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| 1 | National Epidemiology and Evolutionary History of Four Hand, Foot and Mouth Disease-Related Enteroviruses in China from 2008 to 2016显示文摘Hand, foot and mouth disease(HFMD) is a major public health concern in China. The most predominant enteroviruses that cause HFMD have traditionally been attributed to enterovirus A71(EVA71) and coxsackievirus A16(CVA16). Since its first large outbreak in 2008, the dominant HFMD pathogens are constantly changing. In 2013 and 2015, CVA6 exceeded both EVA71 and CVA16 to become the leading cause of HFMD in some provinces. However, there still lacks a comprehensive overview on the molecular epidemiology and evolution of HFMD-related enteroviruses at the national level. In this study, we performed systematic epidemiological analyses of HFMD-related enteroviruses using the data of 64 published papers that met the inclusion criteria, and conducted phylogenetic analyses based on 12,080 partial VP1 sequences identified in China before 31 st June 2018. We found that EVA71 prevalence has decreased sharply but other enteroviruses have increased rapidly from 2008 to 2016 and that one subtype of each enterovirus is represented during the epidemic. In addition, four genotypes EVA71_C4, CVA16_B1, CVA6_D and CVA10_C are the most predominant enterovirus strains and collectively they cause over 90% of all HFMD cases in China according to the phylogenetic trees using representative partial VP1 sequences. These four major enterovirus genotypes have different geographical distributions, and they may cocirculate with other genotypes and serotypes. These results suggest that more molecular epidemiological studies should be performed on several enteroviruses simultaneously, and such information should have implications for virological surveillance, disease management, vaccine development and policy-making on the prevention and control of HFMD. | Xuemin Fu Zhenzhou Wan Yanpeng Li Yihong Hu Xia Jin Chiyu Zhang | 2020 | Virologica Sinica2020，35，1： | 31 |
| 2 | The Genome of Cucurbita argyrosperma (Silver- Seed Gourd) Reveals Faster Rates of Protein- Coding Gene and Long Noncoding RNA Turnover and Neofunctionalization within Cucurbita显示文摘Whole-genome duplications are an important source of evolutionary novelties that change the mode and tempo at which genetic elements evolve within a genome. The Cucurbita genus experienced a wholegenome duplication around 30 million years ago, although the evolutionary dynamics of the coding and noncoding genes in this genus have not yet been scrutinized. Here, we analyzed the genomes of four Cucurbita species, in eluding a newly assembled genome of Cucurbita argyrosperma, and compared the gene con tents of these species with those of five other members of the Cucurbitaceae family to assess the evolutionary dynamics of protein-coding and long intergenic noncoding RNA (lincRNA) genes after the genome duplication. We report that Cucurbita genomes have a higher protein-coding gene birth-death rate compared with the genomes of the other members of the Cucurbitaceae family. C. argyrosperma gene families associated with pollination and transmembrane transport had significantly faster evolutionary rates. lincRNA families showed high levels of gene turnover throughout the phylogeny, and 67.7% of the lincRNA families in Cucurbita showed evidence of birth from the neofunctionalization of previously existing protein-coding genes. Collectively, our results suggest that the whole-genome duplication in Cucurbita resulted in faster rates of gene family evolution through the neofunctionalization of duplicated genes. | Josue Barrera-Red on do Enrique Ibarra-Laclette Alejandra Vazquez-Lobo Yocelyn T. Gutierrez-Guerrero Guillermo Sanchez de la Vega Daniel Pinero Salvador Montes-Hernandez Rafael Lira-Saade Luis E. Eguiarte | 2019 | Molecular Plant2019，12，4： | 9 |
| 3 | Comparative plastid genomics of Pinus species:Insights into sequence variations and phylogenetic relationships显示文摘Pinus L.is the largest genus of conifers and provides a classical model for studying species divergence and phylogenetic evolution by gymnosperms.However,our poor understanding of sequence divergence in the whole plastid genomes of Pinus species severely hinders studies of their evolution and phylogeny.Thus,we analyzed the sequences of 97 Pinus plastid genomes,including four newly sequenced genomes and 93 previously published plastomes,to explore the evolution and phylogenetic relationships in the genus Pinus.The complete chloroplast genomes of Pinus species ranged in size from 109640 bp(P.cembra L.)to 121976 bp(P.glabra Walter),and these genomes comprised circular DNA molecules in a similar manner to those of most gymnosperms.We identified 9108 repeats where most of the repeats comprised the dispersed type with 3983(44%),followed by tandem repeats with 2999(33%),and then palindromic repeats with 2126(23%).Sixteen