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
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
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
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
Ulvophytes are attractive model systems for understanding the evolution of growth,development,and environmental stress responses.They are untapped resources for food,fuel,and high-value compounds.The rapid and abundan...Ulvophytes are attractive model systems for understanding the evolution of growth,development,and environmental stress responses.They are untapped resources for food,fuel,and high-value compounds.The rapid and abundant growth of Ulva species makes them key contributors to coastal biogeochemical cycles,which can cause significant environmental problems in the form of green tides and biofouling.Until now,the Ulva mutabilis genome is the only Ulva genome to have been sequenced.To obtain further insights into the evolutionary forces driving divergence in Ulva species,we analyzed 3905 single copy ortholog family from U.mutabilis,Chlamydomonas reinhardtii and Volvox carteri to identify genes under positive selection(GUPS)in U.mutabilis.We detected 63 orthologs in U.mutabilis that were considered to be under positive selection.Functional analyses revealed that several adaptive modifications in photosynthesis,amino acid and protein synthesis,signal transduction and stress-related processes might explain why this alga has evolved the ability to grow very rapidly and cope with the variable coastal ecosystem environments.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
Pacific white shrimp has become a major aquaculture and fishery species worldwide.Although a large scale EST resource has been publicly available since 2008,the data have not yet been widely used for SNP discovery or ...Pacific white shrimp has become a major aquaculture and fishery species worldwide.Although a large scale EST resource has been publicly available since 2008,the data have not yet been widely used for SNP discovery or transcriptome-wide assessment of selective pressure.In this study,a set of 155 411 expressed sequence tags(ESTs) from the NCBI database were computationally analyzed and 17 225 single nucleotide polymorphisms(SNPs) were predicted,including 9 546 transitions,5 124 transversions and 2 481 indels.Among the 7 298 SNP substitutions located in functionally annotated contigs,58.4%(4 262) are non-synonymous SNPs capable of introducing amino acid mutations.Two hundred and fifty nonsynonymous SNPs in genes associated with economic traits have been identified as candidates for markers in selective breeding.Diversity estimates among the synonymous nucleotides were on average 3.49 times greater than those in non-synonymous,suggesting negative selection.Distribution of non-synonymous to synonymous substitutions(Ka/Ks) ratio ranges from 0 to 4.01,(average 0.42,median 0.26),suggesting that the majority of the affected genes are under purifying selection.Enrichment analysis identified multiple gene ontology categories under positive or negative selection.Categories involved in innate immune response and male gamete generation are rich in positively selected genes,which is similar to reports in Drosophila and primates.This work is the first transcriptome-wide assessment of selective pressure in a Penaeid shrimp species.The functionally annotated SNPs provide a valuable resource of potential molecular markers for selective breeding.展开更多
Cloud computing, a recently emerged paradigm faces major challenges in achieving the privacy of migrated data, network security, etc. Too many cryptographic technologies are raised to solve these issues based on ident...Cloud computing, a recently emerged paradigm faces major challenges in achieving the privacy of migrated data, network security, etc. Too many cryptographic technologies are raised to solve these issues based on identity, attributes and prediction algorithms yet;these techniques are highly prone to attackers. This would raise a need of an effective encryption technique, which would ensure secure data migration. With this scenario, our proposed methodology Efficient Probabilistic Public Key Encryption(EPPKE) is optimized with Covariance Matrix Adaptation Evolution Strategies(CMA-ES). It ensures data integrity through the Luhn algorithm with BLAKE 2b encapsulation. This enables an optimized security to the data which is migrated through cloud. The proposed methodology is implemented in Open Stack with Java Language. It achieves better results by providing security compared to other existing techniques like RSA, IBA, ABE, PBE, etc.展开更多
