In this study, a forward cDNA library was constructed by suppression subtractive hybridization using seedling leaves of CN165, a drought-tolerant maize inbred line. In the suppression subtractive hybridization (SSH) l...In this study, a forward cDNA library was constructed by suppression subtractive hybridization using seedling leaves of CN165, a drought-tolerant maize inbred line. In the suppression subtractive hybridization (SSH) library, 672 positive clones were picked up randomly. After polymerase chain reaction (PCR) of each clone, all the single clones were sequenced. Totally 598 available sequences were obtained. After cluster analysis of the EST sequences, 80 uniESTs were obtained, among which 57 uniESTs were contigs and 23 uniESTs were singlets. The results of BLASTN showed that all the uniESTs had homologous sequences in the nr database. The BLASTX results indicated that 68 uniESTs had significant protein homology, 8 uniESTs with homology of unknown proteins and putative proteins, and 4 uniESTs without protein homology. Those drought stress-induced genes were involved in many metabolism pathways to regulate plant growth and development under drought stress.展开更多
AIM: To screen for metronidazole (MTZ)-resistance associated gene fragments of H pylori by suppression subtractive hybridization (SSH). METHODS: Five MTZ-resistant (tester, T) and 1 MTZ-susceptible (driver, D) clinica...AIM: To screen for metronidazole (MTZ)-resistance associated gene fragments of H pylori by suppression subtractive hybridization (SSH). METHODS: Five MTZ-resistant (tester, T) and 1 MTZ-susceptible (driver, D) clinical H pylori isolates were selected. Genomic DNAs were prepared and submitted to RsaⅠdigestion. Then two different adaptors were ligated respectively to the 5'-end of two aliquots of the tester DNA fragments and SSH was made between the tester and driver DNAs. The specific inserts of tester strains were screened and MTZ-resistance related gene fragments were identified by dot blotting. RESULTS: Among the randomly selected 120 subtractive colonies, 37 DNA fragments had a different number of DNA copies (≥ 2 times) in resistant and susceptible strains and 17 of them had a significantly different number of DNA copies (≥ 3 times). Among the sequences obtained from the 17 DNA fragments, new sequences were found in 10 DNA fragments and duplicated sequences in 7 DNA fragments, representing respectively the sequences of depeptide ABC transporter periplasmic dipeptide-binding protein (dppA), permease protein (dppB), ribosomal protein S4 (rps4), ribonuclease Ⅲ (rnc), protease (pqqE), diaminopimelate epimerase (dapF), acetatekinase (ackA), H pylori plasmid pHP51 and H pylori gene 1334. CONCLUSION: Gene fragments specific to MTZ-resistant H pylori strains can be screened by SSH and may be associated with MTZ-resistant H pylori.展开更多
Soybean is planted worldwide and its productivity is significantly hampered by salinity. Development of salt tolerant cultivars is necessary for promoting soybean production. Despite wealth of information generated on...Soybean is planted worldwide and its productivity is significantly hampered by salinity. Development of salt tolerant cultivars is necessary for promoting soybean production. Despite wealth of information generated on salt tolerance mechanism, its basics still remain elusive. A continued effort is needed to understand the salt tolerance mechanism in soybean using suitable molecular tools. To better understand the molecular basis of the responses of soybean to salt stress and to get an enrichment of critical salt stress responsive genes in soybean, suppression subtractive hybridization libraries (SSH) are constructed for the root tissue of two cultivated soybean genotypes, one was tolerant and the other was sensitive to salt stress. To compare the responses of plants in salt treatment and non-treatment, SSH1 was constructed for the salt-tolerant cultivar Wenfeng 7 and SSH2 was constructed for the salt-sensitive cultivar Union. From the two SSH cDNA libraries, a total of 379 high quality ESTs were obtained. These ESTs were then annotated by performing sequence similarity searches against the NCBI nr (National Center for Biotechnology Information protein non-redundant) database using the BLASTX program. Sixty-three genes from SSH1 and 49 genes from SSH2 could be assigned putative function. On the other hand, 25 ESTs of SSH1 which may be not the salt tolerance-related genes were removed by comparing and analyzing the ESTs from the two SSH libraries, which increased the proportion of the genes related to salt tolerance in SSH1. These results suggested that the novel way could realize low background of SSH and high level enrichment of target cDNAs to some extent.展开更多
AIM: To identify potential diagnostic target genes in early reperfusion periods following warm liver ischemia before irreversible liver damage occurs.METHODS: We used two strategies (SSH suppression subtractive hybrid...AIM: To identify potential diagnostic target genes in early reperfusion periods following warm liver ischemia before irreversible liver damage occurs.METHODS: We used two strategies (SSH suppression subtractive hybridization and hybridization of cDNA arrays)to determine early changes in gene expression profiles in a rat model of partial WI/R, comparing postischemic and adjacent nonischemic liver lobes. Differential gene expression was verified (WT/R; 1 h/2 h) and analyzed in more detail after warm ischemia (1 h) in a reperfusion time kinetics (0, 1, 2 and 6 h) and compared to untreated livers by Northern blot hybridizations. Protein expression was examined on Western blots and by immunohistochemistry for four differentially expressed target genes (Hsp70,Hsp27, Gadd45a and IL-1rl).RESULTS: Thirty-two individual WI/R target genes showing