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At least 1,441 records · Page 80

Cross-HLA targeting of intracellular oncoproteins with peptide-centric CARs

The majority of oncogenic drivers are intracellular proteins, thus constraining their immunotherapeutic targeting to mutated peptides (neoantigens) presented by individual human leukocyte antigen (HLA) allotypes. However, most cancers have a modest mutational burden that is insufficient to generate responses using neoantigen-based therapies. Neuroblastoma is a paediatric cancer that harbours few mutations and is instead driven by epigenetically deregulated transcriptional networks. Here we show that the neuroblastoma immunopeptidome is enriched with peptides derived from proteins that are essential for tumourigenesis and focus on targeting the unmutated peptide QYNPIRTTF, discovered on HLA-A*24:02, which is derived from the neuroblastoma dependency gene and master transcriptional regulator PHOX2B. To target QYNPIRTTF, we developed peptide-centric chimeric antigen receptors (CARs) using a counter-panning strategy with predicted potentially cross-reactive peptides. We further hypothesized that peptide-centric CARs could recognize peptides on additional HLA allotypes when presented in a similar manner. Informed by computational modelling, we showed that PHOX2B peptide-centric CARs also recognize QYNPIRTTF presented by HLA-A*23:01 and the highly divergent HLA-B*14:02. Finally, we demonstrated potent and specific killing of neuroblastoma cells expressing these HLAs in vitro and complete tumour regression in mice. These data suggest that peptide-centric CARs have the potential to vastly expand the pool of immunotherapeutic targets to include non-immunogenic intracellular oncoproteins and widen the population of patients who would benefit from such therapy by breaking conventional HLA restriction.

59 BASIC BIOLOGICAL SCIENCES↗

Ferroelectric incommensurate spin crystals

Ferroics, especially ferromagnets, can form complextopological spin structures such as vortices and skyrmions when subjected to particular electrical and mechanical boundary conditions. Simple vortex-like, electric-dipole-based topological structures have been observed in dedicated ferroelectric systems, especially ferroelectric-insulator superlattices such as PbTiO 3 /SrTiO 3 , which was later shown to be a model system owing to its high depolarizing field. To date, the electric dipole equivalent of ordered magnetic spin lattices driven by the Dzyaloshinskii-Moriya interaction (DMi) has not been experimentally observed. Here we examine a domain structure in a single PbTiO 3 epitaxial layer sandwiched between SrRuO 3 electrodes. In this work, we observe periodic clockwise and anticlockwise ferroelectric vortices that are modulated by a second ordering along their toroidal core. The resulting topology, supported by calculations, is a labyrinth-like pattern with two orthogonal periodic modulations that form an incommensurate polar crystal that provides a ferroelectric analogue to the recently discovered incommensurate spin crystals in ferromagnetic materials. These findings further blur the border between emergent ferromagnetic and ferroelectrictopologies, clearing the way for experimental realization of further electric counterparts of magnetic DMi-driven phases.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Instantaneous tracking of earthquake growth with elastogravity signals

Rapid and reliable estimation of large earthquake magnitude (above 8) is key to mitigating the risks associated with strong shaking and tsunamis. Standard early warning systems based on seismic waves fail to rapidly estimate the size of such large earthquakes. Geodesy-based approaches provide better estimations, but are also subject to large uncertainties and latency associated with the slowness of seismic waves. Recently discovered speed-of-light prompt elastogravity signals (PEGS) have raised hopes that these limitations may be overcome, but have not been tested for operational early warning. Here we show that PEGS can be used in real time to track earthquake growth instantaneously after the event reaches a certain magnitude. We develop a deep learning model that leverages the information carried by PEGS recorded by regional broadband seismometers in Japan before the arrival of seismic waves. After training on a database of synthetic waveforms augmented with empirical noise, we show that the algorithm can instantaneously track an earthquake source time function on real data. Our model unlocks ‘true real-time’ access to the rupture evolution of large earthquakes using a portion of seismograms that is routinely treated as noise, and can be immediately transformative for tsunami early warning.

