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
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
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
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
Photosynthetic cyanobacteria have shown great potential as“autotrophic cell factories”for the synthesis of fuels and chemicals.However,poor tolerance to various environmental stressors such as high light and heavy m...Photosynthetic cyanobacteria have shown great potential as“autotrophic cell factories”for the synthesis of fuels and chemicals.However,poor tolerance to various environmental stressors such as high light and heavy metals is an important factor limiting their economic viability.While numerous studies have focused on the tolerance mechanism of cyanobacteria to individual stressors,their response to simultaneous stresses remains to be recovered.To investigate the mechanism of cross tolerance to heavymetal Cd^(2+) and high light,the model cyanobacterium Synechocystis sp.PCC 6803 tolerant to both Cd^(2+) and high light was obtained via about 800 days’cross-adaptive laboratory evolution.Three evolutionary strains capable of tolerating both 5.5 μmol·L^(-1) Cd^(2+) and 600 μmol·m^(-2)·s^(-1) high light were successfully obtained,achieving about 83%enhancement of Cd^(2+) tolerance compared with the parent strain.The different response of parent and evolutionary strains to Cd^(2+) was elucidated via metabolomics.Furthermore,a total of 15 genes that were mutated during evolution were identified by whole-genome re-sequencing.Finally,by single-gene knockout and complementation analysis,four genes including ssl2615,sll1732,ssr1480,and sll1659 involved in the improvement of Cd^(2+) tolerance under high-light condition were successfully identified.This work explored the tolerance mechanism of Synechocystis sp.PCC 6803 to cadmium under high-light condition and provided valuable reference for deciphering multitolerance mechanism of cyanobacteria in the future.展开更多
Concentrate copper grade(CCG)is one of the important production indicators of copper flotation processes,and keeping the CCG at the set value is of great significance to the economic benefit of copper flotation indust...Concentrate copper grade(CCG)is one of the important production indicators of copper flotation processes,and keeping the CCG at the set value is of great significance to the economic benefit of copper flotation industrial processes.This paper addresses the fluctuation problem of CCG through an operational optimization method.Firstly,a density-based affinity propagationalgorithm is proposed so that more ideal working condition categories can be obtained for the complex raw ore properties.Next,a Bayesian network(BN)is applied to explore the relationship between the operational variables and the CCG.Based on the analysis results of BN,a weighted Gaussian process regression model is constructed to predict the CCG that a higher prediction accuracy can be obtained.To ensure the predicted CCG is close to the set value with a smaller magnitude of the operation adjustments and a smaller uncertainty of the prediction results,an index-oriented adaptive differential evolution(IOADE)algorithm is proposed,and the convergence performance of IOADE is superior to the traditional differential evolution and adaptive differential evolution methods.Finally,the effectiveness and feasibility of the proposed methods are verified by the experiments on a copper flotation industrial process.展开更多
Escherichia coli MLB(MG1655ΔpflBΔldhA),which can hardly grow on glucose with little succinate accumulation under anaerobic conditions.Two-stage fermentation is a fermentation in which the first stage is used for cel...Escherichia coli MLB(MG1655ΔpflBΔldhA),which can hardly grow on glucose with little succinate accumulation under anaerobic conditions.Two-stage fermentation is a fermentation in which the first stage is used for cell growth and the second stage is used for product production.The ability of glucose consumption and succinate production of MLB under anaerobic conditions can be improved significantly by using acetate as the solo carbon source under aerobic condition during the two-stage fermentation.Then,the adaptive laboratory evolution(ALE)of growing on acetate was applied here.We assumed that the activities of succinate production related enzymes might be further improved in this study.E.coli MLB46-05 evolved from MLB and it had an improved growth phenotype on acetate.Interestingly,in MLB46-05,the yield and tolerance of succinic acid in the anaerobic condition of two-stage fermentation were improved significantly.According to transcriptome analysis,upregulation of the glyoxylate cycle and the activity of stress regulatory factors are the possible reasons for the elevated yield.And the increased tolerance to acetate made it more tolerant to high concentrations of glucose and succinate.Finally,strain MLB46-05 produced 111 g/L of succinic acid with a product yield of 0.74 g/g glucose.展开更多
