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Molecular patterns of avian influenza A viruses

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Chinese Science Bulletin 2008年第13期53卷 2002-2007页

作者： KOU Zheng LEI FuMin wang shengyue ZHOU YanHong LI TianXian Hubei Bioinformatics and Molecular Imaging Key Laboratory Department of Systems Biology Huazhong University of Science and Technology Wuhan 430074 China State Key Laboratory of Virology Wuhan Institute of Virology Chinese Academy of Sciences Wuhan 430071 China Institute of Zoology Chinese Academy of Sciences Beijing 100080 China Chinese National Human Genome Center Chinese Academy of Sciences Shanghai 201203 China

Avian influenza A viruses could get across the species barrier and be fatal to humans. Highly patho-genic avian influenza H5N1 virus was an example. The mechanism of interspecies transmission is not clear as yet. In this research,the protein sequences of 237 influenza A viruses with different subtypes were transformed into pseudo-signals. The energy features were extracted by the method of wavelet packet decomposition and used for virus classification by the method of hierarchical clustering. The clustering results showed that five patterns existed in avian influenza A viruses,which associated with the phenotype of interspecies transmission,and that avian viruses with patterns C and E could across species barrier and those with patterns A,B and D might not have the abilities. The results could be used to construct an early warning system to predict the transmissibility of avian influenza A viruses to humans.

关键词：禽流感病毒 H5N1 子波分解聚类种间传输

High-efficiency circularly polarized emission from liquid-crystalline platinum complexes

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Chinese Chemical Letters 2023年第6期34卷 310-314页

作者： Peng Fan Zhou Fang shengyue wang Qiwei Dong Chen Xiao Alice J.McEllin Duncan W.Bruce Weiguo Zhu Yafei wang Jiangsu Key Laboratory of Environmentally Friendly Polymeric Materials Jiangsu Collaborative Innovation Center of Photovoltaic Science and EngineeringJiangsu Engineering Laboratory of Light-Electricity-Heat Energy-Converting Materials and ApplicationsSchool of Materials Science&EngineeringChangzhou UniversityChangzhou 213164China Department of Chemistry University of YorkYork YO105DDUnited Kingdom Anhui Sholon New Material Technology Co. Ltd.Chuzhou 239500China

Realizing both a high emission efficiency and luminescence dissymmetry factor(g_(lum))in circularly polarized solution processable organic light-emitting diodes(CP-OLEDs)remains a significant *** this contribution,two chiral phosphorescent liquid crystals based on cyclometalated platinum complexes are prepared,in which the chiral s-2-methyl-1-butyl group is introduced into the cyclometalating ligand and the mesogenic fragment is attached to the periphery of the ancillary *** platinum complexes exhibit both smectic and chiral nematic phases as evidenced by polarized optical microscopy,differential scanning calorimetry and small-angle X-ray ***,a high photoluminescent quantum efficiency of over 78%and clear circularly polarized luminescent signal with g_(PL)of about 10^(-2)are observed for the ***,solution-processed CP-OLEDs show maximum external quantum efficiencies(EQE)of over 15%and strong circularly polarized electroluminescent signals with a g_(EL)≈10^(-2).This research demonstrates that both liquid crystallinity and the number of chiral centers play key roles in improving the chiroptical property,paving the way for a new approach for the design of high-efficiency CPL emitters.

关键词： Circularly polarized emission Liquid-crystalline Platinum complex Organic light-emitting diodes

Single-cell atlas reveals a distinct immune profile fostered by T cell-B cell crosstalk in triple negative breast cancer

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Cancer Communications 2023年第6期43卷 661-684页

作者： Shuning Ding Niu Qiao Qingchen Zhu Yiwei Tong shengyue wang Xiaosong Chen Qiang Tian Yichuan Xiao Kunwei Shen Department of General Surgery Comprehensive Breast Health CenterRuijin HospitalShanghai Jiao Tong University School of MedicineShanghaiP.R.China Shanghai Institute of Hematology State Key Laboratory of Medical GenomicsNational Research Center for Translational Medicine at ShanghaiRuijin Hospital Affiliated to Shanghai Jiao Tong University School of MedicineShanghaiP.R.China Chinese Academy of Sciences Key Laboratory of Tissue Microenvironment and Tumor Shanghai Institute of Nutrition and HealthChinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghaiP.R.China

