AIM To clarify the mechanisms of HOX transcript antisense intergenic RNA(HOTAIR) in gastric cancer(GC) migration and invasion.METHODS Quantitative real-time polymerase chain reaction(qp CR) was used to detect the expr...AIM To clarify the mechanisms of HOX transcript antisense intergenic RNA(HOTAIR) in gastric cancer(GC) migration and invasion.METHODS Quantitative real-time polymerase chain reaction(qp CR) was used to detect the expression level of HOTAIR in GC tissues. The correlation of its expression with clinicopathological features was analyzed. Area under receiver operating characteristic curve(AUCROC) was constructed to evaluate the diagnostic value of HOTAIR. Wound-healing assay and Transwell assay were performed to detect the biological effects of HOTAIR in GC cells. qp CR,western blot and immunohistochemistry were used to evaluate the m RNA and protein expression of E-cadherin. RNAbinding protein immunoprecipitation was used for the analysis of EZH2 interactions with HOTAIR. Chromatin immunoprecipitation assay was performed to investigate direct interactions between EZH2 and E-cadherin.RESULTS The expression of HOTAIR was up-regulated in GC tumorous tissues compared with the para-tumorous tissues(p < 0.001). Its over-expression was correlated with tumor-node-metastasis(TNM) stage(p = 0.024),tumor invasion(p = 0.018),lymph node metastasis(p = 0.023),and poor prognosis(p < 0.001). Multivariate Cox regression analysis confirmed expression of HOTAIR as an independent predictor of overall survival(p = 0.033),together with TNM stage(p = 0.002) and lymph node metastasis(p = 0.002). The AUCROC was up to 0.709(95%CI: 0.623-0.785,p < 0.001). Knockdown of HOTAIR by si RNA in GC cells suppressed the migration and invasion of GC cells. Significantly negative correlation between HOTAIR and E-cadherin was found in GC tissues and cell lines,and HOTAIR contributed to the regulation of E-cadherin through binding to EZH2 with the E-cadherin promoter. CONCLUSION HOTAIR may play a pivotal role in tumor cell migration and invasion. It can be used as a potential diagnostic and prognostic biomarker for GC.展开更多
Phylogenetic relationships of Arundinaria and related genera (Pleioblastus, Pseudosasa, Oligostachyum, Bashania, Clavinodum, etc.) were assessed by analyzing the sequences of the nrDNA internal transcribed spacer (ITS...Phylogenetic relationships of Arundinaria and related genera (Pleioblastus, Pseudosasa, Oligostachyum, Bashania, Clavinodum, etc.) were assessed by analyzing the sequences of the nrDNA internal transcribed spacer (ITS) and the cpDNA trnL-F intergenic spacer (IGS). Comparison with trnL-F IGS sequence, the ITS region provided the higher number of parsimony informative characters, and the interspecific variation of the ITS sequence was higher than that of the trnL-F IGS sequence.The tree obtained by combining both sets of data showed that the species sampled in Arundinaria and the related genera were monophyletic and divided into two clades. The relationships and positioning of all the taxa surveryed (including A. oleosa, A. hsienchuensis, A. chino, A. amara, A. yixingensis, A. amabilis, A. fortunei, A. pygmaea, A. gramineus, A. fargesii, A. faberi, A. hupehense, Pseudosasa japonica cv. Tsutsumiana, P. japonica and Brachystachyum densiflorum) were also discussed. The results from the sequences were broadly consistent with morphological characters, appearing all these taxa sampled belong to the genus of Arundinaria. The topologies of the trees generated from individual data and the combined data were similar.展开更多
Objective Cytokine responses to activation of innate immunity differ between individuals,yet the genomic and tissue-specific transcriptomic determinants of inflammatory responsiveness are not well understood. We hypot...Objective Cytokine responses to activation of innate immunity differ between individuals,yet the genomic and tissue-specific transcriptomic determinants of inflammatory responsiveness are not well understood. We hypothesized that tissue-specific mRNA and long intergenic non-coding RNA (lincRNA) induction differs between individuals with divergent evoked inflammatory responses.展开更多
An improved method of PCR in which the small segment of conchocelis is amplified directly without DNA extraction was used to amplify a RUBISCO intergenic spacer DNA fragment from nine species of red algal genus Porphy...An improved method of PCR in which the small segment of conchocelis is amplified directly without DNA extraction was used to amplify a RUBISCO intergenic spacer DNA fragment from nine species of red algal genus Porphyra(Bangiales,Rhodophyta),including Porphyra yezoensis(Jiangsu,China),P.haitanensis(Fujian,China),P.oligospermatangia(Qingdao,China),P.katadai(Qingdao,China),P.tenera(Qingdao,China),P.suborboculata(Fujian,China),P.pseudolinearis(Kogendo,Korea),P.linearis(Devon,England),and P.fallax(Seattle,USA).Standard PCR and the method developed here were both conducted using primers specific for the RUBISCO spacer region,after which the two PCR products were sequenced.The sequencing data of the amplicons obtained using both methods were identical,suggesting that the improved PCR method was functional.These findings indicate that the method developed here may be useful for the rapid identification of species of Porphyra in a germplasm bank.In addition,a phylogenetic tree was constructed using the RUBISCO spacer and partial rbcS sequence,and the results were in concordant with possible alternative phylogenies based on traditional morphological taxonomic characteristics,indicating that the RUBISCO spacer is a useful region for phylogenetic studies.展开更多
