Near-Earth objects are important not only in studying the early formation of the Solar System,but also because they pose a serious hazard to humanity when they make close approaches to the Earth.Study of their physica...Near-Earth objects are important not only in studying the early formation of the Solar System,but also because they pose a serious hazard to humanity when they make close approaches to the Earth.Study of their physical properties can provide useful information on their origin,evolution,and hazard to human beings.However,it remains challenging to investigate small,newly discovered,near-Earth objects because of our limited observational window.This investigation seeks to determine the visible colors of near-Earth asteroids(NEAs),perform an initial taxonomic classification based on visible colors and analyze possible correlations between the distribution of taxonomic classification and asteroid size or orbital parameters.Observations were performed in the broadband BVRI Johnson−Cousins photometric system,applied to images from the Yaoan High Precision Telescope and the 1.88 m telescope at the Kottamia Astronomical Observatory.We present new photometric observations of 84 near-Earth asteroids,and classify 80 of them taxonomically,based on their photometric colors.We find that nearly half(46.3%)of the objects in our sample can be classified as S-complex,26.3%as C-complex,6%as D-complex,and 15.0%as X-complex;the remaining belong to the A-or V-types.Additionally,we identify three P-type NEAs in our sample,according to the Tholen scheme.The fractional abundances of the C/X-complex members with absolute magnitude H≥17.0 were more than twice as large as those with H<17.0.However,the fractions of C-and S-complex members with diameters≤1 km and>1 km are nearly equal,while X-complex members tend to have sub-kilometer diameters.In our sample,the C/D-complex objects are predominant among those with a Jovian Tisserand parameter of T_(J)<3.1.These bodies could have a cometary origin.C-and S-complex members account for a considerable proportion of the asteroids that are potentially hazardous.展开更多
Accurate taxonomic classification is essential to understanding microbial diversity and function through metagenomic sequencing.However,this task is complicated by the vast variety of microbial genomes and the computa...Accurate taxonomic classification is essential to understanding microbial diversity and function through metagenomic sequencing.However,this task is complicated by the vast variety of microbial genomes and the computational limitations of bioinformatics tools.The aim of this study was to evaluate the impact of reference database selection and confidence score(CS)settings on the performance of Kraken2,a widely used k-mer-based metagenomic classifier.In this study,we generated simulated metagenomic datasets to systematically evaluate how the choice of reference databases,from the compact Minikraken v1 to the expansive nt-and GTDB r202,and different CS(from 0 to 1.0)affect the key performance metrics of Kraken2.These metrics include classification rate,precision,recall,F1 score,and accuracy of true versus calculated bacterial abundance estimation.Our results show that higher CS,which increases the rigor of taxonomic classification by requiring greater k-mer agreement,generally decreases the classification rate.This effect is particularly pronounced for smaller databases such as Minikraken and Standard-16,where no reads could be classified when the CS was above 0.4.In contrast,for larger databases such as Standard,nt and GTDB r202,precision and F1 scores improved significantly with increasing CS,highlighting their robustness to stringent conditions.Recovery rates were mostly stable,indicating consistent detection of species under different CS settings.Crucially,the results show that a comprehensive reference database combined with a moderate CS(0.2 or 0.4)significantly improves classification accuracy and sensitivity.This finding underscores the need for careful selection of database and CS parameters tailored to specific scientific questions and available computational resources to optimize the results of metagenomic analyses.展开更多
The Cheng index distinguishes indica andjaponica rice based on six taxonomic traits.This index has been widely used for classifi- cation of indica and japonica varieties in China.In this study,a double haploid(DH)popu...The Cheng index distinguishes indica andjaponica rice based on six taxonomic traits.This index has been widely used for classifi- cation of indica and japonica varieties in China.In this study,a double haploid(DH)popula-tion derived from anther culture of ZYQ8/JX17 F,a typical inter-subspecies hybrid,was used to investigate the six taxonomictraits,i.e.leaf hairiness(LH),color of hullwhen heading(CHH),hairiness of hull(HH),length of the first and second panicle internode(LPI),length/width of grain(L/W),andphenol reaction(PH).The morphological in- dex(MI)was also calculated.Based on themolecular linkage map constructed from this展开更多
