Subtropical evergreen broad-leaved trees are usually vulnerable to freezing stress,while hexaploid wild Camellia oleifera shows strong freezing tolerance.As a valuable genetic resource of woody oil crop C.oleifera,wil...Subtropical evergreen broad-leaved trees are usually vulnerable to freezing stress,while hexaploid wild Camellia oleifera shows strong freezing tolerance.As a valuable genetic resource of woody oil crop C.oleifera,wild C.oleifera can serve as a case for studying the molecular bases of adaptive evolution to freezing stress.Here,47 wild C.oleifera from 11 natural distribution sites in China and 4 relative species of C.oleifera were selected for genome sequencing.“Min Temperature of Coldest Month”(BIO6)had the highest comprehensive contribution to wild C.oleifera distribution.The population genetic structure of wild C.oleifera could be divided into two groups:in cold winter(BIO6≤0℃)and warm winter(BIO6>0℃)areas.Wild C.oleifera in cold winter areas might have experienced stronger selection pressures and population bottlenecks with lower N_(e) than those in warm winter areas.155 singlenucleotide polymorphisms(SNPs)were significantly correlated with the key bioclimatic variables(106 SNPs significantly correlated with BIO6).Twenty key SNPs and 15 key copy number variation regions(CNVRs)were found with genotype differentiation>50%between the two groups of wild C.oleifera.Key SNPs in cis-regulatory elements might affect the expression of key genes associated with freezing tolerance,and they were also found within a CNVR suggesting interactions between them.Some key CNVRs in the exon regions were closely related to the differentially expressed genes under freezing stress.The findings suggest that rich SNPs and CNVRs in polyploid trees may contribute to the adaptive evolution to freezing stress.展开更多
Saccharomyces cerevisiae is not naturally capable of efficiently utilizing xylose as a carbon source.When cultured with lignocellulosic hydrolysates containing pretreatment-derived inhibitors,S.cerevisiae suffers from...Saccharomyces cerevisiae is not naturally capable of efficiently utilizing xylose as a carbon source.When cultured with lignocellulosic hydrolysates containing pretreatment-derived inhibitors,S.cerevisiae suffers from much lower sugar uptake,ethanol yield and fermentation efficiency.Thus,considering efficient xylose conversion into ethanol during non-detoxified hydrolysate culture,genetic engineering and adaptive evolution of S.cerevisiae might be a promising joint strategy for improving xylose uptake and ethanol production.In this study,an inhibitor-tolerant strain S.cerevisiae SPSC01-TAF94 was genetically engineered by overexpressing both xylose transport-and metabolism-related genes(N360F,Ru-xyl A,TAL1,TKL1,RKI1 and RPE1),yielding the xylose-utilizing strain TAF94-X,followed by three-stage adaptation in non-detoxified corn stover hydrolysate containing 5 g·L^(-1)acetic acid,0.32 g·L^(-1)furfural,0.17 g·L(-1)HMF and 0.19 g·L^(-1)vanillin as the major inhibitors as well as 20,40 and 60 g·L^(-1)xylose adjusted as the major carbon source,respectively.Finally,an active xylose-utilizing and ethanolproducing strain TAF94-X60 was obtained,which achieved 44.9 g·L^(-1)ethanol with yield of0.41 g·g^(-1),productivity of 0.62 g·L^(-1)·h^(-1)and xylose consumption rate of 0.42 g·L^(-1)·h^(-1)during hydrolysate culture,compared to those of 36.5 g·L^(-1),0.38 g·g^(-1),0.50 g·L^(-1)·h^(-1)and 0.20 g·L^(-1)·h^(-1)obtained with the control strain TAF94-X.The proposed joint strategy effectively utilizes hydrolyzed sugars while eliminating the need for conventional detoxification or water washing processes,thus enhancing the economic feasibility of large-scale lignocellulosic ethanol production.展开更多
The globin superfamily,central to oxygen(O_(2))cascade dynamics,exemplifies how canalization—evolutionary stabilization of phenotypic traits—enables vertebrates to thrive in extreme environments.In birds,hemoglobins...The globin superfamily,central to oxygen(O_(2))cascade dynamics,exemplifies how canalization—evolutionary stabilization of phenotypic traits—enables vertebrates to thrive in extreme environments.In birds,hemoglobins(Hbs)serve as a paradigm of this process,with structural and functional canalization underpinning their exceptional aerobic capacity and elevational diversification.Despite significant advances of globins in our understanding of avian aerobic adaptation,a comprehensive synthesis of functional diversity,molecular evolution,and structural innovation is essential to fully elucidate their canalized roles in O_(2)homeostasis.Integrating perspectives on globin functional diversity and structural evolution,this review examines how chance(mutation/fixation biases)and contingency(historical genetic/epistatic constraints)shape Hb divergence and