Changes in genome architecture and transcriptional dynamics progress independently of sensory experience during post-natal brain development.

Both transcription and three-dimensional (3D) architecture of the mammalian genome play critical roles in neurodevelopment and its disorders. However, 3D genome structures of single brain cells have not been solved; little is known about the dynamics of single-cell transcriptome and 3D genome after birth. Here, we generated a transcriptome (3,517 cells) and 3D genome (3,646 cells) atlas of the developing mouse cortex and hippocampus by using our high-resolution multiple annealing and looping-based amplification cycles for digital transcriptomics (MALBAC-DT) and diploid chromatin conformation capture (Dip-C) methods and developing multi-omic analysis pipelines. In adults, 3D genome "structure types" delineate all major cell types, with high correlation between chromatin A/B compartments and gene expression. During development, both transcriptome and 3D genome are extensively transformed in the first post-natal month. In neurons, 3D genome is rewired across scales, correlated with gene expression modules, and independent of sensory experience. Finally, we examine allele-specific structure of imprinted genes, revealing local and chromosome (chr)-wide differences. These findings uncover an unknown dimension of neurodevelopment.

Structurally Resolved SARS-CoV-2 Antibody Shows High Efficacy in Severely Infected Hamsters and Provides a Potent Cocktail Pairing Strategy.

Understanding how potent neutralizing antibodies (NAbs) inhibit SARS-CoV-2 is critical for effective therapeutic development. We previously described BD-368-2, a SARS-CoV-2 NAb with high potency; however, its neutralization mechanism is largely unknown. Here, we report the 3.5-Å cryo-EM structure of BD-368-2/trimeric-spike complex, revealing that BD-368-2 fully blocks ACE2 recognition by occupying all three receptor-binding domains (RBDs) simultaneously, regardless of their "up" or "down" conformations. Also, BD-368-2 treats infected adult hamsters at low dosages and at various administering windows, in contrast to placebo hamsters that manifested severe interstitial pneumonia. Moreover, BD-368-2's epitope completely avoids the common binding site of VH3-53/VH3-66 recurrent NAbs, evidenced by tripartite co-crystal structures with RBDs. Pairing BD-368-2 with a potent recurrent NAb neutralizes SARS-CoV-2 pseudovirus at pM level and rescues mutation-induced neutralization escapes. Together, our results rationalized a new RBD epitope that leads to high neutralization potency and demonstrated BD-368-2's therapeutic potential in treating COVID-19.

Potent Neutralizing Antibodies against SARS-CoV-2 Identified by High-Throughput Single-Cell Sequencing of Convalescent Patients' B Cells.

The COVID-19 pandemic urgently needs therapeutic and prophylactic interventions. Here, we report the rapid identification of SARS-CoV-2-neutralizing antibodies by high-throughput single-cell RNA and VDJ sequencing of antigen-enriched B cells from 60 convalescent patients. From 8,558 antigen-binding IgG1+ clonotypes, 14 potent neutralizing antibodies were identified, with the most potent one, BD-368-2, exhibiting an IC50 of 1.2 and 15 ng/mL against pseudotyped and authentic SARS-CoV-2, respectively. BD-368-2 also displayed strong therapeutic and prophylactic efficacy in SARS-CoV-2-infected hACE2-transgenic mice. Additionally, the 3.8 Å cryo-EM structure of a neutralizing antibody in complex with the spike-ectodomain trimer revealed the antibody's epitope overlaps with the ACE2 binding site. Moreover, we demonstrated that SARS-CoV-2-neutralizing antibodies could be directly selected based on similarities of their predicted CDR3H structures to those of SARS-CoV-neutralizing antibodies. Altogether, we showed that human neutralizing antibodies could be efficiently discovered by high-throughput single B cell sequencing in response to pandemic infectious diseases.

Simultaneous single-cell three-dimensional genome and gene expression profiling uncovers dynamic enhancer connectivity underlying olfactory receptor choice.

The simultaneous measurement of three-dimensional (3D) genome structure and gene expression of individual cells is critical for understanding a genome's structure-function relationship, yet this is challenging for existing methods. Here we present 'Linking mRNA to Chromatin Architecture (LiMCA)', which jointly profiles the 3D genome and transcriptome with exceptional sensitivity and from low-input materials. Combining LiMCA and our high-resolution scATAC-seq assay, METATAC, we successfully characterized chromatin accessibility, as well as paired 3D genome structures and gene expression information, of individual developing olfactory sensory neurons. We expanded the repertoire of known olfactory receptor (OR) enhancers and discovered unexpected rules of their dynamics: OR genes and their enhancers are most accessible during early differentiation. Furthermore, we revealed the dynamic spatial relationship between ORs and enhancers behind stepwise OR expression. These findings offer valuable insights into how 3D connectivity of ORs and enhancers dynamically orchestrate the 'one neuron-one receptor' selection process.