To address the problem of network security situation assessment in the Industrial Internet,this paper adopts the evidential reasoning(ER)algorithm and belief rule base(BRB)method to establish an assessment model.First...To address the problem of network security situation assessment in the Industrial Internet,this paper adopts the evidential reasoning(ER)algorithm and belief rule base(BRB)method to establish an assessment model.First,this paper analyzes the influencing factors of the Industrial Internet and selects evaluation indicators that contain not only quantitative data but also qualitative knowledge.Second,the evaluation indicators are fused with expert knowledge and the ER algorithm.According to the fusion results,a network security situation assessment model of the Industrial Internet based on the ER and BRB method is established,and the projection covariance matrix adaptive evolution strategy(P-CMA-ES)is used to optimize the model parameters.This method can not only utilize semiquantitative information effectively but also use more uncertain information and prevent the problem of combinatorial explosion.Moreover,it solves the problem of the uncertainty of expert knowledge and overcomes the problem of low modeling accuracy caused by insufficient data.Finally,a network security situation assessment case of the Industrial Internet is analyzed to verify the effectiveness and superiority of the method.The research results showthat this method has strong applicability to the network security situation assessment of complex Industrial Internet systems.It can accurately reflect the actual network security situation of Industrial Internet systems and provide safe and reliable suggestions for network administrators to take timely countermeasures,thereby improving the risk monitoring and emergency response capabilities of the Industrial Internet.展开更多
The advanced optimization method named as adaptive range differential evolution (ARDE) is developed. The optimization performance of ARDE is demonstrated using a typical mathematical test and compared with the stand...The advanced optimization method named as adaptive range differential evolution (ARDE) is developed. The optimization performance of ARDE is demonstrated using a typical mathematical test and compared with the standard genetic algorithm and differential evolution. Combined with parallel ARDE, surface modeling method and Navier-Stokes solution, a new automatic aerodynamic optimization method is presented. A low aspect ratio transonic turbine stage is optimized for the maximization of the isentropic efficiency with forty-one design variables in total. The coarse-grained parallel strategy is applied to accelerate the design process using 15 CPUs. The isentropic efficiency of the optimum design is 1.6% higher than that of the reference design. The aerodynamic performance of the optimal design is much better than that of the reference design.展开更多
Pangolins(Pholidota,Manidae)are classified as an evolutionarily distinct and globally endangered mammal due to their unique morphology(nail-like scales and a myrmecophagous diet)and being the victim of heavy poaching ...Pangolins(Pholidota,Manidae)are classified as an evolutionarily distinct and globally endangered mammal due to their unique morphology(nail-like scales and a myrmecophagous diet)and being the victim of heavy poaching and worldwide trafficking.As such,pangolins serve as a textbook example for studying the special phenotypic evolutionary adaptations and conservation genetics of an endangered species.Recent years have demonstrated significant advancements in the fields of molecular genetics and genomics,which have translated to a series of important research achievements and breakthroughs concerning the evolution and conservation genetics of pangolins.This review comprehensively presents the hitherto advances in phylogeny,adaptive evolution,conservation genetics,and conservation genomics that are related to pangolins,which will provide an ample understanding of their diversity,molecular adaptation mechanisms,and evolutionary potentials.In addition,we highlight the priority of investigating species/population diversity among pangolins and suggest several avenues of research that are highly relevant for future pangolin conservation.展开更多
Toll-like receptors(TLRs),the key sensor molecules in vertebrates,trigger the innate immunity and prime the adaptive immune system.The TLR family of rodents,the largest order of mammals,typically contains 13 TLR genes...Toll-like receptors(TLRs),the key sensor molecules in vertebrates,trigger the innate immunity and prime the adaptive immune system.The TLR family of rodents,the largest order of mammals,typically contains 13 TLR genes.However,a clear picture of the evolution of the rodent TLR family has not yet emerged and the TLR evolutionary patterns are unclear in rodent clades.Here,we analyzed the natural variation and the evolutionary processes acting on the TLR family in rodents at both the interspecific and population levels.Our results showed that rodent TLRs were dominated by purifying selection,but a series of positively selected sites(PSSs)primarily located in the ligand-binding domain was also identified.The numbers of PSSs differed among TLRs,and nonviralsensing TLRs had more PSSs than those in viral-sensing TLRs.Gene-conversion events were found between TLR1 and TLR6 in most rodent species.Population genetic analyses showed that TLR2,TLR8,and TLR12 were under positive selection in Rattus norvegicus and R.tanezumi,whereas positive selection also acted on TLR5 and TLR9 in the former species,as well as TLR1 and TLR7 in the latter species.Moreover,we found that the proportion of polymorphisms with potentially functional change was much lower in viral-sensing TLRs than in nonviral-sensing TLRs in both of these rat species.Our findings revealed the first thorough insight into the evolution of the rodent TLR genetic variability and provided important novel insights into the evolutionary history of TLRs over long and short timescales.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
