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P Liang

Publications and source records attributed to P Liang.

At least 19 recordsLinked to original sources
PubMed2002

Differential display technology: a general guide.

The 10 years since the invention of differential display technology (DD) has produced a massive amount of literature detailing problems and improvements to the technique, successful gene expression studies and studies done using genes found through the use of DD. In this review we summarise the results of 10 years of research that has focussed on improving DD and discuss how some of the problems associated with DD can be resolved or minimised. In addition to discussing DD, we address issues related to other differential gene expression analysis techniques and try to illustrate how these techniques can be used to complement one's use of DD. This review also serves as an introduction to the taxa-specific DD review articles that are found in this issue.

Adenosine↗
PubMed2002

Differential display analysis of gene expression in mammals: a p53 story.

Differential display is used worldwide as a method to identify changes in gene expression and to discover novel genes that are involved in important biological pathways. The principle of differential display is the systematic amplification of the 3' termini of messenger RNAs by using anchored oligo-dT primers in combination with upstream arbitrary primers. The separation of the polymerase chain reaction products by gel electrophoresis and their direct comparison allows the identification of differentially regulated genes. Recently, fluorescent differential display was established as the first nonradioactive differential display system with equivalent sensitivity to originally 33P isotopic labeling method. Because of its simplicity, sensitivity, reproducibility and automation, which increase the throughput and accuracy, differential display has become one of the most widely used gene-screening methods in biomedical research involving mammals. This chapter provides a glimpse of the application of differential display in search of target genes of the p53 tumor suppressor gene.

Animals↗
PubMed2001

[Functional assessment of infiltrating immunocytes in patients with primary hepatocellular carcinoma after percutaneous microwave coagulation therapy].

OBJECTIVE: To assess the function local immune cells in patients with primary hepatocellular carcinoma (HCC) after percutaneous microwave coagulation therapy (PMCT). METHODS: Thirty-eight patients with histologically proved primary HCC underwent ultrasound guided PMCT. Specimens were taken from the lesion site before and 17 days after PMCT respectively using 18-guage core needle through US-guide biopsy, embedded in paraffin, and stained by immunohistochemistry. The panel of monoclonal antibodies of CD3, CD56, CD68 and Fas-L were used to detect the CD3+, CD56+, CD68+ cells and T lymphocyte Fas-ligand. The positive cells were detected under light microscopy. Their diameter and area and the Fas-L expression rate of T lymphocytes and changes of secondary lysosomes in macrophages were measured by computer. RESULTS: Before PMCT, only a few infiltrating immunocytes were seen in the tumor specimens; the diameter of most CD3+ and CD56+ cells was less than 10 microns and the diameter of CD68+ cells was less than 18 microns. The amount and volume of CD3+, CD56+, and CD68+ cells significantly increased after PMCT (t = 3.48, P = 0.025 for CD3+ cells, t = -4.76, P = 0.000 for CD56+ cells, and t = -2.46, P = 0.028 for CD68+ cells). The percentage of CD3+ and CD56+ cells with the largest diameter > 10 microns increased from 10.4% and 20.1% respectively before PMCT to 24.9% and 30.2% respectively after PMCT. The percentage of CD68+ cells with the largest diameter > 18 microns increased from 10.2% before PMCT to 33.4% after PMCT. The Fas-l expression rate of T lymphocytes increased from 7.2% to 20.1% (t = -19.12, P = 0.000). The secondary lysosomes and cellular debris within microphages and the cellular organs in T lymphocytes significantly increased. CONCLUSION: The function of intratumaral infiltrating immunocytes is significantly enhanced after PMCT.

Adult↗
PubMed2001

A functional update of the Escherichia coli K-12 genome.