One adult α-globin gene and one β-globin gene have been cloned from the large yellow croaker Pseudosciaena crocea. Linkage analysis indicated that the α- and β-globin genes were oriented head-to-head relative to e...One adult α-globin gene and one β-globin gene have been cloned from the large yellow croaker Pseudosciaena crocea. Linkage analysis indicated that the α- and β-globin genes were oriented head-to-head relative to each other. To identify the regulatory elements present in the intergenic and intragenic regions of the globin complex, the intergenic region alone or together with the β-globin gene first intron was cloned into the luciferase-reporter vector pGL3-Basic respectively, and the chimeric constructs were tran- siently transfected into Vero cells and primary fish erythrocytes. The intergenic region cannot support the high-level expression of luciferase. However, the promoter activity of the intergenic region was strongly stimulated by the positive regulatory elements （PRE） located in the β-globin gene intron 1. Thus, it is proposed that the intergenic promoters and intragenic PRE were necessary for the effective expression of the linked α- and β-globin genes.展开更多
China is currently the world＇s leading producer of Lentinula edodes and owns many cultivated strains of this species. This study was performed in order to investigate intergenic spacer I （IGS1） polymorphism and cla...China is currently the world＇s leading producer of Lentinula edodes and owns many cultivated strains of this species. This study was performed in order to investigate intergenic spacer I （IGS1） polymorphism and classification among 49 popular cultivated strains. The great majority of the 49 strains possessed two different IGS1 sequences, with distinct lengths and homologies. Based on the length and homology of the IGS1 sequences of the 49 strains, the strains were classified into two groups： A and B. Group A was subdivided into six subgroups. Forty-seven strains were homozygous or heterozygous among these six subgroups in group A, Cr01 was heterozygous between A and B, and Guangxiang 9 was homozygous in group B. An IGS1 polymorphism map of each cultivated L. edodes strain is reported for the first time and could be used as a marker for the initial classification and management of cultivated L. edodes strains in China.展开更多
To re-identify and further group 25 isolates of Trichosporon spp. identified morphologically previously, sequences of D1/D2 region of large subunit （LSU） of ribosomal DNA （rDNA） of 25 tested strains for identifica...To re-identify and further group 25 isolates of Trichosporon spp. identified morphologically previously, sequences of D1/D2 region of large subunit （LSU） of ribosomal DNA （rDNA） of 25 tested strains for identification and those of ribosomal intergenic space 1 （IGS1） region of 11 strains for subgrouping were detected. The identifications of tested strains were changed except 6 strains. According to the alignment of the IGS1 region, 6 T. asahii isolates tested fell into 4 groups and 5 T. faecale isolates into 3 groups. Polymorphism of 2 T. japonicum isolates was found in 10 positions. With the alignments obtained in this research compared with the relative GenBank entries, it was found that T. asahii, T. faecale and T. japonicum species were divided into 7, 3 and 2 subtypes respectively. Morphological and biophysical methods are not sufficient for Trichosporon spp. identification. Sequencing becomes necessary for Trichosporon diagnosis. There is obvious diversity within a species.展开更多
BACKGROUND Cholangiocarcinoma(CCA)represents a rare but highly aggressive malignancy that is often challenging to diagnose,especially in early stages.The role of existing tumor biomarkers for CCA diagnosis,remains con...BACKGROUND Cholangiocarcinoma(CCA)represents a rare but highly aggressive malignancy that is often challenging to diagnose,especially in early stages.The role of existing tumor biomarkers for CCA diagnosis,remains controversial due to their low sensitivity and specificity.Increasing evidence has implicated long non-coding ribonucleic acid polymorphisms with cancer susceptibility in a variety of tumor types.The association between long non-coding ribonucleic acid homeobox protein transcript antisense intergenic ribonucleic acid(HOTAIR)polymorphisms and CCA risk has not been reported yet.AIM To investigate the influence of HOTAIR variants on the risk of CCA development.METHODS We conducted a case-control study in which three HOTAIR single nucleotide polymorphisms(rs920778,rs4759314 and rs7958904)were genotyped in a Greek cohort.Our study population included 122 CCA patients(80 males and 42 females)and 165 healthy controls.The polymorphisms under investigation were examined in peripheral blood samples.RESULTS HOTAIR rs4759314 AG and GG genotypes were associated with a significantly increased CCA risk[P=0.004,odds ratio:3.13;95%confidence interval:1.65-5.91 and P=0.005,odds ratio:12.31;95%confidence interval:1.48-101.87,respectively].However,no significant associations of HOTAIR rs920778,and rs7958904 were detected.Similarly,we found no significant associations between rs4759314 AA genotype and CCA susceptibility.CONCLUSION HOTAIR rs4759314 AG and GG genotypes may be implicated with CCA development and may serve as a potential diagnostic biomarker.展开更多
