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| 1 | The origin, diversification and adaptation of a major mangrove clade (Rhizophoreae) revealed by whole-genome sequencing显示文摘Mangroves invade some very marginal habitats for woody plants—at the interface between land and sea.Since mangroves anchor tropical coastal communities globally, their origin, diversification and adaptation are of scientific significance, particularly at a time of global climate change. In this study, a combination of single-molecule long reads and the more conventional short reads are generated from Rhizophora apiculata for the de novo assembly of its genome to a near chromosome level. The longest scaffold, N50 and N90 for the R. apiculata genome, are 13.3 Mb, 5.4 Mb and 1.0 Mb, respectively. Short reads for the genomes and transcriptomes of eight related species are also generated. We find that the ancestor of Rhizophoreae experienced a whole-genome duplication ~70 Myrs ago, which is followed rather quickly by colonization and species diversification. Mangroves exhibit pan-exome modifications of amino acid(AA) usage as well as unusual AA substitutions among closely related species. The usage and substitution of AAs, unique among plants surveyed, is correlated with the rapid evolution of proteins in mangroves. A small subset of these substitutions is associated with mangroves' highly specialized traits(vivipary and red bark) thought to be adaptive in the intertidal habitats. Despite the many adaptive features, mangroves are among the least genetically diverse plants, likely the result of continual habitat turnovers caused by repeated rises and falls of sea level in the geologically recent past. Mangrove genomes thus inform about their past evolutionary success as well as portend a possibly difficult future. | Shaohua Xu Ziwen He Zhang Zhang Zixiao Guo Wuxia Guo Haomin Lyu Jianfang Li Ming Yang Zhenglin Du Yelin Huang Renchao Zhou Cairong Zhong David E. Boufford Manuel Lerdau Chung-I Wu Norman C. Duke Suhua Shi | 2017 | National Science Review2017，4，5： | 7 |
| 2 | Whole Genome Analyses of Chinese Population and De Novo Assembly of A Northern Han Genome显示文摘To unravel the genetic mechanisms of disease and physiological traits,it requires comprehensive sequencing analysis of large sample size in Chinese populations.Here,we report the primary results of the Chinese Academy of Sciences Precision Medicine Initiative(CASPMI)project launched by the Chinese Academy of Sciences,including the de novo assembly of a northern Han reference genome(NH1.0)and whole genome analyses of 597 healthy people coming from most areas in China.Given the two existing reference genomes for Han Chinese(YH and HX1)were both from the south,we constructed NH1.0,a new reference genome from a northern individual,by combining the sequencing strategies of PacBio,10×Genomics,and Bionano mapping.Using this integrated approach,we obtained an N50 scaffold size of 46.63 Mb for the NH1.0 genome and performed a comparative genome analysis of NH1.0 with YH and HX1.In order to generate a genomic variation map of Chinese populations,we performed the whole-genome sequencing of 597 participants and identified 24.85 million(M)single nucleotide variants(SNVs),3.85 M small indels,and 106,382 structural variations.In the association analysis with collected phenotypes,we found that the T allele of rs1549293 in KAT8 significantly correlated with the waist circumference in northern Han males.Moreover,significant genetic diversity in MTHFR,TCN2,FADS1,and FADS2,which associate with circulating folate,vitamin B12,or lipid metabolism,was observed between northerners and southerners.Especially,for the homocysteine-increasing allele of rs1801133(MTHFR 677T),we hypothesize that there exists a “comfort”zone for a high frequency of 677T between latitudes of 35–45 degree North.Taken together,our results provide a high-quality northern Han reference genome and novel population-specific data sets of genetic variants for use in the personalized and precision medicine. | Zhenglin Du Liang Ma Hongzhu Qu Wei Chen Bing Zhang Xi Lu Weibo Zhai Xin Sheng Yongqiao Sun Wenjie Li Meng Lei Qiuhui Qi Na Yuan Shuo Shi Jingyao Zeng Jinyue Wang Yadong Yang Qi Liu Yaqiang Hong Lili Dong Zhewen Zhang Dong Zou Yanqing Wang Shuhui Song Fan Liu Xiangdong Fang Hua Chen Xin Liu Jingfa Xiao Changqing Zeng | 2019 | Genomics, Proteomics & Bioinformatics2019，17，3： | 4 |
