The present paper predicted the function of unknow genes by analyzing the co-expression data of Arabidopsis thaliana from biological pathway based on the shortest-path algorithm. This paper proposed that transitive co...The present paper predicted the function of unknow genes by analyzing the co-expression data of Arabidopsis thaliana from biological pathway based on the shortest-path algorithm. This paper proposed that transitive co-expression among genes can be used as an important attribute to link genes of the same biological pathway. The genes from the same biological pathway with similar functions are strongly correlated in expression. Moreover,the function of unknown genes can be predicted by the known genes where they are strongly correlated in expression lying on the same shortest-path from the biological pathway. Analyzing the Arabidopsis thaliana from the biological pathway,this study showed that this method can reliably reveal function of the unknown Arabidopsis thaliana genes and the approach of predicting gene function by transitiving co-expression in shortest-path is feasible and effective.展开更多
Obtaining transgenic plants is a common method for analyzing gene function.Unfortunately,stable genetic transformation is difficult to achieve,especially for plants(e.g.,soybean),which are recalcitrant to genetic tran...Obtaining transgenic plants is a common method for analyzing gene function.Unfortunately,stable genetic transformation is difficult to achieve,especially for plants(e.g.,soybean),which are recalcitrant to genetic transformation.Transient expression systems,such as Arabidopsis protoplast,Nicotiana leaves,and onion bulb leaves are widely used for gene functional studies.A simple method for obtaining transgenic soybean callus tissues was reported recently.We extend this system with simplified culture conditions to gene functional studies,including promoter analysis,expression and subcellular localization of the target protein,and protein-protein interaction.We also evaluate the plasticity of this system with soybean varieties,different vector constructs,and various Agrobacterium strains.The results indicated that the callus transformation system is efficient and adaptable for gene functional investigation in soybean genotype-,vector-,and Agrobacterium strain-independent modes.We demonstrated an easy set-up and practical homologous strategy for soybean gene functional studies.展开更多
Perennial grasses have developed intricate mechanisms to adapt to diverse environments,enabling their resistance to various biotic and abiotic stressors.These mechanisms arise from strong natural selection that contri...Perennial grasses have developed intricate mechanisms to adapt to diverse environments,enabling their resistance to various biotic and abiotic stressors.These mechanisms arise from strong natural selection that contributes to enhancing the adaptation of forage plants to various stress conditions.Methods such as antisense RNA technology,CRISPR/Cas9 screening,virus-induced gene silencing,and transgenic technology,are commonly utilized for investigating the stress response functionalities of grass genes in both warm-season and cool-season varieties.This review focuses on the functional identification of stress-resistance genes and regulatory elements in grasses.It synthesizes recent studies on mining functional genes,regulatory genes,and protein kinase-like signaling factors involved in stress responses in grasses.Additionally,the review outlines future research directions,providing theoretical support and references for further exploration of(i)molecular mechanisms underlying grass stress responses,(ii)cultivation and domestication of herbage,(iii)development of high-yield varieties resistant to stress,and(iv)mechanisms and breeding strategies for stress resistance in grasses.展开更多
A GoBlast system was built to predict gene function by integrating Blast search and Gene Ontology(GO)annotations together.The operation system was based on Debian Linux 3.1,with Apache as the web server and Mysql data...A GoBlast system was built to predict gene function by integrating Blast search and Gene Ontology(GO)annotations together.The operation system was based on Debian Linux 3.1,with Apache as the web server and Mysql database as the data storage system.FASTA files with GO annotations were taken as the sequence source for blast alignment,which were formatted by wu-formatdb program.The GoBlast system includes three Bioperl modules in Perl:a data input module,a data process module and a data output module.A GoBlast query starts with an amino acid or nucleotide sequence.It ends with an output in an html page,presenting high scoring gene products which are of a high homology to the queried sequence and listing associated GO terms beside respective gene poducts.A simple click on a GO term leads to the detailed explanation of the specific gene function.This avails gene function prediction by Blast.GoBlast can be a very useful tool for functional genome research and is available for free at http://bioq.org/goblast.展开更多
Ion channels are crucial in the generation and modulation of excitability in the nervous system and have been implicated in human epilepsy. Forty-one epilepsyassociated ion channel genes and their mutations are system...Ion channels are crucial in the generation and modulation of excitability in the nervous system and have been implicated in human epilepsy. Forty-one epilepsyassociated ion channel genes and their mutations are systematically reviewed. In this paper, we analyzed the genotypes, functional alterations（funotypes）, and phenotypes of these mutations. Eleven genes featured loss-offunction mutations and six had gain-of-function mutations.Nine genes displayed diversified funotypes, among which a distinct funotype-phenotype correlation was found in SCN1A. These data suggest that the funotype is an essential consideration in evaluating the pathogenicity of mutations and a distinct funotype or funotype-phenotype correlation helps to define the pathogenic potential of a gene.展开更多