parallelism,thereby bridging molecular mechanisms with physiological adaptation in birds.We highlight how avian Hbs,canalized through compensatory substitutions and allosteric regulation,achieves a balance between evolutionary robustness and adaptive plasticity.However,critical gaps remain persist:the roles of understudied globins(e.g.,neuroglobin,globin E)and the mechanisms of genetic assimilation in migratory taxa.We propose an integrative framework that incorporates ecological divergence(elevation,flight endurance),phylogenetic timescales,and systems biology to unravel how canalization directs adaptive compromise.By focusing on birds within the amniotes,this synthesis advances a cohesive model for vertebrate evolution,wherein canalized globins reconcile metabolic precision with ecological innovation.Ultimately,this review refines hypotheses of O_(2)cascade evolution and calls for cross-disciplinary studies to decode the genetic and physiological architecture underlying adaptive canalization in extreme environments.展开更多
In underwater target search path planning,the accuracy of sonar models directly dictates the accurate assessment of search coverage.In contrast to physics-informed sonar models,traditional geometric sonar models fail ...In underwater target search path planning,the accuracy of sonar models directly dictates the accurate assessment of search coverage.In contrast to physics-informed sonar models,traditional geometric sonar models fail to accurately characterize the complex influence of marine environments.To overcome these challenges,we propose an acoustic physics-informed intelligent path planning framework for underwater target search,integrating three core modules:The acoustic-physical modeling module adopts 3D ray-tracing theory and the active sonar equation to construct a physics-driven sonar detection model,explicitly accounting for environmental factors that influence sonar performance across heterogeneous spaces.The hybrid parallel computing module adopts a message passing interface(MPI)/open multi-processing(Open MP)hybrid strategy for large-scale acoustic simulations,combining computational domain decomposition and physics-intensive task acceleration.The search path optimization module adopts the covariance matrix adaptation evolution algorithm to solve continuous optimization problems of heading angles,which ensures maximum search coverage for targets.Largescale experiments conducted in the Pacific and Atlantic Oceans demonstrate the framework's effectiveness:(1)Precise capture of sonar detection range variations from 5.45 km to 50 km in heterogeneous marine environments.(2)Significant speedup of 453.43×for acoustic physics modeling through hybrid parallelization.(3)Notable improvements of 7.23%in detection coverage and 15.86%reduction in optimization time compared to the optimal baseline method.The framework provides a robust solution for underwater search missions in complex marine environments.展开更多
For developing efficient vaccines, it is essential to identify which amino acid changes are most important to the survival of the virus. We investigate the amino acid substitution features in the Avian Infectious Bron...For developing efficient vaccines, it is essential to identify which amino acid changes are most important to the survival of the virus. We investigate the amino acid substitution features in the Avian Infectious Bronchitis Virus （AIBV） antigenic domain of a vaccine serotype （DE072） and a virulent viral strain （GA98） to better understand adaptive evolution of AIBV. In addition, the SARS Coronavirus （SARS-CoV） was also analyzed in the same way. It is interesting to find that extreme comparability exists between AIBV and SARS in amino acid substitution pattern. It suggests that amino acid changes that result in overall shift of residue charge and polarity should be paid special attention to during the development of vaccines.展开更多
Acetic acid and furfural are known as prevalent inhibitors deriving from pretreatment during lignocellulosic ethanol production.They negatively impact cell growth,glucose uptake and ethanol biosynthesis of Saccharomyc...Acetic acid and furfural are known as prevalent inhibitors deriving from pretreatment during lignocellulosic ethanol production.They negatively impact cell growth,glucose uptake and ethanol biosynthesis of Saccharomyces cerevisiae strains.Development of industrial S.cerevisiae strains with high tolerance towards these inhibitors is thus critical for efficient lignocellulosic ethanol production.In this study,the acetic acid or furfural tolerance of different S.cerevisiae strains could be significantly enhanced after adaptive evolution via serial cultivation for 40 generations under stress conditions.The acetic acid-based adaptive strain SPSC01-TA9 produced 30.5 g·L^(-1)ethanol with a