Chinese shrimp （Fenneropenaeus chinensis） is an economically important aquaculture species in China. However, cytogenetic and genomic data is limited in the organism partly because the chromosomes are difficult to i...Chinese shrimp （Fenneropenaeus chinensis） is an economically important aquaculture species in China. However, cytogenetic and genomic data is limited in the organism partly because the chromosomes are difficult to isolate and analyze. In this study, fluorescence in-situ hybridization （FISH） was used to identify the chromosomes of F. chinensis. The 5S ribosomal RNA gene （rDNA） of F. chinensis was isolated, cloned and then used as a hybridization probe. The results show that the 5S rDNA was located on one pair of homologous chromosomes in F chinensis. In addition, triploid shrimp were used to evaluate the feasibility of chromosome identification using FISH and to validate the method. It was confirmed that 5S rDNA can be used as a chromosome-specific probe for chromosome identification in E chinensis. The successful application ofFISH in E chinensis shows that chromosome-specific probes can be developed and this finding will facilitate further research on the chromosomes ofpenaeid shrimps.展开更多
In situ loop-mediated isothermal amplification （in situ LAMP） combines in situ hybridization and loop-mediated isothermal amplification （LAMP） techniques for chromosomal localization of DNA sequences. In situ LAMP...In situ loop-mediated isothermal amplification （in situ LAMP） combines in situ hybridization and loop-mediated isothermal amplification （LAMP） techniques for chromosomal localization of DNA sequences. In situ LAMP is a method that is generally more specific and sensitive than conventional techniques such as fluorescence in situ hybridization （FISH）, primed in situ labeling （PRINS）, and cycling primed in situ labeling （C-PRINS）. Here, we describe the development and application of in situ LAMP to identify the chromosomal localization of DNA sequences. To benchmark this technique, we successfully applied this technique to localize the major ribosomal RNA gene on the chromosomes of the Zhikong scallop （ Chlarnys farreri）.展开更多
A total of 1,160 differentially expressed genes induced by Marssonina brunnea f.sp.muhigermtubi were identified in Populus deltoides cv.'Lux'(1-69/55)with two-colour cDNA microarray including 2,952 cDNAs from ...A total of 1,160 differentially expressed genes induced by Marssonina brunnea f.sp.muhigermtubi were identified in Populus deltoides cv.'Lux'(1-69/55)with two-colour cDNA microarray including 2,952 cDNAs from two cDNA libraries constructed with 72 h inoculated poplar leaves.Functional analysis showed that 1,160 genes were classified into 11 functional categories that are involved in metabolism(15.9%),signal transduction(9.5%),transcription and replication(8.7%),and cell rescue and defense(7.8%).Among them,926 genes were sporadically localized on 19 linkage groups.Chromosome 2 contained 102(11%)differentially expressed genes,followed by chromosome 1 which contains 93 genes(10%),and chromosome 17 had the least number of differentially expressed genes.Clustering of expressed sequence tags(ESTs)in poplar genome was observed at the terminal regions of several chromosomes.The relationship between cluster of genes and plant defense response would be further studied.展开更多
Genetic resistance is the most economical method of reducing yield losses caused by wheat leaf rust. To identify the leaf rust resistance genes in commonly used parental germplasm and released cultivars become very ...Genetic resistance is the most economical method of reducing yield losses caused by wheat leaf rust. To identify the leaf rust resistance genes in commonly used parental germplasm and released cultivars become very important for utilizing the genetic resistance to wheat leaf rust fully. Up to date, about 90 leaf rust resistance genes have been found, of which 51 genes have been located and mapped to special chromosomes, and 56 genes have been designated officially according to the standards set forth in the Catalogue of Gene Symbols for wheat. Twenty-four wheat leaf rust resistance genes have been developed for their molecular markers. It is very important to isolate, characterize, and map leaf rust resistance genes due to the resistance losses of the genes caused by the pathogen continuously.展开更多
Affymetrix U133A oligonucleotide microarrays were used to study the differences of gene expressions between high （H） metastatic ovarian cancer cell line, HO-8910PM, and normal ovarian tissues （C）. Bioinformatics w...Affymetrix U133A oligonucleotide microarrays were used to study the differences of gene expressions between high （H） metastatic ovarian cancer cell line, HO-8910PM, and normal ovarian tissues （C）. Bioinformatics was used to identify their chromosomal localizations. A total of 1,237 genes were found to have a difference in expression levels more than eight times. Among them 597 were upregulated [Signal Log Ratio （SLR） ≥3], and 640 genes were downregulated （SLR≤-3）. Except one gene, whose location was unknown, all these genes were randomly distributed on all the chromosomes. However, chromosome 1 contained the most differentially expressed genes （115 genes, 9.3%）, followed by chromosome 2 （94 genes, 7.6%）, chromosome 12 （88 genes, 7.1%）, chromosome 11 （76 genes, 6.1%）, chromosomes X （71 genes, 5.7%）, and chromosomes l7 （69 genes, 5.6%）. These genes were localized on short-arm of chromosome （q）, which had 805 （65.1%） genes, and the short arms of No.13, 14, 15, 21, and 22 chromosomes were the only parts of the chromosomes where the differentially expressed genes were localized. Functional classification showed that most of the genes （306 genes, 24.7%） belonged to the enzymes and their regulator groups. The subsequent group was the nucleic acid binding genes （144 genes, 11.6%）. The rest of the top two groups were signal transduction genes （137 genes, 11.1%） and proteins binding genes （116 genes, 9.4%）. These comprised 56.8% of all the differentially expressed genes. There were also 207 genes whose functions were unknown （16.7 %）. Therefore it was concluded that differentially expressed genes in high metastatic ovarian cancer cell were supposed to be randomly distributed across the genome, but the majority were found on chromosomes 1, 2, 12, 11, 17, and X. Abnormality in four groups of genes, including in enzyme and its regulator, nucleic acid binding, signal transduction and protein binding associated genes, might play important roles in ovarian cancer metastasis. Those genes need to be further studied.展开更多
