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There are 21 papers published in subject: > since this site started. |
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1. Identification of two dazl splicing variants in Japanese flounder (Paralichthys olivaceus) | |||
WANG Xubo,JIANG Jiajun,ZHANG Quanqi | |||
Biology 16 May 2016 | |||
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Abstract:DAZL is an RNA-binding protein of DAZ family, playing key roles in reproduction of organisms. Here in this study, we clone and identify the dazl gene in a kind of flatfish, Japanese flounder (Paralichthys olivaceus). Two different splicing variants of dazl mRNAs are found, and they differ from each other by a 51-bp insertion/deletion. We characterize the two mRNA variants by qPCR and in situ hybridization and prove their germ cell specific expression patterns. Results of western blot and immunohistochemistry show that the two isoforms of their translational production also express specifically in germ cells of both sexes. The similar expression patterns of the two variants may imply their complementary functions in germ cell development. But there are also differences in their functions. By RNA-binding protein immunoprecipitation, we find Podazl-I and Podazl-II may be the target of both PODAZL isoforms. More sequencing results will offer more detailed and accurate information on their functions. Studies on the two dazl variants in Japanese flounder are rare in teleosts. Our results may facilitate further studies on reproduction related genes and germ cell development. | |||
TO cite this article:WANG Xubo,JIANG Jiajun,ZHANG Quanqi. Identification of two dazl splicing variants in Japanese flounder (Paralichthys olivaceus)[OL].[16 May 2016] http://en.paper.edu.cn/en_releasepaper/content/4689150 |
2. Comparisons of several softwares to detect medium- and large-sized deletions based on next generation sequencing data | |||
Yao Wen,Xie Weibo | |||
Biology 25 November 2015 | |||
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Abstract:Next generation sequencing (NGS) technologies have enabled us to detect sequence variations effectively. And there are many softwares developed to facilitate and simplify this task. In this study, we carry out detailed comparisons between BreakDancer, Pindel, CNV-seq, CNVnator, inGAP-sv and Defind using both simulation data and real data to detect medium- and large-sized deletions. Defind and CNVnator are the only two methods capable of detecting the completed deletion of Ghd7 in the rice cultivar Zhenshan 97 and Defind performs robustly at different sequence coverage with different read length in the simulation study. The results demonstrate the advantage of combining different types of signature in NGS data to identify deletions. Our studies also provided a significant practical guidance to select appropriate methods to detect medium- and large-sized genomic deletions using NGS data. | |||
TO cite this article:Yao Wen,Xie Weibo. Comparisons of several softwares to detect medium- and large-sized deletions based on next generation sequencing data[OL].[25 November 2015] http://en.paper.edu.cn/en_releasepaper/content/4664949 |
3. Genetic diversity of Hirsutella sinensis revealed by EST-SSR | |||
YUAN Feng,YU Hong,ZUO Shimei | |||
Biology 19 November 2014 | |||
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Abstract:In recent years, expressed sequence tags has been used as a new approach to develop markers, as they rapidly accumulated in databases. In the present study, EST-SSR markers of the genus Hirsutella have been identified using primers designed from ESTs pools of Paecilomyces militaris and were found to have well transferability from Paecilomyces to Hirsutella. These markers were used to evaluate genetic diversity and structure within and between 8 populations of Hirsutella sinensis. The genetic differentiation of H. sinensis was relatively astonishing between populations (67.49%). The Nm was 0.2408, indicating serious lack of gene flow among populations of H. sinensis. The genetic distance and geographical distance were significantly positively correlated relationship (P = 0.04). And the analysis of mismatch distribution indicated the populations of H. sinensis underwent population expansion recently. It was also found that H. robertsii might originate from H. sinensis. The EST-SSR markers were proved to be an informative and useful tool for assaying genetic diversity and authenticating species of Hirsutella. | |||
TO cite this article:YUAN Feng,YU Hong,ZUO Shimei. Genetic diversity of Hirsutella sinensis revealed by EST-SSR[OL].[19 November 2014] http://en.paper.edu.cn/en_releasepaper/content/4619402 |
