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| 1 | rMVP: A Memory-efficient, Visualization-enhanced, and Parallel-accelerated Tool for Genome-wide Association Study显示文摘Along with the develoipment of high-throughput sequencing technologies,both sample size and SNP number are increasing rapidly in genome-wide association studies(GWAS),and the associated computation is more challenging than ever.Here,we present a memory-efficient,visualization-enhanced,and parallel-accelerated R package called“r MVP”to address the need for improved GWAS computation.r MVP can 1)effectively process large GWAS data,2)rapidly evaluate population structure,3)efficiently estimate variance components by Efficient Mixed-Model Association e Xpedited(EMMAX),Factored Spectrally Transformed Linear Mixed Models(Fa ST-LMM),and Haseman-Elston(HE)regression algorithms,4)implement parallel-accelerated association tests of markers using general linear model(GLM),mixed linear model(MLM),and fixed and random model circulating probability unification(Farm CPU)methods,5)compute fast with a globally efficient design in the GWAS processes,and 6)generate various visualizations of GWASrelated information.Accelerated by block matrix multiplication strategy and multiple threads,the association test methods embedded in r MVP are significantly faster than PLINK,GEMMA,and Farm CPU_pkg.r MVP is freely available at http://gffzz188fe103f8f1460asu55uk6cqubwc6f9u.ffgz.tsg.suse.edu.cn/xiaolei-lab/r MVP. | Lilin Yin Haohao Zhang Zhenshuang Tang Jingya Xu Dong Yin Zhiwu Zhang Xiaohui Yuan Mengjin Zhu Shuhong Zhao Xinyun Li Xiaolei Liu | 2021 | Genomics, Proteomics & Bioinformatics2021，19，4： | 12 |
| 2 | Porcine Immunoglobulin Fc Fused P30/P54 Protein of African Swine Fever Virus Displaying on Surface of S. cerevisiae Elicit Strong Antibody Production in Swine显示文摘African swine fever virus(ASFV)infects domestic pigs and European wild boars with strong,hemorrhagic and high mortality.The primary cellular targets of ASFV is the porcine macrophages.Up to now,no commercial vaccine or effective treatment available to control the disease.In this study,three recombinant Saccharomyces cerevisiae(S.cerevisiae)strains expressing fused ASFV proteins-porcine Ig heavy chains were constructed and the immunogenicity of the S.cerevisiae-vectored cocktail ASFV feeding vaccine was further evaluated.To be specific,the P30-Fcγand P54-Fcαfusion proteins displaying on surface of S.cerevisiae cells were produced by fusing the Fc fragment of porcine immunoglobulin IgG1 or IgA1 with p30 or p54 gene of ASFV respectively.The recombinant P30-Fcγand P54-Fcαfusion proteins expressed by S.cerevisiae were verified by Western blotting,flow cytometry and immunofluorescence assay.Porcine immunoglobulin Fc fragment fused P30/P54 proteins elicited P30/P54-specific antibody production and induced higher mucosal immunity in swine.The absorption and phagocytosis of recombinant S.cerevisiae strains in IPEC-J2 cells or porcine alveolar macrophage(PAM)cells were significantly enhanced,too.Here,we introduce a kind of cheap and safe oral S.cerevisiae-vectored vaccine,which could activate the specific mucosal immunity for controlling ASFV infection. | Chen Chen Deping Hua Jingxuan Shi Zheng Tan Min Zhu Kun Tan Lilin Zhang Jinhai Huang | 2021 | Virologica Sinica2021，36，2： | 7 |
