Visualizing the Local Twist Angle Variation within and between Domains of Twisted Bilayer Graphene

Moirésuperlattices in twisted two-dimensional materials have emerged as ideal platforms for engineering quantum phenomena,which are highly sensitive to twist angles,including both the global value and the spatial inhomogeneity.However,only a few methods provide spatial-resolved information for characterizing local twist angle distribution.

Formation of Two-Dimensional AgTe Monolayer Atomic Crystal on Ag(111) Substrate

We report on the formation of two-dimensional monolayer AgTe crystal on Ag(111) substrates. The samples are prepared in ultrahigh vacuum by deposition of Te on Ag(111) followed by annealing. Using a scanning tunneling microscope(STM) and low electron energy diffraction(LEED), we investigate the atomic structure of the samples.The STM images and the LEED pattern show that monolayer AgTe crystal is formed on Ag(111). Four kinds of atomic structures of AgTe and Ag(111) are observed:(i) flat honeycomb structure,(ii) bulked honeycomb,(iii)stripe structure,(iv) hexagonal structure. The structural analysis indicates that the formation of the different atomic structures is due to the lattice mismatch and relief of the intrinsic strain in the AgTe layer. Our results provide a simple and convenient method to produce monolayer AgTe atomic crystal on Ag(111) and a template for study of novel physical properties and for future quantum devices.

Construction of monolayer IrTe2 and the structural transition under low temperatures

Bulk iridium ditelluride(IrTe2)is a layered material and is known for its interesting electronic and structural properties,such as large spin-orbit coupling,charge ordering,and superconductivity.However,so far there is no experimental study about the fabrication of monolayer IrTe2.Here we report the formation of IrTe2 monolayer on Ir(111)substrate by direct tellurization method.Scanning tunneling microscope(STM)images show the coexistence of 1/5 phase and 1/6 phase structures of IrTe2 at room temperature.We also obtained STM images showing distorted stripe feature under low temperatures.This stripe feature is possibly induced by the strain between the IrTe2 monolayer and the metal substrate.Density functional theory(DFT)calculations show that the IrTe2 monolayer has strong interaction with the underlying Ir(111)substrate.

A high-resolution transcriptomic atlas depicting nitrogen fixation and nodule development in soybean

Although root nodules are essential for biological nitrogen fixation in legumes,the cell types and molecular regulatory mechanisms contributing to nodule development and nitrogen fixation in determinate nodule legumes,such as soybean(Glycine max),remain incompletely understood.Here,we generated a single-nucleus resolution transcriptomic atlas of soybean roots and nodules at 14 days post inoculation(dpi)and annotated 17 major cell types,including six that are specific to nodules.We identified the specific cell types responsible for each step in the ureides synthesis pathway,which enables spatial compartmentalization of biochemical reactions during soybean nitrogen fixation.By utilizing RNA velocity analysis,we reconstructed the differentiation dynamics of soybean nodules,which differs from those of indeterminate nodules in Medicago truncatula.Moreover,we identified several putative regulators of soybean nodulation and two of these genes,GmbHLH93 and GmSCL1,were as-yet uncharacterized in soybean.Overexpression of each gene in soybean hairy root systems validated their respective roles in nodulation.Notably,enrichment for cytokinin-related genes in soybean nodules led to identification of the cytokinin receptor,GmCRE1,as a prominent component of the nodulation pathway.GmCRE1 knockout in soybean resulted in a striking nodule phenotype with decreased nitrogen fixation zone and depletion of leghemoglobins,accompanied by downregulation of nodule-specific gene expression,as well as almost complete abrogation of biological nitrogen fixation.In summary,this study provides a comprehensive perspective of the cellular landscape during soybean nodulation,shedding light on the underlying metabolic and developmental mechanisms of soybean nodule formation.