Messenger RNA-like non-coding RNAs （mlncRNAs） are a newly identified group of non-coding RNAs （ncRNAs） that may be involved in a number of critical cellular events. In this study, 93 candidate porcine mlncRNAs wer...Messenger RNA-like non-coding RNAs （mlncRNAs） are a newly identified group of non-coding RNAs （ncRNAs） that may be involved in a number of critical cellular events. In this study, 93 candidate porcine mlncRNAs were obtained by computational prediction and screening, among which 72 were mapped to the porcine genome. Further analysis of 8 representative candidates revealed that these mlncRNA candidates are not highly conserved among species. Remarkably, one of the candidates, sTF35495, was found to be precursor of a putative porcine microRNA. By RACE PCR, we determined that the full length of sTF35495 was 3 kb. The protein-coding potential of this RNA was tested in silico with no significant finding. Semi-quantitative RT-PCR analysis of the subgroup of 8 candidates revealed two distinct expression profiles and two molecules were further validated by real-time PCR. The predicted pre-microRNA sequence in this study provides a potentially interesting insight into the in vivo function of porcine mlncRNAs and our findings suggest that they play key biological roles in Sus scrofa.展开更多
Objective： To study the difference of gene expression and screen the carcinogenesis associated gene in gastric mucosa by oligonucleotide microarray. Methods： Using the U133A gene chip to detect the gene expression p...Objective： To study the difference of gene expression and screen the carcinogenesis associated gene in gastric mucosa by oligonucleotide microarray. Methods： Using the U133A gene chip to detect the gene expression profile difference between pericancerous mucosa （mucosa inside nearly 2 cm by cancer） and normal section of gastric mucosa. Bioinformatics was used to analyze the detected result on their localization and function in chromosome. Results＂ （1） A total of 150 genes with a difference of more than 3 times in expression levels by comparing the pericancerous mucosa with normal gastric mucosa, of 130 genes were up-regulated （SLR〉I.5）, and 20 were down- regulated （SLR〈 -1.5）. From the gene expression difference was to do the function classification, among those 22 enzyme and 6 enzyme regular genes were most one （18.7%）. The next were 17 nucleic acid binding associated genes （11.3%）. The third were 15 signal transduction associated genes （10%）. Fourth, were 13 protein binding associated genes （8.7%）. Besides the 40 genes were unknown their function, above mentioned 4 groups were 48.7% of the gene total number; （2） The pericancerous mucosa （P） and gastric cancer （T） were simultaneously compared with normal gastric mucosa, which had 71 genes with the same expression difference, of 61 genes were up-regulated （pericancerous SLR〉I.5）, and other 10 genes were down-regulated （pericancerous SLR〈 -1.5）. From their localization on the chromosome, there was simultaneously 71 genes appearance both in the pericancerous mucosa and in gastric cancer. The most one was 11 abnormal genes on the No. 19 chromosome. The next was No. 1, 2, 16 and 17 chromosomes which had 6 genes, respectively. It was not finding an abnormal gene on the No. 5, 14, 22 and Y chromosome. Conclusion： It suggested those genes may be related to the promotion in early gastric carcinogenesis and their progress. Four main groups （enzyme and enzyme regular, nucleic acid binding, signal transduction, protein binding） that associated gene＇s abnormality be played an importance role in studying the carcinogenesis of gastric cancer. The No. 19 and No. 1, 2, 16, 17 chromosomes are important sites of the oncogene transformation.展开更多
基金Supported by the Key Program of the National Natural ScienceFoundation of China(No.30730071)the National High-Tech Researchand Development Program of China(863 program)(No.2007AA09Z430)the General Program of National Natural Science Foundation of China(Nos.30471347&40706048)
文摘Chinese shrimp （Fenneropenaeus chinensis） is an economically important aquaculture species in China. However, cytogenetic and genomic data is limited in the organism partly because the chromosomes are difficult to isolate and analyze. In this study, fluorescence in-situ hybridization （FISH） was used to identify the chromosomes of F. chinensis. The 5S ribosomal RNA gene （rDNA） of F. chinensis was isolated, cloned and then used as a hybridization probe. The results show that the 5S rDNA was located on one pair of homologous chromosomes in F chinensis. In addition, triploid shrimp were used to evaluate the feasibility of chromosome identification using FISH and to validate the method. It was confirmed that 5S rDNA can be used as a chromosome-specific probe for chromosome identification in E chinensis. The successful application ofFISH in E chinensis shows that chromosome-specific probes can be developed and this finding will facilitate further research on the chromosomes ofpenaeid shrimps.