| 3 | The histone methyltransferase EZH2 primes the early differentiation of follicular helper T cells during acute viral infection显示文摘Epigenetic modifications to histones dictate the differentiation of naïve CD4^(+) T cells into different subsets of effector T helper(TH)cells.The histone methyltransferase enhancer of zeste homolog 2(EZH2)has been implicated in the mechanism regulating the differentiation of TH1,TH2 and regulatory T(Treg)cells.However,whether and how EZH2 regulates follicular helper T(TFH)cell differentiation remain unknown.Using a mouse model of acute lymphocytic choriomeningitis virus(LCMV)infection,we observed abundant EZH2 expression and associated H3K27me3 modifications preferentially in the early committed virus-specific TFH cells compared to those in TH1 cells.Ablation of EZH2 in LCMV-specific CD4^(+) T cells leads to a selective impairment of early TFH cell fate commitment,but not late TFH differentiation or memory TFH maintenance.Mechanistically,EZH2 specifically stabilizes the chromatin accessibility of a cluster of genes that are important for TFH fate commitment,particularly B cell lymphoma 6(Bcl6),and thus directs TFH cell commitment.Therefore,we identified the chromatin-modifying enzyme EZH2 as a novel regulator of early TFH differentiation during acute viral infection. | Xiangyu Chen Guoshuai Cao Jialin Wu Xinxin Wang Zhiwei Pan Jianbao Gao Qin Tian Lifan Xu Zhirong Li Yaxing Hao Qizhao Huang Pengcheng Wang Minglu Xiao Luoyingzi Xie Shupei Tang Zhenyu Liu Li Hu Jianfang Tang Ran He Li Wang Xinyuan Zhou Yuzhang Wu Mengjie Chen Beicheng Sun Bo Zhu Jun Huang Lilin Ye | 2020 | Cellular & Molecular Immunology2020，17，3： | 4 |
| 4 | SOME RESULTS OF UPPER ATMOSPHERIC COMPOSITION MEASUREMENTS BY A MASS-SPECTROMETER ON BOARD 'SZ-2':CHANGE OF COMPOSITIONS DURING SOLAR AND GEOMAGNETIC DISTURBANCES显示文摘Upper atmosphere composition data were obtained for the last half year with a quadruple mass spectrometer on board spacecraft 'SZ-2' launched on 10 Jan uary 2001. Based on the analysis of these data, the variations of atmospheric compositions in solar and geomagnetic quiet conditions are reported first, then a detailed discussion on the atmospheric composition variations under the so lar and geomagnetic disturbed conditions is given. The results show that near the altitude of 400 km the variations of main atmospheric compositions corre sponding to solar disturbances are more remarkable in the sunlit area than in the shade area. On the contrary, in geomagnetic disturbance events the corre sponding variations are more obvious in the shade area, an evident increase of N2 density at relatively higher latitudes was observed. | QIN Guotai QIU Shiyan HE Aiqing ZHU Yiqiang SUN Lilin LIN Xianwen LI Hong XU Xuepei | 2002 | 空间科学学报2002，22，z1： | 2 |
| 5 | The C/EBPβ-Dependent Induction of TFDP2 Facilitates Porcine Reproductive and Respiratory Syndrome Virus Proliferation显示文摘Porcine reproductive and respiratory syndrome(PRRS) is an important infectious disease caused by porcine reproductive and respiratory syndrome virus(PRRSV), leading to significant economic losses in swine industry worldwide. Although several studies have shown that PRRSV can affect the cell cycle of infected cells, it is still unclear how it manipulates the cell cycle to facilitate its proliferation. In this study, we analyzed the mRNA expression profiles of transcription factors in PRRSV-infected 3D4/21 cells by RNA-sequencing. The result shows that the expression of transcription factor DP2(TFDP2) is remarkably upregulated in PRRSV-infected cells. Further studies show that TFDP2 contributes to PRRSV proliferation and the PRRSV nucleocapsid(N) protein induces TFDP2 expression by activating C/EBPb. TFDP2 positively regulates cyclin A expression and triggers a less proportion of cells in the S phase, which contributes to PRRSV proliferation. This study proposes a novel mechanism by which PRRSV utilizes host protein to regulate the cell cycle to favor its infection. Findings from this study will help us for a better understanding of PRRSV pathogenesis. | Min Zhu Xiaoyang Li Ruiqi Sun Peidian Shi Aiping Cao Lilin Zhang Yanyu Guo Jinhai Huang | 2021 | Virologica Sinica2021，36，6： | 2 |