Although a great deal of research has been undertaken in the area of the annotation of gene structure, predictive techniques are still not fully developed. In this paper, based on the characteristics of base compositi...Although a great deal of research has been undertaken in the area of the annotation of gene structure, predictive techniques are still not fully developed. In this paper, based on the characteristics of base composition of sequences and conservative of nucleotides at exon/intron splicing site, a least increment of diversity al-gorithm (LIDA) is developed for studying and predicting three kinds of coding exons, introns and intergenic regions. At first, by selecting the 64 trinucleotides composition and 120 position parameters of the four bases as informational parameters, coding exon, intron and intergenic sequence are predicted. The results show that overall predicted accuracies are 91.1% and 88.4%, respectively for A. thaliana and C. ele-gans genome. Subsequently, based on the po-sition frequencies of four kinds of bases in regions near intron/coding exon boundary, initia-tion and termination site of translation, 12 position parameters are selected as diversity source. And three kinds of the coding exons are predicted by use of the LIDA. The predicted successful rates are higher than 80%. These results can be used in sequence annotation.展开更多
Objective To set up a rapid and simple method for identificating bacteria by 16S 23SrDNA intergenic spacer regions (ISRs) Methods Polymorphic products of PCR from ISRs were selected on agarose gel and sequenced ...Objective To set up a rapid and simple method for identificating bacteria by 16S 23SrDNA intergenic spacer regions (ISRs) Methods Polymorphic products of PCR from ISRs were selected on agarose gel and sequenced directly using purified fragments by excising the gel without cloning Nucleotide sequences were compared with GenBank databases and analyzed by DNAMAN program Results There was only a single product in streptococcus genus after PCR amplification of 16S 23SrDNA ISRs Five streptococcal species were obtained from 7 strains of streptococcus Two major amplicons were consistently generated for 8 strains of Haemophilus influenzae (H influenzae) The sequence data showed that they all belonged to H influenzae type b on GenBank databases Conclusion PCR and direct sequencing of 16S 23SrDNA ISRs were very successful methods for bacterial species identification展开更多
Although there is an accumulating appreciation of the key roles that long intergenic non-coding RNAs （lincRNAs） play in diverse cellular processes, our knowledge of how lincRNAs function in cancer remains sparse. He...Although there is an accumulating appreciation of the key roles that long intergenic non-coding RNAs （lincRNAs） play in diverse cellular processes, our knowledge of how lincRNAs function in cancer remains sparse. Here, we present a comprehensive landscape of RNA-seq transcriptome profiles of lung adenocarcinomas and their paired normal counterparts to unravel gene regulation rules of lincRNAs. Consistent with previous findings of co-expression between neighboring protein-coding genes, lincRNAs were typically co-expressed with their neighboring genes, which was found in both cancerous and normal tissues. By building a mathematical model based on correlated gene expression, we distinguished an additional subset of lincRNAs termed ＂regulatory lincRNAs＂, representing their dominant roles in gene regulation. The number of regulatory lincRNAs was significantly higher in cancerous compared to normal tissues, and most of them positively regulated protein-coding genes in trans. Functional validation, using knockdown, determined that regulatory lincRNA, GASS, affected its predicted protein-coding targets. Moreover, we discovered hundreds of differentially expressed regulatory lincRNAs with inclusion of some cancer-associated lincRNAs. Our integrated analysis reveals enhanced regulatory effects of lincRNAs and provides a resource for the study of regulatory lincRNAs that play critical roles in lung adenocarcinoma.展开更多
Cotton leaf curl virus (CLCuV) is a type of single-stranded DMA virus, belonging to geminivirus of subgroup Ⅲ. In order to determine the function of CLCuV large intergenic region (LIR), total DNA of CLCuV-infected co...Cotton leaf curl virus (CLCuV) is a type of single-stranded DMA virus, belonging to geminivirus of subgroup Ⅲ. In order to determine the function of CLCuV large intergenic region (LIR), total DNA of CLCuV-infected cotton leaves was used as template, and fragment of LIR was obtained by PCR and inserted into clone vector. The fragment of LIR was fused with gus reporter gene and nos terminator in the orientation of transcription of virion sense and complementary sense respectively, and the plant expression vectors were constructed. GUS activity of Agrobacte-rium-mediated transgenic tobacco was measured. The result indicated that LIR showed strong promoter activity in complementary sense gene orientation. Average GUS activity of the complementary sense promoter was 5-6 times that of CaMV 35S promoter, and the highest GUS activity of individual plant was ten times of that of CaMV 35S promoter. Histochemical localization confirmed its activity in both mesophyll and vascular tissues. Activity of virion sense of LIR was rather low. Thus LIR isolated from CLCuV could be used as a novel strong promoter in plant genetic manipulation.展开更多
