Early screening is crucial for the prevention of intestinal-type gastric cancer.The current study aimed to ascertain the molecular evolution of intestinal-type gastric cancer based on the Correa cascade for precise ga...Early screening is crucial for the prevention of intestinal-type gastric cancer.The current study aimed to ascertain the molecular evolution of intestinal-type gastric cancer based on the Correa cascade for precise gastric cancer screening.We collected sequential lesions of the Correa cascade in the formalin-fixed and paraffin-embedded endoscopic submucosal dissection(ESD)-resected specimens from 14 Chinese patients by microdissection,and subsequently determined the profiles of somatic aberrations during gastric carcinogenesis using whole-exome sequencing,identifying multiple variants at different Correa stages.The results showed that TP53,PCLO,and PRKDC were the most frequently mutated genes in early gastric cancer(EGC).We found a high frequency of TP53 alterations in low-grade intraepithelial neoplasia(LGIN),which further increased in high-grade intraepithelial neoplasia(HGIN)and EGC.Intestinal metaplasia(IM)showed no significant correlation with EGC in terms of mutational spectra,whereas both LGIN and HGIN showed higher genomic similarities to EGC,compared with IM.Based on Jaccard similarity coefficients,we constructed three evolutionary models,with most patients showing linear progression from LGIN to HGIN,ultimately resulting in EGC.The extracellular matrix-receptor interaction pathway was revealed to be involved in the linear evolution.Additionally,the retrospective validation study of 39 patients diagnosed with LGIN indicated that PRKDC mutations,in addition to TP53 mutations,may drive LGIN progression to HGIN or EGC.In conclusion,the current study unveils the genomic evolution across the Correa cascade of intestinal-type gastric cancer,elucidates the underlying molecular mechanisms of gastric carcinogenesis,and provides evidence for potential personalized gastric cancer surveillance.展开更多
Porous molecular sieve catalysts,including aluminosilicate zeolites and silicoaluminophosphate(SAPO)molecular sieves,have found widespread use in heterogeneous catalysis and are expected to play a key role in advancin...Porous molecular sieve catalysts,including aluminosilicate zeolites and silicoaluminophosphate(SAPO)molecular sieves,have found widespread use in heterogeneous catalysis and are expected to play a key role in advancing carbon neutrality and sustainable development.Given the ubiquitous presence of water during catalyst synthesis,storage,and application,the interactions between water and molecular sieves as well as their consequent effects on frameworks and catalytic reactions have attracted considerable attention.These effects are inherently complex and highly dependent on various factors such as temperature,water phase,and partial pressure.In this review,we provide a comprehensive overview of the current understanding of water-molecular sieve interactions and their roles in catalysis,based on both experimental and theoretical calculation results.Special attention is paid to water-induced reversible and irreversible structural changes in aluminosilicate and SAPO frameworks at the atomic level,underscoring the dynamic and labile nature of these frameworks in water environments.The influence of water on catalytic performance and reaction kinetics in molecular sieve-catalyzed reactions is discussed from two perspectives:(1)its participation in reaction through hydrogen bonding interactions,such as competitive adsorption at active sites,stabilization of ground and transition states,and proton transfer bridge;(2)its role as a direct reactant forming new species via reactions with other vip molecules.Recent advancements in this area provide valuable insights for the rational design and optimization of catalysts for water-involved reactions.展开更多
The search for photoactive materials that are able to efficiently produce solar fuels is a growing research field to tackle the current energy crisis.Herein,we have prepared two ionic non-noble metallo-supramolecular ...The search for photoactive materials that are able to efficiently produce solar fuels is a growing research field to tackle the current energy crisis.Herein,we have prepared two ionic non-noble metallo-supramolecular polymers Se-MTpy(M=Co or Ni),and constructed their composites with single-walled carbon nanotubes(CNTs)via electrostatic attraction andπ-πinteractions for efficient and stable photocatalytic hydrogen evolution.In the photocatalytic system,the cationic Se-MTpy as host and anionic CNTs as vip are assembled into a binary composite,which exhibits superior photocatalytic activity under visible light irradiation(>420 nm).The optimized CNT@Se-CoTpy composite,containing 1.2 wt%metal loading,achieves 7 times higher hydrogen evolution rate(2.47 mmol g^(-1)h^(-1))than bare Se-CoTpy(0.35 mmol g^(-1)h^(-1)).This is attributed to the constructive formation of junctions between polymer and CNTs,facilitating interfacial charge transfer and transport for efficient proton reduction.The composite system also shows high photostability after continuous irradiation for~30 h.The combination of experimental and theoretical analysis demonstrates the higher activity for reducing H_(2)O to H_(2)of Se-CoTpy than Se-NiTpy.The feasible interfacial architecture proposed in this study represents an effective approach to achieve high photocatalytic performance.展开更多
The molecular composition and evolution of the chalcone synthase (CHS) gene family from five species in Camellia (Theaceae) are explored in this study. Sixteen CHS exon 2 from four Camellia species were amplified from...The molecular composition and evolution of the chalcone synthase (CHS) gene family from five species in Camellia (Theaceae) are explored in this study. Sixteen CHS exon 2 from four Camellia species were amplified from total DNA by PCR method. Three sequences of the fifth species in Camellia and two sequences of Glycine max as the designated outgroups were obtained from GenBank. Our results indicated that CHS gene family in Camellia was differentiated to three subfamilies (A, B, C) during the evolutionary history with six groups (A1, A2, A3, BI, B2, C). Among them, only group A2 was possessed by all five species in this study. However, the other five groups were detected only in some species of the plants studied. All members of CHS gene family in this study had high sequence similarity, more than 90% among the members in the same subfamily and more than 78% among different subfamilies at nucleotide level., According to the estimated components of amino acids, the function of CHS genes in Camellia had been diverged. The nucleotide substitutions of the different groups were not identical. Based on phylogenetic analyse inferred from sequences of CHS genes and their deduced amino acid sequences, we concluded that the CHS genes with new function in this genus were evolved either by mutations on several important sites or by accumulation of the mutations after the gene duplication. A further analysis showed that the diversification of CHS genes in Camellia still occurred recently, and the evolutionary models were different to some extant among different species. So we assumed that the different evolutionary models resulted from the impacts of variable environmental elements after the events of speciation.展开更多
