A 1440bp open-reading frame encoding D-hydantoinase from Pseudomonas putida YZ-26 was cloned and sequenced（ GenBank AY387829）. The DNA fragment was inserted into Nde and BamHI sites of vector pET-3a, yielding a reco...A 1440bp open-reading frame encoding D-hydantoinase from Pseudomonas putida YZ-26 was cloned and sequenced（ GenBank AY387829）. The DNA fragment was inserted into Nde and BamHI sites of vector pET-3a, yielding a recombinant plasmid, pET-HDT. After being transferred into the host strain, the artificial strain, pET-HDT/ E. coli BL21 can express the D-hydantoinase as the soluble form in the Lura-Bertani medium without addition of any inducers. The activity of the enzyme toward substrate DL-hydantoin can reach 3000-4000 IU per cells from one-liter bacterial culture incubated at 30 ℃ for 10-12 h. By the comparison of amino acid sequence homology, hydrophobic residues analysis and secondary structure prediction, it was found that D-hydantoinase reported herein is quite similar to that from Pseudomonas putdia CCRC12857, and alike to that from Pseudomonas putdia DSM84 or other bacteria. A rapid and efficient purification procedure of the enzyme was performed by a three-step procedure： ammonium sulfate fractionation, phenyl Sepharose hydrophobic interaction chromatography and Sephacryl S-200 gel filtration. The molecular mass of the monomeric enzyme is 52042 Da as determined by MALDI-TOF mass spectrometry.展开更多
Songliao Basin is filled predominantly with continental facies sediments including alluvial fan, fluvial plain, fan delta, lacustrine delta, shore - shallow lacustrine, beach salty flat, semi - deep to deep lacustrine...Songliao Basin is filled predominantly with continental facies sediments including alluvial fan, fluvial plain, fan delta, lacustrine delta, shore - shallow lacustrine, beach salty flat, semi - deep to deep lacustrine, subaqueous gravity flow,lacustrine swamp and pyroclastic sediments. However, some event units were formed during lake - marine linking periods of the Mid - Cretaceous in the basin, which include black shales with high values for salinity (Sr/Ba) , alkalinity ( Ca + Mg)/(Si + Al) , reducibility (Ni + Zn)/Ga and sulfide sulfur as well as heavy isotopes. The Breitenholz -section to be represented for facies comparison with the Cretaceous evaporitic series in Northeast China is localized in Southwest Germany. Stratigraphically it belongs to the Crabfeld Formation of Keuper of the Germanic Triassic corresponding to Ladinian - Carnian of the international reference scale, and is generally called Lower Gipskeuper. The Germanic Triassic was deposited in the epicontinental (cratonic) central Europe Basin. It covered the area in between Great Britain, North Sea, Poland and Southern Germany. It is composed of cyclic deposits of multicolored mudstones, gypsum/anhydrite, and dolomite beds. The two cases of marine ingression - influenced sequences share some common features.展开更多
The study and comparison of sequences of characters from a finite alphabet is relevant to various areas of science, notably molecular biology. The measurement of sequence similarity involves the consideration of the p...The study and comparison of sequences of characters from a finite alphabet is relevant to various areas of science, notably molecular biology. The measurement of sequence similarity involves the consideration of the possible sequence alignments in order to find an optimal one for which the “distance” between sequences is minimum. In biology informatics area, it is a more important and difficult problem due to the long length (100 at least) of sequence, this cause the compute complexity and large memory require. By associating a path in a lattice to each alignment, a geometric insight can be brought into the problem of finding an optimal alignment, this give an obvious encoding of each path. This problem can be solved by applying genetic algorithm, which is more efficient than dynamic programming and hidden Markov model using commomly now.展开更多