altered RNA levels after confirmation by Northern blot analyzes were identified. Among them, six functionally uncharacteristic expressed sequences and 26 known genes (12 induced in postischemic liver lobes, 14 with higher transcriptional expression in adjacent nonischemic liver lobes). Functional categories of the verified marker genes indicate on the one hand cellular stress and tissue damage but otherwise activation of protective cellular reactions (AP-1 transcription factors, apoptosis related genes, heat shock genes). In order to assign the transcriptional status to the biological relevant protein level we demonstrated that Hsp70, Hsp27, Gadd45a and IL-1rI were clearly up-regulated comparing postischemic and untreated rat livers, suggesting their involvement in the WI/R context.CONCLUSION: This study unveils a WI/R response gene set that will help to explore molecular pathways involved in the tissue damage after WI/R. In addition, these genes especially Hsp70and Gadd45a might represent promising new candidates indicating WI/R liver damage.展开更多
For the purpose of screening and analyzing the differentially expressed genes from the salivary gland of Rhipicephalus haemaphysaloides, two salivary gland-subtracted cDNA libraries of partially fed female ticks and f...For the purpose of screening and analyzing the differentially expressed genes from the salivary gland of Rhipicephalus haemaphysaloides, two salivary gland-subtracted cDNA libraries of partially fed female ticks and fed male ticks were constructed using suppression subtractive hybridization (SSH). A total of 247 female expression sequence tags (ESTs) and 168 male ESTs were obtained from the two SSH cDNA libraries. It is predicted that 25 female ESTs and 44 female ESTs contain the 5′and 3′ends, respectively, and that 53 male ESTs and 74 male ESTs contain the 5′and 3′ends, respectively. To identify the subtraction rate of the two SSH cDNA libraries, the RT-PCR method was used to test 24 female ESTs and 21 male ESTs selected randomly but not repeatedly. The results showed that there were 13 upregulated or differentially expressed genes in the partially fed salivary gland of the female R. haemaphysaloides and that the differentially expressed rate was 54%. In addition, they indicated that there were 9 upregulated or differently expressed genes in the fed salivary gland of the male R. haemaphysaloides and that the differentially expressed rate was 43%. Putative translations of 141 (57%) female ESTs and 125 (74%) male ESTs had similarity to GenBank sequences, and 32 (23%) female ESTs and 29 (23%) male ESTs exhibited similarity to tick proteins, which showed that most of the proteins in the libraries were mainly related to the feeding blood physiology of the ticks.展开更多
[Objectives]This study was conducted to construct forward and reserve libraries of suppression subtractive hybridization (SSH) in the testis of male tilapia under the stress of methomyl by using SSH technology.[Method...[Objectives]This study was conducted to construct forward and reserve libraries of suppression subtractive hybridization (SSH) in the testis of male tilapia under the stress of methomyl by using SSH technology.[Methods]Using male tilapia as the test animal,the forward and reserve libraries of SSH in the testis of tilapia under the stress of methomyl were constructed by using the SSH technology.[Results]45 expressed sequence tags (ESTs) were obtained,and 25 expressed sequence tags were successfully noted,including 13 forward libraries and 12 reverse libraries.The genes with confirmed functions were classified into five types.Genes related to catalytic activity and cell characteristics were up-regulated,while genes related to structural molecule's activity and biological process were down-regulated.The expression amount of integrin β1 was up-regulated,while serine/threonine protein kinase pim-3,Ca^2+-ATPase,Na^+-K^+-ATPase and ribosomal protein L22 were down-regulated.[Conclusions]The research results could lay a foundation for revealing the molecular mechanism of methomyl's reproductive toxicity to tilapia.展开更多
A cDNA subtractive library enriched for dark-induced up-regulated ESTs was constructed by suppression subtractive hybridization(SSH) from leaf tissues of soybean cultivar DongNong L13 treated with short-day(8-h light/...A cDNA subtractive library enriched for dark-induced up-regulated ESTs was constructed by suppression subtractive hybridization(SSH) from leaf tissues of soybean cultivar DongNong L13 treated with short-day(8-h light/16-h dark) and long-day(16-h light/8-h dark) conditions.A total of 148 clones were sequenced,representing 76 unique ESTs which corresponded to about 20% of 738 clones from the cDNA library and showed a significant up-regulation of at least three fold verified by dot blot hybridization.The putative functions of ESTs were predicted by Blastn and Blastx.The 43 differentially expressed genes identified by subtractions were classified according to their putative functions generated by Blast analysis.Genetic functional analysis indicated that putative proteins encoded by these genes were related to diverse functions during organism development,which include biological regulation pathways such as transcription,signal transduction and programmed cell death,protein,nucleic acid and carbohydrate macromolecule degradation,the cell wall modification,primary and secondary metabolism and stress response.Two soybean transcription factors enhanced in SD conditions,GAMYB-binding protein and DNA binding protein RAV cDNAs that may be involved in SD soybean photoperiod response,had been isolated using 5'-and 3'-rapid amplification of cDNA ends(RACE)(Genbank Accession numbers DQ112540 and DQ147914).展开更多