[Objective]To construct an Escherichia coli mutant strain that accumulates pyruvate by genetic modification guided by the genome-scale metabolic network model.[Methods]Using a genome-scale metabolic network model as a...[Objective]To construct an Escherichia coli mutant strain that accumulates pyruvate by genetic modification guided by the genome-scale metabolic network model.[Methods]Using a genome-scale metabolic network model as a guide,we simulated pyruvate production of E.coli,screened key genes in metabolic pathways,and developed gene editing procedures accordingly.We knocked out the acetate kinase gene ackA,phosphate acetyltransferase gene pta,alcohol dehydrogenase adhE,glycogen synthase gene glgA,glycogen phosphorylase gene glgP,phosphoribosyl pyrophosphate(PRPP)synthase gene prs,ribose 1,5-bisphosphate phosphokinase gene phnN,and transporter encoding gene proP.Furthermore,we knocked in the transporter encoding gene ompC,flavonoid toxin gene fldA,and D-serine ammonia lyase gene dsdA.[Results]A shake flask process with the genetically edited mutant strain MG1655-6-2 under anaerobic conditions produced pyruvate at a titer of 10.46 g/L and a yield of 0.69 g/g.Metabolomic analysis revealed a significant increase in the pyruvate level in the fermentation broth,accompanied by notable decreases in the levels of certain related metabolic byproducts.Through 5 L fed-batch fermentation and an adaptive laboratory evolution,the strain finally achieved a pyruvate titer of 45.86 g/L.[Conclusion]This study illustrated the efficacy of a gene editing strategy predicted by a genome-scale metabolic network model in enhancing pyruvate accumulation in E.coli under anaerobic conditions and provided novel insights for microbial metabolic engineering.展开更多
Despite most eel gobies(Gobionellidae:Amblyopinae)have inhabited brackish or marine waters,few species(such as Taenioides sp.)have been found to invade multiple inland freshwaters via artificial water transfer project...Despite most eel gobies(Gobionellidae:Amblyopinae)have inhabited brackish or marine waters,few species(such as Taenioides sp.)have been found to invade multiple inland freshwaters via artificial water transfer projects.The habitat transfers from brackish water to freshwater zones of Taenioides sp.have caused severe damage to Chinese aquatic ecosystems in recent years.Unfortunately,the molecular mechanism underlying freshwater invasion remains poorly understood.Considering changes of environmental factors,especially salinity,are bound to adjust the demands for energy affected by mitochondria via oxidative phosphorylation,13 Amblyopinae mitogenomes were compared,including the newly assembled Taenioides sp.mitogenome in this study.Comparative mitogenomic analyses revealed a highly conserved structure,composition and arrangements,with the exception of variable control region(CR).All of the CRs possessed tandem repeat sequences except Trypauchenopsis sp.G341,differing in motifs and number of copies,which was the dominant factor resulting in length heterogeneity of CR.The phylogenetic trees reconfirmed the paraphyletic origin of Amblyopinae with respect to Oxudercinae,supporting that these two subfamilies should be merged as an expansion of phenotypic variation within the“terrestrial goby”clade.Furthermore,four protein coding genes(COI,ND3,ND5 and Cyt b)in Taenioides sp.mitogenome have experienced adaptive evolution,indicating their important roles in enhancing the efficiency of ATP production to cope with the osmotic regulation adjustment and reach its current widespread distribution in multiple inland freshwaters of China.These results revealed the functional importance of mitochondrial genes,and provided fresh insights into the molecular mechanisms underlying the freshwater invasion.Also,our results may provide critical reference value for the future control of other invasive species.展开更多
Some of the most interesting areas in aerospace science and technologies are on either higher,faster,and larger systems or lower,slower,and smaller flying capabilities.In this paper,we present our perspectives on the ...Some of the most interesting areas in aerospace science and technologies are on either higher,faster,and larger systems or lower,slower,and smaller flying capabilities.In this paper,we present our perspectives on the aerodynamics related to small,fixed-wing as well as flapping-wing flight vehicles.From an evolutionary viewpoint,flyers have gone through many iterations,adaptations,and optimizations to balance their biological functions,including flight.In the low-Reynolds-number regime,the aerodynamic characteristics around a solid object differ from those observed at the scale of passenger-airplanes.Consequently,the optimal airfoil and wing shapes vary with vehicle size.As vehicle dimensions vary,non-proportional scaling between surface areas and weight shifts the dominance of physical mechanisms,leading to distinct operational parameters and technical requirements.With smaller flight vehicles,structural flexibility as well as anisotropic material properties become more pronounced,which causes qualitative changes in aerodynamics.The flapping motion of the wings,the interactions between wings,the synergistic characteristics of wing and tail,and the development of soft structures for better agility and flight performance are discussed.Low-Reynolds-number aerodynamics require collaborative innovation to optimize shape,motion,and structure of vehicles in accordance with the scaling laws.Together,progress on these fronts is reshaping the design paradigm of air vehicles and other types of robots with shrinking physical dimensions and more versatile capabilities to meet wider ranges of missions.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
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(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
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
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 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 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.