AIM： To investigate the hoLspoLs, direction, and the time course of evolution of hepatitis A virus in the process of consecutive cell culture passage in human KMB17 diploid cells.METHODS： Wild type hepatitis A virus...AIM： To investigate the hoLspoLs, direction, and the time course of evolution of hepatitis A virus in the process of consecutive cell culture passage in human KMB17 diploid cells.METHODS： Wild type hepatitis A virus H2w was serially propagated in KMB17 cells until passage 30, and the fulllength genomes of H2w and its six chosen progenies were determined by directly sequencing RT-PCR products amplified from viral genomic RNA. Alignment comparison of sequences from H2w with its six progenies and phylogenetic analysis of the whole VP1 region from H2w, progenies of H2w, and other cell culture adapted hepatitis A virus were then carried out to obtain data on the molecular evolution of hepatitis A virus in the process of consecutive passage in KMB17 cells.RESULTS： Most of the mutations occurred by passage 5 and several hotspots related to adaptation of the virus during cell growth were observed. After that stage, few additional mutations occurred through the remaining duration of passage in KMB17 cells except for mutation in the virulence determinants, which occurred in the vicinity of passage 15. The phylogenetic analysis of the whole VP1 region suggested that the progenies of H2w evolved closely to other cell culture adapted hepatitis A virus, i.e. MBB, L-A-l, other than its progenitor H2w.CONCLUSION： Hepatitis A virus served as a useful model for studying molecular evolution of viruses in a given environment. The information obtained in this study may provide assistance in cultivating the next generation of a seed virus for live hepatitis A vaccine production.展开更多
Heterogeneous oxidation by gas-phase oxidants is an important chemical transformation pathway of secondary organic aerosol(SOA)and plays an important role in controlling the abundance,properties,as well as climate and...Heterogeneous oxidation by gas-phase oxidants is an important chemical transformation pathway of secondary organic aerosol(SOA)and plays an important role in controlling the abundance,properties,as well as climate and health impacts of aerosols.However,our knowledge on this heterogeneous chemistry remains inadequate.In this study,the heterogeneous oxidation ofα-pinene ozonolysis SOA by hydroxyl(OH)radicals was investigated under both low and high relative humidity(RH)conditions,with an emphasis on the evolution of molecular composition of SOA and its RH dependence.It is found that the heterogeneous oxidation of SOA at an OH exposure level equivalent to 12 hr of atmospheric aging leads to particle mass loss of 60%at 25%RH and 95%at 90%RH.The heterogeneous oxidation strongly changes the molecular composition of SOA.The dimer-to-monomer signal ratios increase dramatically with rising OH exposure,in particular under high RH conditions,suggesting that aerosol water stimulates the reaction of monomers with OH radicals more than that of dimers.In addition,the typical SOA tracer compounds such as pinic acid,pinonic acid,hydroxy pinonic acid and dimer esters(e.g.,C17H26O8 and C19H28O7)have lifetimes of several hours against heterogeneous OH oxidation under typical atmospheric conditions,which highlights the need for the consideration of their heterogeneous loss in the estimation of monoterpene SOA concentrations using tracer-based methods.Our study sheds lights on the heterogeneous oxidation chemistry ofmonoterpene SOA andwould help to understand their evolution and impacts in the atmosphere.展开更多
[Objective] The aim of this study was to analyze the sequence characteristics and molecular evolution of ubiquitins encoded by baculoviruses.[Methods]Clustal W software was used for multiple sequence alignment analysi...[Objective] The aim of this study was to analyze the sequence characteristics and molecular evolution of ubiquitins encoded by baculoviruses.[Methods]Clustal W software was used for multiple sequence alignment analysis,and neighbor-joining method（NJ）and maximum parsimony method（MP）were used for the construction of phylogenetic tree.[Results]The baculoviral ubiquitins showed 73%-86% sequence identity to eukaryotic ubiquitin.Two heterogeneous regions of baculoviral ubiquitins were observed：one was the residues from 15-32,the other was located from residues 53 to 60.The else parts were conserved,where many functional amino acids were also observed.Phylogenetic analysis indicated that baculoviral ubiquitins could be divided into three sub-families,including sub-family GV,sub-family I and sub-family II.The molecular evolution of baculoviral ubiquitins might be under negative selection to maintain their functional and structural stability.[Conclusion]The analysis had provided reference for the researches on functional characterization of baculoviral ubiquitins.展开更多
Pseudogene and fibrin peptide which has rapid evolve speed and good stability are used in this study to determine the divergence date among groups.Through calculating the evolutionary rate of hemoglobin α chain,γ ch...Pseudogene and fibrin peptide which has rapid evolve speed and good stability are used in this study to determine the divergence date among groups.Through calculating the evolutionary rate of hemoglobin α chain,γ chain in vertebrate（including birds and mammals）,it is concluded that the evolutionary rate of hemoglobin α chain,γ chain is not invariable.It shows different evolutionary rates in different periods,that is,faster in early evolution stage and relatively slow in later stage.展开更多
