Denitrification effect and strengthening mechanism of SAD/A system at low temperature by gel-immobilization technology.

Sulfur autotrophic denitrification coupled anaerobic ammonia oxidation (SAD/A) has several advantages over other denitrification processes; for example, it does not consume the organic carbon source, has low operation costs, and produces less excess sludge; however, it has certain disadvantages as well, such as a long start-up time, easy loss of bacteria, and low microbial activity at low temperature. The use of microbial immobilization technology to embed functional bacteria provides a feasible method of resolving the above problems. In this study polyvinyl alcohol­sodium alginate was used to prepare a composite carrier for fixing anaerobic ammonia oxidizing bacteria (AAOB) and sulfur oxidizing bacteria (SOB), and the structure and morphology of the encapsulated bodies were characterized by scanning electron microscopy and Fourier transform infrared spectroscopy. Subsequently, the nitrogen removal performance of the immobilized microbial carriers in the gradient cooling process (30 °C to 10 °C) was determined, and the corresponding mechanism was discussed. The results showed that the nitrate-removal efficiencies observed with granular sludge and gel embedding were at 10 °C 21.44 % and 14.31 % lower, than those at 30 °C, respectively, whereas the ammonia-removal efficiency decreased by up to approximately three-fold. The main mechanism was the 'insulation' provided by the external gel composed of PVA and SA for the internal sludge and subsequent improvement of its low temperature resistance, while protecting AAOB and SOB from oxygen inhibition, which is conducive to enriching denitrifying bacteria. In addition, the gel does not change the internal sludge species, it can shift the dominance of specific microorganisms and improve the removal efficiency of nitrogen. In summary, the immobilization of AAOB and SOB by the gel can achieve effectively mitigate nitrogen pollution in low temperature environments, thus indicating that the SAD/A process has broad engineering application prospects.

Identification of critical prognosis signature associated with lymph node metastasis of stomach adenocarcinomas.

Lymph node metastasis (LNM) is an important factor affecting the prognosis of patients with gastric adenocarcinoma (STAD), which is the most common malignancy of the human digestive system. Current detection techniques have limited sensitivity and specificity, and there is a lack of effective biomarkers to screen for LNM. Therefore, it is critical to screen for biomarkers that predict LNM in STAD. Gene expression differential analysis (false discovery rate < 0.05, |log2Fold change| ≥1.5) was performed on 102 LNM samples, 224 non-LNM samples, and 29 normal gastric tissue samples from The Cancer Genome Atlas (TCGA) STAD dataset, and 269 LNM-specific genes (DEGs) were obtained. Enrichment analysis showed that LNM-specific genes functioned mainly in cytokine-cytokine receptor interactions, calcium signaling, and other pathways. Ten DEGs significantly associated with overall survival in STAD patients were screened by multivariate Cox regression, and an LNM-based 10-mRNA prognostic signature was established (Logrank P < 0.0001). This 10-mRNA signature was well predicted in both the TCGA training set and the Gene Expression Omnibus validation dataset (GSE84437) and was associated with survival in patients with LNM or advanced-stage STAD. Using Kaplan-Meier survival, receiver operating characteristic curve, C-index analysis, and decision curve analysis, the 10-mRNA signature was found to be a more effective predictor of prognosis in STAD patients than the other two reported models (P < 0.0005). Protein-protein interaction network and gene set enrichment analysis of the 10-mRNA signature revealed that the signature may affect the expression of multiple biological pathways and related genes. Finally, the expression levels of prognostic genes in STAD tissues and cell lines were verified using qRT-PCR, Western blot, and the Human Protein Atlas database. Taken together, the prognostic signature constructed in this study may become an indicator for clinical prognostic assessment of LNM-STAD and provide a new strategy for future targeted therapy.

Construction of mRNA prognosis signature associated with differentially expressed genes in early stage of stomach adenocarcinomas based on TCGA and GEO datasets.