Rice is a model plant for genomic study of grass species. Functional identification and definition of rice genes becomes the object of its functional genomics research. WRKY gene superfamily, one of the transcription ...Rice is a model plant for genomic study of grass species. Functional identification and definition of rice genes becomes the object of its functional genomics research. WRKY gene superfamily, one of the transcription factor gene families, was recently suggested to play important roles in plant development and stress response. In rice, the results of analyses of expression pattern and ectopic overexpressor lines also support this viewpoint, and the evidences implicate rice WRKY proteins in transcriptional reprogramming during biotic or abiotic stresses, senescence, sugar metabolites, and morphological architecture. In this paper, we review the advance in study of rice WRKY gene family and also propose unified nomenclature for rice WRKY factors to eliminate confusion.展开更多
It is very important in the field of bioinformatics to apply computer to perform the function annotation for new sequenced bio-sequences. Based on GO database and BLAST program, a novel method for the function annotat...It is very important in the field of bioinformatics to apply computer to perform the function annotation for new sequenced bio-sequences. Based on GO database and BLAST program, a novel method for the function annotation of new biological sequences is presented by using the variable-precision rough set theory. The proposed method is applied to the real data in GO database to examine its effectiveness. Numerical results show that the proposed method has better precision, recall-rate and harmonic mean value compared with existing methods.展开更多
Plant expression vectors are essential tools for gene functional analysis and molecular plant breeding.The gene of interest is transferred to the vector by molecular cloning technology.Nimble Cloning is a newly develo...Plant expression vectors are essential tools for gene functional analysis and molecular plant breeding.The gene of interest is transferred to the vector by molecular cloning technology.Nimble Cloning is a newly developed molecular cloning method with the advantages of simplicity,efficiency,and standardization.In this study,we developed a"pNC"vector system that contains 55 Nimble Cloning-compatible vectors for functional analysis of genes in plants.These vectors contain the NC frame flanked by unique adapters for one-step and standardized Nimble Cloning.We demonstrate that the pNC vectors are convenient and effective for the functional analysis of plant genes,including the study of gene ectopic expression,protein subcellular localization,protein-protein interaction,gene silencing(RNAi),virus-induced gene silencing,promoter activity,and CRISPR-Cas9-mediated genome editing.The"pNC"vector system represents a high-throughput toolkit that can facilitate the large-scale analysis of plant functional genomics.展开更多
Taking AuCu3-type sublattice system as an example, three discoveries have been presented: First, the third barrier hindering the progress in metal materials science is that researchers have got used to recognizing exp...Taking AuCu3-type sublattice system as an example, three discoveries have been presented: First, the third barrier hindering the progress in metal materials science is that researchers have got used to recognizing experimental phenomena of alloy phase transitions during extremely slow variation in temperature by equilibrium thinking mode and then taking erroneous knowledge of experimental phenomena as selected information for establishing Gibbs energy function and so-called equilibrium phase diagram. Second, the equilibrium holographic network phase diagrams of AuCu3-type sublattice system may be used to describe systematic correlativity of the composition?temperature-dependent alloy gene arranging structures and complete thermodynamic properties, and to be a standard for studying experimental subequilibrium order-disorder transition. Third, the equilibrium transition of each alloy is a homogeneous single-phase rather than a heterogeneous two-phase, and there exists a single-phase boundary curve without two-phase region of the ordered and disordered phases; the composition and temperature of the top point on the phase-boundary curve are far away from the ones of the critical point of the AuCu3 compound.展开更多
Taking Au3Cu-type sublattice system as an example, three discoveries have been presented. First, the fourth barrier to hinder the progress of metal materials science is that today’s researchers do not understand that...Taking Au3Cu-type sublattice system as an example, three discoveries have been presented. First, the fourth barrier to hinder the progress of metal materials science is that today’s researchers do not understand that the Gibbs energy function of an alloy phase should be derived from Gibbs energy partition function constructed of alloy gene sequence and their Gibbs energy sequence. Second, the six rules for establishing alloy gene Gibbs energy partition function have been discovered, and it has been specially proved that the probabilities of structure units occupied at the Gibbs energy levels in the degeneracy factor for calculating configuration entropy should be degenerated as ones of component atoms occupied at the lattice points. Third, the main characteristics unexpected by today’s researchers are as follows. There exists a single-phase boundary curve without two-phase region coexisting by the ordered and disordered phases. The composition and temperature of the top point on the phase-boundary curve are far away from those of the critical point of the Au3Cu compound; At 0 K, the composition of the lowest point on the composition-dependent Gibbs energy curve is notably deviated from that of the Au3Cu compounds. The theoretical limit composition range of long range ordered Au3Cu-type alloys is determined by the first jumping order degree.展开更多
