3D Genome of macaque fetal brain reveals evolutionary innovations during primate corticogenesis.

Elucidating the regulatory mechanisms of human brain evolution is essential to understanding human cognition and mental disorders. We generated multi-omics profiles and constructed a high-resolution map of 3D genome architecture of rhesus macaque during corticogenesis. By comparing the 3D genomes of human, macaque, and mouse brains, we identified many human-specific chromatin structure changes, including 499 topologically associating domains (TADs) and 1,266 chromatin loops. The human-specific loops are significantly enriched in enhancer-enhancer interactions, and the regulated genes show human-specific expression changes in the subplate, a transient zone of the developing brain critical for neural circuit formation and plasticity. Notably, many human-specific sequence changes are located in the human-specific TAD boundaries and loop anchors, which may generate new transcription factor binding sites and chromatin structures in human. Collectively, the presented data highlight the value of comparative 3D genome analyses in dissecting the regulatory mechanisms of brain development and evolution.

Somatic Mutations Increase Hepatic Clonal Fitness and Regeneration in Chronic Liver Disease.

Normal tissues accumulate genetic changes with age, but it is unknown if somatic mutations promote clonal expansion of non-malignant cells in the setting of chronic degenerative diseases. Exome sequencing of diseased liver samples from 82 patients revealed a complex mutational landscape in cirrhosis. Additional ultra-deep sequencing identified recurrent mutations in PKD1, PPARGC1B, KMT2D, and ARID1A. The number and size of mutant clones increased as a function of fibrosis stage and tissue damage. To interrogate the functional impact of mutated genes, a pooled in vivo CRISPR screening approach was established. In agreement with sequencing results, examination of 147 genes again revealed that loss of Pkd1, Kmt2d, and Arid1a promoted clonal expansion. Conditional heterozygous deletion of these genes in mice was also hepatoprotective in injury assays. Pre-malignant somatic alterations are often viewed through the lens of cancer, but we show that mutations can promote regeneration, likely independent of carcinogenesis.

Ultracold field-linked tetratomic molecules.

Ultracold polyatomic molecules offer opportunities1 in cold chemistry2,3, precision measurements4 and quantum information processing5,6, because of their rich internal structure. However, their increased complexity compared with diatomic molecules presents a challenge in using conventional cooling techniques. Here we demonstrate an approach to create weakly bound ultracold polyatomic molecules by electroassociation7 (F.D. et al., manuscript in preparation) in a degenerate Fermi gas of microwave-dressed polar molecules through a field-linked resonance8-11. Starting from ground-state NaK molecules, we create around 1.1 × 103 weakly bound tetratomic (NaK)2 molecules, with a phase space density of 0.040(3) at a temperature of 134(3) nK, more than 3,000 times colder than previously realized tetratomic molecules12. We observe a maximum tetramer lifetime of 8(2) ms in free space without a notable change in the presence of an optical dipole trap, indicating that these tetramers are collisionally stable. Moreover, we directly image the dissociated tetramers through microwave-field modulation to probe the anisotropy of their wavefunction in momentum space. Our result demonstrates a universal tool for assembling weakly bound ultracold polyatomic molecules from smaller polar molecules, which is a crucial step towards Bose-Einstein condensation of polyatomic molecules and towards a new crossover from a dipolar Bardeen-Cooper-Schrieffer superfluid13-15 to a Bose-Einstein condensation of tetramers. Moreover, the long-lived field-linked state provides an ideal starting point for deterministic optical transfer to deeply bound tetramer states16-18.

Homogenized contact in all-perovskite tandems using tailored 2D perovskite.

