficiency results in stabilization of CHD1, which in turn engages the trimethyl lysine-4 histone H3 modification to activate transcription of the pro-tumorigenic TNF–NF-κB gene network. This study identifies a novel PTEN pathway in cancer and provides a framework for the discovery of ‘trackable’ targetsin cancers that harbour specific tumour-suppressor deficiencies.
Whole-exome analysis of individuals with developmental disorders shows that de novo mutations can equally cause loss or altered protein function, but that most mutations causing altered protein function have not yet been described.
Neutrinos are much lighter than the other constituents of matter. One explanation for this could be that neutrinos are their own antiparticles and belong to a new class of 'Majorana' particle. An experiment sets strong constraints on this scenario.
The human dispersal out of Africa that populated the world was probably paced by climate changes. This is the inference drawn from computer modelling of climate variability during the time of early human migration.
Underactivity of the transcription factor p53 can lead to tumour development. The discovery that the SET protein binds to and inhibits p53 points to a way to unleash the tumour suppressor's activity.
Deadly coral snakes warn predators through striking red-black banding. New data confirm that many harmless snakes have evolved to resemble coral snakes, and suggest that the evolution of this Batesian mimicry is not always a one-way street.