Small RNAs （sRNAs） are non-coding transcripts exerting their functions in the cells directly. Identification of sRNAs is a difficult task due to the lack of clear sequence and structural biases. Most sRNAs are ident...Small RNAs （sRNAs） are non-coding transcripts exerting their functions in the cells directly. Identification of sRNAs is a difficult task due to the lack of clear sequence and structural biases. Most sRNAs are identified within genus specific intergenic regions in related genomes. However, several of these regions remain un-annotated due to lack of sequence homology and/or potent statistical identification tools. A computational engine has been built to search within the intergenic regions to identify and roughly annotate new putative sRNA regions in Enterobacteriaceae genomes. It utilizes experimentally known sRNA data and their flanking genes/KEGG Orthology （KO） numbers as templates to identify similar sRNA regions in related query genomes. The search engine not only has the capability to locate putative intergenic regions for specific sRNAs, but also has the potency to locate conserved, shuffled or deleted gene clusters in query genomes. Because it uses the KO terms for locating functionally important regions such as sRNAs, any further KO number assignment to additional genes will increase the sensitivity. The PsRNA server is used for the identification of putative sRNA regions through the information retrieved from the sRNA of interest. The computing engine is available online at http：//bioserver 1 .physics.iisc.ernet.in/psrna/and http：//bicmku.in： 8081/psrna/.展开更多
In the past few decades, scientists from all over the world have taken a keen interest in novel functional units such as small regulatory RNAs, small open reading frames, pseudogenes, transposons, integrase binding at...In the past few decades, scientists from all over the world have taken a keen interest in novel functional units such as small regulatory RNAs, small open reading frames, pseudogenes, transposons, integrase binding attB/attP sites, repeat elements within the bacterial intergenic regions （IGRs） and in the analysis of those ＂junk＂ regions for ge- nomic complexity. Here we have developed a web server, named Junker, to facilitate the in-depth analysis of IGRs for examining their length distribution, four-quadrant plots, GC percentage and repeat details. Upon selection of a particular bacterial genome, the physical genome map is displayed as a multiple loci with options to view any loci of interest in detail. In addition, an IGR statistics module has been created and implemented in the web server to analyze the length distribution of the IGRs and to understand the disordered grouping of IGRs across the genome by generating the four-quadrant plots. The proposed web server is freely available at the URL http：//pranag.physics.iisc.ernet.in/junker/.展开更多
Objective To explore the relationships intergenic region in mtDNA with PCOS. of variations in D-loop and COH-tRNA^Lys Methods A total of 77 PCOS and 45 non-PCOS patients were enrolled, whose D-loop and COH-tRNA^Lys in...Objective To explore the relationships intergenic region in mtDNA with PCOS. of variations in D-loop and COH-tRNA^Lys Methods A total of 77 PCOS and 45 non-PCOS patients were enrolled, whose D-loop and COH-tRNA^Lys intergenic region in mtDNA were amplified and sequenced; sexual hormone assay, oral glucose tolerance test （OGTT） and insulin releasing test were carried out. Then variations found in mtDNA were compared between the two groups, the correlations between variations and clinical indexes were analyzed in all subjects. Results Nucleotide variations found in mtDNA were not different between the two groups, but the mutation of 16 094T/C was found associated with the serum levels ofT and fasting insulin; （303-317）CnTC, associated with the serum levels of A and LH; 195C/T with A level and 491T/C with LH level; （8 272-8 289）（ACCCCCTCT）, was associated with the serum level of 1 h glucose. Conclusion Noncoding region mutations in mtDNA perhaps associate with PCOS clinical symptoms and involve in PCOS development.展开更多
Non-alcoholic fatty liver disease(NAFLD)is emerging as a common cause of chronic liver disease in children and adults.NAFLD can progress to steatohepa-titis and potentially even hepatocellular carcinoma.Early identifi...Non-alcoholic fatty liver disease(NAFLD)is emerging as a common cause of chronic liver disease in children and adults.NAFLD can progress to steatohepa-titis and potentially even hepatocellular carcinoma.Early identification of pati-ents at risk for progressive disease is crucial for managing NAFLD.Recent studies have identified long noncoding RNAs(lncRNAs),circular RNAs,and microRNAs as playing important roles in the pathogenesis of NAFLD.These noncoding RNAs are involved in modulating several metabolic pathways such as hepatic glucose and lipid metabolism,oxidative stress,and even carcinogenesis.Elevated levels of lncARSR and lncRNA nuclear-enriched abundant transcript 1 have been found in patients with NAFLD.In addition,lncRNAs such as PRYP4-3 and RP11-128N14.5 can distinguish patients with NAFLD from healthy indi-viduals.Increased MEG3 expression has been observed in both NAFLD and non-alcoholic steatohepatitis,suggesting that it may help predict patients at risk for disease progression.With advances in transcriptomics,we may discover additional targets to help in the identification and prognostication of NAFLD.展开更多
