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1. 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 |
2. 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 |
3. 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 |
4. Major histocompatibility complex II B allele polymorphism and its association with Vibrio anguillarum infection in half-smooth tongue sole | |||
WANG Xubo,LI Chunmei,QI Jie,WANG Zhigang,YU Haiyang | |||
Biology 14 July 2011 | |||
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Abstract:Major histocompatibility complex (MHC) class II B molecules play an important role in the adaptive immune response in fish. Previous study has reported that two highly polymorphic class II B genes, Cyse-DAB and Cyse-DBB exist in half-smooth tongue sole (Cynoglossus semilaevis). In this study, the polymorphism within exon 2 of the class II B genes following bacterial challenge was evaluated. Two hundred individuals were injected intraperitoneally with Vibrio anguillarum. Muscle tissue from the first 20 dead and 20 of the survivors was collected for genotyping. Sixty alleles from the 40 individuals were isolated, of which 32 belonged to Cyse-DAB and 28 belonged to Cyse-DBB. The rate of dN (non-synonymous substitution) was higher than that of dS (synonymous substitution) in the PBRs (peptide binding residues) of both class II B genes. Conversely, the rate of dS was higher than dN in the non-PBRs and the complete exon 2 sequence. Thus, the results suggest that positive selection has occurred in the PBRs and purifying selection in the non-PBRs and exon 2. Thirteen class II B alleles were used to study the association between alleles and resistance to infection. Though not significant, alleles Cyse-DAB*0601, Cyse-DAB*0706, and Cyse-DBB*0101, Cyse-DBB*1301 were only found in surviving individuals and may represent alleles that have resistance against V. anguillarum infection. Alleles Cyse-DAB*0701 and Cyse-DAB*1301 were significantly more prevalent in dead individuals than in surviving ones and may represent alleles that are associated with increased susceptibility to V. anguillarum infection. | |||
TO cite this article:WANG Xubo,LI Chunmei,QI Jie, et al. Major histocompatibility complex II B allele polymorphism and its association with Vibrio anguillarum infection in half-smooth tongue sole[OL].[14 July 2011] http://en.paper.edu.cn/en_releasepaper/content/4435459 |
5. Origin and differentiation of a special fragment from Capra hircus agouti gene | |||
Weiwei WU,Xianglong LI,Rongyan ZHOU,Lanhui LI,Huiqin ZHENG | |||
Biology 15 March 2010 | |||
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Abstract:A special fragment, 136 bp fragment previously considered only existed in Capra hircus agouti gene but not in agouti gene of cow, sheep, pig, and horse, was analyzed using BLAST program in NCBI and some powerful molecular biology softwares. The results indicated that the special fragment existed in different regions of the agouti gene of Capra hircus and Ovis aries, but not in the agouti gene of Bos taurus. Meanwhile, it appeared in coding or non-coding regions with forward and reverse sequence in other genes of Ovis aries and Bos taurus. The number of forward sequences was higher than that of reverse ones in Bos taurus, but with similar genetic diversity. While the reverse sequence from Ovis aries had higher genetic diversity than forward ones. The differentiation between Bos taurus and Capra hircus was more obvious than between Bos taurus and Ovis aries, but not within species. The BACR5 (AC150540) from Bos taurus and OEEF2 (EE751186) from Ovis aries could be considered as the farmost ancestral sequences. | |||
TO cite this article:Weiwei WU,Xianglong LI,Rongyan ZHOU, et al. Origin and differentiation of a special fragment from Capra hircus agouti gene[OL].[15 March 2010] http://en.paper.edu.cn/en_releasepaper/content/40689 |
6. Bioinformatics analysis of tyrosinase-related protein 1 gene (TYRP1) from different species | |||
Huiqin Zheng,Xianglong Li,Rongyan Zhou,Lanhui Li,Xiuli Guo,Jingfen Kang,Dongfeng Li | |||
Biology 25 January 2010 | |||
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Abstract:As one member of tyrosinase-related family directly involved in the production of melanin, TYRP1 is involved in not only melanogenesis but also prevention of melanocyte death, stabilizing tyrosinase and helping determine the shape of melanosomes, etc. Multi-species sequence comparisons showed that there were two evolutionally conserved non-coding regions (from -1306 to -733 and from -642 to -515 according to AL138753) upstream of translational initiation sites, representing putative regulatory regions subject to subsequent experimental test. CDS length variation and genetic diversity analysis showed that Felis catus, Homo sapiens and Canis familiaris had more genetic diversities than the other species for TYRP1, especially Felis catus that could be a better choice for studying the TYRP1-associated genetic basis underlying the color diversity. As a 75 kDa type-1 transmembrane glycoprotein, Mature TYRP1 possesses about 17 kDa modifying components, whose function predominantly depends on the existing glycosyl- groups and the Cu components. In addition, the mutated amino acids within species and the highly conserved amino acids among species were listed in our paper. | |||