基金Supported by the National Natural Science Foundation of China (Nos.31270047, 30901096)the National Key Technology R&D Program of China(Nos. 2011BAD45B01, 2011BAD13B05)the Earmarked Fund For Modern Agro-Industry Technology Research System to Dr. Zhenmin BAO
文摘In situ loop-mediated isothermal amplification （in situ LAMP） combines in situ hybridization and loop-mediated isothermal amplification （LAMP） techniques for chromosomal localization of DNA sequences. In situ LAMP is a method that is generally more specific and sensitive than conventional techniques such as fluorescence in situ hybridization （FISH）, primed in situ labeling （PRINS）, and cycling primed in situ labeling （C-PRINS）. Here, we describe the development and application of in situ LAMP to identify the chromosomal localization of DNA sequences. To benchmark this technique, we successfully applied this technique to localize the major ribosomal RNA gene on the chromosomes of the Zhikong scallop （ Chlarnys farreri）.
基金National Natural Science Foundation of China(No.30230300).
文摘A total of 1,160 differentially expressed genes induced by Marssonina brunnea f.sp.muhigermtubi were identified in Populus deltoides cv.'Lux'(1-69/55)with two-colour cDNA microarray including 2,952 cDNAs from two cDNA libraries constructed with 72 h inoculated poplar leaves.Functional analysis showed that 1,160 genes were classified into 11 functional categories that are involved in metabolism(15.9%),signal transduction(9.5%),transcription and replication(8.7%),and cell rescue and defense(7.8%).Among them,926 genes were sporadically localized on 19 linkage groups.Chromosome 2 contained 102(11%)differentially expressed genes,followed by chromosome 1 which contains 93 genes(10%),and chromosome 17 had the least number of differentially expressed genes.Clustering of expressed sequence tags(ESTs)in poplar genome was observed at the terminal regions of several chromosomes.The relationship between cluster of genes and plant defense response would be further studied.
基金This study was supported by the National Natural Science Foundation of China(30170602)the Biological Control Center of Plant Pathogens and Plant Pests of Hebei Province.
文摘Genetic resistance is the most economical method of reducing yield losses caused by wheat leaf rust. To identify the leaf rust resistance genes in commonly used parental germplasm and released cultivars become very important for utilizing the genetic resistance to wheat leaf rust fully. Up to date, about 90 leaf rust resistance genes have been found, of which 51 genes have been located and mapped to special chromosomes, and 56 genes have been designated officially according to the standards set forth in the Catalogue of Gene Symbols for wheat. Twenty-four wheat leaf rust resistance genes have been developed for their molecular markers. It is very important to isolate, characterize, and map leaf rust resistance genes due to the resistance losses of the genes caused by the pathogen continuously.
基金National Natural Science Foundation of China (No. 30471819).