| 3 | The Global Landscape of SARS-CoV-2 Genomes, Variants, and Haplotypes in 2019nCoVR显示文摘On January 22,2020,China National Center for Bioinformation(CNCB)released the 2019 Novel Coronavirus Resource(2019nCoVR),an open-access information resource for the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2).2019nCoVR features a comprehensive integration of sequence and clinical information for all publicly available SARS-CoV-2 isolates,which are manually curated with value-added annotations and quality evaluated by an automated in-house pipeline.Of particular note,2019nCoVR offers systematic analyses to generate a dynamic landscape of SARS-CoV-2 genomic variations at a global scale.It provides all identified variants and their detailed statistics for each virus isolate,and congregates the quality score,functional annotation,and population frequency for each variant.Spatiotemporal change for each variant can be visualized and historical viral haplotype network maps for the course of the outbreak are also generated based on all complete and high-quality genomes available.Moreover,2019nCoVR provides a full collection of SARS-CoV-2 relevant literature on the coronavirus disease 2019(COVID-19),including published papers from PubMed as well as preprints from services such as bioRxiv and medRxiv through Europe PMC.Furthermore,by linking with relevant databases in CNCB,2019nCoVR offers data submission services for raw sequence reads and assembled genomes,and data sharing with NCBI.Collectively,SARS-CoV-2 is updated daily to collect the latest information on genome sequences,variants,haplotypes,and literature for a timely reflection,making 2019nCoVR a valuable resource for the global research community.2019nCoVR is accessible at https://bigd.big.ac.cn/ncov/. | Shuhui Song Lina Ma Dong Zou Dongmei Tian Cuiping Li Junwei Zhu Meili Chen Anke Wang Yingke Ma Mengwei Li Xufei Teng Ying Cui Guangya Duan Mochen Zhang Tong Jin Chengmin Shi Zhenglin Du Yadong Zhang Chuandong Liu Rujiao Li Jingyao Zeng Lili Hao Shuai Jiang Hua Chen Dali Han Jingfa Xiao Zhang Zhang Wenming Zhao Yongbiao Xue Yiming Bao | 2020 | Genomics, Proteomics & Bioinformatics2020，18，6： | 4 |
| 4 | Study of the intrinsic mechanisms of nickel additive for grain refinement and strength enhancement of laser aided additively manufactured Ti–6Al–4V显示文摘It is well-known that grain refiners can tailor the microstructure and enhance the mechanical properties of titanium alloys fabricated by additive manufacturing(AM). However, the intrinsic mechanisms of Ni addition on AM-built Ti–6Al–4V alloy is not well established. This limits its industrial applications. This work systematically investigated the influence of Ni additive on Ti–6Al–4V alloy fabricated by laser aided additive manufacturing(LAAM). The results showed that Ni addition yields three key effects on the microstructural evolution of LAAM-built Ti–6Al–4V alloy.(a) Ni additive remarkably refines the prior-β grains, which is due to the widened solidification range. As the Ni addition increased from 0 to 2.5 wt. %, the major-axis length and aspect ratio of the prior-β grains reduced from over 1500 μm and 7 to 97.7 μm and1.46, respectively.(b) Ni additive can discernibly induce the formation of globular α phase,which is attributed to the enhanced concentration gradient between the β and α phases. This is the driving force of globularization according to the termination mass transfer theory. The aspect ratio of the α laths decreased from 4.14 to 2.79 as the Ni addition increased from 0 to2.5 wt. %.(c) Ni as a well-known β-stabilizer and it can remarkably increase the volume fraction of β phase. Room-temperature tensile results demonstrated an increase in mechanical strength and an almost linearly decreasing elongation with increasing Ni addition. A modified mathematical model was used to quantitatively analyze the strengthening mechanism. It was evident from the results that the α lath phase and the solid solutes contribute the most to the overall yield strength of the LAAM-built Ti–6Al–4V–x Ni alloys in this work. Furthermore, the decrease in elongation with increasing Ni addition is due to the deterioration in deformability of the β phase caused by a large amount of solid-solution Ni atoms. These findings can accelerate the development of additively manufactured titanium alloys. | Shang Sui Youxiang Chew Fei Weng Chaolin Tan Zhenglin Du Guijun Bi | 2022 | International Journal of Extreme Manufacturing2022，4，3： | 1 |