Plants reshape their transcriptomes, proteomes and metabolomes in response to insect damage. In this study, we used suppression subtractive hybridization to investigate the transcriptomes of two cotton varieties(CCRI4...Plants reshape their transcriptomes, proteomes and metabolomes in response to insect damage. In this study, we used suppression subtractive hybridization to investigate the transcriptomes of two cotton varieties(CCRI41 and CCRI23) under Apolygus lucorum damage. From the CCRI23 libraries we obtained 92 transcripts and from the CCRI41 libraries we obtained 96 transcripts. 26 and 63 of the transcripts from CCRI23 and CCRI41, respectively, had known functions. Using reverse transcription PCR, we detected expression profile of genes with known functions. Ultimately, we identified eight significantly regulated genes, including one downregulated and four upregulated genes from the CCRI41 libraries, and one downregulated and two upregulated genes from the CCRI23 libraries. Only the gene encoding the polyphenol oxidase(PPO) is involved in plant defense against insect herbivores, and the others are related to improving tolerance to insect damage. Quantitative real-time PCR was used to study changes in expression levels during A. lucorum damage in CCRI23 and CCRI41. Significantly regulated genes from CCRI23 showed a response in CCRI23 but not response in CCRI41. Similarly, significantly regulated genes from CCRI41 showed a response in CCRI41 but not response in CCRI23. The results showed that, among transcriptomes of cotton varieties, there are different responses to A. lucorum damage.展开更多
AIM:To clone and identify human genes transactivated by PS1TP5 by constructing a cDNA subtractive library with suppression subtractive hybridization(SSH)technique.METHODS:SSH and bioinformatics techniques were used fo...AIM:To clone and identify human genes transactivated by PS1TP5 by constructing a cDNA subtractive library with suppression subtractive hybridization(SSH)technique.METHODS:SSH and bioinformatics techniques were used for screening and cloning of the target genes transactivated by PS1TP5 protein.The mRNA was isolated from HepG2 cells transfected with pcDNA3.1(-)-myc-his(A)-PS1TP5 and pcDNA3.1(-)-myc-his(A)empty vector,respectively,and SSH technique was employed to analyze the differentially expressed DNA sequence between the two groups.After digestion with restriction enzyme RsaⅠ,small size cDNAs were obtained.Then tester cDNA was divided into two groups and ligated to the specific adaptor 1 and adaptor 2,respectively.The tester cDNA was hybridized with driver cDNA twice and subjected to nested PCR for two times,and then subcloned into T/A plasmid vectors to set up the subtractive library.Amplification of the library was carried out with E.coli strain DH5α.The cDNA was sequenced and analyzed in GenBank with Vector NTI 9.1 and NCBI BLAST software after PCR amplification.RESULTS:The subtractive library of genes transactivated by PS1TP5 was constructed successfully.The amplified library contained 90 positive clones.Colony PCR showed that 70 clones contained 200-1000-bp inserts.Sequence analysis was performed in 30 clones randomly,and the full-length sequences were obtained by bioinformatics technique.Altogether 24 coding sequences were obtained,which consisted of 23 known and 1 unknown.One novel gene with unknown functions was found and named as PS1TP5TP1 after being electronically spliced,and deposited in GenBank(accession number:DQ487761).CONCLUSION:PS1TP5 is closely correlated with immunoregulation,carbohydrate metabolism,signal transduction,formation mechanism of hepatic fibrosis,and occurrence and development of tumor.Understanding PS1TP5 transactive proteins may help to bring some new clues for further studying the biological functions of pre-S1 protein.展开更多
Suppression subtractive hybridization (SSH) was employed to investigate bioluminescence in Panellus stipticus (Bull.) P. Karst. by detecting proteins differentially expressed in bioluminescent and luminescent strains....Suppression subtractive hybridization (SSH) was employed to investigate bioluminescence in Panellus stipticus (Bull.) P. Karst. by detecting proteins differentially expressed in bioluminescent and luminescent strains. Comparisons of luminescent and non-luminescent monokaryon cultures of North American strains revealed differences in transcript levels of proteins responsible for post-translational modification (PTM) of enzymes. A similar comparison of a luminescent strain of P. stipticus from North America with a non-luminescent European strain revealed the presence of extracellular manganese superoxide dismutase (MnSOD) in the luminescent form, in addition to proteins involved in PTM. The application of MnSOD-specific inhibitors to luminescent mycelium resulted in the rapid loss of luminescence. The relevance to luminescence of proteins involved in PTM is discussed, together with a possible role for MnSOD that considers the potential for SODs to form stable complexes with catechols revealed in previously published research. In light of the recent discovery that hispidine may be the precursor of fungal luciferin, we consider a hypothetical mechanism for fungal luminescence in which the ο-hydroquinone moiety of a hispidine derivative ligates with the extracellular form of MnSOD producing a semiquinone-radical complex, with the resultant semiquinonato complex potentially reacting with molecular oxygen or other reactive oxygen species to produce sufficiently excited intermediates to emit light on relaxation.展开更多
Background and Objective The invasion and metastasis are not only the malignant markers and characteristics of lung cancer, but also the leading cause of failure to treatment and patient’