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 grants from the National Key Research and Development Programof China(2018YFA0903600)well as the National Natural Science Foundation of China(32371486 and 32270091).
文摘Photosynthetic cyanobacteria have shown great potential as“autotrophic cell factories”for the synthesis of fuels and chemicals.However,poor tolerance to various environmental stressors such as high light and heavy metals is an important factor limiting their economic viability.While numerous studies have focused on the tolerance mechanism of cyanobacteria to individual stressors,their response to simultaneous stresses remains to be recovered.To investigate the mechanism of cross tolerance to heavymetal Cd^(2+) and high light,the model cyanobacterium Synechocystis sp.PCC 6803 tolerant to both Cd^(2+) and high light was obtained via about 800 days’cross-adaptive laboratory evolution.Three evolutionary strains capable of tolerating both 5.5 μmol·L^(-1) Cd^(2+) and 600 μmol·m^(-2)·s^(-1) high light were successfully obtained,achieving about 83%enhancement of Cd^(2+) tolerance compared with the parent strain.The different response of parent and evolutionary strains to Cd^(2+) was elucidated via metabolomics.Furthermore,a total of 15 genes that were mutated during evolution were identified by whole-genome re-sequencing.Finally,by single-gene knockout and complementation analysis,four genes including ssl2615,sll1732,ssr1480,and sll1659 involved in the improvement of Cd^(2+) tolerance under high-light condition were successfully identified.This work explored the tolerance mechanism of Synechocystis sp.PCC 6803 to cadmium under high-light condition and provided valuable reference for deciphering multitolerance mechanism of cyanobacteria in the future.
基金supported in part by the National Key Research and Development Program of China(2021YFC2902703)the National Natural Science Foundation of China(62173078,61773105,61533007,61873049,61873053,61703085,61374147)。
文摘Concentrate copper grade(CCG)is one of the important production indicators of copper flotation processes,and keeping the CCG at the set value is of great significance to the economic benefit of copper flotation industrial processes.This paper addresses the fluctuation problem of CCG through an operational optimization method.Firstly,a density-based affinity propagationalgorithm is proposed so that more ideal working condition categories can be obtained for the complex raw ore properties.Next,a Bayesian network(BN)is applied to explore the relationship between the operational variables and the CCG.Based on the analysis results of BN,a weighted Gaussian process regression model is constructed to predict the CCG that a higher prediction accuracy can be obtained.To ensure the predicted CCG is close to the set value with a smaller magnitude of the operation adjustments and a smaller uncertainty of the prediction results,an index-oriented adaptive differential evolution(IOADE)algorithm is proposed,and the convergence performance of IOADE is superior to the traditional differential evolution and adaptive differential evolution methods.Finally,the effectiveness and feasibility of the proposed methods are verified by the experiments on a copper flotation industrial process.
基金supported by the National Key R&D Program of China(2021YFC2101300)Science and Technology Commission of Shanghai Municipality(21DZ1209100)Partially supported by Open Funding Project of the State Key Laboratory of Bioreactor Engineering.
文摘Escherichia coli MLB(MG1655ΔpflBΔldhA),which can hardly grow on glucose with little succinate accumulation under anaerobic conditions.Two-stage fermentation is a fermentation in which the first stage is used for cell growth and the second stage is used for product production.The ability of glucose consumption and succinate production of MLB under anaerobic conditions can be improved significantly by using acetate as the solo carbon source under aerobic condition during the two-stage fermentation.Then,the adaptive laboratory evolution(ALE)of growing on acetate was applied here.We assumed that the activities of succinate production related enzymes might be further improved in this study.E.coli MLB46-05 evolved from MLB and it had an improved growth phenotype on acetate.Interestingly,in MLB46-05,the yield and tolerance of succinic acid in the anaerobic condition of two-stage fermentation were improved significantly.According to transcriptome analysis,upregulation of the glyoxylate cycle and the activity of stress regulatory factors are the possible reasons for the elevated yield.And the increased tolerance to acetate made it more tolerant to high concentrations of glucose and succinate.Finally,strain MLB46-05 produced 111 g/L of succinic acid with a product yield of 0.74 g/g glucose.