Evidence for a mouse origin of the SARS-CoV-2 Omicron variant

The rapid accumulation of mutations in the SARS-CoV-2 Omicron variant that enabled its outbreak raises questions as to whether its proximal origin occurred in humans or another mammalian host. Here, we identified 45 point mutations that Omicron acquired since divergence from the B.1.1 lineage. We found that the Omicron spike protein sequence was subjected to stronger positive selection than that of any reported SARS-CoV-2 variants known to evolve persistently in human hosts, suggesting a possibility of hostjumping. The molecular spectrum of mutations(i.e., the relative frequency of the 12 types of base substitutions) acquired by the progenitor of Omicron was significantly different from the spectrum for viruses that evolved in human patients but resembled the spectra associated with virus evolution in a mouse cellular environment. Furthermore, mutations in the Omicron spike protein significantly overlapped with SARS-CoV-2 mutations known to promote adaptation to mouse hosts, particularly through enhanced spike protein binding affinity for the mouse cell entry receptor. Collectively, our results suggest that the progenitor of Omicron jumped from humans to mice, rapidly accumulated mutations conducive to infecting that host,then jumped back into humans, indicating an inter-species evolutionary trajectory for the Omicron outbreak.

Single-cell transcriptome atlas of the leaf and root of rice seedlings

As a multicellular organism,rice flourishes relying on gene expression diversity among cells of various functions.However,cellular-resolution transcriptome features are yet to be fully recognized,let alone cell-specific transcriptional responses to environmental stimuli.In this study,we apply single-cell RNA sequencing to both shoot and root of rice seedlings growing in Kimura B nutrient solution or exposed to various abiotic stresses and characterize transcriptomes for a total of 237,431 individual cells.We identify 15 and 9 cell types in the leaf and root,respectively,and observe that common transcriptome features are often shared between leaves and roots in the same tissue layer,except for endodermis or epidermis.Abiotic stress stimuli alter gene expression largely in a cell type-specific manner,but for a given cell type,different stresses often trigger transcriptional regulation of roughly the same set of genes.Besides,we detect proportional changes in cell populations in response to abiotic stress and investigate the underlying molecular mechanisms through single-cell reconstruction of the developmental trajectory.Collectively,our study represents a benchmark-setting data resource of single-cell transcriptome atlas for rice seedlings and an illustration of exploiting such resources to drive discoveries in plant biology.

Surface morphology and electronic structure in stoichiometric superconductor CaKFe_(4)As_(4) robed by scanning tunneling microscopy/spectroscopy

CaKFe_(4)As_(4) is a new-type superconductor with a relatively high transition temperature of 35 K among stoichiometric iron-based superconductors. Based on scanning tunneling microscopy/spectroscopy, the surface morphology and electronic structure of CaKFe_(4)As_(4) single crystal were systematically investigated. The cleaved CaKFe_(4)As_(4) showed various morphologies, such as atomically resolved 1×1, 1×2, and √2×√2 lattices. By analyzing the geometrical correlations of these morphologies, the 1×1 and 1×2 lattices were identified as the original and reconstructed As layers, respectively, whereas the √2×√2 lattice was distinguished as the reconstructed alkaline-earth-metal or alkali-metal layer. The superconducting energy gap of 7.3 me V and bosonic mode of 12.7 me V were resolved in the scanning tunneling spectra. In addition, the superconducting energy gaps measured on different terminations were identical and consistent with the values obtained by bulk-sensitive techniques, indicating that the electronic structures of CaKFe_(4)As_(4) were insensitive to the surface reconstructions. Our study clarifies the relationships between complex surface reconstructions and surface terminations and preliminarily presents that there is no obvious effect of surface reconstructions on electronic states.

