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The quantum simulation of driven, strongly correlated phases at large scales is challenging, primarily due to detrimental heating effects. Now, a large-scale interacting Mott–Meissner phase has been realized in a neutral atom quantum simulator.

The authors study a Pt/Nb hybrid structure by scanning microscopy and muon spin rotation. They find an anomalous absence of Meissner screening near the Pt/Nb interface due to spin-triplet pair correlations driven by spin-orbit coupling alone with no ferromagnetic layer necessary.

Josephson vortices (JVs) play an important role in superconducting quantum devices, but they remain difficult to be observed and manipulated. Here, Dremov et al. report magnetic fingerprint of JVs in magnetic force microscopy experiments, which paves a way to generate and control JVs.

The study of magnetic-related phenomena under high-pressure conditions currently presents significant challenges. The authors develop an in-situ magnetic imaging technique at megabar pressures, revealing the magnetic transition of magnetite.

Elements in the alkali metal series are regarded as unlikely superconductors because of their monovalent character. This paper reports that lithium (the lightest alkali element) is a superconductor at ambient pressure with a transition temperature of 0.4 mK.

Interaction between Cooper pairs and other collective excitations may reveal important information about the pairing mechanism. Here, the authors observe a universal jump in the phase of the driven Higgs oscillations in cuprate thin films, indicating the presence of a coupled collective mode, as well as a nonvanishing Higgs-like response at high temperatures, suggesting a potential nonzero pairing amplitude above Tc.

Whole-genome bisulfite sequencing analysis of human embryonic stem cells shows that DNMT3 deficiency leads to global and local demethylation, which depends on TET activity. Dynamic loci overlap with putative somatic enhancers that are highly methylated in ESCs.

Controlling the motion and pinning of vortices is essential for developing superconducting electronics. Here, the authors reveal the vortex pinning nano-network in thin superconducting niobium films by developing a scanning quantum vortex microscopy approach.

Reduced representation bisulphite sequencing is used to generate genome-scale DNA methylation maps in mouse gametes and several stages of early, pre-implantation embryogenesis, allowing a base-pair resolution timeline of the changes in DNA methylation during developmental transitions.

Here the authors show that active DNA demethylation and transcription factor occupation at distal regulatory elements is essential for pluripotency maintenance in dormancy conditions.

Alexander Meissner and colleagues use CRISPR/Cas9 genome editing to inactivate the DNA methyltransferases DNMT1, DNMT3A and DNMT3B in human embryonic stem cells (ESCs). They find an essential role for DNMT1 in human ESCs and generate genome-wide maps of the DNA methylation changes that occur following inactivation of these enzymes.

To celebrate the first 20 years of Nature Reviews Genetics, we asked 12 leading scientists to reflect on the key challenges and opportunities faced by the field of genetics and genomics.

The Palaeocene–Eocene Thermal Maximum was associated with warming and seafloor carbonate dissolution. Numerical simulations suggest that the spread of deep corrosive water from the North Atlantic can explain the observed dissolution patterns.

Alex Meissner and colleagues report base pair–resolution methylation maps from donor fibroblasts and nuclear transfer–reconstructed mouse embryos. They compare methylation profiles to that present during normal fertilization and find that specific promoters and repeat elements exhibit differential dynamics.

Here, Libertini and colleagues devise a computation tool that can analyze whole-genome bisulfite sequencing (WGBS) data to recover of ∼30% of the lost differential methylation position information. They use COMETgazer and COMETvintage to analyze 13 diffferent methylome data to demonstrate their performance.

We report an ensemble of cold ⁸⁵Rb atoms strongly coupled to a superconducting resonator and optical cavity, resulting in the demonstration of quantum-enabled transduction of millimetre wave photons to optical photons.

Lineage-specific transcription factors and signalling pathways cooperate with pluripotency regulators to control the transcriptional networks that drive cell specification and exit from an embryonic stem cell state; here, we report genome-wide binding data for 38 transcription factors combined with analysis of epigenomic and gene expression data during the differentiation of human embryonic stem cells into the three germ layers.

A qPCR ScoreCard assay provides a faster, more quantitative and scalable alternative to the teratoma assay for evaluating human stem cell lines.

The authors present a characterization of complex X-linked lncRNA loci with sex- and allele-specific epigenetic signatures that serve as a platform for the largest chromatin structures in mammals, thereby elucidating diverse phenotypes and combinatorial effects on autosomes.

