The structure genes spike(S) ,nucleocapsid(N) ,membrane(M) ,small membrane(sM) of a porcine epidemic diarrhea virus(PEDV) strain DX isolated in Gansu province,North-west of China,were cloned,sequenced and compared wit...The structure genes spike(S) ,nucleocapsid(N) ,membrane(M) ,small membrane(sM) of a porcine epidemic diarrhea virus(PEDV) strain DX isolated in Gansu province,North-west of China,were cloned,sequenced and compared with published sequences of PEDV strains. The nucleotide sequences encoding the entire S,sM,M and N genes open reading frame(ORF) of DX were 4 152,231,681 and 1 326 bases long respectively. There were transcription regulatory sequences(TRSs) upstream of the initiator ATG of the S,N and M genes. The amino acids sequences of S,M and N contained 30,3 and 7 potential asparagine(N) -linked glycosylation sites. Homologous analysis and phylogenetic trees showed that DX had the closest relationship with strains LJB/06,JS-2004-2Z and CH/HLJH/06 that were also isolated from China and indicated the prevalence of some PEDV isolates in China were widespread since the JS-2004-2Z strain originated from the south of the China,and LJB/06 and CH/HLJH/06 were isolated from northeast China. The N gene was cloned using two primers which contained Nco I and BamH I restriction enzyme sites and subcloned into expression vector pET30a. The recombinant plasmid was then transformed into E.coli Rossta. SDS-PAGE showed there was a protein of about 55kDa as expected and Western blot indicated the N protein had biological activity.展开更多
Population-wide genetic structure was studied using fluorescent-AFLP markers on 85 apricot （Prunus armeniaca L.） cultivars collected from Kuche, Kashi, Hetian in the Tarim Basin, southern Xinjiang Uygur Autonomous R...Population-wide genetic structure was studied using fluorescent-AFLP markers on 85 apricot （Prunus armeniaca L.） cultivars collected from Kuche, Kashi, Hetian in the Tarim Basin, southern Xinjiang Uygur Autonomous Region of China. The purpose of this study was to determine the genetic structure and genotypic diversity among the different eco-geographical populations. Based on the results from this study, 8 pairs of fluorescent-AFLP primers showed clear electrophoregram and high polymorphism amongst the 64 pairs of EcoR Ⅰ/Mse Ⅰ （Mse Ⅰ - a FAM fluorescent marked primer） primers screened. There was a significant polymorphic difference for the same primer pair in different populations and for the same population with different primer pairs. The percentage of polymorphic loci （P） at species level was higher than Kuche, Hetian, Kashi population levels, respectively. The Nei＇s gene diversity index （H） and Shannon＇s information index （I） at species level were higher than those of Kuche, Hetian, and Kashi at population level, respectively. H and I of Kuche population were the highest amongst the three populations. Apricot population genetic diversity was found mainly within the population, Genetic differentiation coefficient between populations （GST） was 0.0882. Gene flow Nm between the populations was 5.1689. Population genetic identity was between 0.9772-0.9811 and genetic distance was between 0.0191-0.0232. These results further indicated that the similarity between populations was higher and the genetic distance between populations was smaller. The UPGMA cluster analysis indicates that the geographical populations at Kuche, Kashi, Hetian were relatively independent Mendelian populations. Concurrently, there was also partial gene exchange between the populations. All the evidences indicated that the genetic diversity in Kuche population was the highest, suggesting that it could be a transition population from wild apricot to cultivated apricot. There were abundant genetic diversities in apricot cultivar populations in southern Xinjiang, China, which provide promising germplasm for further breeding and theoretical basis for biodiversity conservation and utilization for apricot population in this area.展开更多
Diaphanes is the fourth largest genus in Lampyridae, but no luciferase gene from this genus has been reported. In this paper, by PCR amplification of the genomic DNA, the luciferase gene of Diaphanes pectinealis, whic...Diaphanes is the fourth largest genus in Lampyridae, but no luciferase gene from this genus has been reported. In this paper, by PCR amplification of the genomic DNA, the luciferase gene of Diaphanes pectinealis, which is the first case from Diaphanes, was identified and sequenced. The luciferase gene from D. pectinealis spans 1958 base pairs （bp） from the start to the stop codon, including seven exons separated by six introns, and encoding a 547-residuelong polypeptide. Its deduced amino acid sequence showed high protein similarity to those of the Lampyrini tribe （93 - 94% ） and the Cratomorphini tribe （92%）, while low similarity was found with the North American firefly Photinus pyralis （83%） of the Photinini tribe within the same subfamily Lampyrinae. The phylogenetic analysis performed with the deduced amino acid sequences of the luciferase gene further confirms that D. pectinealis, Pyrocoelia, Lampyris, Cratomorphus, and Photinus belong to the same subfamily Lampyrinae, and Diaphanes is closely related to Pyrocoelia, Lampyris, and Cratomorphus. Furthemore, the phylogenetic analysis based on the nucleotide sequences of the luciferase gene indicates Diaphanes is a sister to Lampyris. The phylogenetic analyses are partly consistent with morphological （Branham ＆ Wenzel, 2003） and mitochondrial DNA analyses （Li et al, 2006）.展开更多
Acyl-coenzyme A dehydrogenases （ACAD） are a family of nuclear-coded, mitochondrial flavoenzymes that catalyze the alpha, and beta-dehydrogenation of fatty acids. The eighth member of this family, ACAD8 catalyzes the...Acyl-coenzyme A dehydrogenases （ACAD） are a family of nuclear-coded, mitochondrial flavoenzymes that catalyze the alpha, and beta-dehydrogenation of fatty acids. The eighth member of this family, ACAD8 catalyzes the valine catabolism. In this study, the bovine ACAD8 full-length mRNA and genomic DNA sequence were obtained and its gene structure was determined through alignment of the genomic DNA sequence to the mRNA sequence. The mRNA sequence consisted of a 1,251 bp open reading frame （ORF） flanked by a 37 bp 5＇-untranslated region （UTR） and a 444 bp 3＇-UTR; and its full-length genomic DNA sequence was 13,814 bp in length and included 11 exons and 10 introns. One A-G single nucleotide polymorphism （SNP） was revealed at nucleotide 13,408 （GenBank accession No. DQ435445） in the bovine ACAD8 gene by sequencing the polymerase chain reaction （PCR） products of 6 randomly selected individuals from the sample population. Different genotypes were determined by restriction fragment length polymorphism （RFLP）. The association analysis of this SNP in bovine ACAD8 with production traits in 178 unrelated steers from 5 breeds showed that it had a significant effect on the daily gain and the beef tenderness （P〈0.05）. Cattle with the G allele grew more rapidly and the beef they produced was more tender than those with the A allele. Thus, this SNP of the bovine ACAD8 gene can be used as an indicator to improve the growth rate and the beef tenderness.展开更多
Genes homologous to members of the MRP gene family in Caenorhabditis elegans are important in drug resistance.To further explore the molecular mechanism of drug resistance in pine wood nematode(Bursaphelenchus xylophi...Genes homologous to members of the MRP gene family in Caenorhabditis elegans are important in drug resistance.To further explore the molecular mechanism of drug resistance in pine wood nematode(Bursaphelenchus xylophilus),we used bioinformatics approaches to analyze genomic data for B.xylophilus and identified Bx-MRP genes.We predicted the structure and function of the genes and encoded proteins.Using bioinformatics programs to predict and analyze various properties of the predicted proteins,including hydrophobicity,transmembrane regions,phosphorylation sites,and topologically isomeric structures,of these Bx-MRP genes,we determined that they function in transmembrane transport.From the results of RT-qPCR,the Bx-MRP family members confer significant differential resistance to different drug treatments.After treatment with different concentrations of emamectin benzoate,avermectin and matrine,the expression of each gene increased with increasing drug concentrations,indicating that the family members play a positive role in the regulation of multidrug resistance.展开更多
