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
Aspergillus species are ubiquitous fungi that produce mycotoxins(secondary metabolites)known as sterigmatocystin and aflatoxins in many different kinds of foods,which leads to serious contamination in agricultural pro...Aspergillus species are ubiquitous fungi that produce mycotoxins(secondary metabolites)known as sterigmatocystin and aflatoxins in many different kinds of foods,which leads to serious contamination in agricultural products,thereby endangering human health.Extensive studies on Aspergillus fungi have been conducted on growth and development,aflatoxin biosynthesis,and their interactions with environment.Here,we summarized a series of functional genes of the main Aspergillus fungi relative to toxins occurrence in foods,which revealed the signal transduction mechanisms of their involvement in growth and development,toxin production,and response to light,anticipating providing theoretical guidance on developing control and prevention technologies for mycotoxin contamination in agricultural products to ensure food safety.展开更多
Antibiotic contamination has garnered significant attention,particularly given the growing pressures from aquaculture,a key contributor to environmental antibiotic loads.Addressing both antibiotic and nitrogen polluti...Antibiotic contamination has garnered significant attention,particularly given the growing pressures from aquaculture,a key contributor to environmental antibiotic loads.Addressing both antibiotic and nitrogen pollution in such ecosystems is critical.In this study,the aerobic denitrifying bacterium Marinobacter hydrocarbonoclasticus RAD-2,previously isolated in our laboratory,was subjected to a series of concentration gradients(0,20,40,60,80,100 mg/L)to evaluate the single and combined effects of tetracycline(TET)and chlortetracycline(CTC)on the aerobic denitrification process.Among them,the combined effects of antibiotics were set up in a full-factor experimental design(a total of 30 treatment combinations)on the basis of the single-factor experiments of TET and CTC.Results demonstrated that the inhibitory impact of both antibiotics intensified with increasing concentration,with CTC exerting a more pronounced inhibitory effect.Notably,RAD-2 was unable to proliferate at 100 mg/L of TET or 80 mg/L of CTC.High concentrations of either antibiotic significantly suppressed the expression of key denitrification functional genes,including nirX,napA,norB,and nosZ.Furthermore,simultaneous exposure to both antibiotics led to a rapid decline in nitrogen removal efficiency(TET or CTC>60 mg/L),alongside substantial inhibition of bacterial growth and functional gene expression,except for napA.Under specific concentration ranges,the combination of TET and CTC exhibits a certain degree of antagonistic effect.These findings provide critical insights into the restoration of wetland ecosystem health and inform strategies to mitigate the dual challenges of antibiotic and nitrogen pollution in aquaculture effluents.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
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
Dear Editor,A few studies have focused on exploring APOE gene- related effects on cognitive functions and brain activities in healthy populations. Bondi et aL found that ε4 carriers perform significantly worse on the...Dear Editor,A few studies have focused on exploring APOE gene- related effects on cognitive functions and brain activities in healthy populations. Bondi et aL found that ε4 carriers perform significantly worse on the California Verbal Learning Test than non-carriers in non-demented old subjects （mean age, 72 years）ε11. But the results are not entirely consistent. For example, Scarmeas et aL found no effect of the E4 allele on neuropsychological performance[2] in young adults, and Jochemsen et al. found that the ε4 allele is associated with age-related cognitive decline[3]. Furthermore, protective and negative effects of the E2 allele on cognition are inconsistent[4＇ s]. APOE E2 is thought to be a protective allele for AD in the elderly population due to its role in the superior cognitive performance of ε2 carriers compared to E3 or E4 carriers[5]. However, the ε2 allele has also been found to have a negative effect on AD pathology[4].展开更多
