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Nature is the international weekly journal of science: a magazine style journal that publishes full-length research papers in all disciplines of science, as well as News and Views, reviews, news, features, commentaries, web focuses and more, covering all branches of science and how science impacts upon all aspects of society and life.

Last feed update: Monday November 20th, 2017 10:19:43 AM

Graduate students face alarming tax hike

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Adding to PhD students’ woes will undermine US research and economy.

Chemists get faster on the draw

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A Nature journals guide to drawing the structures of molecules should aid expert and casual chemists alike.

How China could make the most of its beamlines

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More international collaboration could build capacity at big physics facilities especially in the south.

Immunization needs a technology boost

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Tracking who receives vaccines is essential, but will be impossible without innovations in digital technologies, says Seth Berkley.

New Delhi smog, death-sentence appeal and a porpoise setback

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The week in science: 11–16 November 2017.

Archaeologists say human-evolution study used stolen bone

Monday November 13th, 2017 12:00:00 AM
Bizarre tale of theft and suspicious packages casts doubt on claims for early-human occupation in northern Europe.

Lab mice's ancestral ‘Eve’ gets her genome sequenced

Monday November 13th, 2017 12:00:00 AM
Effort aims to help scientists understand how generations of inbreeding have altered the genetics of research rodents.

UK government appoints next chief scientific adviser

Wednesday November 8th, 2017 12:00:00 AM
A former pharmaceutical boss will help navigate the UK’s exit from the European Union.

Puerto Rico struggles to assess hurricane’s health effects

Wednesday November 15th, 2017 12:00:00 AM
While dealing with their own losses, public-health researchers are regrouping to study the aftermath of Hurricane Maria.

World’s carbon emissions set to spike by 2% in 2017

Monday November 13th, 2017 12:00:00 AM
Increased coal use in China appears to be driving the first increase in global greenhouse-gas output since 2014.

China fires up next-generation neutron-science facility

Tuesday November 14th, 2017 12:00:00 AM
Beam generator puts country in elite company for doing experiments in materials science and other fields.

Biology’s beloved amphibian — the axolotl — is racing towards extinction

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Although abundant in captivity, the salamander has nearly disappeared from its natural habitat, and that’s a problem.

Chemists can help to solve the air-pollution health crisis

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Learning more about how pollutants enter and damage the body would reduce disease and deaths, say Jos Lelieveld and Ulrich Pöschl.

Boycott products from states with dirty energy

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Consumer pressure could encourage regions to switch from fossil fuels to cleaner sources of electricity, argues Christopher Kennedy.

Bioethics: Justice in genomics

Wednesday November 15th, 2017 12:00:00 AM
Rosario Isasi examines a study on the societal impact of grand sequencing projects.

Economics: How science got a golden ticket

Wednesday November 15th, 2017 12:00:00 AM
Ehsan Masood hails an account of the mixed implications of governments valuing research as an investment.

Computer science: Visionary of virtual reality

Wednesday November 15th, 2017 12:00:00 AM
Aldo Faisal explores the immersive journey of technology pioneer Jaron Lanier.

Fires: fund research for citizen safety

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Fires: degree courses for fire professionals

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International funding: Empower Africa’s electricity sector

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Preclinical research: Meet patients to sharpen up research

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Research reports: An open market for scientific verbiage?

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Survival stories: science endures

Wednesday November 15th, 2017 12:00:00 AM
Scientists hit hard by powerful hurricanes in 2017 share tips for weathering future disasters.

Turning point: Gourmet investigator

Wednesday November 15th, 2017 12:00:00 AM
Cross-cultural chef-turned-scientist cooks up recipe for diversity outreach.

Those who favour fire

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A final farewell.

