Objective:Osteoarthritis(OA)and sarcopenia are significant health concerns in the elderly,substantially impacting their daily activities and quality of life.However,the relationship between them remains poorly underst...Objective:Osteoarthritis(OA)and sarcopenia are significant health concerns in the elderly,substantially impacting their daily activities and quality of life.However,the relationship between them remains poorly understood.This study aims to uncover common biomarkers and pathways associated with both OA and sarcopenia.Methods:Gene expression profiles related to OA and sarcopenia were retrieved from the Gene Expression Omnibus(GEO)database.Differentially expressed genes(DEGs)between disease and control groups were identified using R software.Common DEGs were extracted via Venn diagram analysis.Gene ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)enrichment analyses were conducted to identify biological processes and pathways associated with shared DEGs.Protein-protein interaction(PPI)networks were constructed,and candidate hub genes were ranked using the maximal clique centrality(MCC)algorithm.Further validation of hub gene expression was performed using 2 independent datasets.Receiver operating characteristic(ROC)curve analysis was used to evaluate the predictive value of key genes for OA and sarcopenia.Mouse models of OA and sarcopenia were established.Hematoxylin-eosin and Safranin O/Fast Green staining were used to validate the OA model.The sarcopenia model was validated via rotarod testing and quadriceps muscle mass measurement.Real-time reverse transcription PCR(real-time RT-PCR)was employed to assess the mRNA expression levels of candidate key genes in both models.Gene set enrichment analysis(GSEA)was conducted to identify pathways associated with the selected shared key genes in both diseases.Results:A total of 89 common DEGs were identified in the gene expression profiles of OA and sarcopenia,including 76 upregulated and 13 downregulated genes.These 89 DEGs were significantly enriched in protein digestion and absorption,the PI3K-Akt signaling pathway,and extracellular matrix-receptor interaction.PPI network analysis and MCC algorithm analysis of the 89 common DEGs identified the top 17 candidate hub genes.Based on the differential expression analysis of these 17 candidate hub genes in the validation datasets,AEBP1 and COL8A2 were ultimately selected as the common key genes for both diseases,both of which showed a significant upregulation trend in the disease groups(all P<0.05).The value of area under the curve(AUC)for AEBP1 and COL8A2 in the OA and sarcopenia datasets were all greater than 0.7,indicating that both genes have potential value in predicting OA and sarcopenia.Real-time RT-PCR results showed that the mRNA expression levels of AEBP1 and COL8A2 were significantly upregulated in the disease groups(all P<0.05),consistent with the results observed in the bioinformatics analysis.GSEA revealed that AEBP1 and COL8A2 were closely related to extracellular matrix-receptor interaction,ribosome,and oxidative phosphorylation in OA and sarcopenia.Conclusion:AEBP1 and COL8A2 have the potential to serve as common biomarkers for OA and sarcopenia.The extracellular matrix-receptor interaction pathway may represent a potential target for the prevention and treatment of both OA and sarcopenia.展开更多
The nuclear receptor peroxisome proliferator-activated receptor γ（PPAR-γ） is a key transcriptional regulator of adipocyte differentiation.It also modulates the synthesis of adipocytokines in the adipose tissue.Its...The nuclear receptor peroxisome proliferator-activated receptor γ（PPAR-γ） is a key transcriptional regulator of adipocyte differentiation.It also modulates the synthesis of adipocytokines in the adipose tissue.Its polymorphisms are associated with the risk of type Ⅱ diabetes,obesity,cardiovascular diseases and cancer.In the present study,to investigate the regulatory mechanism of PPAR-γ gene on lipid metabolism,the computational prediction of peroxisome proliferator response elements（PPREs） was pursued with a genome-wide scale by using MEME/MAST method based on the information of TRANSFAC database,then GO and KEGG analyses were carried out.The results showed that a huge number of predicted target genes of PPAR-γ were significantly enriched in 36 GO terms（P〈0.05） and 10 KEGG pathways（P〈0.05） which were related closely to the lipid metabolism.The results should be a valuable resource for elucidation of the regulatory mechanism of PPAR-γ influence on lipid metabolism,also of the major importance to the diagnosis,prevention and treatment of the complex diseases such as obesity and diabete.展开更多