Acyl-CoA-binding proteins(ACBPs)are important for the transport of acyl groups for macro molecular biosynthesis involved in plant growth,development,and diverse stress(e.g.,cold,drought,salinity,and heavy metals)respo...Acyl-CoA-binding proteins(ACBPs)are important for the transport of acyl groups for macro molecular biosynthesis involved in plant growth,development,and diverse stress(e.g.,cold,drought,salinity,and heavy metals)responses.Here,we report the phylogeny and characteristics of the ACBP family in the woody plant Populus trichocarpa.Eight genes encoding ACBP proteins were identified,and they are distributed on eight chromosomes in P.trichocarpa.These PtACBP genes were divided into four subgroups according to gene structure,conserved motifs and phylogenetic relationship.Promoter analysis revealed that cis-elements were related to stress response,phytohormone response,and physical and reproductive growth regulation.Expression levels of PtACBP genes varied among different organs,with the highest expression in leaves and the lowest in stems.Quantitative real-time PCR(qRT-PCR)analysis showed that under salinity-alkali stresses(i.e.,200 mM NaCl,75 mM Na2CO3,and 100 mM NaHCO3),four(PtACBP1,PtACBP3,PtACBP4 and PtACBP8)of eight PtACBP genes were significantly induced in roots and leaves.These data provide a comprehensive analysis of the ACBPs family in P.trichocarpa,which could be useful for gene function analyses.展开更多
[Objectives]This study aimed to investigate the sequence structure and function of Myostatin(MSTN)gene in the hybrid grouper(Epinephelus fuscoguttatus,♀×Epinephelus polyphekadion,♂).[Methods]Genetic DNA samples...[Objectives]This study aimed to investigate the sequence structure and function of Myostatin(MSTN)gene in the hybrid grouper(Epinephelus fuscoguttatus,♀×Epinephelus polyphekadion,♂).[Methods]Genetic DNA samples were extracted from the caudal fins of the hybrid grouper and its parents to amplify their MSTN genes.Then,MSTN gene sequences were analyzed using bioinformatics tools to predict their protein structures and functions.[Results]The hybrid grouper and its parents shared the same MSTN gene structure,consisting of three exons and two introns.Nucleotide sequence of the gene could be translated into 376 amino acids,including an N-terminal signal peptide,a proteolytic processing site(RXXR motif),and nine conserved cysteine residues at C-terminal,which were the typical features of transforming growth factor beta(TGF-β)superfamily proteins.Alignment of protein sequence showed that MSTN was highly conserved between the hybrid grouper and its parents.Especially,exon 3,an important functional domain,exhibited a sequence similarity of 100%among them.In addition,four variable amino acid residues were detected in exon 2 at positions 141,153,185 and 186 in the hybrid grouper,but they did not affect the secondary structure of the protein.[Conclusion]These results will provide molecular information for future investigation on the growth and heterosis of hybrid grouper species,and on the roles of MSTN gene in regulating the growth traits of the hybrid grouper.展开更多
Fructan is not only a carbon source for storage but also plays an important role as anti-stress agents in many plant species. Complex fructans having both β-（2,1）- and β-（2,6）-linked fructosyl units accumulate i...Fructan is not only a carbon source for storage but also plays an important role as anti-stress agents in many plant species. Complex fructans having both β-（2,1）- and β-（2,6）-linked fructosyl units accumulate in Triticeae plants commonly. Three enzymes （sucrose： sucrose 1-fructosyltransferase, 1-SST, EC： 2.4.1.99; sucrose： fructan 6-fructosyltransferase, 6- SFT, EC： 2.4.1.10; and fructan： fructan 1-fructosyltransferase, 1-FFT, EC： 2.4.1.100） were involved in fructan biosynthesis in Triticeae plant species. We successfully isolated these genes from tetraploid wheat （Triticum turgidum, genotype： AABB）, common wheat （Triticum aestivum L., genotype： AABBDD） and three wild relatives of common wheat, Triticum urartu Thum. （the origin of the AA genome）, Aegilops speltoides （Tausch） Gren. （the putative source of the SS genome） and Aegilops tauschii Coss. （the source of the DD genome）. Sequence analysis revealed that all the FBEs （fructan biosynthetic enzymes） had three highly conserved functional motifs except 1-SST （EU981912） from tetraploid wheat species only with conserved DPNG. Low pI （isoelectric point） and potential N-glycosylation sites were predicted, which were crucial for protein compartmentation and post-translational process. Analysis on subcelluar localization signals showed that only 6-SFT had vacuolar-directed signal. Sequences alignment result showed that 1-SST and 1-FFT were more conservative and had closer relationship each other, while 6-SFT was more active during the evolution processing. According to the syntenic relationship between wheat and rice genome, FBEs were predicated to be located on the homeologous group 6 and group 2 chromosomes. Expression profile confirmed that expression of all the three FBEs were drought-stress induced. This study can assist to establish a useful theoretical platform for cold- or drought-tolerant improvement of wheat by modulating FBEs expression.展开更多
Genetic structure of Iraqi buffalo population, in the South, Middle and North area of the country was characterized, using six microsatellite markers （ETHI52, ETH02, ETH225, CSSM060, BM1706 and INRA005）. Seventy all...Genetic structure of Iraqi buffalo population, in the South, Middle and North area of the country was characterized, using six microsatellite markers （ETHI52, ETH02, ETH225, CSSM060, BM1706 and INRA005）. Seventy alleles were detected across the six loci. Total number of alleles per locus （TNA） varied from 3 （INRA005 locus） to 16 （ETH 152 locus）. The mean number of allele （MNA） across the six loci in Iraqi indigenous buffalo was 11.4. The locus ETHI52 was the most polymorphic marker according to its number of allele （16）, the expected heterozygosity （0.86） and polymorphism information content （0.80） number of alleles （3）, expected Heterozygosity （0.1-0.2） and polymorphism information content （0.1-0.2）. Results showed that these markers were suitable in population genetics researches. It was concluded that a high degree of genetic diversity exist in the Iraqi buffalo populations.展开更多
Methylation of the N6 position of adenine, termed N6-methyladenine, protects DNA from restriction endonucleases via the host-specific restriction-modification system. N6-methyladenine was discovered and has been well ...Methylation of the N6 position of adenine, termed N6-methyladenine, protects DNA from restriction endonucleases via the host-specific restriction-modification system. N6-methyladenine was discovered and has been well studied in bacteria. N6-adenine-specific DNA methyltransferase（N6AMT） is the main enzyme catalyzing the methylation of the adenine base and knowledge of this enzyme was mainly derived from work in prokaryotic models. However, large-scale gene discovery at the genome level in many model organisms indicated that the N6AMT gene also exists in eukaryotes, such as humans, mice, fruit flies and plants. Here, we cloned a N6AMT gene from Nilaparvata lugens（Nlu-N6AMT） and amplified its fulllength transcript. Then, we carried out a systematic investigation of N6AMT in 33 publically available insect genomes, indicating that all studied insects had N6AMT. Genomic structure analysis showed that insect N6AMT has short introns compared with the mammalian homologs. Domain and phylogenetic analysis indicated that insect N6AMT had a conserved N6-adenine Mlase domain that is specific to catalyze the adenine methylation. Nlu-N6AMT was highly expressed in the adult female. We knocked down Nlu-N6AMT by feeding ds RNA from the second instar nymph to adult female, inducing retard development of adult female. In all, we provide the first genome-wide analysis of N6AMT in insects and presented the experimental evidence that N6AMT might have important functions in reproductive development and ovary maturation.展开更多