The changes of microbial community structures and functional genes during the biodegradation of single phenol and phenol plus p-cresol under high salt condition were explored.It was found that the phenol-fed system（...The changes of microbial community structures and functional genes during the biodegradation of single phenol and phenol plus p-cresol under high salt condition were explored.It was found that the phenol-fed system（PFS） exhibited stronger degrading abilities and more stable biomass than that of the phenol plus p-cresol-fed system（PCFS）.The microbial community structures were revealed by a modern DNA fingerprint technique,ribosomal intergenic spacer analysis（RISA）.The results indicated that the microbial community of PFS changed obviously when gradually increased phenol concentration,while PCFS showed a little change.16S rRNA sequence analysis of the major bands showed that Alcanivorax sp.genus was predominant species during phenolic compounds degradation.Furthermore,amplified functional DNA restriction analysis（AFDRA） on phenol hydroxylase genes showed that the fingerprints were substantially different in the two systems,and the fingerprints were not the same during the different operational periods.展开更多
基金Supported by the Shandong Provincial Natural Science Foundation of China,No.ZR2016HQ08Shandong Province Medical Science and Technology Development Projects of China,No.2016WS0151the Jining Municipal Project on Science and Technology Development of China,No.2013jnwk58
文摘AIM To clarify the mechanisms of HOX transcript antisense intergenic RNA(HOTAIR) in gastric cancer(GC) migration and invasion.METHODS Quantitative real-time polymerase chain reaction(qp CR) was used to detect the expression level of HOTAIR in GC tissues. The correlation of its expression with clinicopathological features was analyzed. Area under receiver operating characteristic curve(AUCROC) was constructed to evaluate the diagnostic value of HOTAIR. Wound-healing assay and Transwell assay were performed to detect the biological effects of HOTAIR in GC cells. qp CR,western blot and immunohistochemistry were used to evaluate the m RNA and protein expression of E-cadherin. RNAbinding protein immunoprecipitation was used for the analysis of EZH2 interactions with HOTAIR. Chromatin immunoprecipitation assay was performed to investigate direct interactions between EZH2 and E-cadherin.RESULTS The expression of HOTAIR was up-regulated in GC tumorous tissues compared with the para-tumorous tissues(p < 0.001). Its over-expression was correlated with tumor-node-metastasis(TNM) stage(p = 0.024),tumor invasion(p = 0.018),lymph node metastasis(p = 0.023),and poor prognosis(p < 0.001). Multivariate Cox regression analysis confirmed expression of HOTAIR as an independent predictor of overall survival(p = 0.033),together with TNM stage(p = 0.002) and lymph node metastasis(p = 0.002). The AUCROC was up to 0.709(95%CI: 0.623-0.785,p < 0.001). Knockdown of HOTAIR by si RNA in GC cells suppressed the migration and invasion of GC cells. Significantly negative correlation between HOTAIR and E-cadherin was found in GC tissues and cell lines,and HOTAIR contributed to the regulation of E-cadherin through binding to EZH2 with the E-cadherin promoter. CONCLUSION HOTAIR may play a pivotal role in tumor cell migration and invasion. It can be used as a potential diagnostic and prognostic biomarker for GC.
文摘Phylogenetic relationships of Arundinaria and related genera (Pleioblastus, Pseudosasa, Oligostachyum, Bashania, Clavinodum, etc.) were assessed by analyzing the sequences of the nrDNA internal transcribed spacer (ITS) and the cpDNA trnL-F intergenic spacer (IGS). Comparison with trnL-F IGS sequence, the ITS region provided the higher number of parsimony informative characters, and the interspecific variation of the ITS sequence was higher than that of the trnL-F IGS sequence.The tree obtained by combining both sets of data showed that the species sampled in Arundinaria and the related genera were monophyletic and divided into two clades. The relationships and positioning of all the taxa surveryed (including A. oleosa, A. hsienchuensis, A. chino, A. amara, A. yixingensis, A. amabilis, A. fortunei, A. pygmaea, A. gramineus, A. fargesii, A. faberi, A. hupehense, Pseudosasa japonica cv. Tsutsumiana, P. japonica and Brachystachyum densiflorum) were also discussed. The results from the sequences were broadly consistent with morphological characters, appearing all these taxa sampled belong to the genus of Arundinaria. The topologies of the trees generated from individual data and the combined data were similar.
文摘Objective Cytokine responses to activation of innate immunity differ between individuals,yet the genomic and tissue-specific transcriptomic determinants of inflammatory responsiveness are not well understood. We hypothesized that tissue-specific mRNA and long intergenic non-coding RNA (lincRNA) induction differs between individuals with divergent evoked inflammatory responses.