Objective To construct and screen the suppression subtractive hybridization (SSH) library of human renal cell carcinoma (RCC). Methods Poly A+ RNA was isolated from RCC lines 786-O(tester) and renal cell(RC) lines HK-...Objective To construct and screen the suppression subtractive hybridization (SSH) library of human renal cell carcinoma (RCC). Methods Poly A+ RNA was isolated from RCC lines 786-O(tester) and renal cell(RC) lines HK-2 ( driver), respectiely. SSH procedure was performed according to the protocol of the PCR-Select cDNA Subtraction Kit ( Clontech), and PCR products were cloned into pT-Adv vector and transformed E. coli TOP10F’. All positive clones picked out were digested and some of which were sequenced. Results The SSH library contained 362 clones with SSH cDNA fragments distributed mainly from 0.3 to 0.9 kb. Among 50 clones sequenced randomly,2 represented unknown genes and the other 48 derived from 36 known genes. Conclusion The quality of the SSH library of human RCC is reliable and is construction is the basis for further screening differentially expressed genes of RCC. 6 refs,4 figs, 1 tab.展开更多
BACKGROUND:Interferon-alpha(IFN-α)is an important cytokine with multiple functions,but the target genes transactivated by IFN-αremain largely unknown.A study of such genes will help to understand the mechanism of fu...BACKGROUND:Interferon-alpha(IFN-α)is an important cytokine with multiple functions,but the target genes transactivated by IFN-αremain largely unknown.A study of such genes will help to understand the mechanism of function of IFN-α.To isolate the gene transcripts specifically upregulated by IFN-αin HepG2 cells,we conducted suppressive subtractive hybridization(SSH) analysis. METHODS:SSH was used to analyze the target genes transactivated by recombinant IFN-αprotein,and a subtractive cDNA library was constructed from HepG2 cells treated with recombinant IFN-α(rIFN-α,2000 IU/ml)for 16 hours as tester,and cells not treated with rIFN-αas driver.The SSH PCR products from the library were cloned into pGEM-T easy vector and with BLASTX, the positive clones were randomly selected,sequenced and compared to the database in GenBank of the 35 differentially expressed gene fragments from the library, 6 clones showed significant homology to other known proteins. RESULTS:The subtractive cDNA library of genes upregulated by IFN-αwas constructed successfully. rIFN-αupregulated the expression of the RAN bindingprotein 5(RANBP5),NADH dehydrogenase,exosome component 3(EXOSC3),zinc finger RNA binding protein, Dickkopf homolog 1(DKK1)and acetyl-coenzyme A acetyltransferase 2(ACAT2). CONCLUSIONS:These results suggest that rIFN-αcan upregulate the expression of important genes to exert its functions,and provide new clues for discovering the molecular mechanisms of action of IFN-α.展开更多
In searching for differentially expressed genes in human uterine leiomyomas (ULs), suppression sub-tractive hybridization was used to construct an UL up-regulated library, which turned out to represent 88genes. After ...In searching for differentially expressed genes in human uterine leiomyomas (ULs), suppression sub-tractive hybridization was used to construct an UL up-regulated library, which turned out to represent 88genes. After two rounds of screening by reverse Northern analysis, twenty genes were proved to be up-regulated, including seventeen known genes and three genes with unknown function. All these genes werefirstly associated with UL. Three genes with notable difference were selected for Northern confirmationOur results proved the authenticity of the twenty genes. One gene named Phospholipase A2 (PLA2) showedup-regulation in 4/6 of the patients and investigation of tissue distribution indicated that it had obviousexpression in prostate, testis, liver, heart and skeletal muscle.展开更多
In searching for differentially expressed genes in human uterine leiomyomas (ULs), suppression sub-tractive hybridization was used to construct an UL up-regulated library, which turned out to represent 88genes. After ...In searching for differentially expressed genes in human uterine leiomyomas (ULs), suppression sub-tractive hybridization was used to construct an UL up-regulated library, which turned out to represent 88genes. After two rounds of screening by reverse Northern analysis, twenty genes were proved to be up-regulated, including seventeen known genes and three genes with unknown function. All these genes werefirstly associated with UL. Three genes with notable difference were selected for Northern confirmationOur results proved the authenticity of the twenty genes. One gene named Phospholipase A2 (PLA2) showedup-regulation in 4/6 of the patients and investigation of tissue distribution indicated that it had obviousexpression in prostate, testis, liver, heart and skeletal muscle.展开更多
In order to isolate genes related to anther development and understand molecular basis of male sterility,cDNA library of Zinnia elegans was constructed using suppression subtractive hybridization(SSH) approach.672 dif...In order to isolate genes related to anther development and understand molecular basis of male sterility,cDNA library of Zinnia elegans was constructed using suppression subtractive hybridization(SSH) approach.672 different expressed clones were selected from the fertile disk floret buds.PCR results showed that cDNA inserts were ranged from 100 to 750 bp.303 positive clones screened by dot-blot hybridization were sequenced.273 out of 303 sequenced clones produced readable sequences;these sequences represent 87 non-repetitive sequences.The homology alignment showed that 76 expressed sequence tags(ESTs) had functional annotations in GenBank,the other 11 ESTs without any homology to the known gene.In addition,87 ESTs were divided into 17 groups according to MIPS of Arabidopsis thaliana database.Sequence data from the cDNA library have been deposited with the GenBank under the accession numbers GT067016-GT067085.As an important result in this study,7 genes related to anther development were isolated.Results from semi-quantitative RT-PCR showed 6 genes were expressed only in disk florets of fertile plants compared with that of male sterile plants.These ESTs obtained provide important clues for further isolation and identification of fertility-related genes in Z.elegans.展开更多
