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Atsushi Watanabe - One of the best experts on this subject based on the ideXlab platform.
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spatiotemporal gene expression profiles associated with male strobilus development in cryptomeria japonica by Suppression Subtractive Hybridization
Breeding Science, 2011Co-Authors: Manabu Kurita, Ryogo Nakada, Teiji Kondo, Toru Taniguchi, Atsushi WatanabeAbstract:To identify the genes associated with the formation and development of the male strobilus of Cryptomeria japonica D. Don (Sugi), male strobilus-specific Suppression Subtractive Hybridization (SSH) libraries were constructed from three different stages of male strobilus development. From these SSH libraries, 1,012 unigene sets including 314 contigs were assembled from 2,448 sequences. The profiles of the genes isolated from the SSH libraries differed strongly according to developmental stage: 49%, 13% and 29% of genes were unique to the early stage (stage E), tetrad stage (stage T), and mature stage (stage M) SSH libraries, respectively. To evaluate the reliability of the SSH libraries, we focused on the eight genes strongly concentrated in the three SSH libraries and performed RT-PCR analysis. All genes tested were expressed more strongly in the male strobilus than in the shoot. Our findings suggest that the gene profiles associated with male strobilus development differ in both number and kind of dominantly expressed genes.
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spatiotemporal gene expression profiles associated with male strobilus development in cryptomeria japonica by Suppression Subtractive Hybridization
Breeding Science, 2011Co-Authors: Manabu Kurita, Ryogo Nakada, Teiji Kondo, Toru Taniguchi, Atsushi WatanabeAbstract:To identify the genes associated with the formation and development of the male strobilus of Cryptomeria japonica D. Don (Sugi), male strobilus-specific Suppression Subtractive Hybridization (SSH) libraries were constructed from three different stages of male strobilus development. From these SSH libraries, 1,012 unigene sets including 314 contigs were assembled from 2,448 sequences. The profiles of the genes isolated from the SSH libraries differed strongly according to developmental stage: 49%, 13% and 29% of genes were unique to the early stage (stage E), tetrad stage (stage T), and mature stage (stage M) SSH libraries, respectively. To evaluate the reliability of the SSH libraries, we focused on the eight genes strongly concentrated in the three SSH libraries and performed RT-PCR analysis. All genes tested were expressed more strongly in the male strobilus than in the shoot. Our findings suggest that the gene profiles associated with male strobilus development differ in both number and kind of dominantly expressed genes.
Xavier Foissac - One of the best experts on this subject based on the ideXlab platform.
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stolbur phytoplasma genome survey achieved using a Suppression Subtractive Hybridization approach with high specificity
Applied and Environmental Microbiology, 2006Co-Authors: Agni S Cimerman, Guillaume Arnaud, Xavier FoissacAbstract:Phytoplasmas are unculturable bacterial plant pathogens transmitted by phloem-feeding hemipteran insects. DNA of phytoplasmas is difficult to purify because of their exclusive phloem location and low abundance in plants. To overcome this constraint, Suppression Subtractive Hybridization (SSH) was modified and used to selectively amplify DNA of the stolbur phytoplasma infecting a periwinkle plant. Plasmid libraries were constructed, and the origins of the DNA inserts were verified by Hybridization and PCR screenings. After a single round of SSH, there was still a significant level of contamination with plant DNA (around 50%). However, the modified SSH, which included a second round of subtraction (double SSH), resulted in an increased phytoplasma DNA purity (97%). Results validated double SSH as an efficient way to produce a genome survey for microbial agents unavailable in culture. Assembly of 266 insert sequences revealed 181 phytoplasma genetic loci which were annotated. Comparative analysis of 113 kbp indicated that among 217 protein coding sequences, 83% were homologous to "Candidatus Phytoplasma asteris" (OY-M strain) genes, with hits widely distributed along the chromosome. Most of the stolbur-specific SSH sequences were orphan genes, with the exception of two partial coding sequences encoding proteins homologous to a mycoplasma surface protein and riboflavin kinase.