The partial sequences of exon Ⅰ of hormone-sensitive lipase （HSL） genes in yak （Bos grunniens）, cattle （Bos taurus）, zebu （Bos indicus）, and buffalo （Bubalus bubalis） were analyzed. Comparisons of these seq...The partial sequences of exon Ⅰ of hormone-sensitive lipase （HSL） genes in yak （Bos grunniens）, cattle （Bos taurus）, zebu （Bos indicus）, and buffalo （Bubalus bubalis） were analyzed. Comparisons of these sequences and the deduced amino acid sequences with the homologous HSL gene and protein sequences in other mammalian species including pig （Sus scrofa）, human （Homo sapiens）, mouse （Mus musculus）, and rat （Rattus sp.） retrieved from the GenBank were carried out and finally a phylogenetic tree was constructed using the partial DNA sequences of the HSL genes in all species. The results showed that the homologies of the partial exon Ⅰ sequences of the HSL genes between yak and cattle, zebu, buffalo, pig, human, mouse, and rat were as high as 99.8%, 99.6%, 97.4%, 90.6%, 88.4%, 83.5%, and 82.3%, respectively. This was accompanied by highly homologous amino acid sequences of the HSLs： 100%, 100%, 98.2%, 94.0%, 92.2%, 89.8%, and 89.8% identity, respectively. There are more transitions, less transversions, and no insertion or deletion in variable nucleotides of the HSL genes between the yak and other species. The majority of the variable mutations was synonymous and was found most frequently at the third codon, followed by the first and second codons, a finding that was in accordance with the neutralism hypothesis for molecular evolution. In the phylogenetic tree, the cattle and zebu were clustered together first, followed by the yak, buffalo, pig, human, mouse, and rat. This was in agreement with taxonomy suggesting that the partial sequences of exon Ⅰ of the HSL genes were useful in constructing the phylogenetic tree of mammalian species. Among the four species of Bovidae, genetic differentiation in the HSL genes between yak and buffalo is equivalent to that between buffalo and cattle and between buffalo and zebu. Furthermore, the genetic distances in the HSL genes are much smaller between yak, cattle, and zebu than those between each of the three species and the buffalo. Therefore, it is reasonable to consider yak as an independent species of the genus Bos.展开更多
Many eukaryotic genes are members of multi-gene families due to gene duplications, which generate new copies that allow functional divergence. However, the relationship between
In this work, molecular dynamics simulations have been performed to explore the structural evolution and underlying sintering mechanism of aluminum nanoparticles. The structural evolution during sintering was firstly ...In this work, molecular dynamics simulations have been performed to explore the structural evolution and underlying sintering mechanism of aluminum nanoparticles. The structural evolution during sintering was firstly monitored through radial distribution function and atomic migration, and the underlying sintering mechanism was further quantitatively characterized in terms of average displacement, mean squared distance(MSD), radius ratio(i.e., the ratio of the neck radius to the particle radius), shrinkage and radius of gyration, crystalline orientations, particle size, etc. Results show that the surface atoms of nanoparticles are more active than the internal atoms, favoring the mechanical rotation of nanoparticles during sintering. During the sintering process, average displacement, radius ratio and the shrinkage rate have undergone three stages with increasing the temperature:(1) a slow increase and subsequent abrupt hike after reaching the sintering temperature;(2) an almost plateau region over a wide span of temperature;(3) finally a sharp increase again after reaching the melting temperature. In contrast, MSD remains basically unchanged before melting, close to zero, followed by a sudden increase after melting temperature. Although the radius of gyration also experiences three stages, nonetheless it exhibits almost completely contrary trend. It has also been found that both sintering temperature and melting temperature demonstrate an almost linear increase with the increase of nanoparticle size ranging from4.0, 6.0, 8.0 to 10.0 nm in diameter. Finally, we also found that the particle direction has limited effect on neck growth during sintering.展开更多
Water oxidation is one of the most important reactions in natural and artificial energy conversion schemes.In nature,solar energy is converted to chemical energy via water oxidation at the oxygen-evolving center of ph...Water oxidation is one of the most important reactions in natural and artificial energy conversion schemes.In nature,solar energy is converted to chemical energy via water oxidation at the oxygen-evolving center of photosystem II to generate dioxygen,protons,and electrons.In artificial energy schemes,water oxidation is one of the half reactions of water splitting,which is an appealing strategy for energy conversion via photocatalytic,electrocatalytic,or photoelectrocatalytic processes.Because it is thermodynamically unfavorable and kinetically slow,water oxidation is the bottleneck for achieving large-scale water splitting.Thus,developing highly efficient water oxidation catalysts has attracted the interests of researchers in the past decades.The formation of O-O bonds is typically the rate-determining step of the water oxidation catalytic cycle.Therefore,better understanding this key step is critical for the rational design of more efficient catalysts.This review focuses on elucidating the evolution of metal-oxygen species during transition metal-catalyzed water oxidation,and more importantly,on discussing the feasible O-O bond formation mechanisms during the oxygen evolution reaction over synthetic molecular catalysts.展开更多
Objective Two important geological issues have long been controversial in the Xing-Meng area of North China. The first concerns the final closure of Paleo-Asian Ocean in Xing-Meng area, and the other concerns the fol...Objective Two important geological issues have long been controversial in the Xing-Meng area of North China. The first concerns the final closure of Paleo-Asian Ocean in Xing-Meng area, and the other concerns the folding and lifting of the Xing-Meng Trough. The focus of thses issues is the Late Permian sedimentary environment, which is generally considered to be either an exclusively continental environment or from the closed inland sea environment in the Early to Middle stage to continental lacustrine environment in the late stage. In recent years, we have successively discovered abundant typical marine fossils （e.g., bryozoans and calcareous algae） in the Upper Permian thick limestone layer from Linxi County and Ar Horqin Banner in eastern region of Inner Mongolia and Jiutain County in Jilin Province. These significant findings have attracted the attention from fellow academics.展开更多