Microorganisms actively participate in biogeochemical cycling processes and play a crucial role in maintaining the dynamic balance of hot spring ecosystems.However,the distribution of microbial functional genes and th...Microorganisms actively participate in biogeochemical cycling processes and play a crucial role in maintaining the dynamic balance of hot spring ecosystems.However,the distribution of microbial functional genes and their influencing factors in hot springs remain largely unclear.Therefore,this study investigated the microbial functional genes and their potential for controlling biogeochemical cycles(C,N,S,and P) in the hot Springs of Tengchong,China,using the Geochip method,a functional gene microarray technology.The examined hot springs have very different microbial functional genes.A total of 22 736 gene probe signals were identified,belonging to 567 functional genes and associated with 15 ecological functions,mainly involving stress response,carbon cycle,nitrogen cycle,sulfur cycle,phosphorus cycle and energy processes.The amyA,narG,dsrA and ppx genes were most abundant in carbon,nitrogen,sulfur and phosphorus cycles,respectively,and were significantly correlated with pH,temperature and SO_(4)^(2-).The diversity and abundance of detected gene probes were negatively correlated with temperature.The α-diversity(i.e.,Shannon index) was high at low temperature and low pH.Molecular functional interactions revealed by the gene connectivity levels were negatively correlated with temperature,pH and SO_(4)^(2-).These results suggested that the abundance,diversity and interactions of microbial functional genes were significantly influenced by geochemical parameters.-In addition,some genera possessed functional genes related to carbon,nitrogen,sulfur,and phosphorus cycles and can synergistically control the biogeochemical cycles of carbon,nitrogen,sulfur and phosphorus.These findings provide new insights into the functional potentials of microorganisms to participate in biogeochemical cycles and their responses to environmental factors in hot springs.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
Low temperature is one of the main environmental stress factors influenc- ing plant growth and development and crop yield. Cold tolerance genes and progress of their application in genetic engineering of plant for col...Low temperature is one of the main environmental stress factors influenc- ing plant growth and development and crop yield. Cold tolerance genes and progress of their application in genetic engineering of plant for cold tolerance were reviewed comprehensively and systematically from the aspect of genes that are in- volved in biosynthesis of osmotic substances, genes coding fatty acid desaturation enzymes, antifreeze protein genes, genes coding antioxidant enzymes and so on, aiming at laying the foundation for genetic improvement of cold tolerance and breeding of plants.展开更多
Leaf thickness in rice critically influences photosynthetic efficiency and yield,yet its genetic basis remains poorly understood,with few functional genes previously characterized.In this study,we employ a pangenome-w...Leaf thickness in rice critically influences photosynthetic efficiency and yield,yet its genetic basis remains poorly understood,with few functional genes previously characterized.In this study,we employ a pangenome-wide association study(Pan-GWAS)on 302 diverse rice accessions from southern China,identifying 49 quantitative trait loci(QTLs)associated with leaf thickness.The most significant locus,qLT9,is fine-mapped to a 79-kb region on chromosome 9.Transcriptomic and genomic sequence analyses identify LOC_Os09g33480,which encodes a protein belonging to Multiple Organellar RNA Editing Factor family,as the key candidate gene.Overexpression and complementation transgenic experiments confirm LOC_Os09g33480(OsLT9)as the functional gene underlying qLT9,demonstrating a 24-bp Indel in its promoter correlates with the expression levels and leaf thickness.Notably,OsLT9 overexpression lines show not only thicker leaf,but also significantly enhanced photosynthetic efficiency and grain yield,establishing a link between leaf thickness modulation and yield enhancement.Population genomic analyses indicate strong selection for OsLT9 during domestication and breeding,with modern cultivars favoring thick leaf haplotype of OsLT9.This study establishes OsLT9 as a key regulator controlling leaf thickness in rice,and provides a valuable genetic resource for molecular breeding of high-yielding rice through optimization of plant architecture.展开更多
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
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