The fabrication of scalable all-perovskite tandem solar cells is considered an attractive route to commercialize perovskite photovoltaic modules1. However, The certified efficiency of 1-cm2 scale all-perovskite tandem solar cells lags behind their small-area (~0.1 cm2) counterparts2,3. This performance deficit originates from inhomogeneity in wide-bandgap (WBG) perovskite solar cells (PSCs) at a large scale. The inhomogeneity is known to be introduced at the bottom interface and within the perovskite bulk itself4,5. Here we uncover another crucial source for the inhomogeneity - the top interface formed during the deposition of the electron transport layer (ETL, C60). Meanwhile, the poor ETL interface is also a significant limitation of device performance. We address this issue by introducing a mixture of 4-fluorophenethylamine (F-PEA) and 4-trifluoromethyl-phenylammonium (CF3-PA) to create a tailored two-dimensional perovskite layer (TTDL), in which F-PEA forms a two-dimensional perovskite at the surface reducing contact losses and inhomogeneity, CF3-PA enhances charge extraction and transport. As a result, we demonstrate a high open-circuit voltage of 1.35 V and an efficiency of 20.5% in 1.77-eV WBG PSCs at a square centimeter scale. By stacking with a narrow-bandgap perovskite sub-cell, we report 1.05 cm2 all-perovskite tandem cells delivering 28.5% (certified 28.2%) efficiency, the highest among all reported so far. Our work showcases the importance of treating the top perovskite/ETL contact for upscaling perovskite solar cells.

Field-linked resonances of polar molecules.

Scattering resonances are an essential tool for controlling the interactions of ultracold atoms and molecules. However, conventional Feshbach scattering resonances1, which have been extensively studied in various platforms1-7, are not expected to exist in most ultracold polar molecules because of the fast loss that occurs when two molecules approach at a close distance8-10. Here we demonstrate a new type of scattering resonance that is universal for a wide range of polar molecules. The so-called field-linked resonances11-14 occur in the scattering of microwave-dressed molecules because of stable macroscopic tetramer states in the intermolecular potential. We identify two resonances between ultracold ground-state sodium-potassium molecules and use the microwave frequencies and polarizations to tune the inelastic collision rate by three orders of magnitude, from the unitary limit to well below the universal regime. The field-linked resonance provides a tuning knob to independently control the elastic contact interaction and the dipole-dipole interaction, which we observe as a modification in the thermalization rate. Our result provides a general strategy for resonant scattering between ultracold polar molecules, which paves the way for realizing dipolar superfluids15 and molecular supersolids16, as well as assembling ultracold polyatomic molecules.

Evaporation of microwave-shielded polar molecules to quantum degeneracy.

Ultracold polar molecules offer strong electric dipole moments and rich internal structure, which makes them ideal building blocks to explore exotic quantum matter1-9, implement quantum information schemes10-12 and test the fundamental symmetries of nature13. Realizing their full potential requires cooling interacting molecular gases deeply into the quantum-degenerate regime. However, the intrinsically unstable collisions between molecules at short range have so far prevented direct cooling through elastic collisions to quantum degeneracy in three dimensions. Here we demonstrate evaporative cooling of a three-dimensional gas of fermionic sodium-potassium molecules to well below the Fermi temperature using microwave shielding. The molecules are protected from reaching short range with a repulsive barrier engineered by coupling rotational states with a blue-detuned circularly polarized microwave. The microwave dressing induces strong tunable dipolar interactions between the molecules, leading to high elastic collision rates that can exceed the inelastic ones by at least a factor of 460. This large elastic-to-inelastic collision ratio allows us to cool the molecular gas to 21 nanokelvin, corresponding to 0.36 times the Fermi temperature. Such cold and dense samples of polar molecules open the path to the exploration of many-body phenomena with strong dipolar interactions.

STING controls nociception via type I interferon signalling in sensory neurons.