Sox genes are transcription factors that ubiquitously exist in animal species, and share a conserved high mobility group(HMG) box. They play important biological roles in diverse developmental processes, such as sex d...Sox genes are transcription factors that ubiquitously exist in animal species, and share a conserved high mobility group(HMG) box. They play important biological roles in diverse developmental processes, such as sex determination and differentiation, chondrogenesis, neurogenesis, and early embryonic development. In this study, we identified 25 sox genes from genome and transcriptome of Japanese flounder Paralichthys olivaceus. These s ox genes could be mainly classified into seven subfamilies(B1, B2, C, D, E, F, and K), and each subfamily exhibited a relatively conserved gene structure. Besides, subfamilies A and G were found exclusively in human and mouse, and sox 32 in subfamily K only existed in teleosts. Compared with other mammals, some s ox genes in teleosts had two duplicates. The loss, duplication, and divergence of sox genes during evolution provided an evidence for whole-genome duplication that occurred in the radiation of teleosts. The expression of Japanese flounder sox genes was also analyzed by FPKM value. Our results showed that certain s ox genes exhibited obviously tissue-specific and spatio-temproal expression. Especially, gonal-basied expression analysis uncovered that s ox7 and s ox2 were ovary-biased, and s ox8 b was testis-biased. Moreover, sox10 a was expressed specifically in ovary, and sox8 a in testis. Therefore this study provide a solid foundation for future functional and evolutionary analysis of sox genes in Japanese flounder.展开更多
Resistance genes enable plants to fight against plant pathogens. Plant resistance genes （R gene） are organized complexly in genome. Some resistance gene sequence data enable an insight into R gene structure and gene...Resistance genes enable plants to fight against plant pathogens. Plant resistance genes （R gene） are organized complexly in genome. Some resistance gene sequence data enable an insight into R gene structure and gene evolution. Some sites like Leucine-Rich Repeat （LRR） are of specific interest since homologous recombination can happen. Crossing over, transposon insertion and excision and mutation can produce new specificity. Three models explaining R gene evolution were discussed. More information needed for dissection of R gene evolution though some step can be inferred from genetic and sequence analysis.展开更多
RNA-Seq, a high-throughput （HT） sequencing technique, has been used effectively in large-scale transcriptomic studies, and is particularly useful for improving gene structure information and mining of new genes. In ...RNA-Seq, a high-throughput （HT） sequencing technique, has been used effectively in large-scale transcriptomic studies, and is particularly useful for improving gene structure information and mining of new genes. In this study, RNA-Seq HT technology was employed to analyze the transcriptome of yak ovary. After lllurrlina-Solexa deep sequencing, 26826516 clean reads with a total of 4828772880 bp were obtained from the ovary library. Alignment analysis showed that 16992 yak genes mapped to the yak genome and 3734 of these genes were involved in alternative splicing. Gene structure refinement analysis showed that 7340 genes that were annotated in the yak genome could be extended at the 5＇ or 3＇ ends based on the alignments been the transcripts and the genome sequence. Novel transcript prediction analysis identified 6321 new transcripts with lengths ranging from 180 to 14884 bp, and 2267 of them were predicted to code proteins. BLAST analysis of the new transcripts showed that 1200-4933 mapped to the non-redundant （nr）, nucleotide （nt） and/or SwissProt sequence databases. Comparative statistical analysis of the new mapped transcripts showed that the majority of them were similar to genes in Bos taurus （41.4%）, Bos grunniens mutus （33.0%）, Ovis aries （6.3%）, Homo sapiens （2.8%）, Mus musculus （1.6%） and other species. Functional analy- sis showed that these expressed genes were involved in various Gene Ontology （GO） categories and Kyoto Encyclopedia of Genes and Genomes pathways. GO analysis of the new transcripts found that the largest proportion of them was associated with reproduction. The results of this study will provide a basis for describing the normal transcriptome map of yak ovary and for future studies on yak breeding performance. Moreover, the results confirmed that RNA-Seq HT technology is highly ad- vantageous in improving gene structure information and mining of new genes, as well as in providing valuable data to expand the yak genome information.展开更多
How the structure and base composition of genes changed with the evolution of vertebrates remains a puzzling question. Here we analyzed 895 orthologous protein-coding genes in six multicellular animals： human, chicke...How the structure and base composition of genes changed with the evolution of vertebrates remains a puzzling question. Here we analyzed 895 orthologous protein-coding genes in six multicellular animals： human, chicken, zebrafish, sea squirt, fruit fly, and worm. Our analyses reveal that many gene regions, particularly intron and 3~ UTR, gradually expanded throughout the evolution of vertebrates from their invertebrate ancestors, and that the number of exons per gene increased. Studies based on all protein-coding genes in each genome provide consistent results. We also find that GC-content increased in many gene regions （especially 5＇ UTR） in the evolution of endotherms, except in coding-exons. Analysis of individual genomes shows that 3t UTR demonstrated stronger length and GC-content correlation with intron than 5~ UTR, and gene with large intron in all six species demonstrated relatively similar GC-content. Our data indicates a great increase in complexity in vertebrate genes and we propose that the requirement for morphological and functional changes is probably the driving force behind the evolution of structure and base composition complexity in multicellular animal genes.展开更多
On the basis of a long-term（30 years） field experiment that involved four rotation systems, rice-rice-winter fallow（RRF）, rice-rice-ryegrass（RRG）, rice-rice-rape（RRP）, and rice-rice-milk vetch（RRV）, this stu...On the basis of a long-term（30 years） field experiment that involved four rotation systems, rice-rice-winter fallow（RRF）, rice-rice-ryegrass（RRG）, rice-rice-rape（RRP）, and rice-rice-milk vetch（RRV）, this study described the effects of green manure on the microbial communities in the red paddy soils using 454 pyrosequencing for the 16 S r RNA gene. The Chao1 richness and non-parametric Shannon＇s index increased in all soil samples that received green manure treatments. The communities＇ structures with the green manure applications were significantly dissimilar from that under the winter fallow. Using Metastats tests, many genera in the RRG, RRP and RRV soils were significantly different from those in the RRF soil, including a number of genera that functioned in the nitrogen and sulfur cycles. Analyses of the genera with these functions revealed the shifts in microbial ecosystem functions after long-term green manuring. Changes in the microbial communities increased the ammonium supply and decreased the soil acidification in green-manure-amended soils. Together, these data suggested powerful effects of green manure on both the microbial communities and the biogeochemical cycle driven by the shifts in bacterial functional groups.展开更多
Restriction fragments of HBV-DNA, cleaved by endonuclease HhaI,containing HBcAg gene were trimmed by BAL-31 exonuclease to remove different lengths of the precore sequence.They were inserted into plasmid pUR222 at Eco...Restriction fragments of HBV-DNA, cleaved by endonuclease HhaI,containing HBcAg gene were trimmed by BAL-31 exonuclease to remove different lengths of the precore sequence.They were inserted into plasmid pUR222 at EcoRI site through synthetic linker ligation. Transformants in E.coli BMH7118 showing different levels of HBcAg gene expression were screened and analyzed for their nucleotide sequences in the junction region both by Maxam and Gilbert's chemical degradation method and by M13 chain termination method. Results of sequence analysis of different transformants revealed a partial palindromic (loop and stem) structure, at -7 to -35 nucleotide with regard to ATG of the HBcAg gene as position +1, which has dramatic effect on the level of expression of the inserted gene using the same promoter,SD sequence and identical N-terminus.The amount of HBcAg synthesized differed from 9% in the high expressing plasmid to less than 0.01% of the total cell proteins in the low expressing transformants.The findings were compared to results obtained by other workers in studies of HBcAg expression in procaryotes and their significance in the expression of eucaryotic genes in procaryotic cells were discussed.展开更多