The archaeological site of the Sanxingdui may date back as far as 5,000 years ago. The typical profiles of Palaeo-Stagnic-Anthrosols near the ancient site were selected, which aimed to identify diagnostic horizons emp...The archaeological site of the Sanxingdui may date back as far as 5,000 years ago. The typical profiles of Palaeo-Stagnic-Anthrosols near the ancient site were selected, which aimed to identify diagnostic horizons employing methodology of soil taxonomic classification and to reveal the micromorphological properties of the paleosols. Under long-term anthropogenic mellowing, the discernible differentiation between anthrostagnic epipedon and its subhorizons as well as hydragric horizon and its subhorizons occurred in Paleo-Stagnie-Anthrosols at the archaeological site of the Sanxingdui. The mieromorphological properties diversified among each specific diagnostic subhorizon, e.g., the developed microstructure in cultivated subhorizon within anthrostagnic epipedon, closely arranged particles and considerable micropores beneficial to both of water conservation and filtration in plow subhorizon within anthrostagnic epipedon, and automorphic optical-orientation clays and calcareous corrosion in hydragric horizons. The findings above of micromorphological features related with diagnostic horizons are significant for soil taxonomic classification.展开更多
According to the literature data on the chemical composition of the Trichilia genus performed in this work, it can be concluded that 334 different compounds were isolated and identified, distributed in monoterpenes, s...According to the literature data on the chemical composition of the Trichilia genus performed in this work, it can be concluded that 334 different compounds were isolated and identified, distributed in monoterpenes, sesquiterpenes, diterpenes, triterpenes, steroids, limonoids, coumarins, flavonoids, lignans, phenolic acids, amino acids and lactones. Together with the structures of this compound, data from botanical classification and pharmaco-logical results from extracts and pure compounds on the Trichilia genus were also described. The compounds derived from terpenes pathway were more significant, corresponding to about 87.7% of isolated and identified compounds from various Trichilia species. Among the different terpenoid skeletons of this kind, limonoids were meanly reported, appearing a total of 33.9% of compounds isolated from several Trichilia species.展开更多
Arbuscular mycorrhizal fungi(AMF)are plant root symbionts that play key roles in plant growth and soil fertility.They are obligate biotrophic fungi that form coenocytic multinucleated hyphae and spores.Numerous studie...Arbuscular mycorrhizal fungi(AMF)are plant root symbionts that play key roles in plant growth and soil fertility.They are obligate biotrophic fungi that form coenocytic multinucleated hyphae and spores.Numerous studies have shown that diverse microorganisms live on the surface of and inside their mycelia,resulting in a metagenome when whole-genome sequencing(WGS)data are obtained from sequencing AMF cultivated in vivo.The metagenome contains not only the AMF sequences,but also those from associated microorganisms.In this study,we introduce a novel bioinformatics program,Spore-associated Symbiotic Microbes(SeSaMe),designed for taxonomic classification of short sequences obtained by next-generation DNA sequencing.A genus-specific usage bias database was created based on amino acid usage and codon usage of a three consecutive codon DNA 9-mer encoding an amino acid trimer in a protein secondary structure.The program distinguishes between coding sequence(CDS)and non-CDS,and classifies a query sequence into a genus group out of 54 genera used as reference.The mean percentages of correct predictions of the CDS and the non-CDS test sets at the genus level were 71% and 50% for bacteria,68% and 73% for fungi(excluding AMF),and 49% and 72% for AMF(Rhizophagus irregularis),respectively.SeSaMe provides not only a means for estimating taxonomic diversity and abundance but also the gene reservoir of the reference taxonomic groups associated with AMF.Therefore,it enables users to study the symbiotic roles of associated microorganisms.It can also be applicable to other microorganisms as well as soil metagenomes.SeSaMe is freely available at www.fungalsesame.org.展开更多
基金funded by the China National Space Administration(KJSP2023020105)supported by the National Key R&D Program of China(Grant No.2023YFA1608100)+2 种基金the NSFC(Grant No.62227901)the Minor Planet Foundationsupported by the Egyptian Science,Technology&Innovation Funding Authority(STDF)under Grant No.48102.