Using suppression subtractive hybridization, a renal cell carcinoma (RCC) cDNA subtractive library which only contains differently expressed cDNAs between human RCC and normal kidney has been constructed. 200 clones w...Using suppression subtractive hybridization, a renal cell carcinoma (RCC) cDNA subtractive library which only contains differently expressed cDNAs between human RCC and normal kidney has been constructed. 200 clones were picked out randomly to perform enzyme digest analysis, a part of them underwent sequence analysis and Northern blot to identify RCC specially expressed genes. Results showed that 190 clones contain 50-400 bp inserts respectively. Sequence analysis was performed in 10 clones. All the 10 sequences were unknown before and derived from 6 unique novel genes among which the cDNA insert RCC18 has five copies. Northern blot analysis showed that RCC18 cDNA expressed highly in RCC, but there was no signal detected in normal kidney, and the full length of RCC18 was about 2.5 kb. The constructed cDNA subtractive library of human RCC is a highly efficient one and lays the solid foundation for large-scale screening and cloning new and specific oncogenes or tumor suppressor genes of RCC. The novel展开更多
文摘In this study, a forward cDNA library was constructed by suppression subtractive hybridization using seedling leaves of CN165, a drought-tolerant maize inbred line. In the suppression subtractive hybridization (SSH) library, 672 positive clones were picked up randomly. After polymerase chain reaction (PCR) of each clone, all the single clones were sequenced. Totally 598 available sequences were obtained. After cluster analysis of the EST sequences, 80 uniESTs were obtained, among which 57 uniESTs were contigs and 23 uniESTs were singlets. The results of BLASTN showed that all the uniESTs had homologous sequences in the nr database. The BLASTX results indicated that 68 uniESTs had significant protein homology, 8 uniESTs with homology of unknown proteins and putative proteins, and 4 uniESTs without protein homology. Those drought stress-induced genes were involved in many metabolism pathways to regulate plant growth and development under drought stress.
基金Supported by the Natural Science Foundation of ZhejiangProvince, No. 29801
文摘AIM: To screen for metronidazole (MTZ)-resistance associated gene fragments of H pylori by suppression subtractive hybridization (SSH). METHODS: Five MTZ-resistant (tester, T) and 1 MTZ-susceptible (driver, D) clinical H pylori isolates were selected. Genomic DNAs were prepared and submitted to RsaⅠdigestion. Then two different adaptors were ligated respectively to the 5'-end of two aliquots of the tester DNA fragments and SSH was made between the tester and driver DNAs. The specific inserts of tester strains were screened and MTZ-resistance related gene fragments were identified by dot blotting. RESULTS: Among the randomly selected 120 subtractive colonies, 37 DNA fragments had a different number of DNA copies (≥ 2 times) in resistant and susceptible strains and 17 of them had a significantly different number of DNA copies (≥ 3 times). Among the sequences obtained from the 17 DNA fragments, new sequences were found in 10 DNA fragments and duplicated sequences in 7 DNA fragments, representing respectively the sequences of depeptide ABC transporter periplasmic dipeptide-binding protein (dppA), permease protein (dppB), ribosomal protein S4 (rps4), ribonuclease Ⅲ (rnc), protease (pqqE), diaminopimelate epimerase (dapF), acetatekinase (ackA), H pylori plasmid pHP51 and H pylori gene 1334. CONCLUSION: Gene fragments specific to MTZ-resistant H pylori strains can be screened by SSH and may be associated with MTZ-resistant H pylori.
基金the National Natural Science Foundation of China (30771358)
文摘Soybean is planted worldwide and its productivity is significantly hampered by salinity. Development of salt tolerant cultivars is necessary for promoting soybean production. Despite wealth of information generated on salt tolerance mechanism, its basics still remain elusive. A continued effort is needed to understand the salt tolerance mechanism in soybean using suitable molecular tools. To better understand the molecular basis of the responses of soybean to salt stress and to get an enrichment of critical salt stress responsive genes in soybean, suppression subtractive hybridization libraries (SSH) are constructed for the root tissue of two cultivated soybean genotypes, one was tolerant and the other was sensitive to salt stress. To compare the responses of plants in salt treatment and non-treatment, SSH1 was constructed for the salt-tolerant cultivar Wenfeng 7 and SSH2 was constructed for the salt-sensitive cultivar Union. From the two SSH cDNA libraries, a total of 379 high quality ESTs were obtained. These ESTs were then annotated by performing sequence similarity searches against the NCBI nr (National Center for Biotechnology Information protein non-redundant) database using the BLASTX program. Sixty-three genes from SSH1 and 49 genes from SSH2 could be assigned putative function. On the other hand, 25 ESTs of SSH1 which may be not the salt tolerance-related genes were removed by comparing and analyzing the ESTs from the two SSH libraries, which increased the proportion of the genes related to salt tolerance in SSH1. These results suggested that the novel way could realize low background of SSH and high level enrichment of target cDNAs to some extent.