The nuclear factor Y(NF-Y) gene family is a class of transcription factors that are widely distributed in eukaryotes and are involved in various biological processes. However, the NF-Y gene family members in watermelo...The nuclear factor Y(NF-Y) gene family is a class of transcription factors that are widely distributed in eukaryotes and are involved in various biological processes. However, the NF-Y gene family members in watermelon, a valued and nutritious fruit, remain largely unknown and their functions have not been characterized. In the present study, 22 ClNF-Y genes in watermelon, 29 CsNF-Y genes in cucumber, and 24CmNF-Y genes in melon were identified based on the whole-genome investigation and their protein properties, gene location, gene structure, motif composition, conserved domain, and evolutionary relationship were investigated. ClNF-YB9 from watermelon and its homologs in cucumber and melon were expressed specifically in seeds. Its expression remained low in the early stages of watermelon seed development,increased at 20 days after pollination(DAP), and peaked at 45–50 DAP. Moreover, the knockout mutant Clnf-yb9 exhibited abnormal leafy cotyledon phenotype, implying its critical role during seed formation.Finally, protein interaction assays showed that ClNF-YB9 interacts with all ClNF-YCs and the ClNF-YB9-YC4 heterodimer was able to recruit a ClNF-YA7 subunit to assemble a complete NF-Y complex, which may function in seed development. This study revealed the structure and evolutionary relationships of the NF-Y gene family in Cucurbitaceae and the novel function of ClNF-YB9 in regulating seed development in watermelon.展开更多
Field resistances of nine accessions of common wild rice （Oryza rufipogon Griff.） and one rice variety （IR24） were evaluated by using nine strains of bacterial blight pathogen （Xanthomonas oryzae pv. oryzae） fro...Field resistances of nine accessions of common wild rice （Oryza rufipogon Griff.） and one rice variety （IR24） were evaluated by using nine strains of bacterial blight pathogen （Xanthomonas oryzae pv. oryzae） from the Philippines. IR24 was highly susceptible to all the strains, and six common wild rice accessions resisted all the nine strains, with a resistance frequency of 67%. The accessions Yulin and Wanning were only susceptible to PXO280 and PXO71, respectively. The accession Gaozhou was susceptible to the three strains PXO79, PXO99 and PXO339, whereas resistant to the other six strains. It could be concluded that there is at least one resistance gene in each common wild rice accession. The functional markers of the genes xa5, xa13, Xa21 and Xa27 were used to detect the presence of these resistance genes in the nine tested wild rice accessions, and it was found that four wild rice accessions contained heterozygous xa13. Among the nine common wild rice accessions, five were homozygous for Xa27 and three homozygous for xa27, and the accession Laibin contained neither xa27 nor Xa27. In addition, there were no xa5 and Xa21 in all of these accessions.展开更多
Gene Ontology(GO)has been widely used to annotate functions of genes and gene products.Here,we proposed a new method,Triplet GO,to deduce GO terms of protein-coding and noncoding genes,through the integration of four ...Gene Ontology(GO)has been widely used to annotate functions of genes and gene products.Here,we proposed a new method,Triplet GO,to deduce GO terms of protein-coding and noncoding genes,through the integration of four complementary pipelines built on transcript expression profile,genetic sequence alignment,protein sequence alignment,and naīve probability.Triplet GO was tested on a large set of 5754 genes from 8 species(human,mouse,Arabidopsis,rat,fly,budding yeast,fission yeast,and nematoda)and 2433 proteins with available expression data from the third Critical Assessment of Protein Function Annotation challenge(CAFA3).Experimental results show that Triplet GO achieves function annotation accuracy significantly beyond the current state-of-the-art approaches.Detailed analyses show that the major advantage of Triplet GO lies in the coupling of a new triplet network-based profiling method with the feature space mapping technique,which can accurately recognize function patterns from transcript expression profiles.Meanwhile,the combination of multiple complementary models,especially those from transcript expression and protein-level alignments,improves the coverage and accuracy of the final GO annotation results.The standalone package and an online server of Triplet GO are freely available at https://zhanggroup.org/Triplet GO/.展开更多
Computational analysis is essential for transforming the masses of microarray datainto a mechanistic understanding of cancer. Here we present a method for findinggene functional modules of cancer from microarray data ...Computational analysis is essential for transforming the masses of microarray datainto a mechanistic understanding of cancer. Here we present a method for findinggene functional modules of cancer from microarray data and have applied it tocolon cancer. First, a colon cancer gene network and a normal colon tissue genenetwork were constructed using correlations between the genes. Then the modulesthat tended to have a homogeneous functional composition were identified by split-ting up the network. Analysis of both networks revealed that they are scale-free.Comparison of the gene functional modules for colon cancer and normal tissuesshowed that the modules’ functions changed with their structures.展开更多
With the development of bioinformatics,it is easy to obtain information and data about thousands of genes,but the determi nation of the functions of these genes depends on methods for rapid and effective functi on al ...With the development of bioinformatics,it is easy to obtain information and data about thousands of genes,but the determi nation of the functions of these genes depends on methods for rapid and effective functi on al identification.Virus-induced gene sile ncing(VIGS)is a mature method of gene functional identification developed over the last 20 years,which has been widely used in many research fields involving many species.Fruit quality formation is a complex biological process,which is closely related to ripening.Here,we review the progress and contribution of VIGS to our understanding of fruit biology and its advantages and disadvantages in determining gene function.展开更多