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Stolbur Phytoplasma Genome Survey Achieved Using a Suppression Subtractive Hybridization Approach with High Specificity†
2005Co-Authors: Agni S Cimerman, Guillaume Arnaud, Xavier FoissacAbstract:Phytoplasmas are unculturable bacterial plant pathogens transmitted by phloem-feeding hemipteran insects. DNA of phytoplasmas is difficult to purify because of their exclusive phloem location and low abundance in plants. To overcome this constraint, Suppression Subtractive Hybridization (SSH) was modified and used to selectively amplify DNA of the stolbur phytoplasma infecting a periwinkle plant. Plasmid libraries were constructed, and the origins of the DNA inserts were verified by Hybridization and PCR screenings. After a single round of SSH, there was still a significant level of contamination with plant DNA (around 50%). However, the modified SSH, which included a second round of subtraction (double SSH), resulted in an increased phytoplasma DNA purity (97%). Results validated double SSH as an efficient way to produce a genome survey for microbial agents unavailable in culture. Assembly of 266 insert sequences revealed 181 phytoplasma genetic loci which were annotated. Comparative analysis of 113 kbp indicated that among 217 protein coding sequences, 83 % were homologous to “Candidatus Phytoplasma asteris ” (OY-M strain) genes, with hits widely distributed along the chromosome. Most of the stolbur-specific SSH sequences were orphan genes, with the exception of two partial coding sequences encoding proteins homologous to a mycoplasma surface protein and riboflavin kinase. Phytoplasmas are responsible for plant diseases that damag
Manabu Kurita - One of the best experts on this subject based on the ideXlab platform.
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spatiotemporal gene expression profiles associated with male strobilus development in cryptomeria japonica by Suppression Subtractive Hybridization
Breeding Science, 2011Co-Authors: Manabu Kurita, Ryogo Nakada, Teiji Kondo, Toru Taniguchi, Atsushi WatanabeAbstract:To identify the genes associated with the formation and development of the male strobilus of Cryptomeria japonica D. Don (Sugi), male strobilus-specific Suppression Subtractive Hybridization (SSH) libraries were constructed from three different stages of male strobilus development. From these SSH libraries, 1,012 unigene sets including 314 contigs were assembled from 2,448 sequences. The profiles of the genes isolated from the SSH libraries differed strongly according to developmental stage: 49%, 13% and 29% of genes were unique to the early stage (stage E), tetrad stage (stage T), and mature stage (stage M) SSH libraries, respectively. To evaluate the reliability of the SSH libraries, we focused on the eight genes strongly concentrated in the three SSH libraries and performed RT-PCR analysis. All genes tested were expressed more strongly in the male strobilus than in the shoot. Our findings suggest that the gene profiles associated with male strobilus development differ in both number and kind of dominantly expressed genes.
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spatiotemporal gene expression profiles associated with male strobilus development in cryptomeria japonica by Suppression Subtractive Hybridization
Breeding Science, 2011Co-Authors: Manabu Kurita, Ryogo Nakada, Teiji Kondo, Toru Taniguchi, Atsushi WatanabeAbstract:To identify the genes associated with the formation and development of the male strobilus of Cryptomeria japonica D. Don (Sugi), male strobilus-specific Suppression Subtractive Hybridization (SSH) libraries were constructed from three different stages of male strobilus development. From these SSH libraries, 1,012 unigene sets including 314 contigs were assembled from 2,448 sequences. The profiles of the genes isolated from the SSH libraries differed strongly according to developmental stage: 49%, 13% and 29% of genes were unique to the early stage (stage E), tetrad stage (stage T), and mature stage (stage M) SSH libraries, respectively. To evaluate the reliability of the SSH libraries, we focused on the eight genes strongly concentrated in the three SSH libraries and performed RT-PCR analysis. All genes tested were expressed more strongly in the male strobilus than in the shoot. Our findings suggest that the gene profiles associated with male strobilus development differ in both number and kind of dominantly expressed genes.
Adelino V M Canario - One of the best experts on this subject based on the ideXlab platform.
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identification of estrogen responsive genes in the testis of sea bream sparus auratus using Suppression Subtractive Hybridization
Molecular Reproduction and Development, 2006Co-Authors: Patricia Pinto, H R Teodosio, Malyka Galayburgos, Deborah M Power, Glen E Sweeney, Adelino V M CanarioAbstract:There is growing evidence that estrogens play important roles in both normal and xenoestrogen disrupted testis physiology. However, the mechanisms and signaling pathways involved, in particular in fish, are largely unknown. We have used Suppression Subtractive Hybridization to isolate 152 candidate estrogen-responsive genes in the testis of male estradiol (E2)-treated sea bream (Sparus aurata). The E2 up-regulation of some of the genes (e.g., choriogenin L and H, vitellogenin I and II, apolipoprotein A-I, fibrinogen β and γ, and thyroid receptor interacting protein 4) was confirmed by reverse transcriptase polymerase chain reaction in fish treated with 0.1–10 mg/kg E2. Many of these genes are typical E2-induced genes in liver, and this is the first report of its up regulation with E2 in testis. Moreover, low levels of expression were also found for nontreated fish. Hepatic differential expression for these genes was also confirmed, although, contrary to testis, fibrinogen β, and γ were downregulated. The possible significance of these findings in normal testis physiology and in endocrine disruption is discussed.