文摘AIM: To identify potential diagnostic target genes in early reperfusion periods following warm liver ischemia before irreversible liver damage occurs.METHODS: We used two strategies (SSH suppression subtractive hybridization and hybridization of cDNA arrays)to determine early changes in gene expression profiles in a rat model of partial WI/R, comparing postischemic and adjacent nonischemic liver lobes. Differential gene expression was verified (WT/R; 1 h/2 h) and analyzed in more detail after warm ischemia (1 h) in a reperfusion time kinetics (0, 1, 2 and 6 h) and compared to untreated livers by Northern blot hybridizations. Protein expression was examined on Western blots and by immunohistochemistry for four differentially expressed target genes (Hsp70,Hsp27, Gadd45a and IL-1rl).RESULTS: Thirty-two individual WI/R target genes showing altered RNA levels after confirmation by Northern blot analyzes were identified. Among them, six functionally uncharacteristic expressed sequences and 26 known genes (12 induced in postischemic liver lobes, 14 with higher transcriptional expression in adjacent nonischemic liver lobes). Functional categories of the verified marker genes indicate on the one hand cellular stress and tissue damage but otherwise activation of protective cellular reactions (AP-1 transcription factors, apoptosis related genes, heat shock genes). In order to assign the transcriptional status to the biological relevant protein level we demonstrated that Hsp70, Hsp27, Gadd45a and IL-1rI were clearly up-regulated comparing postischemic and untreated rat livers, suggesting their involvement in the WI/R context.CONCLUSION: This study unveils a WI/R response gene set that will help to explore molecular pathways involved in the tissue damage after WI/R. In addition, these genes especially Hsp70and Gadd45a might represent promising new candidates indicating WI/R liver damage.
基金the National Natural Science Foundation of China (31172095)
文摘For the purpose of screening and analyzing the differentially expressed genes from the salivary gland of Rhipicephalus haemaphysaloides, two salivary gland-subtracted cDNA libraries of partially fed female ticks and fed male ticks were constructed using suppression subtractive hybridization (SSH). A total of 247 female expression sequence tags (ESTs) and 168 male ESTs were obtained from the two SSH cDNA libraries. It is predicted that 25 female ESTs and 44 female ESTs contain the 5′and 3′ends, respectively, and that 53 male ESTs and 74 male ESTs contain the 5′and 3′ends, respectively. To identify the subtraction rate of the two SSH cDNA libraries, the RT-PCR method was used to test 24 female ESTs and 21 male ESTs selected randomly but not repeatedly. The results showed that there were 13 upregulated or differentially expressed genes in the partially fed salivary gland of the female R. haemaphysaloides and that the differentially expressed rate was 54%. In addition, they indicated that there were 9 upregulated or differently expressed genes in the fed salivary gland of the male R. haemaphysaloides and that the differentially expressed rate was 43%. Putative translations of 141 (57%) female ESTs and 125 (74%) male ESTs had similarity to GenBank sequences, and 32 (23%) female ESTs and 29 (23%) male ESTs exhibited similarity to tick proteins, which showed that most of the proteins in the libraries were mainly related to the feeding blood physiology of the ticks.
基金Supported by Basic Scientific Research Fund for Chinese Academy of Fishery Sciences(2015C02XK01)Youth Natural Scientific Foundation of Jiansu Province(BK20150117)Earmarked Fund for China Agriculture Research System(CARS-46)
文摘[Objectives]This study was conducted to construct forward and reserve libraries of suppression subtractive hybridization (SSH) in the testis of male tilapia under the stress of methomyl by using SSH technology.[Methods]Using male tilapia as the test animal,the forward and reserve libraries of SSH in the testis of tilapia under the stress of methomyl were constructed by using the SSH technology.[Results]45 expressed sequence tags (ESTs) were obtained,and 25 expressed sequence tags were successfully noted,including 13 forward libraries and 12 reverse libraries.The genes with confirmed functions were classified into five types.Genes related to catalytic activity and cell characteristics were up-regulated,while genes related to structural molecule's activity and biological process were down-regulated.The expression amount of integrin β1 was up-regulated,while serine/threonine protein kinase pim-3,Ca^2+-ATPase,Na^+-K^+-ATPase and ribosomal protein L22 were down-regulated.[Conclusions]The research results could lay a foundation for revealing the molecular mechanism of methomyl's reproductive toxicity to tilapia.
文摘A cDNA subtractive library enriched for dark-induced up-regulated ESTs was constructed by suppression subtractive hybridization(SSH) from leaf tissues of soybean cultivar DongNong L13 treated with short-day(8-h light/16-h dark) and long-day(16-h light/8-h dark) conditions.A total of 148 clones were sequenced,representing 76 unique ESTs which corresponded to about 20% of 738 clones from the cDNA library and showed a significant up-regulation of at least three fold verified by dot blot hybridization.The putative functions of ESTs were predicted by Blastn and Blastx.The 43 differentially expressed genes identified by subtractions were classified according to their putative functions generated by Blast analysis.Genetic functional analysis indicated that putative proteins encoded by these genes were related to diverse functions during organism development,which include biological regulation pathways such as transcription,signal transduction and programmed cell death,protein,nucleic acid and carbohydrate macromolecule degradation,the cell wall modification,primary and secondary metabolism and stress response.Two soybean transcription factors enhanced in SD conditions,GAMYB-binding protein and DNA binding protein RAV cDNAs that may be involved in SD soybean photoperiod response,had been isolated using 5'-and 3'-rapid amplification of cDNA ends(RACE)(Genbank Accession numbers DQ112540 and DQ147914).