Lagerstroemia L.(Lythraceae)is a widely distributed genus of trees and shrubs native to tropical and subtropical environments from Southeast Asia to Australia,with numerous species highly valued as ornamentals.Althoug...Lagerstroemia L.(Lythraceae)is a widely distributed genus of trees and shrubs native to tropical and subtropical environments from Southeast Asia to Australia,with numerous species highly valued as ornamentals.Although the plastomes of many species in this genus have been sequenced,the rates of functional gene evolution and their effect on phylogenetic analyses have not been thoroughly examined.We compared three plastome sequence matrices to elucidate how differences in these datasets affected phylogenetic analyses.Robust phylogenetic relationships for Lagerstroemia species were reconstructed based on different plastome sequence partitions and multiple phylogenetic methods.Identification of single-nucleotide variants within different genes also provides basic data on the patterns of functional gene evolution in Lagerstroemia and may provide insights into how those mutations affect protein structure and potentially drive divergence via cytonuclear incompatibility.These results as well as analyses of non-synonymous and synonymous mutations,indicate that heterotachic modes of evolution are present in functional plastome genes and should be accounted for in the analyses of molecular evolution.In addition,divergence events within the Lagerstroemia were dated for the first time.Several of the divergence estimates corresponded to well-known Earth history events,such as the reduction in global temperatures at the Eocene/Oligocene boundary.Our analyses conducted in Lagerstroemia here dissects the various patterns in the divergence of Lagerstroemia and may provide a useful guide to help plant breeders,as well as the necessity of using plastomic data and as possible as to combine evidence from morphological characteristics to investigate the complicated interspecies relationship and the evolutionary dynamics of species.展开更多
HSP90 AA1 is part of the heat shock protein 90 gene family and has important functions against heat stress. We report a case of molecular level parallel evolution of the HSP90 AA1 gene in high elevation amphibians. HS...HSP90 AA1 is part of the heat shock protein 90 gene family and has important functions against heat stress. We report a case of molecular level parallel evolution of the HSP90 AA1 gene in high elevation amphibians. HSP90 AA1 gene sequences of four high-elevation anurans, Bufo gargarizans, Nanorana parkeri, Rana kukunoris, and Scutiger boulengeri, were compared along with five of their low-elevation relatives. A total of 16 amino-acid sites were identified as parallel evolution between N. parkeri and R. kukunoris. We generated both model based（Zhang and Kumar＇s test） and empirical data based（parallel/divergence plotting） null distributions for non-parallel evolution, and both methods clearly determined that the observed number of parallel substitutions were significantly more than the null expectation. Furthermore, on the HSP90 AA1 gene tree, N. parkeri and R. kukunoris formed a strongly supported clade that was away from their respective relatives. This study provides a clear case of molecular parallel evolution, which may have significant implications in understanding the genetic mechanisms of high-elevation adaptation.展开更多
A major research topic within molecular evolution studies is to understand more about the causes of the molecular evolutionary patterns that are recorded within and between taxa. The amount of germ cell divisions in f...A major research topic within molecular evolution studies is to understand more about the causes of the molecular evolutionary patterns that are recorded within and between taxa. The amount of germ cell divisions in females and males causes the majority of mutations, during DNA replication, that impact molecular evolution. In an XX female and an XY male system of diploid animals, the autosomes come in duplicates, with one copy from the male and female parent. Because of this, the idea that evolution is driven by male mutations has become increasingly more likely. This paper looks at the different male-mutation rates and determines that the male-mutation rate is much higher than female-mutation rates. Ry/a to be approximately 2.2, which means that Ry is approximately -24.2. From software analysis, x was approximated to be about 0.5. And since x and Ry are known, Ry/x was determined to be -49. The results for this paper show the calculated Rx/a and Ry/a are similar to the results of another study, but they are unique in that they produced a relatively high negative number for the Ry/a, which was about -49. This provides evidence that the male-mutation rate is higher than the female-mutation rate. This is interesting because this suggests that, from the data, the mutation rate in males is the defining force in molecular evolution. And because the rate goes beyond the prescribed model, future models of molecular systems will need to consider the rate of male mutations, as well as clarifying this male-mutation rate and calculating the rate of mutation in other sex-determinant systems.展开更多
Reptiles are the most morphologically and physiologically diverse tetrapods,with the squamates having the most diverse habitats.Lizard is an important model system for understanding the role of visual ecology,phylogen...Reptiles are the most morphologically and physiologically diverse tetrapods,with the squamates having the most diverse habitats.Lizard is an important model system for understanding the role of visual ecology,phylogeny and behavior on the structure of visual systems.In this study,we compared three opsin genes(RH2,LWS and SWS1)among 49 reptile species to detect positively selected genes as well as amino acid sites.Our results indicated that visual opsin genes have undergone divergent selection pressures in all lizards and RH2 and LWS suffered stronger positive selection than SWS1.Twelve positively selected sites were picked out for RH2 and LWS.Moreover,many diagnostic sites were found between geckos and non-gecko lizards,most of which were located near the positively selected sites and some of them have already been reported to be responsible for significant shifts of the wavelength of maximum absorption(λ_(max)).The results indicated that the gecko lineage accelerated the evolution of these genes to adapt to the dim-light environment or nocturnality as well as the switch between nocturnality and diurnality.展开更多
基金supported by the National Natural Science Foundation of China(Grant Nos.81871959,82373143,and 82003180).