| 6 | Arabidopsis immune-associated nucleotide-binding genes repress heat tolerance at the reproductive stage by inhibiting the unfolded protein response and promoting cell death显示文摘Plants are vulnerable to heat stress,especially during reproductive development.The heat shock response(HSR)in the cytosol and nucleus,as well as the unfolded protein response(UPR)in the endoplasmic reticulum(ER),are two mechanisms that enable plants to survive heat stress.Excessive heat or ER stresses lead to cell death when the UPR cannot repair stress damage,but the means by which cell survival or death is determined remains unclear.In this study,we used a genome-wide association study(GWAS)to identify that a cluster of five Immune-associated nucleotide-binding protein(IAN)genes(IAN2 to IAN6)is responsible for variation in heat tolerance at the reproductive stage in Arabidopsis thaliana.These IAN genes have both unique and overlapping functions in the negative regulation of heat tolerance,and their loss of function singly or in combination confers increased heat tolerance,measured by a lower number of barren siliques and a higher seedling survival rate under heat.The loss of rice IAN1 gene function also leads to enhanced heat tolerance,suggesting a conserved function of plant IANs.Transcriptome analysis revealed enhanced expression of HSR and UPR genes,as well as reduced cell death,under heat and ER stress in the mutant of IAN6,a major effect member in Arabidopsis.Furthermore,the IAN proteins were found to promote cell death induced by heat stress,ER stress,and cell death-inducing molecules.Thus,the Arabidopsis IAN genes repress heat tolerance,probably through the HSR and UPR and by enhancing the cell death pathway.The IAN2 to IAN6 proteins are partially localized to the ER,suggesting a direct role in the UPR and UPR-mediated cell death.In addition,a natural IAN6 variant from more heat-tolerant Arabidopsis accessions confers greater heat tolerance and induces less cell death compared with the natural variant from less heat-tolerant accessions.The heat-tolerant IAN6 variant is associated with a higher maximum temperature of the warmest month at its collection sites compared with the heat-sensitive variant.Taken together,these results reveal an important role of Arabidopsis IAN2 to IAN6 genes in the regulation of the HSR,UPR,and cell death,and suggest that their natural variations have adaptive functions in heat tolerance. | Shan Lu Tianquan Zhu Zhixue Wang Lilin Luo Shuai Wang Minghui Lu Yongmei Cui Baohong Zou Jian Hua | 2021 | Molecular Plant2021，14，2： | 2 |
| 7 | Retrorsine Cooperates with Gut Microbiota to Promote Hepatic Sinusoidal Obstruction Syndrome by Disrupting the Gut Barrier显示文摘Background and Aims:Hepatic sinusoidal obstruction syndrome(HSOS)is a life-threatening syndrome,and a cause is exposure to pyrrolizidine alkaloid(PA)-containing products.It is well-established that retrorsine(RTS),a rep-resentative Pas,insults hepatic sinusoidal endothelial cells and ensues congestion of hepatic sinusoids.However,little known about the impact of Pas on gut microbiota and intesti-nal barrier and inflammation in HSOS.Methods:Mice were gavaged with or without nonabsorbable antibiotics(ABX),followed by a single dose of RTS.The gut microbiota was examined by 16S rDNA sequencing.Results:ABX pretreat-ment significantly reversed RTS-induced liver damage.RTS altered gut microbiota composition,increasing Gram-nega-tive bacteria and resulting in a sharp elevation of circulating lipopolysaccharides(LPS)in HSOS mice.Gut decontamina-tion with ABX alleviated RTS-induced intestine inflamma-tion,protected against disruption of the intestinal epithelial barrier and gut vascular barrier(GVB),and suppressed he-patic LPS-NF-κB pathway activation in RTS-induced HSOS.Importantly,the LPS level was positively correlated with