The genus Citrus L. has a long controversial taxonomy history, and a well-resolved molecular phylogeny of the ＂true citrus fruit trees＂ group in the future will provide new information for advancing breeding techniq...The genus Citrus L. has a long controversial taxonomy history, and a well-resolved molecular phylogeny of the ＂true citrus fruit trees＂ group in the future will provide new information for advancing breeding techniques and developing better conservation strategies. In the present study, three cpDNA fragments （TrnL-TrnF, PsbH-PetB, and TrnS-TrnG） of 30 genotypes chosen from the six genera of the ＂true citrus fruit trees＂ group were analyzed. A molecular phylogenetic tree of the ＂true citrus fruit trees＂ group ＂~as reconstructed based on plastid DNA sequences. The results confirmed that the ＂true citrus fruit trees＂ group was monophyletic, and thereby the group was divided into genera as previously suggested based on morphological characters. The cpDNA data also suggested that Poncirus might be the first genus separated from the other five genera in the group. The genus Fortunella were of hybrid origin and Citrus might be as its putative paternal parent. The genera Microcitrus, Eremocitrus, and Clymenia were possibly monophyletic and their common ancestor might branch out from Citrus. Furthermore, the phylogenetic relationships within the Citrus genus were discussed.展开更多
The augmented Zagreb index displays a good correlation with the formation heat of octanes and heptanes. The augmented Zagreb index of catacondensed hexagonal systems and molecular trees was discussed. By using the met...The augmented Zagreb index displays a good correlation with the formation heat of octanes and heptanes. The augmented Zagreb index of catacondensed hexagonal systems and molecular trees was discussed. By using the methods of analysis of graph structure and mathematical induction,the catacondensed hexagonal systems with extreme augmented Zagreb index were characterized.The lower bound for augmented Zagreb index of molecular trees with fixed numbers of pendent vertices was given,and the extremal trees were characterized. From these results,we can compare the formation heat of catacondensed hexagonal systems and molecular trees.展开更多
Objective To trace the source of human H7N9 cases in Huai＇an and elucidate the genetic characterization of Huai＇an strains associated with both humans and birds in live poultry market.Methods An enhanced surveillanc...Objective To trace the source of human H7N9 cases in Huai＇an and elucidate the genetic characterization of Huai＇an strains associated with both humans and birds in live poultry market.Methods An enhanced surveillance was implemented when the first human H7N9 case was confirmed in Huai＇an.Clinical specimens,cloacal swabs,and fecal samples were collected and screened by real-time reverse transcription-polymerase chain reaction（RT-PCR） for H7N9 virus.The positive samples were subjected to further RT-PCR and genome sequencing.The phylodynamic patterns of H7N9 virus within and separated from Huai＇an and evolutionary dynamics of the virus were analyzed.Results Six patients with H7N9 infection were previously exposed to live poultry market and presented symptoms such as fever（〉38.0 °C） and headaches.Results of this study support the hypothesis that live poultry markets were the source of human H7N9 exposure.Phylogenetic analysis revealed that all novel H7N9 viruses,including Huai＇an strains,could be classified into two distinct clades,A and B.Additionally,the diversified H7N9 virus circulated in live poultry markets in Huai＇an.Interestingly,the common ancestors of the Huai＇an H7N9 virus existed in January 2012.The mean nucleotide substitution rates for each gene segment of the H7N9 virus were（3.09-7.26）×10-3 substitutions/site per year（95% HPD：1.72×10-3 to 1.16×10-2）.Conclusion Overall,the source of exposure of human H7N9 cases in Huai＇an was live poultry market,and our study highlights the presence of divergent genetic lineage of H7N9 virus in both humans and poultry specimens in Huai＇an.展开更多
According to the contradictions about classification on Trimeresurus between ＂China＇s Fauna＂ and international database, the rationality about Trimeresurus divided to multiple genera based on molecular systematies ...According to the contradictions about classification on Trimeresurus between ＂China＇s Fauna＂ and international database, the rationality about Trimeresurus divided to multiple genera based on molecular systematies was discussed. The genetic distance was calculated by sequencing 12S gene of the original Trimeresurus snakes, including 80 individuals of 33 species ; and the molecular phylogenetie tree was established by taking Hypnale hypnale as the outgroup. The results showed that the topological structures of ME tree and ML tree were basically consistent, and all of the species in the molecular trees were divided into 8 branches; and the difference of T. albolabris between Hainan and other locations is not obvious. The viewpoint that original Trimeresurus genera subdivided into 8 genera was more rational, and new authoritative reference books are expected to be published in China.展开更多