Single-cell bisulfite-free 5mC and 5hmC sequencing with high sensitivity and scalability.

Existing single-cell bisulfite-based DNA methylation analysis is limited by low DNA recovery, and the measurement of 5hmC at single-base resolution remains challenging. Here, we present a bisulfite-free single-cell whole-genome 5mC and 5hmC profiling technique, named Cabernet, which can characterize 5mC and 5hmC at single-base resolution with high genomic coverage. Cabernet utilizes Tn5 transposome for DNA fragmentation, which enables the discrimination between different alleles for measuring hemi-methylation status. Using Cabernet, we revealed the 5mC, hemi-5mC and 5hmC dynamics during early mouse embryo development, uncovering genomic regions exclusively governed by active or passive demethylation. We show that hemi-methylation status can be used to distinguish between pre- and post-replication cells, enabling more efficient cell grouping when integrated with 5mC profiles. The property of Tn5 naturally enables Cabernet to achieve high-throughput single-cell methylome profiling, where we probed mouse cortical neurons and embryonic day 7.5 (E7.5) embryos, and constructed the library for thousands of single cells at high efficiency, demonstrating its potential for analyzing complex tissues at substantially low cost. Together, we present a way of high-throughput methylome and hydroxymethylome detection at single-cell resolution, enabling efficient analysis of the epigenetic status of biological systems with complicated nature such as neurons and cancer cells.

Highly sensitive single-cell chromatin accessibility assay and transcriptome coassay with METATAC.

Recent advances in single-cell assay for transposase accessible chromatin using sequencing (scATAC-seq) and its coassays have transformed the field of single-cell epigenomics and transcriptomics. However, the low detection efficiency of current methods has limited our understanding of the true complexity of chromatin accessibility and its relationship with gene expression in single cells. Here, we report a high-sensitivity scATAC-seq method, termed multiplexed end-tagging amplification of transposase accessible chromatin (METATAC), which detects a large number of accessible sites per cell and is compatible with automation. Our high detectability and statistical framework allowed precise linking of enhancers to promoters without merging single cells. We systematically investigated allele-specific accessibility in the mouse cerebral cortex, revealing allele-specific accessibility of promotors of certain imprinted genes but biallelic accessibility of their enhancers. Finally, we combined METATAC with our high-sensitivity single-cell RNA sequencing (scRNA-seq) method, multiple annealing and looping based amplification cycles for digital transcriptomics (MALBAC-DT), to develop a joint ATAC-RNA assay, termed METATAC and MALBAC-DT coassay by sequencing (M2C-seq). M2C-seq achieved significant improvements for both ATAC and RNA compared with previous methods, with consistent performance across cell lines and early mouse embryos.

Phase-matching of high-order harmonic generation in the extreme ultraviolet region with orbital angular momentum.

High-order harmonics can generate vortex beams with orbital angular momentum (OAM) in the extreme ultraviolet region. However, experimental research on their phase-matching (PM) characteristics is limited. In this study, vortex high-order harmonic generation (HHG) in the extreme ultraviolet region was generated with Ar gas. Phase-matched HHG with OAM was obtained by optimizing the focus position, laser energy, and gas pressure. The dependence of the PM characteristics on these parameters was analyzed. In addition, we conducted an experimental analysis of the dimensional properties of vortex harmonics under PM conditions. This study is a contribution towards the intense vortex high-order harmonic light sources and their applications.

Resonance absorption of the inner shell during high-order harmonic generation.

In this work, we report the observation of resonance absorption of the inner shell during the high-order harmonic generation (HHG) from xenon (Xe) and krypton (Kr). The absorption peaks show a periodic variation with the change of carrier-envelope phase of driving laser pulses and the delay of two-color laser field, which indicates the absorption peaks come from the collective multielectron effects during the HHG. With the increase of gas pressure, the depth of absorption peak will continue to increase, while due to the phase matching effect, there will be an optimal pressure for the intensity of harmonic signal. Our experimental results pave the way to uncover the physical mechanism of the collective multielectron effects involving inner-shell electrons in the HHG process.

Controlling of the harmonic generation induced by the Berry curvature.