Auxin response factors(ARFs) are transcription factors that activate or repress the expression of primary/early auxin response genes by binding to auxin-responsive elements(Aux REs) in their promoter regions. The ARFs...Auxin response factors(ARFs) are transcription factors that activate or repress the expression of primary/early auxin response genes by binding to auxin-responsive elements(Aux REs) in their promoter regions. The ARFs play important roles in diverse developmental processes.To explore the ARF gene family in hot pepper(Capsicum annuum L.), we performed a genome-wide identification and expression analysis. In this study, 19 pepper ARF genes(Ca ARFs) clustered into three phylogenetic groups(I, II, and III) were comprehensively analyzed. Conserved domain analysis showed that all Ca ARFs contained a B3 DNA-binding domain and a middle domain, but two members lacked the carboxyterminal dimerization(CTD) domain. The number of introns in Ca ARF genes ranged from 1 to 13 and the gene structure was similar among genes in the same phylogenetic group. Additionally, prediction of Ca ARFs promoter elements and putative targets for micro RNAs suggested that the regulation of Ca ARFs may occur at both transcriptional and posttranscriptional levels. Most Ca ARFs were expressed in more than one tested tissue, and most Ca ARFs were identified as being responsive to exogenous auxin. Moreover, time-course transcription profiles of Ca ARFs revealed their roles in adventitious rooting of hypocotyl cuttings from pepper seedlings. Therefore, our results will provide a foundation for better understanding the regulatory mechanisms and molecular functions of Ca ARFs in hot pepper.展开更多
GINS, a heterotetramer of SLD5, PSF1, PSF2, and PSF3 proteins, is an emerging chromatin factor recognized to be involved in the initiation and elongation step of DNA replication. Although the yeast and Xenopus GINS ge...GINS, a heterotetramer of SLD5, PSF1, PSF2, and PSF3 proteins, is an emerging chromatin factor recognized to be involved in the initiation and elongation step of DNA replication. Although the yeast and Xenopus GINS genes are well documented, their orthologous genes in higher eukaryotes are not fully characterized. In this study, we report the genomic structure and transcriptional regulation of mammalian GINS genes. Serum stimulation increased the GINS mRNA levels in human cells. Reporter gene assay using putative GINS promoter sequences revealed that the expression of mammalian GINS is regulated by 17β-Estradiolstimulated estrogen receptor a, and human PSF3 acts as a gene responsive to transcription factor E2F1. The goal of this study is to present the current data so as to encourage further work in the field of GINS gene regulation and functions in mammalian cells.展开更多
The RNA interference(RNAi)phenomenon is a recently observed process in which the introduction of a double-stranded,small interfering RNA(siRNA)into a cell causes the specific degradation of a homologous single-strande...The RNA interference(RNAi)phenomenon is a recently observed process in which the introduction of a double-stranded,small interfering RNA(siRNA)into a cell causes the specific degradation of a homologous single-stranded RNA.It represents an exciting new technology that could have therapeutic applications for the treatment of viral infections.Since hepatitis G virus(HGV)genome is a positive-sense single-stranded RNA,the replication of HGV does not lead to an integrated DNA genome,suggesting a particularly attractive target for RNAi study that could eliminate viral RNA from infected cells.The eukaryotic expression vector pVAX.EH containing the cDNA sequences of the entire HGV structural genes and hygromycin resistance gene downstream from the encephalomyocarditis virus(ECMV)internal ribosome entry site(IRES)was constructed and transfected into human hepatoma cell Huh-7.The modified cleavage products of the structural proteins of HGV expressed in hygromycin-resistant cell line Huh-7-EH were confirmed by RT-PCR and Western blot methods.Two specific HGV E2 siRNAs(1-E2siRNA,2-E2 siRNA)synthesized with T7 RNA polymerase by transcription in vitro were transfected into the Huh-7-EH cells.With the analyses of Western blot and the formation of hygromycin-resistant colonies,the inhibitions of expression of HGV structural protein by two HGV E2siRNAs were detected and found lasting at least one week.The inhibition of 2-E2 siRNA was stronger and only 1%of the cells treated with 2-E2 siRNA formed hygromycin-resistant colonies.These results support that specific HGV 2-E2 siRNAs mediate the degradation of mRNA spanning from HGV structural gene cDNA to hygromycin resistance gene in a majority of cells.In conclusion,the Huh-7-EH cells expressing HGV structural proteins stably can be used as a cell model for studying the replication of HGV and RNAi and the enlargement of RNAi may exist,in mammalian cells.展开更多
In order to evaluate the impact of reclaimed water on the ecology of bacterial communities in the Typha angustifolia L. rhizosphere soil, bacterial community structure was investigated using a combination of terminal ...In order to evaluate the impact of reclaimed water on the ecology of bacterial communities in the Typha angustifolia L. rhizosphere soil, bacterial community structure was investigated using a combination of terminal restriction fragment length polymorphism and 16S rRNA gene clone library. The results revealed significant spatial variation of bacterial communities along the river from upstream and downstream. For example, a higher relative abundance of γ-Proteobacteria, Firmicutes, Chloroflexi and a lower proportion of β-Proteobacteria and ε-Proteobacteria was detected at the downstream site compared to the upstream site. Additionally, with an increase of the reclaimed water interference intensity, the rhizosphere bacterial community showed a decrease in taxon richness, evenness and diversity. The relative abundance of bacteria closely related to the resistant of heavy-metal was markedly increased, while the bacteria related for carbon/nitrogen/phosphorus/sulfur cycling wasn＇t strikingly changed. Besides that, the pathogenic bacteria markedly increased in the downstream rhizosphere soil since reclaimed water supplement, while the possible plant growth-promoting rhizobacteria obviously reduced in the downstream sediment. Together these data suggest cause and effect between reclaimed water input into the wetland, shift in bacterial communities through habitat change, and alteration of capacity for biogeochemical cycling of contaminants.展开更多
基金National Basic Research Program (2004CCA00500)National High-tech Development Research Program of China (2006AA02Z440)
文摘The structure genes spike(S) ,nucleocapsid(N) ,membrane(M) ,small membrane(sM) of a porcine epidemic diarrhea virus(PEDV) strain DX isolated in Gansu province,North-west of China,were cloned,sequenced and compared with published sequences of PEDV strains. The nucleotide sequences encoding the entire S,sM,M and N genes open reading frame(ORF) of DX were 4 152,231,681 and 1 326 bases long respectively. There were transcription regulatory sequences(TRSs) upstream of the initiator ATG of the S,N and M genes. The amino acids sequences of S,M and N contained 30,3 and 7 potential asparagine(N) -linked glycosylation sites. Homologous analysis and phylogenetic trees showed that DX had the closest relationship with strains LJB/06,JS-2004-2Z and CH/HLJH/06 that were also isolated from China and indicated the prevalence of some PEDV isolates in China were widespread since the JS-2004-2Z strain originated from the south of the China,and LJB/06 and CH/HLJH/06 were isolated from northeast China. The N gene was cloned using two primers which contained Nco I and BamH I restriction enzyme sites and subcloned into expression vector pET30a. The recombinant plasmid was then transformed into E.coli Rossta. SDS-PAGE showed there was a protein of about 55kDa as expected and Western blot indicated the N protein had biological activity.