Native animals are facing long-term coexistence with invasive plants worldwide,the impacts of which on animal behavior remain poorly known.Potential ecological traps could threaten native birds breeding in invasive pl...Native animals are facing long-term coexistence with invasive plants worldwide,the impacts of which on animal behavior remain poorly known.Potential ecological traps could threaten native birds breeding in invasive plant habitats,but behavioral strategies for birds to avoid such risks are few concerned.The invasion of Smooth Cordgrass(Spartina alterniflra) has seriously varied the vegetation landscape in the coastal wetlands of eastern China,and affected the habitat selection of native birds.Here,we investigated the nesting and breeding characteristics of a common native passerine,the Vinous-throated Parrotbill(Sinosuthora webbiana),in habitats dominated by native Common Reed(Phragmites australis) and exotic cordgrass.We found that parrotbills could complete their breeding cycle in cordgrass habitat.Most nest failure was attributed to predation in native habitat but tide inundation in cordgrass habitat.However,the nest success rate and daily survival rate(DSR) in cordgrass habitat were higher.Moreover,nest height was markedly higher in cordgrass habitat and was the most important influencing variable(positively correlated with the DSR).These results suggest that cordgrass habitat is a potential ecological trap due to the tide inundation,but some parrotbills seem to effectively avoid this risk by increasing nest height.Our study reveals that a native passerine changes its nesting behavior to accommodate invasive plant habitat and highlights that habitat changes caused by invasive plants may drive the adaptive evolution of native animal behavior.The limitation of these results must be acknowledged for the small sample size,and there is a need for a larger sample and long-term data for further verification.展开更多
Higher levels of acetaldehyde in beer are one of the major concerns in the current beer industry.Yeast produces acetaldehyde during alcoholic fermentation,and its modification significantly affects beer flavor and qua...Higher levels of acetaldehyde in beer are one of the major concerns in the current beer industry.Yeast produces acetaldehyde during alcoholic fermentation,and its modification significantly affects beer flavor and quality.A different mutant strain with lower acetaldehyde production and improved ethanol tolerance was constructed using the ARTP-ALE mutagenesis strategy with 4-methylpyrazole-disulfiram.As a result of the mutation,the alcohol dehydrogenase activity of the mutant strain decreased to about 71.22%of that of the wild-type strain.At the same time,the fermentation properties and genetic stability of the newly screened strain showed slight differences from the wild-type strain,and there were no safety concerns regarding industrial use of the mutant strain.展开更多
Selecting design variables and determining optimal hard⁃point coordinates are subjective in the traditional multiobjective optimization of geometric design of vehicle suspension,thereby usually resulting in poor overa...Selecting design variables and determining optimal hard⁃point coordinates are subjective in the traditional multiobjective optimization of geometric design of vehicle suspension,thereby usually resulting in poor overall suspension kinematic performance.To eliminate the subjectivity of selection,a method transferring multiobjective optimization function into a single⁃objective one through the integrated use of grey relational analysis(GRA)and improved entropy weight method(IEWM)is proposed.First,a comprehensive evaluation index of sensitivities was formulated to facilitate the objective selection of design variables by using GRA,in which IEWM was used to determine the weight of each subindex.Second,approximate models between the variations of the front wheel alignment parameters and the design variables were developed on the basis of support vector regression(SVR)and the fruit fly optimization algorithm(FOA).Subsequently,to eliminate the subjectivity and improve the computational efficiency of multiobjective optimization(MOO)of hard⁃point coordinates,the MOO functions were transformed into a single⁃objective optimization(SOO)function by using the GRA-IEWM method again.Finally,the SOO problem was solved by the self⁃adaptive differential evolution(jDE)algorithm.Simulation results indicate that the GRA⁃IEWM method outperforms the traditional multiobjective optimization method and the original coordinate scheme remarkably in terms of kinematic performance.展开更多
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.
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.
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.