基金supported by the National Natural Science Foundation of China (31201518)
文摘Plants reshape their transcriptomes, proteomes and metabolomes in response to insect damage. In this study, we used suppression subtractive hybridization to investigate the transcriptomes of two cotton varieties(CCRI41 and CCRI23) under Apolygus lucorum damage. From the CCRI23 libraries we obtained 92 transcripts and from the CCRI41 libraries we obtained 96 transcripts. 26 and 63 of the transcripts from CCRI23 and CCRI41, respectively, had known functions. Using reverse transcription PCR, we detected expression profile of genes with known functions. Ultimately, we identified eight significantly regulated genes, including one downregulated and four upregulated genes from the CCRI41 libraries, and one downregulated and two upregulated genes from the CCRI23 libraries. Only the gene encoding the polyphenol oxidase(PPO) is involved in plant defense against insect herbivores, and the others are related to improving tolerance to insect damage. Quantitative real-time PCR was used to study changes in expression levels during A. lucorum damage in CCRI23 and CCRI41. Significantly regulated genes from CCRI23 showed a response in CCRI23 but not response in CCRI41. Similarly, significantly regulated genes from CCRI41 showed a response in CCRI41 but not response in CCRI23. The results showed that, among transcriptomes of cotton varieties, there are different responses to A. lucorum damage.
基金Supported by the National Natural Science Foundation,No. 30371288Beijing Natural Science Foundation,No. 5042024
文摘AIM:To clone and identify human genes transactivated by PS1TP5 by constructing a cDNA subtractive library with suppression subtractive hybridization(SSH)technique.METHODS:SSH and bioinformatics techniques were used for screening and cloning of the target genes transactivated by PS1TP5 protein.The mRNA was isolated from HepG2 cells transfected with pcDNA3.1(-)-myc-his(A)-PS1TP5 and pcDNA3.1(-)-myc-his(A)empty vector,respectively,and SSH technique was employed to analyze the differentially expressed DNA sequence between the two groups.After digestion with restriction enzyme RsaⅠ,small size cDNAs were obtained.Then tester cDNA was divided into two groups and ligated to the specific adaptor 1 and adaptor 2,respectively.The tester cDNA was hybridized with driver cDNA twice and subjected to nested PCR for two times,and then subcloned into T/A plasmid vectors to set up the subtractive library.Amplification of the library was carried out with E.coli strain DH5α.The cDNA was sequenced and analyzed in GenBank with Vector NTI 9.1 and NCBI BLAST software after PCR amplification.RESULTS:The subtractive library of genes transactivated by PS1TP5 was constructed successfully.The amplified library contained 90 positive clones.Colony PCR showed that 70 clones contained 200-1000-bp inserts.Sequence analysis was performed in 30 clones randomly,and the full-length sequences were obtained by bioinformatics technique.Altogether 24 coding sequences were obtained,which consisted of 23 known and 1 unknown.One novel gene with unknown functions was found and named as PS1TP5TP1 after being electronically spliced,and deposited in GenBank(accession number:DQ487761).CONCLUSION:PS1TP5 is closely correlated with immunoregulation,carbohydrate metabolism,signal transduction,formation mechanism of hepatic fibrosis,and occurrence and development of tumor.Understanding PS1TP5 transactive proteins may help to bring some new clues for further studying the biological functions of pre-S1 protein.
文摘Suppression subtractive hybridization (SSH) was employed to investigate bioluminescence in Panellus stipticus (Bull.) P. Karst. by detecting proteins differentially expressed in bioluminescent and luminescent strains. Comparisons of luminescent and non-luminescent monokaryon cultures of North American strains revealed differences in transcript levels of proteins responsible for post-translational modification (PTM) of enzymes. A similar comparison of a luminescent strain of P. stipticus from North America with a non-luminescent European strain revealed the presence of extracellular manganese superoxide dismutase (MnSOD) in the luminescent form, in addition to proteins involved in PTM. The application of MnSOD-specific inhibitors to luminescent mycelium resulted in the rapid loss of luminescence. The relevance to luminescence of proteins involved in PTM is discussed, together with a possible role for MnSOD that considers the potential for SODs to form stable complexes with catechols revealed in previously published research. In light of the recent discovery that hispidine may be the precursor of fungal luciferin, we consider a hypothetical mechanism for fungal luminescence in which the ο-hydroquinone moiety of a hispidine derivative ligates with the extracellular form of MnSOD producing a semiquinone-radical complex, with the resultant semiquinonato complex potentially reacting with molecular oxygen or other reactive oxygen species to produce sufficiently excited intermediates to emit light on relaxation.
基金supported by a grant from the key project of the National Natural Science Foundation of China (to Qinghua ZHOU)(No. 30430300)National Natural Science Foundation of China (to Qinghua ZHOU)(No. 30670922)INTERNATION Scienc and Techniquie COOPRATION PROGRAM OFCHINA (ISCP) (to Qinghua ZHOU)(No.2006DFB32330)
文摘Background and Objective The invasion and metastasis are not only the malignant markers and characteristics of lung cancer, but also the leading cause of failure to treatment and patient’
文摘Objective To construct and screen the suppression subtractive hybridization (SSH) library of human renal cell carcinoma (RCC). Methods Poly A+ RNA was isolated from RCC lines 786-O(tester) and renal cell(RC) lines HK-2 ( driver), respectiely. SSH procedure was performed according to the protocol of the PCR-Select cDNA Subtraction Kit ( Clontech), and PCR products were cloned into pT-Adv vector and transformed E. coli TOP10F’. All positive clones picked out were digested and some of which were sequenced. Results The SSH library contained 362 clones with SSH cDNA fragments distributed mainly from 0.3 to 0.9 kb. Among 50 clones sequenced randomly,2 represented unknown genes and the other 48 derived from 36 known genes. Conclusion The quality of the SSH library of human RCC is reliable and is construction is the basis for further screening differentially expressed genes of RCC. 6 refs,4 figs, 1 tab.