Zostera marina, a monocotyledonous angiosperm, is one of the most important seagrass species. To inves- tigate the salt-tolerance mechanism and discover salt-tolerant genes in Z. marina, a cDNA library was con- struct...Zostera marina, a monocotyledonous angiosperm, is one of the most important seagrass species. To inves- tigate the salt-tolerance mechanism and discover salt-tolerant genes in Z. marina, a cDNA library was con- structed. Single-pass sequencing of the 5＇ ends of 4 081 clones yielded 4 002 high quality expressed sequence tags （ESTs）, which were assembled into 241 contigs and 1 673 singletons, representing 1 914 unigenes. The average length of the ESTs was 582 bp, with sizes ranging from 100-1 500 bp. Basic Local Alignment Search Tool （BLASTX） analysis revealed that 1 664 unigenes had significant homology to known genes in the Na- tional Center for Biotechnology Information （NCBI） non-redundant （nr） database （E-value≤5-10）. Among them, the two most abundant genes encoded metallothionein （157 ESTs） and chlorophyll a/b-binding pro- tein （38 ESTs）, accounting for 7.1% and 1.7% of the total ESTs, respectively. Using Kyoto Encyclopedia of Genes and Genomes （KEGG）, 1 462 unigenes were assigned to 1 161 pathways （E-value≤5-10）. A total of 938 unigenes were assigned Gene Ontology （GO） terms based on the GO hierarchy analysis, and InterProScan searches recognized 1 003 InterPro families. Three genes for metallothionein in Z. marina that belonged to Class II was identified. Results of this study will improve understanding of the molecular mechanisms of saline tolerance in Z. marina.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
Curvularia leaf spot, caused mainly by Curvularia lunata, is a widespread plant disease in China. In the recent years, di- rectional host selection by the pathogen, which likely results in the virulence differentiatio...Curvularia leaf spot, caused mainly by Curvularia lunata, is a widespread plant disease in China. In the recent years, di- rectional host selection by the pathogen, which likely results in the virulence differentiation in pathogens, is widely reported. Among the hallmarks potentially associated to pathogen variation in virulence, superoxide dismutase gene Sod has been found to be closely related to the enhancement of virulence. In the present study, the full-length of Sod was obtained via Blastn alignment against GenBank and the whole genome of C. lunata. In order to understand the role of Sod in the vir- ulence variation in C. lunata, targeted gene disruption was performed to construct Sod mutants. The cell wall degrading enzyme （CWDE） activities and toxin production of ASod were not distinctly different from wild-type strain CX-3 and its complon. However, at an early stage of infection, 3Sod virulence appeared to be lower than CX-3 and the complon, while at a later stage, its virulence gradually returned to the level of CX-3 and the complon. Furthermore, the melanin production of ASod was significantly reduced compared to CX-3 and the complon, suggesting that Sod gene influences the virulence by regulating melanin production at an early stage of infection but is not essential for pathogenicity. However, the disruption of Sod did not significantly affect the transcriptional expression of the melanin biosynthesis-associated genes, bml and scd. Therefore, we infer that Sod in C. lunata are involved, to some extent, with the virulence in maize leaf, but still needs further studies to have a clear understanding of its mechanism.展开更多
Members of the activity of bc1 complex (ABC1) family are protein kinases that are widely found in prokaryotes and eukaryotes. Previous studies showed that several plant ABC1 genes participated in the abiotic stress re...Members of the activity of bc1 complex (ABC1) family are protein kinases that are widely found in prokaryotes and eukaryotes. Previous studies showed that several plant ABC1 genes participated in the abiotic stress response. Here, we present the systematic identification of rice and Arabidopsis ABC1 genes and the expression analysis of rice ABC1 genes. A total of 15 and 17 ABC1 genes from the rice and Arabidopsis genomes, respectively, were identified using a bioinformatics approach. Phylogenetic analyses of these proteins suggested that the divergence of this family had occurred and their main characteristics were established before the monocot-dicot split. Indeed, species-specific expansion contributed to the evolution of this family in rice and Arabidopsis after the monocot-dicot split. Intron/exon structure analysis indicated that most of the orthologous genes had similar exon sizes, but diverse intron sizes, and the rice genes contained larger introns, moreover, intron gain was an important event accompanying the recent evolution of the rice ABC1 family. Multiple sequence alignment revealed one conserved amino acid segment and four conserved amino acids in the ABC1 domain. Online subcellular localization predicted that nine rice ABC1 proteins were localized in chloroplasts. Real-time RT-PCR established that the rice ABC1 genes were primarily expressed in leaves and the expression could be modulated by a broad range of abiotic factors such as H2O2, abscisic acid, low temperature, drought, darkness and high salinity. These results reveal that the rice ABC1 gene family plays roles in the environmental stress response and specific biological processes of rice.展开更多