yield of 0.46 g·g^(-1)in the presence of 9 g·L^(-1)acetic acid,while the acetic acid/furfural-based adaptive strain SPSC01-TAF94 produced more ethanol of 36.2 g·L^(-1)with increased yield up to 0.49 g·g^(-1)in the presence of both 9 g·L^(-1)acetic acid and 4 g·L^(-1)furfural.Significant improvements were also observed during non-detoxified corn stover hydrolysate culture by SPSC01-TAF94,which achieved ethanol production and yield of 29.1 g·L^(-1)and 0.49 g·g^(-1),respectively,the growth and fermentation efficiency of acetic acid/furfural-based adaptive strain in hydrolysate was 95%higher than those of wildtype strains,indicating the acetic acid-and furfural-based adaptive evolution strategy could be an effective approach for improving lignocellulosic ethanol production.The adapted strains developed in this study with enhanced tolerance against acetic acid and furfural could be potentially contribute to economically feasible and sustainable lignocellulosic biorefinery.展开更多
Pikas(Lagomorpha:Ochotonidae)are small mouselike lagomorphs.To investigate their adaptation to different ecological environments during their dispersal from the Qinghai-Xizang(Tibet)Plateau(QTP),we collected 226 pikas...Pikas(Lagomorpha:Ochotonidae)are small mouselike lagomorphs.To investigate their adaptation to different ecological environments during their dispersal from the Qinghai-Xizang(Tibet)Plateau(QTP),we collected 226 pikas and measured 20 morphological characteristics and recorded habitat information.We also sequenced the genome of 81specimens,representing 27 putative pika species.The genome-wide tree based on 4?090 coding genes identified five subgenera,i.e.,Alienauroa,Conothoa,Lagotona,Ochotona,and Pika,consistent with morphometric data.Morphologically,Alienauroa and Ochotona had similar traits,including smaller size and earlier divergence time compared to other pikas.Consistently,the habitats of Alienauroa and Ochotona differed from those of the remaining subgenera.Phylogenetic signal analysis detected 83 genes significantly related to morphological characteristics,including several visual and hearingrelated genes.Analysis of shared amino acid substitutions and positively selected genes(PSGs)in Alienauroa and Ochotona identified two genes,i.e.,mitochondrial function-related TSFM(p.Q155E)and low-light visual sensitivity-related PROM1(p.H419Y).Functional experiments demonstrated that TSFM-155E significantly enhanced mitochondrial function compared to TSFM-155Q in other pikas,and PROM1-419Y decreased the modeling of dynamic intracellular chloride efflux upon calcium uptake.Alienauroa and Ochotona individuals mostly inhabit different environments(e.g.,subtropical forests)than other pikas,suggesting that a shift from the larger ancestral type and changes in sensory acuity and energy enhancement may have been required in their new environments.This study increases our understanding of the evolutionary history of pikas.展开更多
Next-generation sequencing technology has transformed our ability to assess the taxonomic composition functions of host-associated microbiota and microbiomes. More human microbiome research projects—particularly thos...Next-generation sequencing technology has transformed our ability to assess the taxonomic composition functions of host-associated microbiota and microbiomes. More human microbiome research projects—particularly those that explore genomic mutations within the microbiome—will be launched in the next decade. This review focuses on the coevolution of microbes within a microbiome, which shapes strain-level diversity both within and between host species. We also explore the correlation between microbial genomic mutations and common metabolic diseases, and the adaptive evolution of pathogens and probiotics during invasion and colonization. Finally, we discuss advances in methods and algorithms for annotating and analyzing microbial genomic mutations.展开更多
Meiotic recombination is essential for sexual reproduction and its regulation has been extensively studied in many taxa.However,genome-wide recombination landscape has not been reported in ciliates and it remains unkn...Meiotic recombination is essential for sexual reproduction and its regulation has been extensively studied in many taxa.However,genome-wide recombination landscape has not been reported in ciliates and it remains unknown how it is affected by the unique features of ciliates:the synaptonemal complex(SC)-independent meiosis and the nuclear dimorphism.Here,we show the recombination landscape in the model ciliate Tetrahymena thermophila by analyzing single-nucleotide polymorphism datasets from 38 hybrid progeny.We detect 1021 crossover(CO)events(35.8 per meiosis),corresponding to an overall CO rate of 9.9 cM/Mb.However,gene conversion by non-crossover is rare(1.03 per meiosis)and not biased towards G or C alleles.Consistent with the reported roles of SC in CO interference,we find no obvious sign of CO interference.CO tends to occur within germ-soma common genomic regions and many of the 44 identified CO hotspots localize at the centromeric or subtelomeric regions.Gene ontology analyses show that CO hotspots are strongly associated with genes responding to environmental changes.We discuss these results with respect to how nuclear dimorphism has potentially driven the formation of the observed recombination landscape to facilitate environmental adaptation and the sharing of machinery among meiotic and somatic recombination.展开更多
