Single-cell chromatin accessibility profiling of cell-state-specific gene regulatory programs during mouse organogenesis

In mammals, early organogenesis begins soon after gastrulation, accompanied by specification of various type of progenitor/precusor cells. In order to reveal dynamic chromatin landscape of precursor cells and decipher the underlying molecular mechanism driving early mouse organogenesis, we performed single-cell ATAC-seq of E8.5-E10.5 mouse embryos. We profiled a total of 101,599 single cells and identified 41 specific cell types at these stages. Besides, by performing integrated analysis of scATAC-seq and public scRNA-seq data, we identified the critical cis-regulatory elements and key transcription factors which drving development of spinal cord and somitogenesis. Furthermore, we intersected accessible peaks with human diseases/traits-related loci and found potential clinical associated single nucleotide variants (SNPs). Overall, our work provides a fundamental source for understanding cell fate determination and revealing the underlying mechanism during postimplantation embryonic development, and expand our knowledge of pathology for human developmental malformations

Deconvolution of single-cell multi-omics layers reveals regulatory heterogeneity

Heterogeneity in gene expression and epigenetic states exists across individual cells. Here, the authors develop scCAT-seq, a technique for simultaneously performing ATAC-seq and RNA-seq within the same single cell

Effect of Control Strategies on Prevalence, Incidence and Re-infection of Clonorchiasis in Endemic Areas of China

Clonorchiasis is a liver fluke disease prevalent in East Asia, which is transmitted to humans mainly by eating raw freshwater fish. It induces various complications in the liver or bile duct including cholelithiasis, cholecystitis, cholangitis, and cirrhosis. Clonorchis sinensis has been known to cause cholangiocarcinoma, and is still a major health problem in endemic areas. People in endemic areas are repeatedly infected with C. sinensis, as they continue to consume raw freshwater fish in spite of control activities and availability of a highly effective drug, praziquantel. Reservoir hosts such as cats, dogs, and pigs supply eggs continuously to the environment and act as a source of infection. The present study analyzed the data produced by the Korea-China collaborative project for helminthiasis control in China during 2001–2004 to find out effective chemotherapeutic control strategies with praziquantel in endemic areas and to evaluate their effects on the transmission of C. sinensis infection by repeated mass or selective treatment. The four-year control trial found that repeated treatment is essential to the effective reduction of prevalence and infection intensity in heavily endemic areas. Mass chemotherapy is more effective than selective treatment, and more repeated treatments produce better outcomes in clonorchiasis control. Health education to change the habit of consuming raw or undercooked fish is an important and practical measure to prevent and reduce human infections in endemic areas. Together with chemotherapy, health education could be highly effective and produce sustainable effects in clonorchiasis control. Treatment of reservoirs, if applicable, will contribute to reduce the source of infection

Cell transcriptomic atlas of the non-human primate Macaca fascicularis.

Studying tissue composition and function in non-human primates (NHPs) is crucial to understand the nature of our own species. Here we present a large-scale cell transcriptomic atlas that encompasses over 1 million cells from 45 tissues of the adult NHP Macaca fascicularis. This dataset provides a vast annotated resource to study a species phylogenetically close to humans. To demonstrate the utility of the atlas, we have reconstructed the cell-cell interaction networks that drive Wnt signalling across the body, mapped the distribution of receptors and co-receptors for viruses causing human infectious diseases, and intersected our data with human genetic disease orthologues to establish potential clinical associations. Our M. fascicularis cell atlas constitutes an essential reference for future studies in humans and NHPs.We thank W. Liu and L. Xu from the Huazhen Laboratory Animal Breeding Centre for helping in the collection of monkey tissues, D. Zhu and H. Li from the Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory) for technical help, G. Guo and H. Sun from Zhejiang University for providing HCL and MCA gene expression data matrices, G. Dong and C. Liu from BGI Research, and X. Zhang, P. Li and C. Qi from the Guangzhou Institutes of Biomedicine and Health for experimental advice or providing reagents. This work was supported by the Shenzhen Basic Research Project for Excellent Young Scholars (RCYX20200714114644191), Shenzhen Key Laboratory of Single-Cell Omics (ZDSYS20190902093613831), Shenzhen Bay Laboratory (SZBL2019062801012) and Guangdong Provincial Key Laboratory of Genome Read and Write (2017B030301011). In addition, L.L. was supported by the National Natural Science Foundation of China (31900466), Y. Hou was supported by the Natural Science Foundation of Guangdong Province (2018A030313379) and M.A.E. was supported by a Changbai Mountain Scholar award (419020201252), the Strategic Priority Research Program of the Chinese Academy of Sciences (XDA16030502), a Chinese Academy of Sciences–Japan Society for the Promotion of Science joint research project (GJHZ2093), the National Natural Science Foundation of China (92068106, U20A2015) and the Guangdong Basic and Applied Basic Research Foundation (2021B1515120075). M.L. was supported by the National Key Research and Development Program of China (2021YFC2600200).S

Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays.