Agrobacterium tumefaciens-mediated transformation has been widely adopted for plant genetic engineering and the study of gene function(Krenek et al.,2015).This method is prevalent in the genetic transformation of herb...Agrobacterium tumefaciens-mediated transformation has been widely adopted for plant genetic engineering and the study of gene function(Krenek et al.,2015).This method is prevalent in the genetic transformation of herbaceous plants,with notable applications in species such as Arabidopsis(Yin et al.,2024),soybean(Zhang et al.,2024),rice(Zhang et al.,2020),and Chinese cabbage(Li et al.,2021).However,its application in fruit trees is limited.This is primarily due to their long growth cycles and lack of rapid,efficient,and stable transgenic systems,which severely hinders foundational research involving plant genetic transformation(Mei et al.,2024).Furthermore,for subtropical fruit trees,the presence of recalcitrant seeds adds an extra layer of difficulty to genetic transformation(Umarani et al.,2015),as most methods rely on seed germination as a basis for transformation.展开更多
Inflammatory bowel disease(IBD)is an incurable disease of the digestive system;however,the therapeutic methods for IBD remain limited.The pathogenesis of IBD was systematically discussed and compared in this paper,pri...Inflammatory bowel disease(IBD)is an incurable disease of the digestive system;however,the therapeutic methods for IBD remain limited.The pathogenesis of IBD was systematically discussed and compared in this paper,primarily comprising Crohn’s disease and ulcerative colitis.This paper focused on six common aspects:(1)Dysregulated immune responses;(2)Gene function changes;(3)Intestinal microbes disorder and imbalance;(4)Microbial infections;(5)Associations between IBD and other inflammatory diseases;and(6)Other factors.In addition,the pathogenesis differences between these two forms of IBD were unraveled and clearly distinguished.These unique aspects of pathogenesis provide crucial insights for the precise treatment of both Crohn’s disease and ulcerative colitis.This paper illustrates the root causes and beneficial factors of resistance to IBD,which provides novel insights on early prevention,development of new therapeutic agents,and treatment options of this disease.展开更多
The long-term impact of fulvic acid(FA)on partial nitritation(PN)systemwas initially examined in this study.The obtained results revealed that the FA lower than 50 mg/L had negligible effect on the nitrite accumulatio...The long-term impact of fulvic acid(FA)on partial nitritation(PN)systemwas initially examined in this study.The obtained results revealed that the FA lower than 50 mg/L had negligible effect on the nitrite accumulation rate(NAR nearly 100%)and ammonium removal rate(ARR 56.85%),while FA over 50 mg/L decreased ARR from 56.85%to 0.7%.Sludge characteristics analysis found that appropriate FA(<50 mg/L)exposure promoted the settling performance and granulation of PN sludge by removing Bacteroidetes and accumulating Chloroflexi.The analysis of metagenomics suggested that the presence of limited FA(0-50 mg/L)stimulated the generation of NADH,which favors the denitrification and nitrite reduction.The negative impact of FA on the PN system could be divided into two stages.Initially,limited FA(50-120 mg/L)was decomposed by Anaerolineae to stimulate the growth and propagation of heterotrophic bacteria(Thauera).Increasing heterotrophs competed with AOB(Nitrosomonas)for dissolved oxygen,causing AOB to be eliminated and ARR to declined.Subsequently,when FA dosage was over 120 mg/L,Anaerolineae were inhibited and heterotrophic bacteria reduced,resulting in the abundance of AOB recovered.Nevertheless,the ammonium transformation pathway was suppressed because genes amoABC and hao were obviously reduced,leading to the deterioration of reactor performance.Overall,these results provide theoretical guidance for the practical application of PN for the treatment of FA-containing sewage.展开更多
Rice with low glutelin content is suitable as functional food for patients affected by kidney failure. Low glutelincontent gene Lgc1 in rice has a 3.5-kb deletion between two highly similar glutelin genes GluB4 and Gl...Rice with low glutelin content is suitable as functional food for patients affected by kidney failure. Low glutelincontent gene Lgc1 in rice has a 3.5-kb deletion between two highly similar glutelin genes GluB4 and GluB5, which locates on the short arm of chromosome 2. To improve the selection efficiency in low glutelin-content rice breeding, two molecular markers designated as InDel-Lgc1-1 and InDel-Lgc1-2 were developed to detect the low glutelin-content gene Lgc1. A double PCR detection indicated that combined use of the two markers could easily distinguish the genotypes of Lgc1 from different rice varieties. Therefore, as a simple and low-cost technique, the molecular marker could be widely used to identify different varieties with Lgc1 gene and applied in marker-assisted selection of low glutelin-content rice.展开更多
基金Supported by Shanghai Municipal Education Committee Educationand Scientific Research (Grant No. 07ZZ60)~~
文摘The present paper predicted the function of unknow genes by analyzing the co-expression data of Arabidopsis thaliana from biological pathway based on the shortest-path algorithm. This paper proposed that transitive co-expression among genes can be used as an important attribute to link genes of the same biological pathway. The genes from the same biological pathway with similar functions are strongly correlated in expression. Moreover,the function of unknown genes can be predicted by the known genes where they are strongly correlated in expression lying on the same shortest-path from the biological pathway. Analyzing the Arabidopsis thaliana from the biological pathway,this study showed that this method can reliably reveal function of the unknown Arabidopsis thaliana genes and the approach of predicting gene function by transitiving co-expression in shortest-path is feasible and effective.