The coat protein （CP） genes were cloned and sequenced from viral particles of 11 isolates of citrus tristeza virus （CTV） collected from wild citrus plants in China and 4 Chinese isolates from cultivated sweet oran...The coat protein （CP） genes were cloned and sequenced from viral particles of 11 isolates of citrus tristeza virus （CTV） collected from wild citrus plants in China and 4 Chinese isolates from cultivated sweet orange and pummelo varieties, respectively. By analyzing and comparing the nucleotide and amino acid sequences of CP genes, the 11 wild CTV isolates were found over 92% identical with 4 Chinese CTV isolates and 21 exotic CTV isolates from cultivated citrus. From 91 to 100% of the CTV CP gene sequences in wild type citrus plants were generally well conserved. Genetic evolution analysis indicated that the GC% of the CP gene was less than AT%, and more transition were found in the CP genes than transversion with the transition/transversion ratio ranging from 6.3 to 7.0 among species. The substitution frequency was the highest at the third codon, followed by the first and second codon. The ratio of non-synonymous mutations （du） to synonymous mutations （ds） was far lower than 1, suggesting that the CP gene might have experienced purifying selection in the evolution. Phylogenetic analysis revealed that the 11 CTV isolates in Chinese wild type citrus belonged to different phylogenetic clusters, and shared higher homology and closer relationships with other cultivated citrus CTV isolates from different countries, which indicated complicated genetic relationships among the CTV isolates. In addition, CTV isolates with similar biological characteristics usually located into the same clusters. Therefore, the conclusion was drawn that pathogenicity was critical to evolution and origin of CTV.展开更多
Biology sequence comparison is a fundamental task in computational biology.According to the hydropathy profile of amino acids,a protein sequence is taken as a string with three letters.Three curves of the new protein ...Biology sequence comparison is a fundamental task in computational biology.According to the hydropathy profile of amino acids,a protein sequence is taken as a string with three letters.Three curves of the new protein sequence were defined to describe the protein sequence.A new method to analyze the similarity/dissimilarity of protein sequence was proposed based on the conditional probability of the protein sequence.Finally,the protein sequences of ND6(NADH dehydrogenase subunit 6)protein of eight species were taken as an example to illustrate the new approach.The results demonstrated that the method is convenient and efficient.展开更多
Citrus Tristeza Virus(CTV),usually occurs in nature as a mixture of genotypes.Six naturally infected citrus(Citrus sinensis)trees grafted on sour orange rootstock were collected from three citrus growing governorates ...Citrus Tristeza Virus(CTV),usually occurs in nature as a mixture of genotypes.Six naturally infected citrus(Citrus sinensis)trees grafted on sour orange rootstock were collected from three citrus growing governorates in Egypt(Sharqia,Qalyubia and Garbia).In this study,RT-PCR,Single-Strand Conformation Polymorphism(SSCP)and nucleotide sequence analysis were used for four independent CTV genomic regions(p65,p18,p20,and p23)to detect and assess the sequence and genetic variabilities among CTV Egyptian isolates.RTPCR products(650 bp)for the CTV p23 gene obtained from the selected isolates were used for the SSCP analysis and DNA sequencing.SSCP patterns of p23 gene for individual isolates yielded different complex haplotype patterns.Nucleotide sequence analysis of p23 region amplified from six isolates under study revealed that p23 shared high nucleotide identity 98.7%with T36 isolate from USA,Florida.Phylogenetic analysis of p23 gene indicated a close evolutionary relationship between all examined isolates and Qaha isolate(T36 isolate group),suggesting that they may have originated from closely related ancestors.Nucleotide sequence analysis of the three genes located on CTV 3′-coterminal overhang,p18,p20 and p65,amplified from isolate A3,Sharqia governorate,revealed that the p18,p65,and p20 genes were related to the T3-KB isolate from South Africa with 99%–100%sequence homology.Phylogenetic relationship analysis for p65,p18 and p20 ORFs clustered the current A3 isolate with T3 genotype group.The recombination analysis identified three of six isolates from Sharqia,and Garbia as potential recombinant for p23 gene.The isolates T36 and T3 were identified as major donors for recombination events in isolate A3.Our results concluded that p23 ORF likely to be as a hotspot region for recombination and originated through recombination event.The current study indicated that recombination is an important factor for the origin of CTV strains in Egypt.展开更多