Whole-genome bisulphite sequencing data from diverse human cell and tissue types shows that only about 22% of CpGs change their methylation state across these cell types; most of these CpGs are located at gene regulatory elements, particularly enhancers and transcription-factor-binding sites, and these selected regions with dynamic DNA methylation patterns could help to define putative regulatory elements further.

The canonical DNA methylation maintenance enzyme Dnmt1 displays global de novo methylation activity with greater targeting towards IAP transposons, which may contribute to their stable repression during early development.

This study describes the integrative analysis of 111 reference human epigenomes, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression; the results annotate candidate regulatory elements in diverse tissues and cell types, their candidate regulators, and the set of human traits for which they show genetic variant enrichment, providing a resource for interpreting the molecular basis of human disease.

Direct measurements of carbon fixation rates in groundwater suggest a substantial contribution of in situ primary production to subsurface ecosystem processes.

Batki, Hetzel et al. report a lineage-tracing strategy to track extraembryonic gut endoderm cells over development. They find that these cells are eventually eliminated in a p53-dependent manner and neighbouring embryonic cells clear their remnants.

The integrative analysis of epigenetic footprints along consecutive stages of neural progenitors derived from human ES cells reveals regulatory mechanisms that orchestrate stage-specific differentiation.

Slide-seq profiling of mouse embryos at the onset of organogenesis (embryonic days 8.5–9.5) coupled with a new three-dimensional reconstruction and visualization tool (sc3D) provides high-resolution maps of spatiotemporal gene expression dynamics.

The presence of axion-like dark matter candidates is expected to induce an oscillating magnetic field, enhanced by a ferromagnet. Limits on the electromagnetic coupling strength of axion-like particles are reported over a mass range spanning three decades.

The establishment of a drug-discovery screening pipeline for cryptosporidiosis, and identification of pyrazolopyridines as selective ATP-competitive inhibitors of the Cryptosporidium lipid kinase PI(4)K.

In hepatocellular carcinoma driven by non-alcoholic steatohepatitis, aberrant T cell activation and impaired immune surveillance seem to make hepatocellular carcinoma less responsive to anti-PD1 or anti-PDL1 immunotherapy.

Analysis of global remethylation in mouse embryos at several developmental stages identifies an epigenetic landscape that partitions extraembryonic tissues within the embryo and resembles a frequent, global departure in genome regulation in human cancers.

A connectome of the right optic lobe from a male fruitfly is presented together with an extensive collection of genetic drivers matched to a comprehensive neuron-type catalogue.

A multi-channel molecular recording technique is applied as a lineage tracer to assemble cell-fate maps from fertilization through gastrulation in the mouse, providing insights into ontogeny in a complex multicellular organism.

A lag in nascent strand DNA methylation contributes to heterogeneous methylation in asynchronous cell populations, but cancer cells and active transcription factor binding sites preserve heterogeneity even after cell cycle arrest.

Barriers underlying the inefficiency of reprogramming cells to pluripotency are poorly defined. Here the authors identify a transient interval soon after pluripotency exit that permits high-efficiency reprogramming and is facilitated by OCT4 bound elements displaying unique silencing behaviour during differentiation.

A nonreciprocal critical current is known as the superconducting diode effect (SDE). Here, the authors use SQUID-on-tip to study SDE in a EuS/Nb bilayer and find that the stray field from magnetized EuS creates screening currents in the Nb, which lead to SDE by affecting vortex flow dynamics.

Weigert et al. show that an antagonistic relationship between DNA methyltransferase and Polycomb activity is globally responsible for the maintenance of intermediate methylation levels observed in trophoblast stem cells.

In the superconductor Sr2RuO4, in-plane strain is known to enhance both the superconducting transition temperature Tc and upper critical field Hc2, but the effect of out-of-plane strain has not been studied. Here, the authors find that Hc2 is enhanced under out-of-plane strain, but Tc unexpectedly decreases.

An experimental and analytical pipeline is used to assess, at the single-cell level, complex transcriptional and morphological mutant phenotypes that occur in mouse embryos during gastrulation.

The addition of a Notch signaling inhibitor to both mouse and human keratinocytes bypasses the use of oncogenes and p53 to increase transcription factor mediated–pluripotent stem cell reprogramming through blocking p21 expression.