| 5 | The effects of bonding conditions on the propagation of acoustic waves along a cased borehole显示文摘Based on the wave equations in cylindrically layered structures and boundary conditions, the frequency equation for axisymmetric guided waves and the expression for sound fields in a cased borehole excited by a monopole or multipole source have been derived. The synthetic full waveforms excited by the monopole and dipole source are simulated using a real axis integration and FFT method. According to the axisymmetric guided wave modes, the synthetic full waveforms and the effects of the interface conditions on the sound field in a cased borehole have been analyzed and studied respectively. Numerical results indicate that it may be difficult to distinguish well bonded, poorly bonded or unbonded intermediate layer between the steel pipe and formation if only using a monopole source or dipole source. To properly estimate the case boundary conditions, a combination of monopole source logging with dipole source logging is suggested. | LI Zhenglin, DU Guangsheng, WANG Yaojun (The State Key Laboratory of Modern Acoustics, Nanjing University Nanjing 210093) | 2001 | Chinese Journal of Acoustics2001，20，3： | 1 |
| 6 | Long noncoding RNA(lncRNA)H19:An essential developmental regulator with expanding roles in cancer,stem cell differentiation,and metabolic diseases显示文摘Recent advances in deep sequencing technologies have revealed that,while less than 2%of the human genome is transcribed into mRNA for protein synthesis,over 80%of the genome is transcribed,leading to the production of large amounts of noncoding RNAs(ncRNAs).It has been shown that ncRNAs,especially long non-coding RNAs(lncRNAs),may play crucial regulatory roles in gene expression.As one of the first isolated and reported lncRNAs,H19 has gained much attention due to its essential roles in regulating many physiological and/or pathological processes including embryogenesis,development,tumorigenesis,osteogen-esis,and metabolism.Mechanistically,H19 mediates diverse regulatory functions by serving as competing endogenous RNAs(CeRNAs),Igf2/H19 imprinted tandem gene,modular scaffold,cooperating with H19 antisense,and acting directly with other mRNAs or lncRNAs.Here,we summarized the current understanding of H19 in embryogenesis and development,cancer development and progression,mesenchymal stem cell lineage-specific differentiation,and metabolic diseases.We discussed the potential regulatory mechanisms underlying H19’s func-tions in those processes although more in-depth studies are warranted to delineate the exact molecular,cellular,epigenetic,and genomic regulatory mechanisms underlying the physiolog-ical and pathological roles of H19.Ultimately,these lines of investigation may lead to the development of novel therapeutics for human diseases by exploiting H19 functions. | Junyi Liao Bowen Chen Zhenglin Zhu Chengcheng Du Shengqiang Gao Guozhi Zhao Piao Zhao Yonghui Wang Annie Wang Zander Schwartz Lily Song Jeffrey Hong William Wagstaff Rex CHaydon Hue HLuu Jiaming Fan Russell RReid Tong-Chuan He Lewis Shi Ning Hu Wei Huang | 2023 | Genes & Diseases2023，10，4： | 1 |
| 7 | Metagenomic evidence for the co-existence of SARS and H1N1 in patients from 2007-2012 flu seasons in France显示文摘By re-analzying public metagenomic data from 101 patients infected with influenza A virus during the 2007–2012 H1N1 flu seasons in France,we identified 22 samples with SARS-CoV sequences.In three of them,the SARS genome sequences could be fully assembled out of each.These sequences are highly similar(99.99%and 99.70%)to the artificially constructed recombinant SARS-CoV(SARSr-CoV)strains generated by the J.Craig Venter Institute in the USA.Moreover,samples from different flu seasons have different SARS-CoV strains,and the divergence between these strains cannot be explained by natural evolution.Our study also shows that retrospective studies using public metagenomic data from past major epidemic outbreaks serve as a genomic strategy for the research of the origins or spread of infectious diseases. | Qi Liu Zhenglin Du Sihui Zhu Wenming Zhao Hua Chen Yongbiao Xue | 2021 | Biosafety and Health2021，3，6： | 0 |
