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| 1 | Building a sequence map of the pig pan-genome from multiple de novo assemblies and Hi-C data显示文摘Pigs were domesticated independently in the Near East and China,indicating that a single reference genome from one individual is unable to represent the full spectrum of divergent sequences in pigs worldwide.Therefore,12 de novo pig assemblies from Eurasia were compared in this study to identify the missing sequences from the reference genome.As a result,72.5 Mb of nonredundant sequences(~3% of the genome)were found to be absent from the reference genome(Sscrofa11.1)and were defined as pan-sequences.Of the pan-sequences,9.0 Mb were dominant in Chinese pigs,in contrast with their low frequency in European pigs.One sequence dominant in Chinese pigs contained the complete genic region of the tazarotene-induced gene 3(TIG3)gene which is involved in fatty acid metabolism.Using flanking sequences and Hi-C based methods,27.7% of the sequences could be anchored to the reference genome.The supplementation of these sequences could contribute to the accurate interpretation of the 3D chromatin structure.A web-based pan-genome database was further provided to serve as a primary resource for exploration of genetic diversity and promote pig breeding and biomedical research. | Xiaomeng Tian Ran Li Weiwei Fu Yan Li Xihong Wang Ming Li Duo Du Qianzi Tang Yudong Cai Yiming Long Yue Zhao Mingzhou Li Yu Jiang | 2020 | Science China(Life Sciences)2020，63，5： | 7 |
| 2 | Prevalence and Phylogenetic Analysis of Crimean-Congo Hemorrhagic Fever Virus in Ticks from Different Ecosystems in Xinjiang,China显示文摘The Crimean-Congo hemorrhagic fever virus(CCHFV),a member of the genus Orthonairovirus and family Nairoviridae,is transmitted by ticks and causes severe hemorrhagic disease in humans.To study the epidemiology of CCHFV in different ecosystems in Xinjiang,China,a total of 58,932 ticks were collected from Tarim Basin,Junggar Basin,Tianshan Mountain,and Altai Mountain from 2014 to 2017.Hyalomma asiaticum asiaticum was the dominant tick species in Tarim and Junggar basins,whereas Dermacentor nuttalli and Hyalomma detritum were found in Tianshan Mountain and Altai Mountain,respectively.Reverse transcription-polymerase chain reaction of the CCHFV small(S)genome segment was used for the molecular detection.The CCHFV-positive percentage was 5.26%,6.85%,1.94%,and 5.56% in Tarim Basin,Junggar Basin,Tianshan Mountain,and Altai Mountain,respectively.Sequences of the S segment were used for phylogenetic analysis and the results showed that the newly identified CCHFV strains belonged to two clades.Our study confirms that H.asiaticum asiaticum is the major vector of CCHFV in desert habitats which is consistent with previous studies,and also suggests that H.detritum and D.nuttalli are emerging vectors for CCHFV in Xinjiang.Moreover,this study reports the presence of CCHFV in the mountain habitat of Xinjiang for the first time,suggesting that future surveillance of CCHFV should also include mountainous areas. | Abulimiti Moming Xihong Yue Shu Shen Chenchen Chang Cheng Wang Tao Luo Yanfang Zhang Rong Guo Zhihong Hu Yujiang Zhang Fei Deng Surong Sun | 2018 | Virologica Sinica2018，33，1： | 5 |
| 3 | A new cell death program regulated by toll-like receptor 9 through p38 mitogen-activated protein kinase signaling pathway in a neonatal rat model with sepsis associated encephalopathy显示文摘Background:Sepsis,a serious condition with high mortality,usually causes sepsis associated encephalopathy(SAE)that involves neuronal cell death.However,the cell death programs involved and their underlying mechanisms are not clear.This study aimed to explore the regulatory mechanisms of different cell death programs in SAE.Methods:A neonatal rat model of SAE was established by cecal ligation and perforation.Survival rate and vital signs(mean arterial pressure and heart rate)were monitored,nerve reflexes were evaluated,and cortical pathological changes were observed by hematoxylin and eosin staining.The expression of pyroptosis,apoptosis,and necroptosis(PANoptosis)-related proteins,mitogen-activated protein kinase(MAPK),and its upstream regulator toll-like receptor 9(TLR9)were detected.The expression of TLR9 in neurons was observed by immunofluorescence staining.The ultrastructure of neurons was observed by transmission electron microscope.Results:First,PANoptosis was found in cortical nerve cells of the SAE rats.Meanwhile,the subunits of MAPKs,p38 MAPK,Jun N-terminal kinase,and extracellular signal-regulated kinase(ERK)were activated.After pharmacologically inhibiting