Lipoxygenase 3 (LOX3) is a major component of the LOX isozymes in mature rice seeds. To investigate the role of LOX3 gene under stresses, a plant expression vector containing antisense cDNA of LOX3 was constructed. Ri...Lipoxygenase 3 (LOX3) is a major component of the LOX isozymes in mature rice seeds. To investigate the role of LOX3 gene under stresses, a plant expression vector containing antisense cDNA of LOX3 was constructed. Rice varieties Wuyunjing 7 and Kasalath were transformed by the Agrobacterium-mediated method and transgenic rice plants were generated. PCR and Southern blot results showed that the antisense LOX3 gene was integrated into the rice genome. Analyses of embryo LOX3 deletion and semi-quantitative RT-PCR confirmed the antisense suppression of LOX3 gene in transgenic plants. The T2 antisense plants of LOX3 were sensitive to drought stress, rice blast and bacterial blight compared with non-transgenic plants. These results suggest that the LOX3 gene might function in response to stresses.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
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 key project of National Natural Sciences Foundation of China(U22A20551,32030085)the Major Project of Hubei Hongshan Laboratory,China(2021hszd015)+2 种基金the Hubei Province Major Science and Technology Special Project,China(2023BBA002)the National Natural Sciences Foundation of China(U22A20551)the National Natural Science Foundation of China Excellent Youth Fund(32422072)。
文摘Aspergillus species are ubiquitous fungi that produce mycotoxins(secondary metabolites)known as sterigmatocystin and aflatoxins in many different kinds of foods,which leads to serious contamination in agricultural products,thereby endangering human health.Extensive studies on Aspergillus fungi have been conducted on growth and development,aflatoxin biosynthesis,and their interactions with environment.Here,we summarized a series of functional genes of the main Aspergillus fungi relative to toxins occurrence in foods,which revealed the signal transduction mechanisms of their involvement in growth and development,toxin production,and response to light,anticipating providing theoretical guidance on developing control and prevention technologies for mycotoxin contamination in agricultural products to ensure food safety.
基金supported by the Science Fund for Distinguished Young Scholars of Zhejiang Province(No.LR22C190001)the National Natural Science Foundation of China(No.41401556).
文摘Antibiotic contamination has garnered significant attention,particularly given the growing pressures from aquaculture,a key contributor to environmental antibiotic loads.Addressing both antibiotic and nitrogen pollution in such ecosystems is critical.In this study,the aerobic denitrifying bacterium Marinobacter hydrocarbonoclasticus RAD-2,previously isolated in our laboratory,was subjected to a series of concentration gradients(0,20,40,60,80,100 mg/L)to evaluate the single and combined effects of tetracycline(TET)and chlortetracycline(CTC)on the aerobic denitrification process.Among them,the combined effects of antibiotics were set up in a full-factor experimental design(a total of 30 treatment combinations)on the basis of the single-factor experiments of TET and CTC.Results demonstrated that the inhibitory impact of both antibiotics intensified with increasing concentration,with CTC exerting a more pronounced inhibitory effect.Notably,RAD-2 was unable to proliferate at 100 mg/L of TET or 80 mg/L of CTC.High concentrations of either antibiotic significantly suppressed the expression of key denitrification functional genes,including nirX,napA,norB,and nosZ.Furthermore,simultaneous exposure to both antibiotics led to a rapid decline in nitrogen removal efficiency(TET or CTC>60 mg/L),alongside substantial inhibition of bacterial growth and functional gene expression,except for napA.Under specific concentration ranges,the combination of TET and CTC exhibits a certain degree of antagonistic effect.These findings provide critical insights into the restoration of wetland ecosystem health and inform strategies to mitigate the dual challenges of antibiotic and nitrogen pollution in aquaculture effluents.