Background:Characterizing the unique immune microenvironment of each tumor is of great importance for better predicting prognosis and guiding cancer ***,the unique features of the immune microenvironment of triple negative breast cancer(TNBC)compared with other subtypes of breast cancer remain ***,we aimed to depict and compare the immune landscape among TNBC,human epidermal growth factor receptor 2-positive(HER2^(+))breast cancer,and luminal-like breast ***:Single-cell RNA sequencing(scRNA-seq)was performed on CD45^(+)immune cells isolated from human normal breast tissues and primary breast tumors of various *** analyzing the scRNA-seq data,immune cell clusters were identified and their proportions as well as transcriptome features were compared among TNBC,human HER2^(+)breast cancer,and luminal-like breast *** and cell-cell communication analyses were also conducted to characterize the immune ***:ScRNA-seq data of 117,958 immune cells were obtained and 31 immune clusters were identified.A unique immunosuppressive microenvironment in TNBC was decoded as compared to that in HER2^(+)or luminal-like breast cancer,which was characterized by higher proportions of regulatory T cells(Tregs)and exhausted CD8+T cells and accompanied by more abundant plasma *** and exhausted CD8+T cells in TNBC exhibited increased immunosuppression signature and dysfunctional *** analyses showed that B cells tended to differentiate to plasma cells in ***-cell communication analyses indicated that these unique features are fostered by the diversified T cell-B cell crosstalk in *** on the T cell-B cell crosstalk,a prognostic signaturewas established that could effectively predict the prognosis status for patients with ***,it was found that TNBC had a higher proportion of cytotoxic natural killer(NK)cells,whereas HER2^(+)or luminal-like breast cancer lost this f

关键词： breast cancer prognostic signature single-cell RNA sequencing T cell-B cell crosstalk triplenegative breast cancer tumor immune microenvironment

Integrated analysis of gut microbiome and host immune responses in COVID-19

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Frontiers of Medicine 2022年第2期16卷 263-275页

作者： Xiaoguang Xu Wei Zhang Mingquan Guo Chenlu Xiao Ziyu Fu Shuting Yu Lu Jiang shengyue wang Yun Ling Feng Liu Yun Tan Saijuan Chen Shanghai Institute of Hematology State Key Laboratory of Medical GenomicsNational Research Center for Translational Medicine at ShanghaiRuijin Hospital Affiliated to Shanghai Jiao Tong University School ofMedicineShanghai 200025China Schoolof Life Sciences and Biotechnology Shanghai Jiao Tong UniversityShanghai 200240China Shanghai Public Health Clinical Center Shanghai 201508China Department of Laboratory Medicine Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of MedicineShanghai 200025China

Emerging evidence indicates that the gut microbiome contributes to the host immune response to infectious ***,to explore the role of the gut microbiome in the host immune responses in COVID-19,we conducted shotgun metagenomic sequencing and immune profiling of 14 severe/critical and 24 mild/moderate COVID-19 cases as well as 31 healthy control *** found that the diversity of the gut microbiome was reduced in severe/critical COVID-19 cases compared to mild/moderate *** identified the abundance of some gut microbes altered post-SARS-CoV-2 infection and related to disease severity,such as Enterococcus faecium,Coprococcus comes,Roseburia intestinalis,Akkermansia ntuciniphila,Bacteroides cellulosilyticus and Blautia *** further analyzed the correlation between the abundance of gut microbes and host responses,and obtained a correlation map between clinical features of COVID-19 and 16 severity-related gut microbe,including Coprococcus comes that was positively correlated with CD3^(+)/CD4^(+)/CD8^(+)lymphocyte *** addition,an integrative analysis of gut microbiome and the transcriptome of peripheral blood mononuclear cells(PBMCs)showed that genes related to viral transcription and apoptosis were up-regulated in Coprococcus comes low ***,a number of metabolic pathways in gut microbes were also found to be differentially enriched in severe/critical or mild/moderate COVID-19 cases,including the superpathways of polyamine biosynthesis II and sulfur oxidation that were suppressed in severe/critical ***,our study highlighted a potential regulatory role of severity related gut microbes in the immune response of host.