BACKGROUND: Stomach adenocarcinomas (STAD) are the most common malignancy of the human digestive system and represent the fourth leading cause of cancer-related deaths. As early-stage STAD are generally mild or asymptomatic, patients with advanced STAD have short overall survival. Early diagnosis of STAD has a considerable influence on clinical outcomes. METHODS: The mRNA expression data and clinical indicators of STAD and normal tissues were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database. The gene expression differences were analyzed by R packages, and gene function enrichment analysis was performed. Kaplan-Meier method and univariate Cox proportional risk regression analysis were used to screen differential expressed genes (DEGs) related to survival of STAD patients. Multivariate Cox proportional risk regression analysis was used to further screen and determine the prognostic DEGs in STAD patients, and to construct a multigene prognostic prediction signature. The accuracy of predictive signature was tested by receiver operating characteristic (ROC) curve software package, and the nomogram of patients with STAD was drawn. Cox regression was used to investigate the correlation between multigene prognostic signature and clinical factors. The predictive performance of this model was compared with two other models proposed in previous studies using KM survival analysis, ROC curve analysis, Harrell consistency index and decision curve analysis (DCA). qRT-PCR and Western blot were used to verify the expression levels of prognostic genes. The pathways and functions of possible involvement of features were predicted using the GSEA method. RESULTS: A total of 569 early-stage specific DEGs were retrieved from TCGA-STAD dataset, including 229 up-regulated genes and 340 down-regulated genes. Enrichment analysis showed that the early-stage specific DEGs were associated with cytokine-cytokine receptor interaction, neuroactive ligand-receptor interaction, and calcium signaling pathway. Multiple Cox regression algorithm was used to identify 10 early-stage specific DEGs associated with overall survival (P < 0.01) of STAD patients, and a multi-mRNA prognosis signature was established. The patients were divided into high-risk group and low-risk group according to the risk score. In the training set, the prognostic signature was positively correlated with tumor size and stage (P < 0.05), survival curve (P < 0.001) and time-dependent ROC (AUC = 0.625). In the training dataset and test dataset, the both signatures had good predictive efficiencies. Cox regression and DCA analysis revealed that the prognostic signature was an independent factor and had a better predict effect than the conventional TNM stage classification method and the earlier published biomarkers on the prognosis of STAD patients. CONCLUSION: In this study, based on the early-stage specifically expressed genes, the prognostic signature constructed through TCGA and GEO datasets may become an indicator for clinical prognosis assessment of STAD and a new strategy for targeted therapy in the future.

Integrating transcriptome and chemical analyses to reveal the anti-Alzheimer's disease components in Verbena officinalis Linn.

Verbena officinalis Linn. is a kind of traditional Chinese medicine, which has a long history of application and shows good effects on neuroprotection. Therefore, we consider that V. officinalis may be a potential drug for treating Alzheimer's disease (AD). First, ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) pointed out that the main chemical components in V. officinalis were iridoid glycosides, phenylethanoid glycosides, and flavonoids. These compounds were used for molecular docking and the results showed that these compounds had good anti-AD activity. To explore the biosynthetic pathway of anti-AD components in V. officinalis, UPLC and ultraviolet (UV) spectrophotometry were used for contents determination and the result was leaf > stem > root. At the same time, 92,867 unigenes were annotated in V. officinalis transcriptome; 206, 229, 115 related unigenes were, respectively, annotated in iridoid glycoside, phenylethanoid glycoside, and flavonoid pathway, of which 61, 73, and 35 were differential expression genes. The components had relatively high expression in leaves, which was consistent with the quantitative results. In addition, the tissue distribution particularity of verbenalin may be related to the branching of pathways. Meanwhile transcription factors VoWRKY6 and VoWRKY7 may be involved in the regulation of iridoid glycoside biosynthesis. Further, VoWRKY3, VoWRKY9, and VoWRKY12 may be related to flavonoid biosynthesis. The above research is helpful to explore the biosynthetic pathway of anti-AD components and the regulation mechanism of active components and to further explore the anti-AD effect of V. officinalis.

Screening of Genes Related to Sex Determination and Differentiation in Mandarin Fish (Siniperca chuatsi).