Part 5＇ UTR region of pig SRPK1 gene was cloned by inverse PCR （I-PCR）, then a 425 bp gene sequence was acquired. A promoter region in -1--309 bp was predicted by online tool （TFSEARCH） and 32 binding sites of tr...Part 5＇ UTR region of pig SRPK1 gene was cloned by inverse PCR （I-PCR）, then a 425 bp gene sequence was acquired. A promoter region in -1--309 bp was predicted by online tool （TFSEARCH） and 32 binding sites of transcription with scores higher than 85 were getten, of which scores of Spl, MyoD, and HSF2 were over 90. Some of these binding sites of transcription factors were connected with promoters, but TATA-box, which was important to gene expression, hadn＇t been found in this region. By using PCR-SSCP method to search SNPs this part （5＇ UTR of SRPK1 in pig）, total of 40 Large White pigs were obtained as the research objects, but no polymorphism were found. Thus, 5＇ UTR of SRPK1 was speculated with a characteristic of high conservation, while it might have been directly or indirectly selected in commercial breeding. The paper provided a further feature of SRPK1 gene in molecular genetics.展开更多
TDF1(transcription-drived fragment) was homologous to the predicted S. lycopersicum nonspecific lipid-transfer protein,nsLTP 2-like(91%), and it was significantly upregulated in response to C. fulvum(cladosporium fulv...TDF1(transcription-drived fragment) was homologous to the predicted S. lycopersicum nonspecific lipid-transfer protein,nsLTP 2-like(91%), and it was significantly upregulated in response to C. fulvum(cladosporium fulvum) infection in tomato plants.In this experiment, the full-length cDNA of nsLTP 2-like was cloned using RACE technology based on the sequence of TDF1(GenBank: JZ717725). A full-length, 625 bp(GenBank: KU366289), cDNA sequence, which with 98% similarity to nsLTP 2-like gene(GenBank: XM015233692) was obtained. This cDNA contains an ORF(open reading frame) with full-length of 345 bp, coding of 114 amino acids, including 12.3% Ala and Gly. Protein molecular weight was 11.51 ku, the isoelectric point(pI) was 8.99, and average overall hydrophilicity was 0.412, with one phosphorylation sites, belonging to volatile acidic nuclear protein. Secondary structure prediction showed that α-Helix accounts for 30.7%, extension chain for 12.28%, β-corner for 9.65%, and random coil for 47.37%. Through comparative analysis of the homology among species, it was found that the amino acid sequence of tomato nsLTP 2-like protein had a high similarity with other plants, and with a specific conserved sequence which might related features in nsLTP 2-like protein. It also be analyzed the gene expression pattern of tomato in different parts and under different stress conditions.The results showed that nsLTP 2-like gene was up-regulated in varying degrees, under the condition of cold stress, exogenous hormone spraying and cladosporium fulvum infection. Therefore, it was speculated that the gene played a role in response to abiotic and biotic stress in tomato.展开更多
The regulating axillary branch gene was cloned and named as CsCCD7.Using a series bioinformatic computer softwares,database and online programes,CsCCD7 nucleotide sequence and CsCCD7 amino acid sequence were analyzed ...The regulating axillary branch gene was cloned and named as CsCCD7.Using a series bioinformatic computer softwares,database and online programes,CsCCD7 nucleotide sequence and CsCCD7 amino acid sequence were analyzed and CsCCD7 function was predicted.The results showed that CsCCD7 cDNA full length sequence was 2 136 bp,and included a 1 665 bp ORF which encoded a 554 AA protein;there were 32 kinds of cis-acting regulating element in 2 136 bp cDNA sequence;CsCCD7 was an unstable protein（the unstable coefficient：40.77）,including many phosphorylation sites related with CsCCD7 function;CsCCD7 had no transmembrane domain,and its subcellular localization was in chloroplast.CsCCD7 secondary structure contained four conformations including α-helix,β-sheet,β-turn and random coil.CsCCD7 protein had no signal peptide,so was non-secretory protein and hydrophilicity protein（grand average of hydropathicity：-0.401）.Both CsCCD7 secondary and tertiary structure prediction results showed that it was classified as carotenoid oxygenase family.Phylogenetic tree drew by Geneious showed that CsCCD7 was more closely related to AtCCD7 than any other Arabidopsis CCD protein.展开更多
At the early stage,the transcriptome sequencing technique was used to detect the differentially expressed gene CsFK111 between vine cucumber and dwarf cucumber D0462.The gene was cloned,and bioinformatics software too...At the early stage,the transcriptome sequencing technique was used to detect the differentially expressed gene CsFK111 between vine cucumber and dwarf cucumber D0462.The gene was cloned,and bioinformatics software tools were used to analyze and predict the gene family and this gene.There were 30 members of the cucumber F-box gene family.The coding region of the cucumber CsFK111 gene was full-length 1314 bp,which encoded 437 amino acids and was predicted to be located in the nucleus.The protein encoded by this gene was a non-transmembrane protein,and the prediction of the secondary structure showed thatβ-lamellar structure and irregular crimp were dominant.A comparison of the phylogenetic tree showed that it was closest to cantaloupe and belonged to the same branch.The results provided a basis for future study on the regulation mechanism of the CsFK111 gene on cucumber dwarfing and also laid a foundation for further study of FBK family proteins.展开更多