High-order harmonic generation in solid state has attracted a lot of attentions. The Berry curvature (BC), a geometrical property of the Bloch energy band, plays an important role for the harmonic generation in crystal. As we all know, the influence of BC on the harmonic emission has been investigated before and BC is simplified as a 1D structure. However, many other materials including MoS2 are 2D materials. In this work, we extend the investigation for BC to 2D structure and get a generalized equation, which not only gives a new method to control the harmonic emission with BC, but also gives a deeper understanding for the influence of the BC. We show the ability to control the harmonic emission related to the BC using the orthogonal two-color (OTC) laser field. By tuning the delay of OTC laser field, one can steer the trajectory of electrons and modulate the emission of harmonics. This study can provide us a deeper insight into the role of the BC which is difficult to be measured experimentally.

Laser-induced inner-shell excitations through direct electron re-collision versus indirect collision.

The dynamics and the decay processes of inner-shell excited atoms are of great interest in physics, chemistry, biology, and technology. The highly excited state decays very quickly through different channels, both radiative and non-radiative. It is therefore a long-standing goal to study such dynamics directly in the time domain. Using few-cycle infrared laser pulses, we investigated the excitation and ionization of inner-shell electrons through laser-induced electron re-collision with the original parent ions and measured the dependence of the emitted x-ray spectra on the intensity and ellipticity of the driving laser. These directly re-colliding electrons can be used as the initiating pump step in pump/probe experiments for studying core-hole dynamics at their natural temporal scale. In our experiment we found that the dependence of the x-ray emission spectrum on the laser intensity and polarization state varies distinctly for the two kinds of atomic systems. Relying on our data and numerical simulations, we explain this behavior by the presence of different excitation mechanisms that are contributing in different ratios to the respective overall x-ray emission yields. Direct re-collision excitation competes with indirect collisions with neighboring atoms by electrons having "drifted away" from the original parent ion.

Infrared-laser-induced ultrafast modulation on the spectrum of an extreme-ultraviolet attosecond pulse.

We present a theoretical investigation of the isolated extreme-ultraviolet (XUV) attosecond pulse propagating in the ionizing gas induced by a synchronized strong infrared (IR) laser, with the numerical solution of the nonadiabatic one-dimensional propagation model. Upon scanning the relative delay between the XUV and the IR pulse, it is found that the delay-dependent XUV transmission spectrogram exhibits the unique pattern that is controllable by the chirp of the XUV pulse. Furthermore, we demonstrate that this kind of spectrum modulation can be attributed to the term of the light energy loss involved in the propagation equation. The characteristics of the spectrum modulation dependent on the XUV chirp might provide an all-optical way for the reconstruction of the XUV spectral phase.

Functional disruption of the dystrophin gene in rhesus monkey using CRISPR/Cas9.

CRISPR/Cas9 has been used to genetically modify genomes in a variety of species, including non-human primates. Unfortunately, this new technology does cause mosaic mutations, and we do not yet know whether such mutations can functionally disrupt the targeted gene or cause the pathology seen in human disease. Addressing these issues is necessary if we are to generate large animal models of human diseases using CRISPR/Cas9. Here we used CRISPR/Cas9 to target the monkey dystrophin gene to create mutations that lead to Duchenne muscular dystrophy (DMD), a recessive X-linked form of muscular dystrophy. Examination of the relative targeting rate revealed that Crispr/Cas9 targeting could lead to mosaic mutations in up to 87% of the dystrophin alleles in monkey muscle. Moreover, CRISPR/Cas9 induced mutations in both male and female monkeys, with the markedly depleted dystrophin and muscle degeneration seen in early DMD. Our findings indicate that CRISPR/Cas9 can efficiently generate monkey models of human diseases, regardless of inheritance patterns. The presence of degenerated muscle cells in newborn Cas9-targeted monkeys suggests that therapeutic interventions at the early disease stage may be effective at alleviating the myopathy.

Attosecond chirp effect on the transient absorption spectrum of laser-dressed helium atom.

We theoretically investigate the attosecond transient absorption spectrum of helium atom in the presence of an infrared-dressed laser pulse upon scanning their relative delay, with the particular emphasis on the chirp effect of the attosecond pulse. By numerically solving the fully three-dimensional time-dependent Schrödinger equation, we identify the attoscecond chirp can induce the temporal shift of the absorption spectrogram along the delay axis. Additionally, it is found that the extent of the temporal shift is dependent on both the position of the absorption line and the infrared pulse wavelength, which is well confirmed and reproduced by a three-level model. Moreover, we demonstrate that the observed features can be quantitatively explained in terms of the indirect two-photon absorption processes through some virtual states. This effect might provide a way to measure the chirp of attosecond pulse in an all-optical way.

Frequency modulation of high-order harmonic generation in an orthogonally polarized two-color laser field.

