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Gastric cancers overexpress DARPP-32 and a novel isoform, t-DARPP.

Gastric carcinoma is the second most common cause of cancer-related death worldwide. Recently, we have demonstrated that expressed sequence tag AA552509 was frequently amplified and the most consistently overexpressed target at 17q in gastric cancers. Herein, we report that DARPP-32 (dopamine and cAMP-regulated phosphoprotein of M(r) 32,000) is the target gene for overexpression of expressed sequence tag AA552509. In addition, we have identified full-length cDNA of DARPP-32 (GenBank accession number AF464196) with 467 bp of additional untranslated mRNA nucleotides upstream of the previously known translation start site in exon 1. Additionally, we have discovered a novel truncated isoform of DARPP-32 that we named t-DARPP (GenBank accession number AY070271), which is also overexpressed in gastric cancers. Using quantitative real-time reverse transcription-PCR, Western blots, and staining of tumor tissue arrays, the two DARPP mRNA transcripts and proteins were overexpressed in gastric cancer cells and exhibited abundant protein overexpression in neoplastic but not normal gastric epithelial cells. DARPP-32 is the only known protein that acts as a protein phosphatase 1 inhibitor or a protein kinase A inhibitor. The novel truncated isoform, t-DARPP, lacks the phosphorylation site related to protein phosphatase 1 inhibition but maintains the phosphorylation site with the protein kinase A inhibitory effect. Our results reveal for the first time the presence of these signaling molecules in human cancer and suggest that they may be important for gastric tumorigenesis.

Blotting, Western↗

Cloning and characterization of the kinesin-related protein, Krp1p, in Schizosaccharomyces pombe.

Kinesin have been cloned in many organisms. They played important roles in the transport of cell organelles, polarized growth, and secretion. We report here the identification of a kinesin-related protein in Schizosaccharomyces pombe, which was named kinesin-related protein (Krplp). The primer sequences were driven from the highly conserved area of the kinesin genes in other organisms. We cloned kinesin genes from S. pombe using the PCR technique. Sequence analysis revealed that krp1+ has a 1,665 bp open-reading frame (ORF) that encoded a protein that consisted of 554 amino acids with a molecular weight of 61,900. It is homologous to the proteins that belong to the kinesin heavy chain (KHC) superfamily [GenBank accession No. AF156966 (genomic DNA) and AF247188 (mRNA)]. To characterize Krplp, the gene was disrupted and overexpressed in S. pombe. Cells that contained a krp1+ null allele were viable. Overexpression of Krp1p resulted in the inhibition of mitotic growth; cells became elongated, branched, and formed aberrant septa. To identify proteins that interact with Krplp, the yeast two-hybrid system was used. As a result, the novel protein, designated kinesin associated protein (Kap1p), was identified and showed structural homology to the proteins of the myosin family (GenBank accession No. AF351206). The data from the overexpression and two-hybrid study of Krplp may provide information that Krplp can have roles in cytokinesis with myosin.

Base Sequence↗

[Detection and identification of the transgenes in genetically modified plants on the example of Bt-potato].

We have developed diagnostic system for revealing 35S promoter CaMV and transgene CryIIIA in transgenic potato NL Russet Burbank and NL Superior companies Monsanto. Using the data about nucleotide sequences of 35S promoter (AF234316 GenBank) and gene CryIIIA (X70979 GenBank) oligonucleotides primers were synthesized for polymerase chain reaction (PCR). The technique of genomic DNA isolation from plant material, suitable for PCR has been optimized. Using Touchdown PCR method presence of specific transgene in a Bt-potato was shown. This method can be used in routine laboratory practice for revealing 35S promoter in genetically modified plants and for identification of specific transgene CryIIIA in the transformed Bt-plants.

Bacillus thuringiensis Toxins↗

[Identification of a snoRNA47 gene cluster in Oryza sativa].