MicroRNAs, a class of endogenous non-coding small RNAs about 21 nucleotides in length, play pivotal roles in plant physiological and biochemical processes. Tomato is important economic crop throughout the world. Recen...MicroRNAs, a class of endogenous non-coding small RNAs about 21 nucleotides in length, play pivotal roles in plant physiological and biochemical processes. Tomato is important economic crop throughout the world. Recently, involvement of miRNAs in tomato has received significant attention. MiR172 is one of the conserved miRNAs in tomato. Investigation into the roles and the target genes of this small RNA molecular in Arabidopsis illustrated that miR172 functions in regulating the transitions between developmental stages and in specifying floral organ identify. Herein, we combined bioinformatics and molecular biology approaches to profile the functional characteristics of miR172 in tomato. The results of target prediction showed that AP2-like ethylene-responsive transcription factors were major targets of miR172, analysis of upstream sequence indicated the presence of stress-related cis-elements in its promoter regions, and further analysis of qRT-PCR confirmed that miR172 participated in various stress responses. Our research provided a paradigm for further in-depth investigation of the functional characteristics of miRNAs in tomato.展开更多
基金supported by the National Natural Science Foundation of China(82060418).
文摘Objective:Osteoarthritis(OA)and sarcopenia are significant health concerns in the elderly,substantially impacting their daily activities and quality of life.However,the relationship between them remains poorly understood.This study aims to uncover common biomarkers and pathways associated with both OA and sarcopenia.Methods:Gene expression profiles related to OA and sarcopenia were retrieved from the Gene Expression Omnibus(GEO)database.Differentially expressed genes(DEGs)between disease and control groups were identified using R software.Common DEGs were extracted via Venn diagram analysis.Gene ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)enrichment analyses were conducted to identify biological processes and pathways associated with shared DEGs.Protein-protein interaction(PPI)networks were constructed,and candidate hub genes were ranked using the maximal clique centrality(MCC)algorithm.Further validation of hub gene expression was performed using 2 independent datasets.Receiver operating characteristic(ROC)curve analysis was used to evaluate the predictive value of key genes for OA and sarcopenia.Mouse models of OA and sarcopenia were established.Hematoxylin-eosin and Safranin O/Fast Green staining were used to validate the OA model.The sarcopenia model was validated via rotarod testing and quadriceps muscle mass measurement.Real-time reverse transcription PCR(real-time RT-PCR)was employed to assess the mRNA expression levels of candidate key genes in both models.Gene set enrichment analysis(GSEA)was conducted to identify pathways associated with the selected shared key genes in both diseases.Results:A total of 89 common DEGs were identified in the gene expression profiles of OA and sarcopenia,including 76 upregulated and 13 downregulated genes.These 89 DEGs were significantly enriched in protein digestion and absorption,the PI3K-Akt signaling pathway,and extracellular matrix-receptor interaction.PPI network analysis and MCC algorithm analysis of the 89 common DEGs identified the top 17 candidate hub genes.Based on the differential expression analysis of these 17 candidate hub genes in the validation datasets,AEBP1 and COL8A2 were ultimately selected as the common key genes for both diseases,both of which showed a significant upregulation trend in the disease groups(all P<0.05).The value of area under the curve(AUC)for AEBP1 and COL8A2 in the OA and sarcopenia datasets were all greater than 0.7,indicating that both genes have potential value in predicting OA and sarcopenia.Real-time RT-PCR results showed that the mRNA expression levels of AEBP1 and COL8A2 were significantly upregulated in the disease groups(all P<0.05),consistent with the results observed in the bioinformatics analysis.GSEA revealed that AEBP1 and COL8A2 were closely related to extracellular matrix-receptor interaction,ribosome,and oxidative phosphorylation in OA and sarcopenia.Conclusion:AEBP1 and COL8A2 have the potential to serve as common biomarkers for OA and sarcopenia.The extracellular matrix-receptor interaction pathway may represent a potential target for the prevention and treatment of both OA and sarcopenia.