Single unmanned aerial vehicle(UAV)multitasking plays an important role in multiple UAVs cooperative control,which is as well as the most complicated and hardest part.This paper establishes a threedimensional topograp...Single unmanned aerial vehicle(UAV)multitasking plays an important role in multiple UAVs cooperative control,which is as well as the most complicated and hardest part.This paper establishes a threedimensional topographical map,and an improved adaptive differential evolution(IADE)algorithm is proposed for single UAV multitasking.As an optimized problem,the efficiency of using standard differential evolution to obtain the global optimal solution is very low to avoid this problem.Therefore,the algorithm adopts the mutation factor and crossover factor into dynamic adaptive functions,which makes the crossover factor and variation factor can be adjusted with the number of population iteration and individual fitness value,letting the algorithm exploration and development more reasonable.The experimental results implicate that the IADE algorithm has better performance,higher convergence and efficiency to solve the multitasking problem compared with other algorithms.展开更多
In the field of phylogenetic analyses, the rbcL gene encoded large subunit Ribulose-1,5-biphosphate carboxylase/oxygenase （Rubisco, EC4.1.1.39）, which plays a crucial role in the process of photosynthesis for most ...In the field of phylogenetic analyses, the rbcL gene encoded large subunit Ribulose-1,5-biphosphate carboxylase/oxygenase （Rubisco, EC4.1.1.39）, which plays a crucial role in the process of photosynthesis for most terrestrial plants, has been considered to be conserved; however, recent controversy regarding rbcL conservation has appeared since it was proposed to be under natural selection within all principal lineages of land plants. In this study, by examining the variation of DNA and protein sequences among 17 species in the family Tamaricaceae, three nonsynonymous mutations were identified to be under positive selection. The favored sites were located in the alph-helix domains of Rubisco, with decreased hydrophobicity and increased entropy, which could facilitate C〇 2 penetration into the active site of Rubisco. We also found that the expression level of rbcL in different genotypes of Reaumuria soongarica shifted in response to various stresses such as drought, temperature, salt, and light. This study not only sheds light on the functional/structural features of Rubisco in the evolution scenarios from 〇 3-like into C4 in Tamaricaceae but also provides useful information on directing genetic performance to enhance photosynthesis efficiency of desert plants for sustaining fragile desert ecosystems; fur-thermore, it promotes the ability to cope with desert aridification and global warming.展开更多
Effective constrained optimization algorithms have been proposed for engineering problems recently.It is common to consider constraint violation and optimization algorithm as two separate parts.In this study,a pbest s...Effective constrained optimization algorithms have been proposed for engineering problems recently.It is common to consider constraint violation and optimization algorithm as two separate parts.In this study,a pbest selection mechanism is proposed to integrate the current mutation strategy in constrained optimization problems.Based on the improved pbest selection method,an adaptive differential evolution approach is proposed,which helps the population jump out of the infeasible region.If all the individuals are infeasible,the top 5%of infeasible individuals are selected.In addition,a modified truncatedε-level method is proposed to avoid trapping in infeasible regions.The proposed adaptive differential evolution approach with an improvedεconstraint processmechanism(IεJADE)is examined on CEC 2006 and CEC 2010 constrained benchmark function series.Besides,a standard IEEE-30 bus test system is studied on the efficiency of the IεJADE.The numerical analysis verifies the IεJADE algorithm is effective in comparisonwith other effective algorithms.展开更多
基金funded by the National Natural Science Foundation of China(grant no.32270238 and 31870311).