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Foundation item:The National Key Research and Development Program of China under contract No.2016YFC1402102the Central Public-interest Scientific Institution Basal Research Fund,CAFS under contract Nos 2020TD19 and 2020TD27+3 种基金the Major Scientific and Technological Innovation Project of Shandong Provincial Key Research and Development Program under contract No.2019JZZY020706the National Natural Science Foundation of China under contract No.31770393the Earmarked Fund for China Agriculture Research System under contract No.CARS-50the Taishan Scholars Funding of Shandong Province.
文摘Ulvophytes are attractive model systems for understanding the evolution of growth,development,and environmental stress responses.They are untapped resources for food,fuel,and high-value compounds.The rapid and abundant growth of Ulva species makes them key contributors to coastal biogeochemical cycles,which can cause significant environmental problems in the form of green tides and biofouling.Until now,the Ulva mutabilis genome is the only Ulva genome to have been sequenced.To obtain further insights into the evolutionary forces driving divergence in Ulva species,we analyzed 3905 single copy ortholog family from U.mutabilis,Chlamydomonas reinhardtii and Volvox carteri to identify genes under positive selection(GUPS)in U.mutabilis.We detected 63 orthologs in U.mutabilis that were considered to be under positive selection.Functional analyses revealed that several adaptive modifications in photosynthesis,amino acid and protein synthesis,signal transduction and stress-related processes might explain why this alga has evolved the ability to grow very rapidly and cope with the variable coastal ecosystem environments.
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 Key Program of National Natural Science Foundation of China (No.30730071)the National High Technology R&D Program of China(863 Program)(No.2012AA10A404)the Agricultural Science and Technology Achievements Transformation Funds Project(No.2010GB24910700)
文摘Pacific white shrimp has become a major aquaculture and fishery species worldwide.Although a large scale EST resource has been publicly available since 2008,the data have not yet been widely used for SNP discovery or transcriptome-wide assessment of selective pressure.In this study,a set of 155 411 expressed sequence tags(ESTs) from the NCBI database were computationally analyzed and 17 225 single nucleotide polymorphisms(SNPs) were predicted,including 9 546 transitions,5 124 transversions and 2 481 indels.Among the 7 298 SNP substitutions located in functionally annotated contigs,58.4%(4 262) are non-synonymous SNPs capable of introducing amino acid mutations.Two hundred and fifty nonsynonymous SNPs in genes associated with economic traits have been identified as candidates for markers in selective breeding.Diversity estimates among the synonymous nucleotides were on average 3.49 times greater than those in non-synonymous,suggesting negative selection.Distribution of non-synonymous to synonymous substitutions(Ka/Ks) ratio ranges from 0 to 4.01,(average 0.42,median 0.26),suggesting that the majority of the affected genes are under purifying selection.Enrichment analysis identified multiple gene ontology categories under positive or negative selection.Categories involved in innate immune response and male gamete generation are rich in positively selected genes,which is similar to reports in Drosophila and primates.This work is the first transcriptome-wide assessment of selective pressure in a Penaeid shrimp species.The functionally annotated SNPs provide a valuable resource of potential molecular markers for selective breeding.
文摘Cloud computing, a recently emerged paradigm faces major challenges in achieving the privacy of migrated data, network security, etc. Too many cryptographic technologies are raised to solve these issues based on identity, attributes and prediction algorithms yet;these techniques are highly prone to attackers. This would raise a need of an effective encryption technique, which would ensure secure data migration. With this scenario, our proposed methodology Efficient Probabilistic Public Key Encryption(EPPKE) is optimized with Covariance Matrix Adaptation Evolution Strategies(CMA-ES). It ensures data integrity through the Luhn algorithm with BLAKE 2b encapsulation. This enables an optimized security to the data which is migrated through cloud. The proposed methodology is implemented in Open Stack with Java Language. It achieves better results by providing security compared to other existing techniques like RSA, IBA, ABE, PBE, etc.
基金supported by the Provincial Universities Basic Business Expense Scientific Research Projects of Heilongjiang Province(No.2021-KYYWF-0179)the Science and Technology Project of Henan Province(No.212102310991)+2 种基金the Opening Project of Shanghai Key Laboratory of Integrated Administration Technologies for Information Security(No.AGK2015003)the Key Scientific Research Project of Henan Province(No.21A413001)the Postgraduate Innovation Project of Harbin Normal University(No.HSDSSCX2021-121).