基金supported by the Transgenic Programs,China(2014ZX0800930B and 2016ZX08009-001)the National Natural Science Found of China(31371703)
文摘Obtaining transgenic plants is a common method for analyzing gene function.Unfortunately,stable genetic transformation is difficult to achieve,especially for plants(e.g.,soybean),which are recalcitrant to genetic transformation.Transient expression systems,such as Arabidopsis protoplast,Nicotiana leaves,and onion bulb leaves are widely used for gene functional studies.A simple method for obtaining transgenic soybean callus tissues was reported recently.We extend this system with simplified culture conditions to gene functional studies,including promoter analysis,expression and subcellular localization of the target protein,and protein-protein interaction.We also evaluate the plasticity of this system with soybean varieties,different vector constructs,and various Agrobacterium strains.The results indicated that the callus transformation system is efficient and adaptable for gene functional investigation in soybean genotype-,vector-,and Agrobacterium strain-independent modes.We demonstrated an easy set-up and practical homologous strategy for soybean gene functional studies.
基金supported by the Chief Scientist Program of Qinghai Province(2024-SF-101).
文摘Perennial grasses have developed intricate mechanisms to adapt to diverse environments,enabling their resistance to various biotic and abiotic stressors.These mechanisms arise from strong natural selection that contributes to enhancing the adaptation of forage plants to various stress conditions.Methods such as antisense RNA technology,CRISPR/Cas9 screening,virus-induced gene silencing,and transgenic technology,are commonly utilized for investigating the stress response functionalities of grass genes in both warm-season and cool-season varieties.This review focuses on the functional identification of stress-resistance genes and regulatory elements in grasses.It synthesizes recent studies on mining functional genes,regulatory genes,and protein kinase-like signaling factors involved in stress responses in grasses.Additionally,the review outlines future research directions,providing theoretical support and references for further exploration of(i)molecular mechanisms underlying grass stress responses,(ii)cultivation and domestication of herbage,(iii)development of high-yield varieties resistant to stress,and(iv)mechanisms and breeding strategies for stress resistance in grasses.
文摘A GoBlast system was built to predict gene function by integrating Blast search and Gene Ontology(GO)annotations together.The operation system was based on Debian Linux 3.1,with Apache as the web server and Mysql database as the data storage system.FASTA files with GO annotations were taken as the sequence source for blast alignment,which were formatted by wu-formatdb program.The GoBlast system includes three Bioperl modules in Perl:a data input module,a data process module and a data output module.A GoBlast query starts with an amino acid or nucleotide sequence.It ends with an output in an html page,presenting high scoring gene products which are of a high homology to the queried sequence and listing associated GO terms beside respective gene poducts.A simple click on a GO term leads to the detailed explanation of the specific gene function.This avails gene function prediction by Blast.GoBlast can be a very useful tool for functional genome research and is available for free at http://bioq.org/goblast.
基金supported by the National Natural Science Foundation of China (81571273,81571274,81501124,81271434,and 81301107)Omics-based precision medicine of epilepsy being entrusted by Key Research Project of the Ministry of Science and Technology of China (2016YFC0904400)+5 种基金the Natural Science Foundation of Guangdong Province,China (2014A030313489)Science and Technology Planning Projects of Guangdong Province,China (2012B031800404 and 2013B051000084)the Department of Education of Guangdong Province,China (2013CXZDA022,2013KJCX0156,and 2012KJCX009)the Foundation for High-level Talents in Higher Education of Guangdong Province,China (2013-167)Yangcheng Scholar Research Projects of Guangzhou Municipal College (12A016S and 12A017G)Science and Technology Projects of Guangzhou,Guangdong Province,China (2014J4100069,201508020011,201604020161,and 201607010002)
文摘Ion channels are crucial in the generation and modulation of excitability in the nervous system and have been implicated in human epilepsy. Forty-one epilepsyassociated ion channel genes and their mutations are systematically reviewed. In this paper, we analyzed the genotypes, functional alterations（funotypes）, and phenotypes of these mutations. Eleven genes featured loss-offunction mutations and six had gain-of-function mutations.Nine genes displayed diversified funotypes, among which a distinct funotype-phenotype correlation was found in SCN1A. These data suggest that the funotype is an essential consideration in evaluating the pathogenicity of mutations and a distinct funotype or funotype-phenotype correlation helps to define the pathogenic potential of a gene.
基金supported by the Science Foundation of the Chinese Academy of Sciences (Grant No.KSCX2-YW-N-007)the National Natural Science Foundation of China (Grant No.30370803)+1 种基金the Ministry of Science and Technology of China (Grant No.2005DKA21006)‘Hundred Talents’ Program of the Chinese Academy of Sciences
文摘Rice is a model plant for genomic study of grass species. Functional identification and definition of rice genes becomes the object of its functional genomics research. WRKY gene superfamily, one of the transcription factor gene families, was recently suggested to play important roles in plant development and stress response. In rice, the results of analyses of expression pattern and ectopic overexpressor lines also support this viewpoint, and the evidences implicate rice WRKY proteins in transcriptional reprogramming during biotic or abiotic stresses, senescence, sugar metabolites, and morphological architecture. In this paper, we review the advance in study of rice WRKY gene family and also propose unified nomenclature for rice WRKY factors to eliminate confusion.
基金the support of the National Natural Science Foundation of China under Grant No.60673023,60433020,10501017,3040016the European Commission for TH/Asia Link/010 under Grant No.111084.