The innate immune regulator STING is a critical sensor of self- and pathogen-derived DNA. DNA sensing by STING leads to the induction of type-I interferons (IFN-I) and other cytokines, which promote immune-cell-mediated eradication of pathogens and neoplastic cells1,2. STING is also a robust driver of antitumour immunity, which has led to the development of STING activators and small-molecule agonists as adjuvants for cancer immunotherapy3. Pain, transmitted by peripheral nociceptive sensory neurons (nociceptors), also aids in host defence by alerting organisms to the presence of potentially damaging stimuli, including pathogens and cancer cells4,5. Here we demonstrate that STING is a critical regulator of nociception through IFN-I signalling in peripheral nociceptors. We show that mice lacking STING or IFN-I signalling exhibit hypersensitivity to nociceptive stimuli and heightened nociceptor excitability. Conversely, intrathecal activation of STING produces robust antinociception in mice and non-human primates. STING-mediated antinociception is governed by IFN-Is, which rapidly suppress excitability of mouse, monkey and human nociceptors. Our findings establish the STING-IFN-I signalling axis as a critical regulator of physiological nociception and a promising new target for treating chronic pain.

Virtual-scanning light-field microscopy for robust snapshot high-resolution volumetric imaging.

High-speed three-dimensional (3D) intravital imaging in animals is useful for studying transient subcellular interactions and functions in health and disease. Light-field microscopy (LFM) provides a computational solution for snapshot 3D imaging with low phototoxicity but is restricted by low resolution and reconstruction artifacts induced by optical aberrations, motion and noise. Here, we propose virtual-scanning LFM (VsLFM), a physics-based deep learning framework to increase the resolution of LFM up to the diffraction limit within a snapshot. By constructing a 40 GB high-resolution scanning LFM dataset across different species, we exploit physical priors between phase-correlated angular views to address the frequency aliasing problem. This enables us to bypass hardware scanning and associated motion artifacts. Here, we show that VsLFM achieves ultrafast 3D imaging of diverse processes such as the beating heart in embryonic zebrafish, voltage activity in Drosophila brains and neutrophil migration in the mouse liver at up to 500 volumes per second.

Engineering covalently bonded 2D layered materials by self-intercalation.

Two-dimensional (2D) materials1-5 offer a unique platform from which to explore the physics of topology and many-body phenomena. New properties can be generated by filling the van der Waals gap of 2D materials with intercalants6,7; however, post-growth intercalation has usually been limited to alkali metals8-10. Here we show that the self-intercalation of native atoms11,12 into bilayer transition metal dichalcogenides during growth generates a class of ultrathin, covalently bonded materials, which we name ic-2D. The stoichiometry of these materials is defined by periodic occupancy patterns of the octahedral vacancy sites in the van der Waals gap, and their properties can be tuned by varying the coverage and the spatial arrangement of the filled sites7,13. By performing growth under high metal chemical potential14,15 we can access a range of tantalum-intercalated TaS(Se)y, including 25% Ta-intercalated Ta9S16, 33.3% Ta-intercalated Ta7S12, 50% Ta-intercalated Ta10S16, 66.7% Ta-intercalated Ta8Se12 (which forms a Kagome lattice) and 100% Ta-intercalated Ta9Se12. Ferromagnetic order was detected in some of these intercalated phases. We also demonstrate that self-intercalated V11S16, In11Se16 and FexTey can be grown under metal-rich conditions. Our work establishes self-intercalation as an approach through which to grow a new class of 2D materials with stoichiometry- or composition-dependent properties.

On-device phase engineering.

In situ tailoring of two-dimensional materials' phases under external stimulus facilitates the manipulation of their properties for electronic, quantum and energy applications. However, current methods are mainly limited to the transitions among phases with unchanged chemical stoichiometry. Here we propose on-device phase engineering that allows us to realize various lattice phases with distinct chemical stoichiometries. Using palladium and selenide as a model system, we show that a PdSe2 channel with prepatterned Pd electrodes can be transformed into Pd17Se15 and Pd4Se by thermally tailoring the chemical composition ratio of the channel. Different phase configurations can be obtained by precisely controlling the thickness and spacing of the electrodes. The device can be thus engineered to implement versatile functions in situ, such as exhibiting superconducting behaviour and achieving ultralow-contact resistance, as well as customizing the synthesis of electrocatalysts. The proposed on-device phase engineering approach exhibits a universal mechanism and can be expanded to 29 element combinations between a metal and chalcogen. Our work highlights on-device phase engineering as a promising research approach through which to exploit fundamental properties as well as their applications.