基金Supported by the National High Technology Research and Development Program of China (863 Program)(No 2006AA10A402)Project for Supporting National Development (No 2006BAD09A04)+2 种基金the National Natural Science Foundation of China (Nos U0633006,40476059)the Natural Science Foundation of Qingdao (No 05-2-p-2)the Knowledge Innovation Program of the Chinese Academy of Sciences (No KZCX2-211)
文摘An improved method of PCR in which the small segment of conchocelis is amplified directly without DNA extraction was used to amplify a RUBISCO intergenic spacer DNA fragment from nine species of red algal genus Porphyra(Bangiales,Rhodophyta),including Porphyra yezoensis(Jiangsu,China),P.haitanensis(Fujian,China),P.oligospermatangia(Qingdao,China),P.katadai(Qingdao,China),P.tenera(Qingdao,China),P.suborboculata(Fujian,China),P.pseudolinearis(Kogendo,Korea),P.linearis(Devon,England),and P.fallax(Seattle,USA).Standard PCR and the method developed here were both conducted using primers specific for the RUBISCO spacer region,after which the two PCR products were sequenced.The sequencing data of the amplicons obtained using both methods were identical,suggesting that the improved PCR method was functional.These findings indicate that the method developed here may be useful for the rapid identification of species of Porphyra in a germplasm bank.In addition,a phylogenetic tree was constructed using the RUBISCO spacer and partial rbcS sequence,and the results were in concordant with possible alternative phylogenies based on traditional morphological taxonomic characteristics,indicating that the RUBISCO spacer is a useful region for phylogenetic studies.
基金The National Natural Science Foundation of China under contract Nos 30640015 and 30771644the Major Program of Zhejiang Province of China under contract No. 2005C23085
文摘One adult α-globin gene and one β-globin gene have been cloned from the large yellow croaker Pseudosciaena crocea. Linkage analysis indicated that the α- and β-globin genes were oriented head-to-head relative to each other. To identify the regulatory elements present in the intergenic and intragenic regions of the globin complex, the intergenic region alone or together with the β-globin gene first intron was cloned into the luciferase-reporter vector pGL3-Basic respectively, and the chimeric constructs were tran- siently transfected into Vero cells and primary fish erythrocytes. The intergenic region cannot support the high-level expression of luciferase. However, the promoter activity of the intergenic region was strongly stimulated by the positive regulatory elements （PRE） located in the β-globin gene intron 1. Thus, it is proposed that the intergenic promoters and intragenic PRE were necessary for the effective expression of the linked α- and β-globin genes.
基金supported by the earmarked fund for China Agriculture Research System (CARS-20)the Youth Talent Development Plan of Shanghai Municipal Agricultural System, China (20160113)the Agriculture Research System of Shanghai, China (201809)
文摘China is currently the world＇s leading producer of Lentinula edodes and owns many cultivated strains of this species. This study was performed in order to investigate intergenic spacer I （IGS1） polymorphism and classification among 49 popular cultivated strains. The great majority of the 49 strains possessed two different IGS1 sequences, with distinct lengths and homologies. Based on the length and homology of the IGS1 sequences of the 49 strains, the strains were classified into two groups： A and B. Group A was subdivided into six subgroups. Forty-seven strains were homozygous or heterozygous among these six subgroups in group A, Cr01 was heterozygous between A and B, and Guangxiang 9 was homozygous in group B. An IGS1 polymorphism map of each cultivated L. edodes strain is reported for the first time and could be used as a marker for the initial classification and management of cultivated L. edodes strains in China.
基金supported by the National Bio-Resource Project "Pathogenic microbes" from the Ministry of Education,Culture,Sports,Science and Technology of the Japanese Governments
文摘To re-identify and further group 25 isolates of Trichosporon spp. identified morphologically previously, sequences of D1/D2 region of large subunit （LSU） of ribosomal DNA （rDNA） of 25 tested strains for identification and those of ribosomal intergenic space 1 （IGS1） region of 11 strains for subgrouping were detected. The identifications of tested strains were changed except 6 strains. According to the alignment of the IGS1 region, 6 T. asahii isolates tested fell into 4 groups and 5 T. faecale isolates into 3 groups. Polymorphism of 2 T. japonicum isolates was found in 10 positions. With the alignments obtained in this research compared with the relative GenBank entries, it was found that T. asahii, T. faecale and T. japonicum species were divided into 7, 3 and 2 subtypes respectively. Morphological and biophysical methods are not sufficient for Trichosporon spp. identification. Sequencing becomes necessary for Trichosporon diagnosis. There is obvious diversity within a species.
基金The Hellenic Society of Medical Oncology,No.8021/25.09.2020.
文摘BACKGROUND Cholangiocarcinoma(CCA)represents a rare but highly aggressive malignancy that is often challenging to diagnose,especially in early stages.The role of existing tumor biomarkers for CCA diagnosis,remains controversial due to their low sensitivity and specificity.Increasing evidence has implicated long non-coding ribonucleic acid polymorphisms with cancer susceptibility in a variety of tumor types.The association between long non-coding ribonucleic acid homeobox protein transcript antisense intergenic ribonucleic acid(HOTAIR)polymorphisms and CCA risk has not been reported yet.AIM To investigate the influence of HOTAIR variants on the risk of CCA development.METHODS We conducted a case-control study in which three HOTAIR single nucleotide polymorphisms(rs920778,rs4759314 and rs7958904)were genotyped in a Greek cohort.Our study population included 122 CCA patients(80 males and 42 females)and 165 healthy controls.The polymorphisms under investigation were examined in peripheral blood samples.RESULTS HOTAIR rs4759314 AG and GG genotypes were associated with a significantly increased CCA risk[P=0.004,odds ratio:3.13;95%confidence interval:1.65-5.91 and P=0.005,odds ratio:12.31;95%confidence interval:1.48-101.87,respectively].However,no significant associations of HOTAIR rs920778,and rs7958904 were detected.Similarly,we found no significant associations between rs4759314 AA genotype and CCA susceptibility.CONCLUSION HOTAIR rs4759314 AG and GG genotypes may be implicated with CCA development and may serve as a potential diagnostic biomarker.