文摘Early screening is crucial for the prevention of intestinal-type gastric cancer.The current study aimed to ascertain the molecular evolution of intestinal-type gastric cancer based on the Correa cascade for precise gastric cancer screening.We collected sequential lesions of the Correa cascade in the formalin-fixed and paraffin-embedded endoscopic submucosal dissection(ESD)-resected specimens from 14 Chinese patients by microdissection,and subsequently determined the profiles of somatic aberrations during gastric carcinogenesis using whole-exome sequencing,identifying multiple variants at different Correa stages.The results showed that TP53,PCLO,and PRKDC were the most frequently mutated genes in early gastric cancer(EGC).We found a high frequency of TP53 alterations in low-grade intraepithelial neoplasia(LGIN),which further increased in high-grade intraepithelial neoplasia(HGIN)and EGC.Intestinal metaplasia(IM)showed no significant correlation with EGC in terms of mutational spectra,whereas both LGIN and HGIN showed higher genomic similarities to EGC,compared with IM.Based on Jaccard similarity coefficients,we constructed three evolutionary models,with most patients showing linear progression from LGIN to HGIN,ultimately resulting in EGC.The extracellular matrix-receptor interaction pathway was revealed to be involved in the linear evolution.Additionally,the retrospective validation study of 39 patients diagnosed with LGIN indicated that PRKDC mutations,in addition to TP53 mutations,may drive LGIN progression to HGIN or EGC.In conclusion,the current study unveils the genomic evolution across the Correa cascade of intestinal-type gastric cancer,elucidates the underlying molecular mechanisms of gastric carcinogenesis,and provides evidence for potential personalized gastric cancer surveillance.
文摘Porous molecular sieve catalysts,including aluminosilicate zeolites and silicoaluminophosphate(SAPO)molecular sieves,have found widespread use in heterogeneous catalysis and are expected to play a key role in advancing carbon neutrality and sustainable development.Given the ubiquitous presence of water during catalyst synthesis,storage,and application,the interactions between water and molecular sieves as well as their consequent effects on frameworks and catalytic reactions have attracted considerable attention.These effects are inherently complex and highly dependent on various factors such as temperature,water phase,and partial pressure.In this review,we provide a comprehensive overview of the current understanding of water-molecular sieve interactions and their roles in catalysis,based on both experimental and theoretical calculation results.Special attention is paid to water-induced reversible and irreversible structural changes in aluminosilicate and SAPO frameworks at the atomic level,underscoring the dynamic and labile nature of these frameworks in water environments.The influence of water on catalytic performance and reaction kinetics in molecular sieve-catalyzed reactions is discussed from two perspectives:(1)its participation in reaction through hydrogen bonding interactions,such as competitive adsorption at active sites,stabilization of ground and transition states,and proton transfer bridge;(2)its role as a direct reactant forming new species via reactions with other vip molecules.Recent advancements in this area provide valuable insights for the rational design and optimization of catalysts for water-involved reactions.
基金supported by the RGC Senior Research Fellowship Scheme(Grant No.SRFS2021-5S01)the Hong Kong Research Grants Council(Grant No.PolyU 15307321)+2 种基金Research Institute for Smart Energy(CDAQ),Research Centre for Nanoscience and Nanotechnology(CE2H),Research Centre for Carbon-Strategic Catalysis(CE2L)Miss Clarea Au for the Endowed Professorship in Energy(Grant No.847S)National Natural Science Foundation of China(Grant No.62205277).
文摘The search for photoactive materials that are able to efficiently produce solar fuels is a growing research field to tackle the current energy crisis.Herein,we have prepared two ionic non-noble metallo-supramolecular polymers Se-MTpy(M=Co or Ni),and constructed their composites with single-walled carbon nanotubes(CNTs)via electrostatic attraction andπ-πinteractions for efficient and stable photocatalytic hydrogen evolution.In the photocatalytic system,the cationic Se-MTpy as host and anionic CNTs as vip are assembled into a binary composite,which exhibits superior photocatalytic activity under visible light irradiation(>420 nm).The optimized CNT@Se-CoTpy composite,containing 1.2 wt%metal loading,achieves 7 times higher hydrogen evolution rate(2.47 mmol g^(-1)h^(-1))than bare Se-CoTpy(0.35 mmol g^(-1)h^(-1)).This is attributed to the constructive formation of junctions between polymer and CNTs,facilitating interfacial charge transfer and transport for efficient proton reduction.The composite system also shows high photostability after continuous irradiation for~30 h.The combination of experimental and theoretical analysis demonstrates the higher activity for reducing H_(2)O to H_(2)of Se-CoTpy than Se-NiTpy.The feasible interfacial architecture proposed in this study represents an effective approach to achieve high photocatalytic performance.