MELD score in patients with HSOS.Elevated LPS in patients with HSOS confirmed that Gram-negative bacteria were in-volved in the pathogenesis of HSOS.Conclusions:RTS,a PA,cooperated with gut dysbiosis to cause intestinal inflam-mation and gut barrier compromise that increased transport of gut-derived LPS into the liver through the portal vein,which contributed to the pathology of HSOS.Modulating the gut microbiota,protecting the intestinal barrier,and sup-pressing intestinal inflammation with prebiotics or antibiot-ics might be a useful pharmacologic intervention in HSOS. | Li Xiao Lilin Hu Huikuan Chu Liuying Chen Jingjing Yan Weijun Wang Xiaoqian Yang Qingjing Zhu Fan Du Yuhu Song Peng Chen Xiaohua Hou Ling Yang | 2022 | Journal of Clinical and Translational Hepatology2022，10，6： | 2 |
| 8 | CHANGES OF THE THERMOSPHERE DENSITY IN THE SUNSHINE AND SHADE AREA OBSERVED BY 'SZ-2' ATMOSPHERIC DENSITY DETECTOR显示文摘In this paper, thermosphere density data of 'SZ-2' Atmospheric Density Detec tor From February to April 2001 are used to study the changes of the thermo sphere density in the sunshine and shaded area during solar and geomagnetic activity. The results show that in the sunshine area, the peak value of atmo spheric density changes as F10.7 varies; during geomagnetic activity, the peak value of atmospheric density in the shaded area increases as Ap increases, and start off with higher latitude, therefore move to lower latitude. | QIN Guotai QIU Shiyan HE Aiqing ZHU Yiqiang SUN Lilin LIN Xianwen LI Hong XU Xuepei | 2002 | 空间科学学报2002，22，z1： | 1 |
| 9 | The gut microbiome and metabolome of Himalayan Griffons(Gyps himalayensis):insights into the adaptation to carrion-feeding habits in avian scavengers显示文摘Background:Himalayan Griffons(Gyps himalayensis),large scavenging raptors widely distributed in Qinghai-Tibetan Plateau,have evolved a remarkable ability to feed on carcasses without suffering any adverse effects.The gut microbiome plays an important role in animal physiological and pathological processes,and has also been found to play a health protective role in the vulture adaptation to scavenging.However,the microbial taxonomic diversity(including nonculturable and culturable microbes),functions,and metabolites related to Himalayan Griffons have not been fully explored.Methods:In the present study,the 28 fecal samples of the Himalayan Griffons and 8 carrion samples were collected and sequenced using high-throughput 16 S rRNA gene sequencing methods to analyze the composition and functional structures of the microbiomes.Twelve fecal samples of the Himalayan Griffons were analyzed using untargeted Liquid Chromatography Mass Spectroscopy(LC-MS)to identify metabolites.We used different culture conditions to grow Himalayan Griffons gut microbes.Inhibitory effects of gut beneficial bacteria on 5 common pathogenic bacteria were also tested using the Oxford cup method.Results:According to the results of the culture-independent method,a high abundance of four major phyla in Himalayan Griffons were identified,including Fusobacteria,Firmicutes,Bacteroidetes,and Proteobacteria.The most abundant genera were Fusobacterium,followed by Clostridium_sensu_stricto_1,Cetobacterium,Epulopiscium,and Bacteroides.The predicted primary functional categories of the Himalayan Griffons'gut microbiome were associated with carbohydrate and amino acid metabolism,replication and repair,and membrane transport.LC-MS metabolomic analysis showed a total of 154 metabolites in all the fecal samples.Cultivation yielded 184 bacterial isolates with Escherichia coli,Enterococcus faecium,Enterococcus hirae,and Paeniclostridium sordellii as most common isolates.Moreover,7 potential beneficial gut bacteria isolated showed certain inhibition to 5 common pathogenic bacteria.Conclusions:Our findings broaden and deepen the understanding of Himalayan Griffons'gut microbiome,and highlighted the importance of gut microbiome-mediated adaptation to scavenging habits.In particular,our results highlighted the protective role of gut beneficial bacteria in the Himalayan Griffons against pathogenic bacteria that appear in rotten food resources. | Wen Wang Xiaolong Gao Sisi Zheng Zhuoma Lancuo Ying Li Lilin Zhu Jianping Hou Jiayi Hai Xin Long Hanxi Chen Alexey Druzyaka Kirill Sharshov | 2021 | Avian Research2021，12，4： | 1 |