Mandarin fish has an XX/XY sex-determination system. The female mandarin fish is typically larger than the male. Sex identification and the discovery of genes related to sex determination in mandarin fish have important theoretical significance in the elucidation of the regulation and evolutionary mechanism of animal reproductive development. In this study, the chromosome-level genome of a female mandarin fish was assembled, and we found that LG24 of the genome was an X chromosome. A total of 61 genes on the X chromosome showed sex-biased expression. Only six gonadal genes (LG24G00426, LG24G003280, LG24G003300, LG24G003730, LG24G004200, and LG24G004770) were expressed in the testes, and the expression of the other gene LG24G003870 isoform 1 in the ovaries was significantly higher than that in the testes (p < 0.01). Five (except LG24G003280 and LG24G003300) of the seven aforementioned genes were expressed at the embryonic development stage, suggesting their involvement in early sex determination. The expression of LG24G004770 (encoding HS6ST 3-B-like) was also significantly higher in female muscles than in male muscles (p < 0.01), indicating other functions related to female growth. ZP3 encoded by LG24G003870 isoform 1 increased the C-terminal transmembrane domain, compared with that encoded by other fish zp3 isoforms, indicating their different functions in sex determination or differentiation. This study provides a foundation for the identification of sex-determining genes in mandarin fish.

Integrated metabolomic and transcriptomic analysis reveals variation in the metabolites and genes of Platycodon grandiflorus roots from different regions.

INTRODUCTION: Platycodon grandiflorum root (PG), a popular traditional Chinese medicine, contains considerable chemical components with broad pharmacological activities. The complexity and diversity of the chemical components of PG from different origins contribute to its broad biological activities. The quality of southern PG is superior to that of northern PG, but the mechanisms underlying these differences remain unclear. OBJECTIVES: In order to study variation in the differentially accumulated metabolites (DAMs), differentially expressed genes (DEGs), as well as their interactions and signalling pathways among PG from Anhui and Liaoning. METHODS: The metabolomes based on liquid chromatography-tandem mass spectrometry (LC-MS/MS) and the transcriptome based on high-throughput sequencing technology were combined to comprehensively analyse PGn and PGb. RESULTS: A total of 6515 DEGs and 83 DAMs from the comparison of PG from Anhui and Liaoning were detected. Integrated analysis of metabolomic and transcriptomic data revealed that 215 DEGs and 57 DAMs were significantly enriched in 48 pathways according to KEGG pathway enrichment analysis, and 15 DEGs and 10 DAMs significantly enriched in the main pathway sesquiterpenoid and triterpenoid and phenylpropanoid biosynthesis might play a key role in complex response or regulatory processes. CONCLUSION: Differences in PG from southern and northern China might thus stem from differences in environmental factors, such as precipitation, light duration, and humidity. The results of our study provide new insight into geographic variation in gene expression and metabolite accumulation and will enhance the utilisation of PG resources.

Selection and Evaluation of a Thornless and HLB-Tolerant Bud-Sport of Pummelo Citrus With an Emphasis on Molecular Mechanisms.

The selection of elite bud-sports is an important breeding approach in horticulture. We discovered and evaluated a thornless pummelo bud-sport (TL) that grew more vigorously and was more tolerant to Huanglongbing (HLB) than the thorny wild type (W). To reveal the underlying molecular mechanisms, we carried out whole-genome sequencing of W, and transcriptome comparisons of W, TL, and partially recovered thorny "mutants" (T). The results showed W, TL, and T varied in gene expression, allelic expression, and alternative splicing. Most genes/pathways with significantly altered expression in TL compared to W remained similarly altered in T. Pathway and gene ontology enrichment analysis revealed that the expression of multiple pathways, including photosynthesis and cell wall biosynthesis, was altered among the three genotypes. Remarkably, two polar auxin transporter genes, PIN7 and LAX3, were expressed at a significantly lower level in TL than in both W and T, implying alternation of polar auxin transport in TL may be responsible for the vigorous growth and thornless phenotype. Furthermore, 131 and 68 plant defense-related genes were significantly upregulated and downregulated, respectively, in TL and T compared with W. These genes may be involved in enhanced salicylic acid (SA) dependent defense and repression of defense inducing callose deposition and programmed cell death. Overall, these results indicated that the phenotype changes of the TL bud-sport were associated with tremendous transcriptome alterations, providing new clues and targets for breeding and gene editing for citrus improvement.

[Transcriptome analysis of Platycodon grandiflorum at different growth years and discovery of key genes for platycodin biosynthesis].