The effectiveness of expanded carrier screening based on next-generation sequencing for severe monogenic genetic diseases.

Expanded carrier screening (ECS) based on next-generation sequencing has been the subject of few studies to estimate the effectiveness of ECS in the Chinese population. A total of 3737 individuals from Southwest China or the general Chinese population, including 1048 pairs and 1641 individuals, were analysed by ECS for 155 monogenetic diseases. An ECS panel was used to detect 147 genes and 10,449 variants in 145 autosomal recessive and 10 X-linked recessive disorders. A total of 43.27% (1617/3737) were found to be carriers of at least one of the 155 monogenetic diseases. The average number of carriers of these recessive mutations was 0.54 and ranged from 0 to 4. Of the 1048 couples, 74.81% (n = 784) were found to have at least one partner carrying more than one disease. In addition, 5.34% of the couples at risk (n = 56) were heterozygous for the same autosomal recessive disease, and 0.37% of the women (9/2440) were carriers of X-linked diseases. Our study demonstrated the clinical significance of ECS in Chinese populations and the need for a programme of familial screening for the prevention of severe recessive monogenetic diseases.

Evaluating the role of DNA methyltransferases in trophoblast fusion and preeclampsia development: Insights from methylation-regulated genes.

The etiology of preeclampsia (PE), a complex and multifactorial condition, remains incompletely understood. DNA methylation, which is primarily regulated by three DNA methyltransferases (DNMTs), DNMT1, DNMT3A, and DNMT3B, plays a vital role in early embryonic development and trophectoderm differentiation. Yet, how DNMTs modulate trophoblast fusion and PE development remains unclear. In this study, we found that the DNMTs expression was downregulated during trophoblast cells fusion. Downregulation of DNMTs was observed during the reconstruction of the denuded syncytiotrophoblast (STB) layer of placental explants. Additionally, overexpression of DNMTs inhibited trophoblast fusion. Conversely, treatment with the DNA methylation inhibitor 5-aza-CdR decreased the expression of DNMTs and promoted trophoblast fusion. A combined analysis of DNA methylation data and gene transcriptome data obtained from the primary cytotrophoblasts (CTBs) fusion process identified 104 potential methylation-regulated differentially expressed genes (MeDEGs) with upregulated expression due to DNA demethylation, including CD59, TNFAIP3, SDC1, and CDK6. The transcription regulation region (TRR) of TNFAIP3 showed a hypomethylation with induction of 5-aza-CdR, which facilitated CREB recruitment and thereby participated in regulating trophoblast fusion. More importantly, clinical correlation analysis of PE showed that the abnormal increase in DNMTs may be involved in the development of PE. This study identified placental DNA methylation-regulated genes that may contribute to PE, offering a novel perspective on the role of epigenetics in trophoblast fusion and its implication in PE development.

CNTools: A computational toolbox for cellular neighborhood analysis from multiplexed images.

Recent studies show that cellular neighborhoods play an important role in evolving biological events such as cancer and diabetes. Therefore, it is critical to accurately and efficiently identify cellular neighborhoods from spatially-resolved single-cell transcriptomic data or single-cell resolution tissue imaging data. In this work, we develop CNTools, a computational toolbox for end-to-end cellular neighborhood analysis on annotated cell images, comprising both the identification and analysis steps. It includes state-of-the-art cellular neighborhood identification methods and post-identification smoothing techniques, with our newly proposed Cellular Neighbor Embedding (CNE) method and Naive Smoothing technique, as well as several established downstream analysis approaches. We applied CNTools on three real-world CODEX datasets and evaluated identification methods with smoothing techniques quantitatively and qualitatively. It shows that CNE with Naive Smoothing overall outperformed other methods and revealed more convincing biological insights. We also provided suggestions on how to choose proper identification methods and smoothing techniques according to input data.