基金Supported by National 973 Project of China (2006CB102105)Natural Science Foundation Key Project of Heilongjiang Province (ZJN0604-01)National 863 Project of China (2006AA10A120)
文摘The nuclear receptor peroxisome proliferator-activated receptor γ（PPAR-γ） is a key transcriptional regulator of adipocyte differentiation.It also modulates the synthesis of adipocytokines in the adipose tissue.Its polymorphisms are associated with the risk of type Ⅱ diabetes,obesity,cardiovascular diseases and cancer.In the present study,to investigate the regulatory mechanism of PPAR-γ gene on lipid metabolism,the computational prediction of peroxisome proliferator response elements（PPREs） was pursued with a genome-wide scale by using MEME/MAST method based on the information of TRANSFAC database,then GO and KEGG analyses were carried out.The results showed that a huge number of predicted target genes of PPAR-γ were significantly enriched in 36 GO terms（P〈0.05） and 10 KEGG pathways（P〈0.05） which were related closely to the lipid metabolism.The results should be a valuable resource for elucidation of the regulatory mechanism of PPAR-γ influence on lipid metabolism,also of the major importance to the diagnosis,prevention and treatment of the complex diseases such as obesity and diabete.
基金Supported by 11th Five-year Plan Key Projects of National Science and Technology (2008BADB2B01)
文摘Part 5＇ UTR region of pig SRPK1 gene was cloned by inverse PCR （I-PCR）, then a 425 bp gene sequence was acquired. A promoter region in -1--309 bp was predicted by online tool （TFSEARCH） and 32 binding sites of transcription with scores higher than 85 were getten, of which scores of Spl, MyoD, and HSF2 were over 90. Some of these binding sites of transcription factors were connected with promoters, but TATA-box, which was important to gene expression, hadn＇t been found in this region. By using PCR-SSCP method to search SNPs this part （5＇ UTR of SRPK1 in pig）, total of 40 Large White pigs were obtained as the research objects, but no polymorphism were found. Thus, 5＇ UTR of SRPK1 was speculated with a characteristic of high conservation, while it might have been directly or indirectly selected in commercial breeding. The paper provided a further feature of SRPK1 gene in molecular genetics.