We have experimentally investigated the frequency modulation of high-order harmonics in an orthogonally polarized two-color laser field consisting of a mid-infrared 1800nm fundamental pulse and its second harmonic pulse. It is demonstrated that the high harmonic spectra can be fine-tuned as we slightly change the relative delay of the two-color laser pulses. By analyzing the relative frequency shift of each harmonic at different two-color delays, the nonadiabatic spectral shift induced by the rapid variation of the intensity-dependent intrinsic dipole phase can be distinguished from the blueshift induced by the change of the refractive index during self-phase modulation (SPM). Our comprehensive analysis shows that the frequency modulation pattern is a reflection of the average emission time of high-order harmonic generation (HHG), thus offering a simple method to fine-tune the spectra of the harmonics on a sub-cycle time scale.

Effect of nuclear motion on spectral broadening of high-order harmonic generation.

High-order harmonic generation (HHG) in molecular targets is experimentally investigated in order to reveal the role of the nuclear motion played in the harmonic generation process. An obvious broadening in the harmonic spectrum from the H2 molecule is observed in comparison with the harmonic spectrum generated from other molecules with relatively heavy nuclei. We also find that the harmonic yield from the H2 molecule is much weaker than the yield from those gas targets with the similar ionization potentials, such as Ar atom and N2 molecule. The yield suppression and the spectrum broadening of HHG can be attributed to the vibrational motion of nuclear induced by the driving laser pulse. Moreover, the one-dimensional (1D) time-dependent Schrödinger equation (TDSE) with the non-Born-Oppenheimer (NBO) treatment is numerically solved to provide a theoretical support to our explanation.

Enhanced high-order harmonic generation from spatially prepared filamentation in argon.

We experimentally demonstrate enhanced high-order harmonic generation (HHG) from spatially prepared filamentation in Argon. Upon shifting the focus position of an elliptically polarized laser pulse over the filament induced by a linearly polarized laser pulse, an obvious enhancement of harmonic yield by nearly one order of magnitude is observed. The result could be interpreted in terms of the double contributions from both the excited states of target atom and the phase-matching effect of harmonic beam. In contrast to the enhancement phenomena, an obvious suppression of harmonic yield is also presented, which could be attributed to both the ground-state depletion and the plasma effect.

CEP-controlled supercontinuum generation during filamentation with mid-infrared laser pulse.

With carrier-envelope phase (CEP) stabilized mid-infrared (MIR) laser pulse, the CEP-controlled supercontinuum generation can be distinctly observed in a very small distance range when the focus of the laser pulse closes to the exit surface of the fused silica (FS). This CEP effect will be gradually weakened and finally disappears if the laser focus moves out of this range. With numerical simulation, we find that although the CEP effect starts from the tunneling ionization of the electron, it can be observed only when the supercontinuum mainly comes from the self-phase modulation (SPM) and self-steepening of the laser pulse and too much electrons will make it ambiguous.

Carrier-envelope phase effects on the spatial coherence of high-order harmonics.

In this work, we report the Carrier-Envelope Phase Effects on the Spatial Coherence of High-order Harmonics driven by phase-stabilized few-cycle mid-infrared laser pulses. The degree of coherence varies with carrier-envelope phase periodically with a period of π. At the same time, as the harmonic orders increase, the extreme points on the curve of coherence degree vs. carrier-envelope phase shift toward the direction of carrier-envelope phase increasing. Through theoretical analysis, we find that the ionization induced frequency chirp plays an important role in the Carrier-Envelope Phase Effects on the Spatial Coherence. This effect suggests a possible method to optimize the spatial coherence of harmonics by tuning the carrier-envelope phase of the driving field.

Spatially and spectrally resolved quantum-path tracing in high-order harmonic generation.

We experimentally demonstrate the macroscopic evolution of quantum-path distributions in harmonic emission with spatial and spectral resolution from an argon gas jet, and obviously observe that the spatial profiles of harmonics are gradually split into two components (the red and blue shifts) when the driving laser intensity is increased. Moreover, the red and blue shifts in quantum-path distributions are experimentally traced and clarified in the spatial and spectral domain by choosing the focal position. These results give a more comprehensive understanding and therefore a better control of harmonic emission.

Observation of CEP effect via filamentation in transparent solids.

We report on the first direct observation of carrier-envelope-phase (CEP) effect during the interaction between few-cycle laser pulses and bulk solid materials. Using 2-cycle mid-infrared laser pulses with stabilized CEP, the CEP effect of tunneling ionization during the laser filamentation in a fused silica is revealed. The phase variation of the accompanying supercontinuum (SC) emission with filamentation at different CEPs of laser pulses can be measured by means of spectral interference technique, as a direct manifestation of the strong field tunneling ionization dynamics in transparent solids.