通过离子液体选择性调控铜氧化物中的易失和非易失超导电性

高效、可靠地调控铜氧化物超导体的超导态,对其在下一代电子学中的应用具有重要意义.本文研究了绝缘Pr2CuO4±δ(PCO)薄膜的离子液体调控行为,发现可以利用两种不同的调控机制分别诱导出易失和非易失的超导态.在正电场调控下,薄膜可以在超导态和非超导态之间可逆转换,这归因于载流子的掺杂效应.另外,对绝缘的样品进行负偏压的调控,当偏压加至-4 V时,样品的电阻明显增大.值得关注的是,一旦撤去栅极电压,样品获得了非易失的超导电性.高分辨扫描电子显微镜和原位X射线衍射实验的结果表明,负向调控过程修复了铜氧面中的氧空位.对于电子型铜氧化物而言,这是一种诱导超导电性的独特途径.在同一个铜氧化物母体中有效地调控易失和非易失超导电性,为超导电子器件和高温超导体中量子相变的研究提供了新的渠道.

HeteroMeth： A Database of Cell-to-cell Heterogeneity in DNA Methylation

DNA methylation is an important epigenetic mark that plays a vital role in gene expression and cell differentiation. The average DNA methylation level among a group of cells has been extensively documented. However, the cell-to-cell heterogeneity in DNA methylation, which reflects the differentiation of epigenetic status among cells, remains less investigated. Here we established a gold standard of the cell-to-cell heterogeneity in DNA methylation based on single-cell bisulfite sequencing （BS-seq） data. With that, we optimized a computational pipeline for estimating the heterogeneity in DNA methylation from bulk BS-seq data. We further built HeteroMeth, a database for searching, browsing, visualizing, and downloading the data for heterogeneity in DNA methylation for a total of 141 samples in humans, mice, Arabidopsis, and rice. Three genes are used as examples to illustrate the power of HeteroMeth in the identification of unique features in DNA methylation. The optimization of the computational strategy and the construction of the database in this study complement the recent experimental attempts on single-cell DNA methylomes and will facilitate the understanding of epigenetic mechanisms underlying cell differentiation and embryonic development. HeteroMeth is publicly available at http：//qianlab.genetics.ac.cn/HeteroMeth.

Transcriptome-wide Analysis Of Vernalization Reveals Conserved and Species-specific Mechanisms in Brachypodium

Several temperate cereals need vernalization to promote flowering. Little, however, is known about the vernalization-memory-related genes, and almost no comparative analysis has been performed. Here, RNA- Seq was used for transcriptome analysis in non-vernalized, vernalized and post-vernalized Brachypodium distachyon （L.） Beauv. seedlings. In total, the expression of 1,665 genes showed significant changes （fold change 〉4） in response to vernalization. Among them, 674 putative vernalization-memory-related genes with a constant response to vernalization were significantly enriched in transcriptional regulation and monooxygenase-mediated biological processes. Comparative analysis of vernalization-memory-related genes with barley demonstrated that the oxidative-stress response was the most conserved pathway between these two plant species. Moreover, Brachypodium preferred to regulate transcription and protein phosphorylation processes, while vernalization-memory-related genes, whose products are cytoplasmic membrane-bound-vesicle-located proteins, were preferred to be regulated in barley. Correlation analysis of the vernalization-related genes with barley revealed that the vernalization mechanism was conserved between these two plant species. In summary, vernalization, including its memory mechanism, is conserved between Brachypodium and barley, although several species-specific features also exist. The data reported here will provide primary resources for subsequent functional research in vernalization.

Host-specific asymmetric accumulation of mutation types reveals that the origin of SARS-CoV-2 is consistent with a natural process