文摘Although a great deal of research has been undertaken in the area of the annotation of gene structure, predictive techniques are still not fully developed. In this paper, based on the characteristics of base composition of sequences and conservative of nucleotides at exon/intron splicing site, a least increment of diversity al-gorithm (LIDA) is developed for studying and predicting three kinds of coding exons, introns and intergenic regions. At first, by selecting the 64 trinucleotides composition and 120 position parameters of the four bases as informational parameters, coding exon, intron and intergenic sequence are predicted. The results show that overall predicted accuracies are 91.1% and 88.4%, respectively for A. thaliana and C. ele-gans genome. Subsequently, based on the po-sition frequencies of four kinds of bases in regions near intron/coding exon boundary, initia-tion and termination site of translation, 12 position parameters are selected as diversity source. And three kinds of the coding exons are predicted by use of the LIDA. The predicted successful rates are higher than 80%. These results can be used in sequence annotation.
文摘Objective To set up a rapid and simple method for identificating bacteria by 16S 23SrDNA intergenic spacer regions (ISRs) Methods Polymorphic products of PCR from ISRs were selected on agarose gel and sequenced directly using purified fragments by excising the gel without cloning Nucleotide sequences were compared with GenBank databases and analyzed by DNAMAN program Results There was only a single product in streptococcus genus after PCR amplification of 16S 23SrDNA ISRs Five streptococcal species were obtained from 7 strains of streptococcus Two major amplicons were consistently generated for 8 strains of Haemophilus influenzae (H influenzae) The sequence data showed that they all belonged to H influenzae type b on GenBank databases Conclusion PCR and direct sequencing of 16S 23SrDNA ISRs were very successful methods for bacterial species identification
基金supported by the National Basic Research Program of China (No. 2011CB510100)the National Natural Science Foundation of China (No. 81030015)
文摘Although there is an accumulating appreciation of the key roles that long intergenic non-coding RNAs （lincRNAs） play in diverse cellular processes, our knowledge of how lincRNAs function in cancer remains sparse. Here, we present a comprehensive landscape of RNA-seq transcriptome profiles of lung adenocarcinomas and their paired normal counterparts to unravel gene regulation rules of lincRNAs. Consistent with previous findings of co-expression between neighboring protein-coding genes, lincRNAs were typically co-expressed with their neighboring genes, which was found in both cancerous and normal tissues. By building a mathematical model based on correlated gene expression, we distinguished an additional subset of lincRNAs termed ＂regulatory lincRNAs＂, representing their dominant roles in gene regulation. The number of regulatory lincRNAs was significantly higher in cancerous compared to normal tissues, and most of them positively regulated protein-coding genes in trans. Functional validation, using knockdown, determined that regulatory lincRNA, GASS, affected its predicted protein-coding targets. Moreover, we discovered hundreds of differentially expressed regulatory lincRNAs with inclusion of some cancer-associated lincRNAs. Our integrated analysis reveals enhanced regulatory effects of lincRNAs and provides a resource for the study of regulatory lincRNAs that play critical roles in lung adenocarcinoma.
基金This work has been registered as national patent (patent applying number: 99103044.3).theMomentous Project of Chinese Academy of Sciences, National High Science and Technology Program, National Special Program for Research and Industrialization of Tran
文摘Cotton leaf curl virus (CLCuV) is a type of single-stranded DMA virus, belonging to geminivirus of subgroup Ⅲ. In order to determine the function of CLCuV large intergenic region (LIR), total DNA of CLCuV-infected cotton leaves was used as template, and fragment of LIR was obtained by PCR and inserted into clone vector. The fragment of LIR was fused with gus reporter gene and nos terminator in the orientation of transcription of virion sense and complementary sense respectively, and the plant expression vectors were constructed. GUS activity of Agrobacte-rium-mediated transgenic tobacco was measured. The result indicated that LIR showed strong promoter activity in complementary sense gene orientation. Average GUS activity of the complementary sense promoter was 5-6 times that of CaMV 35S promoter, and the highest GUS activity of individual plant was ten times of that of CaMV 35S promoter. Histochemical localization confirmed its activity in both mesophyll and vascular tissues. Activity of virion sense of LIR was rather low. Thus LIR isolated from CLCuV could be used as a novel strong promoter in plant genetic manipulation.