BACKGROUND: Since the genome of Escherichia coli K-12 was initially annotated in 1997, additional functional information based on biological characterization and functions of sequence-similar proteins has become available. On the basis of this new information, an updated version of the annotated chromosome has been generated. RESULTS: The E. coli K-12 chromosome is currently represented by 4,401 genes encoding 116 RNAs and 4,285 proteins. The boundaries of the genes identified in the GenBank Accession U00096 were used. Some protein-coding sequences are compound and encode multimodular proteins. The coding sequences (CDSs) are represented by modules (protein elements of at least 100 amino acids with biological activity and independent evolutionary history). There are 4,616 identified modules in the 4,285 proteins. Of these, 48.9% have been characterized, 29.5% have an imputed function, 2.1% have a phenotype and 19.5% have no function assignment. Only 7% of the modules appear unique to E. coli, and this number is expected to be reduced as more genome data becomes available. The imputed functions were assigned on the basis of manual evaluation of functions predicted by BLAST and DARWIN analyses and by the MAGPIE genome annotation system. CONCLUSIONS: Much knowledge has been gained about functions encoded by the E. coli K-12 genome since the 1997 annotation was published. The data presented here should be useful for analysis of E. coli gene products as well as gene products encoded by other genomes.

Bacterial Proteins↗
PubMed2001

Differential display analysis of gene expression altered by ras oncogene.

The goal of the signal transduction pathways, such as those controlled by Ras, is in large part to ensure highly stringent regulation of the target genes in the nucleus, which are collectively responsible for the signal output, or phenotypes, of the cell. Understanding of the Ras effect ultimately requires the identification of these downstream target genes. Reverse genetic approaches would trace back the pathways by which they are regulated by Ras. While newer methods such as DNA microarray are emerging, differential display has allowed the identification of a greater number of differentially expressed genes than have been cloned by all the other methods combined, based on Medline search. Much of this success has been attributed to its simplicity (RT-PCR and DNA-sequencing gel) and versatility (compare more than two RNAs for both up- and downregulated genes). It has become obvious that finding the genes by either differential display or DNA microarray is only the first step toward the understanding of biological problems under investigation. It is hoped that finding the right genes through careful experimental designs, such as outlined here, will narrow down the number of relevant genes and increase the odds for solving the puzzles of nature, such as ras.

Animals↗
PubMed2001

Glutathione-S-Transferase M1 null genotype in autoimmune hepatitis.

Autoimmune hepatitis is associated with genes located in the major histocompatibility complex. The search for genes at other loci that may play a role in disease susceptibility and/or severity is an area of active investigation in autoimmune liver diseases. Genes for glutathione-S-transferases, enzymes that are widely distributed and collectively metabolize carcinogens, pollutants, drugs, and a broad spectrum of harmful, foreign compounds have been associated with liver disease. The objective of this study was to search for a relationship between the glutathione-S-transferase Ml null genotype and autoimmune hepatitis using polymerase chain reaction analysis. The findings indicate that the frequency of the null genotype is not increased in patients with autoimmune hepatitis when compared to control subjects. These results coupled with similar ones in primary biliary cirrhosis do not support a role for this mutation in autoimmune liver disease.

Adolescent↗
PubMed2001

Computer-aided dynamic simulation of microwave-induced thermal distribution in coagulation of liver cancer.

To develop a method of dynamic three-dimensional (3-D) simulation of thermal distribution in ultrasound-guided microwave coagulation therapy of liver cancer and to verify its accuracy. The specific absorption rate (SAR) values were established by measuring the temperature in equivalent phantom tests. Those values were different under different power output condition. Dynamic 3-D temperature distributions were reconstructed with a finite-element model. Testing and rectification were performed through animal experiments and clinical trials, respectively. The temperature curves in the experiments corresponded well with simulated ones in vitro--91.4% and 88.9% using single and double electrodes, respectively. The measured coagulated boundary and simulated temperature boundary had a good correspondence in 85.7% of the specimens. In both in vivo experiments and clinical trials, blood perfusion influenced the rise in temperature significantly. Temperature curves between the simulations and actual measured results showed good correspondence--67.8% (19/28) in the patients with hepatocellular carcinoma. Distance between electrodes and combined thermal distributions were both optimized with computer-aided simulation during simultaneous two-electrode coagulation. The results demonstrated that computer-aided simulation of microwave thermal distribution is an accurate and reliable method which provides a theoretical and technical basis for controlling coagulated tissue volume and placement of the electrodes during microwave coagulation therapy of liver cancer.