Spatially resolved transcriptomic technologies are promising tools to study complex biological processes such as mammalian embryogenesis. However, the imbalance between resolution, gene capture, and field of view of current methodologies precludes their systematic application to analyze relatively large and three-dimensional mid- and late-gestation embryos. Here, we combined DNA nanoball (DNB)-patterned arrays and in situ RNA capture to create spatial enhanced resolution omics-sequencing (Stereo-seq). We applied Stereo-seq to generate the mouse organogenesis spatiotemporal transcriptomic atlas (MOSTA), which maps with single-cell resolution and high sensitivity the kinetics and directionality of transcriptional variation during mouse organogenesis. We used this information to gain insight into the molecular basis of spatial cell heterogeneity and cell fate specification in developing tissues such as the dorsal midbrain. Our panoramic atlas will facilitate in-depth investigation of longstanding questions concerning normal and abnormal mammalian development.This work is part of the ‘‘SpatioTemporal Omics Consortium’’ (STOC) paper package. A list of STOC members is available at: http://sto-consortium.org. We would like to thank the MOTIC China Group, Rongqin Ke (Huaqiao University, Xiamen, China), Jiazuan Ni (Shenzhen University, Shenzhen, China), Wei Huang (Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China), and Jonathan S. Weissman (Whitehead Institute, Boston, USA) for their help. This work was supported by the grant of Top Ten Foundamental Research Institutes of Shenzhen, the Shenzhen Key Laboratory of Single-Cell Omics (ZDSYS20190902093613831), and the Guangdong Provincial Key Laboratory of Genome Read and Write (2017B030301011); Longqi Liu was supported by the National Natural Science Foundation of China (31900466) and Miguel A. Esteban’s laboratory at the Guangzhou Institutes of Biomedicine and Health by the Strategic Priority Research Program of the Chinese Academy of Sciences (XDA16030502), National Natural Science Foundation of China (92068106), and the Guangdong Basic and Applied Basic Research Foundation (2021B1515120075).S

Tuning flexural elastic wave propagation in electroactive phononic crystals

In this paper, we investigate the flexural elastic wave propagation properties in phononic crystals (PCs) consisting of co-axial steel and electrorheological (ER) elastomer pillars deposited on a thin plate. The finite element method and the super cell technique are used to calculate the band structures and transmission spectra. It is found that the band gap boundaries of the PCs can be tuned by applying an electric field to the ER elastomer component. The relationship between the band gap boundaries and the electric field is given. It is also found that point and line defects can be created by properly applying an electric field to some of the cells. These defects bring defect bands inside the original band gaps and lead to elastic wave confinement in the point defect or along the line defect. The dependence of the defect band frequencies on the electric field is expounded. Band gap tunability, wave confinement, and wave guiding achieved by applying electric field in this paper are useful in applications of flexural vibration reduction and energy harvesting in engineering.Published versio

Assessment of light pollution risk level

Artificial light has both positive and negative effects, affecting different sites in different ways. The level of light pollution is influenced by the level of local development, population, biodiversity, geography and climate. Therefore, it is important to assess the risk level of light pollution and to study the impact of different interventions to reduce light pollution in different locations. In this paper, four different types of representative locations in China were selected for calculation using the LPRL assessment model. Protected land locations have the lowest L1 values. Urban communities have the highest LPRL of L7. Rural and urban communities have LPRLs of L2 and L5, respectively. the results show that for rural communities, SI works best. It increased LPRL from L2 to L1. however, SII and SIII had no effect on LPRL. For urban communities, SIII had a significant effect in that it increased LPRL from L7 to L5. Therefore, it was necessary to focus on this aspect to develop the most effective intervention strategy for an urban community in Hangzhou, and a 1-page flyer was created to promote the strategy at this site