表达基因鉴定的一种新策略:筛选poly(dA/dT)^-cDNAs

低丰度表达基因及组织细胞等特异基因的鉴定是人类表达基因鉴定的瓶颈 ,Wang等认为cDNA中的长序列poly(dA/dT)是限制低丰度表达基因等鉴定效率的主要原因。为此提出了一种新策略 ,即用 3′端锚定oligo(dT) 11代替常规oligo(dT)引物逆转录合成cDNA ,并将 3′端携带 11个 (dA/dT)s序列的cDNA称之为poly(dA/dT) -cDNA。筛选poly(dA/dT)

Expression and Identification of Mycoplasma penetrans P35 Lipoprotein

Objective: To study the biological activity of Myco-plasma penetrans 35kDa lipoprotein(P35) in vitro, prokaryotic expression vector pQE31//p35 was constructed and recombinant fusion protein P35 (rP35) was expressed in E.coli. Methods: The p35 gene was amplified by polymerase chain reaction(PCR), cloned to pQE31, and a positive clone was screened. PCR-mediated mutagenesis was used to change the two "TGA" triplets to "TGG" triplets within the p35 gene. Production of the recombinant protein was induced by the addition of IPTG to the E.coli culture. rP35 was purified with a Ni-NTA Spin Kit and rP35 purification was analyzed by Western blot. Results: About 1Kb PCR amplification was cloned into pQE31. The two "TGA" triplets within the p35 gene were successfully changed to "TGG" triplets. The pQE31/p35 vector expressed a protein with a calculated molecular mass of 37.4kDa in E.coli. Western blot indicated the 37.4kDa protein was rP35 . Conclusion: PQE31/p35, a prokaryotic expression vector containing p35 gene, was successfully constructed and expressed in E.coli.

Identification of differentially expressed genes in human uterine leiomyomas using differential display

In searching of differentially expressed genes in human uterine leiomyomas, differential display was used with twelve pairs of primers to compare human uterine leiomyomas with matched myometrium. False positives were eliminated by reverse Northern analysis. Positives were confirmed by Northern blot analysis. RESULTS: Four of 69 cDNA fragments (3 up-regulated named L1, L2 and L3 and 1 down-regulated named M1 in leiomyoma) were confirmed by Northern analysis. Sequence comparison and Northern analysis proved that L1 is exactly the human ribosomal protein S19. It was present ubiquitously in 13 tissues tested but in various levels and even in different size. L1 was highly expressed in parotidean cystadenocarcinoma, pancreatic cancer and breast cancer examined. No mutations have been found in human uterine leiomyomas (n=6). CONCLUSIONS: hRPS19 overexpression might be a universal signal in rapid cell growth tissues.

Identification and characterization of new plant microRNAs using EST analysis

Seventy-five previously known plant microRNAs (miRNAs) were classified into 14 families according to their gene sequence identity. A total of 18,694 plant expressed sequence tags (EST) were found in the GenBank EST databases by comparing all previously known Arabidopsis miRNAs to GenBank’s plant EST databases with BLAST algorithms. After removing the EST sequences with high numbers (more than 2) of mismatched nucleotides, a total of 812 EST contigs were identified. After predicting and scoring the RNA secondary structure of the 812 EST sequences using mFold software, 338 new potential miRNAs were identified in 60 plant species. miRNAs are widespread. Some microRNAs may highly conserve in the plant kingdom, and they may have the same ancestor in very early evolution. There is no nucleotide substitution in most miRNAs among many plant species. Some of the new identified potential miRNAs may be induced and regulated by environmental biotic and abiotic stresses. Some may be preferentially expressed in specific tissues, and are regulated by developmental switching. These findings suggest that EST analysis is a good alternative strategy for identifying new miRNA candidates, their targets, and other genes. A large number of miRNAs exist in different plant species and play important roles in plant developmental switching and plant responses to environmental abiotic and biotic stresses as well as signal transduction. Environmental stresses and developmental switching may be the signals for synthesis and regulation of miRNAs in plants. A model for miRNA induction and expression, and gene regulation by miRNA is hypothesized.

Identification and expression analysis of bovine ANGPTL gene family

Encoded by seven genes, angiopoietin-like （ANGPTL） family members structurally similar to the angiogenic regulating factor angiopoietin are known to possess biological activities in angiogenesis and metabolism. Here we reports for the first time the identification and expression analysis of all the seven members of bovine ANGPTL gene family, which were designated bANGPTL1 to bANGPTL7 in order. The seven bANGPTL genes consist of 4-9 exons, span 3800M-3000 bp and are located on different chromosomes. The deduced amino acid sequences of the members all possess an N-terminal coiled-coil domain and a C-terminal fibrinogen-like domain, both characteristics of angiopoietins. Phylogenetic analysis showed that the 32 identified ANGPTL homologs from 9 species could be classified into two major groups. Real-time quantitative PCR （Q-PCR） analysis revealed that the bANGPTL family members have different expression patterns. This study will be helpful for investigation on the biological role of the bANGPTL family in this economically important species. Furthermore, it provides an insight into the molecular evolution of the emerging ANGPTL family