The Yellow Sea Cold Water Mass(YSCWM)is a distinct hydrographic phenomenon of the Yellow Sea,and the distribution pattern of meio-and macrobenthos diff ers inside and outside of the YSCWM.However,such a pattern has ne...The Yellow Sea Cold Water Mass(YSCWM)is a distinct hydrographic phenomenon of the Yellow Sea,and the distribution pattern of meio-and macrobenthos diff ers inside and outside of the YSCWM.However,such a pattern has never been observed in the microbenthic ciliate communities.Therefore,we hypothesized that benthic ciliates followed a similar distribution pattern as meio-and macrobenthos,but this pattern has not been uncovered by morphological methods.We evaluated the diversity and distribution of benthic ciliates at fi ve stations along hydrographic gradients across the YSCWM and adjacent shallow water by using morphology and DNA and complementary DNA(cDNA)high-throughput sequencing of the V4 region of 18S rRNA gene.Results showed that the diversity of benthic ciliates detected by DNA(303 OTUs),and the cDNA(611 OTUs)sequencing was much higher than that detected by the morphological method(79 species).Morphological method detected roughly diff erent ciliate communities inside and outside of the YSCWM,but without statistical signifi cance.No clear pattern was obtained by DNA sequencing.In contrast,cDNA sequencing revealed a distinct distribution pattern of benthic ciliate communities like meioand macrobenthos,which coincided well with the results of the environmental parameter analysis.More than half of the total sequences detected by DNA sequencing belonged to planktonic ciliates,most(if not all)of which were recovered from historic DNA originating through the sedimentation of pelagic forms because none of them were observed morphologically.The irrelevant historic DNA greatly infl uenced the recovery of rare species and thus limited the understanding of the benthic ciliate diversity and distribution.Our research indicates that the methods used have signifi cant eff ects on the investigation of benthic ciliate communities and highlights that cDNA sequencing has great advantages in estimating the diversity and distribution of benthic ciliates,as well as the potential for benthic environmental assessments.展开更多
Purpose:Generally,the scientific comparison has been done with the help of the overall impact of scholars.Although it is very easy to compare scholars,but how can we assess the scientific impact of scholars who have d...Purpose:Generally,the scientific comparison has been done with the help of the overall impact of scholars.Although it is very easy to compare scholars,but how can we assess the scientific impact of scholars who have different research careers?It is very obvious,the scholars may gain a high impact if they have more research experience or have spent more time(in terms of research career in a year).Then we cannot compare two scholars who have different research careers.Many bibliometrics indicators address the time-span of scholars.In this series,the h-index sequence and EM/EM’-index sequence have been introduced for assessment and comparison of the scientific impact of scholars.The h-index sequence,EM-index sequence,and EM’-index sequence consider the yearly impact of scholars,and comparison is done by the index value along with their component value.The time-series indicators fail to give a comparative analysis between senior and junior scholars if there is a huge difference in both scholars’research careers.Design/methodology/approach:We have proposed the cumulative index calculation method to appraise the scientific impact of scholars till that age and tested it with 89 scholars data.Findings:The proposed mechanism is implemented and tested on 89 scholars’publication data,providing a clear difference between the scientific impact of two scholars.This also helps in predicting future prominent scholars based on their research impact.Research limitations:This study adopts a simplistic approach by assigning equal credit to all authors,regardless of their individual contributions.Further,the potential impact of career breaks on research productivity is not taken into account.These assumptions may limit the generalizability of our findings Practical implications:The proposed method can be used by respected institutions to compare their scholars impact.Funding agencies can also use it for similar purposes.Originality/value:This research adds to the existing literature by introducing a novel methodology for comparing the scientific impact of scholars.The outcomes of this research have notable implications for the development of more precise and unbiased research assessment frameworks,enabling a more equitable evaluation of scholarly contributions.展开更多