Planetary science: Haze cools Pluto's atmosphere

Wednesday November 15th, 2017 12:00:00 AM
Modelling suggests that Pluto's atmospheric temperature is regulated by haze, unlike the other planetary bodies in the Solar System. The finding has implications for our understanding of exoplanetary atmospheres. See Letter p.352

Microbiology: Bacteria disarm host-defence proteins

Wednesday October 25th, 2017 12:00:00 AM
Infection with Shigella flexneri bacteria is a major cause of infant death. It emerges that S. flexneri evades intracellular defences by releasing a protein that triggers the destruction of members of a key family of host enzymes. See Letter p.378

50 & 100 Years Ago

Wednesday November 15th, 2017 12:00:00 AM
50 Years AgoLast week's first Saturn V flight (called Apollo 4) may have helped NASA to catch up on the lagging timetable for landing two Americans on the Moon by 1970. By combining in one flight the first operational tests of several important components,

Biogeochemistry: Ocean hotspots of nitrogen loss

Wednesday November 15th, 2017 12:00:00 AM
Microbial activity in the sea results in a loss of bioavailable nitrogen. It emerges that the climate phenomenon called the El Niño–Southern Oscillation has a surprisingly large effect on the size of this loss.

Gene therapy: Transgenic stem cells replace skin

Wednesday November 8th, 2017 12:00:00 AM
The treatment of a patient affected by an incurable genetic skin disease demonstrates the efficacy, feasibility and safety of replacing almost the whole skin using genetically corrected stem cells. See Letter p.327

Geophysics: The buoyancy of Earth's deep mantle

Wednesday November 15th, 2017 12:00:00 AM
The physical nature of two regions called large low-shear-velocity provinces at the base of Earth's mantle is uncertain. A measurement of their density has implications for our understanding of mantle dynamics. See Article p.321

Ecology: The effect of conservation spending

Wednesday October 25th, 2017 12:00:00 AM
Statistical analysis of data on threatened species provides a model that can predict how rates of investment in conservation affect biodiversity under changing human population levels and agricultural and economic conditions. See Letter p.364

Influenza: A broadly protective antibody

Wednesday November 15th, 2017 12:00:00 AM
A single antibody uses multiple antiviral mechanisms to block the replication of influenza B viruses in mice and ferrets. The development could inform research into improved flu vaccines.

Progress in and promise of bacterial quorum sensing research

Wednesday November 15th, 2017 12:00:00 AM
This Review highlights how we can build upon the relatively new and rapidly developing field of research into bacterial quorum sensing (QS). We now have a depth of knowledge about how bacteria use QS signals to communicate with each other and to coordinate their activities.

Tidal tomography constrains Earth’s deep-mantle buoyancy

Wednesday November 15th, 2017 12:00:00 AM
Earth’s body tide—also known as the solid Earth tide, the displacement of the solid Earth’s surface caused by gravitational forces from the Moon and the Sun—is sensitive to the density of the two Large Low Shear Velocity Provinces (LLSVPs) beneath Africa and the Pacific. These

Regeneration of the entire human epidermis using transgenic stem cells

Wednesday November 8th, 2017 12:00:00 AM
Junctional epidermolysis bullosa (JEB) is a severe and often lethal genetic disease caused by mutations in genes encoding the basement membrane component laminin-332. Surviving patients with JEB develop chronic wounds to the skin and mucosa, which impair their quality of life and lead to skin

A single-cell survey of the small intestinal epithelium

Wednesday November 8th, 2017 12:00:00 AM
Intestinal epithelial cells absorb nutrients, respond to microbes, function as a barrier and help to coordinate immune responses. Here we report profiling of 53,193 individual epithelial cells from the small intestine and organoids of mice, which enabled the identification and characterization of previously unknown subtypes

Inflammation-induced IgA+ cells dismantle anti-liver cancer immunity

Wednesday November 8th, 2017 12:00:00 AM
The role of adaptive immunity in early cancer development is controversial. Here we show that chronic inflammation and fibrosis in humans and mice with non-alcoholic fatty liver disease is accompanied by accumulation of liver-resident immunoglobulin-A-producing (IgA+) cells. These cells also express programmed death

Dynamics of P-type ATPase transport revealed by single-molecule FRET

Wednesday November 8th, 2017 12:00:00 AM
Phosphorylation-type (P-type) ATPases are ubiquitous primary transporters that pump cations across cell membranes through the formation and breakdown of a phosphoenzyme intermediate. Structural investigations suggest that the transport mechanism is defined by conformational changes in the cytoplasmic domains of the protein that are allosterically coupled

