Genome-Wide Analysis of Gene Expression Provides New Insights into Cold Responses in Thellungiella salsuginea

Low temperature is one of the major environmental stresses that affects plant growth and development, and leads to decrease in crop yield and quality. Thellungiella salsuginea (salt cress) exhibits high tolerance to chilling, is an appropriate model to investigate the molecular mechanisms of cold tolerance. Here, we compared transcription changes in the roots and leaves of T. salsuginea under cold stress using RNA-seq. We identified 2,782 and 1,430 differentially expressed genes (DEGs) in leaves and roots upon cold treatment, respectively. The expression levels of some genes were validated by quantitative real-time-PCR (qRT-PCR). Among these DEGs, 159 (11.1%) genes in roots and 232 (8.3%) genes in leaves were annotated as various types of transcription factors. We found that five aquaporin genes (three TIPs, one PIPs, and one NIPs) responded to cold treatment. In addition, the expression of COR47, ICE1, and CBF1 genes of DREB1/CBF-dependent cold signaling pathway genes altered in response to low temperature. KEGG pathway analysis indicated that these cold regulated genes were enriched in metabolism, photosynthesis, circadian rhythm, and transcriptional regulation. Our findings provided a complete picture of the regulatory network of cold stress response in T. salsuginea. These cold-responsive genes could be targeted for detail functional study and utilization in crop cold tolerance improvement

Prevalence of hyperuricemia and the population attributable fraction of modifiable risk factors: Evidence from a general population cohort in China

Data on updated hyperuricemia prevalence in Beijing-Tianjin-Hebei (BTH) region in China, which is one of the world-class urban agglomerations, is sparse. Overweight/obesity, alcohol consumption, smoking and sedentary behavior are modifiable risk factors (MRFs) for elevated serum uric acid (SUA), but their population attributable fractions (PAFs) for hyperuricemia is still unclear. Using baseline data from the BTH Physical Examination General Population Cohort, we calculated the crude- and adjusted-prevalence of hyperuricemia based on the 30,158 participants aged 18–80 years. Hyperuricemia was defined as SUA >420 μmol/L in men and >360 μmol/L in women, or currently use of uric acid lowering drugs. Overweight/obesity, alcohol consumption, smoking and sedentary behavior were considered as MRFs and their adjusted PAFs were estimated. The prevalence of hyperuricemia was 19.37%, 27.72% in men and 10.69% in women. The PAFs and 95% confidence intervals for overweight, obesity were 16.25% (14.26–18.25%) and 12.08% (11.40–12.77%) in men, 13.95% (12.31–15.59%) and 6.35% (5.97–6.74%) in women, respectively. Alcohol consumption can explain 4.64% (2.72–6.56%) hyperuricemia cases in men, but with no statistical significance in women. Cigarette smoking contributed to 3.15% (1.09–5.21%) cases in men, but a much lower fraction in women (0.85%, 0.49–1.22%). Compared with sedentary time <2 h per day, the PAFs of 2–4 h, 4–6 h, and more than 6 h per day were 3.14% (1.34–4.93%), 6.72% (4.44–8.99%) and 8.04% (4.95–11.13%) in men, respectively. Sedentary time was not found to be associated with hyperuricemia in women. These findings concluded that hyperuricemia is prevalent in this representative Chinese adult general population with substantial sex difference. Four MRFs (overweight/obesity, alcohol consumption, cigarette smoking and sedentary behavior) accounted for a notable proportion of hyperuricemia cases. The PAF estimations enable the exploration of the expected proportion of hyperuricemia cases that could be prevented if the MRFs were removed, which warrants the public health significance of life-style intervention

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

Epidemiological characteristics and risk factors for cystic and alveolar echinococcosis in China: an analysis of a national population-based field survey

Background Human cystic and alveolar echinococcosis are neglected tropical diseases that WHO has prioritized for control in recent years. Both diseases impose substantial burdens on public health and the socio-economy in China. In this study, which is based on the national echinococcosis survey from 2012 to 2016, we aim to describe the spatial prevalence and demographic characteristics of cystic and alveolar echinococcosis infections in humans and assess the impact of environmental, biological and social factors on both types of the disease. Methods We computed the sex-, age group-, occupation- and education level-specific prevalences of cystic and alveolar echinococcosis at national and sub-national levels. We mapped the geographical distribution of echinococcosis prevalence at the province, city and county levels. Finally, by analyzing the county-level echinococcosis cases combined with a range of associated environmental, biological and social factors, we identified and quantified the potential risk factors for echinococcosis using a generalized linear model. Results A total of 1,150,723 residents were selected and included in the national echinococcosis survey between 2012 and 2016, of whom 4161 and 1055 tested positive for cystic and alveolar echinococcosis, respectively. Female gender, older age, occupation at herdsman, occupation as religious worker and illiteracy were identified as risk factors for both types of echinococcosis. The prevalence of echinococcosis was found to vary geographically, with areas of high endemicity observed in the Tibetan Plateau region. Cystic echinococcosis prevalence was positively correlated with cattle density, cattle prevalence, dog density, dog prevalence, number of livestock slaughtered, elevation and grass area, and negatively associated with temperature and gross domestic product (GDP). Alveolar echinococcosis prevalence was positively correlated with precipitation, level of awareness, elevation, rodent density and rodent prevalence, and negatively correlated with forest area, temperature and GDP. Our results also implied that drinking water sources are significantly associated with both diseases. Conclusions The results of this study provide a comprehensive understanding of geographical patterns, demographic characteristics and risk factors of cystic and alveolar echinococcosis in China. This important information will contribute towards developing targeted prevention measures and controlling diseases from the public health perspective. Graphical Abstract

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

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

The Final Step in the Application of Perovskite Solar Cells

Since 2009, there has been renewed interest in perovskite materials due to the rise of metal halide perovskite photoelectric materials, especially in the field of perovskite solar cells (PSCs) [...

Geo-environmental and mechanical behaviors of As(V) and Cd(II) co-contaminated soils stabilized by goethite nanoparticles modified biochar

Abstract Goethite nanoparticles modified biochar (FBC) could address the weak effectiveness of conventional biochar commonly to process heavy metal(loids)  (HMs) co-contamination with different charges. However, few studies have focused on the change of soil mechanical properties after stabilization. In this study, FBC was synthesized to stabilize simultaneously arsenic (As (V)) (anions) and cadmium (Cd (II)) (cations) in co-contaminated soils. Batch adsorption, leaching toxicity, geotechnical properties and micro-spectroscopic tests were comprehensively adopted to investigate the stabilization mechanism. The results showed that FBC could immobilize As (V) mainly through redox and surface precipitation while stabilizing Cd (II) by electrostatic attraction and complexation, causing soil agglomeration and ultimately making rougher surface and stronger sliding friction of contaminated soils. The maximum adsorption capacity of FBC for As (V) and Cd (II) was 31.96 mg g−1 and 129.31 mg g−1, respectively. Besides, the dosages of FBC required in contaminated soils generally were approximately 57% higher than those in contaminated water. FBC promoted the formation of small macroaggregates (0.25–2 mm) and the shear strengths of co-contaminated soils by 21.40% and 8.34%, respectively. Furthermore, the soil reutilization level was significantly improved from 0.14–0.46 to 0.76–0.83 after FBC stabilization according to TOPSIS method (i.e., technique for order preference by similarity to an ideal solution). These findings confirm the potential of FBC in immobilizing As (V) and Cd (II) of co-contaminated soils and provide a useful reference for green stabilization and remediation of HMs co-contaminated sites. Graphical Abstrac