divergence hotspot regions were identified in Pinus plastid genomes,which could be useful molecular markers for future population genetics studies.Phylogenetic analysis showed that Pinus species could be divided into two diverged clades comprising the subgenera Strobus(single needle section)and Pinus(double needles section).Molecular dating suggested that the genus Pinus originated approximately 130.38 Mya during the late Cretaceous.The two subgenera subsequently split 85.86 Mya,which was largely consistent with the other molecular results based on partial DNA markers.These findings provide important insights into the sequence variations and phylogenetic evolution of Pinus plastid genomes. | Umar Zeb Wan-Lin Dong Ting-Ting Zhang Ruo-Nan Wang Khurram Shahzad Xiong-Feng Ma Zhong-Hu Li | 2020 | Journal of Systematics and Evolution2020，58，2： | 3 |
| 4 | Phylogeographic analysis of human papillomavirus 58显示文摘Human papillomavirus 58 (HPV58) is one type of HPV with high risk of causing cervical cancer. Unusually high prevalence of HPV58 has been reported in Asia, Africa and some other areas. However, due to the scattered distribution of global data, in addition to the lack of data of some HPV58 high-incidence nations and regions, like China's Mainland, a comprehensive analysis of the global geographical distribution of HPV58 remains blank so far. In this study, HPV58 from the human cervical cancer tissue was detected in China's Mainland, and 14 new HPV58-E6/L1 gene sequences were obtained. Moreover, phylogeographic analysis has been conducted combining the HPV58 sequences that have been deposited in GenBank since 1985. The study result shows that the sequences detected from the Shanghai, Jiangsu and Sichuan areas are homologous with those found in the past from Hong Kong and Xi'an, China, as well as Japan and other Southeast Asian areas. Furthermore, Western Africa is considered to be the 'root' source of the HPV58 variant, while China's Mainland and Southeast Asia are 'transit points' and the new sources of HPV58 after receiving the isolates from the 'root' source; like HPV16 and HPV18, the HPV58 might also be one of the major HPV types associated with the development and spread of cervical cancer. | LI YanYun1, LI ZuoFeng2, HE YiFeng1, KANG Yu1, ZHANG XiaoYan1, CHENG MingJun1, ZHONG Yang2, 3· & XU CongJian1· 1 Obstetrics and Gynecology Hospital of Fudan University, Shanghai 200011, China 2 Shanghai Bioinformation Research Center, Shanghai 200235, China 3 School of Life Sciences, Fudan University, Shanghai 200433, China | 2009 | Science China(Life Sciences)2009，52，12： | 2 |
| 5 | Fast docking of drug molecules to their receptor显示文摘AEDock based on AutoDock2.4 is developed with annealing evolution algorithm (AEA) in place of simulated annealing algorithm (SA) for supermolecular conformation searching. Because AEA takes advantage of both the genetic algorithm (GA) and the simulated annealing algorithm, the results of AEDock show that AEA can predict the binding conformations of ligands with up to 10 rotatable bonds to a rigid macromolecular target. The case of 1 hvr is only one of six cases where SA in AutoDock 2.4 failed to find an energy less than that of the crystal. It is used here to compare the performance of SA with AEA. The results of comparison show that fewer states are needed in AEA than in SA, but the success rate of AEA is much higher. | Jianquan Chen Hanlin Chi | 1999 | Chinese Science Bulletin1999，44，10： | 2 |
| 6 | A new method of research on molecular evolution of proteinase superfamily显示文摘The molecular evolutionary tree, also known as a phylogenetic tree, of the serine proteinase superfamily was constructed by means of structural alignment. Three-dimensional structures of proteins were aligned by the SSAP program of Orengo and Taylor to obtain evolutionary distances. The resulting evolutionary tree provides a topology graph that can reflect the evolution of structure and function of homology proteinase. Moreover, study on evolution of the serine proteinase superfamily can lead to better understanding of the relationship and evolutionary difference among proteins of the superfamily, and is of significance to protein engineering, molecular design and protein structure prediction. Structure alignment is one of the useful methods of research on molecular evolution of protein. | SUN Zhirong JI Xinglai HU Shengmin WANG Yu HE Fuchu | 2001 | Chinese Science Bulletin2001，46，7： | 1 |