Characterization of reference genes for qPCR analysis in various tissues of the Fujian oyster Crassostrea angulata

Accurate quantification of transcripts using quantitative real-time polymerase chain reaction （qPCR） depends on the identification of reliable reference genes for normalization. This study aimed to identify and validate seven reference genes, including actin-2 （ACT-2）, elongation factor 1 alpha （EF-1α）, elongation factor 1 beta （EF-1β）, glyceraldehyde-3-phosphate dehydrogenase （GAPDH）, ubiquitin （UBQ）, β-tubulin （β-TUB）, and 18 S ribosomal RNA, from Crassostrea angulata, a valuable marine bivalve cultured worldwide. Transcript levels of the candidate reference genes were examined using qPCR analysis and showed differential expression patterns in the mantle, gill, adductor muscle, labial palp, visceral mass, hemolymph and gonad tissues. Quantitative data were analyzed using the geNorm software to assess the expression stability of the candidate reference genes, revealing that β-TUB and UBQ were the most stable genes. The commonly used GAPDH and 18S rRNA showed low stability, making them unsuitable candidates in this system. The expression pattern of the G protein β-subunit gene （Gβ） across tissue types was also examined and normalized to the expression of each or both of UBQ andβ-TUB as internal controls. This revealed consistent trends with all three normalization approaches, thus validating the reliability of UBQ and β-TUB as optimal internal controls. The study provides the first validated reference genes for accurate data normalization in transcript profiling in Crassostrea angulata, which will be indispensable for further fimetional genomics studies in this economically valuable marine bivalve.

Identification of Differentially Expressed Genes in Grape Skin at Veraison and Maturity and Construction of Co-expression Network

The ripening process of grape is an important stage during grape growth and development. During this process, color of grape skin is the most obvious change. The molecular mechanism for the ripening of grape(a non-climacteric fruit, which ripens without ethylene and respiration bursts) is still unclear. Although numerous studies have been done on the changes in the contents of metabolites during grape ripening, the differentially expressed genes at veraison and maturity stages have not been systematically analyzed. In this study, 1 524 genes that are significantly differentially expressed in grape(Pinot Noir) skin at veraison and maturity stages were identified, and a co-expression network of these genes was built. Some of the eight co-expression modules we identified may be closely related to the synthesis or metabolism of anthocyanins, sugar acids, and other flavor substances. The transcription factor families WRKY, b ZIP, HSF and WOX may play an important role in the regulation of anthocyanin synthesis or metabolism. The results provide a foundation for further study of the molecular mechanism of grape ripening.

Identification of differential gene expressions in colorectal cancer and polyp by cDNA microarray

AIM： TO screen the differential expressed genes in colorectal cancer and polyp tissue samples. METHODS： Tissue specimens containing 16 cases of colorectal adenocarcinoma and colorectal polyp vs nor- mal mucosae were collected and subjected to cDNA microarray and bioinformatical analyses. Quantitative reverse transcription-polymerase chain reaction （qRT- PCR） was used to confirm some of the cDNA microarray data.RESULTS： The experimental data showed that eight genes were differentially expressed, most of which were upregulated in adenomatous polyp lesions. Forty-six genes expressions were altered in colorectal cancers, of which 29 were upregulated and 17 downregulated, as compared to the normal mucosae. In addition, 18 genes were similarly altered in both adenomatous polyps and colorectal cancer, qRT-PCR analyses confirmed the cDNA microarray data for four of those 18 genes： MTA1, PDCD4, TSC1 and PDGFRA. CONCLUSION： These differentially expressed genes likely represent biomarkers for early detection of co- Iorectal cancer and may be potential therapeutic targets after confirmed by further studies.

Identification of Light-Harvesting Chlorophyll a/b-Binding Protein Genes of Zostera marina L.and Their Expression Under Different Environmental Conditions

Photosynthesis includes the collection of light and a/b-binding （LHC） proteins. In high plants, the LHC gene family constituting the light-harvesting complex ofphotosystems I and II. the transfer of solar energy using light-harvesting chlorophyll includes LHCA and LHCB sub-families, which encode proteins Zostera marina L. is a monocotyledonous angiosperm and inhab- its submerged marine environments rather than land environments. We characterized the Lhca and Lhcb gene families of Z. marina from the expressed sequence tags （EST） database. In total, 13 unigenes were annotated as ZmLhc, 6 in Lhca family and 7 in ZmLhcb family. ZmLHCA and ZmLHCB contained the conservative LHC motifs and amino acid residues binding chlorophyll. The average similarity among mature ZmLHCA and ZmLHCB was 48.91% and 48.66%, respectively, which indicated a high degree of diver- gence within ZmLHChc gene family. The reconstructed phylogenetic tree showed that the tree topology and phylogenetic relation- ship were similar to those reported in other high plants, suggesting that the Lhc genes were highly conservative and the classification of ZmLhc genes was consistent with the evolutionary position of Z. marina. Real-time reverse transcription （RT） PCR analysis showed that different members of ZmLhca and ZmLhcb responded to a stress in different expression patterns. Salinity, temperature, light intensity and light quality may affect the expression of most ZmLhca and ZmLhcb genes. Inorganic carbon concentration and acidity had no obvious effect on ZmLhca and ZmLhcb gene expression, except for ZmLhca6.