文摘Near-Earth objects are important not only in studying the early formation of the Solar System,but also because they pose a serious hazard to humanity when they make close approaches to the Earth.Study of their physical properties can provide useful information on their origin,evolution,and hazard to human beings.However,it remains challenging to investigate small,newly discovered,near-Earth objects because of our limited observational window.This investigation seeks to determine the visible colors of near-Earth asteroids(NEAs),perform an initial taxonomic classification based on visible colors and analyze possible correlations between the distribution of taxonomic classification and asteroid size or orbital parameters.Observations were performed in the broadband BVRI Johnson−Cousins photometric system,applied to images from the Yaoan High Precision Telescope and the 1.88 m telescope at the Kottamia Astronomical Observatory.We present new photometric observations of 84 near-Earth asteroids,and classify 80 of them taxonomically,based on their photometric colors.We find that nearly half(46.3%)of the objects in our sample can be classified as S-complex,26.3%as C-complex,6%as D-complex,and 15.0%as X-complex;the remaining belong to the A-or V-types.Additionally,we identify three P-type NEAs in our sample,according to the Tholen scheme.The fractional abundances of the C/X-complex members with absolute magnitude H≥17.0 were more than twice as large as those with H<17.0.However,the fractions of C-and S-complex members with diameters≤1 km and>1 km are nearly equal,while X-complex members tend to have sub-kilometer diameters.In our sample,the C/D-complex objects are predominant among those with a Jovian Tisserand parameter of T_(J)<3.1.These bodies could have a cometary origin.C-and S-complex members account for a considerable proportion of the asteroids that are potentially hazardous.
基金supported by the Central Public-Interest Scientific Institution Basal Research Fund of the Chinese Academy of Agricultural Sciences(Y2022QC10)Agricultural Sciences and Technology Innovation Program of the Chinese Academy of Agricultural Sciences(CAAS-IFRZDRW202404,CAAS-ASTIP-2023-IFR-04).
文摘Accurate taxonomic classification is essential to understanding microbial diversity and function through metagenomic sequencing.However,this task is complicated by the vast variety of microbial genomes and the computational limitations of bioinformatics tools.The aim of this study was to evaluate the impact of reference database selection and confidence score(CS)settings on the performance of Kraken2,a widely used k-mer-based metagenomic classifier.In this study,we generated simulated metagenomic datasets to systematically evaluate how the choice of reference databases,from the compact Minikraken v1 to the expansive nt-and GTDB r202,and different CS(from 0 to 1.0)affect the key performance metrics of Kraken2.These metrics include classification rate,precision,recall,F1 score,and accuracy of true versus calculated bacterial abundance estimation.Our results show that higher CS,which increases the rigor of taxonomic classification by requiring greater k-mer agreement,generally decreases the classification rate.This effect is particularly pronounced for smaller databases such as Minikraken and Standard-16,where no reads could be classified when the CS was above 0.4.In contrast,for larger databases such as Standard,nt and GTDB r202,precision and F1 scores improved significantly with increasing CS,highlighting their robustness to stringent conditions.Recovery rates were mostly stable,indicating consistent detection of species under different CS settings.Crucially,the results show that a comprehensive reference database combined with a moderate CS(0.2 or 0.4)significantly improves classification accuracy and sensitivity.This finding underscores the need for careful selection of database and CS parameters tailored to specific scientific questions and available computational resources to optimize the results of metagenomic analyses.