The amniote pallium,a vital component of the forebrain,exhibits considerable evolutionary divergence across species and mediates diverse functions,including sensory processing,memory formation,and learning.However,the...The amniote pallium,a vital component of the forebrain,exhibits considerable evolutionary divergence across species and mediates diverse functions,including sensory processing,memory formation,and learning.However,the relationships among pallial subregions in different species remain poorly characterized,particularly regarding the identification of homologous neurons and their transcriptional signatures.In this study,we utilized singlenucleus RNA sequencing to examine over 130?000 nuclei from the macaque(Macaca fascicularis)neocortex,complemented by datasets from humans(Homo sapiens),mice(Mus musculus),zebra finches(Taeniopygia guttata),turtles(Chrysemys picta bellii),and lizards(Pogona vitticeps),enablingcomprehensivecross-species comparison.Results revealed transcriptomic conservation and species-specific distinctions within the amniote pallium.Notable similarities were observed among cell subtypes,particularly within PVALB+inhibitory neurons,which exhibited species-preferred subtypes.Furthermore,correlations between pallial subregions and several transcription factor candidates were identified,including RARB,DLX2,STAT6,NR3C1,and THRB,with potential regulatory roles in gene expression in mammalian pallial neurons compared to their avian and reptilian counterparts.These results highlight the conserved nature of inhibitory neurons,remarkable regional divergence of excitatory neurons,and species-specific gene expression and regulation in amniote pallial neurons.Collectively,these findings provide valuable insights into the evolutionary dynamics of the amniote pallium.展开更多
The rapid expansion of the number of viral genome sequences in public databases necessitates a scalable,universal,and automated preliminary taxonomic framework for comprehensive Virus studies.Here,we introduce Virus S...The rapid expansion of the number of viral genome sequences in public databases necessitates a scalable,universal,and automated preliminary taxonomic framework for comprehensive Virus studies.Here,we introduce Virus Sequence-based Taxonomy Assignment(VISTA),a computa-tional tool that employs a novel pairwise sequence comparison system and an automatic demarcation threshold identification framework for vi-rus taxonomy.Leveraging physio-chemical property sequences,k-mer profiles,and machine learning techniques,ViSTA constructs a robust distance-based framework for taxonomic assignment.Functionally similar to Pairwise Sequence Comparison(PAsC),a widely used virus as-signment tool based on pairwise sequence comparison,VisTA demonstrates superior performance by providing significantly improved separa-tion for taxonomic groups,more objective taxonomic demarcation thresholds,greatly enhanced speed,and a wider application scope.We suc-cessfully applied ViSTA to 38 virus families,as well as to the class Caudoviricetes.This demonstrates VISTA's scalability,robustness,and ability to automatically and accurately assign taxonomy to both prokaryotic and eukaryotic viruses.Furthermore,the application of ViSTA to 679 unclas-sified prokaryotic virus genomes recovered from metagenomic data identified 46 novel virus families.VisTA is available as both a command line toolandauser-friendlywebportal athttps:/ngdc.cncb.ac.cn/vista.展开更多
基金Supported by the Natural Science Foundation of Shanxi Province(No.20031042).
文摘A 1440bp open-reading frame encoding D-hydantoinase from Pseudomonas putida YZ-26 was cloned and sequenced（ GenBank AY387829）. The DNA fragment was inserted into Nde and BamHI sites of vector pET-3a, yielding a recombinant plasmid, pET-HDT. After being transferred into the host strain, the artificial strain, pET-HDT/ E. coli BL21 can express the D-hydantoinase as the soluble form in the Lura-Bertani medium without addition of any inducers. The activity of the enzyme toward substrate DL-hydantoin can reach 3000-4000 IU per cells from one-liter bacterial culture incubated at 30 ℃ for 10-12 h. By the comparison of amino acid sequence homology, hydrophobic residues analysis and secondary structure prediction, it was found that D-hydantoinase reported herein is quite similar to that from Pseudomonas putdia CCRC12857, and alike to that from Pseudomonas putdia DSM84 or other bacteria. A rapid and efficient purification procedure of the enzyme was performed by a three-step procedure： ammonium sulfate fractionation, phenyl Sepharose hydrophobic interaction chromatography and Sephacryl S-200 gel filtration. The molecular mass of the monomeric enzyme is 52042 Da as determined by MALDI-TOF mass spectrometry.
基金NSFC (National Science Foundation of China) Project No. 4967212, attained with the assistance of the AvH (Alexander von Humboldt Foundation) of Germany.