58 GEOSCIENCES↗

A detailed map of Higgs boson interactions by the ATLAS experiment ten years after the discovery

The standard model of particle physics describes the known fundamental particles and forces that make up our Universe, with the exception of gravity. One of the central features of the standard model is a field that permeates all of space and interacts with fundamental particles. The quantum excitation of this field, known as the Higgs field, manifests itself as the Higgs boson, the only fundamental particle with no spin. In 2012, a particle with properties consistent with the Higgs boson of the standard model was observed by the ATLAS and CMS experiments at the Large Hadron Collider at CERN. Since then, more than 30 times as many Higgs bosons have been recorded by the ATLAS experiment, enabling much more precise measurements and new tests of the theory. Here, on the basis of this larger dataset, we combine an unprecedented number of production and decay processes of the Higgs boson to scrutinize its interactions with elementary particles. Interactions with gluons, photons, and W and Z bosons—the carriers of the strong, electromagnetic and weak forces—are studied in detail. Interactions with three third-generation matter particles (bottom (b) and top (t) quarks, and tau leptons (τ)) are well measured and indications of interactions with a second-generation particle (muons, μ) are emerging. These tests reveal that the Higgs boson discovered ten years ago is remarkably consistent with the predictions of the theory and provide stringent constraints on many models of new phenomena beyond the standard model.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Borgs are giant genetic elements with potential to expand metabolic capacity

Anaerobic methane oxidation exerts a key control on greenhouse gas emissions1, yet factors that modulate the activity of microorganisms performing this function remain poorly understood. Here we discovered extraordinarily large, diverse DNA sequences that primarily encode hypothetical proteins through studying groundwater, sediments and wetland soil where methane production and oxidation occur. Four curated, complete genomes are linear, up to approximately 1 Mb in length and share genome organization, including replichore structure, long inverted terminal repeats and genome-wide unique perfect tandem direct repeats that are intergenic or generate amino acid repeats. We infer that these are highly divergent archaeal extrachromosomal elements with a distinct evolutionary origin. Gene sequence similarity, phylogeny and local divergence of sequence composition indicate that many of their genes were assimilated from methane-oxidizing Methanoperedens archaea. We refer to these elements as ‘Borgs’. We identified at least 19 different Borg types coexisting with Methanoperedens spp. in four distinct ecosystems. Borgs provide methane-oxidizing Methanoperedens archaea access to genes encoding proteins involved in redox reactions and energy conservation (for example, clusters of multihaem cytochromes and methyl coenzyme M reductase). These data suggest that Borgs might have previously unrecognized roles in the metabolism of this group of archaea, which are known to modulate greenhouse gas emissions, but further studies are now needed to establish their functional relevance.

59 BASIC BIOLOGICAL SCIENCES↗

Anomalous thermal transport under high pressure in boron arsenide

High pressure represents extreme environments and provides opportunities for materials discovery. Thermal transport under high hydrostatic pressure has been investigated for more than 100 years and all measurements of crystals so far have indicated a monotonically increasing lattice thermal conductivity. Here we report in situ thermal transport measurements in the newly discovered semiconductor crystal boron arsenide, and observe an anomalous pressure dependence of the thermal conductivity. We use ultrafast optics, Raman spectroscopy and inelastic X-ray scattering measurements to examine the phonon bandstructure evolution of the optical and acoustic branches, as well as thermal conductivity under varied temperatures and pressures up to 32 gigapascals. Using atomistic theory, we attribute the anomalous high-pressure behaviour to competitive heat conduction channels from interactive high-order anharmonicity physics inherent to the unique phonon bandstructure. Our study verifies ab initio theory calculations and we show that the phonon dynamics—resulting from competing three-phonon and four-phonon scattering processes—are beyond those expected from classical models and seen in common materials. In conclusion, this work uses high-pressure spectroscopy combined with atomistic theory as a powerful approach to probe complex phonon physics and provide fundamental insights for understanding microscopic energy transport in materials of extreme properties.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