Platycodon grandiflorum is a medicinal and edible medicinal material. Our study is aimed to explore the differences in the gene expression of P. grandiflorum in different growth years, and the expression rules of key genes in the biosynthesis of the main active substances of P. grandiflorum. Illumina Hiseq 4000 sequencing platform was used to sequence the transcriptome of P. grandiflorum in different years. Then, 59 654 unigenes were obtained through filtering, assembly, splicing and bioinformatics analysis of the sequencing data, of which 1 671 unigenes were differentially expressed between at least two samples. The results of cluster analysis showed that there was a great difference in the gene expression of P. grandiflorum from one-year-old to two/three-year-old. There were 1 128 different genes between one-and three-year old P. grandiflorum, and only 57 different genes between two-and three-year-old P. grandiflorum. KEGG enrichment results showed that the differential genes of P. grandiflorum in different years were mainly concentra-ted in the biosynthesis of sesquiterpenes and triterpenes, and the biosynthesis of terpenoid skeletons. In the triterpenoid biosynthesis-related pathways, a total of 15 unigenes were identified, involving 5 enzymes. The expression levels of ACAT, HMGR, FDFT1, SQLE decreased with the increase of the growth year of P. grandiflorum. The expression of HMGS was the highest in the one-year-old P. grandiflorum, followed by the three-year-old sample. This study provides useful data for the development of P. grandiflorum, and also provides a basis for the study of related genes in the biosynthetic pathway of platycodin.

Transcriptome analysis of Platycodon grandiflorum at different growth years and discovery of key genes for platycodin biosynthesis / 中国中药杂志

Platycodon grandiflorum is a medicinal and edible medicinal material. Our study is aimed to explore the differences in the gene expression of P. grandiflorum in different growth years, and the expression rules of key genes in the biosynthesis of the main active substances of P. grandiflorum. Illumina Hiseq 4000 sequencing platform was used to sequence the transcriptome of P. grandiflorum in different years. Then, 59 654 unigenes were obtained through filtering, assembly, splicing and bioinformatics analysis of the sequencing data, of which 1 671 unigenes were differentially expressed between at least two samples. The results of cluster analysis showed that there was a great difference in the gene expression of P. grandiflorum from one-year-old to two/three-year-old. There were 1 128 different genes between one-and three-year old P. grandiflorum, and only 57 different genes between two-and three-year-old P. grandiflorum. KEGG enrichment results showed that the differential genes of P. grandiflorum in different years were mainly concentra-ted in the biosynthesis of sesquiterpenes and triterpenes, and the biosynthesis of terpenoid skeletons. In the triterpenoid biosynthesis-related pathways, a total of 15 unigenes were identified, involving 5 enzymes. The expression levels of ACAT, HMGR, FDFT1, SQLE decreased with the increase of the growth year of P. grandiflorum. The expression of HMGS was the highest in the one-year-old P. grandiflorum, followed by the three-year-old sample. This study provides useful data for the development of P. grandiflorum, and also provides a basis for the study of related genes in the biosynthetic pathway of platycodin.

Presence-absence polymorphisms of single-copy genes in the stony coral Acropora digitifera.

BACKGROUND: Despite the importance of characterizing genetic variation among coral individuals for understanding phenotypic variation, the correlation between coral genomic diversity and phenotypic expression is still poorly understood. RESULTS: In this study, we detected a high frequency of genes showing presence-absence polymorphisms (PAPs) for single-copy genes in Acropora digitifera. Among 10,455 single-copy genes, 516 (5%) exhibited PAPs, including 32 transposable element (TE)-related genes. Five hundred sixteen genes exhibited a homozygous absence in one (102) or more than one (414) individuals (n = 33), indicating that most of the absent alleles were not rare variants. Among genes showing PAPs (PAP genes), roughly half were expressed in adults and/or larvae, and the PAP status was associated with differential expression among individuals. Although 85% of PAP genes were uncharacterized or had ambiguous annotations, 70% of these genes were specifically distributed in cnidarian lineages in eumetazoa, suggesting that these genes have functional roles related to traits related to cnidarians or the family Acroporidae or the genus Acropora. Indeed, four of these genes encoded toxins that are usually components of venom in cnidarian-specific cnidocytes. At least 17% of A. digitifera PAP genes were also PAPs in A. tenuis, the basal lineage in the genus Acropora, indicating that PAPs were shared among species in Acropora. CONCLUSIONS: Expression differences caused by a high frequency of PAP genes may be a novel genomic feature in the genus Acropora; these findings will contribute to improve our understanding of correlation between genetic and phenotypic variation in corals.