PARP-1 Controls the Adipogenic Transcriptional Program by PARylating C/EBPß and Modulating Its Transcriptional Activity.

Poly(ADP-ribosyl)ation (PARylation) is a post-translational modification of proteins mediated by PARP family members, such as PARP-1. Although PARylation has been studied extensively, few examples of definitive biological roles for site-specific PARylation have been reported. Here we show that C/EBPß, a key pro-adipogenic transcription factor, is PARylated by PARP-1 on three amino acids in a conserved regulatory domain. PARylation at these sites inhibits C/EBPß's DNA binding and transcriptional activities and attenuates adipogenesis in various genetic and cell-based models. Interestingly, PARP-1 catalytic activity drops precipitously during the first 48 hr of differentiation, corresponding to a release of C/EBPß from PARylation-mediated inhibition. This promotes the binding of C/EBPß at enhancers controlling the expression of adipogenic target genes and continued differentiation. Depletion or chemical inhibition of PARP-1, or mutation of the PARylation sites on C/EBPß, enhances these early adipogenic events. Collectively, our results provide a clear example of how site-specific PARylation drives biological outcomes.

Framework nucleic acid-based nanoparticles enhance temozolomide sensitivity in glioblastoma.

O6-methylguanine DNA methyltransferase (MGMT) is a crucial determinant of temozolomide (TMZ) sensitivity in patients with glioblastoma (GBM). The therapeutic potential of small interfering RNA (siRNA) targeting MGMT to enhance TMZ sensitivity has been hampered by serum nuclease degradation, off-target effects, poor accumulation at tumor sites, and low circulation in blood stream. In this study, we developed a framework nucleic acid-based nanoparticles (FNN), which is constructed from a six-helix DNA bundle, to encapsulate and protect siMGMT for improving TMZ sensitivity in GBM treatment. For better blood-brain barrier (BBB) penetration and GBM targeting, we conjugated Angiopep-2 (ANG) targeting modules to each end of the FNN. Nucleolin (NCL)-responsive locks were engineered along the sides of the six-helix DNA bundle, which safeguard siMGMT before tumor entry. Upon interaction with tumor-overexpressed NCL, these locks unlock, exposing siMGMT, this allows for effective suppression of MGMT, resulting in a significant improvement of TMZ therapeutic efficacy in GBM. This innovative strategy has the potential to transform the current treatment landscape for GBM.

Characteristic Plasmon Energies for 2D In2Se3 Phase Identification at Nanoscale.

Two-dimensional (2D) materials with competing polymorphs offer remarkable potential to switch the associated 2D functionalities for novel device applications. Probing their phase transition and competition mechanisms requires nanoscale characterization techniques that can sensitively detect the nucleation of secondary phases down to single-layer thickness. Here we demonstrate nanoscale phase identification on 2D In2Se3 polymorphs, utilizing their distinct plasmon energies that can be distinguished by electron energy-loss spectroscopy (EELS). The characteristic plasmon energies of In2Se3 polymorphs have been validated by first-principles calculations, and also been successfully applied to reveal phase transitions using in situ EELS. Correlating with in situ X-ray diffraction, we further derive a subtle difference in the valence electron density of In2Se3 polymorphs, consistent with their disparate electronic properties. The nanometer resolution and independence of orientation make plasmon-energy mapping a versatile technique for nanoscale phase identification on 2D materials.

Improvement in ORR Durability of Fe Single-Atom Carbon Catalysts Hybridized with CeO2 Nanozyme.

FeNC catalysts are considered one of the most promising alternatives to platinum group metals for the oxygen reduction reaction (ORR). Despite the extensive research on improving ORR activity, the undesirable durability of FeNC is still a critical issue for its practical application. Herein, inspired by the antioxidant mechanism of natural enzymes, CeO2 nanozymes featuring catalase-like and superoxide dismutase-like activities were coupled with FeNC to mitigate the attack of reactive oxygen species (ROS) for improving durability. Benefiting from the multienzyme-like activities of CeO2, ROS generated from FeNC is instantaneously eliminated to alleviate the corrosion of carbon and demetallization of metal sites. Consequently, FeNC/CeO2 exhibits better ORR durability with a decay of only 5 mV compared to FeNC (18 mV) in neutral electrolyte after 10k cycles. The FeNC/CeO2-based zinc-air battery also shows minimal voltage decay over 140 h in galvanostatic discharge-charge cycling tests, outperforming FeNC and commercial Pt/C.