| 8 | Deep Sc-RNA sequencing decoding the molecular dynamic architecture of the human retina显示文摘The human retina serves as a light detector and signals transmission tissue.Advanced insights into retinal disease mechanisms and therapeutic strategies require a deep understanding of healthy retina molecular events.Here,we sequenced the m RNA of over 0.6 million single cells from human retinas across six regions at nine different ages.Sixty cell sub-types have been identified from the human mature retinas with unique markers.We revealed regional and age differences of gene expression profiles within the human retina.Cell-cell interaction analysis indicated a rich synaptic connection within the retinal cells.Gene expression regulon analysis revealed the specific expression of transcription factors and their regulated genes in human retina cell types.Some of the gene’s expression,such as DKK3,are elevated in aged retinas.A further functional investigation suggested that over expression of DKK3 could impact mitochondrial stability.Overall,decoding the molecular dynamic architecture of the human retina improves our understanding of the vision system. | Lulin Huang Runze Li Lin Ye Shanshan Zhang Huaping Tian Mingyan Du Chao Qu Shujin Li Jie Li Mu Yang Biao Wu Ran Chen Guo Huang Ling Zhong Hongjie Yang Man Yu Yi Shi Changguan Wang Houbin Zhang Wei Chen Zhenglin Yang | 2023 | Science China(Life Sciences)2023，66，3： | 0 |
| 9 | LncRNA H19 mediates BMP9-induced angiogenesis in mesenchymal stem cells by promoting the p53-Notch1 angiogenic signaling axis显示文摘BMP9 mediated osteogenic differentiation mechanisms of MSCs were widely explored, however, mechanisms of BMP9-induced angiogenesis still need to be clarified. We previously characterized that Notch1 promoted BMP9-induced osteogenesis–angiogenesis coupling process in mesenchymal stem cells (MSCs). Here, we explored the underlying mechanisms of lncRNA H19 (H19) mediated regulation of BMP9-induced angiogenesis through activating Notch1 signaling. We demonstrated that basal expression level of H19 was high in MSCs, and silencing H19 attenuates BMP9-induced osteogenesis and angiogenesis of MSCs both in vitro and in vivo. Meanwhile, we identified that BMP9-induced production of CD31+ cells was indispensable for BMP9-induced bone formation, and silencing H19 dramatically blocked BMP9-induced production of CD31^(+) cells. In addition, we found that down-regulation of H19 inhibited BMP9 mediated blood vessel formation and followed subsequent bone formation in vivo. Mechanistically, we clarified that H19 promoted p53 phosphorylation by direct interacting and phosphorylating binding, and phosphorylated p53 potentiated Notch1 expression and activation of Notch1 targeting genes by binding on the promoter area of Notch1 gene. These findings suggested that H19 regulated BMP9-induced angiogenesis of MSCs by promoting the p53-Notch1 angiogenic signaling axis. | Chengcheng Du Qiang Cheng Piao Zhao Claire Wang Zhenglin Zhu Xiangdong Wu Shengqiang Gao Bowen Chen Jing Zou Wei Huang Junyi Liao | 2023 | Genes & Diseases2023，10，3： | 0 |
| 10 | C–H…S Hydrogen Bond Assisted Supramolecular Encapsulation of Fullerenes with Nanobelts显示文摘Hydrogen-bonded capsules have been widely employed as supramolecular hosts for organic molecular guests.Encapsulation of fullerenes by capsules is relatively scarce,especially those that utilize sulfur atoms as hydrogen-bond acceptors.Herein,we describe,in both solution and solid state,a bowl-shaped nanobelt[8]cyclophenoxathiin 1a and its tetra-methylated derivative 1b that can form C–H⋯S hydrogen-bonded capsules induced by complexation with suitable fullerenes.1a strongly encapsulates C60,C70,or 6,6-phenyl-C61-butyric acid methyl ester(PC61BM)to form a 2∶1 ternary complex featuring 16 equatorial(sp2)C–H⋯S hydrogen bonds.A pseudorotaxane structure was further obtained for the complex of 1a with PC61BM.Conversely,a 1∶1 inclusion complex was observed for binding C60 or PC61BM with 1b indicating the reduced tendency to form capsules by introducing methyl groups into the belt.Surprisingly,the capsule-like structure was retained for the 1:2 complex of C70 with 1b as observed by the presence of multiple(sp3)C–H⋯S hydrogen bonds.The strong binding affinity and tailorable complexation mode enable further applications of nanobelts in fullerene chemistry. | Jialin Xie Xia Li Zhenglin Du Yandie Liu Kelong Zhu | 2023 | CCS Chemistry2023，5，4： | 0 |
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