关键词： COVID-19 SARS-COV-2 gut microbiome immune response

Primary assessment of the diversity of Omicron sublineages and the epidemiologic features of autumn/winter 2022 COVID-19 wave in Chinese mainland

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Frontiers of Medicine 2023年第4期17卷 758-767页

作者： Gang Lu Yun Ling Minghao Jiang Yun Tan Dong Wei Lu Jiang Shuting Yu Fangying Jiang Shuai wang Yao Dai Jinzeng wang Geng Wu Xinxin Zhang Guoyu Meng shengyue wang Feng Liu Xiaohong Fan Saijuan Chen Shanghai Institute of Hematology National Research Center for Translational MedicineState Key Laboratory of Medical GenomicsRuijin Hospital Affiliated to Shanghai Jiao Tong University School of MedicineShanghai 200025China Shanghai Public Health Clinical Center Fudan UniversityShanghai 200083China Department of Infectious Diseases Research Laboratory of Clinical VirologyNational Research Center for Translational MedicineRuijin Hospital Affiliated to Shanghai Jiao Tong University School of MedicineShanghai 200025China State Key Laboratory of Microbial Metabolism School of Life Sciences and BiotechnologyThe Joint International Research Laboratory of Metabolic and Developmental SciencesShanghai Jiao Tong UniversityShanghai 200240China

With the recent ongoing autumn/winter 2022 COVID-19 wave and the adjustment of public health control measures,there have been widespread SARS-CoV-2 infections in Chinese *** we have analyzed 369 viral genomes from recently diagnosed COVID-19 patients in Shanghai,identifying a large number of sublineages of the SARS-CoV-2 Omicron *** analysis,coupled with contact history tracing,revealed simultaneous community transmission of two Omicron sublineages dominating the infections in some areas of China(BA.5.2 mainly in Guangzhou and Shanghai,and BF.7 mainly in Beijing)and two highly infectious sublineages recently imported from abroad(XBB and BQ.1).Publicly available data from August 31 to November 29,2022 indicated an overall severe/critical case rate of 0.035%nationwide,while analysis of 5706 symptomatic patients treated at the Shanghai Public Health Center between September 1 and December 26,2022 showed that 20 cases(0.35%)without comorbidities progressed into severe/critical conditions and 153 cases(2.68%)with COVID-19-exacerbated comorbidities progressed into severe/critical *** observations shall alert healthcare providers to place more resources for the treatment of severe/critical ***,mathematical modeling predicts this autumn/winter wave might pass through major cities in China by the end of the year,whereas some middle and western provinces and rural areas would be hit by the upcoming infection wave in mid-to-late January 2023,and the duration and magnitude of upcoming outbreak could be dramatically enhanced by the extensive travels during the Spring Festival(January 21,2023).Altogether,these preliminary data highlight the needs to allocate resources to early diagnosis and effective treatment of severe cases and the protection of vulnerable population,especially in the rural areas,to ensure the country’s smooth exit from the ongoing pandemic and accelerate socio-economic recovery.

关键词： SARS-CoV-2 COVID-19 Omicron genomic epidemiology

Host protection against Omicron BA.2.2 sublineages by prior vaccination in spring 2022 COVID-19 outbreak in Shanghai

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Frontiers of Medicine 2023年第3期17卷 562-575页

作者： Ziyu Fu Dongguo Liang Wei Zhang Dongling Shi Yuhua Ma Dong Wei Junxiang Xi Sizhe Yang Xiaoguang Xu Di Tian Zhaoqing Zhu Mingquan Guo Lu Jiang Shuting Yu Shuai wang Fangyin Jiang Yun Ling shengyue wang Saijuan Chen Feng Liu Yun Tan Xiaohong Fan Shanghai Institute of Hematology National Research Center for Translational MedicineState Key Laboratory of Medical GenomicsRuijin Hospital Affiliated to Shanghai Jiao Tong University(SJTU)School of MedicineShanghai 200025China National Translational Science Center for Molecular Medicine&Department of Cell Biology Fourth Military Medical UniversityXi’an 710032China Shanghai Public Health Clinical Center Fudan UniversityShanghai 201508China Department of Nephrology Traditional Chinese Medicine Hospital of KunShanSuzhou 215300China Department of Infectious Diseases Ruijin Hospital Affiliated to Shanghai Jiao Tong University(SJTU)School of MedicineShanghai 200025China

The Omicron family of SARS-CoV-2 variants are currently driving the COVID-19 *** we analyzed the clinical laboratory test results of 9911 Omicron BA.2.2 sublineages-infected symptomatic patients without earlier infection histories during a SARS-CoV-2 outbreak in Shanghai in spring *** to an earlier patient cohort infected by SARS-CoV-2 prototype strains in 2020,BA.2.2 infection led to distinct fluctuations of pathophysiological markers in the peripheral *** particular,severe/critical cases of COVID19 post BA.2.2 infection were associated with less pro-inflammatory macrophage activation and stronger interferon alpha response in the bronchoalveolar ***,the abnormal biomarkers were significantly subdued in individuals who had been immunized by 2 or 3 doses of SARS-CoV-2 prototypeinactivated vaccines,supporting the estimation of an overall 96.02% of protection rate against severe/critical disease in the 4854 cases in our BA.2.2 patient cohort with traceable vaccination ***,even though age was a critical risk factor of the severity of COVID-19 post BA.2.2 infection,vaccination-elicited protection against severe/critical COVID-19 reached 90.15% in patients aged≥60 years ***,our study delineates the pathophysiological features of Omicron BA.2.2 sublineages and demonstrates significant protection conferred by prior prototype-based inactivated vaccines.