TO cite this article:Huiqin Zheng,Xianglong Li,Rongyan Zhou, et al. Bioinformatics analysis of tyrosinase-related protein 1 gene (TYRP1) from different species[OL].[25 January 2010] http://en.paper.edu.cn/en_releasepaper/content/39346 |
7. ESTs involved in interaction between genomic and plasmid DNA in E. coli JM109 | |||
Yao Xinling,Ma Yijing,Zhiping Hong,Qin Wu,Aiguang Guo | |||
Biology 14 January 2010 | |||
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Abstract:An essential issue for genome annotation is to identify genes involving in interaction between genomes in the same cell. It is difficult to do so in eukaryotic cells, because each type of genome is required for cell survival. Escherichia coli, however, is a suitable model for the study of specific gene interactions, because E. coli can grow in the presence or absence of a plasmid. In this paper, genes that are expressed in a cell-specific manner were tested using E. coli JM109 with or without plasmid with modified suppression subtractive hybridization, named transcript subtractive hybridization (TSH). Four out of five genes that were specific to the plasmid were detected by the SSH. Meanwhile, 10 expressed sequence tags (ESTs) were identified that may be involved in interaction between the JM109 genome and the plasmid. This technique provides a potential approach for the study of interaction between genomes in prokaryotes. | |||
TO cite this article:Yao Xinling,Ma Yijing,Zhiping Hong, et al. ESTs involved in interaction between genomic and plasmid DNA in E. coli JM109[OL].[14 January 2010] http://en.paper.edu.cn/en_releasepaper/content/38944 |
8. Relationship between trehalose accumulation and freeze tolerance of baker’s yeast | |||
Xiao Dongguang ,Zhang Cuiying ,Lv Ye | |||
Biology 30 October 2009 | |||
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Abstract:Accumulation of trehalose is suggested to be a critical determinant in improving the stress tolerance of the yeast Saccharomyces cerevisiae. To test the influence of trehalose accumulation on response to freeze stress, we constructed all single and double gene disruption mutants of the trehalase genes ATH1, NTH1 and NTH2 and examined the changes of their trehalose accumulations and their freeze tolerance. Under the condition of freeze stress, three mutants, Δnth1, Δnth2Δnth1, and Δath1Δnth1, all of which carry the NTH1 gene disruption, showed increased trehalose accumulation as compared to the parent strain and other mutants. Moreover, compared with the parent strain BY-6, the NTH1 disruption mutants possessed higher cell survival ratios and greater relative leavening abilities. The results indicated that NTH1 gene is important for trehalose degradation under conditions of freeze stress, thus closely correlated with freeze tolerance of baker’s yeast. | |||
TO cite this article:Xiao Dongguang ,Zhang Cuiying ,Lv Ye . Relationship between trehalose accumulation and freeze tolerance of baker’s yeast[OL].[30 October 2009] http://en.paper.edu.cn/en_releasepaper/content/36281 |
9. Isolation and expression of a new high molecular weight glutenin subunit gene at the Glu-D-1-2 locus from Aegilops tauschii | |||
Yanzhen Zhang,An Xueli,Li Xiaohui,Chen Shaoming,Wang Ke,Wang Ke,Wang Shunli ,Yueming Yan | |||
Biology 14 January 2009 | |||
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Abstract:Two new y-type HMW-GSs in Ae. tauschii, 1Dy12.1*t and 1Dy12.2t with the mobility order of 1Dy12.2t>1Dy12.1*t>1Dy12.1t>1Dy12, were identified by both SDS-PAGE and MALDI-TOF-MS. Molecular cloning and sequencing showed that the genes encoding subunits 1Dy12.1*t and 1Dy12.2t had identical nucleotide acid sequences with 1,947bp encoding a mature protein of 627 residues. Their deduced molecular weights were 67,347.6Da, satisfactorily corresponding to that of 1Dy12.2t subunit determined by MALDI-TOF-MS (67,015.7Da), but was significantly smaller than that of the the 1Dy12.1*t subunit (68,577.1Da). Both subunits showed high similarities to 1Dy10, suggesting that they could have a positive effect on bread-making quality. Interestingly, the expressed protein of the cloned ORF from accessions TD87 and TD130 in E. coli co-migrated with subunit 1Dy12.2t, but moved slightly faster than 1Dy12.1*t on SDS-PAGE. The expressed protein in transgenic tobacco seeds, however, had the same mobility as the 1Dy12.1*t subunit, as confirmed by both SDS-PAGE and Western blotting. Although direct evidence of phosphoprotein or glycoprotein could not be obtained by specific staining methods, certain types of post-translational modifications (PTMs) of the 1Dy12.1*t subunit could not be excluded. We believe PTMs might be responsible for the molecular weight difference between the subunits 1Dy12.1*t and 1Dy12.2t. | |||
TO cite this article:Yanzhen Zhang,An Xueli,Li Xiaohui, et al. Isolation and expression of a new high molecular weight glutenin subunit gene at the Glu-D-1-2 locus from Aegilops tauschii[OL].[14 January 2009] http://en.paper.edu.cn/en_releasepaper/content/27797 |
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