A swapped genetic code prevents viral infections and gene transfer

Engineering the genetic code of an organism has been proposed to provide a firewall from natural ecosystems by preventing viral infections and gene transfer. However, numerous viruses and mobile genetic elements encode parts of the translational apparatus, potentially rendering a genetic-code-based firewall ineffective. Here we show that such mobile transfer RNAs (tRNAs) enable gene transfer and allow viral replication in Escherichia coli despite the genome-wide removal of 3 of the 64 codons and the previously essential cognate tRNA and release factor genes. We then establish a genetic firewall by discovering viral tRNAs that provide exceptionally efficient codon reassignment allowing us to develop cells bearing an amino acid-swapped genetic code that reassigns two of the six serine codons to leucine during translation. This amino acid-swapped genetic code renders cells resistant to viral infections by mistranslating viral proteomes and prevents the escape of synthetic genetic information by engineered reliance on serine codons to produce leucine-requiring proteins. As these cells may have a selective advantage over wild organisms due to virus resistance, we also repurpose a third codon to biocontain this virus-resistant host through dependence on an amino acid not found in nature. Furthermore, our results may provide the basis for a general strategy to make any organism safely resistant to all natural viruses and prevent genetic information flow into and out of genetically modified organisms.

59 BASIC BIOLOGICAL SCIENCES↗

Ubiquitin-like conjugation by bacterial cGAS enhances anti-phage defence

Abstract cGAS is an evolutionarily conserved enzyme that has a pivotal role in immune defence against infection 1–3 . In vertebrate animals, cGAS is activated by DNA to produce cyclic GMP–AMP (cGAMP) 4,5 , which leads to the expression of antimicrobial genes 6,7 . In bacteria, cyclic dinucleotide (CDN)-based anti-phage signalling systems (CBASS) have been discovered 8–11 . These systems are composed of cGAS-like enzymes and various effector proteins that kill bacteria on phage infection, thereby stopping phage spread. Of the CBASS systems reported, approximately 39% contain Cap2 and Cap3 , which encode proteins with homology to ubiquitin conjugating (E1/E2) and deconjugating enzymes, respectively 8,12 . Although these proteins are required to prevent infection of some bacteriophages 8 , the mechanism by which the enzymatic activities exert an anti-phage effect is unknown. Here we show that Cap2 forms a thioester bond with the C-terminal glycine of cGAS and promotes conjugation of cGAS to target proteins in a process that resembles ubiquitin conjugation. The covalent conjugation of cGAS increases the production of cGAMP. Using a genetic screen, we found that the phage protein Vs.4 antagonized cGAS signalling by binding tightly to cGAMP (dissociation constant of approximately 30 nM) and sequestering it. A crystal structure of Vs.4 bound to cGAMP showed that Vs.4 formed a hexamer that was bound to three molecules of cGAMP. These results reveal a ubiquitin-like conjugation mechanism that regulates cGAS activity in bacteria and illustrates an arms race between bacteria and viruses through controlling CDN levels.

Science & Technology - Other Topics↗

Detection of a pair density wave state in UTe2

Abstract Spin-triplet topological superconductors should exhibit many unprecedented electronic properties, including fractionalized electronic states relevant to quantum information processing. Although UTe 2 may embody such bulk topological superconductivity 1–11 , its superconductive order parameter Δ( k ) remains unknown 12 . Many diverse forms for Δ( k ) are physically possible 12 in such heavy fermion materials 13 . Moreover, intertwined 14,15 density waves of spin (SDW), charge (CDW) and pair (PDW) may interpose, with the latter exhibiting spatially modulating 14,15 superconductive order parameter Δ( r ), electron-pair density 16–19 and pairing energy gap 17,20–23 . Hence, the newly discovered CDW state 24 in UTe 2 motivates the prospect that a PDW state may exist in this material 24,25 . To search for it, we visualize the pairing energy gap with μeV-scale energy resolution using superconductive scanning tunnelling microscopy (STM) tips 26–31 . We detect three PDWs, each with peak-to-peak gap modulations of around 10 μeV and at incommensurate wavevectors P i =1,2,3 that are indistinguishable from the wavevectors Q i =1,2,3 of the prevenient 24 CDW. Concurrent visualization of the UTe 2 superconductive PDWs and the non-superconductive CDWs shows that every P i : Q i pair exhibits a relative spatial phase δϕ ≈ π. From these observations, and given UTe 2 as a spin-triplet superconductor 12 , this PDW state should be a spin-triplet PDW 24,25 . Although such states do exist 32 in superfluid 3 He, for superconductors, they are unprecedented.

