Selection of reliable reference genes for gene expression study in nasopharyngeal carcinoma.

Aim: To construct a system for selecting reference genes (RGs) and to select the most optimal RGs for gene expression studies in nasopharyngeal carcinoma (NPC).

Methods: The total RNAs from 20 NPC samples were each labeled with Cy5-dUTP. To create a common control, the total RNA from 15 nasopharyngeal phlogistic (NP) tissues was mixed and labeled via reverse transcription with Cy3-dUTP.

Grb10 interacts with Bim L and inhibits apoptosis.

Bim is a proapoptotic member of the Bcl-2 family and is primarily involved in the regulation of the intrinsic apoptotic pathway. However, the detail of regulation of Bim's proapoptotic activity has not been clarified yet. Using Bim L as bait, we screened a human fetal cDNA library for interacting proteins and identified Grb10 as an interactor.

A stochastic model for identifying differential gene pair co-expression patterns in prostate cancer progression.

Background: The identification of gene differential co-expression patterns between cancer stages is a newly developing method to reveal the underlying molecular mechanisms of carcinogenesis. Most researches of this subject lack an algorithm useful for performing a statistical significance assessment involving cancer progression. Lacking this specific algorithm is apparently absent in identifying precise gene pairs correlating to cancer progression.

Discovery and analysis of pancreatic adenocarcinoma genes using cDNA microarrays.

Aim: To study the pathogenetic processes and the role of gene expression by microarray analyses in expediting our understanding of the molecular pathophysiology of pancreatic adenocarcinoma, and to identify the novel cancer-associated genes.

Methods: Nine histologically defined pancreatic head adenocarcinoma specimens associated with clinical data were studied. Total RNA and mRNA were isolated and labeled by reverse transcription reaction with Cy5 and Cy3 for cDNA probe.

[Impacts of donor and recipient's SNP of cytokine and cytokine receptor on early acute renal allograft rejection].

Objective: To investigate the impact of donor and recipient's SNP of cytokine and cytokine receptor on early acute rejection after renal transplantation.

Methods: (1) 129 cases of cadaveric renal allograft recipients were divided into two groups according to the presence or absence of acute graft rejection. The distribution of 21 single nucleotide polymorphisms in cytokines and cytokine receptors gene were compared between two groups as well as latent factors affecting the development of acute rejection.

Analysis of common gene expression patterns in four human tumor cell lines exposed to camptothecin using cDNA microarray: identification of topoisomerase-mediated DNA damage response pathways.

Camptothecin (CPT) is a potent inhibitor of DNA topoisomerase I with a wide spectrum of anti-tumor activity. Relatively little information is available regarding the relation of known topoisomerase-mediated DNA damage with other intracellular pathways. To gain an insight into the intracellular molecular mechanisms of Topoisomerase I inhibitor camptothecin-mediated DNA damage leading to cell death, we used a high-density cDNA microarray to assess sensitive early gene expression profiles in SGC7901 (gastric cancer), Hela (cervical adenocarcinoma), K562 (chronic myelogenous leukemia) and HL60 (promyelocytic leukemia) tumor cells stimulated with camptothecin for 1 h at the concentrations of GI50 (50 % growth inhibition after 24 h of treatment).

[Application of oligonucleotide array in single nucleotide polymorphism typing of cytokines and cytokine receptors].

Objective: To develop an oligonucleotide array for single nucleotide polymorphism (SNP) typing of cytokines, such as tumor necrosis factor (TNF)-a, interleukin (IL)-10, tumor growth factor (TGF)-betal, IL-4, and IL-6, and their receptors and evaluate its function by direct sequencing.

Methods: According to relevant literature, SNP database of NCBI and SNP500 Cancer database of NCI, SNP loci and sequences of cytokines of clinical importance, TNF-a, IL-10, TGF-bl, IL-4 and IL-6, and matched cytokine receptors were chosen and 59 synthesized oligonucleotide probes were immobilized on a glass support, then the primer and Cy5-dCTP were used in multi-PCR, thus the products were labeled with Cy5. The labeled PCR products were hybridized with the probes in the array, and the signals were scanned by Scanner and then analyzed by Image software.