基金This work was supported by the National Natural Science Foundation (No. 30471196)the Special Program for Doctorial Site of Universities (No. 200404344011).
文摘Population-wide genetic structure was studied using fluorescent-AFLP markers on 85 apricot （Prunus armeniaca L.） cultivars collected from Kuche, Kashi, Hetian in the Tarim Basin, southern Xinjiang Uygur Autonomous Region of China. The purpose of this study was to determine the genetic structure and genotypic diversity among the different eco-geographical populations. Based on the results from this study, 8 pairs of fluorescent-AFLP primers showed clear electrophoregram and high polymorphism amongst the 64 pairs of EcoR Ⅰ/Mse Ⅰ （Mse Ⅰ - a FAM fluorescent marked primer） primers screened. There was a significant polymorphic difference for the same primer pair in different populations and for the same population with different primer pairs. The percentage of polymorphic loci （P） at species level was higher than Kuche, Hetian, Kashi population levels, respectively. The Nei＇s gene diversity index （H） and Shannon＇s information index （I） at species level were higher than those of Kuche, Hetian, and Kashi at population level, respectively. H and I of Kuche population were the highest amongst the three populations. Apricot population genetic diversity was found mainly within the population, Genetic differentiation coefficient between populations （GST） was 0.0882. Gene flow Nm between the populations was 5.1689. Population genetic identity was between 0.9772-0.9811 and genetic distance was between 0.0191-0.0232. These results further indicated that the similarity between populations was higher and the genetic distance between populations was smaller. The UPGMA cluster analysis indicates that the geographical populations at Kuche, Kashi, Hetian were relatively independent Mendelian populations. Concurrently, there was also partial gene exchange between the populations. All the evidences indicated that the genetic diversity in Kuche population was the highest, suggesting that it could be a transition population from wild apricot to cultivated apricot. There were abundant genetic diversities in apricot cultivar populations in southern Xinjiang, China, which provide promising germplasm for further breeding and theoretical basis for biodiversity conservation and utilization for apricot population in this area.
文摘Diaphanes is the fourth largest genus in Lampyridae, but no luciferase gene from this genus has been reported. In this paper, by PCR amplification of the genomic DNA, the luciferase gene of Diaphanes pectinealis, which is the first case from Diaphanes, was identified and sequenced. The luciferase gene from D. pectinealis spans 1958 base pairs （bp） from the start to the stop codon, including seven exons separated by six introns, and encoding a 547-residuelong polypeptide. Its deduced amino acid sequence showed high protein similarity to those of the Lampyrini tribe （93 - 94% ） and the Cratomorphini tribe （92%）, while low similarity was found with the North American firefly Photinus pyralis （83%） of the Photinini tribe within the same subfamily Lampyrinae. The phylogenetic analysis performed with the deduced amino acid sequences of the luciferase gene further confirms that D. pectinealis, Pyrocoelia, Lampyris, Cratomorphus, and Photinus belong to the same subfamily Lampyrinae, and Diaphanes is closely related to Pyrocoelia, Lampyris, and Cratomorphus. Furthemore, the phylogenetic analysis based on the nucleotide sequences of the luciferase gene indicates Diaphanes is a sister to Lampyris. The phylogenetic analyses are partly consistent with morphological （Branham ＆ Wenzel, 2003） and mitochondrial DNA analyses （Li et al, 2006）.
基金This work was supported by Chinese National Programs for High Technology Research and Development (No. 2002AA242011)the 10th Five Years Key Problems for Science and Technology Development of China (No. 2002BA518A14).
文摘Acyl-coenzyme A dehydrogenases （ACAD） are a family of nuclear-coded, mitochondrial flavoenzymes that catalyze the alpha, and beta-dehydrogenation of fatty acids. The eighth member of this family, ACAD8 catalyzes the valine catabolism. In this study, the bovine ACAD8 full-length mRNA and genomic DNA sequence were obtained and its gene structure was determined through alignment of the genomic DNA sequence to the mRNA sequence. The mRNA sequence consisted of a 1,251 bp open reading frame （ORF） flanked by a 37 bp 5＇-untranslated region （UTR） and a 444 bp 3＇-UTR; and its full-length genomic DNA sequence was 13,814 bp in length and included 11 exons and 10 introns. One A-G single nucleotide polymorphism （SNP） was revealed at nucleotide 13,408 （GenBank accession No. DQ435445） in the bovine ACAD8 gene by sequencing the polymerase chain reaction （PCR） products of 6 randomly selected individuals from the sample population. Different genotypes were determined by restriction fragment length polymorphism （RFLP）. The association analysis of this SNP in bovine ACAD8 with production traits in 178 unrelated steers from 5 breeds showed that it had a significant effect on the daily gain and the beef tenderness （P〈0.05）. Cattle with the G allele grew more rapidly and the beef they produced was more tender than those with the A allele. Thus, this SNP of the bovine ACAD8 gene can be used as an indicator to improve the growth rate and the beef tenderness.
基金supported by the National Key Research and Development Program of China(2017YFD0600101).