| 10 | Peroxyoxalate Chemiluminescence Based on Fluorescent Conjugated Polymer for the Determination of Triton X-IO0显示文摘 | Jin, Yingqiong Sun, Lilin Hao, Dan Yu, Rui Qian, Zhangsheng Zhu, Changqing | 2011 | Chinese Journal of Chemistry2011，29，3： | 1 |
| 11 | Whole genome variants across 57 pig breeds enable comprehensive identification of genetic signatures that underlie breed features显示文摘Background:A large number of pig breeds are distributed around the world,their features and characteristics vary among breeds,and they are valuable resources.Understanding the underlying genetic mechanisms that explain across-breed variation can help breeders develop improved pig breeds.Results:In this study,we performed GWAS using a standard mixed linear model with three types of genome variants(SNP,InDel,and CNV)that were identified from public,whole-genome,sequencing data sets.We used 469 pigs of 57 breeds,and we identified and analyzed approximately 19 million SNPs,1.8 million InDels,and 18,016 CNVs.We defined six biological phenotypes by the characteristics of breed features to identify the associated genome variants and candidate genes,which included coat color,ear shape,gradient zone,body weight,body length,and body height.A total of 37 candidate genes was identified,which included 27 that were reported previously(e.g.,PLAG1 for body weight),but the other 10 were newly detected candidate genes(e.g.,ADAMTS9 for coat color).Conclusion:Our study indicated that using GWAS across a modest number of breeds with high density genome variants provided efficient mapping of complex traits. | Jingya Xu Yuhua Fu Yan Hu Lilin Yin Zhenshuang Tang Dong Yin Mengjin Zhu Mei Yu Xinyun Li Yang Zhou Shuhong Zhao Xiaolei Liu | 2021 | Journal of Animal Science and Biotechnology2021，12，2： | 1 |
| 12 | A potent human monoclonal antibody with pan-neutralizing activities directly dislocates S trimer of SARS-CoV-2 through binding both up and down forms of RBD显示文摘The severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)has caused a global pandemic of novel coronavirus disease(COVID-19).The neutralizing monoclonal antibodies(mAbs)targeting the receptor-binding domain(RBD)of SARS-CoV-2 are among the most promising strategies to prevent and treat COVID-19.However,SARS-CoV-2 variants of concern(VOCs)profoundly reduced the efficacies of most of mAbs and vaccines approved for clinical use.Herein,we demonstrated mAb 35B5 efficiently neutralizes both wild-type(WT)SARS-CoV-2 and VOCs. | Xiaofei Wang Ao Hu Xiangyu Chen Yixin Zhang Fei Yu Shuai Yue Arong Li Junsong Zhang Zhiwei Pan Yang Yang Yao Lin Leiqiong Gao Jing Zhou Jing Zhao Fang Li Yaling Shi Feng Huang Xiaofan Yang Yi Peng Luoyang Tu Huan Zhang Huanying Zheng Jun He Hui Zhang Lifan Xu Qizhao Huang Yongqun Zhu Kai Deng Lilin Ye | 2022 | Signal Transduction and Targeted Therapy2022，7，5： | 1 |