Small nucleolar RNAs (snoRNAs) are required for ribose 2'-O-methylation of eukaryotic ribosomal RNA. By researching in international rice genome databases, a snoRNA gene cluster, consisting of three box C/D snoRNA gene candidates, was found on chromosome 6. All of snoRNA coding sequences in this cluster exhibited the characteristic structure of box C/D antisense snoRNA. They shared conserved box C and box D motifs, a stable terminal stem formed by a 4-6 nt-long inverted repetition sequence located upstream of box C and downstream of box D. All candidates had a 12 nt-long sequence complementary to the region from 621 nt to 6 32 nt in rice 18 S rRNA (nt numbering according to GenBank accession No. X00755), and might mediate the ribose 2'-O-methylation of A(623) in rice 18 S rRNA. Comparison of these sequences showed that these three rice snoRNAs were homologue of yeast snR47. These three rice snoRNAs were named as OSsnR47.1, OSsnR47.2 and OSsnR47.3, respectively. Primer extension assay showed that these three snoRNAs were transcribed in vivo and determined the 5' ends of each snoRNA. RT-PCR detected transcripts containing linked snoRNA47s and this suggested that the snoRNAs encoded in the cluster might be transcribed as a polycistronic transcript under the control of a single upstream promoter. The gene sequences encoding these three snoRNAs had been deposited in GenBank under accession number of AF453504 AF453503 an d AF453502.

Base Sequence↗

NCBI genetic resources supporting immunogenetic research.

The NCBI creates and maintains a set of integrated bibliographic, sequence, map, structure and other database resources to promote the efficient retrieval of information and the discovery of novel relationships. The connections made between elements of these resources permit researchers to start a search from a wide spectrum of entry points. These multiple dimensions of data can be roughly categorized by primary content as text or bibliographic (PubMed, PubMedCentral, OMIM, LocusLink), sequence (GenBank, Reference Sequence Project (RefSeq), dbSNP, MMDB), protein structure (MMDB) or map position (MapView). They can also becategorized by level of expert curation, which may range from validation of submissions from external groups (GenBank, PubMed, PubMedCentral,), to automatic computation (HomoloGene, UniGene), and to highly reviewed and corrected (LocusLink, MMDB, OMIM, RefSeq). Searches can be made by words (in an article title, key words, sequence annotation, database value, author) by sequence (BLAST or e-PCR against multiple sequence databases), or by map coordinates. By computing or curating bi-directional links between related objects, NCBI can represent content on the genetics, molecular biology, and clinical considerations of interest to immunogeneticists. There is also an emerging resource developed by the NCBI in collaboration with the IHWG devoted to the presentation of MHC data (dbMHC). How dbMHC will augment existing resources at the NCBI is described.

Computational Biology↗

Identification of Streptococcus species and Haemophilus influenzae by direct sequencing of PCR products from 16S-23SrDNA intergenic spacer regions.

OBJECTIVE: To set up a rapid and simple method for identificating bacteria by 16S-23SrDNA intergenic spacer regions (ISRs). METHODS: Polymorphic products of PCR from ISRs were selected on agarose gel and sequenced directly using purified fragments by excising the gel without cloning. Nucleotide sequences were compared with GenBank databases and analyzed by DNAMAN program. RESULTS: There was only a single product in streptococcus genus after PCR amplification of 16S-23SrDNA ISRs. Five streptococcal species were obtained from 7 strains of streptococcus. Two major amplicons were consistently generated for 8 strains of Haemophilus influenzae (H. influenzae). The sequence data showed that they all belonged to H. influenzae type b on GenBank databases. CONCLUSION: PCR and direct sequencing of 16S-23SrDNA ISRs were very successful methods for bacterial species identification.

Base Sequence↗

[Molecular cloning of SRG2, a mouse testis spermatocyte apoptosis-related gene].

A novel mouse gene full-length cDNA sequence-SRG2 were identified (GenBank accession number AF395083), which was significantly changed in cryptorchidism, from a mouse testis cDNA library using a cDNA fragment (GenBank accession number BE644542) as an electronic probe. SRG2 was 1058 bp in length. The putative protein encoded by this gene was 295 amino acids with a theoretical molecular weight of 33 579 and isoelectric point of 9.64. The sequence shared no significant homology with any known protein in databases except TSARG2, with which its homology was 78%. RT-PCR showed that SRG2 was expressed significantly in testis.