each of the subunits,only p38 MAPK was found to be associated with PANoptosis.Furthermore,blocking the p38 MAPK signaling pathway activated necroptosis but inhibited apoptosis and pyroptosis.When necroptosis was pharmacologically inhibited,apoptosis and pyroptosis were reactivated.Finally,we found that the expression of TLR9,a regulator of MAPKs,was significantly increased in this model.After down-regulation of TLR9,p38 MAPK,and ERK signaling pathways were inhibited,which led to the inhibition of PANoptosis.Further analysis found that down-regulation of TLR9 improved the survival rate and reduced the pathological changes in SAE rats.Conclusions:Our study showed that the programs comprising PANoptosis are activated simultaneously in SAE rats.TLR9 activated PANoptosis through the p38 MAPK signaling pathway.TLR9 may work as a potential target for SAE treatment. | Ruixi Zhou Junjie Ying Xia Qiu Luting Yu Yan Yue Qian Liu Jing Shi Xihong Li Yi Qu Dezhi Mu | 2022 | Chinese Medical Journal2022，，12： | 3 |
| 4 | Modes of genetic adaptations underlying functional innovations in the rumen显示文摘The rumen is the hallmark organ of ruminants and hosts a diverse ecosystem of microorganisms that facilitates efficient digestion of plant fibers.We analyzed 897 transcriptomes from three Cetartiodactyla lineages:ruminants,camels and cetaceans,as well as data from ruminant comparative genomics and functional assays to explore the genetic basis of rumen functional innovations.We identified genes with relatively high expression in the rumen,of which many appeared to be recruited from other tissues.These genes show functional enrichment in ketone body metabolism,regulation of microbial community,and epithelium absorption,which are the most prominent biological processes involved in rumen innovations.Several modes of genetic change underlying rumen functional innovations were uncovered,including coding mutations,genes newly evolved,and changes of regulatory elements.We validated that the key ketogenesis rate-limiting gene(HMGCS2)with five ruminant-specific mutations was under positive selection and exhibits higher synthesis activity than those of other mammals.Two newly evolved genes(LYZ1 and DEFB1)are resistant to Gram-positive bacteria and thereby may regulate microbial community equilibrium.Furthermore,we confirmed that the changes of regulatory elements accounted for the majority of rumen gene recruitment.These results greatly improve our understanding of rumen evolution and organ evo-devo in general. | Xiangyu Pan Yudong Cai Zongjun Li Xianqing Chen Rasmus Heller Nini Wang Yu Wang Chen Zhao Yong Wang Han Xu Songhai Li Ming Li Cunyuan Li Shengwei Hu Hui Li Kun Wang Lei Chen Bin Wei Zhuqing Zheng Weiwei Fu Yue Yang Tingting Zhang Zhuoting Hou Yueyang Yan Xiaoyang Lv Wei Sun Xinyu Li Shisheng Huang Lixiang Liu Shengyong Mao Wenqing Liu Jinlian Hua Zhipeng Li Guojie Zhang Yulin Chen Xihong Wang Qiang Qiu Brian PDalrymple Wen Wang Yu Jiang | 2021 | Science China(Life Sciences)2021，64，1： | 3 |
| 5 | Experimental Study for the Cementation Effect of Dust Soil by Using Soybean Urease显示文摘Dust is an environmental and health hazard.In this study,a new technology for dust suppressant is introduced using soybean urease with an optimal cementing solution.Calcium carbonate is produced by soybean urease and cementing solution,which bonds the soil particles towards a dust suppressant.A laboratory wind tunnel test is carried out to examine its effectiveness and discover possible optimization solutions.Several factors,including soybean meal concentration,cementing solution concentration,and volume of solution per unit area,are examined to quantify their influences on soil transport mass,evaporation ratio,evaporation rate,surface strength,water retention ratio,and infiltration rate of soil treated by different dust suppressants.Field tests are conducted to explore the performance of this method in the natural environment.The results show that compared with other dust suppressants,the optimized soybean urease has the smallest evaporation rate,a moderate infiltration rate,the largest water retention ratio and surface strength.The indexes of soybean urease for dust suppressant are found to be better than traditional materials.In the natural environment,soybean urease has a stronger anti-disturbance ability.This study concludes that soybean urease dust suppressant has great application potential as a cheap and green method. | Jianwei Zhang Yue Yin Lei Shi Yi Han Mi Zhou Xihong Zhang | 2023 | Journal of Renewable Materials2023，11，6： | 0 |
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