Science & Technology - Other Topics↗

Quantum textures of the many-body wavefunctions in magic-angle graphene

Interactions among electrons create novel many-body quantum phases of matter with wavefunctions that often reflect electronic correlation effects, broken symmetries, and novel collective excitations. A wide range of quantum phases has been discovered in MATBG, including correlated insulating, unconventional superconducting, and magnetic topological phases. The lack of microscopic information, including precise knowledge of possible broken symmetries, has thus far hampered our understanding of MATBG's correlated phases. Here we use high-resolution scanning tunneling microscopy to directly probe the wavefunctions of the correlated phases in MATBG. The squares of the wavefunctions of gapped phases, including those of the correlated insulators, pseudogap, and superconducting phases, show distinct patterns of broken symmetry with a √3 x √3 super-periodicity on the graphene atomic lattice that has a complex spatial dependence on the moiré superlattice scale. We introduce a symmetry-based analysis to describe our measurements of the wavefunctions of MATBG's correlated phases with a set of complex-valued local order parameters. For the correlated insulators in MATBG, at fillings of ±2 electrons per moiré unit cell relative to charge neutrality, we compare the observed quantum textures to those expected for proposed theoretical ground states. In typical MATBG devices, the textures of correlated insulators' wavefunctions closely match those of the theoretically proposed IKS order, while in ultra-low-strain samples our data has local symmetries like those of a T-IVC phase. Here, we also study the wavefunction of MATBG's superconducting state, revealing strong signatures of intervalley coherence that can only be distinguished from those of the insulator with our phase-sensitive measurements.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Single-cell quantification of ribosome occupancy in early mouse development

Translation regulation is critical for early mammalian embryonic development. However, previous studies had been restricted to bulk measurements, precluding precise determination of translation regulation including allele-specific analyses. Here, to address this challenge, we developed a novel microfluidic isotachophoresis (ITP) approach, named RIBOsome profiling via ITP (Ribo-ITP), and characterized translation in single oocytes and embryos during early mouse development. We identified differential translation efficiency as a key mechanism regulating genes involved in centrosome organization and N 6 -methyladenosine modification of RNAs. Our high-coverage measurements enabled, to our knowledge, the first analysis of allele-specific ribosome engagement in early development. These led to the discovery of stage-specific differential engagement of zygotic RNAs with ribosomes and reduced translation efficiency of transcripts exhibiting allele-biased expression. By integrating our measurements with proteomics data, we discovered that ribosome occupancy in germinal vesicle-stage oocytes is the predominant determinant of protein abundance in the zygote. The Ribo-ITP approach will enable numerous applications by providing high-coverage and high-resolution ribosome occupancy measurements from ultra-low input samples including single cells.

59 BASIC BIOLOGICAL SCIENCES↗

Targeting of intracellular oncoproteins with peptide-centric CARs

The majority of oncogenic drivers are intracellular proteins, constraining their immunotherapeutic targeting to mutated peptides (neoantigens) presented by individual human leukocyte antigen (HLA) allotypes. However, most cancers have a modest mutational burden that is insufficient for generating responses using neoantigen-based therapies. Neuroblastoma is a paediatric cancer that harbours few mutations and is instead driven by epigenetically deregulated transcriptional networks. Here we show that the neuroblastoma immunopeptidome is enriched with peptides derived from proteins essential for tumorigenesis. We focused on targeting the unmutated peptide QYNPIRTTF discovered on HLA-A*24:02, which is derived from the neuroblastoma-dependency gene and master transcriptional regulator PHOX2B. To target QYNPIRTTF, we developed peptide-centric chimeric antigen receptors (PC-CARs) through a counter panning strategy using predicted potentially cross-reactive peptides. We further proposed that PC-CARs can recognize peptides on additional HLA allotypes when presenting a similar overall molecular surface. Informed by our computational modelling results, we show that PHOX2B PC-CARs also recognize QYNPIRTTF presented by HLA-A*23:01, the most common non-A2 allele in people with African ancestry. Finally, we demonstrate potent and specific killing of neuroblastoma cells expressing these HLAs in vitro and complete tumour regression in mice. These data suggest that PC-CARs have the potential to expand the pool of immunotherapeutic targets to include non-immunogenic intracellular oncoproteins and allow targeting through additional HLA allotypes in a clinical setting.