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 the National Natural Science Foundation of China (81130024)the National Key Technology R & D Program of the Ministry of Science and Technology of China during the 12th Five-Year Plan (2012BAI01B06)
文摘Dear Editor,A few studies have focused on exploring APOE gene- related effects on cognitive functions and brain activities in healthy populations. Bondi et aL found that ε4 carriers perform significantly worse on the California Verbal Learning Test than non-carriers in non-demented old subjects （mean age, 72 years）ε11. But the results are not entirely consistent. For example, Scarmeas et aL found no effect of the E4 allele on neuropsychological performance[2] in young adults, and Jochemsen et al. found that the ε4 allele is associated with age-related cognitive decline[3]. Furthermore, protective and negative effects of the E2 allele on cognition are inconsistent[4＇ s]. APOE E2 is thought to be a protective allele for AD in the elderly population due to its role in the superior cognitive performance of ε2 carriers compared to E3 or E4 carriers[5]. However, the ε2 allele has also been found to have a negative effect on AD pathology[4].
基金supported by grants from the National Natural Science Foundation of China(Nos.42172339,91951205)。
文摘Microorganisms actively participate in biogeochemical cycling processes and play a crucial role in maintaining the dynamic balance of hot spring ecosystems.However,the distribution of microbial functional genes and their influencing factors in hot springs remain largely unclear.Therefore,this study investigated the microbial functional genes and their potential for controlling biogeochemical cycles(C,N,S,and P) in the hot Springs of Tengchong,China,using the Geochip method,a functional gene microarray technology.The examined hot springs have very different microbial functional genes.A total of 22 736 gene probe signals were identified,belonging to 567 functional genes and associated with 15 ecological functions,mainly involving stress response,carbon cycle,nitrogen cycle,sulfur cycle,phosphorus cycle and energy processes.The amyA,narG,dsrA and ppx genes were most abundant in carbon,nitrogen,sulfur and phosphorus cycles,respectively,and were significantly correlated with pH,temperature and SO_(4)^(2-).The diversity and abundance of detected gene probes were negatively correlated with temperature.The α-diversity(i.e.,Shannon index) was high at low temperature and low pH.Molecular functional interactions revealed by the gene connectivity levels were negatively correlated with temperature,pH and SO_(4)^(2-).These results suggested that the abundance,diversity and interactions of microbial functional genes were significantly influenced by geochemical parameters.-In addition,some genera possessed functional genes related to carbon,nitrogen,sulfur,and phosphorus cycles and can synergistically control the biogeochemical cycles of carbon,nitrogen,sulfur and phosphorus.These findings provide new insights into the functional potentials of microorganisms to participate in biogeochemical cycles and their responses to environmental factors in hot springs.
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 National Natural Science Foundation of China(30871512,31000701)Startup Foundation for Advanced Talents of Henan Academy of Agricultural Sciences(2060503)~~
文摘Low temperature is one of the main environmental stress factors influenc- ing plant growth and development and crop yield. Cold tolerance genes and progress of their application in genetic engineering of plant for cold tolerance were reviewed comprehensively and systematically from the aspect of genes that are in- volved in biosynthesis of osmotic substances, genes coding fatty acid desaturation enzymes, antifreeze protein genes, genes coding antioxidant enzymes and so on, aiming at laying the foundation for genetic improvement of cold tolerance and breeding of plants.