Animals↗
PubMed2001

High glucose concentrations induce oxidative damage to mitochondrial DNA in explanted vascular smooth muscle cells.

Oxidative stress is considered to be one of the mechanisms leading to atherosclerosis. It occurs in response to injury or to altered metabolic state. Alterations in cell growth (proliferation or apoptosis) can also contribute to the pathogenesis of atherosclerosis and is influenced by oxidative stress. Smooth muscle cells (SMC) from aortic explants of JCR:LA-cp homozygous cp/cp corpulent rats who are genetically predisposed to develop atherosclerosis exhibit increased SMC proliferation, which can be attenuated by exercise and food restriction. This study was conducted to characterize the effects fo oxidative stress and high glucose media on cell growth and its relationship to mitochondrial DNA integrity and gene expression in explanted aortic SMC from corpulent and lean JCR:LA-cp rats. The results show that SMC from the cp/cp rat appear to be resistant to oxidant-induced cell death and that they accumulate mitochondrial DNA mutations, probably as a result of a reduction in apoptosis. These data suggest that susceptibility to age- and glucose-related atherosclerosis may be related to alterations in redox signaling.

Animals↗
PubMed2001

Detection of an mRNA polymorphism by differential display.

Differential Display (DD) technology was utilized to compare programs of gene expression in primary cultures of human skin fibroblasts from normal volunteers and patients diagnosed with melancholic depression. Polymorphic transcripts of a single gene differing by one tandem repeat sequence of four nucleotides (TGAT) in the 3' noncoding region were detected.

3' Untranslated Regions↗
PubMed2001

Multicolor fluorescent differential display.

Differential display and DNA microarray have emerged as the two most popular methods for gene expression profiling. Here, we developed a multicolor fluorescent differential display (FDD) method that combines the virtues of both differential display in signal amplification and DNA microarray in signal analysis. As in DNA microarray, RNA samples being compared can be labeled with either a red or green fluorescent dye and displayed in a single lane, allowing convenient scoring and quantification of the differentially expressed messages. In addition, the multicolor FDD has a built-in signal proofreading capability that is achieved by labeling each RNA sample from a comparative study with both red and green fluorescent dyes followed by their reciprocal mixings in color. Thus, the multicolor FDD provides a platform upon which a sensitive and accurate gene expression profiling by differential display can be automated and digitally analyzed. It is envisioned that cDNAs generated by the multicolor FDD may also be used directly as probes for DNA microarray, allowing an integration of the two most widely used technologies for comprehensive analysis of gene expression.

Animals↗
PubMed2001

[Kinetic study on photocatalytic degradation of p-chlorobenzoate at different light intensities].

Kinetics of photocatalytic degradation were investigated at different light intensities using para-chlorobenzoate as a model pollutant. It was experimentally found that the Langmuir-Hinshelwood model could satisfactorily describe all the kinetic processes. However, the two crucial parameters involved in the L-H model were dependent of the incident light intensity. With elevated light intensity, the rate constant, kr, increased whereas the apparent adsorption constant, Ks, decreased. Grossly, both kr and Ks-1 were correlated with the light intensity in a power law. The experimental discovery implies that the photonic efficiency would be much deteriorated with increased radiation intensity although the reaction rate can be enhanced. Applying mild light intensity might be one of the critical strategies in photocatalytic reactor design to improve the photonic efficiency.

Catalysis↗
PubMed2001

[Construction of a subtracted cDNA library of differentially expressed genes in human normal liver tissue and primary hepatocellular carcinoma tissue].