| 7 | Molecular phylogeny of the genus Clibanarius(Decapoda: Anomura: Diogenidae) based on mitochondrial and nuclear DNA sequences显示文摘Clibanarius , a genus of hermit crabs, is one of the most diverse genera within Diogenidae. However, studies on the phylogeny within Clibanarius is very limited. We reconstruct the molecular phylogeny of the genus Clibanarius based on two mitochondrial (16S rRNA and COI) and two nuclear protein-coding (NaK and PEPCK) genes using a multigene phylogenetic approach. Eleven selected Clibanarius species from the Indo-West Pacifi c are analyzed and the Bayesian and maximum likelihood analyses produced identical results in topology. Results suggest that C . rutilus and C . infraspinatus are more closely related to each other than to C . snelliusi , and C . striolatus shows a close relationship to C . longitarsus . The close association of C . merguiensis with C . englaucus and C . humilis is strongly supported by the divergence of C . virescens from them. Our phylogenetic results contradict the morphological classifi cation scheme proposed for Clibanarius and indicate that the relative length of dactyls and propodi is not phylogenetically signifi cant in Clibanarius . In addition, we speculate that the morphological characteristic of the median cleft of the telson might be phylogenetically important for Clibanarius . | LI Wenjie CHENG Jiao HUI Min SHA Zhongli | 2019 | Journal of Oceanology and Limnology2019，37，5： | 1 |
| 8 | Nickel Complexes with Non-innocent Ligands as Highly Active Electrocatalysts for Hydrogen Evolution显示文摘Rational design of a molecular catalyst for a hydrogen evolution reaction (HER)with both high rates and low overpotential remains a chal- lenge.Here we report a series of Ni-based catalysts incorporating non-innocent ligands and aimed at reduction of the overpotential by reserving electrons in the ligand,which could decouple the correlation between metal center reduction and metal hydride formation.The third-order rate constant of our catalysts can be increased by 2 orders of magnitude without increase of overpotential by altering the substituents in the imide since the electronic effect of substituents can change the kinetics of metal hydride formation dramatically.Furthermore,constructing a proton shuttle in the ligand further improves the activity.The catalyst with both of these features can catalyze HER at a turnover frequency of 2572s^-1 with low concentrations of acid and an extremely high third-order rate constant of 2.7×10^6M^-2·s^-1 at a low overpotential. | Zhixin Chen Tao Wang Tingting Sun Zhiyong Chen Tian Sheng Yu-Hao Hong Zi-Ang Nan Jun Zhu Zhi-You Zhou Haiping Xia Shi-Gang Sun | 2018 | Chinese Journal of Chemistry2018，36，12： | 1 |
| 9 | Jump further,leap higher,and consolidate stronger:A brief review of the long-term partnership between Kunming Institute of Zoology(KIZ)and the Chinese University of Hong Kong(CUHK)in bioresources and molecular research显示文摘The molecular etiologies of many prevalent diseases stem from genetic variations that arise during evolution and natural selection,as well as from environmental effects.The study of genetic diversity in human populations and analysis of molecular evolution in primates and other animal species can provide important insights regarding the pathogenesis of common diseases in both human and animal populations. | Nelson Tang Yong-Tang Zheng Hui Zhao Wai-Yee Chan Yong-Gang Yao | 2023 | Zoological Research2023，44，3： | 0 |
| 10 | Sequencing of p35 Gene from Heliothis armigera Polyhedrosis Virus and Its Homologous Comparison显示文摘Heliothisarmigeranuclearpolyhedrosisvirus(HaNPV),amemberofBaculoviridae,isaspecialspecies.withadouble-strained,circularDNAofa... | Wang Ye-fu Qi Yi-peng Li Zhi-da Zhu Ying Su fei | 1999 | Wuhan University Journal of Natural Sciences1999，4，2： | 0 |
| 11 | Primary Structural Characterization of Phospholipid Hydroperoxide Glutathione Peroxidase显示文摘More than 20 sequences of phospholipid hydroperoxide glutathione peroxidase (PHGPX) from a sequence database were analyzed. The analyses show that the primary structures of most PHGPX proteins have three highly conserved regions forming a catalytic center and have more than 50% amino acid sequence identity in common. However, two PHGPXs from bovine and swine with the same function have very low similarity with typical PHGPXs and do not have the three highly conserved regions. Thus, the PHGPX proteins are divided into two types: those with the three highly conserved regions, designated as PHGPX I, and the others as PHGPX II. In general, type I proteins are composed of ca.170 amino acid residues; a few of them have an extra signal peptide sequence at the N terminal of the protein. The composition of plant and animal PHGPX amino acids is very different, with most plant PHGPXs being weak acidic, while most animal ones are alkaline. Another specific conservative motif is also found in plant PHGPX proteins. System evolution analysis shows that ortholog and paralog evolution models both exist in PHGPXs, with the plant PHGPX and the animal PHGPX diverging exclusively into two branches in PHGPX I. The information revealed by the evolution tree agrees with the general species evolution process from low to advanced and from simple to complicated. | 王泽斌 杨晓东 赵南明 刘进元 | 2002 | Tsinghua Science and Technology2002，7，4： | 0 |
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