Hydrogen bonds (H-bonds) play a key role in both the formation and stabilization of protein structures. H-bonds involving atoms from residues that are close to each other in the main-chain sequence stabilize secondary...Hydrogen bonds (H-bonds) play a key role in both the formation and stabilization of protein structures. H-bonds involving atoms from residues that are close to each other in the main-chain sequence stabilize secondary structure elements. H-bonds between atoms from distant residues stabilize a protein’s tertiary structure. However, H-bonds greatly vary in stability. They form and break while a protein deforms. For instance, the transition of a protein from a non-functional to a functional state may require some H-bonds to break and others to form. The intrinsic strength of an individual H-bond has been studied from an energetic viewpoint, but energy alone may not be a very good predictor. Other local interactions may reinforce (or weaken) an H-bond. This paper describes inductive learning methods to train a protein-independent probabilistic model of H-bond stability from molecular dynamics (MD) simulation trajectories. The training data describes H-bond occurrences at successive times along these trajectories by the values of attributes called predictors. A trained model is constructed in the form of a regression tree in which each non-leaf node is a Boolean test (split) on a predictor. Each occurrence of an H-bond maps to a path in this tree from the root to a leaf node. Its predicted stability is associated with the leaf node. Experimental results demonstrate that such models can predict H-bond stability quite well. In particular, their performance is roughly 20% better than that of models based on H-bond energy alone. In addition, they can accurately identify a large fraction of the least stable H-bonds in a given conformation. The paper discusses several extensions that may yield further improvements.展开更多
In this study, we report that we successfully cloned and sequenced a chitinase gene from the ovotestis of Kuroda’s sea hare Aplysia kurodai. By using reverse transcription-polymerase chain reaction (RT-PCR) and a sys...In this study, we report that we successfully cloned and sequenced a chitinase gene from the ovotestis of Kuroda’s sea hare Aplysia kurodai. By using reverse transcription-polymerase chain reaction (RT-PCR) and a system for the 5’ and 3’ rapid amplification of cDNA ends, we obtained a 1352 bp chitinase gene (AkChi) from the ovotestis of A. kurodai. AkChi contains a 1263 bp open reading frame that encodes 421 amino acids. The domain structure predicted from the deduced amino acid sequence was an N-terminal signal peptide and a catalytic domain of glycoside hydrolase (GH) family 18 chitinase. A comparative analysis of the deduced amino acid sequences of AkChi with those of the acidic mammalian chitinase of the California sea hare Aplysia californica revealed the highest homology at 83%. The purified chitinase from the ovotestis was digested by trypsin, and 119 residues of digested peptides were consistent with the deduced amino acid sequence of AkChi. We used RT-PCR to evaluate the expression of AkChi in various tissues of A. kurodai, and we observed that AkChi was expressed only in the ovotestis. A phylogenetic tree analysis, performed using the amino acid sequences of AkChi and known GH family 18 chitinases, showed that AkChi was separated from the molluscan chitinases with a chitin binding domain. To our knowledge, this is the first study demonstrating the cDNA cloning of an ovotestis chitinase from a sea hare.展开更多
基金supported by the National Natural Science Foundation of China (NSFC, 30671450)
文摘The genus Citrus L. has a long controversial taxonomy history, and a well-resolved molecular phylogeny of the ＂true citrus fruit trees＂ group in the future will provide new information for advancing breeding techniques and developing better conservation strategies. In the present study, three cpDNA fragments （TrnL-TrnF, PsbH-PetB, and TrnS-TrnG） of 30 genotypes chosen from the six genera of the ＂true citrus fruit trees＂ group were analyzed. A molecular phylogenetic tree of the ＂true citrus fruit trees＂ group ＂~as reconstructed based on plastid DNA sequences. The results confirmed that the ＂true citrus fruit trees＂ group was monophyletic, and thereby the group was divided into genera as previously suggested based on morphological characters. The cpDNA data also suggested that Poncirus might be the first genus separated from the other five genera in the group. The genus Fortunella were of hybrid origin and Citrus might be as its putative paternal parent. The genera Microcitrus, Eremocitrus, and Clymenia were possibly monophyletic and their common ancestor might branch out from Citrus. Furthermore, the phylogenetic relationships within the Citrus genus were discussed.