文摘Genes homologous to members of the MRP gene family in Caenorhabditis elegans are important in drug resistance.To further explore the molecular mechanism of drug resistance in pine wood nematode(Bursaphelenchus xylophilus),we used bioinformatics approaches to analyze genomic data for B.xylophilus and identified Bx-MRP genes.We predicted the structure and function of the genes and encoded proteins.Using bioinformatics programs to predict and analyze various properties of the predicted proteins,including hydrophobicity,transmembrane regions,phosphorylation sites,and topologically isomeric structures,of these Bx-MRP genes,we determined that they function in transmembrane transport.From the results of RT-qPCR,the Bx-MRP family members confer significant differential resistance to different drug treatments.After treatment with different concentrations of emamectin benzoate,avermectin and matrine,the expression of each gene increased with increasing drug concentrations,indicating that the family members play a positive role in the regulation of multidrug resistance.
基金supported by grants from the Fundamental Research Funds for the Central Universities(Nos.2572018B03)the College Students Innovations Special Project funded by NEFU(No.202010225173)+1 种基金the Fundamental Research Funds for the Central Universities(Nos.2572019CT03)the Natural Science Foundation of Heilongjiang Province(No.ZD2019C003)。
文摘Acyl-CoA-binding proteins(ACBPs)are important for the transport of acyl groups for macro molecular biosynthesis involved in plant growth,development,and diverse stress(e.g.,cold,drought,salinity,and heavy metals)responses.Here,we report the phylogeny and characteristics of the ACBP family in the woody plant Populus trichocarpa.Eight genes encoding ACBP proteins were identified,and they are distributed on eight chromosomes in P.trichocarpa.These PtACBP genes were divided into four subgroups according to gene structure,conserved motifs and phylogenetic relationship.Promoter analysis revealed that cis-elements were related to stress response,phytohormone response,and physical and reproductive growth regulation.Expression levels of PtACBP genes varied among different organs,with the highest expression in leaves and the lowest in stems.Quantitative real-time PCR(qRT-PCR)analysis showed that under salinity-alkali stresses(i.e.,200 mM NaCl,75 mM Na2CO3,and 100 mM NaHCO3),four(PtACBP1,PtACBP3,PtACBP4 and PtACBP8)of eight PtACBP genes were significantly induced in roots and leaves.These data provide a comprehensive analysis of the ACBPs family in P.trichocarpa,which could be useful for gene function analyses.
基金Supported by the Innovation Platform for Academicians of Hainan Province(YSPTZX202103)Hainan Provincial Natural Science Foundation of China(321QN263)+3 种基金National Natural Science Foundation of China(32160861)the Major Science and Technology Plan of Hainan Province(ZDKJ2021017)State Key Laboratory of Developmental Biology of Freshwater Fish(2020KF001)Scientific Research Foundation of Hainan Tropical Ocean University(RHDRC202010)。
文摘[Objectives]This study aimed to investigate the sequence structure and function of Myostatin(MSTN)gene in the hybrid grouper(Epinephelus fuscoguttatus,♀×Epinephelus polyphekadion,♂).[Methods]Genetic DNA samples were extracted from the caudal fins of the hybrid grouper and its parents to amplify their MSTN genes.Then,MSTN gene sequences were analyzed using bioinformatics tools to predict their protein structures and functions.[Results]The hybrid grouper and its parents shared the same MSTN gene structure,consisting of three exons and two introns.Nucleotide sequence of the gene could be translated into 376 amino acids,including an N-terminal signal peptide,a proteolytic processing site(RXXR motif),and nine conserved cysteine residues at C-terminal,which were the typical features of transforming growth factor beta(TGF-β)superfamily proteins.Alignment of protein sequence showed that MSTN was highly conserved between the hybrid grouper and its parents.Especially,exon 3,an important functional domain,exhibited a sequence similarity of 100%among them.In addition,four variable amino acid residues were detected in exon 2 at positions 141,153,185 and 186 in the hybrid grouper,but they did not affect the secondary structure of the protein.[Conclusion]These results will provide molecular information for future investigation on the growth and heterosis of hybrid grouper species,and on the roles of MSTN gene in regulating the growth traits of the hybrid grouper.
基金funded by the National High-Tech R&D Program of China (863 Program of China,2007AA10Z129)
文摘Fructan is not only a carbon source for storage but also plays an important role as anti-stress agents in many plant species. Complex fructans having both β-（2,1）- and β-（2,6）-linked fructosyl units accumulate in Triticeae plants commonly. Three enzymes （sucrose： sucrose 1-fructosyltransferase, 1-SST, EC： 2.4.1.99; sucrose： fructan 6-fructosyltransferase, 6- SFT, EC： 2.4.1.10; and fructan： fructan 1-fructosyltransferase, 1-FFT, EC： 2.4.1.100） were involved in fructan biosynthesis in Triticeae plant species. We successfully isolated these genes from tetraploid wheat （Triticum turgidum, genotype： AABB）, common wheat （Triticum aestivum L., genotype： AABBDD） and three wild relatives of common wheat, Triticum urartu Thum. （the origin of the AA genome）, Aegilops speltoides （Tausch） Gren. （the putative source of the SS genome） and Aegilops tauschii Coss. （the source of the DD genome）. Sequence analysis revealed that all the FBEs （fructan biosynthetic enzymes） had three highly conserved functional motifs except 1-SST （EU981912） from tetraploid wheat species only with conserved DPNG. Low pI （isoelectric point） and potential N-glycosylation sites were predicted, which were crucial for protein compartmentation and post-translational process. Analysis on subcelluar localization signals showed that only 6-SFT had vacuolar-directed signal. Sequences alignment result showed that 1-SST and 1-FFT were more conservative and had closer relationship each other, while 6-SFT was more active during the evolution processing. According to the syntenic relationship between wheat and rice genome, FBEs were predicated to be located on the homeologous group 6 and group 2 chromosomes. Expression profile confirmed that expression of all the three FBEs were drought-stress induced. This study can assist to establish a useful theoretical platform for cold- or drought-tolerant improvement of wheat by modulating FBEs expression.
文摘Genetic structure of Iraqi buffalo population, in the South, Middle and North area of the country was characterized, using six microsatellite markers （ETHI52, ETH02, ETH225, CSSM060, BM1706 and INRA005）. Seventy alleles were detected across the six loci. Total number of alleles per locus （TNA） varied from 3 （INRA005 locus） to 16 （ETH 152 locus）. The mean number of allele （MNA） across the six loci in Iraqi indigenous buffalo was 11.4. The locus ETHI52 was the most polymorphic marker according to its number of allele （16）, the expected heterozygosity （0.86） and polymorphism information content （0.80） number of alleles （3）, expected Heterozygosity （0.1-0.2） and polymorphism information content （0.1-0.2）. Results showed that these markers were suitable in population genetics researches. It was concluded that a high degree of genetic diversity exist in the Iraqi buffalo populations.