[Tumor relevance analysis of a highly conserved gene by using gene microarray hybridization].

Preliminary function research of a highly conserved human gene,which was cloned from human fetal cDNA library during large-scale cDNA sequencing,is illustrated in this article. Bioinformatics analysis indicates that this gene is highly conserved in human, mouse, fruit fly, thaliana and fission yeast. Other bioinformatics analysis implies its relevance with tumors.

[RAPD study of populations of Glycine tabacina].

The ecological genetic research on Glycine tabacina populations was based on RAPD technique, which revealed 100% polymorphisms, with minimum value of 0.41 in population MM, and maximum value of 0.82 in population PT.

[Detecting genetic polymorphisms of CYP1 A1 and GSTM1 simultaneously with oligonucleotide microarray].

Cytochrome P4501A1 plays a major role in the bioactivation of a number of tobacco procarcinogens. Glutathione S-transferase( GSTM1), a member of the class of GST gene family, has been shown to be polymorphic because of gene deletion resulting in a failure to express the GSTM1 gene in 50% approximately 60% of individuals. Some CYP1 A1/GSTM1 null genotype combinations seem to predispose the lung, esophagus, and oral cavity of smokers to an even higher risk for cancer or DNA damage, requiring, however, confirmation.

Over-expression of Bim alpha3, a novel isoform of human Bim, result in cell apoptosis.

Bim proteins are essential factors of apoptosis. Nine isoforms of Bim have been submitted to GenBank database. In order to improve the understanding of the regulation of Bims' proapoptotic activity, we screened a multiple tissue cDNA panels for Bim isoforms and tested their proapoptotic activity by over-expression.

Cloning and expression of human GTDC1 gene (glycosyltransferase-like domain containing 1) from human fetal library.

The glycosyltransferases (GTs) catalyze the synthesis of the carbohydrate portions of glycoproteins, glycolipids, and proteoglycans. Here we report the cloning and characterization of a novel human GTDC1 (glycosyltransferase-like domain containing 1) gene, which locates on human chromosome 2q22. The GTDC1 cDNA is 2954 bp in length, encoding a putative protein of 458 amino acids.

Cloning and identification of a novel human RNPC3 gene that encodes a protein with two RRM domains and is expressed in the cell nucleus.

The RNA recognition motifs (RRM) domain is one of the most common eukaryotic protein folds. Proteins containing RRM domains function in important steps of posttranscriptional regulation of gene expression and are involved in processing and transport of mRNA precursors. Here we describe the cloning and characterization of a novel human RNPC3 gene containing two RNA recognition motifs.

Analysis of gene expression profiles in human HL-60 cell exposed to cantharidin using cDNA microarray.

Cantharidin is a natural toxin that has antitumor properties and causes leukocytosis as well as increasing sensitivity of tumor cells resistant to other chemotherapeutic agents. There is limited information, however, on the molecular pharmacological mechanisms of cantharidin on human cancer cells. We have used cDNA microarrays to identify gene expression changes in HL-60 promyeloid leukemia cells exposed to cantharidin.

Assignment of human sprouty 4 gene to chromosome segment 5q32 approximately 33 and analysis of its pattern of expression.

The human sprouty 4 (SPRY4) gene was localized to chromosome band 5q32 approximately 33 by screening the Stanford radiation hybrid G3 panel using a SPRY4-specific primer pair for PCR. Northern blot analysis revealed two different mRNAs (5 kb and 2 kb) in liver, skeletal muscle, heart, lung, kidney, spleen, placenta and small intestine. Reverse transcriptase-PCR analysis showed that SPRY4 was expressed in all tested tissues to different levels.

Cloning and identification of a novel cDNA which encodes a putative protein with a DnaJ domain and a thioredoxin active motif, human macrothioredoxin.