Amino Acid Sequence↗

Acquisition of expressed sequence tags from Schistosoma japonicum cercariae (mainland China strain) and its homology analysis.

OBJECTIVE: To understand the general profiles of the genes included in Schistosoma japonicum (Sj) cercarriae cDNA library that we have constructed for the purpose of identifying novel genes. METHODS: The phages in Sj cercariae cDNA library were transformed into plasmids after they had invaded into E.coli BM25.8, and the E.coli clones containing the plasmids were cultured in LB medium supplemented with aminobenzylpenicillin. The isolated colonies were selected for plasmid extraction and the DNAs subsequently extracted from the plasmids underwent sequence analysis with a sequencing primer to obtain the expressed sequence tags (ESTs). After sequence editing of the resulted ESTs, comparison of these sequences with those listed in the GenBank database was performed for homology analysis. The new sequences generated from the analysis were submitted to GenBank and the accession numbers acquired. RESULTS and CONCLUSION :Altogether 58 ESTs were identified among which 3 possed highly homologous nucleotide sequences with the known genes of Sj, 2 showed the homology with Schistosoma mansori genes, 7 had the homologous protein sequences, but not the nucleotide sequences, with other species, and another 27 were poorly homologous in terms of both the nucleotide and protein sequences.

Journal Article↗

Determination and analysis of complete nucleotide sequence of Chinese genotype D hepatitis B virus: the first report.

OBJECTIVE: To determine the complete nucleotide sequence of a Chinese hepatitis B virus (HBV) strain of genotype D. METHOD: The complete nucleotide sequence of HBV derived from a Chinese chronic asymptomatic carrier was amplified by PCR and cloned to conduct sequence analysis. Homology of the resulted nucleotide sequence with those of published HBV strains was assessed by using DNASIS, and complete sequence analysis of the phylogenetic tree of 30 genotype D HBV strains conducted by the assistance of Clustalw. RESULTS: With the complete nucleotide sequnce of 3 182 bp, this HBV strain belongs to ayw3 subtype and D genotype, with the Genebank accession number AF280817. Its complete nucleotide homology is 98.3% to 94.5% with the published sequences of genotype D HBV strains and less than 89.5% with the other HBV strains of genotype A, B, C, E, F and G published in GenBank. CONCLUSION: The evolutionary relations of the complete nucleotide sequence of this HBV strain is the closest to those of the 4 Swedish strains out of the 30 genotype D strains published in GenBank.

Journal Article↗

Generation and analysis of 113 adult stage Schistosoma japonicum (Chinese strain) expressed sequence tags.

OBJECTIVE: To rapidly and economically obtain knowledge about adult stage Schistosoma japonicum (Chinese strain) expressed genes using expressed sequence tag (EST). METHODS: A directional cDNA library constructed from Schistosoma japonicum (Chinese strain) adult stage RNA was used to generate expressed sequence tags (ESTs). These were compared against an EMBL-parasites database and GENBANK database by BLASTn and BLASTx. RESULTS: A total of 314 phage clones were randomly selected for generating expressed sequence tags (ESTs). From these clones, 132 EST-quality sequence were obtained. Among these EST-quality sequences, 113 ESTs were successfully submitted to the dbEST at GenBanK. A total of 7.6% of these EST-quality sequences were previously identified sequence of Schistosoma japonicum, while 4.5% were putatively identified sequences of Schistosoma japonicum. A total of 23.5% of these EST-quality sequences were putatively identified sequence of Schistosoma mansoni or other organisms. 57.6% had no matches in the database and were classified as unknown sequences. Most ESTs with the putative protein identified belonged to housekeeping proteins. Information about several interesting genes was found. CONCLUSION: Partial cDNA sequencing to generate expressed sequence tags (ESTs) has the potential to rapidly and economically increase our knowledge about adult stage Schistosoma japonicum (Chinese strain) expressed genes.

Animals↗

[Cloning of differentially expressed cDNA sequences involved in malignant transformation induced by benzo(a)pyrene metabolite dihydroxyepoxy benzo pyrene].