文摘It is very important in the field of bioinformatics to apply computer to perform the function annotation for new sequenced bio-sequences. Based on GO database and BLAST program, a novel method for the function annotation of new biological sequences is presented by using the variable-precision rough set theory. The proposed method is applied to the real data in GO database to examine its effectiveness. Numerical results show that the proposed method has better precision, recall-rate and harmonic mean value compared with existing methods.
基金the Hainan Provincial Natural Science Foundation of China(320RC706 and 322RC760)the Central Public-interest Scientific Institution Basal Research Fund(no.1630052022004).
文摘Plant expression vectors are essential tools for gene functional analysis and molecular plant breeding.The gene of interest is transferred to the vector by molecular cloning technology.Nimble Cloning is a newly developed molecular cloning method with the advantages of simplicity,efficiency,and standardization.In this study,we developed a"pNC"vector system that contains 55 Nimble Cloning-compatible vectors for functional analysis of genes in plants.These vectors contain the NC frame flanked by unique adapters for one-step and standardized Nimble Cloning.We demonstrate that the pNC vectors are convenient and effective for the functional analysis of plant genes,including the study of gene ectopic expression,protein subcellular localization,protein-protein interaction,gene silencing(RNAi),virus-induced gene silencing,promoter activity,and CRISPR-Cas9-mediated genome editing.The"pNC"vector system represents a high-throughput toolkit that can facilitate the large-scale analysis of plant functional genomics.
基金Project(51071181)supported by the National Natural Science Foundation of ChinaProject(2013FJ4043)supported by the Natural Science Foundation of Hunan Province,China
文摘Taking AuCu3-type sublattice system as an example, three discoveries have been presented: First, the third barrier hindering the progress in metal materials science is that researchers have got used to recognizing experimental phenomena of alloy phase transitions during extremely slow variation in temperature by equilibrium thinking mode and then taking erroneous knowledge of experimental phenomena as selected information for establishing Gibbs energy function and so-called equilibrium phase diagram. Second, the equilibrium holographic network phase diagrams of AuCu3-type sublattice system may be used to describe systematic correlativity of the composition?temperature-dependent alloy gene arranging structures and complete thermodynamic properties, and to be a standard for studying experimental subequilibrium order-disorder transition. Third, the equilibrium transition of each alloy is a homogeneous single-phase rather than a heterogeneous two-phase, and there exists a single-phase boundary curve without two-phase region of the ordered and disordered phases; the composition and temperature of the top point on the phase-boundary curve are far away from the ones of the critical point of the AuCu3 compound.
基金Project(51071181)supported by the National Natural Science Foundation of ChinaProject(2013FJ4043)supported by the Natural Science Foundation of Hunan Province,China
文摘Taking Au3Cu-type sublattice system as an example, three discoveries have been presented. First, the fourth barrier to hinder the progress of metal materials science is that today’s researchers do not understand that the Gibbs energy function of an alloy phase should be derived from Gibbs energy partition function constructed of alloy gene sequence and their Gibbs energy sequence. Second, the six rules for establishing alloy gene Gibbs energy partition function have been discovered, and it has been specially proved that the probabilities of structure units occupied at the Gibbs energy levels in the degeneracy factor for calculating configuration entropy should be degenerated as ones of component atoms occupied at the lattice points. Third, the main characteristics unexpected by today’s researchers are as follows. There exists a single-phase boundary curve without two-phase region coexisting by the ordered and disordered phases. The composition and temperature of the top point on the phase-boundary curve are far away from those of the critical point of the Au3Cu compound; At 0 K, the composition of the lowest point on the composition-dependent Gibbs energy curve is notably deviated from that of the Au3Cu compounds. The theoretical limit composition range of long range ordered Au3Cu-type alloys is determined by the first jumping order degree.
基金supported by the National Youth Talent Program (A279021801)Key-Area R&D Program of Guangdong province (2022B0202060001)+4 种基金Key R&D Program of Shaanxi Province (2023-YBNY-008)the Science and Technology Innovation Team of Shaanxi (2021TD-32)the Natural Science Foundation of Shaanxi Province (2021JM-089, 2022JM-112 and 2022JQ-162)the Key R&D Project from Yangling Seed Industry Innovation Center (K3031322016)the Fundamental Research Fund from Northwest A&F University (2452022111)。
文摘The nuclear factor Y(NF-Y) gene family is a class of transcription factors that are widely distributed in eukaryotes and are involved in various biological processes. However, the NF-Y gene family members in watermelon, a valued and nutritious fruit, remain largely unknown and their functions have not been characterized. In the present study, 22 ClNF-Y genes in watermelon, 29 CsNF-Y genes in cucumber, and 24CmNF-Y genes in melon were identified based on the whole-genome investigation and their protein properties, gene location, gene structure, motif composition, conserved domain, and evolutionary relationship were investigated. ClNF-YB9 from watermelon and its homologs in cucumber and melon were expressed specifically in seeds. Its expression remained low in the early stages of watermelon seed development,increased at 20 days after pollination(DAP), and peaked at 45–50 DAP. Moreover, the knockout mutant Clnf-yb9 exhibited abnormal leafy cotyledon phenotype, implying its critical role during seed formation.Finally, protein interaction assays showed that ClNF-YB9 interacts with all ClNF-YCs and the ClNF-YB9-YC4 heterodimer was able to recruit a ClNF-YA7 subunit to assemble a complete NF-Y complex, which may function in seed development. This study revealed the structure and evolutionary relationships of the NF-Y gene family in Cucurbitaceae and the novel function of ClNF-YB9 in regulating seed development in watermelon.