| 13 | Transcriptomic basis of neutrophil ratio variation induced by poly I:C stimulation in porcine peripheral blood显示文摘Neutrophils are vital components of defense mechanisms against invading pathogens and are closely linked with the individual antiviral capacity of pigs and other mammals. Neutrophilia is a well-known clinical characteristic of viral and bacterial infections. Using Affymetrix porcine genome microarrays, we investigated the gene expression profiles associated with neutrophil variation in porcine peripheral blood before and after polyriboinosinic-polyribocytidylic acid stimulation. Transcriptomic analysis showed 796 differentially expressed genes(DEGs) in extreme response(ER) pigs and 192 DEGs in moderate response(MR) pigs. Most DEGs were related to immune responses, included MXD1, CXCR4,CREG1, My D88, CD14, TLR2, TLR4, IRF3 and IRF7.Gene ontology analysis indicated that the DEGs of both ER and MR pigs were involved in common biological processes, such as cell proliferation, growth regulation,immune response, inflammatory response and cell activation. The ER and MR groups also showed differences in DEGs involved in biological processes. DEGs involved in cell division and cell cycle were specifically found in the ER pigs, whereas DEGs involved in cell migration were specifically found in the MR pigs. The study provides a basic understanding of the molecular basis for the antiviral capacity of pigs and other mammals. | Haiyan WANG Qiaoxia ZHANG Lilin YIN Xiangdong LIU Shuhong ZHAO Mengjin ZHU Changchun LI | 2017 | Frontiers of Agricultural Science and Engineering2017，4，3： | 0 |
| 14 | Tumor-specific memory CD8^(+)T cells are strictly resident in draining lymph nodes during tumorigenesis显示文摘The functional exhaustion of CD8^(+)T cells represents a fundamental hallmark of chronic viral infection and cancer and,in both scenarios,is driven by prolonged exposure to persistent cognate antigens in the context of an immunoinhibitory microenvironment.Exhausted CD8^(+)T cells upregulate the expression of a wide diversity of coinhibitory immunoreceptors(also referred to as immune checkpoint receptors),such as PD-1,Tim-3,LAG-3,and TIGIT.Concomitantly,exhausted CD8^(+)T cells lose their potential to differentiate into functional memory cells and are characterized by hierarchical loss of effector function,leading to compromised tumor control and viral eradication[1,2]. | Qiao Liu Ling Ran Zhengliang Yue Xingxing Su Lisha Wang Shuqiong Wen Shun Lei Xiaofan Yang Yan Zhang Jianjun Hu Jianfang Tang Zhirong Li Li Hu Bo Zhu Lifan Xu Lilin Ye Qizhao Huang | 2023 | Cellular & Molecular Immunology2023，20，4： | 0 |
| 15 | Author Correction:Tumor-specific memory CD8^(+)T cells are strictly resident in draining lymph nodes during tumorigenesis显示文摘 | Qiao Liu Ling Ran Zhengliang Yue Xingxing Su Lisha Wang Shuqiong Wen Shun Lei Xiaofan Yang Yan Zhang Jianjun Hu Jianfang Tang Zhirong Li Li Hu Bo Zhu Lifan Xu Lilin Ye Qizhao Huang | 2023 | Cellular & Molecular Immunology2023，20，7： | 0 |
| 16 | Variations of Thermosphere Density Based on Joint Analysis of In-Situ Measurement Data From Shenzhou Spacecrafts显示文摘Based on the measurements made by Atmospheric Density Detectors(ADDs) onboard Chinese spacecraft Shenzhou 2-4,the variations of thermosphere density are revealed.During the quiet period,the density at spacecraft altitude of 330~410 km exhibited a dominant diurnal variation,with high value on dayside and low value on nightside.The ratio of the diurnal maximum density to the minimum ranged from 1.7 to 2.0.The ratio shows a positive correlation with the level of solar activity and a negative correlation with the level of geomagnetic activity.When a geomagnetic disturbance comes,the atmospheric density at the altitude of 330~410 km displayed a global enhancement.For a strong geomagnetic disturbance,the atmospheric density increased by about 56%,and reached its maximum about 6~7 hours after the geomagnetic disturbance peak. The density asymmetry was also observed both in the southern and northern hemisphere during the geomagnetic disturbance peak. | SUN Lilin QIN Guotai ZHU Guangwu | 2012 | 空间科学学报2012，32，2： | 0 |
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