文摘Subtropical evergreen broad-leaved trees are usually vulnerable to freezing stress,while hexaploid wild Camellia oleifera shows strong freezing tolerance.As a valuable genetic resource of woody oil crop C.oleifera,wild C.oleifera can serve as a case for studying the molecular bases of adaptive evolution to freezing stress.Here,47 wild C.oleifera from 11 natural distribution sites in China and 4 relative species of C.oleifera were selected for genome sequencing.“Min Temperature of Coldest Month”(BIO6)had the highest comprehensive contribution to wild C.oleifera distribution.The population genetic structure of wild C.oleifera could be divided into two groups:in cold winter(BIO6≤0℃)and warm winter(BIO6>0℃)areas.Wild C.oleifera in cold winter areas might have experienced stronger selection pressures and population bottlenecks with lower N_(e) than those in warm winter areas.155 singlenucleotide polymorphisms(SNPs)were significantly correlated with the key bioclimatic variables(106 SNPs significantly correlated with BIO6).Twenty key SNPs and 15 key copy number variation regions(CNVRs)were found with genotype differentiation>50%between the two groups of wild C.oleifera.Key SNPs in cis-regulatory elements might affect the expression of key genes associated with freezing tolerance,and they were also found within a CNVR suggesting interactions between them.Some key CNVRs in the exon regions were closely related to the differentially expressed genes under freezing stress.The findings suggest that rich SNPs and CNVRs in polyploid trees may contribute to the adaptive evolution to freezing stress.
基金supported by the National Key Research and Development Program of China(2021YFC2101303)the National Natural Science Foundation of China(U22A20424 and 22378048)+5 种基金the Major scientific and technological projects of Sinopecthe Dalian Technology Talents Project for Distinguished Young Scholars(2021RJ03)the Fundamental Research Funds for the Central Universities(DUT25LAB104)the Liaoning Revitalization Talents Program(XLYC2202049)the Ningbo Natural Science Foundation(2022J013)the Ningbo Municipal Public Welfare Science and Technology Foundation(2024S004)。
文摘Saccharomyces cerevisiae is not naturally capable of efficiently utilizing xylose as a carbon source.When cultured with lignocellulosic hydrolysates containing pretreatment-derived inhibitors,S.cerevisiae suffers from much lower sugar uptake,ethanol yield and fermentation efficiency.Thus,considering efficient xylose conversion into ethanol during non-detoxified hydrolysate culture,genetic engineering and adaptive evolution of S.cerevisiae might be a promising joint strategy for improving xylose uptake and ethanol production.In this study,an inhibitor-tolerant strain S.cerevisiae SPSC01-TAF94 was genetically engineered by overexpressing both xylose transport-and metabolism-related genes(N360F,Ru-xyl A,TAL1,TKL1,RKI1 and RPE1),yielding the xylose-utilizing strain TAF94-X,followed by three-stage adaptation in non-detoxified corn stover hydrolysate containing 5 g·L^(-1)acetic acid,0.32 g·L^(-1)furfural,0.17 g·L(-1)HMF and 0.19 g·L^(-1)vanillin as the major inhibitors as well as 20,40 and 60 g·L^(-1)xylose adjusted as the major carbon source,respectively.Finally,an active xylose-utilizing and ethanolproducing strain TAF94-X60 was obtained,which achieved 44.9 g·L^(-1)ethanol with yield of0.41 g·g^(-1),productivity of 0.62 g·L^(-1)·h^(-1)and xylose consumption rate of 0.42 g·L^(-1)·h^(-1)during hydrolysate culture,compared to those of 36.5 g·L^(-1),0.38 g·g^(-1),0.50 g·L^(-1)·h^(-1)and 0.20 g·L^(-1)·h^(-1)obtained with the control strain TAF94-X.The proposed joint strategy effectively utilizes hydrolyzed sugars while eliminating the need for conventional detoxification or water washing processes,thus enhancing the economic feasibility of large-scale lignocellulosic ethanol production.