The capacity of RNA viruses to adapt to new hosts and rapidly escape the host immune system is largely attributable to de novo genetic diversity that emerges through mutations in RNA.Although the molecular spectrum of de novo mutations—the relative rates at which various base substitutions occur—are widely recognized as informative toward understanding the evolution of a viral genome,little attention has been paid to the possibility of using molecular spectra to infer the host origins of a virus.Here,we characterize the molecular spectrum of de novo mutations for SARS-CoV-2 from transcriptomic data obtained from virus-infected cell lines,enabled by the use of sporadic junctions formed during discontinuous transcription as molecular barcodes.We find that de novo mutations are generated in a replication-independent manner,typically on the genomic strand,and highly dependent on mutagenic mechanisms specific to the host cellular environment.De novo mutations will then strongly influence the types of base substitutions accumulated during SARS-CoV-2 evolution,in an asymmetric manner favoring specific mutation types.Consequently,similarities between the mutation spectra of SARS-CoV-2 and the bat coronavirus RaTG13,which have accumulated since their divergence strongly suggest that SARS-CoV-2 evolved in a host cellular environment highly similar to that of bats before its zoonotic transfer into humans.Collectively,our findings provide data-driven support for the natural origin of SARS-CoV-2.

Construction of poly-naphthalocyanine linked by [4]-radialene-like structures on silver surfaces

Cyclic-conjugated linkages between planar-macrocydic molecules contribute to the robustness of the two-dimensional (2D) polymerization and extension of π-interactions. The fabrication of such linkages in 2D polymers remains challenging. Combining scanning tunneling microscope (STM) measurements and density functional theory (DFT) calculations, we demonstrate a linear polymerization of metal-free naphthalocyanine (NPc) molecules with [4]-radialene-like linkages on silver surfaces. Experimentally, by depositing NPc molecules on the Ag(110) surface and subsequent annealing up to 750 K, one-dimensional polymers are constructed along the [\(1\overline 1 0\)] direction. High-resolution STM images show a stem-leaf-like feature. STM simulations based on a linear polymer of NPc molecules linked by four-membered carbon rings, [4]-radialene-like structure, agree well with the experimental observations. DFT calculations reveal that the polymerization process includes detaching two-terminal H atoms of NPc molecules along [\(1\overline 1 0\)] direction, then bonding with a neighboring dehydrogenated NPc molecule by forming a four-membered ring. The dehydrogenation process can be promoted by on-surface impurities such as additional H atoms. Similar polymerizations have been achieved on Ag(111) surfaces in an amorphous way. Moreover, the energy gap of the NPc molecule decreases after linear polymerization, suggesting a red-shift for its optical absorption/scattering spectrum. Our study offers a new route to polymerize conjugated molecules with extended planar π-interactions.

跨学科壁挂艺术:模仿、模拟和转换

本文从纤维艺术的哲学体系出发,结合作者的壁挂作品,探讨了支撑理论的方法,以及深度的专业化会推动形式、内容和隐喻的多样性。基于这种对专业性的理解,进而在创作中寻找更多可能性的方法。

纺织艺术策展--在国际双年展和三年展中的历史、实践和观念

什么是纺织艺术策展?在国际双年展或三年展中,纺织艺术策展有哪些经验?如果有一些经验,那么在当代视觉文化和实践中这些策展经验对纺织品的定位起到什么作用?这些策展经验对该领域的文化认知和社会认知有什么影响?这些策展活动又是如何定义和固化这些认知的?对这些问题的解答,有利于我们探索策展过程中的管控模式,以便于指导在策展工作过程中发挥创造性、批判性和经验性。这些策展经验对当代艺术实践及其传播平台有何影响?虽然,我们很难在双年展的背景中勾勒出一个清晰或连续的纺织双年展历史,但是本文试图了解这些展览活动在全球化背景中的地位,以及在全球化中,当艺术和纺织艺术重新定义了其媒介和本体的界限时,纺织艺术和艺术之间潜在的相互关系和相互影响,反之亦然。受到后现代主义和后殖民主义趋势的影响,重新评估了对艺术和视觉或物质文化范畴的划分,试图消解艺术市场及围绕着艺术市场的相关话语。(1)然而,这些重新定义是否能让人们重新理解艺术实践?基于政治和经济的影响以及"明星策展人"的出现,当代艺术双年展的模式在哪些方面影响了该领域的道德伦理?在这种日益发展的趋势下,人们如何理解纺织品所处的社会和地域背景?