文摘The molecular composition and evolution of the chalcone synthase (CHS) gene family from five species in Camellia (Theaceae) are explored in this study. Sixteen CHS exon 2 from four Camellia species were amplified from total DNA by PCR method. Three sequences of the fifth species in Camellia and two sequences of Glycine max as the designated outgroups were obtained from GenBank. Our results indicated that CHS gene family in Camellia was differentiated to three subfamilies (A, B, C) during the evolutionary history with six groups (A1, A2, A3, BI, B2, C). Among them, only group A2 was possessed by all five species in this study. However, the other five groups were detected only in some species of the plants studied. All members of CHS gene family in this study had high sequence similarity, more than 90% among the members in the same subfamily and more than 78% among different subfamilies at nucleotide level., According to the estimated components of amino acids, the function of CHS genes in Camellia had been diverged. The nucleotide substitutions of the different groups were not identical. Based on phylogenetic analyse inferred from sequences of CHS genes and their deduced amino acid sequences, we concluded that the CHS genes with new function in this genus were evolved either by mutations on several important sites or by accumulation of the mutations after the gene duplication. A further analysis showed that the diversification of CHS genes in Camellia still occurred recently, and the evolutionary models were different to some extant among different species. So we assumed that the different evolutionary models resulted from the impacts of variable environmental elements after the events of speciation.
文摘AIM： To investigate the hoLspoLs, direction, and the time course of evolution of hepatitis A virus in the process of consecutive cell culture passage in human KMB17 diploid cells.METHODS： Wild type hepatitis A virus H2w was serially propagated in KMB17 cells until passage 30, and the fulllength genomes of H2w and its six chosen progenies were determined by directly sequencing RT-PCR products amplified from viral genomic RNA. Alignment comparison of sequences from H2w with its six progenies and phylogenetic analysis of the whole VP1 region from H2w, progenies of H2w, and other cell culture adapted hepatitis A virus were then carried out to obtain data on the molecular evolution of hepatitis A virus in the process of consecutive passage in KMB17 cells.RESULTS： Most of the mutations occurred by passage 5 and several hotspots related to adaptation of the virus during cell growth were observed. After that stage, few additional mutations occurred through the remaining duration of passage in KMB17 cells except for mutation in the virulence determinants, which occurred in the vicinity of passage 15. The phylogenetic analysis of the whole VP1 region suggested that the progenies of H2w evolved closely to other cell culture adapted hepatitis A virus, i.e. MBB, L-A-l, other than its progenitor H2w.CONCLUSION： Hepatitis A virus served as a useful model for studying molecular evolution of viruses in a given environment. The information obtained in this study may provide assistance in cultivating the next generation of a seed virus for live hepatitis A vaccine production.
基金supported by the National Natural Science Foundation of China (Nos.22022607 and 42005090)the Shanghai Pujiang Program (No.20PJ1407600)。
文摘Heterogeneous oxidation by gas-phase oxidants is an important chemical transformation pathway of secondary organic aerosol(SOA)and plays an important role in controlling the abundance,properties,as well as climate and health impacts of aerosols.However,our knowledge on this heterogeneous chemistry remains inadequate.In this study,the heterogeneous oxidation ofα-pinene ozonolysis SOA by hydroxyl(OH)radicals was investigated under both low and high relative humidity(RH)conditions,with an emphasis on the evolution of molecular composition of SOA and its RH dependence.It is found that the heterogeneous oxidation of SOA at an OH exposure level equivalent to 12 hr of atmospheric aging leads to particle mass loss of 60%at 25%RH and 95%at 90%RH.The heterogeneous oxidation strongly changes the molecular composition of SOA.The dimer-to-monomer signal ratios increase dramatically with rising OH exposure,in particular under high RH conditions,suggesting that aerosol water stimulates the reaction of monomers with OH radicals more than that of dimers.In addition,the typical SOA tracer compounds such as pinic acid,pinonic acid,hydroxy pinonic acid and dimer esters(e.g.,C17H26O8 and C19H28O7)have lifetimes of several hours against heterogeneous OH oxidation under typical atmospheric conditions,which highlights the need for the consideration of their heterogeneous loss in the estimation of monoterpene SOA concentrations using tracer-based methods.Our study sheds lights on the heterogeneous oxidation chemistry ofmonoterpene SOA andwould help to understand their evolution and impacts in the atmosphere.
基金Supported by China Postdoctoral Scientific Foundation(201004713-87)Natural Science Foundation for Universities of Jiangsu Province(07KJB180013)Foundation for Talented Man in Jiangsu University(05JDG048)~~
文摘[Objective] The aim of this study was to analyze the sequence characteristics and molecular evolution of ubiquitins encoded by baculoviruses.[Methods]Clustal W software was used for multiple sequence alignment analysis,and neighbor-joining method（NJ）and maximum parsimony method（MP）were used for the construction of phylogenetic tree.[Results]The baculoviral ubiquitins showed 73%-86% sequence identity to eukaryotic ubiquitin.Two heterogeneous regions of baculoviral ubiquitins were observed：one was the residues from 15-32,the other was located from residues 53 to 60.The else parts were conserved,where many functional amino acids were also observed.Phylogenetic analysis indicated that baculoviral ubiquitins could be divided into three sub-families,including sub-family GV,sub-family I and sub-family II.The molecular evolution of baculoviral ubiquitins might be under negative selection to maintain their functional and structural stability.[Conclusion]The analysis had provided reference for the researches on functional characterization of baculoviral ubiquitins.
基金Supported by Youth Foundation of Hunan Institution of Humanities,Science and Technology(2009QN08)Educational Reform Project of Hunan Institution of Humanities,Science and Technology(RKJGZ1013)~~
文摘Pseudogene and fibrin peptide which has rapid evolve speed and good stability are used in this study to determine the divergence date among groups.Through calculating the evolutionary rate of hemoglobin α chain,γ chain in vertebrate（including birds and mammals）,it is concluded that the evolutionary rate of hemoglobin α chain,γ chain is not invariable.It shows different evolutionary rates in different periods,that is,faster in early evolution stage and relatively slow in later stage.