基金supported by the National Natural Science Foundation of China(NSFC 31900313)to X.Z.the Central guide local science and technology development funds(XZ202301YD0007C)to L.Y.+1 种基金NSFC(32471572)National Key Research and Development Program of China(2024YFC2310303)to D.L。
文摘The globin superfamily,central to oxygen(O_(2))cascade dynamics,exemplifies how canalization—evolutionary stabilization of phenotypic traits—enables vertebrates to thrive in extreme environments.In birds,hemoglobins(Hbs)serve as a paradigm of this process,with structural and functional canalization underpinning their exceptional aerobic capacity and elevational diversification.Despite significant advances of globins in our understanding of avian aerobic adaptation,a comprehensive synthesis of functional diversity,molecular evolution,and structural innovation is essential to fully elucidate their canalized roles in O_(2)homeostasis.Integrating perspectives on globin functional diversity and structural evolution,this review examines how chance(mutation/fixation biases)and contingency(historical genetic/epistatic constraints)shape Hb divergence and parallelism,thereby bridging molecular mechanisms with physiological adaptation in birds.We highlight how avian Hbs,canalized through compensatory substitutions and allosteric regulation,achieves a balance between evolutionary robustness and adaptive plasticity.However,critical gaps remain persist:the roles of understudied globins(e.g.,neuroglobin,globin E)and the mechanisms of genetic assimilation in migratory taxa.We propose an integrative framework that incorporates ecological divergence(elevation,flight endurance),phylogenetic timescales,and systems biology to unravel how canalization directs adaptive compromise.By focusing on birds within the amniotes,this synthesis advances a cohesive model for vertebrate evolution,wherein canalized globins reconcile metabolic precision with ecological innovation.Ultimately,this review refines hypotheses of O_(2)cascade evolution and calls for cross-disciplinary studies to decode the genetic and physiological architecture underlying adaptive canalization in extreme environments.
基金supported by Natural Science Foundation of Hu'nan Province(2024JJ5409)。
文摘In underwater target search path planning,the accuracy of sonar models directly dictates the accurate assessment of search coverage.In contrast to physics-informed sonar models,traditional geometric sonar models fail to accurately characterize the complex influence of marine environments.To overcome these challenges,we propose an acoustic physics-informed intelligent path planning framework for underwater target search,integrating three core modules:The acoustic-physical modeling module adopts 3D ray-tracing theory and the active sonar equation to construct a physics-driven sonar detection model,explicitly accounting for environmental factors that influence sonar performance across heterogeneous spaces.The hybrid parallel computing module adopts a message passing interface(MPI)/open multi-processing(Open MP)hybrid strategy for large-scale acoustic simulations,combining computational domain decomposition and physics-intensive task acceleration.The search path optimization module adopts the covariance matrix adaptation evolution algorithm to solve continuous optimization problems of heading angles,which ensures maximum search coverage for targets.Largescale experiments conducted in the Pacific and Atlantic Oceans demonstrate the framework's effectiveness:(1)Precise capture of sonar detection range variations from 5.45 km to 50 km in heterogeneous marine environments.(2)Significant speedup of 453.43×for acoustic physics modeling through hybrid parallelization.(3)Notable improvements of 7.23%in detection coverage and 15.86%reduction in optimization time compared to the optimal baseline method.The framework provides a robust solution for underwater search missions in complex marine environments.
文摘For developing efficient vaccines, it is essential to identify which amino acid changes are most important to the survival of the virus. We investigate the amino acid substitution features in the Avian Infectious Bronchitis Virus （AIBV） antigenic domain of a vaccine serotype （DE072） and a virulent viral strain （GA98） to better understand adaptive evolution of AIBV. In addition, the SARS Coronavirus （SARS-CoV） was also analyzed in the same way. It is interesting to find that extreme comparability exists between AIBV and SARS in amino acid substitution pattern. It suggests that amino acid changes that result in overall shift of residue charge and polarity should be paid special attention to during the development of vaccines.