基金supported by the Hebei Provincial Key Research and Development Project(21372803D)。
文摘[Objective]To construct an Escherichia coli mutant strain that accumulates pyruvate by genetic modification guided by the genome-scale metabolic network model.[Methods]Using a genome-scale metabolic network model as a guide,we simulated pyruvate production of E.coli,screened key genes in metabolic pathways,and developed gene editing procedures accordingly.We knocked out the acetate kinase gene ackA,phosphate acetyltransferase gene pta,alcohol dehydrogenase adhE,glycogen synthase gene glgA,glycogen phosphorylase gene glgP,phosphoribosyl pyrophosphate(PRPP)synthase gene prs,ribose 1,5-bisphosphate phosphokinase gene phnN,and transporter encoding gene proP.Furthermore,we knocked in the transporter encoding gene ompC,flavonoid toxin gene fldA,and D-serine ammonia lyase gene dsdA.[Results]A shake flask process with the genetically edited mutant strain MG1655-6-2 under anaerobic conditions produced pyruvate at a titer of 10.46 g/L and a yield of 0.69 g/g.Metabolomic analysis revealed a significant increase in the pyruvate level in the fermentation broth,accompanied by notable decreases in the levels of certain related metabolic byproducts.Through 5 L fed-batch fermentation and an adaptive laboratory evolution,the strain finally achieved a pyruvate titer of 45.86 g/L.[Conclusion]This study illustrated the efficacy of a gene editing strategy predicted by a genome-scale metabolic network model in enhancing pyruvate accumulation in E.coli under anaerobic conditions and provided novel insights for microbial metabolic engineering.
基金The National Natural Science Foundation of China under contract Nos 42171069 and 41976121.
文摘Despite most eel gobies(Gobionellidae:Amblyopinae)have inhabited brackish or marine waters,few species(such as Taenioides sp.)have been found to invade multiple inland freshwaters via artificial water transfer projects.The habitat transfers from brackish water to freshwater zones of Taenioides sp.have caused severe damage to Chinese aquatic ecosystems in recent years.Unfortunately,the molecular mechanism underlying freshwater invasion remains poorly understood.Considering changes of environmental factors,especially salinity,are bound to adjust the demands for energy affected by mitochondria via oxidative phosphorylation,13 Amblyopinae mitogenomes were compared,including the newly assembled Taenioides sp.mitogenome in this study.Comparative mitogenomic analyses revealed a highly conserved structure,composition and arrangements,with the exception of variable control region(CR).All of the CRs possessed tandem repeat sequences except Trypauchenopsis sp.G341,differing in motifs and number of copies,which was the dominant factor resulting in length heterogeneity of CR.The phylogenetic trees reconfirmed the paraphyletic origin of Amblyopinae with respect to Oxudercinae,supporting that these two subfamilies should be merged as an expansion of phenotypic variation within the“terrestrial goby”clade.Furthermore,four protein coding genes(COI,ND3,ND5 and Cyt b)in Taenioides sp.mitogenome have experienced adaptive evolution,indicating their important roles in enhancing the efficiency of ATP production to cope with the osmotic regulation adjustment and reach its current widespread distribution in multiple inland freshwaters of China.These results revealed the functional importance of mitochondrial genes,and provided fresh insights into the molecular mechanisms underlying the freshwater invasion.Also,our results may provide critical reference value for the future control of other invasive species.
基金supported by the Research Grants Council(RGC)of the Government of Hong Kong Special Administrative Region(HKSAR)with RGC/GRF Project(Grant Nos.16206321 and 14113824).
文摘Some of the most interesting areas in aerospace science and technologies are on either higher,faster,and larger systems or lower,slower,and smaller flying capabilities.In this paper,we present our perspectives on the aerodynamics related to small,fixed-wing as well as flapping-wing flight vehicles.From an evolutionary viewpoint,flyers have gone through many iterations,adaptations,and optimizations to balance their biological functions,including flight.In the low-Reynolds-number regime,the aerodynamic characteristics around a solid object differ from those observed at the scale of passenger-airplanes.Consequently,the optimal airfoil and wing shapes vary with vehicle size.As vehicle dimensions vary,non-proportional scaling between surface areas and weight shifts the dominance of physical mechanisms,leading to distinct operational parameters and technical requirements.With smaller flight vehicles,structural flexibility as well as anisotropic material properties become more pronounced,which causes qualitative changes in aerodynamics.The flapping motion of the wings,the interactions between wings,the synergistic characteristics of wing and tail,and the development of soft structures for better agility and flight performance are discussed.Low-Reynolds-number aerodynamics require collaborative innovation to optimize shape,motion,and structure of vehicles in accordance with the scaling laws.Together,progress on these fronts is reshaping the design paradigm of air vehicles and other types of robots with shrinking physical dimensions and more versatile capabilities to meet wider ranges of missions.
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 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.
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.