文摘Songliao Basin is filled predominantly with continental facies sediments including alluvial fan, fluvial plain, fan delta, lacustrine delta, shore - shallow lacustrine, beach salty flat, semi - deep to deep lacustrine, subaqueous gravity flow,lacustrine swamp and pyroclastic sediments. However, some event units were formed during lake - marine linking periods of the Mid - Cretaceous in the basin, which include black shales with high values for salinity (Sr/Ba) , alkalinity ( Ca + Mg)/(Si + Al) , reducibility (Ni + Zn)/Ga and sulfide sulfur as well as heavy isotopes. The Breitenholz -section to be represented for facies comparison with the Cretaceous evaporitic series in Northeast China is localized in Southwest Germany. Stratigraphically it belongs to the Crabfeld Formation of Keuper of the Germanic Triassic corresponding to Ladinian - Carnian of the international reference scale, and is generally called Lower Gipskeuper. The Germanic Triassic was deposited in the epicontinental (cratonic) central Europe Basin. It covered the area in between Great Britain, North Sea, Poland and Southern Germany. It is composed of cyclic deposits of multicolored mudstones, gypsum/anhydrite, and dolomite beds. The two cases of marine ingression - influenced sequences share some common features.
文摘The study and comparison of sequences of characters from a finite alphabet is relevant to various areas of science, notably molecular biology. The measurement of sequence similarity involves the consideration of the possible sequence alignments in order to find an optimal one for which the “distance” between sequences is minimum. In biology informatics area, it is a more important and difficult problem due to the long length (100 at least) of sequence, this cause the compute complexity and large memory require. By associating a path in a lattice to each alignment, a geometric insight can be brought into the problem of finding an optimal alignment, this give an obvious encoding of each path. This problem can be solved by applying genetic algorithm, which is more efficient than dynamic programming and hidden Markov model using commomly now.
基金supported by the National Natural Science Foundation of China (30900977)the Key Project 210111 of Chinese Ministry of Education and Natural Science Foundation Project of CQ CSTC (2009BB1310)
文摘The coat protein （CP） genes were cloned and sequenced from viral particles of 11 isolates of citrus tristeza virus （CTV） collected from wild citrus plants in China and 4 Chinese isolates from cultivated sweet orange and pummelo varieties, respectively. By analyzing and comparing the nucleotide and amino acid sequences of CP genes, the 11 wild CTV isolates were found over 92% identical with 4 Chinese CTV isolates and 21 exotic CTV isolates from cultivated citrus. From 91 to 100% of the CTV CP gene sequences in wild type citrus plants were generally well conserved. Genetic evolution analysis indicated that the GC% of the CP gene was less than AT%, and more transition were found in the CP genes than transversion with the transition/transversion ratio ranging from 6.3 to 7.0 among species. The substitution frequency was the highest at the third codon, followed by the first and second codon. The ratio of non-synonymous mutations （du） to synonymous mutations （ds） was far lower than 1, suggesting that the CP gene might have experienced purifying selection in the evolution. Phylogenetic analysis revealed that the 11 CTV isolates in Chinese wild type citrus belonged to different phylogenetic clusters, and shared higher homology and closer relationships with other cultivated citrus CTV isolates from different countries, which indicated complicated genetic relationships among the CTV isolates. In addition, CTV isolates with similar biological characteristics usually located into the same clusters. Therefore, the conclusion was drawn that pathogenicity was critical to evolution and origin of CTV.
基金Project(No.Z111020834)supported by 08 Special Talent Fund of Northwest A&F University,China
文摘Biology sequence comparison is a fundamental task in computational biology.According to the hydropathy profile of amino acids,a protein sequence is taken as a string with three letters.Three curves of the new protein sequence were defined to describe the protein sequence.A new method to analyze the similarity/dissimilarity of protein sequence was proposed based on the conditional probability of the protein sequence.Finally,the protein sequences of ND6(NADH dehydrogenase subunit 6)protein of eight species were taken as an example to illustrate the new approach.The results demonstrated that the method is convenient and efficient.
基金Authors extend their appreciation to Deanship of Scientific Research,King Faisal University,Saudi Arabia,for supporting this research(GRANT494).