基金supported by the National Key Research and Development Program of China(2021YFC2101303)the National Natural Science Foundation of China(U22A20424 and 22378048)+6 种基金the Major Scientific and Technological Projects of Sinopecthe Dalian Technology Talents Project for Distinguished Young Scholars(2021RJ03)the Yunnan Provincial Rural Energy Engineering Key Laboratory(2022KF003)the National Natural Science Foundation of Liaoning Province(2023-MS-110)the Liaoning Revitalization Talents Program(XLYC2202049)the Fundamental Research Funds for the Central Universities(DUT22LK22)the CAS Key Laboratory of Renewable Energy,Guangzhou Institute of Energy Conversion(E229kf0401)。
文摘Acetic acid and furfural are known as prevalent inhibitors deriving from pretreatment during lignocellulosic ethanol production.They negatively impact cell growth,glucose uptake and ethanol biosynthesis of Saccharomyces cerevisiae strains.Development of industrial S.cerevisiae strains with high tolerance towards these inhibitors is thus critical for efficient lignocellulosic ethanol production.In this study,the acetic acid or furfural tolerance of different S.cerevisiae strains could be significantly enhanced after adaptive evolution via serial cultivation for 40 generations under stress conditions.The acetic acid-based adaptive strain SPSC01-TA9 produced 30.5 g·L^(-1)ethanol with a yield of 0.46 g·g^(-1)in the presence of 9 g·L^(-1)acetic acid,while the acetic acid/furfural-based adaptive strain SPSC01-TAF94 produced more ethanol of 36.2 g·L^(-1)with increased yield up to 0.49 g·g^(-1)in the presence of both 9 g·L^(-1)acetic acid and 4 g·L^(-1)furfural.Significant improvements were also observed during non-detoxified corn stover hydrolysate culture by SPSC01-TAF94,which achieved ethanol production and yield of 29.1 g·L^(-1)and 0.49 g·g^(-1),respectively,the growth and fermentation efficiency of acetic acid/furfural-based adaptive strain in hydrolysate was 95%higher than those of wildtype strains,indicating the acetic acid-and furfural-based adaptive evolution strategy could be an effective approach for improving lignocellulosic ethanol production.The adapted strains developed in this study with enhanced tolerance against acetic acid and furfural could be potentially contribute to economically feasible and sustainable lignocellulosic biorefinery.
基金supported by the National Natural Science Foundation of China(31470110,31970399)China National GeneBank(CNGB)。
文摘Pikas(Lagomorpha:Ochotonidae)are small mouselike lagomorphs.To investigate their adaptation to different ecological environments during their dispersal from the Qinghai-Xizang(Tibet)Plateau(QTP),we collected 226 pikas and measured 20 morphological characteristics and recorded habitat information.We also sequenced the genome of 81specimens,representing 27 putative pika species.The genome-wide tree based on 4?090 coding genes identified five subgenera,i.e.,Alienauroa,Conothoa,Lagotona,Ochotona,and Pika,consistent with morphometric data.Morphologically,Alienauroa and Ochotona had similar traits,including smaller size and earlier divergence time compared to other pikas.Consistently,the habitats of Alienauroa and Ochotona differed from those of the remaining subgenera.Phylogenetic signal analysis detected 83 genes significantly related to morphological characteristics,including several visual and hearingrelated genes.Analysis of shared amino acid substitutions and positively selected genes(PSGs)in Alienauroa and Ochotona identified two genes,i.e.,mitochondrial function-related TSFM(p.Q155E)and low-light visual sensitivity-related PROM1(p.H419Y).Functional experiments demonstrated that TSFM-155E significantly enhanced mitochondrial function compared to TSFM-155Q in other pikas,and PROM1-419Y decreased the modeling of dynamic intracellular chloride efflux upon calcium uptake.Alienauroa and Ochotona individuals mostly inhabit different environments(e.g.,subtropical forests)than other pikas,suggesting that a shift from the larger ancestral type and changes in sensory acuity and energy enhancement may have been required in their new environments.This study increases our understanding of the evolutionary history of pikas.
基金supported by the National Natural Science Foundation of China(31701577).
文摘Next-generation sequencing technology has transformed our ability to assess the taxonomic composition functions of host-associated microbiota and microbiomes. More human microbiome research projects—particularly those that explore genomic mutations within the microbiome—will be launched in the next decade. This review focuses on the coevolution of microbes within a microbiome, which shapes strain-level diversity both within and between host species. We also explore the correlation between microbial genomic mutations and common metabolic diseases, and the adaptive evolution of pathogens and probiotics during invasion and colonization. Finally, we discuss advances in methods and algorithms for annotating and analyzing microbial genomic mutations.
基金supported by the Wuhan Branch,Supercomputing Center,Chinese Academy of Sciences,Chinasupported by the National Aquatic Biological Resource Center(NABRC)+4 种基金supported by the Bureau of Frontier Sciences and Education,Chinese Academy of Sciences(ZDBS-LY-SM026)the National Natural Science Foundation of China(32370457,32122015,32130011,31900316,and 31900339)the Strategic Priority Research Program of the Chinese Academy of Sciences(XDB0480000)PJA3 grant of ARC Foundation(ARCPJA2021060003830)Equipes 2022 grant of Foundation Recherche Medicale(EQU202203014651).