基金supported by the National Natural Science Foundation of China(32301845)GuangDong Basic and Applied Basic Research Foundation(2022A1515012339)+3 种基金the National Key R&D Program of China(2024YFD1200801)Seed industry revitalization project of special fund for rural revitalization strategy in Guangdong Province(2024-NPY-00-001)Modern Seed Industry Innovation Capacity Enhancement Progject of Guangdong Academy of Agricultural Sciences,Elite Rice Plan of GDRRI(2023YG01)Guangdong Key Laboratory of Rice Science and Technology(2023B1212060042).
文摘Leaf thickness in rice critically influences photosynthetic efficiency and yield,yet its genetic basis remains poorly understood,with few functional genes previously characterized.In this study,we employ a pangenome-wide association study(Pan-GWAS)on 302 diverse rice accessions from southern China,identifying 49 quantitative trait loci(QTLs)associated with leaf thickness.The most significant locus,qLT9,is fine-mapped to a 79-kb region on chromosome 9.Transcriptomic and genomic sequence analyses identify LOC_Os09g33480,which encodes a protein belonging to Multiple Organellar RNA Editing Factor family,as the key candidate gene.Overexpression and complementation transgenic experiments confirm LOC_Os09g33480(OsLT9)as the functional gene underlying qLT9,demonstrating a 24-bp Indel in its promoter correlates with the expression levels and leaf thickness.Notably,OsLT9 overexpression lines show not only thicker leaf,but also significantly enhanced photosynthetic efficiency and grain yield,establishing a link between leaf thickness modulation and yield enhancement.Population genomic analyses indicate strong selection for OsLT9 during domestication and breeding,with modern cultivars favoring thick leaf haplotype of OsLT9.This study establishes OsLT9 as a key regulator controlling leaf thickness in rice,and provides a valuable genetic resource for molecular breeding of high-yielding rice through optimization of plant architecture.
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 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 Key Science and Technology Program of Shandong Province under contract No. 2012GHY11527Natural Science Foundation of Shandong Province under contract No. Q2007E02+1 种基金Specialized Research Fund for the Doctoral Program of Higher Education (New Teachers) under contract No. 20070423027the Public Science and Technology Research Funds Projects of Ocean, State Oceanic Administration of the People’s Republic of China under contract No. 201105021-8
文摘Zostera marina, a monocotyledonous angiosperm, is one of the most important seagrass species. To inves- tigate the salt-tolerance mechanism and discover salt-tolerant genes in Z. marina, a cDNA library was con- structed. Single-pass sequencing of the 5＇ ends of 4 081 clones yielded 4 002 high quality expressed sequence tags （ESTs）, which were assembled into 241 contigs and 1 673 singletons, representing 1 914 unigenes. The average length of the ESTs was 582 bp, with sizes ranging from 100-1 500 bp. Basic Local Alignment Search Tool （BLASTX） analysis revealed that 1 664 unigenes had significant homology to known genes in the Na- tional Center for Biotechnology Information （NCBI） non-redundant （nr） database （E-value≤5-10）. Among them, the two most abundant genes encoded metallothionein （157 ESTs） and chlorophyll a/b-binding pro- tein （38 ESTs）, accounting for 7.1% and 1.7% of the total ESTs, respectively. Using Kyoto Encyclopedia of Genes and Genomes （KEGG）, 1 462 unigenes were assigned to 1 161 pathways （E-value≤5-10）. A total of 938 unigenes were assigned Gene Ontology （GO） terms based on the GO hierarchy analysis, and InterProScan searches recognized 1 003 InterPro families. Three genes for metallothionein in Z. marina that belonged to Class II was identified. Results of this study will improve understanding of the molecular mechanisms of saline tolerance in Z. marina.