文摘The Cheng index distinguishes indica andjaponica rice based on six taxonomic traits.This index has been widely used for classifi- cation of indica and japonica varieties in China.In this study,a double haploid(DH)popula-tion derived from anther culture of ZYQ8/JX17 F,a typical inter-subspecies hybrid,was used to investigate the six taxonomictraits,i.e.leaf hairiness(LH),color of hullwhen heading(CHH),hairiness of hull(HH),length of the first and second panicle internode(LPI),length/width of grain(L/W),andphenol reaction(PH).The morphological in- dex(MI)was also calculated.Based on themolecular linkage map constructed from this
基金supported by the Knowledge Innovation Program of the Chinese Academy of Sciences (Grant No KZCX2-YW-409)
文摘The archaeological site of the Sanxingdui may date back as far as 5,000 years ago. The typical profiles of Palaeo-Stagnic-Anthrosols near the ancient site were selected, which aimed to identify diagnostic horizons employing methodology of soil taxonomic classification and to reveal the micromorphological properties of the paleosols. Under long-term anthropogenic mellowing, the discernible differentiation between anthrostagnic epipedon and its subhorizons as well as hydragric horizon and its subhorizons occurred in Paleo-Stagnie-Anthrosols at the archaeological site of the Sanxingdui. The mieromorphological properties diversified among each specific diagnostic subhorizon, e.g., the developed microstructure in cultivated subhorizon within anthrostagnic epipedon, closely arranged particles and considerable micropores beneficial to both of water conservation and filtration in plow subhorizon within anthrostagnic epipedon, and automorphic optical-orientation clays and calcareous corrosion in hydragric horizons. The findings above of micromorphological features related with diagnostic horizons are significant for soil taxonomic classification.
基金The authors are thankful to FAPERJ,Fundacao Carlos Chagas Filho de AmparoàPesquisa do Estado do Rio de Janeiro(N˚do Processo E-26/111.898/2012)for financial support.
文摘According to the literature data on the chemical composition of the Trichilia genus performed in this work, it can be concluded that 334 different compounds were isolated and identified, distributed in monoterpenes, sesquiterpenes, diterpenes, triterpenes, steroids, limonoids, coumarins, flavonoids, lignans, phenolic acids, amino acids and lactones. Together with the structures of this compound, data from botanical classification and pharmaco-logical results from extracts and pure compounds on the Trichilia genus were also described. The compounds derived from terpenes pathway were more significant, corresponding to about 87.7% of isolated and identified compounds from various Trichilia species. Among the different terpenoid skeletons of this kind, limonoids were meanly reported, appearing a total of 33.9% of compounds isolated from several Trichilia species.
文摘Arbuscular mycorrhizal fungi(AMF)are plant root symbionts that play key roles in plant growth and soil fertility.They are obligate biotrophic fungi that form coenocytic multinucleated hyphae and spores.Numerous studies have shown that diverse microorganisms live on the surface of and inside their mycelia,resulting in a metagenome when whole-genome sequencing(WGS)data are obtained from sequencing AMF cultivated in vivo.The metagenome contains not only the AMF sequences,but also those from associated microorganisms.In this study,we introduce a novel bioinformatics program,Spore-associated Symbiotic Microbes(SeSaMe),designed for taxonomic classification of short sequences obtained by next-generation DNA sequencing.A genus-specific usage bias database was created based on amino acid usage and codon usage of a three consecutive codon DNA 9-mer encoding an amino acid trimer in a protein secondary structure.The program distinguishes between coding sequence(CDS)and non-CDS,and classifies a query sequence into a genus group out of 54 genera used as reference.The mean percentages of correct predictions of the CDS and the non-CDS test sets at the genus level were 71% and 50% for bacteria,68% and 73% for fungi(excluding AMF),and 49% and 72% for AMF(Rhizophagus irregularis),respectively.SeSaMe provides not only a means for estimating taxonomic diversity and abundance but also the gene reservoir of the reference taxonomic groups associated with AMF.Therefore,it enables users to study the symbiotic roles of associated microorganisms.It can also be applicable to other microorganisms as well as soil metagenomes.SeSaMe is freely available at www.fungalsesame.org.