基金supported by the National Basic Research Program of China (2012CB114102)
文摘Methylation of the N6 position of adenine, termed N6-methyladenine, protects DNA from restriction endonucleases via the host-specific restriction-modification system. N6-methyladenine was discovered and has been well studied in bacteria. N6-adenine-specific DNA methyltransferase（N6AMT） is the main enzyme catalyzing the methylation of the adenine base and knowledge of this enzyme was mainly derived from work in prokaryotic models. However, large-scale gene discovery at the genome level in many model organisms indicated that the N6AMT gene also exists in eukaryotes, such as humans, mice, fruit flies and plants. Here, we cloned a N6AMT gene from Nilaparvata lugens（Nlu-N6AMT） and amplified its fulllength transcript. Then, we carried out a systematic investigation of N6AMT in 33 publically available insect genomes, indicating that all studied insects had N6AMT. Genomic structure analysis showed that insect N6AMT has short introns compared with the mammalian homologs. Domain and phylogenetic analysis indicated that insect N6AMT had a conserved N6-adenine Mlase domain that is specific to catalyze the adenine methylation. Nlu-N6AMT was highly expressed in the adult female. We knocked down Nlu-N6AMT by feeding ds RNA from the second instar nymph to adult female, inducing retard development of adult female. In all, we provide the first genome-wide analysis of N6AMT in insects and presented the experimental evidence that N6AMT might have important functions in reproductive development and ovary maturation.
基金Supported by the National Natural Science Foundation of China(No.31672646)the Fundamental Research Funds for the Central Universities(No.201762016)
文摘Sox genes are transcription factors that ubiquitously exist in animal species, and share a conserved high mobility group(HMG) box. They play important biological roles in diverse developmental processes, such as sex determination and differentiation, chondrogenesis, neurogenesis, and early embryonic development. In this study, we identified 25 sox genes from genome and transcriptome of Japanese flounder Paralichthys olivaceus. These s ox genes could be mainly classified into seven subfamilies(B1, B2, C, D, E, F, and K), and each subfamily exhibited a relatively conserved gene structure. Besides, subfamilies A and G were found exclusively in human and mouse, and sox 32 in subfamily K only existed in teleosts. Compared with other mammals, some s ox genes in teleosts had two duplicates. The loss, duplication, and divergence of sox genes during evolution provided an evidence for whole-genome duplication that occurred in the radiation of teleosts. The expression of Japanese flounder sox genes was also analyzed by FPKM value. Our results showed that certain s ox genes exhibited obviously tissue-specific and spatio-temproal expression. Especially, gonal-basied expression analysis uncovered that s ox7 and s ox2 were ovary-biased, and s ox8 b was testis-biased. Moreover, sox10 a was expressed specifically in ovary, and sox8 a in testis. Therefore this study provide a solid foundation for future functional and evolutionary analysis of sox genes in Japanese flounder.
文摘Resistance genes enable plants to fight against plant pathogens. Plant resistance genes （R gene） are organized complexly in genome. Some resistance gene sequence data enable an insight into R gene structure and gene evolution. Some sites like Leucine-Rich Repeat （LRR） are of specific interest since homologous recombination can happen. Crossing over, transposon insertion and excision and mutation can produce new specificity. Three models explaining R gene evolution were discussed. More information needed for dissection of R gene evolution though some step can be inferred from genetic and sequence analysis.
基金supported by the National Science&Technology Pillar Program of China(2012BAD13B06)the Special Fund for Agroscientific Research in the Public Interest(201203009)
文摘RNA-Seq, a high-throughput （HT） sequencing technique, has been used effectively in large-scale transcriptomic studies, and is particularly useful for improving gene structure information and mining of new genes. In this study, RNA-Seq HT technology was employed to analyze the transcriptome of yak ovary. After lllurrlina-Solexa deep sequencing, 26826516 clean reads with a total of 4828772880 bp were obtained from the ovary library. Alignment analysis showed that 16992 yak genes mapped to the yak genome and 3734 of these genes were involved in alternative splicing. Gene structure refinement analysis showed that 7340 genes that were annotated in the yak genome could be extended at the 5＇ or 3＇ ends based on the alignments been the transcripts and the genome sequence. Novel transcript prediction analysis identified 6321 new transcripts with lengths ranging from 180 to 14884 bp, and 2267 of them were predicted to code proteins. BLAST analysis of the new transcripts showed that 1200-4933 mapped to the non-redundant （nr）, nucleotide （nt） and/or SwissProt sequence databases. Comparative statistical analysis of the new mapped transcripts showed that the majority of them were similar to genes in Bos taurus （41.4%）, Bos grunniens mutus （33.0%）, Ovis aries （6.3%）, Homo sapiens （2.8%）, Mus musculus （1.6%） and other species. Functional analy- sis showed that these expressed genes were involved in various Gene Ontology （GO） categories and Kyoto Encyclopedia of Genes and Genomes pathways. GO analysis of the new transcripts found that the largest proportion of them was associated with reproduction. The results of this study will provide a basis for describing the normal transcriptome map of yak ovary and for future studies on yak breeding performance. Moreover, the results confirmed that RNA-Seq HT technology is highly ad- vantageous in improving gene structure information and mining of new genes, as well as in providing valuable data to expand the yak genome information.
基金supported by the National Natural Science Foundation of China(Nos.30930049 and 30870176(gsl))to D.T.or J-Q.C
文摘How the structure and base composition of genes changed with the evolution of vertebrates remains a puzzling question. Here we analyzed 895 orthologous protein-coding genes in six multicellular animals： human, chicken, zebrafish, sea squirt, fruit fly, and worm. Our analyses reveal that many gene regions, particularly intron and 3~ UTR, gradually expanded throughout the evolution of vertebrates from their invertebrate ancestors, and that the number of exons per gene increased. Studies based on all protein-coding genes in each genome provide consistent results. We also find that GC-content increased in many gene regions （especially 5＇ UTR） in the evolution of endotherms, except in coding-exons. Analysis of individual genomes shows that 3t UTR demonstrated stronger length and GC-content correlation with intron than 5~ UTR, and gene with large intron in all six species demonstrated relatively similar GC-content. Our data indicates a great increase in complexity in vertebrate genes and we propose that the requirement for morphological and functional changes is probably the driving force behind the evolution of structure and base composition complexity in multicellular animal genes.
基金supported by the Special Fund for Agro-scientific Research in the Public Interest of China(201103005)the Science and Technology Innovation Project of Chinese Academy of Agricultural Sciences(2013–2017)
文摘On the basis of a long-term（30 years） field experiment that involved four rotation systems, rice-rice-winter fallow（RRF）, rice-rice-ryegrass（RRG）, rice-rice-rape（RRP）, and rice-rice-milk vetch（RRV）, this study described the effects of green manure on the microbial communities in the red paddy soils using 454 pyrosequencing for the 16 S r RNA gene. The Chao1 richness and non-parametric Shannon＇s index increased in all soil samples that received green manure treatments. The communities＇ structures with the green manure applications were significantly dissimilar from that under the winter fallow. Using Metastats tests, many genera in the RRG, RRP and RRV soils were significantly different from those in the RRF soil, including a number of genera that functioned in the nitrogen and sulfur cycles. Analyses of the genera with these functions revealed the shifts in microbial ecosystem functions after long-term green manuring. Changes in the microbial communities increased the ammonium supply and decreased the soil acidification in green-manure-amended soils. Together, these data suggested powerful effects of green manure on both the microbial communities and the biogeochemical cycle driven by the shifts in bacterial functional groups.