A 3345 bp cDNA was isolated from the fetal brain cDNA library by high throughput cDNA sequencing. The cDNA with an open reading fragment (ORF) of 2241 bp encodes a 747 amino acids putative protein with a DnaJ N-terminus domain and four thioredoxin active sets. So it is named human macrothioredoxin (hMTHr).

[Validation of cDNA microarray technology].

cDNA microarray is a technological approach that has the potential to globally measure changes in mRNA expression levels. Self-comparison experiments with the same kind of tissue and differential expression experiments with the different kinds of tissue have been done to verify the reproducibility and the accuracy of this technique. The parameter of the reliability and the reproducibility of the microarray data were analyzed by correlation coefficient (R), coefficient of variation (CV) and false positive rate (FPR) etc.

Purification, crystallization and preliminary X-ray studies of a p-nitrophenylphosphatase from Bacillus stearothermophilus.

Thermostable p-nitrophenylphosphatase from Bacillus stearothermophilus has been expressed in Escherichia coli, purified and crystallized. The crystals belong to space group C(2), with unit-cell parameters a = 67.17 A, b = 57.

Premature termination of telomeric extension-PCR for detection of telomerase activity.

In this article, we report a simple, rapid, and efficient method to detect telomerase activity: the premature termination of telomeric extension-PCR (PTEP). Similar to the telomeric repeat amplification protocol (TRAP), this method is based on PCR amplification following the in vitro telomerase reaction, while the in vitro telomerase reaction here is prematurely, rather than randomly, terminated. Apart from this, the telomeric extension products are used as initial primers, instead of as templates, to trigger the amplification with a specially constructed plasmid DNA as the template that cannot be directly amplified with the telomerase primer.

Purification, crystallization and preliminary X-ray studies of GMP reductase 2 from human.

GMP reductase 2 from human has been expressed in Escherichia coli, purified and crystallized. The crystals belong to space group P3(2)21, with unit-cell parameters a = b = 110.6, c = 209.

[Optimization of T7-based RNA amplification system for cDNA microarray].

cDNA microarrays are powerful parallel tools for gene expression profiling analysis, which help us to understand the molecular mechanism of diseases and to identify potential targets for therapeutic intervention. However, their broader application are hampered by the large amount of RNA required: up to 200 microg of total RNA or 5 microg of mRNA for one chip, making analysis of small samples difficult. In this work, combined with a template switching effect, the T7 RNA linear amplification procedure was optimized, providing multiple copies of anti-sense RNA with reduced sample inputs: no more than 3 microg total RNA for one chip.

A novel cDNA encodes a putative hRALY-like protein, hRALYL.

High throughput cDNA sequencing and 5'-rapid amplification of cDNA ends (5'RACE) isolated two cDNAs that shared the same open reading fragment (ORF). Northern blot analysis with the fetal brain mRNA blots detected two transcripts with the length of 3.2 kb and 2.

Cloning, expression, and genomic structure of a novel human Rap2 interacting gene (RPIP9).

During a large-scale screen of a human fetal brain cDNA library, a full-length cDNA encoding a novel Rap2 interacting protein was isolated and sequenced. The cDNA is 3397bp long and has a predicted open reading frame encoding a protein of 329 aa. The predicted protein shows high homology to mouse and human RPIP8, and has a RUN domain near its C-terminus.

Purification, crystallization and preliminary X-ray studies of human augmenter of liver regeneration.

Human augmenter of liver regeneration has been expressed in Escherichia coli, purified and crystallized. The crystals belong to space group C222, with unit-cell parameters a=51.7 A, b=78.

Cloning and identification of a cDNA that encodes a novel human protein with thrombospondin type I repeat domain, hPWTSR.

A cDNA was isolated from the fetal brain cDNA library by high throughput cDNA sequencing. The 2390 bp cDNA with an open reading fragment (ORF) of 816 bp encodes a 272 amino acids putative protein with a thrombospondin type I repeat (TSR) domain and a cysteine-rich region at the N-terminus, so it is named hPWTSR. We used Northern blot detected two bands with length of about 3 kb and 4 kb respectively, which expressed in human adult tissues with different intensities.