文摘BACKGROUND:Interferon-alpha(IFN-α)is an important cytokine with multiple functions,but the target genes transactivated by IFN-αremain largely unknown.A study of such genes will help to understand the mechanism of function of IFN-α.To isolate the gene transcripts specifically upregulated by IFN-αin HepG2 cells,we conducted suppressive subtractive hybridization(SSH) analysis. METHODS:SSH was used to analyze the target genes transactivated by recombinant IFN-αprotein,and a subtractive cDNA library was constructed from HepG2 cells treated with recombinant IFN-α(rIFN-α,2000 IU/ml)for 16 hours as tester,and cells not treated with rIFN-αas driver.The SSH PCR products from the library were cloned into pGEM-T easy vector and with BLASTX, the positive clones were randomly selected,sequenced and compared to the database in GenBank of the 35 differentially expressed gene fragments from the library, 6 clones showed significant homology to other known proteins. RESULTS:The subtractive cDNA library of genes upregulated by IFN-αwas constructed successfully. rIFN-αupregulated the expression of the RAN bindingprotein 5(RANBP5),NADH dehydrogenase,exosome component 3(EXOSC3),zinc finger RNA binding protein, Dickkopf homolog 1(DKK1)and acetyl-coenzyme A acetyltransferase 2(ACAT2). CONCLUSIONS:These results suggest that rIFN-αcan upregulate the expression of important genes to exert its functions,and provide new clues for discovering the molecular mechanisms of action of IFN-α.
基金This work was supported by Nationa1 NaturalScience Fundation of China No.39700148 and LifeScience Special fund of CAS supported by ChineseMinisery of Finance.
文摘In searching for differentially expressed genes in human uterine leiomyomas (ULs), suppression sub-tractive hybridization was used to construct an UL up-regulated library, which turned out to represent 88genes. After two rounds of screening by reverse Northern analysis, twenty genes were proved to be up-regulated, including seventeen known genes and three genes with unknown function. All these genes werefirstly associated with UL. Three genes with notable difference were selected for Northern confirmationOur results proved the authenticity of the twenty genes. One gene named Phospholipase A2 (PLA2) showedup-regulation in 4/6 of the patients and investigation of tissue distribution indicated that it had obviousexpression in prostate, testis, liver, heart and skeletal muscle.
文摘In searching for differentially expressed genes in human uterine leiomyomas (ULs), suppression sub-tractive hybridization was used to construct an UL up-regulated library, which turned out to represent 88genes. After two rounds of screening by reverse Northern analysis, twenty genes were proved to be up-regulated, including seventeen known genes and three genes with unknown function. All these genes werefirstly associated with UL. Three genes with notable difference were selected for Northern confirmationOur results proved the authenticity of the twenty genes. One gene named Phospholipase A2 (PLA2) showedup-regulation in 4/6 of the patients and investigation of tissue distribution indicated that it had obviousexpression in prostate, testis, liver, heart and skeletal muscle.
基金funded by the National Natural Science Foundation of China(30771518)
文摘In order to isolate genes related to anther development and understand molecular basis of male sterility,cDNA library of Zinnia elegans was constructed using suppression subtractive hybridization(SSH) approach.672 different expressed clones were selected from the fertile disk floret buds.PCR results showed that cDNA inserts were ranged from 100 to 750 bp.303 positive clones screened by dot-blot hybridization were sequenced.273 out of 303 sequenced clones produced readable sequences;these sequences represent 87 non-repetitive sequences.The homology alignment showed that 76 expressed sequence tags(ESTs) had functional annotations in GenBank,the other 11 ESTs without any homology to the known gene.In addition,87 ESTs were divided into 17 groups according to MIPS of Arabidopsis thaliana database.Sequence data from the cDNA library have been deposited with the GenBank under the accession numbers GT067016-GT067085.As an important result in this study,7 genes related to anther development were isolated.Results from semi-quantitative RT-PCR showed 6 genes were expressed only in disk florets of fertile plants compared with that of male sterile plants.These ESTs obtained provide important clues for further isolation and identification of fertility-related genes in Z.elegans.
基金supported by the National Natural Science Foundation of China(30471123,30571206)Natural Science Foundation of Jiangsu Province,China(BK2005421)New Century Excellent Scholar Project of Ministry of Education of China(NCET-07-0042).
基金This work was supported by the National Natural Science Foundation of China (Grant No. 39870841).
文摘Using suppression subtractive hybridization, a renal cell carcinoma (RCC) cDNA subtractive library which only contains differently expressed cDNAs between human RCC and normal kidney has been constructed. 200 clones were picked out randomly to perform enzyme digest analysis, a part of them underwent sequence analysis and Northern blot to identify RCC specially expressed genes. Results showed that 190 clones contain 50-400 bp inserts respectively. Sequence analysis was performed in 10 clones. All the 10 sequences were unknown before and derived from 6 unique novel genes among which the cDNA insert RCC18 has five copies. Northern blot analysis showed that RCC18 cDNA expressed highly in RCC, but there was no signal detected in normal kidney, and the full length of RCC18 was about 2.5 kb. The constructed cDNA subtractive library of human RCC is a highly efficient one and lays the solid foundation for large-scale screening and cloning new and specific oncogenes or tumor suppressor genes of RCC. The novel