文摘To address the problem of network security situation assessment in the Industrial Internet,this paper adopts the evidential reasoning(ER)algorithm and belief rule base(BRB)method to establish an assessment model.First,this paper analyzes the influencing factors of the Industrial Internet and selects evaluation indicators that contain not only quantitative data but also qualitative knowledge.Second,the evaluation indicators are fused with expert knowledge and the ER algorithm.According to the fusion results,a network security situation assessment model of the Industrial Internet based on the ER and BRB method is established,and the projection covariance matrix adaptive evolution strategy(P-CMA-ES)is used to optimize the model parameters.This method can not only utilize semiquantitative information effectively but also use more uncertain information and prevent the problem of combinatorial explosion.Moreover,it solves the problem of the uncertainty of expert knowledge and overcomes the problem of low modeling accuracy caused by insufficient data.Finally,a network security situation assessment case of the Industrial Internet is analyzed to verify the effectiveness and superiority of the method.The research results showthat this method has strong applicability to the network security situation assessment of complex Industrial Internet systems.It can accurately reflect the actual network security situation of Industrial Internet systems and provide safe and reliable suggestions for network administrators to take timely countermeasures,thereby improving the risk monitoring and emergency response capabilities of the Industrial Internet.
基金This project is supported by Advanced Propulsion Technologies Demonstration Program of Commission of Science Technology and Industry for National Defense of China(No.APTD-0602-04).
文摘The advanced optimization method named as adaptive range differential evolution (ARDE) is developed. The optimization performance of ARDE is demonstrated using a typical mathematical test and compared with the standard genetic algorithm and differential evolution. Combined with parallel ARDE, surface modeling method and Navier-Stokes solution, a new automatic aerodynamic optimization method is presented. A low aspect ratio transonic turbine stage is optimized for the maximization of the isentropic efficiency with forty-one design variables in total. The coarse-grained parallel strategy is applied to accelerate the design process using 15 CPUs. The isentropic efficiency of the optimum design is 1.6% higher than that of the reference design. The aerodynamic performance of the optimal design is much better than that of the reference design.
文摘Pangolins(Pholidota,Manidae)are classified as an evolutionarily distinct and globally endangered mammal due to their unique morphology(nail-like scales and a myrmecophagous diet)and being the victim of heavy poaching and worldwide trafficking.As such,pangolins serve as a textbook example for studying the special phenotypic evolutionary adaptations and conservation genetics of an endangered species.Recent years have demonstrated significant advancements in the fields of molecular genetics and genomics,which have translated to a series of important research achievements and breakthroughs concerning the evolution and conservation genetics of pangolins.This review comprehensively presents the hitherto advances in phylogeny,adaptive evolution,conservation genetics,and conservation genomics that are related to pangolins,which will provide an ample understanding of their diversity,molecular adaptation mechanisms,and evolutionary potentials.In addition,we highlight the priority of investigating species/population diversity among pangolins and suggest several avenues of research that are highly relevant for future pangolin conservation.
基金supported by the Major Program of National Natural Science Foundation of China(32090023)the National Key R&D Program of China(2022YFC2601602)Hunan Provincial Natural Science Foundation of China(2023JJ41038).
文摘Toll-like receptors(TLRs),the key sensor molecules in vertebrates,trigger the innate immunity and prime the adaptive immune system.The TLR family of rodents,the largest order of mammals,typically contains 13 TLR genes.However,a clear picture of the evolution of the rodent TLR family has not yet emerged and the TLR evolutionary patterns are unclear in rodent clades.Here,we analyzed the natural variation and the evolutionary processes acting on the TLR family in rodents at both the interspecific and population levels.Our results showed that rodent TLRs were dominated by purifying selection,but a series of positively selected sites(PSSs)primarily located in the ligand-binding domain was also identified.The numbers of PSSs differed among TLRs,and nonviralsensing TLRs had more PSSs than those in viral-sensing TLRs.Gene-conversion events were found between TLR1 and TLR6 in most rodent species.Population genetic analyses showed that TLR2,TLR8,and TLR12 were under positive selection in Rattus norvegicus and R.tanezumi,whereas positive selection also acted on TLR5 and TLR9 in the former species,as well as TLR1 and TLR7 in the latter species.Moreover,we found that the proportion of polymorphisms with potentially functional change was much lower in viral-sensing TLRs than in nonviral-sensing TLRs in both of these rat species.Our findings revealed the first thorough insight into the evolution of the rodent TLR genetic variability and provided important novel insights into the evolutionary history of TLRs over long and short timescales.