基金supported by the Project of the National Ministry of Science and Technology,China (Grant No.2006AA10Z1C8)the Knowledge Innovative Program of the Chinese Academy of Sciences (Grant Nos.KSCX-YW-N-009-02 and KSCX1-YW-03)+1 种基金the National Basic Research Program of China (Grant No.2009CB126004)the Natural Science Foundation of Hainan Province,China (Grant No.309019)
文摘Field resistances of nine accessions of common wild rice （Oryza rufipogon Griff.） and one rice variety （IR24） were evaluated by using nine strains of bacterial blight pathogen （Xanthomonas oryzae pv. oryzae） from the Philippines. IR24 was highly susceptible to all the strains, and six common wild rice accessions resisted all the nine strains, with a resistance frequency of 67%. The accessions Yulin and Wanning were only susceptible to PXO280 and PXO71, respectively. The accession Gaozhou was susceptible to the three strains PXO79, PXO99 and PXO339, whereas resistant to the other six strains. It could be concluded that there is at least one resistance gene in each common wild rice accession. The functional markers of the genes xa5, xa13, Xa21 and Xa27 were used to detect the presence of these resistance genes in the nine tested wild rice accessions, and it was found that four wild rice accessions contained heterozygous xa13. Among the nine common wild rice accessions, five were homozygous for Xa27 and three homozygous for xa27, and the accession Laibin contained neither xa27 nor Xa27. In addition, there were no xa5 and Xa21 in all of these accessions.
基金supported in part by the National Natural Science Foundation of China(Grant Nos.62072243 and 61772273 to Dong-Jun Yu)the Natural Science Foundation of Jiangsu,China(Grant No.BK20201304 to Dong-Jun Yu)+7 种基金the Foundation of National Defense Key Laboratory of Science and Technology,China(Grant No.JZX7Y202001SY000901 to DongJun Yu)the China Scholarship Council(Grant No.201906840041 to Yi-Heng Zhu)the National Institute of Environmental Health Sciences,USA(Grant No.P30ES017885 to Gilbert S.Omenn)the National Cancer Institute,USA(Grant No.U24CA210967 to Gilbert S.Omenn)the National Institute of General Medical Sciences,USA(Grant Nos.GM136422 and S10OD026825 to Yang Zhang)the National Institute of Allergy and Infectious Diseases,USA(Grant No.AI134678 to Peter L.Freddolino and Yang Zhang)the National Science Foundation,USA(Grant Nos.IIS1901191,DBI2030790,and MTM2025426 to Yang Zhang)used the Extreme Science and Engineering Discovery Environment(XSEDE),which is supported by the National Science Foundation,USA(Grant No.ACI1548562)。
文摘Gene Ontology(GO)has been widely used to annotate functions of genes and gene products.Here,we proposed a new method,Triplet GO,to deduce GO terms of protein-coding and noncoding genes,through the integration of four complementary pipelines built on transcript expression profile,genetic sequence alignment,protein sequence alignment,and naīve probability.Triplet GO was tested on a large set of 5754 genes from 8 species(human,mouse,Arabidopsis,rat,fly,budding yeast,fission yeast,and nematoda)and 2433 proteins with available expression data from the third Critical Assessment of Protein Function Annotation challenge(CAFA3).Experimental results show that Triplet GO achieves function annotation accuracy significantly beyond the current state-of-the-art approaches.Detailed analyses show that the major advantage of Triplet GO lies in the coupling of a new triplet network-based profiling method with the feature space mapping technique,which can accurately recognize function patterns from transcript expression profiles.Meanwhile,the combination of multiple complementary models,especially those from transcript expression and protein-level alignments,improves the coverage and accuracy of the final GO annotation results.The standalone package and an online server of Triplet GO are freely available at https://zhanggroup.org/Triplet GO/.
基金the National Natural Science Foundation of China （Grant No. 60234020）.
文摘Computational analysis is essential for transforming the masses of microarray datainto a mechanistic understanding of cancer. Here we present a method for findinggene functional modules of cancer from microarray data and have applied it tocolon cancer. First, a colon cancer gene network and a normal colon tissue genenetwork were constructed using correlations between the genes. Then the modulesthat tended to have a homogeneous functional composition were identified by split-ting up the network. Analysis of both networks revealed that they are scale-free.Comparison of the gene functional modules for colon cancer and normal tissuesshowed that the modules’ functions changed with their structures.
文摘With the development of bioinformatics,it is easy to obtain information and data about thousands of genes,but the determi nation of the functions of these genes depends on methods for rapid and effective functi on al identification.Virus-induced gene sile ncing(VIGS)is a mature method of gene functional identification developed over the last 20 years,which has been widely used in many research fields involving many species.Fruit quality formation is a complex biological process,which is closely related to ripening.Here,we review the progress and contribution of VIGS to our understanding of fruit biology and its advantages and disadvantages in determining gene function.