4. Genetic Structure of Paecilomyces militaris by EST-SSR | |||
Feng Yuan,Hong Yu,Shi Mei Zuo | |||
Biology 19 November 2014 | |||
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Abstract:The EST-SSR markers of Paecilomyces genus was established with the primers designed according to ESTs pools of Paecilomyces militaris. The markers had well transferability to Paecilomyces hepialid. Genetic diversity and structure were also evaluated within and among 11 populations of P. militaris. Nine primer groups were screened, and a total of 179 DNA fragments were amplified, all of which were polymorphic, averaging 19.9 polymorphic bands per primer. At the species level, the percentage of polymorphic bands was 100.00%, and 28.08% within the 11 populations. The observed number of alleles (Na) was 2.0000 and the effective number of alleles (Ne) was 1.3278; Nei's gene diversity (H) was 0.2128; Shannon's information index (I) was 0.3452. At the population level, Na = 1.3017, Ne = 1.1677, H = 0.0918, and I = 0.1546. Total gene diversity was 0.2027(Ht), the gene diversity within population was 0.0918(Hs), the coefficient of gene differentiation was 0.5472(Gst), and estimated gene flow was 0.4138(Nm). These results indicated the genetic differentiation was relatively higher among populations of P. militaris. The genetic structure had correlation with the geographical source, but not so obvious among the populations in Yunnan. The Paecilomyces sp. isolated from living Hepialus yunnanensis was proved to be Paecilomyces hepialid. The EST-SSR markers were an informative and useful method for assaying genetic diversity and authenticating species of Paecilomyces. The EST-SSR markers would provide for insight into population genetics of Paecilomyces species and help us select genotypes with high adaptability and high content of useful chemical components. | |||
TO cite this article:Feng Yuan,Hong Yu,Shi Mei Zuo. Genetic Structure of Paecilomyces militaris by EST-SSR[OL].[19 November 2014] http://en.paper.edu.cn/en_releasepaper/content/4619399 |
5. Genetic diversity and intraspecific genetic differentiation of Ostryopsis davidiana (Betulaceae) revealed by AFLP | |||
LU Zhiqiang,TIAN Bin,LIU Bingbing,LIU Jianquan,WAN Dongshi | |||
Biology 28 February 2014 | |||
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Abstract:Ostryopsis davidiana is endemic to China and widely distributed in northern China. In this study, AFLP markers were used to estimate the genetic diversity and intraspecific genetic differentiation of this species. Three out of fifteen selective primers combinations were applied to analyze 144 individuals of 18 populations of O. davidiana from entire geographical range in China. Finally, a total of 154 fragments with 84 polymorphic sites were produced. Excluding the average between-population diversity, the total population diversity, average within-population diversity and the Nei's gene diversity of southern group (SG) are higher than northern group (NG). One of the possible explanations for this result is that NG may originate from SG. Moreover, Bayesian clustering analysis (K = 2) suggested that populations of SG and NG were assigned to their respective groups with high possibility. Additionally, UPGMA clustering method further suggested all the populations from O. davidiana were also clustered into two groups corresponding to their geographical distributions. This species expanding from south to north before the time when the fast uplifts of Qing Mountains happened then experiencing a strong intraspecific genetic differentiation for the two groups isolated by the Mountains may provide the most reasonable explanation for these results. | |||
TO cite this article:LU Zhiqiang,TIAN Bin,LIU Bingbing, et al. Genetic diversity and intraspecific genetic differentiation of Ostryopsis davidiana (Betulaceae) revealed by AFLP[OL].[28 February 2014] http://en.paper.edu.cn/en_releasepaper/content/4587889 |
6. Transcriptional analysis of the conidiation pattern shift of entomopathogenic fungus, Metarhizium acridum, in response to different nutrients | |||
zhenglong Wang,yuxian Xia | |||
Biology 24 April 2013 | |||