Expression of the human era cDNA in E.coli

Objective: To amplify human era (Hera) gene, then express it in E.coli. Methods: Human era gene, after amplified by PCR and identified by sequencing, was inserted into the expression vector pGEX-4T3 in which exogenous gene was controlled by Ptac promoter. The recombinant plasmid pGEX-Hera was transformed into DH5 (and induced with IPTG chemically. Results: The human era gene was amplified and the sequence was correct. When the bacteria with pGEX-Hera was induced, an anticipated 65 000 protein band appeared on SDS-PAGE gel and amounted to 23% of total bacterial protein. Conclusion: The human era gene has been successfully amplified and efficiently expressed in E.coli.

CLONING AND CHARACTERIZATION OF HUMANUBIQUITIN BINDING ENZYME 2 cDNA

To clone and identify the gene encoding human ubiquitin binding enzym e 2 and study its expression pattern. Methods. According to the sequence of human EST, which is highly homologous to t he mouse ubiquitin binding/conjugating enzyme (E2), primers were synthesized to screen the human fetal brain cDNA library. The gene was analyzed by bioinformati cs technique and its expression pattern was studied by using multiple tissue No rthern blot. Results. Two cDNA clones encoding human ubiquitin conjugating enzyme have been i solated and identified. Both containing the ubiquitin conjugating domain, the 2 cDNA clones are 88% identical in amino acid sequences and splicing isoforms to each other only with an exon excised to form the short sequence. They belong to a highly conserved and widely expressed E2 enzyme family. Northern blot shows th at they are expressed exclusively in adult human heart, placenta, and pancreas b ut no transcripts can be detected in brain, lung, liver, skeletal muscle or kidn ey. Conclusions. The gene encoding human ubiquitin binding enzyme is expressed under temporal control. As a key enzyme in the degradation of proteins, ubiquitin con jugating enzymes play a central role in the expression regulation on the level o f post translation.

Cloning and Identification of promoter of Pseudomonas Pseudoaligenes

Promoter-probe vector pSUPV4 is used to clone the promoter of Pseudomonas pseudoalcaligenes directly in E. coli, and the recombinant pPA7, which has the highest kanamycin resistance, is obtained. Sequencing the PA7 fragment discloses several motifs similar to the conservative domains of prokaryotic promoters, including -10 box, -35 box, parallel SD fragment essential to transcription initiation, and the translation initiation site ATG. Southern blotting of PA7 indicates that the PA7 fragment comes from P. pseudoalcaligenes genome and has probably one copy. The PA7 fragment is subcloned by PCR, and the result shows that the 5’-flanking fragment from 889 to 1120 bp has promoter activity, which can be enhanced by the 0.7Kb fragment at 5’ end. The fragments of pPA7 and pPA7-2 are transferred into pseudomonas pseudoaligenes by electroporation, and the significant higher kanamycin resistance of transformants than that of control indicates that the PA7 fragment has the promoter activity in P. pseudoaligene.

Identification and expression analysis of OsHsfs in rice

Heat stress transcription factors (Hsfs) are the central regulators of defense response to heat stress. We identified a total of 25 rice Hsf genes by genome-wide analysis of rice (Oryza sativa L.) genome, including the subspecies of O. japonica and O. indica. Proteins encoded by OsHsfs were divided into three classes according to their structures. Digital Northern analysis showed that OsHsfs were expressed constitutively. The expressions of these OsHsfs in response to heat stress and oxidative stress differed among the members of the gene family. Promoter analysis identified a number of stress-related cis-elements in the promoter regions of these OsHsfs. No significant correlation, however, was found between the heat-shock responses of genes and their cis-elements. Overall, our results provide a foundation for future research of OsHsfs function.

Identification of differentially expressed genes from spinal cord after firearm injury to rabbit sciatic nerves

Objective: Peripheral nerve regeneration depends on gene regulation by central neurons. To search for more effective treatment methods to improve the regeneration of wounded peripheral nerves, gene expression profile of spinal cord after firearm injury to rabbit sciatic nerves are studied with DNA micro-array technique. Methods: A total of 54 rabbits were randomly divided into 4 groups: Groups d1, d3, d7 and normal control group. Lumbar spinal cords were sampled. RNA and mRNA were extracted, labeled by Cy3 and Cy5, and analyzed by mouse8192S gene chips. Results: A total of 1367, 923, and 61 genes with differential expression were found on day 1, day 3, and day 7 after trauma respectively. Five expressed sequence tag （EST） sequences demonstrated differential expression during 7 days after trauma. Conclusions: There is complex gene profile with differential expression after firearm nerve injury, among which AW701496, U84291, W13926, X04017 and AW822394 EST sequences may be important regulation factors that involved in regeneration of peripheral nerve injury.