文摘Affymetrix U133A oligonucleotide microarrays were used to study the differences of gene expressions between high （H） metastatic ovarian cancer cell line, HO-8910PM, and normal ovarian tissues （C）. Bioinformatics was used to identify their chromosomal localizations. A total of 1,237 genes were found to have a difference in expression levels more than eight times. Among them 597 were upregulated [Signal Log Ratio （SLR） ≥3], and 640 genes were downregulated （SLR≤-3）. Except one gene, whose location was unknown, all these genes were randomly distributed on all the chromosomes. However, chromosome 1 contained the most differentially expressed genes （115 genes, 9.3%）, followed by chromosome 2 （94 genes, 7.6%）, chromosome 12 （88 genes, 7.1%）, chromosome 11 （76 genes, 6.1%）, chromosomes X （71 genes, 5.7%）, and chromosomes l7 （69 genes, 5.6%）. These genes were localized on short-arm of chromosome （q）, which had 805 （65.1%） genes, and the short arms of No.13, 14, 15, 21, and 22 chromosomes were the only parts of the chromosomes where the differentially expressed genes were localized. Functional classification showed that most of the genes （306 genes, 24.7%） belonged to the enzymes and their regulator groups. The subsequent group was the nucleic acid binding genes （144 genes, 11.6%）. The rest of the top two groups were signal transduction genes （137 genes, 11.1%） and proteins binding genes （116 genes, 9.4%）. These comprised 56.8% of all the differentially expressed genes. There were also 207 genes whose functions were unknown （16.7 %）. Therefore it was concluded that differentially expressed genes in high metastatic ovarian cancer cell were supposed to be randomly distributed across the genome, but the majority were found on chromosomes 1, 2, 12, 11, 17, and X. Abnormality in four groups of genes, including in enzyme and its regulator, nucleic acid binding, signal transduction and protein binding associated genes, might play important roles in ovarian cancer metastasis. Those genes need to be further studied.
基金supported by the National Natural Science Foundation of China (No.30830080 and 30800779)the Natural Science Foundation of Beijing (No.5072035)the Ministry of Science and Technology of China (No.2006AA10Z135,2008AA10Z143,2006CB102105 and 2009CB941604)
文摘Messenger RNA-like non-coding RNAs （mlncRNAs） are a newly identified group of non-coding RNAs （ncRNAs） that may be involved in a number of critical cellular events. In this study, 93 candidate porcine mlncRNAs were obtained by computational prediction and screening, among which 72 were mapped to the porcine genome. Further analysis of 8 representative candidates revealed that these mlncRNA candidates are not highly conserved among species. Remarkably, one of the candidates, sTF35495, was found to be precursor of a putative porcine microRNA. By RACE PCR, we determined that the full length of sTF35495 was 3 kb. The protein-coding potential of this RNA was tested in silico with no significant finding. Semi-quantitative RT-PCR analysis of the subgroup of 8 candidates revealed two distinct expression profiles and two molecules were further validated by real-time PCR. The predicted pre-microRNA sequence in this study provides a potentially interesting insight into the in vivo function of porcine mlncRNAs and our findings suggest that they play key biological roles in Sus scrofa.
文摘Objective： To study the difference of gene expression and screen the carcinogenesis associated gene in gastric mucosa by oligonucleotide microarray. Methods： Using the U133A gene chip to detect the gene expression profile difference between pericancerous mucosa （mucosa inside nearly 2 cm by cancer） and normal section of gastric mucosa. Bioinformatics was used to analyze the detected result on their localization and function in chromosome. Results＂ （1） A total of 150 genes with a difference of more than 3 times in expression levels by comparing the pericancerous mucosa with normal gastric mucosa, of 130 genes were up-regulated （SLR〉I.5）, and 20 were down- regulated （SLR〈 -1.5）. From the gene expression difference was to do the function classification, among those 22 enzyme and 6 enzyme regular genes were most one （18.7%）. The next were 17 nucleic acid binding associated genes （11.3%）. The third were 15 signal transduction associated genes （10%）. Fourth, were 13 protein binding associated genes （8.7%）. Besides the 40 genes were unknown their function, above mentioned 4 groups were 48.7% of the gene total number; （2） The pericancerous mucosa （P） and gastric cancer （T） were simultaneously compared with normal gastric mucosa, which had 71 genes with the same expression difference, of 61 genes were up-regulated （pericancerous SLR〉I.5）, and other 10 genes were down-regulated （pericancerous SLR〈 -1.5）. From their localization on the chromosome, there was simultaneously 71 genes appearance both in the pericancerous mucosa and in gastric cancer. The most one was 11 abnormal genes on the No. 19 chromosome. The next was No. 1, 2, 16 and 17 chromosomes which had 6 genes, respectively. It was not finding an abnormal gene on the No. 5, 14, 22 and Y chromosome. Conclusion： It suggested those genes may be related to the promotion in early gastric carcinogenesis and their progress. Four main groups （enzyme and enzyme regular, nucleic acid binding, signal transduction, protein binding） that associated gene＇s abnormality be played an importance role in studying the carcinogenesis of gastric cancer. The No. 19 and No. 1, 2, 16, 17 chromosomes are important sites of the oncogene transformation.