基金This work was supported by the Foundation of Application and Foundation Research of Sichuan Province in China (No. 03JY029-034).
文摘The partial sequences of exon Ⅰ of hormone-sensitive lipase （HSL） genes in yak （Bos grunniens）, cattle （Bos taurus）, zebu （Bos indicus）, and buffalo （Bubalus bubalis） were analyzed. Comparisons of these sequences and the deduced amino acid sequences with the homologous HSL gene and protein sequences in other mammalian species including pig （Sus scrofa）, human （Homo sapiens）, mouse （Mus musculus）, and rat （Rattus sp.） retrieved from the GenBank were carried out and finally a phylogenetic tree was constructed using the partial DNA sequences of the HSL genes in all species. The results showed that the homologies of the partial exon Ⅰ sequences of the HSL genes between yak and cattle, zebu, buffalo, pig, human, mouse, and rat were as high as 99.8%, 99.6%, 97.4%, 90.6%, 88.4%, 83.5%, and 82.3%, respectively. This was accompanied by highly homologous amino acid sequences of the HSLs： 100%, 100%, 98.2%, 94.0%, 92.2%, 89.8%, and 89.8% identity, respectively. There are more transitions, less transversions, and no insertion or deletion in variable nucleotides of the HSL genes between the yak and other species. The majority of the variable mutations was synonymous and was found most frequently at the third codon, followed by the first and second codons, a finding that was in accordance with the neutralism hypothesis for molecular evolution. In the phylogenetic tree, the cattle and zebu were clustered together first, followed by the yak, buffalo, pig, human, mouse, and rat. This was in agreement with taxonomy suggesting that the partial sequences of exon Ⅰ of the HSL genes were useful in constructing the phylogenetic tree of mammalian species. Among the four species of Bovidae, genetic differentiation in the HSL genes between yak and buffalo is equivalent to that between buffalo and cattle and between buffalo and zebu. Furthermore, the genetic distances in the HSL genes are much smaller between yak, cattle, and zebu than those between each of the three species and the buffalo. Therefore, it is reasonable to consider yak as an independent species of the genus Bos.
文摘Many eukaryotic genes are members of multi-gene families due to gene duplications, which generate new copies that allow functional divergence. However, the relationship between
基金financially supported by the National Natural Science Foundation of China (Nos. 11802027 and 11521062)the State Key Laboratory of Explosion Science and Technology (Nos. JCRC1801, QNKT20-01)Beijing Institute of Technology Research Fund。
文摘In this work, molecular dynamics simulations have been performed to explore the structural evolution and underlying sintering mechanism of aluminum nanoparticles. The structural evolution during sintering was firstly monitored through radial distribution function and atomic migration, and the underlying sintering mechanism was further quantitatively characterized in terms of average displacement, mean squared distance(MSD), radius ratio(i.e., the ratio of the neck radius to the particle radius), shrinkage and radius of gyration, crystalline orientations, particle size, etc. Results show that the surface atoms of nanoparticles are more active than the internal atoms, favoring the mechanical rotation of nanoparticles during sintering. During the sintering process, average displacement, radius ratio and the shrinkage rate have undergone three stages with increasing the temperature:(1) a slow increase and subsequent abrupt hike after reaching the sintering temperature;(2) an almost plateau region over a wide span of temperature;(3) finally a sharp increase again after reaching the melting temperature. In contrast, MSD remains basically unchanged before melting, close to zero, followed by a sudden increase after melting temperature. Although the radius of gyration also experiences three stages, nonetheless it exhibits almost completely contrary trend. It has also been found that both sintering temperature and melting temperature demonstrate an almost linear increase with the increase of nanoparticle size ranging from4.0, 6.0, 8.0 to 10.0 nm in diameter. Finally, we also found that the particle direction has limited effect on neck growth during sintering.
文摘Water oxidation is one of the most important reactions in natural and artificial energy conversion schemes.In nature,solar energy is converted to chemical energy via water oxidation at the oxygen-evolving center of photosystem II to generate dioxygen,protons,and electrons.In artificial energy schemes,water oxidation is one of the half reactions of water splitting,which is an appealing strategy for energy conversion via photocatalytic,electrocatalytic,or photoelectrocatalytic processes.Because it is thermodynamically unfavorable and kinetically slow,water oxidation is the bottleneck for achieving large-scale water splitting.Thus,developing highly efficient water oxidation catalysts has attracted the interests of researchers in the past decades.The formation of O-O bonds is typically the rate-determining step of the water oxidation catalytic cycle.Therefore,better understanding this key step is critical for the rational design of more efficient catalysts.This review focuses on elucidating the evolution of metal-oxygen species during transition metal-catalyzed water oxidation,and more importantly,on discussing the feasible O-O bond formation mechanisms during the oxygen evolution reaction over synthetic molecular catalysts.
基金financially supported by the National Natural Science Foundation of China (grant No.41572098)the geological survey project (grants No.121201103000161114 and 121201103000150019 ) of the China Geological Survey
文摘Objective Two important geological issues have long been controversial in the Xing-Meng area of North China. The first concerns the final closure of Paleo-Asian Ocean in Xing-Meng area, and the other concerns the folding and lifting of the Xing-Meng Trough. The focus of thses issues is the Late Permian sedimentary environment, which is generally considered to be either an exclusively continental environment or from the closed inland sea environment in the Early to Middle stage to continental lacustrine environment in the late stage. In recent years, we have successively discovered abundant typical marine fossils （e.g., bryozoans and calcareous algae） in the Upper Permian thick limestone layer from Linxi County and Ar Horqin Banner in eastern region of Inner Mongolia and Jiutain County in Jilin Province. These significant findings have attracted the attention from fellow academics.