Liquid-Metal-Based Spin-Coating Exfoliation for Atomically Thin Metal Oxide Synthesis.

Two-dimensional (2D) semiconductors possess exceptional electronic, optical, and magnetic properties, making them highly desirable for widespread applications. However, conventional mechanical exfoliation and epitaxial growth methods are insufficient in meeting the demand for atomically thin films covering large areas while maintaining high quality. Herein, leveraging liquid metal oxidation reaction, we propose a motorized spin-coating exfoliation strategy to efficiently produce large-area 2D metal oxide (2DMO) semiconductors with high crystallinity, atomically thin thickness, and flat surfaces on diverse substrates. Moreover, we realized a 2D gallium oxide-based deep ultraviolet solar-blind photodetector featuring a metal-semiconductor-metal structure, showcasing high responsivity (8.24 A W-1) at 254 nm and excellent sensitivity (4.3 × 1012 cm Hz1/2 W-1). This novel liquid-metal-based spin-coating exfoliation strategy offers great potential for synthesizing atomically thin 2D semiconductors, opening new avenues for future functional electronic and optical applications.

Atomically Unraveling Highly Crystalline Self-Intercalated Tantalum Sulfide with Correlated Stacking Registry-Dependent Magnetism.

In self-intercalated two-dimensional (ic-2D) materials, understanding the local chemical environment and the topology of the filling site remains elusive, and the subsequent correlation with the macroscopically manifested physical properties has rarely been investigated. Herein, highly crystalline gram-scale ic-2D Ta1.33S2 crystals were successfully grown by the high-pressure high-temperature method. Employing combined atomic-resolution scanning transmission electron microscopy annular dark field imaging and density functional theory calculations, we systematically unveiled the atomic structures of an atlas of stacking registries in a well-defined √3(a) × âˆš3(a) Ta1.33S2 superlattice. Ferromagnetic order was observed in the AC' stacking registry, and it evolves into an antiferromagnetic state in AA/AB/AB' stacking registries; the AA' stacking registry shows ferrimagnetic ordering. Therefore, we present a novel approach for fabricating large-scale highly crystalline ic-2D crystals and shed light on a powerful means of modulating the magnetic order of ic-2D systems via stacking engineering, i.e., stackingtronics.

Integrative Omics Reveals Rapidly Evolving Regulatory Sequences Driving Primate Brain Evolution.

Although the continual expansion of the brain during primate evolution accounts for our enhanced cognitive capabilities, the drivers of brain evolution have scarcely been explored in these ancestral nodes. Here, we performed large-scale comparative genomic, transcriptomic, and epigenomic analyses to investigate the evolutionary alterations acquired by brain genes and provide comprehensive listings of innovatory genetic elements along the evolutionary path from ancestral primates to human. The regulatory sequences associated with brain-expressed genes experienced rapid change, particularly in the ancestor of the Simiiformes. Extensive comparisons of single-cell and bulk transcriptomic data between primate and nonprimate brains revealed that these regulatory sequences may drive the high expression of certain genes in primate brains. Employing in utero electroporation into mouse embryonic cortex, we show that the primate-specific brain-biased gene BMP7 was recruited, probably in the ancestor of the Simiiformes, to regulate neuronal proliferation in the primate ventricular zone. Our study provides a comprehensive listing of genes and regulatory changes along the brain evolution lineage of ancestral primates leading to human. These data should be invaluable for future functional studies that will deepen our understanding not only of the genetic basis of human brain evolution but also of inherited disease.