关键词： SARS-CoV-2 COVID-19 host response bronchoalveolar lavage fluid(BALF)

The Genome of Artemisia annua Provides Insight into the Evolution of Asteraceae Family and Artemisinin Biosynthesis

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Molecular Plant 2018年第6期11卷 776-788页

作者： Qian Shen Lida Zhang Zhihua Liao shengyue wang Tingxiang Yan Pu Shi Meng Liu Xueqing Fu Qifang Pan Yuliang wang Zongyou Lv Xu Lu Fangyuan Zhang Weimin Jiang Yanan Ma Minghui Chen Xiaolong Hao Ling Li Yueli Tang Gang Lv Yan Zhou Xiaofen Sun Peter E. Brodelius Jocelyn K.C. Rose Kexuan Tang Joint International Research Laboratory of Metabolic & Developmental Sciences Key Laboratory of Urban Agriculture (South) Ministry of Agriculture Plant Biotechnology Research Center Fudan-SJTU-Nottingham Plant Biotechnology R&D Center School of Agriculture and Biology Shanghai Jiao Tong University Shanghai 200240 China SWU-TAAHC Medicinal Plant Joint R&D Centre School of Life Sciences Southwest University Chongqing 400715 China Chinese National Human Genome Center at Shanghai Shanghai 201203 China Plant Biology Section School of Integrative Plant Science Cornell University Ithaca NY 14853 USA Department of Chemistry and Biomedical Sciences Linnaeus University 39182 Kalmar Sweden State Key Laboratory of Natural Medicines China Pharmaceutical University Nanjing 211198 China

Artemisia annua, commonly known as sweet wormwood or Qinghao, is a shrub native to China and has long been used for medicinal purposes. A. annua is now cultivated globally as the only natural source of a potent anti-malarial compound, artemisinin. Here, we report a high-quality draft assembly of the 1.74-gigabase genome of A. annua, which is highly heterozygous, rich in repetitive sequences, and contains 63 226 protein-coding genes, one of the largest numbers among the sequenced plant species. We found that, as one of a few sequenced genomes in the Asteraceae, the A. annua genome contains a large number of genes specific to this large angiosperm clade. Notably, the expansion and functional diversification of genes encoding enzymes involved in terpene biosynthesis are consistent with the evolution of the artemi- sinin biosynthetic pathway. We further revealed by transcriptome profiling that A. annua has evolved the sophisticated transcriptional regulatory networks underlying artemisinin biosynthesis. Based on compre- hensive genomic and transcriptomic analyses we generated transgenic A. annua lines producing high levels of artemisinin, which are now ready for large-scale production and thereby will help meet the chal- lenge of increasing global demand of artemisinin.

关键词： Artemisia annua artemisinin genome evolution transcriptome metabolic engineering

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外磁场诱导下的硫化钴晶相转变

南京师大学报（自然科学版） 2012年第1期35卷 34-38页

作者：王巍王声乐王登志南京师范大学物理科学与技术学院江苏南京210046 东南大学物理系江苏南京210096

利用磁场诱导生长技术,成功地控制了Co9S8晶体向Co3S4晶体的晶相过渡生长.通过对晶体产物的XRD,SEM和TEM分析,证实了这种磁场诱导下的晶相结构转变.研究结果表明,通过设计在完全相同的化学反应条件下施加不同磁场,证明外磁场是该晶相相... 详细信息

利用磁场诱导生长技术,成功地控制了Co9S8晶体向Co3S4晶体的晶相过渡生长.通过对晶体产物的XRD,SEM和TEM分析,证实了这种磁场诱导下的晶相结构转变.研究结果表明,通过设计在完全相同的化学反应条件下施加不同磁场,证明外磁场是该晶相相变的惟一诱导因素.并对诱导相变的机理进行了解释.该成果有望为过渡金属硫化物的低温生长提供新技术.

关键词：硫化钴相变磁场诱导晶体生长

The genome and transcriptome of the hydatid tapeworm Echinococcus granulosus

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The genome and transcriptome of the hydatid tapeworm Echinoc...