OBJECTIVE: To construct a subtracted cDNA library of differentially expressed genes in human normal liver tissue and primary hepatocellular carcinoma (HCC) tissue. METHODS: Using the suppression subtractive hybridization (SSH), a novel technique has been described recently. cDNA fragments of missing or low expressing tumor suppressor genes in HCC tissue were isolated using paracancerous normal liver tissue and HCC tissue as targets. Then these cDNA fragments were directly inserted into T/A cloning vector to set up the subtractive library. Amplification of the library was carried out with transformation of E.coli by high voltage electroperforation. One hundred positive bacteria clones were randomly picked and identified using enzyme restriction method. RESULTS: The amplified library contained more than 4,000 positive bacteria clones. Random analysis of 100 clones with enzyme restriction method showed that all clones contained 200-600 bp inserts. CONCLUSIONS: A subtracted cDNA library of differentially expressed genes in human normal liver tissue and HCC tissue is constructed successfully with SSH and T/A cloning techniques. The library is efficient and lays solid foundation for screening and cloning new and specific missing or low expressing tumor suppressor genes of HCC.

Carcinoma, Hepatocellular↗
PubMed2001

[Effect of mm-LDL on NF-kB activation in endothelial cell].

OBJECTIVE: To investigate the signal transduction pathway of NF-kB activated by minimally modified low density lipoprotein (mm-LDL) in endothelial cells and the effect of NF-kB on platelet derived growth factor b (PDGFb) mRNA expression. METHODS: mm-LDL was prepared through iron oxidation by dialyzing the native LDL against FeSO4 in PBS. Endothelial cells were incubated in a medium containing mm-LDL, TNF, and IL-1 respectively and electrophoretic mobility shift assay (EMSA) was displayed to check on the activation of NF-kB. Luciferase reporter gene was analysed to investigate the effect of nuclear factor inducing kinase (NIK), inhibitor of NF-kB kinase alpha (IKK alpha) and inhibitor of NF-kB kinase beta (IKK beta) on NF-kB activation. In addition, endothelial cells were transfected using PDGFb promoter-luciferase for reporter gene analysis or transfected with mut-NIK for slot blot analysis to study the effect of NF-kB on PDGFb mRNA expression. RESULTS: mm-LDL was able to activate NF-kB in endothelial cells. mut-NIK and mut-IKK beta inhibited luciferase activity induced by mm-LDL. mm-LDL could also enhance luciferase activity controlled by upstream sequence of PDGFb promoter which contains element interacting with NF-kB. Result of slot blot showed inhibition of PDGFb mRNA expression by mut-NIK in the endothelial cells stimulated by mm-LDL. CONCLUSION: mm-LDL may activate NF-kB through NIK-IKK beta pathway and promote PDGFb mRNA expression in endothelial cells.

Cells, Cultured↗
PubMed2001

[Relationship between proteoglycans and apoE on the HepG2 cell surface].

OBJECTIVE: To characterize the associations and functions of apoE with the HepG2 cell surface through the study of the relationship between proteoglycans and apoE on HepG2 cell surface. METHODS: The specific binding of 7C9, a monoclonal antibody against the N-terminal domain of apoE was employed to demonstrate the effects of glycosaminoglycans, heparinase, chondroitinase, xyloside, and chlorate on the apoE of HepG2 cell surface. RESULTS: Growth of cells in beta-D-xyloside decreased cell surface apoE by 45% with a concomitant increase in apoE secretion (4.3-fold), underlining the importance of glycosaminoglycan association of apo E. Incubations with heparinase (3 U/ml) and heparin (1 mg/ml) decreased apoE by 25.0% and 30.5% respectively indicating association through cell surface haparin sulfate proteoglycans. Incubations with chondroitinase ABC (1.5 U/ml) reduced cell surface apoE by 40.0%. Chondroitin sulfate A and chondroitin sulfate B reduced cell surface apoE by 23.6% and 15.3% respectively while incubations with chondrointin sulfate C not effective. Decreasing the levels of cell surface apoE with haparin or chondrointin sulfates A and B increased the subsequent binding of LDL to the HepG2 cell surface. CONCLUSIONS: ApoE associates with the cell surface mainly through chondrointin sulfate proteoglycans and to a lesser extent through heparan sulfate proteoglycans, decreased levels of cell surface apoE increase the binding of LDL to the cell surface.