60 APPLIED LIFE SCIENCES↗

Imaging the Meissner effect in hydride superconductors using quantum sensors

By directly altering microscopic interactions, pressure provides a powerful tuning knob for the exploration of condensed phases and geophysical phenomena. Here, the megabar regime represents an interesting frontier, in which recent discoveries include high-temperature superconductors, as well as structural and valence phase transitions. However, at such high pressures, many conventional measurement techniques fail. Here we demonstrate the ability to perform local magnetometry inside a diamond anvil cell with sub-micron spatial resolution at megabar pressures. Our approach uses a shallow layer of nitrogen-vacancy colour centres implanted directly within the anvil; crucially, we choose a crystal cut compatible with the intrinsic symmetries of the nitrogen-vacancy centre to enable functionality at megabar pressures. We apply our technique to characterize a recently discovered hydride superconductor, CeH 9 . By performing simultaneous magnetometry and electrical transport measurements, we observe the dual signatures of superconductivity: diamagnetism characteristic of the Meissner effect and a sharp drop of the resistance to near zero. By locally mapping both the diamagnetic response and flux trapping, we directly image the geometry of superconducting regions, showing marked inhomogeneities at the micron scale. Our work brings quantum sensing to the megabar frontier and enables the closed-loop optimization of superhydride materials synthesis.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Superconductivity in pressurized trilayer La 4 Ni 3 O 10-$δ$ single crystals

In this study, the pursuit of discovering new high-temperature superconductors that diverge from the copper-based model has profound implications for explaining mechanisms behind superconductivity and may also enable new applications. Here our investigation shows that the application of pressure effectively suppresses the spin–charge order in trilayer nickelate La 4 Ni 3 O 10-δ single crystals, leading to the emergence of superconductivity with a maximum critical temperature (T c ) of around 30 K at 69.0 GPa. The d.c. susceptibility measurements confirm a substantial diamagnetic response below T c , indicating the presence of bulk superconductivity with a volume fraction exceeding 80%. In the normal state, we observe a strange metal behaviour, characterized by a linear temperature-dependent resistance extending up to 300 K. Furthermore, the layer-dependent superconductivity observed hints at a unique interlayer coupling mechanism specific to nickelates, setting them apart from cuprates in this regard. Our findings provide crucial insights into the fundamental mechanisms underpinning superconductivity, while also introducing a new material platform to explore the intricate interplay between the spin–charge order, flat band structures, interlayer coupling, strange metal behaviour and high-temperature superconductivity.

36 MATERIALS SCIENCE↗

Opto-twistronic Hall effect in a three-dimensional spiral lattice

Studies of moire systems have elucidated the exquisite effect of quantum geometry on the electronic bands and their properties, leading to the discovery of new correlated phases. However, most experimental studies have been confined to a few layers in the 2D limit. The extension of twistronics to its 3D limit, where the twist is extended into the third dimension between adjacent layers, remains underexplored due to the challenges in precisely stacking layers. Here, in this study, we focus on 3D twistronics on a platform of self-assembled spiral superlattice of multilayered WS 2 . Our findings reveal an opto-twistronic Hall effect in the spiral superlattice. This mesoscopic response is an experimental manifestation of the noncommutative geometry that arises when translational symmetry is replaced by a non-symmorphic screw operation. We also discover signatures of altered laws of optical excitation, manifested as an unconventional photon momentum-lattice interaction owing to moire of moire modulations in the 3D twistronic system. Crucially, our findings mark the initial identification of higher-order quantum geometrical tensors in light-matter interactions. This breakthrough opens new avenues for designing quantum materials-based optical lattices with large nonlinearities, paving the way for the development of advanced quantum nanophotonic devices.