基金National Natural Science Foundation of China(No.11071227)Shanxi Scholarship Council of China(No.2012-070)Foundation of North University of China(No.2013-12-1)
文摘The augmented Zagreb index displays a good correlation with the formation heat of octanes and heptanes. The augmented Zagreb index of catacondensed hexagonal systems and molecular trees was discussed. By using the methods of analysis of graph structure and mathematical induction,the catacondensed hexagonal systems with extreme augmented Zagreb index were characterized.The lower bound for augmented Zagreb index of molecular trees with fixed numbers of pendent vertices was given,and the extremal trees were characterized. From these results,we can compare the formation heat of catacondensed hexagonal systems and molecular trees.
基金supported by grants HAYf201516 from Huai’an Preventive Medicine Associationgrant HAS2015019-3 from Huai’an Scientific Technological Special Project
文摘Objective To trace the source of human H7N9 cases in Huai＇an and elucidate the genetic characterization of Huai＇an strains associated with both humans and birds in live poultry market.Methods An enhanced surveillance was implemented when the first human H7N9 case was confirmed in Huai＇an.Clinical specimens,cloacal swabs,and fecal samples were collected and screened by real-time reverse transcription-polymerase chain reaction（RT-PCR） for H7N9 virus.The positive samples were subjected to further RT-PCR and genome sequencing.The phylodynamic patterns of H7N9 virus within and separated from Huai＇an and evolutionary dynamics of the virus were analyzed.Results Six patients with H7N9 infection were previously exposed to live poultry market and presented symptoms such as fever（〉38.0 °C） and headaches.Results of this study support the hypothesis that live poultry markets were the source of human H7N9 exposure.Phylogenetic analysis revealed that all novel H7N9 viruses,including Huai＇an strains,could be classified into two distinct clades,A and B.Additionally,the diversified H7N9 virus circulated in live poultry markets in Huai＇an.Interestingly,the common ancestors of the Huai＇an H7N9 virus existed in January 2012.The mean nucleotide substitution rates for each gene segment of the H7N9 virus were（3.09-7.26）×10-3 substitutions/site per year（95% HPD：1.72×10-3 to 1.16×10-2）.Conclusion Overall,the source of exposure of human H7N9 cases in Huai＇an was live poultry market,and our study highlights the presence of divergent genetic lineage of H7N9 virus in both humans and poultry specimens in Huai＇an.