Haze heats Pluto’s atmosphere yet explains its cold temperature

Wednesday November 15th, 2017 12:00:00 AM
Pluto’s atmosphere is cold and hazy. Recent observations have shown it to be much colder than predicted theoretically, suggesting an unknown cooling mechanism. Atmospheric gas molecules, particularly water vapour, have been proposed as a coolant; however, because Pluto’s thermal structure is expected to be in radiative–conductive equilibrium, the required water vapour would need to be supersaturated by many orders of magnitude under thermodynamic equilibrium conditions. Here we report that atmospheric hazes, rather than gases, can explain Pluto’s temperature profile. We find that haze particles have substantially larger solar heating and thermal cooling rates than gas molecules, dominating the atmospheric radiative balance from the ground to an altitude of 700 kilometres, above which heat conduction maintains an isothermal atmosphere. We conclude that Pluto’s atmosphere is unique among Solar System planetary atmospheres, as its radiative energy equilibrium is controlled primarily by haze particles instead of gas molecules. We predict that Pluto is therefore several orders of magnitude brighter at mid-infrared wavelengths than previously thought—a brightness that could be detected by future telescopes.

Collective emission of matter-wave jets from driven Bose–Einstein condensates

Monday November 6th, 2017 12:00:00 AM
Scattering is used to probe matter and its interactions in all areas of physics. In ultracold atomic gases, control over pairwise interactions enables us to investigate scattering in quantum many-body systems. Previous experiments on colliding Bose–Einstein condensates have revealed matter–wave interference, haloes of scattered atoms, four-wave mixing and correlations between counter-propagating pairs. However, a regime with strong stimulation of spontaneous collisions analogous to superradiance has proved elusive. In this regime, the collisions rapidly produce highly correlated states with macroscopic population. Here we find that runaway stimulated collisions in Bose–Einstein condensates with periodically modulated interaction strength cause the collective emission of matter-wave jets that resemble fireworks. Jets appear only above a threshold modulation amplitude and their correlations are invariant even when the number of ejected atoms grows exponentially. Hence, we show that the structures and atom occupancies of the jets stem from the quantum fluctuations of the condensate. Our findings demonstrate the conditions required for runaway stimulated collisions and reveal the quantum nature of matter-wave emission.

Granular materials flow like complex fluids

Wednesday November 1st, 2017 12:00:00 AM
Granular materials such as sand, powders and foams are ubiquitous in daily life and in industrial and geotechnical applications. These disordered systems form stable structures when unperturbed, but in the presence of external influences such as tapping or shear they ‘relax’, becoming fluid in nature. It is often assumed that the relaxation dynamics of granular systems is similar to that of thermal glass-forming systems. However, so far it has not been possible to determine experimentally the dynamic properties of three-dimensional granular systems at the particle level. This lack of experimental data, combined with the fact that the motion of granular particles involves friction (whereas the motion of particles in thermal glass-forming systems does not), means that an accurate description of the relaxation dynamics of granular materials is lacking. Here we use X-ray tomography to determine the microscale relaxation dynamics of hard granular ellipsoids subject to an oscillatory shear. We find that the distribution of the displacements of the ellipsoids is well described by a Gumbel law (which is similar to a Gaussian distribution for small displacements but has a heavier tail for larger displacements), with a shape parameter that is independent of the amplitude of the shear strain and of the time. Despite this universality, the mean squared displacement of an individual ellipsoid follows a power law as a function of time, with an exponent that does depend on the strain amplitude and time. We argue that these results are related to microscale relaxation mechanisms that involve friction and memory effects (whereby the motion of an ellipsoid at a given point in time depends on its previous motion). Our observations demonstrate that, at the particle level, the dynamic behaviour of granular systems is qualitatively different from that of thermal glass-forming systems, and is instead more similar to that of complex fluids. We conclude that granular materials can relax even when the driving strain is weak.