The mechanism of methyl jasmonate-induced accumulation of hydroxysafflor yellow A in safflower of different colors / 药学学报

To explore the mechanism hydroxysafflor yellow A (HSYA) biosynthesis and regulation, the effect of methyl jasmonate (MeJA) treatment on gene expression related to the biosynthesis of hydroxysafflor yellow A (HSYA) was analyzed, and expression differences in genes involved in HSYA biosynthesis in safflower of different colors was quantified. MeJA at concentrations of 0, 50, 100, and 200 μmol·L-1 was sprayed onto safflower florets to determine the optimal concentration of MeJA. Safflower was treated with 100 μmol·L-1 MeJA and florets were harvested 0, 3, 6, 12 and 24 h after treatment. The content of MeJA was determined by high performance liquid chromatography (HPLC). RNA was extracted from safflower florets treated with 100 μmol·L-1 MeJA for 6 h. The transcription of key genes involved in the biosynthesis of HSYA was quantified by qRT-PCR and differentially expressed genes were identified. The content of HSYA increased after treatment with MeJA, with 100 μmol·L-1 MeJA treatment for 6 h having the greatest effect on HSYA accumulation. qRT-PCR results showed that MeJA could significantly increase the transcription of HSYA biosynthesis genes including PAL2, PAL4, 4CL2, 4CL4, 4CL5, CHS3, CHS4 and CHI2. The content of HSYA differed between safflowers of different colors with a trend of red>orange-yellow>yellow>white. The results of qRT-PCR showed that the expression of CHS1 and CHI2 in red, orange and yellow safflower was significantly higher than that in white safflower. These results indicate that MeJA promotes the accumulation of HSYA by up-regulating the expression of genes involved in the biosynthesis of HSYA such as PAL2, PAL4, 4CL2, 4CL4, 4CL5, CHS3, CHS4 and CHI2, and the variation of HSYA content in safflower of different colors was related to a difference in the level of expression of CHS1 and CHI2.

Systematic Analysis of Gene Expression in Lung Adenocarcinoma and Squamous Cell Carcinoma with a Case Study of FAM83A and FAM83B.

INTRODUCTION: In our previous study, we constructed a Lung Cancer Explorer (LCE) database housing lung cancer-specific expression data and clinical data from over 6700 patients in 56 studies. METHODS: Using this dataset of the largest collection of lung cancer gene expression along with our meta-analysis method, we systematically interrogated the association between gene expression and overall survival as well as the expression difference between tumor and normal (adjacent non-malignant tissue) samples in lung adenocarcinoma (ADC) and lung squamous cell carcinoma (SQCC). A case study for FAM83A and FAM83B was performed as a demonstration for hypothesis testing with our database. RESULTS: We showed that the reproducibility of results across studies varied by histological subtype and analysis type. Genes and pathways unique or common to the two histological subtypes were identified and the results were integrated into LCE to facilitate user exploration. In our case study, we verified the findings from a previous study on FAM83A and FAM83B in non-small cell lung cancer. CONCLUSIONS: This study used gene expression data from a large cohort of patients to explore the molecular differences between lung ADC and SQCC.

Clinical Study on Expression of Tumor Abnormal Glycoproteins in Patients with Gastrointestinal Malignancies after Fluorouracil-based Chemotherapy / 中国药学杂志

OBJECTIVE: To acquire the expressing information about tumor abnormal glycoprotein (TAP) in the peripheral blood of the gastric cancer patients who are treated with fluorouracil and the colorectal cancer patients treated with fluorouracil, and to discuss the factors that affect its expression and its clinical significance. METHODS: This research was conducted on the basis of 99 gastric cancer patients and colorectal cancer patients whose diseases were pathologically diagnosed from May to December, 2018, including 53 gastric cancer patients treated with fluorouracil and paclitaxel and 46 colorectal cancer patients treated with fluorouracil and oxaliplatin. It tested their TAP values, collected the basic information, the type of the cancer, the stage of the cancer, serum tumor markers, etc. of the patients as well as analyzed the differences of the expression of TAP in gastrointestinal tumors with different characteristics. RESULTS: The expression value of TAP in the peripheral blood of the gastrointestinal cancer patients is (158.11±33.63), and the expression of TAP value has no statistical differences in the expression of different sexes, ages, types of the cancer, clinical stages and serum tumor markers. CONCLUSION: The fact that the expression of TAP has no differences in the gastrointestinal cancer patients with different characteristics can't be taken as the basis of identifying or diagnosing gastrointestinal tumors which are different in character.