基金supported by the Zhejiang Provincial Natural Science Foundation of China(Grant No.LY21C160001)Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants.
文摘Lagerstroemia L.(Lythraceae)is a widely distributed genus of trees and shrubs native to tropical and subtropical environments from Southeast Asia to Australia,with numerous species highly valued as ornamentals.Although the plastomes of many species in this genus have been sequenced,the rates of functional gene evolution and their effect on phylogenetic analyses have not been thoroughly examined.We compared three plastome sequence matrices to elucidate how differences in these datasets affected phylogenetic analyses.Robust phylogenetic relationships for Lagerstroemia species were reconstructed based on different plastome sequence partitions and multiple phylogenetic methods.Identification of single-nucleotide variants within different genes also provides basic data on the patterns of functional gene evolution in Lagerstroemia and may provide insights into how those mutations affect protein structure and potentially drive divergence via cytonuclear incompatibility.These results as well as analyses of non-synonymous and synonymous mutations,indicate that heterotachic modes of evolution are present in functional plastome genes and should be accounted for in the analyses of molecular evolution.In addition,divergence events within the Lagerstroemia were dated for the first time.Several of the divergence estimates corresponded to well-known Earth history events,such as the reduction in global temperatures at the Eocene/Oligocene boundary.Our analyses conducted in Lagerstroemia here dissects the various patterns in the divergence of Lagerstroemia and may provide a useful guide to help plant breeders,as well as the necessity of using plastomic data and as possible as to combine evidence from morphological characteristics to investigate the complicated interspecies relationship and the evolutionary dynamics of species.
基金supported by the National Nature Science Foundation of China (grant number 31328021 to Jinzhong FU)NSERC of Canada (a discovery grant to Jinzhong FU)
文摘HSP90 AA1 is part of the heat shock protein 90 gene family and has important functions against heat stress. We report a case of molecular level parallel evolution of the HSP90 AA1 gene in high elevation amphibians. HSP90 AA1 gene sequences of four high-elevation anurans, Bufo gargarizans, Nanorana parkeri, Rana kukunoris, and Scutiger boulengeri, were compared along with five of their low-elevation relatives. A total of 16 amino-acid sites were identified as parallel evolution between N. parkeri and R. kukunoris. We generated both model based（Zhang and Kumar＇s test） and empirical data based（parallel/divergence plotting） null distributions for non-parallel evolution, and both methods clearly determined that the observed number of parallel substitutions were significantly more than the null expectation. Furthermore, on the HSP90 AA1 gene tree, N. parkeri and R. kukunoris formed a strongly supported clade that was away from their respective relatives. This study provides a clear case of molecular parallel evolution, which may have significant implications in understanding the genetic mechanisms of high-elevation adaptation.
文摘A major research topic within molecular evolution studies is to understand more about the causes of the molecular evolutionary patterns that are recorded within and between taxa. The amount of germ cell divisions in females and males causes the majority of mutations, during DNA replication, that impact molecular evolution. In an XX female and an XY male system of diploid animals, the autosomes come in duplicates, with one copy from the male and female parent. Because of this, the idea that evolution is driven by male mutations has become increasingly more likely. This paper looks at the different male-mutation rates and determines that the male-mutation rate is much higher than female-mutation rates. Ry/a to be approximately 2.2, which means that Ry is approximately -24.2. From software analysis, x was approximated to be about 0.5. And since x and Ry are known, Ry/x was determined to be -49. The results for this paper show the calculated Rx/a and Ry/a are similar to the results of another study, but they are unique in that they produced a relatively high negative number for the Ry/a, which was about -49. This provides evidence that the male-mutation rate is higher than the female-mutation rate. This is interesting because this suggests that, from the data, the mutation rate in males is the defining force in molecular evolution. And because the rate goes beyond the prescribed model, future models of molecular systems will need to consider the rate of male mutations, as well as clarifying this male-mutation rate and calculating the rate of mutation in other sex-determinant systems.
基金Financial support was provided by the National Natural Science Foundation of China(NSFC)(Grant No.31672269,31000949 to J.YAN)the Natural Science Foundation of the Jiangsu Higher Education Institutions of China(19KJA330001 to P.LI)+1 种基金the Priority Academic Program Development of Jiangsu Higher Education Institutions(PAPD)Top-Notch Academic Programs Project of Jiangsu Higher Education Institutions(TAPP,PPZY2015B117)。
文摘Reptiles are the most morphologically and physiologically diverse tetrapods,with the squamates having the most diverse habitats.Lizard is an important model system for understanding the role of visual ecology,phylogeny and behavior on the structure of visual systems.In this study,we compared three opsin genes(RH2,LWS and SWS1)among 49 reptile species to detect positively selected genes as well as amino acid sites.Our results indicated that visual opsin genes have undergone divergent selection pressures in all lizards and RH2 and LWS suffered stronger positive selection than SWS1.Twelve positively selected sites were picked out for RH2 and LWS.Moreover,many diagnostic sites were found between geckos and non-gecko lizards,most of which were located near the positively selected sites and some of them have already been reported to be responsible for significant shifts of the wavelength of maximum absorption(λ_(max)).The results indicated that the gecko lineage accelerated the evolution of these genes to adapt to the dim-light environment or nocturnality as well as the switch between nocturnality and diurnality.