Reductions in global biodiversity loss predicted from conservation spending

Wednesday October 25th, 2017 12:00:00 AM
Halting global biodiversity loss is central to the Convention on Biological Diversity and United Nations Sustainable Development Goals, but success to date has been very limited. A critical determinant of success in achieving these goals is the financing that is committed to maintaining biodiversity; however, financing decisions are hindered by considerable uncertainty over the likely impact of any conservation investment. For greater effectiveness, we need an evidence-based model that shows how conservation spending quantitatively reduces the rate of biodiversity loss. Here we demonstrate such a model, and empirically quantify how conservation investment between 1996 and 2008 reduced biodiversity loss in 109 countries (signatories to the Convention on Biological Diversity and Sustainable Development Goals), by a median average of 29% per country. We also show that biodiversity changes in signatory countries can be predicted with high accuracy, using a dual model that balances the effects of conservation investment against those of economic, agricultural and population growth (human development pressures). Decision-makers can use this model to forecast the improvement that any proposed biodiversity budget would achieve under various scenarios of human development pressure, and then compare these forecasts to any chosen policy target. We find that the impact of spending decreases as human development pressures grow, which implies that funding may need to increase over time. The model offers a flexible tool for balancing the Sustainable Development Goals of human development and maintaining biodiversity, by predicting the dynamic changes in conservation finance that will be needed as human development proceeds.

Parallel palaeogenomic transects reveal complex genetic history of early European farmers

Wednesday November 8th, 2017 12:00:00 AM
Ancient DNA studies have established that Neolithic European populations were descended from Anatolian migrants who received a limited amount of admixture from resident hunter-gatherers. Many open questions remain, however, about the spatial and temporal dynamics of population interactions and admixture during the Neolithic period. Here we investigate the population dynamics of Neolithization across Europe using a high-resolution genome-wide ancient DNA dataset with a total of 180 samples, of which 130 are newly reported here, from the Neolithic and Chalcolithic periods of Hungary (6000–2900 bc, n = 100), Germany (5500–3000 bc, n = 42) and Spain (5500–2200 bc, n = 38). We find that genetic diversity was shaped predominantly by local processes, with varied sources and proportions of hunter-gatherer ancestry among the three regions and through time. Admixture between groups with different ancestry profiles was pervasive and resulted in observable population transformation across almost all cultural transitions. Our results shed new light on the ways in which gene flow reshaped European populations throughout the Neolithic period and demonstrate the potential of time-series-based sampling and modelling approaches to elucidate multiple dimensions of historical population interactions.

Locomotor speed control circuits in the caudal brainstem

Monday October 23rd, 2017 12:00:00 AM
Locomotion is a universal behaviour that provides animals with the ability to move between places. Classical experiments have used electrical microstimulation to identify brain regions that promote locomotion, but the identity of neurons that act as key intermediaries between higher motor planning centres and executive circuits in the spinal cord has remained controversial. Here we show that the mouse caudal brainstem encompasses functionally heterogeneous neuronal subpopulations that have differential effects on locomotion. These subpopulations are distinguishable by location, neurotransmitter identity and connectivity. Notably, glutamatergic neurons within the lateral paragigantocellular nucleus (LPGi), a small subregion in the caudal brainstem, are essential to support high-speed locomotion, and can positively tune locomotor speed through inputs from glutamatergic neurons of the upstream midbrain locomotor region. By contrast, glycinergic inhibitory neurons can induce different forms of behavioural arrest mapping onto distinct caudal brainstem regions. Anatomically, descending pathways of glutamatergic and glycinergic LPGi subpopulations communicate with distinct effector circuits in the spinal cord. Our results reveal that behaviourally opposing locomotor functions in the caudal brainstem were historically masked by the unexposed diversity of intermingled neuronal subpopulations. We demonstrate how specific brainstem neuron populations represent essential substrates to implement key parameters in the execution of motor programs.