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Abstract:Most fungi have two different conidiation patterns: normal conidiation and microcycle conidiation under different culture conditions, including the nutrients in the medium. However, the mechanism of conidiation pattern shift response to culture conditions is poorly understood. In this study, Metarhizium acridum conducting microcycle conidiation on sucrose yeast extract agar medium (SYA) shifted to normal conidiation when supplemented with sucrose, nitrate, or phosphate. The M. acridum transcripts on SYA, SYA supplemented with sucrose, nitrate or phosphate, and 1/4SDAY were sequenced by Solexa/Illumina deep-sequencing technology. The results showed that 6,931 genes involved in 243 biochemical pathways were either up- or downregulated in response to different nutrients. Comparative analysis demonstrated that 1,859 genes specifically upregulated at the microcycle conidiation stage were selected. One hundred and twelve, 292, or 216 genes might be associated with microcycle conidiation after adding sucrose, nitrate, or phosphates to SYA medium, respectively. Four hundred and seventy genes were specifically upregulated and might be related to normal conidiation. KEGG pathway analysis indicated that these genes were mainly associated with the cell cycle, cell proliferation, metabolism, protein transport and signal transduction, and the mitogen-activated protein kinase signaling and catabolism pathway. Changing sucrose, nitrate or phosphate, led to a shift between microcycle and normal conidiation by perturbing the cell cycle and metabolism of M. acridum. This research provides essential information about the molecular mechanism of conidiation pattern shift induced by single nutrients. | |||
TO cite this article:zhenglong Wang,yuxian Xia. Transcriptional analysis of the conidiation pattern shift of entomopathogenic fungus, Metarhizium acridum, in response to different nutrients[OL].[24 April 2013] http://en.paper.edu.cn/en_releasepaper/content/4536643 |
7. Effects of over-expression of allene oxide cyclase on camptothecin production by cell cultures of Camptotheca acuminata | |||
PI Yan,JIANG Keji,LIN Juan,CAO Ying,WANG Qian,YANG Ji | |||
Biology 21 December 2012 | |||
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Abstract:Camptothecin (CPT) is an anticancer and antiviral monoterpene-derived indole alkaloid which can be induced by plant hormone, jasmonates. To improve the production of the pharmaceuticals, the jasmonate biosynthesis related gene allene oxide cyclase from Camptotheca acuminate was transferred back into Camptotheca acuminate using the method of Agrobacterium-mediated genetic transformation and over expressed. The results of HPLC analysis indicated that the camptothecin content of transgenic callus was higher than that of non-transgenic callus. The highest camptothecin content in transgenic callus was 3.9310 mg/g DW. However, camptothecin content in both transgenic and non-transgenic calli significantly decreased after further extrinsic MeJA's induction, whereas the content of CPT in transgenic callus was still higher than in non-transgenic one. All the results indicated that endogenic jasmonate's accumulation may be promoted after allene oxide cyclase gene was transformed into Camptotheca acuminate and over expressed. In this way, jasmonates can affect second metabolism pathway genes' expression and then the camptothecin content was improved. Inexpectantly, the mechanism of extrinsic jasmonate to secondary metabolism of Camptotheca acuminate was different from that of endogenic jasmonates. | |||
TO cite this article:PI Yan,JIANG Keji,LIN Juan, et al. Effects of over-expression of allene oxide cyclase on camptothecin production by cell cultures of Camptotheca acuminata[J]. |
8. Examination of camptothecin and 10-hydroxycamptothecin in Camptotheca acuminata plant and cell culture, and the affected yields under several cell culture treatments | |||
PI Yan,JIANG Keji,HOU Rong,GONG Yifu,LIN Juan,SUN Xiaofen | |||
Biology 18 December 2012 | |||
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Abstract:Camptothecin and its derivatives are monoterpenoid indole alkaloids exhibiting significant anti-tumor actions. With the aim of improving the production of these pharmaceuticals, the contents of camptothecin and 10-hydroxycamptothecin in different tissues including roots, stems, leaves, young flower buds, opening flowers, fading flowers and seeds from Camptotheca acuminata, were investigated. The young flower buds had the highest alkaloid concentrations (camptothecin, 2.46 mg/g of dry weight; 10-hydroxycamptothecin, 1.41 mg/g of dry weight). Callus showed lower concentrations but it should also be considered as a potential source of these pharmaceuticals. In the present study, the growth rate of Camptotheca acuminata cells in culture did not correlate with contents of camptothecin and 10-hydroxycamptothecin. Alkaloid accumulation by cells under various treatments (heavy metal ions, UV-B), methyl-jasmonate, abscisic acid, salicylic acid and hydrogen peroxide was examined, and the most notable effects appeared in the cells induced by UV-B light (which showed an 11-fold increase in camptothecin concentration) and by salicylic acid (which showed a 25-fold increase in 10-hydroxycamptothecin concentration. These results are significant in the context of the production of both pharmaceuticals. | |||