文摘Meiotic recombination is essential for sexual reproduction and its regulation has been extensively studied in many taxa.However,genome-wide recombination landscape has not been reported in ciliates and it remains unknown how it is affected by the unique features of ciliates:the synaptonemal complex(SC)-independent meiosis and the nuclear dimorphism.Here,we show the recombination landscape in the model ciliate Tetrahymena thermophila by analyzing single-nucleotide polymorphism datasets from 38 hybrid progeny.We detect 1021 crossover(CO)events(35.8 per meiosis),corresponding to an overall CO rate of 9.9 cM/Mb.However,gene conversion by non-crossover is rare(1.03 per meiosis)and not biased towards G or C alleles.Consistent with the reported roles of SC in CO interference,we find no obvious sign of CO interference.CO tends to occur within germ-soma common genomic regions and many of the 44 identified CO hotspots localize at the centromeric or subtelomeric regions.Gene ontology analyses show that CO hotspots are strongly associated with genes responding to environmental changes.We discuss these results with respect to how nuclear dimorphism has potentially driven the formation of the observed recombination landscape to facilitate environmental adaptation and the sharing of machinery among meiotic and somatic recombination.
文摘Single unmanned aerial vehicle(UAV)multitasking plays an important role in multiple UAVs cooperative control,which is as well as the most complicated and hardest part.This paper establishes a threedimensional topographical map,and an improved adaptive differential evolution(IADE)algorithm is proposed for single UAV multitasking.As an optimized problem,the efficiency of using standard differential evolution to obtain the global optimal solution is very low to avoid this problem.Therefore,the algorithm adopts the mutation factor and crossover factor into dynamic adaptive functions,which makes the crossover factor and variation factor can be adjusted with the number of population iteration and individual fitness value,letting the algorithm exploration and development more reasonable.The experimental results implicate that the IADE algorithm has better performance,higher convergence and efficiency to solve the multitasking problem compared with other algorithms.
基金supported by the National Natural Science Foundation of China(NSFC,Grant Nos.31370395 and 31500266)the"One Hundred Talents"project of the Chinese Academy of Sciences(Grant No.29Y127E71)
文摘In the field of phylogenetic analyses, the rbcL gene encoded large subunit Ribulose-1,5-biphosphate carboxylase/oxygenase （Rubisco, EC4.1.1.39）, which plays a crucial role in the process of photosynthesis for most terrestrial plants, has been considered to be conserved; however, recent controversy regarding rbcL conservation has appeared since it was proposed to be under natural selection within all principal lineages of land plants. In this study, by examining the variation of DNA and protein sequences among 17 species in the family Tamaricaceae, three nonsynonymous mutations were identified to be under positive selection. The favored sites were located in the alph-helix domains of Rubisco, with decreased hydrophobicity and increased entropy, which could facilitate C〇 2 penetration into the active site of Rubisco. We also found that the expression level of rbcL in different genotypes of Reaumuria soongarica shifted in response to various stresses such as drought, temperature, salt, and light. This study not only sheds light on the functional/structural features of Rubisco in the evolution scenarios from 〇 3-like into C4 in Tamaricaceae but also provides useful information on directing genetic performance to enhance photosynthesis efficiency of desert plants for sustaining fragile desert ecosystems; fur-thermore, it promotes the ability to cope with desert aridification and global warming.
基金supported by National Natural Science Foundation of China under Grant Nos.52005447,72271222,71371170,71871203,L1924063Zhejiang Provincial Natural Science Foundation of China underGrant No.LQ21E050014Foundation of Zhejiang Education Committee under Grant No.Y201840056.
文摘Effective constrained optimization algorithms have been proposed for engineering problems recently.It is common to consider constraint violation and optimization algorithm as two separate parts.In this study,a pbest selection mechanism is proposed to integrate the current mutation strategy in constrained optimization problems.Based on the improved pbest selection method,an adaptive differential evolution approach is proposed,which helps the population jump out of the infeasible region.If all the individuals are infeasible,the top 5%of infeasible individuals are selected.In addition,a modified truncatedε-level method is proposed to avoid trapping in infeasible regions.The proposed adaptive differential evolution approach with an improvedεconstraint processmechanism(IεJADE)is examined on CEC 2006 and CEC 2010 constrained benchmark function series.Besides,a standard IEEE-30 bus test system is studied on the efficiency of the IεJADE.The numerical analysis verifies the IεJADE algorithm is effective in comparisonwith other effective algorithms.