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the National Natural Science Foundation of China(32171526,32201267)Natural Science Foundation of Anhui Province(2208085QC71)the Key University Science Research Project of Anhui Province(KJ2020A0085,KJ2021A0128).
文摘Native animals are facing long-term coexistence with invasive plants worldwide,the impacts of which on animal behavior remain poorly known.Potential ecological traps could threaten native birds breeding in invasive plant habitats,but behavioral strategies for birds to avoid such risks are few concerned.The invasion of Smooth Cordgrass(Spartina alterniflra) has seriously varied the vegetation landscape in the coastal wetlands of eastern China,and affected the habitat selection of native birds.Here,we investigated the nesting and breeding characteristics of a common native passerine,the Vinous-throated Parrotbill(Sinosuthora webbiana),in habitats dominated by native Common Reed(Phragmites australis) and exotic cordgrass.We found that parrotbills could complete their breeding cycle in cordgrass habitat.Most nest failure was attributed to predation in native habitat but tide inundation in cordgrass habitat.However,the nest success rate and daily survival rate(DSR) in cordgrass habitat were higher.Moreover,nest height was markedly higher in cordgrass habitat and was the most important influencing variable(positively correlated with the DSR).These results suggest that cordgrass habitat is a potential ecological trap due to the tide inundation,but some parrotbills seem to effectively avoid this risk by increasing nest height.Our study reveals that a native passerine changes its nesting behavior to accommodate invasive plant habitat and highlights that habitat changes caused by invasive plants may drive the adaptive evolution of native animal behavior.The limitation of these results must be acknowledged for the small sample size,and there is a need for a larger sample and long-term data for further verification.
基金Supported by Heilongjiang Natural Science Foundation Joint Guide Project(LH2019C022)。
文摘Higher levels of acetaldehyde in beer are one of the major concerns in the current beer industry.Yeast produces acetaldehyde during alcoholic fermentation,and its modification significantly affects beer flavor and quality.A different mutant strain with lower acetaldehyde production and improved ethanol tolerance was constructed using the ARTP-ALE mutagenesis strategy with 4-methylpyrazole-disulfiram.As a result of the mutation,the alcohol dehydrogenase activity of the mutant strain decreased to about 71.22%of that of the wild-type strain.At the same time,the fermentation properties and genetic stability of the newly screened strain showed slight differences from the wild-type strain,and there were no safety concerns regarding industrial use of the mutant strain.
基金Sponsored by the National Natural Science Foundation of China(Grant No.71871078).
文摘Selecting design variables and determining optimal hard⁃point coordinates are subjective in the traditional multiobjective optimization of geometric design of vehicle suspension,thereby usually resulting in poor overall suspension kinematic performance.To eliminate the subjectivity of selection,a method transferring multiobjective optimization function into a single⁃objective one through the integrated use of grey relational analysis(GRA)and improved entropy weight method(IEWM)is proposed.First,a comprehensive evaluation index of sensitivities was formulated to facilitate the objective selection of design variables by using GRA,in which IEWM was used to determine the weight of each subindex.Second,approximate models between the variations of the front wheel alignment parameters and the design variables were developed on the basis of support vector regression(SVR)and the fruit fly optimization algorithm(FOA).Subsequently,to eliminate the subjectivity and improve the computational efficiency of multiobjective optimization(MOO)of hard⁃point coordinates,the MOO functions were transformed into a single⁃objective optimization(SOO)function by using the GRA-IEWM method again.Finally,the SOO problem was solved by the self⁃adaptive differential evolution(jDE)algorithm.Simulation results indicate that the GRA⁃IEWM method outperforms the traditional multiobjective optimization method and the original coordinate scheme remarkably in terms of kinematic performance.