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identification of estrogen responsive genes in the testis of sea bream sparus auratus using Suppression Subtractive Hybridization
Molecular Reproduction and Development, 2006Co-Authors: Patricia Pinto, H R Teodosio, Malyka Galayburgos, Deborah M Power, Glen E Sweeney, Adelino V M CanarioAbstract:There is growing evidence that estrogens play important roles in both normal and xenoestrogen disrupted testis physiology. However, the mechanisms and signaling pathways involved, in particular in fish, are largely unknown. We have used Suppression Subtractive Hybridization to isolate 152 candidate estrogen-responsive genes in the testis of male estradiol (E2)-treated sea bream (Sparus aurata). The E2 up-regulation of some of the genes (e.g., chorio- genin L and H, vitellogenin I and II, apolipoprotein A-I, fibrinogen b and g, and thyroid receptor interacting protein 4) was confirmed by reverse transcriptase polymerase chain reaction in fish treated with 0.1- 10 mg/kg E2. Many of these genes are typical E2- induced genes in liver, and this is the first report of its up regulation with E2 in testis. Moreover, low levels of expression were also found for nontreated fish. Hepatic differential expression for these genes was also con- firmed, although, contrary to testis, fibrinogen b, and g were downregulated. The possible significance of these findings in normal testis physiology and in endocrine disruption is discussed. Mol. Reprod. Dev. 73: 318- 329, 2006. 2005 Wiley-Liss, Inc.
Agni S Cimerman - One of the best experts on this subject based on the ideXlab platform.
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stolbur phytoplasma genome survey achieved using a Suppression Subtractive Hybridization approach with high specificity
Applied and Environmental Microbiology, 2006Co-Authors: Agni S Cimerman, Guillaume Arnaud, Xavier FoissacAbstract:Phytoplasmas are unculturable bacterial plant pathogens transmitted by phloem-feeding hemipteran insects. DNA of phytoplasmas is difficult to purify because of their exclusive phloem location and low abundance in plants. To overcome this constraint, Suppression Subtractive Hybridization (SSH) was modified and used to selectively amplify DNA of the stolbur phytoplasma infecting a periwinkle plant. Plasmid libraries were constructed, and the origins of the DNA inserts were verified by Hybridization and PCR screenings. After a single round of SSH, there was still a significant level of contamination with plant DNA (around 50%). However, the modified SSH, which included a second round of subtraction (double SSH), resulted in an increased phytoplasma DNA purity (97%). Results validated double SSH as an efficient way to produce a genome survey for microbial agents unavailable in culture. Assembly of 266 insert sequences revealed 181 phytoplasma genetic loci which were annotated. Comparative analysis of 113 kbp indicated that among 217 protein coding sequences, 83% were homologous to "Candidatus Phytoplasma asteris" (OY-M strain) genes, with hits widely distributed along the chromosome. Most of the stolbur-specific SSH sequences were orphan genes, with the exception of two partial coding sequences encoding proteins homologous to a mycoplasma surface protein and riboflavin kinase.
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Stolbur Phytoplasma Genome Survey Achieved Using a Suppression Subtractive Hybridization Approach with High Specificity†
2005Co-Authors: Agni S Cimerman, Guillaume Arnaud, Xavier FoissacAbstract:Phytoplasmas are unculturable bacterial plant pathogens transmitted by phloem-feeding hemipteran insects. DNA of phytoplasmas is difficult to purify because of their exclusive phloem location and low abundance in plants. To overcome this constraint, Suppression Subtractive Hybridization (SSH) was modified and used to selectively amplify DNA of the stolbur phytoplasma infecting a periwinkle plant. Plasmid libraries were constructed, and the origins of the DNA inserts were verified by Hybridization and PCR screenings. After a single round of SSH, there was still a significant level of contamination with plant DNA (around 50%). However, the modified SSH, which included a second round of subtraction (double SSH), resulted in an increased phytoplasma DNA purity (97%). Results validated double SSH as an efficient way to produce a genome survey for microbial agents unavailable in culture. Assembly of 266 insert sequences revealed 181 phytoplasma genetic loci which were annotated. Comparative analysis of 113 kbp indicated that among 217 protein coding sequences, 83 % were homologous to “Candidatus Phytoplasma asteris ” (OY-M strain) genes, with hits widely distributed along the chromosome. Most of the stolbur-specific SSH sequences were orphan genes, with the exception of two partial coding sequences encoding proteins homologous to a mycoplasma surface protein and riboflavin kinase. Phytoplasmas are responsible for plant diseases that damag