基金funded by the Key-Area Research and Development Program of Guangdong Province(Grant No.2022B0202070002)the Guangxi Science and Technology Major Program(Grant No.GuikeAA23023007-2)+1 种基金the Guangdong Province Modern Agricultural Industry Technology System Innovation Team Construction Project(2024CXTD19)Guangdong Basic and Applied Basic Research Foundation(Grant No.2023A1515010303)。
文摘Agrobacterium tumefaciens-mediated transformation has been widely adopted for plant genetic engineering and the study of gene function(Krenek et al.,2015).This method is prevalent in the genetic transformation of herbaceous plants,with notable applications in species such as Arabidopsis(Yin et al.,2024),soybean(Zhang et al.,2024),rice(Zhang et al.,2020),and Chinese cabbage(Li et al.,2021).However,its application in fruit trees is limited.This is primarily due to their long growth cycles and lack of rapid,efficient,and stable transgenic systems,which severely hinders foundational research involving plant genetic transformation(Mei et al.,2024).Furthermore,for subtropical fruit trees,the presence of recalcitrant seeds adds an extra layer of difficulty to genetic transformation(Umarani et al.,2015),as most methods rely on seed germination as a basis for transformation.
基金Supported by Tianjin Municipal Science and Technology Commission Grant,No.24ZXRKSY00010Program for Innovative Research Team in Peking Union Medical College,CAMS Initiative for Innovative Medicine,No.2023-I2M-2-008.
文摘Inflammatory bowel disease(IBD)is an incurable disease of the digestive system;however,the therapeutic methods for IBD remain limited.The pathogenesis of IBD was systematically discussed and compared in this paper,primarily comprising Crohn’s disease and ulcerative colitis.This paper focused on six common aspects:(1)Dysregulated immune responses;(2)Gene function changes;(3)Intestinal microbes disorder and imbalance;(4)Microbial infections;(5)Associations between IBD and other inflammatory diseases;and(6)Other factors.In addition,the pathogenesis differences between these two forms of IBD were unraveled and clearly distinguished.These unique aspects of pathogenesis provide crucial insights for the precise treatment of both Crohn’s disease and ulcerative colitis.This paper illustrates the root causes and beneficial factors of resistance to IBD,which provides novel insights on early prevention,development of new therapeutic agents,and treatment options of this disease.
基金supported by the Key Research&Developmental Program of Shandong Province(Nos.2021CXGC011202,2020CXGC011404)the Beijing Natural Science Foundation(No.8192004)the Beijing Major Science and Technology Projects(No.Z181100005318001)
文摘The long-term impact of fulvic acid(FA)on partial nitritation(PN)systemwas initially examined in this study.The obtained results revealed that the FA lower than 50 mg/L had negligible effect on the nitrite accumulation rate(NAR nearly 100%)and ammonium removal rate(ARR 56.85%),while FA over 50 mg/L decreased ARR from 56.85%to 0.7%.Sludge characteristics analysis found that appropriate FA(<50 mg/L)exposure promoted the settling performance and granulation of PN sludge by removing Bacteroidetes and accumulating Chloroflexi.The analysis of metagenomics suggested that the presence of limited FA(0-50 mg/L)stimulated the generation of NADH,which favors the denitrification and nitrite reduction.The negative impact of FA on the PN system could be divided into two stages.Initially,limited FA(50-120 mg/L)was decomposed by Anaerolineae to stimulate the growth and propagation of heterotrophic bacteria(Thauera).Increasing heterotrophs competed with AOB(Nitrosomonas)for dissolved oxygen,causing AOB to be eliminated and ARR to declined.Subsequently,when FA dosage was over 120 mg/L,Anaerolineae were inhibited and heterotrophic bacteria reduced,resulting in the abundance of AOB recovered.Nevertheless,the ammonium transformation pathway was suppressed because genes amoABC and hao were obviously reduced,leading to the deterioration of reactor performance.Overall,these results provide theoretical guidance for the practical application of PN for the treatment of FA-containing sewage.
基金supported by the National Transgenic Crops Program, China (Grant No. 2008ZX08001-006)the Research Funds for Public Benefit in Ministry of Agriculture, China (Grant No. 200803056)+1 种基金the Key Support Program of Jiangsu Science and Technology, China (Grant No. BE2008354)the Self-directed Innovation Fund of Agricultural Science and Technology in Jiangsu Province, China (Grant No. CX [08]603)
文摘Rice with low glutelin content is suitable as functional food for patients affected by kidney failure. Low glutelincontent gene Lgc1 in rice has a 3.5-kb deletion between two highly similar glutelin genes GluB4 and GluB5, which locates on the short arm of chromosome 2. To improve the selection efficiency in low glutelin-content rice breeding, two molecular markers designated as InDel-Lgc1-1 and InDel-Lgc1-2 were developed to detect the low glutelin-content gene Lgc1. A double PCR detection indicated that combined use of the two markers could easily distinguish the genotypes of Lgc1 from different rice varieties. Therefore, as a simple and low-cost technique, the molecular marker could be widely used to identify different varieties with Lgc1 gene and applied in marker-assisted selection of low glutelin-content rice.