TO cite this article:PI Yan,JIANG Keji,HOU Rong, et al. Examination of camptothecin and 10-hydroxycamptothecin in Camptotheca acuminata plant and cell culture, and the affected yields under several cell culture treatments[J]. |
9. PCR and magnetic bead-mediated target capture for the isolation of short interspersed nucleotide elements in fishes | |||
Liu Dong,Zhu Guoli,Tang Wenqiao,Yang Jinquan,Guo Hongyi | |||
Biology 06 September 2012 | |||
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Abstract:Short interspersed nucleotide elements (SINEs), a type of retrotransposon, are widely distributed in various genomes with multiple copies arranged in different orientations, and cause changes to genes and genomes during evolutionary history. This can provide the basis for determining genome diversity, genetic variation and molecular phylogeny, etc. SINE DNA is transcribed into RNA by polymerase III from an internal promoter, which is composed of two conserved boxes, box A and box B. Here we present an approach to isolate novel SINEs based on these promoter elements. Box A of a SINE is obtained via PCR with only one primer identical to box B (B-PCR). Box B and its downstream sequence are acquired by PCR with one primer corresponding to box A (A-PCR). The SINE clone produced by A-PCR is selected as a template to label a probe with biotin. The full-length SINEs are isolated from the genomic pool through complex capture using the biotinylated probe bound to magnetic particles. Using this approach, a novel SINE family, Cn-SINE, from the genomes of Coilia nasus, was isolated. The members are 180-360 bp long. Sequence homology suggests that Cn-SINEs evolved from a leucine tRNA gene. This is first report of a tRNALeu-related SINE obtained without the use of a genomic library or inverse PCR. These results provide new insights into the origin of SINEs. | |||
TO cite this article:Liu Dong,Zhu Guoli,Tang Wenqiao, et al. PCR and magnetic bead-mediated target capture for the isolation of short interspersed nucleotide elements in fishes[OL].[ 6 September 2012] http://en.paper.edu.cn/en_releasepaper/content/4488796 |
10. Molecular identification, polymorphism and association to Vibrio anguillarum infection of major histocompatibility complex class IIAof half-smooth tongue sole (Cynoglossus semilaevis) | |||
WANG Xubo,LI Chunmei,QI Jie,WANG Zhigang,YU Haiyang | |||
Biology 22 July 2011 | |||
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Abstract:Major histocompatibility complex class II antigens are important in vertebrate immune system. In the present study, the full length cDNA sequence of class II A gene was got by RACE-PCR from half-smooth tongue sole (Cynoglossus semilaevis), and its open reading frame (ORF) polymorphism was studied. The whole cDNA sequence was 992 bp in length, including the ORF of 717 bp. Twenty-five alleles were identified and clustered into two distinct groups for the specific nucleotides/ amino acids in specific positions, so they belonged to two class II A genes and dominated as Cyse-DAA and Cyse-DBA with 11 and 14 alleles respectively. Four Cyse-DAA alleles were observed in one individual, and three to five Cyse-DBA alleles in each of three detected individuals, which indicated that at least two loci existed in each gene. Moreover, in order to study the association of the alleles of A genes and resistance to infection, 200 individuals were intraperitoneally injected with Vibrio anguillarum and the first 20 dead individuals and 20 surviving ones were selected for genotypes of A genes. Fifty-six alleles were identified among the 40 individuals, 29 of which belonged to Cyse-DAA and 27 belonged to Cyse-DBA. Eighteen alleles were selected for the association study between alleles and resistance to infection. Though not significant, allele Cyse-DAA*0201, Cyse-DAA*1101, Cyse-DBA*0401, Cyse-DBA*1102, Cyse-DBA*1801 and Cyse-DBA*2201 appeared only in surviving individuals, while allele Cyse-DAA*0901, Cyse-DBA*1101 and Cyse-DBA*1401 occurred more frequently in dead individuals. This study confirmed the existence and polymorphism of two class II A genes and also the association between alleles of class II A genes and disease susceptibility/ resistance in half-smooth tongue sole. | |||
TO cite this article:WANG Xubo,LI Chunmei,QI Jie, et al. Molecular identification, polymorphism and association to Vibrio anguillarum infection of major histocompatibility complex class IIAof half-smooth tongue sole (Cynoglossus semilaevis)[OL].[22 July 2011] http://en.paper.edu.cn/en_releasepaper/content/4435563 |
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