Apolipoproteins E↗
PubMed2001

[Characterization of macrophage cell (THP-1) surface apoE and it's role in metabolism of cell lipids].

OBJECTIVE: To study the characterization of THP-1 cell surface apoE in order to learn the further role of macrophage in development of atherosclerosis. METHODS: Using monoclonal antibodies (7C9,3H1) against apoE to analyze the effects of AcLDL, heparin, chondroitinase, and Liposyn II on the apoE of THP-1 cell surface. RESULTS: Cholesterol (AcLDL) loaded cell demonstrated reduced binding of 125I-7C9 to the cell surface by 19% at 4 degrees C, but if the THP-1 cell incubated at 37 degrees C for 2 hours after the removal of AcLDL there was a increase (25%) in 7C9 bound to loaded cells when compared to the 4 degrees C controls; prior loading with AcLDL also increased the secretion of apoE to the extracellular medium in a time-dependent manner; heparinase or chondroitinase ABC did not reduce the surface apoE associated with unloaded cells; the apoE on the surface of loaded macrophage was only marginally affected (9.3%) by incubation with heparinase but was efficiently reduced (50%) by incubation with chondroitinase ABC; Liposyn II dramatically increased the binding of apoA1 to the cell surface (1.5-1.8 fold), the Liposyn II mediated increased binding of apoA1 was antagonized by pre-incubation of THP-1 cells with 3H1 indicating that it was an apoE-dependent process. CONCLUSIONS: Cell surface apoE of THP-1 macrophage relates to the process of cholesterol loading of macrophage cells and lipid mediated binding of apoA1 to the cell surface. It may affect the process of atherosclerosis development.

Apolipoprotein A-I↗
PubMed2000

E2F1 and p53 are dispensable, whereas p21(Waf1/Cip1) cooperates with Rb to restrict endoreduplication and apoptosis during skeletal myogenesis.

We describe temporal and genetic analyses of partially rescued Rb mutant fetuses, mgRb:Rb-/-, that survive to birth and reveal specific defects in skeletal muscle differentiation. We show that in the absence of Rb, these fetuses exhibit increased apoptosis, bona fide endoreduplication, and incomplete differentiation throughout terminal myogenesis. These defects were further augmented in composite mutant fetuses, mgRb:Rb-/-:p21-/-, lacking both Rb and the cyclin-dependent kinase inhibitor p21(Waf1/Cip1). Although E2F1 and p53 mediate ectopic DNA synthesis and cell death in several tissues in Rb mutant embryos, both endoreduplication and apoptosis persisted in mgRb:Rb-/-:E2F1-/- and mgRb:Rb-/-:p53-/- compound mutant muscles. Thus, combined inactivation of Rb and p21(Waf1/Cip1) augments endoreduplication and apoptosis, whereas E2F1 and p53 are dispensable during aberrant myogenesis in Rb-deficient fetuses.

Animals↗
PubMed2000

Genome sequence of Halobacterium species NRC-1.

We report the complete sequence of an extreme halophile, Halobacterium sp. NRC-1, harboring a dynamic 2,571,010-bp genome containing 91 insertion sequences representing 12 families and organized into a large chromosome and 2 related minichromosomes. The Halobacterium NRC-1 genome codes for 2,630 predicted proteins, 36% of which are unrelated to any previously reported. Analysis of the genome sequence shows the presence of pathways for uptake and utilization of amino acids, active sodium-proton antiporter and potassium uptake systems, sophisticated photosensory and signal transduction pathways, and DNA replication, transcription, and translation systems resembling more complex eukaryotic organisms. Whole proteome comparisons show the definite archaeal nature of this halophile with additional similarities to the Gram-positive Bacillus subtilis and other bacteria. The ease of culturing Halobacterium and the availability of methods for its genetic manipulation in the laboratory, including construction of gene knockouts and replacements, indicate this halophile can serve as an excellent model system among the archaea.

Biological Evolution↗