Ji, Zhurun↗

Signatures of ambient pressure superconductivity in thin film La 3 Ni 2 O 7

Recently, the bilayer nickelate La 3 Ni 2 O 7 has been discovered as a new superconductor with transition temperature T c near 80 K under high pressure. Despite extensive theoretical and experimental work to understand the nature of its superconductivity, the requirement of extreme pressure restricts the use of many experimental probes and limits its application potential. Here, in this work, we present signatures of superconductivity in La 3 Ni 2 O 7 thin films at ambient pressure, facilitated by the application of epitaxial compressive strain. The onset T c varies approximately from 26 K to 42 K, with higher T c values correlating with smaller in-plane lattice constants. We observed the co-existence of other Ruddlesden-Popper phases within the films and dependence of transport behavior with ozone annealing, suggesting that the observed low zero resistance T c of around 2 K can be attributed to stacking defects, grain boundaries, and oxygen stoichiometry. This finding initiates numerous opportunities to stabilize and study superconductivity in bilayer nickelates at ambient pressure, and to facilitate the broad understanding of the ever-growing number of high temperature and unconventional superconductors in the transition metal oxides.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Magnetically and optically active edges in phosphorene nanoribbons

Abstract Nanoribbons, nanometre-wide strips of a two-dimensional material, are a unique system in condensed matter. They combine the exotic electronic structures of low-dimensional materials with an enhanced number of exposed edges, where phenomena including ultralong spin coherence times 1,2 , quantum confinement 3 and topologically protected states 4,5 can emerge. An exciting prospect for this material concept is the potential for both a tunable semiconducting electronic structure and magnetism along the nanoribbon edge, a key property for spin-based electronics such as (low-energy) non-volatile transistors 6 . Here we report the magnetic and semiconducting properties of phosphorene nanoribbons (PNRs). We demonstrate that at room temperature, films of PNRs show macroscopic magnetic properties arising from their edge, with internal fields of roughly 240 to 850 mT. In solution, a giant magnetic anisotropy enables the alignment of PNRs at sub-1-T fields. By leveraging this alignment effect, we discover that on photoexcitation, energy is rapidly funnelled to a state that is localized to the magnetic edge and coupled to a symmetry-forbidden edge phonon mode. Our results establish PNRs as a fascinating system for studying the interplay between magnetism and semiconducting ground states at room temperature and provide a stepping-stone towards using low-dimensional nanomaterials in quantum electronics.

Science & Technology - Other Topics↗

Cooper-pair density modulation state in an iron-based superconductor

Superconducting (SC) states that break space-group symmetries of the underlying crystal can exhibit nontrivial spatial modulation of the order parameter. Previously, such states were intimately associated with the breaking of translational symmetry, resulting in the density-wave orders, with wavelengths spanning several unit cells. However, a related basic concept has long been overlooked: when only intra-unit-cell symmetries of the space group are broken, the SC states can show a distinct type of nontrivial modulation preserving long-range lattice translation. Here, in this study, we refer to this new concept as the pair density modulation (PDM) and report the first observation of a PDM state in exfoliated thin flakes of the iron-based superconductor FeTe 0.55 Se 0.45 . Using scanning tunnelling microscopy (STM), we discover robust SC gap modulation with the wavelength corresponding to the lattice periodicity and the amplitude exceeding 30% of the gap average. Notably, we find that the observed modulation originates from the large difference in SC gaps on the two nominally equivalent iron sublattices. The experimental findings, backed up by model calculations, suggest that, in contrast to the density-wave orders, the PDM state is driven by the interplay of sublattice symmetry breaking and a peculiar nematic distortion specific to the thin flakes. Our results establish new frontiers for exploring the intertwined orders in strong-correlated electronic systems and open a new chapter for iron-based superconductors.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