Ubiquitination and degradation of GBPs by a Shigella effector to suppress host defence

Wednesday October 11th, 2017 12:00:00 AM
Interferon-inducible guanylate-binding proteins (GBPs) mediate cell-autonomous antimicrobial defences. Shigella flexneri, a Gram-negative cytoplasmic free-living bacterium that causes bacillary dysentery, encodes a repertoire of highly similar type III secretion system effectors called invasion plasmid antigen Hs (IpaHs). IpaHs represent a large family of bacterial ubiquitin-ligases, but their function is poorly understood. Here we show that S. flexneri infection induces rapid proteasomal degradation of human guanylate binding protein-1 (hGBP1). We performed a transposon screen to identify a mutation in the S. flexneri gene ipaH9.8 that prevented hGBP1 degradation. IpaH9.8 targets hGBP1 for degradation via Lys48-linked ubiquitination. IpaH9.8 targets multiple GBPs in the cytoplasm independently of their nucleotide-bound states and their differential function in antibacterial defence, promoting S. flexneri replication and resulting in the death of infected mice. In the absence of IpaH9.8, or when binding of GBPs to IpaH9.8 was disrupted, GBPs such as hGBP1 and mouse GBP2 (mGBP2) translocated to intracellular S. flexneri and inhibited bacterial replication. Like wild-type mice, mutant mice deficient in GBP1–3, 5 and 7 succumbed to S. flexneri infection, but unlike wild-type mice, mice deficient in these GBPs were also susceptible to S. flexneri lacking ipaH9.8. The mode of IpaH9.8 action highlights the functional importance of GBPs in antibacterial defences. IpaH9.8 and S. flexneri provide a unique system for dissecting GBP-mediated immunity.

BCAT1 restricts αKG levels in AML stem cells leading to IDHmut-like DNA hypermethylation

Wednesday November 8th, 2017 12:00:00 AM
The branched-chain amino acid (BCAA) pathway and high levels of BCAA transaminase 1 (BCAT1) have recently been associated with aggressiveness in several cancer entities. However, the mechanistic role of BCAT1 in this process remains largely uncertain. Here, by performing high-resolution proteomic analysis of human acute myeloid leukaemia (AML) stem-cell and non-stem-cell populations, we find the BCAA pathway enriched and BCAT1 protein and transcripts overexpressed in leukaemia stem cells. We show that BCAT1, which transfers α-amino groups from BCAAs to α-ketoglutarate (αKG), is a critical regulator of intracellular αKG homeostasis. Further to its role in the tricarboxylic acid cycle, αKG is an essential cofactor for αKG-dependent dioxygenases such as Egl-9 family hypoxia inducible factor 1 (EGLN1) and the ten-eleven translocation (TET) family of DNA demethylases. Knockdown of BCAT1 in leukaemia cells caused accumulation of αKG, leading to EGLN1-mediated HIF1α protein degradation. This resulted in a growth and survival defect and abrogated leukaemia-initiating potential. By contrast, overexpression of BCAT1 in leukaemia cells decreased intracellular αKG levels and caused DNA hypermethylation through altered TET activity. AML with high levels of BCAT1 (BCAT1high) displayed a DNA hypermethylation phenotype similar to cases carrying a mutant isocitrate dehydrogenase (IDHmut), in which TET2 is inhibited by the oncometabolite 2-hydroxyglutarate. High levels of BCAT1 strongly correlate with shorter overall survival in IDHWTTET2WT, but not IDHmut or TET2mut AML. Gene sets characteristic for IDHmut AML were enriched in samples from patients with an IDHWTTET2WTBCAT1high status. BCAT1high AML showed robust enrichment for leukaemia stem-cell signatures, and paired sample analysis showed a significant increase in BCAT1 levels upon disease relapse. In summary, by limiting intracellular αKG, BCAT1 links BCAA catabolism to HIF1α stability and regulation of the epigenomic landscape, mimicking the effects of IDH mutations. Our results suggest the BCAA–BCAT1–αKG pathway as a therapeutic target to compromise leukaemia stem-cell function in patients with IDHWTTET2WT AML.