文摘Restriction fragments of HBV-DNA, cleaved by endonuclease HhaI,containing HBcAg gene were trimmed by BAL-31 exonuclease to remove different lengths of the precore sequence.They were inserted into plasmid pUR222 at EcoRI site through synthetic linker ligation. Transformants in E.coli BMH7118 showing different levels of HBcAg gene expression were screened and analyzed for their nucleotide sequences in the junction region both by Maxam and Gilbert's chemical degradation method and by M13 chain termination method. Results of sequence analysis of different transformants revealed a partial palindromic (loop and stem) structure, at -7 to -35 nucleotide with regard to ATG of the HBcAg gene as position +1, which has dramatic effect on the level of expression of the inserted gene using the same promoter,SD sequence and identical N-terminus.The amount of HBcAg synthesized differed from 9% in the high expressing plasmid to less than 0.01% of the total cell proteins in the low expressing transformants.The findings were compared to results obtained by other workers in studies of HBcAg expression in procaryotes and their significance in the expression of eucaryotic genes in procaryotic cells were discussed.
基金supported by the National Natural Science Foundation of China (31172001)the Special Fund for Agro-scientific Research in the Public Interest (201303014)+1 种基金the China Agriculture Research System (CARS-25)the Science and Technology Innovation Program of Chinese Academy of Agricultural Sciences (CAAS-ASTIP-IVFCAAS)
文摘Auxin response factors(ARFs) are transcription factors that activate or repress the expression of primary/early auxin response genes by binding to auxin-responsive elements(Aux REs) in their promoter regions. The ARFs play important roles in diverse developmental processes.To explore the ARF gene family in hot pepper(Capsicum annuum L.), we performed a genome-wide identification and expression analysis. In this study, 19 pepper ARF genes(Ca ARFs) clustered into three phylogenetic groups(I, II, and III) were comprehensively analyzed. Conserved domain analysis showed that all Ca ARFs contained a B3 DNA-binding domain and a middle domain, but two members lacked the carboxyterminal dimerization(CTD) domain. The number of introns in Ca ARF genes ranged from 1 to 13 and the gene structure was similar among genes in the same phylogenetic group. Additionally, prediction of Ca ARFs promoter elements and putative targets for micro RNAs suggested that the regulation of Ca ARFs may occur at both transcriptional and posttranscriptional levels. Most Ca ARFs were expressed in more than one tested tissue, and most Ca ARFs were identified as being responsive to exogenous auxin. Moreover, time-course transcription profiles of Ca ARFs revealed their roles in adventitious rooting of hypocotyl cuttings from pepper seedlings. Therefore, our results will provide a foundation for better understanding the regulatory mechanisms and molecular functions of Ca ARFs in hot pepper.
文摘GINS, a heterotetramer of SLD5, PSF1, PSF2, and PSF3 proteins, is an emerging chromatin factor recognized to be involved in the initiation and elongation step of DNA replication. Although the yeast and Xenopus GINS genes are well documented, their orthologous genes in higher eukaryotes are not fully characterized. In this study, we report the genomic structure and transcriptional regulation of mammalian GINS genes. Serum stimulation increased the GINS mRNA levels in human cells. Reporter gene assay using putative GINS promoter sequences revealed that the expression of mammalian GINS is regulated by 17β-Estradiolstimulated estrogen receptor a, and human PSF3 acts as a gene responsive to transcription factor E2F1. The goal of this study is to present the current data so as to encourage further work in the field of GINS gene regulation and functions in mammalian cells.
基金This work was supported by the National Basic Research(973)Progrum of China(No.2003CB514129)the National INatural Science Foundation of China(Grant No.30170514).
文摘The RNA interference(RNAi)phenomenon is a recently observed process in which the introduction of a double-stranded,small interfering RNA(siRNA)into a cell causes the specific degradation of a homologous single-stranded RNA.It represents an exciting new technology that could have therapeutic applications for the treatment of viral infections.Since hepatitis G virus(HGV)genome is a positive-sense single-stranded RNA,the replication of HGV does not lead to an integrated DNA genome,suggesting a particularly attractive target for RNAi study that could eliminate viral RNA from infected cells.The eukaryotic expression vector pVAX.EH containing the cDNA sequences of the entire HGV structural genes and hygromycin resistance gene downstream from the encephalomyocarditis virus(ECMV)internal ribosome entry site(IRES)was constructed and transfected into human hepatoma cell Huh-7.The modified cleavage products of the structural proteins of HGV expressed in hygromycin-resistant cell line Huh-7-EH were confirmed by RT-PCR and Western blot methods.Two specific HGV E2 siRNAs(1-E2siRNA,2-E2 siRNA)synthesized with T7 RNA polymerase by transcription in vitro were transfected into the Huh-7-EH cells.With the analyses of Western blot and the formation of hygromycin-resistant colonies,the inhibitions of expression of HGV structural protein by two HGV E2siRNAs were detected and found lasting at least one week.The inhibition of 2-E2 siRNA was stronger and only 1%of the cells treated with 2-E2 siRNA formed hygromycin-resistant colonies.These results support that specific HGV 2-E2 siRNAs mediate the degradation of mRNA spanning from HGV structural gene cDNA to hygromycin resistance gene in a majority of cells.In conclusion,the Huh-7-EH cells expressing HGV structural proteins stably can be used as a cell model for studying the replication of HGV and RNAi and the enlargement of RNAi may exist,in mammalian cells.
基金supported by the National Natural Science Foundation of China(No.40901281)the Beijing of Education Science and Technology Program(No.KM201310028012)the International S&T Cooperation Program of China(No.2014DFA21620)
文摘In order to evaluate the impact of reclaimed water on the ecology of bacterial communities in the Typha angustifolia L. rhizosphere soil, bacterial community structure was investigated using a combination of terminal restriction fragment length polymorphism and 16S rRNA gene clone library. The results revealed significant spatial variation of bacterial communities along the river from upstream and downstream. For example, a higher relative abundance of γ-Proteobacteria, Firmicutes, Chloroflexi and a lower proportion of β-Proteobacteria and ε-Proteobacteria was detected at the downstream site compared to the upstream site. Additionally, with an increase of the reclaimed water interference intensity, the rhizosphere bacterial community showed a decrease in taxon richness, evenness and diversity. The relative abundance of bacteria closely related to the resistant of heavy-metal was markedly increased, while the bacteria related for carbon/nitrogen/phosphorus/sulfur cycling wasn＇t strikingly changed. Besides that, the pathogenic bacteria markedly increased in the downstream rhizosphere soil since reclaimed water supplement, while the possible plant growth-promoting rhizobacteria obviously reduced in the downstream sediment. Together these data suggest cause and effect between reclaimed water input into the wetland, shift in bacterial communities through habitat change, and alteration of capacity for biogeochemical cycling of contaminants.