De novo Assembly and Transcriptome Characterization of Opisthopappus (Asteraceae) for Population Differentiation and Adaption.

Opisthopappus Shih (Asteraceae), an endangered genus endemic to the Taihang Mountains of China, is a high-value ornamental and medicinal plant consisting of two species, Opisthopappus longilobus shih and Opisthopappus taihangensis (Ling) Shih. However, the evolutionary relationships and the taxonomic characteristics between the two species remain unknown. In this study, high-throughput transcriptome sequencing was used to analyze the differential metabolic activity and gene expression and screened special molecular markers for exploring the genetic variation and species differentiation in Opisthopappus Shih. The results showed that 33,974 unigenes with an average size of 801 bp were obtained with optimization of de novo assembly. The comprehensive functional annotation based on Gene Ontology (GO), Cluster of Orthologous Group (COG) and Kyoto Encyclopedia of Genes and Genomes pathway database (KEGG) revealed that these unigenes were mainly related to many physiological, metabolic, and molecular processes. Furthermore, the comparative transcriptome analysis indicated that 3,410 differentially expressed genes were mainly involved in lipid, carbohydrate and amino acid metabolism, xenobiotics biodegradation and metabolism as well as environment adaptation via KEGG. Such as the CYP710A, GST, HSP90A and so on, could be the potential candidate genes for further investigating the molecular mechanism of physiological variations between O. taihangensis and O. longilobus. In addition, the potential 71,804 high quality single nucleotide polymorphisms (SNPs) and 1,444 simple sequence repeats (SSRs) were estimated. Based on the predicted SNP, we have developed eight SNP markers for population genetic analysis in Opisthopappus Shih. A significantly high level of genetic differentiation between the populations of O. longilobus and O. taihangensis were found, and they were clearly grouped into two distinct genetic clusters. These results conformed to the record of Flora Reipublicae Popularis Sinicae (FRPS) and unsupported the taxonomic status in the Flora of China. The transcriptome analysis of Opisthopappus Shih can contribute to in-depth exploring of internal mechanisms in species variation and differentiation based on molecular evidence. With the rich and valuable data resources, the more novel structural, functional, and comparative genomic studies will provide comprehensive insights into the evolutionary relationships between O. taihangensis and O. longilobus.

Analysis of Transcriptomes and Differentially Expressed Genes in Leaves and Roots of Tetrastigma hemsleyanum Diels et Gilg / 中国中医药信息杂志

Objective To obtain the transcriptome database and differentially expressed genes of Tetrastigma hemsleyanum Diels et Gilg. by Illumina HiSeq 4000; To provide important molecular information for its molecular biology research. Methods Leaves and roots of Tetrastigma hemsleyanum Diels et Gilg. were chosen as experimental materials to conduct transcriptome sequencing. Then bioinformatics analysis of gene function annotations, metabolic pathways, and microsatellites was performed on the test data. Results 24.13 Gb Clean Data were assembled. Afer assembly steps, 84 433 of T. hemsleyanum Unigene were obtained, and then they were compared in the 7 gene database, and 47 766 annotated information of Unigene was obtained. There were 27 790 annotations in the GO database. The number of differentially expressed genes in the roots, stems and leaves was 4989, of which 3511 were up-regulated and 1478 were down-regulated. The COG database obtained 16 152 homologous sequences of Unigene, which were divided into 25 categories. In the KEGG database, there were 14 511 Unigene obtained the corresponding Ko number, which could be divided into 130 branches of signal metabolism, among which the number of Unigene in the ribosome synthesis pathway was the most, with 1042, and there was only 1 Unigene in the biosynthetic pathway of isoflavones. Conclusion A large number of transcripts of the transcriptome were obtained through splicing, assembling and functional annotation of Tetrastigma hemsleyanum Diels et Gilg., which can provide genomic database resources for molecular biology research of Tetrastigma hemsleyanum Diels et Gilg.

Comparative expression analysis of Calcineurin B-like family gene CBL10A between salt-tolerant and salt-sensitive cultivars in B. oleracea.