基金funded by the Department of Biotechnology (DBT), Government of India
文摘Small RNAs （sRNAs） are non-coding transcripts exerting their functions in the cells directly. Identification of sRNAs is a difficult task due to the lack of clear sequence and structural biases. Most sRNAs are identified within genus specific intergenic regions in related genomes. However, several of these regions remain un-annotated due to lack of sequence homology and/or potent statistical identification tools. A computational engine has been built to search within the intergenic regions to identify and roughly annotate new putative sRNA regions in Enterobacteriaceae genomes. It utilizes experimentally known sRNA data and their flanking genes/KEGG Orthology （KO） numbers as templates to identify similar sRNA regions in related query genomes. The search engine not only has the capability to locate putative intergenic regions for specific sRNAs, but also has the potency to locate conserved, shuffled or deleted gene clusters in query genomes. Because it uses the KO terms for locating functionally important regions such as sRNAs, any further KO number assignment to additional genes will increase the sensitivity. The PsRNA server is used for the identification of putative sRNA regions through the information retrieved from the sRNA of interest. The computing engine is available online at http：//bioserver 1 .physics.iisc.ernet.in/psrna/and http：//bicmku.in： 8081/psrna/.
文摘In the past few decades, scientists from all over the world have taken a keen interest in novel functional units such as small regulatory RNAs, small open reading frames, pseudogenes, transposons, integrase binding attB/attP sites, repeat elements within the bacterial intergenic regions （IGRs） and in the analysis of those ＂junk＂ regions for ge- nomic complexity. Here we have developed a web server, named Junker, to facilitate the in-depth analysis of IGRs for examining their length distribution, four-quadrant plots, GC percentage and repeat details. Upon selection of a particular bacterial genome, the physical genome map is displayed as a multiple loci with options to view any loci of interest in detail. In addition, an IGR statistics module has been created and implemented in the web server to analyze the length distribution of the IGRs and to understand the disordered grouping of IGRs across the genome by generating the four-quadrant plots. The proposed web server is freely available at the URL http：//pranag.physics.iisc.ernet.in/junker/.
基金supported by a grant from the Foundation of Ministry of Education of China (No. JHG06-7-03)
文摘Objective To explore the relationships intergenic region in mtDNA with PCOS. of variations in D-loop and COH-tRNA^Lys Methods A total of 77 PCOS and 45 non-PCOS patients were enrolled, whose D-loop and COH-tRNA^Lys intergenic region in mtDNA were amplified and sequenced; sexual hormone assay, oral glucose tolerance test （OGTT） and insulin releasing test were carried out. Then variations found in mtDNA were compared between the two groups, the correlations between variations and clinical indexes were analyzed in all subjects. Results Nucleotide variations found in mtDNA were not different between the two groups, but the mutation of 16 094T/C was found associated with the serum levels ofT and fasting insulin; （303-317）CnTC, associated with the serum levels of A and LH; 195C/T with A level and 491T/C with LH level; （8 272-8 289）（ACCCCCTCT）, was associated with the serum level of 1 h glucose. Conclusion Noncoding region mutations in mtDNA perhaps associate with PCOS clinical symptoms and involve in PCOS development.
文摘Non-alcoholic fatty liver disease(NAFLD)is emerging as a common cause of chronic liver disease in children and adults.NAFLD can progress to steatohepa-titis and potentially even hepatocellular carcinoma.Early identification of pati-ents at risk for progressive disease is crucial for managing NAFLD.Recent studies have identified long noncoding RNAs(lncRNAs),circular RNAs,and microRNAs as playing important roles in the pathogenesis of NAFLD.These noncoding RNAs are involved in modulating several metabolic pathways such as hepatic glucose and lipid metabolism,oxidative stress,and even carcinogenesis.Elevated levels of lncARSR and lncRNA nuclear-enriched abundant transcript 1 have been found in patients with NAFLD.In addition,lncRNAs such as PRYP4-3 and RP11-128N14.5 can distinguish patients with NAFLD from healthy indi-viduals.Increased MEG3 expression has been observed in both NAFLD and non-alcoholic steatohepatitis,suggesting that it may help predict patients at risk for disease progression.With advances in transcriptomics,we may discover additional targets to help in the identification and prognostication of NAFLD.
基金supported by the National Natural Science Foundation of China (No. 50608011)
文摘The changes of microbial community structures and functional genes during the biodegradation of single phenol and phenol plus p-cresol under high salt condition were explored.It was found that the phenol-fed system（PFS） exhibited stronger degrading abilities and more stable biomass than that of the phenol plus p-cresol-fed system（PCFS）.The microbial community structures were revealed by a modern DNA fingerprint technique,ribosomal intergenic spacer analysis（RISA）.The results indicated that the microbial community of PFS changed obviously when gradually increased phenol concentration,while PCFS showed a little change.16S rRNA sequence analysis of the major bands showed that Alcanivorax sp.genus was predominant species during phenolic compounds degradation.Furthermore,amplified functional DNA restriction analysis（AFDRA） on phenol hydroxylase genes showed that the fingerprints were substantially different in the two systems,and the fingerprints were not the same during the different operational periods.