文摘Citrus Tristeza Virus(CTV),usually occurs in nature as a mixture of genotypes.Six naturally infected citrus(Citrus sinensis)trees grafted on sour orange rootstock were collected from three citrus growing governorates in Egypt(Sharqia,Qalyubia and Garbia).In this study,RT-PCR,Single-Strand Conformation Polymorphism(SSCP)and nucleotide sequence analysis were used for four independent CTV genomic regions(p65,p18,p20,and p23)to detect and assess the sequence and genetic variabilities among CTV Egyptian isolates.RTPCR products(650 bp)for the CTV p23 gene obtained from the selected isolates were used for the SSCP analysis and DNA sequencing.SSCP patterns of p23 gene for individual isolates yielded different complex haplotype patterns.Nucleotide sequence analysis of p23 region amplified from six isolates under study revealed that p23 shared high nucleotide identity 98.7%with T36 isolate from USA,Florida.Phylogenetic analysis of p23 gene indicated a close evolutionary relationship between all examined isolates and Qaha isolate(T36 isolate group),suggesting that they may have originated from closely related ancestors.Nucleotide sequence analysis of the three genes located on CTV 3′-coterminal overhang,p18,p20 and p65,amplified from isolate A3,Sharqia governorate,revealed that the p18,p65,and p20 genes were related to the T3-KB isolate from South Africa with 99%–100%sequence homology.Phylogenetic relationship analysis for p65,p18 and p20 ORFs clustered the current A3 isolate with T3 genotype group.The recombination analysis identified three of six isolates from Sharqia,and Garbia as potential recombinant for p23 gene.The isolates T36 and T3 were identified as major donors for recombination events in isolate A3.Our results concluded that p23 ORF likely to be as a hotspot region for recombination and originated through recombination event.The current study indicated that recombination is an important factor for the origin of CTV strains in Egypt.
基金Supported by the National Natural Science Foundation of China(Nos.41876171,41506167,41476144)。
文摘The Yellow Sea Cold Water Mass(YSCWM)is a distinct hydrographic phenomenon of the Yellow Sea,and the distribution pattern of meio-and macrobenthos diff ers inside and outside of the YSCWM.However,such a pattern has never been observed in the microbenthic ciliate communities.Therefore,we hypothesized that benthic ciliates followed a similar distribution pattern as meio-and macrobenthos,but this pattern has not been uncovered by morphological methods.We evaluated the diversity and distribution of benthic ciliates at fi ve stations along hydrographic gradients across the YSCWM and adjacent shallow water by using morphology and DNA and complementary DNA(cDNA)high-throughput sequencing of the V4 region of 18S rRNA gene.Results showed that the diversity of benthic ciliates detected by DNA(303 OTUs),and the cDNA(611 OTUs)sequencing was much higher than that detected by the morphological method(79 species).Morphological method detected roughly diff erent ciliate communities inside and outside of the YSCWM,but without statistical signifi cance.No clear pattern was obtained by DNA sequencing.In contrast,cDNA sequencing revealed a distinct distribution pattern of benthic ciliate communities like meioand macrobenthos,which coincided well with the results of the environmental parameter analysis.More than half of the total sequences detected by DNA sequencing belonged to planktonic ciliates,most(if not all)of which were recovered from historic DNA originating through the sedimentation of pelagic forms because none of them were observed morphologically.The irrelevant historic DNA greatly infl uenced the recovery of rare species and thus limited the understanding of the benthic ciliate diversity and distribution.Our research indicates that the methods used have signifi cant eff ects on the investigation of benthic ciliate communities and highlights that cDNA sequencing has great advantages in estimating the diversity and distribution of benthic ciliates,as well as the potential for benthic environmental assessments.