Calcineurin B-like proteins (CBLs) are plant calcium sensors that play a critical role in the regulation of plant growth and response to stress. Many CBLs have been identified in the calcium signaling pathway in both Arabidopsis and rice. However, information about BoCBLs genes from Brassica oleracea has not been reported. In the present study, we identified 13 candidate CBL genes in the B. oleracea genome based on the conserved domain of the Calcineurin B-like family, and we carried out a phylogenetic analysis of CBLs among Arabidopsis, rice, maize, cabbage and B. oleracea. For B. oleracea, the distribution of the predicted BoCBL genes was uneven among the five chromosomes. Sequence analysis showed that the nucleotide sequences and corresponding protein structure of BoCBLs were highly conserved, i.e., all of the putative BoCBLs contained 6-8 introns, and most of the exons of those genes contained the same number of nucleotides and had high sequence identities. All BoCBLs consisted of four EF-Hand functional domains, and the distance between the EF-hand motifs was conserved. Evolutionary analysis revealed that the CBLs were classified into two subgroups. Additionally, the CBL10A gene was cloned from salt-tolerant (CB6) and salt-sensitive (CB3) cultivars using RT-PCR. The results indicated that the cloned gene had a substantial difference in length (741bp in CB3 and 829bp in CB6) between these two cultivars. The deduced CBL10A protein in CB6 had four EF-hand structural domains, which have an irreplaceable role in calcium-binding and have calcineurin A subunit binding sites, while the BoCBL10A protein in CB3 had only two EF-hand structural domains and lacked calcineurin A subunit binding sites. The expression level of the BoCBL10A gene between salt tolerance (CB6)and sensitive varieties(CB3) under salt stress was significantly different (P<0.01 and P<0.05). The expression of BoCBL10A gene was relatively higher in salt-tolerant (CB6) cultivar under salt stress, with a longer period of up-regulation expression and a shorter time responding to salt, compared with the salt-sensitive (CB3) cultivar. We speculate that these differences in the coding region of BoCBL10A may lead to the different salt responses between these two cultivars.

Screening of Stilbene Glucosides Biosynthesis-related Genes in Polygonum multiflorum Thunb. by mRNA Differential Display Reverse Transcription Polymerase Chain Reaction / 广州中医药大学学报

Objective To screen and clone the genes related to stilbene glucosides biosynthesis in Polygonum multiflorum Thunb. Methods The differentially expressed genes in the root, stem and leaf of Polygonum multiflorum which have different contents of stilbene glucosides were screened by differential display reverse transcription polymerase chain reaction (DDRT-PCR). After pMD19-T carrier was inserted into the obtained differential genes for sequencing and comparison, the gene function was analyzed. Results Fifty-one differentially expressed cDNA fragments were found. Of them, 9 were used for the identification by semi-quantitative PCR. The identification results presented 3 positive fragments, one fragment was specifically expressed in the stem and leaf of Polygon-um multiflorum Thunb., sharing high homology with glycine dehydrogenase, and 2 were specifically expressed in the root of Polygonum multiflorum Thunb., having high homology with enoyl-CoA hydratase and aminopeptidase N, respectively. Conclusion Three homologous gene sequences obtained through DDRT-PCR provide a basis for the further study of biosynthetic pathway of stilbene glucoside from Polygonum multiflorum Thunb..

Cloning aged-related gene of mouse thymus / 中国免疫学杂志

Objective:Differential expression analysis and cloning aged related genes of mouse thymus Methods:Different expressions of thymus mRNAs from 1 and 10 month old mouse were analyzed by DDRT PCR and different expression sequence tags (ESTs) were obtained One EST that represented high expressed level in one month mouse thymus was probed to screen mouse thymus cDNA library One 827 bp cDNA fragment was obtained and was extended to 1 406 bp by PCR Results:Homology analysis showed that mt22 1406 contained one 438AA coding region and showed high similarity with human elongation factor1?(EF1?) The Genbank accession number is BE241062 Conclusion:Cloning one gene related with mouse thymus aging

Gene technique and modern Chinese materia medica / 中草药

Chinese materia medica (CMM) has double complexity in bioactive ingredient and its mechanism. It is difficult to explain by the modern biomedicine theory So it seriously restricts the modernization of CMM The modern CMM should have the high quality standard to meet the needs of international standard It can be guaranteed by spreading the GAP for Chinese medicinal materials and GMP for standard production The mechanism depends on using the DNA microarray to set up “the gene expression difference chart”, to study on the combination of CMM and gene expression difference chart Meanwhile, we can establish a totally new method of screening modern CMM based on the gene expression difference chart, it can really make the modernization and internationalization of CMM