基金Supported by Fund for Provincial Key DIscipline in Colleges and Universities of Hainan Province:Zoology(2017-02-01,HNZ201702)General Project of National Natural Science Foundation of Hainan Province(20163073),Study on the taxonomic status of Trimeresurus produced in Hainan+4 种基金Special Fund for Scientific Research Trail-produce Project of Sanya City(2016KS05)Scientific Research Project of Colleges and Universities of Hainan Province(Hnky2017-47),Study on the taxonomic status of the subspecies Trimeresurus stejnegeri chenbihuii in Hainan based on morphologyMajor Science and Technology Planning Project of Hainan Province(ZDKJ2016009-2-1)Agricultural Science and Technology Innovation Project of Sanya City(2016NK13)Key Discipline Construction Fund of School of Ocean Science and Technology(Special Fund for Development of Institutions of Higher Learning in 2017(the fourth batch)):Marine Science
文摘According to the contradictions about classification on Trimeresurus between ＂China＇s Fauna＂ and international database, the rationality about Trimeresurus divided to multiple genera based on molecular systematies was discussed. The genetic distance was calculated by sequencing 12S gene of the original Trimeresurus snakes, including 80 individuals of 33 species ; and the molecular phylogenetie tree was established by taking Hypnale hypnale as the outgroup. The results showed that the topological structures of ME tree and ML tree were basically consistent, and all of the species in the molecular trees were divided into 8 branches; and the difference of T. albolabris between Hainan and other locations is not obvious. The viewpoint that original Trimeresurus genera subdivided into 8 genera was more rational, and new authoritative reference books are expected to be published in China.
文摘Hydrogen bonds (H-bonds) play a key role in both the formation and stabilization of protein structures. H-bonds involving atoms from residues that are close to each other in the main-chain sequence stabilize secondary structure elements. H-bonds between atoms from distant residues stabilize a protein’s tertiary structure. However, H-bonds greatly vary in stability. They form and break while a protein deforms. For instance, the transition of a protein from a non-functional to a functional state may require some H-bonds to break and others to form. The intrinsic strength of an individual H-bond has been studied from an energetic viewpoint, but energy alone may not be a very good predictor. Other local interactions may reinforce (or weaken) an H-bond. This paper describes inductive learning methods to train a protein-independent probabilistic model of H-bond stability from molecular dynamics (MD) simulation trajectories. The training data describes H-bond occurrences at successive times along these trajectories by the values of attributes called predictors. A trained model is constructed in the form of a regression tree in which each non-leaf node is a Boolean test (split) on a predictor. Each occurrence of an H-bond maps to a path in this tree from the root to a leaf node. Its predicted stability is associated with the leaf node. Experimental results demonstrate that such models can predict H-bond stability quite well. In particular, their performance is roughly 20% better than that of models based on H-bond energy alone. In addition, they can accurately identify a large fraction of the least stable H-bonds in a given conformation. The paper discusses several extensions that may yield further improvements.
文摘In this study, we report that we successfully cloned and sequenced a chitinase gene from the ovotestis of Kuroda’s sea hare Aplysia kurodai. By using reverse transcription-polymerase chain reaction (RT-PCR) and a system for the 5’ and 3’ rapid amplification of cDNA ends, we obtained a 1352 bp chitinase gene (AkChi) from the ovotestis of A. kurodai. AkChi contains a 1263 bp open reading frame that encodes 421 amino acids. The domain structure predicted from the deduced amino acid sequence was an N-terminal signal peptide and a catalytic domain of glycoside hydrolase (GH) family 18 chitinase. A comparative analysis of the deduced amino acid sequences of AkChi with those of the acidic mammalian chitinase of the California sea hare Aplysia californica revealed the highest homology at 83%. The purified chitinase from the ovotestis was digested by trypsin, and 119 residues of digested peptides were consistent with the deduced amino acid sequence of AkChi. We used RT-PCR to evaluate the expression of AkChi in various tissues of A. kurodai, and we observed that AkChi was expressed only in the ovotestis. A phylogenetic tree analysis, performed using the amino acid sequences of AkChi and known GH family 18 chitinases, showed that AkChi was separated from the molluscan chitinases with a chitin binding domain. To our knowledge, this is the first study demonstrating the cDNA cloning of an ovotestis chitinase from a sea hare.