OBJECTIVE: To clone differentially expressed cDNA sequences involved in malignant transformation induced by benzo(a)pyrene metabolite dihydroxyepoxy benzo pyrene (BPDE). METHOD: The malignant transformation of human bronchial epithelial cell line 16HBE induced by BPDE in vitro was used as a model for comparing gene expression between the transformed cells and controls. cDNA representational difference analysis (cDNA-RDA) was performed to isolate differentially expressed cDNA fragment in transformed cells. The cDNA fragments were ligated to pGEM-T vector and transformed into JM109 bacteria. The plasmid DNA were sequenced and compared with data in GenBank by BLASTN. RESULTS: Five cDNA sequences were found to be novel ones and were registered in dbest database, which assigned accession numbers in GenBank are BG354691, BG354692, BG354693, BG354694 and BG354695, respectively. Eight of the remaining cDNA sequences showed sequence homology to those previously reported such as ribosomal protein S23, MLN137, ACTN4, transforming growth factor and G protein gene. CONCLUSIONS: These 13 genes may be involved in BPDE-induced malignant transformation, but their biological characteristics and functions are left to further studies.

Benzopyrenes↗

[Cloning of mouse endostatin and primary analysis on its biological activity].

The mouse endostatin cDNA was cloned by the total RNA of Chinese Kunming mouse liver as template with RT-PCR. The results of sequencing showed one base pair difference. The ctg was replaced by gtg(L22545 in GenBank) at position 278 base pair, causing the encoded amino acid from reported Val to Leu in this experiment. This new endostatin cDNA was registered in GenBank with an accession number of AF257775. The recombinant eukaryotic expression plasmid pSecTag2-ES was then constructed and transfected into COS-7 cells for transient expression. The results of testing by Western blotting showed an expression fragment in supernatants of pSecTag2-ES transfected COS-7 cells at 48 and 72 hours of transfection. Cultured HUVECs were used to detect the biological effect of supernatants in pSecTag2-ES transfected COS-7 after 48 hours of transfection. 3H incorporation assay showed an obvious inhibition of endothelial cell prolifetation. The results demonstrated primary that the cloned endostatin cDNA had biological activity.

Angiogenesis Inhibitors↗

[Preliminary study of the gene structure of human glycosylphosphatidylinositol specific phospholipase D].

To explore the cDNA and its genomic gene structure of human glycosylphosphatidylinositol specific phospholipase D (GPI-PLD), the stromal cells from human bone marrow were cultured, and the GPI-PLD cDNA was successfully cloned from stromal cells (GenBank Accession AY007546). After analyzing this cDNA, we found that it codes the signal peptide as well as the mature peptide (817 AA) of GPI-PLD. Compared with the cDNA cloned from human pancreas and liver, the homology of the cDNA is 99% and 95% respectively. After searching GenBank, we aligned the genomic gene of the GPI-PLD by DNATools software, and found that the GPI-PLD genomic gene was located in the human 6p22.1-22.3 and contained 25 exons, TATA box, CAAT box, enhancer and the sequence binding homo domain of Pit-1/GHF-1.

Bone Marrow Cells↗

[Cloning and sequence analysis of the phytase phyA gene of Aspergillus niger N25].

The phyA encoding phytase of Aspergillus niger N25 was amplified by the polymerase chain reaction (PCR) with primers designed according to the sequences of the phyA in GenBank. The amplified fragment was cloned and sequenced. The results show that: the coding region is 1506 bp in size, includes a 102 bp intron, and encodes a peptide of 476 amino acid residues, in which there is a signal peptide with 19 amino acids and a mature peptide of 448 amino acids. Comparison of this sequence with the phyA of the natural A. niger NRRL3135 (GenBank Accession: M94550), the most highly secreting-phytase strain, shows that the nucleotide homology is as high as 96.746%, and the amino acid homology comes up to 97.64%. The phyA of A. niger N25 strain in this paper is appropriate to be used to construct the phytase gene-engineering bacteria.

6-Phytase↗

[Sequencing and analysis of a cDNA clone CO111 of Plasmodium falciparum].