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 National Natural Science Foundation of China(31171798 and 31471734)the China Agriculture Research System,China(CARS-02)
文摘Curvularia leaf spot, caused mainly by Curvularia lunata, is a widespread plant disease in China. In the recent years, di- rectional host selection by the pathogen, which likely results in the virulence differentiation in pathogens, is widely reported. Among the hallmarks potentially associated to pathogen variation in virulence, superoxide dismutase gene Sod has been found to be closely related to the enhancement of virulence. In the present study, the full-length of Sod was obtained via Blastn alignment against GenBank and the whole genome of C. lunata. In order to understand the role of Sod in the vir- ulence variation in C. lunata, targeted gene disruption was performed to construct Sod mutants. The cell wall degrading enzyme （CWDE） activities and toxin production of ASod were not distinctly different from wild-type strain CX-3 and its complon. However, at an early stage of infection, 3Sod virulence appeared to be lower than CX-3 and the complon, while at a later stage, its virulence gradually returned to the level of CX-3 and the complon. Furthermore, the melanin production of ASod was significantly reduced compared to CX-3 and the complon, suggesting that Sod gene influences the virulence by regulating melanin production at an early stage of infection but is not essential for pathogenicity. However, the disruption of Sod did not significantly affect the transcriptional expression of the melanin biosynthesis-associated genes, bml and scd. Therefore, we infer that Sod in C. lunata are involved, to some extent, with the virulence in maize leaf, but still needs further studies to have a clear understanding of its mechanism.
基金supported by grants from the National Program on the Development of Basic Research of China (Grant No. 2006CB101700)the National Natural Science Foundation of China (Grant No. 30971846)the Vital Project of Natural Science in Universities of Jiangsu Province, China (Grant No. 09KJA210002)
文摘Members of the activity of bc1 complex (ABC1) family are protein kinases that are widely found in prokaryotes and eukaryotes. Previous studies showed that several plant ABC1 genes participated in the abiotic stress response. Here, we present the systematic identification of rice and Arabidopsis ABC1 genes and the expression analysis of rice ABC1 genes. A total of 15 and 17 ABC1 genes from the rice and Arabidopsis genomes, respectively, were identified using a bioinformatics approach. Phylogenetic analyses of these proteins suggested that the divergence of this family had occurred and their main characteristics were established before the monocot-dicot split. Indeed, species-specific expansion contributed to the evolution of this family in rice and Arabidopsis after the monocot-dicot split. Intron/exon structure analysis indicated that most of the orthologous genes had similar exon sizes, but diverse intron sizes, and the rice genes contained larger introns, moreover, intron gain was an important event accompanying the recent evolution of the rice ABC1 family. Multiple sequence alignment revealed one conserved amino acid segment and four conserved amino acids in the ABC1 domain. Online subcellular localization predicted that nine rice ABC1 proteins were localized in chloroplasts. Real-time RT-PCR established that the rice ABC1 genes were primarily expressed in leaves and the expression could be modulated by a broad range of abiotic factors such as H2O2, abscisic acid, low temperature, drought, darkness and high salinity. These results reveal that the rice ABC1 gene family plays roles in the environmental stress response and specific biological processes of rice.
基金supported by the grants from the National Basic Research Program of China (Grant No. 2004CB117204 and No. 2006CB100200).
文摘Lipoxygenase 3 (LOX3) is a major component of the LOX isozymes in mature rice seeds. To investigate the role of LOX3 gene under stresses, a plant expression vector containing antisense cDNA of LOX3 was constructed. Rice varieties Wuyunjing 7 and Kasalath were transformed by the Agrobacterium-mediated method and transgenic rice plants were generated. PCR and Southern blot results showed that the antisense LOX3 gene was integrated into the rice genome. Analyses of embryo LOX3 deletion and semi-quantitative RT-PCR confirmed the antisense suppression of LOX3 gene in transgenic plants. The T2 antisense plants of LOX3 were sensitive to drought stress, rice blast and bacterial blight compared with non-transgenic plants. These results suggest that the LOX3 gene might function in response to stresses.
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.