基金Supported by the National Key R&D Program of China(2017YFD0101900)China Agriculture Research System(CARS-23-A-16)the Science Foundation of Heilongjiang Province(C2017024)
文摘TDF1(transcription-drived fragment) was homologous to the predicted S. lycopersicum nonspecific lipid-transfer protein,nsLTP 2-like(91%), and it was significantly upregulated in response to C. fulvum(cladosporium fulvum) infection in tomato plants.In this experiment, the full-length cDNA of nsLTP 2-like was cloned using RACE technology based on the sequence of TDF1(GenBank: JZ717725). A full-length, 625 bp(GenBank: KU366289), cDNA sequence, which with 98% similarity to nsLTP 2-like gene(GenBank: XM015233692) was obtained. This cDNA contains an ORF(open reading frame) with full-length of 345 bp, coding of 114 amino acids, including 12.3% Ala and Gly. Protein molecular weight was 11.51 ku, the isoelectric point(pI) was 8.99, and average overall hydrophilicity was 0.412, with one phosphorylation sites, belonging to volatile acidic nuclear protein. Secondary structure prediction showed that α-Helix accounts for 30.7%, extension chain for 12.28%, β-corner for 9.65%, and random coil for 47.37%. Through comparative analysis of the homology among species, it was found that the amino acid sequence of tomato nsLTP 2-like protein had a high similarity with other plants, and with a specific conserved sequence which might related features in nsLTP 2-like protein. It also be analyzed the gene expression pattern of tomato in different parts and under different stress conditions.The results showed that nsLTP 2-like gene was up-regulated in varying degrees, under the condition of cold stress, exogenous hormone spraying and cladosporium fulvum infection. Therefore, it was speculated that the gene played a role in response to abiotic and biotic stress in tomato.
基金Supported by Doctoral Fund of Ministry of Education of China (200802240008)National 863 Project (2007AA10Z177)
文摘The regulating axillary branch gene was cloned and named as CsCCD7.Using a series bioinformatic computer softwares,database and online programes,CsCCD7 nucleotide sequence and CsCCD7 amino acid sequence were analyzed and CsCCD7 function was predicted.The results showed that CsCCD7 cDNA full length sequence was 2 136 bp,and included a 1 665 bp ORF which encoded a 554 AA protein;there were 32 kinds of cis-acting regulating element in 2 136 bp cDNA sequence;CsCCD7 was an unstable protein（the unstable coefficient：40.77）,including many phosphorylation sites related with CsCCD7 function;CsCCD7 had no transmembrane domain,and its subcellular localization was in chloroplast.CsCCD7 secondary structure contained four conformations including α-helix,β-sheet,β-turn and random coil.CsCCD7 protein had no signal peptide,so was non-secretory protein and hydrophilicity protein（grand average of hydropathicity：-0.401）.Both CsCCD7 secondary and tertiary structure prediction results showed that it was classified as carotenoid oxygenase family.Phylogenetic tree drew by Geneious showed that CsCCD7 was more closely related to AtCCD7 than any other Arabidopsis CCD protein.
基金Supported by the National Natural Science Foundation of China(32272724)the National Science Foundation of Heilongjiang Province,China(LH2019C033)。
文摘At the early stage,the transcriptome sequencing technique was used to detect the differentially expressed gene CsFK111 between vine cucumber and dwarf cucumber D0462.The gene was cloned,and bioinformatics software tools were used to analyze and predict the gene family and this gene.There were 30 members of the cucumber F-box gene family.The coding region of the cucumber CsFK111 gene was full-length 1314 bp,which encoded 437 amino acids and was predicted to be located in the nucleus.The protein encoded by this gene was a non-transmembrane protein,and the prediction of the secondary structure showed thatβ-lamellar structure and irregular crimp were dominant.A comparison of the phylogenetic tree showed that it was closest to cantaloupe and belonged to the same branch.The results provided a basis for future study on the regulation mechanism of the CsFK111 gene on cucumber dwarfing and also laid a foundation for further study of FBK family proteins.
基金Suppported by the National Natural Science Foundation of China(31171971,31272167)
文摘MicroRNAs, a class of endogenous non-coding small RNAs about 21 nucleotides in length, play pivotal roles in plant physiological and biochemical processes. Tomato is important economic crop throughout the world. Recently, involvement of miRNAs in tomato has received significant attention. MiR172 is one of the conserved miRNAs in tomato. Investigation into the roles and the target genes of this small RNA molecular in Arabidopsis illustrated that miR172 functions in regulating the transitions between developmental stages and in specifying floral organ identify. Herein, we combined bioinformatics and molecular biology approaches to profile the functional characteristics of miR172 in tomato. The results of target prediction showed that AP2-like ethylene-responsive transcription factors were major targets of miR172, analysis of upstream sequence indicated the presence of stress-related cis-elements in its promoter regions, and further analysis of qRT-PCR confirmed that miR172 participated in various stress responses. Our research provided a paradigm for further in-depth investigation of the functional characteristics of miRNAs in tomato.