AIM: To sequence and analyse a cDNA clone CO111, reacting with immune sera obtained from rabbits immunized with Plasmodium falciparum and one McAb against P. falciparum. METHODS: cDNA clone was amplified by PCR. The PCR product was purified and polished with Klenow enzyme and ligated into the M13mp18 vector (digested by SamI) and then transformed into E. coli JM109. The positive recombinant was screened out by PCR and sequenced by the PRISM Dye Primer Sequencing Kit(ABI). The sequence was analyzed by the program from Geneva University and was compared by GenBank of EMBL. RESULTS: The nucleotide sequence of this cDNA clone contains an open-reading frame of 233 bp, which encodes a predicted polypeptide of 77 amino acid residues. The ratio between A + T and G + C is 3.16. The polypeptide is highly hydrophilic and flexible. Comparison among cDNA of P. falciparum from GenBank of EMBL showed that no sequence identical to this cDNA was found. CONCLUSION: A novel cDNA clone reacted with the antibodies against P. falciparum was isolated.

Amino Acid Sequence↗

[Cloning and sequence analysis of the light chain variable region gene of monoclonal anti-idiotypic antibody NP30 of Schistosoma japonicum].

OBJECTIVE: To amplify and sequence the light chain of anti-idiotypic monoclonal antibody NP30 of Schistosoma japonicum. METHODS: By comparing the conserved regions at each end of the nucleotide sequences of murine germ-line genes encoding FR1 and FR4 regions of immunoglobulin light chain variable regions, we designed a set of primers for amplification of VL gene. The hybridoma cells secreting anti-idiotypic monoclonal antibody NP30 of Schistosoma japonicum were cultured and their genome DNAs were extracted and used as templates for PCR. The PCR product was then cloned into pUC19 vector. The recombinants were sequenced by Sanger's method. The VL gene was compared with GenBank and published mouse VL genes. RESULTS: The full-length of VL gene was 318 bp. The VL gene was a member of mouse Ig kappa light chain subgroup IV and generated from rearrangement of germ line V and J kappa 4 genes. The VL gene sequence has been registered by GenBank(accession No. AF206720). CONCLUSION: The obtained VL gene was a potentially functional gene of anti-idiotypic monoclonal antibody NP30 of Schistosoma japonicum.

Amino Acid Sequence↗

Identified circadian rhythm genes of ciliary epithelium with differential display.

PURPOSE: To identify differential genes expressed in the rabbit ciliary epithelium during the circadian cycle of aqueous flow. METHODS: Total RNA from ciliary epithelium of rabbits at 8 AM (light on 1 hour) and 8 PM (light off 1 hour) were compared by differential display reverse transcription-polymerase chain reaction (DD RT-PCR), using 6% denaturing polyacrylamide electrophoresis, choose differential display bands, cut and reamplify with the same primer, clone and sequence. Search the database of Genbank, prolong them with 5' RACE and 3' RACE technique then clone, sequence and search database of Genbank. RESULTS: 93 Significant differences gene expression were detected between light on and light off in the rabbit ciliary epithelium. CONCLUSION: Differential display is a powerful tool to screen differentially expressed genes in circadian rhythm of ciliary epithelium.

Animals↗

[Cloning and sequencing of the gp23 gene encoding a surface antigen on sporozoites of Cryptosporidium parvum].

OBJECTIVE: To clone and sequence the gp23 gene encoding a surface antigen on the sporozoites of Cryptosporidium parvum. METHODS: Genomic DNA was isolated from oocysts of Cryptosporidium parvum. The gp23 gene was amplified by polymerase chain reaction (PCR) and cloned into pMD18-T vector and sequenced by the methods of dideoxy-mediated chain termination. RESULTS AND CONCLUSION: The gp23 gene was 345 bp in length and included an open reading frame encoding a protein of 114 amino acid residues. The homology of the nucleotide and amino sequences of the gp23 gene was 97.3% and 98.2% to that in the GenBank, respectively. The gp23 gene cloned contained 6 nucleotides more than that in the GenBank.

Amino Acid Sequence↗