文摘Purpose:Generally,the scientific comparison has been done with the help of the overall impact of scholars.Although it is very easy to compare scholars,but how can we assess the scientific impact of scholars who have different research careers?It is very obvious,the scholars may gain a high impact if they have more research experience or have spent more time(in terms of research career in a year).Then we cannot compare two scholars who have different research careers.Many bibliometrics indicators address the time-span of scholars.In this series,the h-index sequence and EM/EM’-index sequence have been introduced for assessment and comparison of the scientific impact of scholars.The h-index sequence,EM-index sequence,and EM’-index sequence consider the yearly impact of scholars,and comparison is done by the index value along with their component value.The time-series indicators fail to give a comparative analysis between senior and junior scholars if there is a huge difference in both scholars’research careers.Design/methodology/approach:We have proposed the cumulative index calculation method to appraise the scientific impact of scholars till that age and tested it with 89 scholars data.Findings:The proposed mechanism is implemented and tested on 89 scholars’publication data,providing a clear difference between the scientific impact of two scholars.This also helps in predicting future prominent scholars based on their research impact.Research limitations:This study adopts a simplistic approach by assigning equal credit to all authors,regardless of their individual contributions.Further,the potential impact of career breaks on research productivity is not taken into account.These assumptions may limit the generalizability of our findings Practical implications:The proposed method can be used by respected institutions to compare their scholars impact.Funding agencies can also use it for similar purposes.Originality/value:This research adds to the existing literature by introducing a novel methodology for comparing the scientific impact of scholars.The outcomes of this research have notable implications for the development of more precise and unbiased research assessment frameworks,enabling a more equitable evaluation of scholarly contributions.
基金supported by the National Key Research and Development Program (2022YEF0203200)National Science and Technology Innovation 2030 Major Program (STI2030-2021ZD0200100)National Key Research and Development Program (2018YFA0801400,2021YFA0805100)。
文摘The amniote pallium,a vital component of the forebrain,exhibits considerable evolutionary divergence across species and mediates diverse functions,including sensory processing,memory formation,and learning.However,the relationships among pallial subregions in different species remain poorly characterized,particularly regarding the identification of homologous neurons and their transcriptional signatures.In this study,we utilized singlenucleus RNA sequencing to examine over 130?000 nuclei from the macaque(Macaca fascicularis)neocortex,complemented by datasets from humans(Homo sapiens),mice(Mus musculus),zebra finches(Taeniopygia guttata),turtles(Chrysemys picta bellii),and lizards(Pogona vitticeps),enablingcomprehensivecross-species comparison.Results revealed transcriptomic conservation and species-specific distinctions within the amniote pallium.Notable similarities were observed among cell subtypes,particularly within PVALB+inhibitory neurons,which exhibited species-preferred subtypes.Furthermore,correlations between pallial subregions and several transcription factor candidates were identified,including RARB,DLX2,STAT6,NR3C1,and THRB,with potential regulatory roles in gene expression in mammalian pallial neurons compared to their avian and reptilian counterparts.These results highlight the conserved nature of inhibitory neurons,remarkable regional divergence of excitatory neurons,and species-specific gene expression and regulation in amniote pallial neurons.Collectively,these findings provide valuable insights into the evolutionary dynamics of the amniote pallium.
基金funded by the National Natural Science Foundation of China(Grant No.32270019)the Professional Association of the Alliance of International Science Organizations(Grant No.ANSO-PA-2020-07)the Open Biodiversity and Health Big Data Programme of IUBS.
文摘The rapid expansion of the number of viral genome sequences in public databases necessitates a scalable,universal,and automated preliminary taxonomic framework for comprehensive Virus studies.Here,we introduce Virus Sequence-based Taxonomy Assignment(VISTA),a computa-tional tool that employs a novel pairwise sequence comparison system and an automatic demarcation threshold identification framework for vi-rus taxonomy.Leveraging physio-chemical property sequences,k-mer profiles,and machine learning techniques,ViSTA constructs a robust distance-based framework for taxonomic assignment.Functionally similar to Pairwise Sequence Comparison(PAsC),a widely used virus as-signment tool based on pairwise sequence comparison,VisTA demonstrates superior performance by providing significantly improved separa-tion for taxonomic groups,more objective taxonomic demarcation thresholds,greatly enhanced speed,and a wider application scope.We suc-cessfully applied ViSTA to 38 virus families,as well as to the class Caudoviricetes.This demonstrates VISTA's scalability,robustness,and ability to automatically and accurately assign taxonomy to both prokaryotic and eukaryotic viruses.Furthermore,the application of ViSTA to 679 unclas-sified prokaryotic virus genomes recovered from metagenomic data identified 46 novel virus families.VisTA is available as both a command line toolandauser-friendlywebportal athttps:/ngdc.cncb.ac.cn/vista.