A ubiquitin-dependent signalling axis specific for ALKBH-mediated DNA dealkylation repair

Wednesday November 8th, 2017 12:00:00 AM
DNA repair is essential to prevent the cytotoxic or mutagenic effects of various types of DNA lesions, which are sensed by distinct pathways to recruit repair factors specific to the damage type. Although biochemical mechanisms for repairing several forms of genomic insults are well understood, the upstream signalling pathways that trigger repair are established for only certain types of damage, such as double-stranded breaks and interstrand crosslinks. Understanding the upstream signalling events that mediate recognition and repair of DNA alkylation damage is particularly important, since alkylation chemotherapy is one of the most widely used systemic modalities for cancer treatment and because environmental chemicals may trigger DNA alkylation. Here we demonstrate that human cells have a previously unrecognized signalling mechanism for sensing damage induced by alkylation. We find that the alkylation repair complex ASCC (activating signal cointegrator complex) relocalizes to distinct nuclear foci specifically upon exposure of cells to alkylating agents. These foci associate with alkylated nucleotides, and coincide spatially with elongating RNA polymerase II and splicing components. Proper recruitment of the repair complex requires recognition of K63-linked polyubiquitin by the CUE (coupling of ubiquitin conjugation to ER degradation) domain of the subunit ASCC2. Loss of this subunit impedes alkylation adduct repair kinetics and increases sensitivity to alkylating agents, but not other forms of DNA damage. We identify RING finger protein 113A (RNF113A) as the E3 ligase responsible for upstream ubiquitin signalling in the ASCC pathway. Cells from patients with X-linked trichothiodystrophy, which harbour a mutation in RNF113A, are defective in ASCC foci formation and are hypersensitive to alkylating agents. Together, our work reveals a previously unrecognized ubiquitin-dependent pathway induced specifically to repair alkylation damage, shedding light on the molecular mechanism of X-linked trichothiodystrophy.

Structure and assembly of the Ebola virus nucleocapsid

Wednesday November 8th, 2017 12:00:00 AM
Ebola and Marburg viruses are filoviruses: filamentous, enveloped viruses that cause haemorrhagic fever. Filoviruses are within the order Mononegavirales, which also includes rabies virus, measles virus, and respiratory syncytial virus. Mononegaviruses have non-segmented, single-stranded negative-sense RNA genomes that are encapsidated by nucleoprotein and other viral proteins to form a helical nucleocapsid. The nucleocapsid acts as a scaffold for virus assembly and as a template for genome transcription and replication. Insights into nucleoprotein–nucleoprotein interactions have been derived from structural studies of oligomerized, RNA-encapsidating nucleoprotein, and cryo-electron microscopy of nucleocapsid or nucleocapsid-like structures. There have been no high-resolution reconstructions of complete mononegavirus nucleocapsids. Here we apply cryo-electron tomography and subtomogram averaging to determine the structure of Ebola virus nucleocapsid within intact viruses and recombinant nucleocapsid-like assemblies. These structures reveal the identity and arrangement of the nucleocapsid components, and suggest that the formation of an extended α-helix from the disordered carboxy-terminal region of nucleoprotein-core links nucleoprotein oligomerization, nucleocapsid condensation, RNA encapsidation, and accessory protein recruitment.

Corrigendum: Superparamagnetic enhancement of thermoelectric performance

Wednesday November 8th, 2017 12:00:00 AM
Nature549, 247–251 (2017); doi:10.1038/nature23667In the Methods subsection ‘Measure the Hall coefficient’ of this Letter, the equation μH = neσ should read μH = σ/(ne). This error has been corrected online.

Erratum: Non-homeostatic body weight regulation through a brainstem-restricted receptor for GDF15

Wednesday November 8th, 2017 12:00:00 AM
Nature550, 255–259 (2017); doi:10.1038/nature24042Owing to an error during the production process, in Fig. 2c of this Letter, all four groups of mice were incorrectly labelled as ‘WT’ (wild type), but the two groups on the left

Corrigendum: High-throughput discovery of novel developmental phenotypes

Wednesday November 8th, 2017 12:00:00 AM
Nature537, 508–514 (2016); doi:10.1038/nature19356In this Article, the author Wolfgang Wurst was erroneously omitted from the author list. They are associated with the affiliations: HelmholtzZentrum Munich, Institute of Developmental Genetics, 85764 Munich-Neuherberg, Germany; Technical University of Munich,






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