Differentially profiling the low-expression transcriptomes of human hepatoma using a novel SSH/microarray approach

BACKGROUND: The main limitation in performing genome-wide gene-expression profiling is the assay of low-expression genes. Approaches with high throughput and high sensitivity for assaying low-expression transcripts are urgently needed for functional genomic studies. Combination of the suppressive subtractive hybridization (SSH) and cDNA microarray techniques using the subtracted cDNA clones as probes printed on chips has greatly improved the efficiency for fishing out the differentially expressed clones and has been used before. However, it remains tedious and inefficient sequencing works for identifying genes including the great number of redundancy in the subtracted amplicons, and sacrifices the original advantages of high sensitivity of SSH in profiling low-expression transcriptomes. RESULTS: We modified the previous combination of SSH and microarray methods by directly using the subtracted amplicons as targets to hybridize the pre-made cDNA microarrays (named as "SSH/microarray"). mRNA prepared from three pairs of hepatoma and non-hepatoma liver tissues was subjected to the SSH/microarray assays, as well as directly to regular cDNA microarray assays for comparison. As compared to the original SSH and microarray combination assays, the modified SSH/microarray assays allowed for much easier inspection of the subtraction efficiency and identification of genes in the subtracted amplicons without tedious and inefficient sequencing work. On the other hand, 5015 of the 9376 genes originally filtered out by the regular cDNA microarray assays because of low expression became analyzable by the SSH/microarray assays. Moreover, the SSH/microarray assays detected about ten times more (701 vs. 69) HCC differentially expressed genes (at least a two-fold difference and P < 0.01), particularly for those with rare transcripts, than did the regular cDNA microarray assays. The differential expression was validated in 9 randomly selected genes in 18 pairs of hepatoma/non-hepatoma liver tissues using quantitative RT-PCR. The SSH/microarray approaches resulted in identifying many differentially expressed genes implicated in the regulation of cell cycle, cell death, signal transduction and cell morphogenesis, suggesting the involvement of multi-biological processes in hepato-carcinogenesis. CONCLUSION: The modified SSH/microarray approach is a simple but high-sensitive and high-efficient tool for differentially profiling the low-expression transcriptomes. It is most adequate for applying to functional genomic studies

Prevalence and molecular characterization of plasmidmediated beta-lactamase genes among nosocomial Staphylococcus aureus isolated in Taiwan

Purpose: To analyze the drug susceptibility phenotypes and the patterns of plasmid-mediated β- lactamase genes among nosocomial Staphylococcus aureus drug resistance isolates in Taiwan.Methods: The antibiotic susceptibilities of 617 clinical Staphylococcus aureus isolates collected from 2005 - 2009 from Chiayi Christian Hospital (Chiayi, Taiwan) were examined in vitro against 8 antimicrobial agents using agar diffusion method. Among the clinical isolates, 114 strains of methicillinsensitive Staphylococcus aureus and 45 strains of methicillin-resistant Staphylococcus aureus (MRSA) isolates were selected for plasmid profile analysis. The patterns of β-lactamase genes presented in plasmids were investigated by polymerase chain reaction analysis.Results: Most test strains were resistant to multiple antibiotics, particularly for the traditional agents such as ampicillin, penicillin, cephalexin and kanamycin. Plasmid profile analysis revealed that up to 36 % of the clinical strains harbored plasmids and were able to develop multi-drug resistant. Among them, most of the isolates harbored at least one plasmid (range 1 – 7) with a size range of 2.3 to 23 Kb. Among the several types of β-lactamases, blaTEM was the most prevalent.Conclusion: The results obtained from this study can serve as a valuable reference for the future control for clinical antibiotic resistant strains and more thorough discussions on resistance mechanisms.Keywords: Staphylococcus aureus, Antibiotic susceptibility, Nosocomial pathogens, Plasmid profile, β- lactamase

Comparison of secondary signs as shown by unenhanced helical computed tomography in patients with uric acid or calcium ureteral stones

AbstractUnenhanced helical computed tomography (UHCT) has evolved into a well-accepted diagnostic method in patients with suspected ureterolithiasis. UHCT not only shows stones within the lumen of the ureter, it also permits evaluation of the secondary signs associated with ureteral obstruction from stones. However, there we could find no data on how secondary signs might differ in relation to different compositions of ureteral stones. In this study, we compared the degree of secondary signs revealed by UHCT in uric acid stone formers and in patients forming calcium stones. We enrolled 117 patients with ureteral stones who underwent UHCT examination and Fourier transform infra-red analysis of stone samples. Clinical data were collected as follows: age, sex, estimated glomerular filtration rate (eGFR), urine pH, and radiological data on secondary signs apparent on UHCT. The uric acid stone formers had significantly lower urine pH and eGFR in comparison to calcium stone formers, and on UHCT they also had a higher percentage of the secondary signs, including rim sign (78.9% vs. 60.2%), hydroureter (94.7% vs. 89.8%), perirenal stranding (84.2% vs. 59.2%) and kidney density difference (73.7% vs. 50.0%). The radiological difference was statistically significant for perirenal stranding (p=0.041). In conclusion, we found that UHCT scanning reveals secondary signs to be more frequent in patients with uric acid ureteral stones than in patients with calcium stones, a tendency that might result from an acidic urine environment

Experimental Simulation of Larger Quantum Circuits with Fewer Superconducting Qubits

Although near-term quantum computing devices are still limited by the quantity and quality of qubits in the so-called NISQ era, quantum computational advantage has been experimentally demonstrated. Moreover, hybrid architectures of quantum and classical computing have become the main paradigm for exhibiting NISQ applications, where low-depth quantum circuits are repeatedly applied. In order to further scale up the problem size solvable by the NISQ devices, it is also possible to reduce the number of physical qubits by "cutting" the quantum circuit into different pieces. In this work, we experimentally demonstrated a circuit-cutting method for simulating quantum circuits involving many logical qubits, using only a few physical superconducting qubits. By exploiting the symmetry of linear-cluster states, we can estimate the effectiveness of circuit-cutting for simulating up to 33-qubit linear-cluster states, using at most 4 physical qubits for each subcircuit. Specifically, for the 12-qubit linear-cluster state, we found that the experimental fidelity bound can reach as much as 0.734, which is about 19\% higher than a direct simulation {on the same} 12-qubit superconducting processor. Our results indicate that circuit-cutting represents a feasible approach of simulating quantum circuits using much fewer qubits, while achieving a much higher circuit fidelity

Tyrosinase inhibitors and insecticidal materials produced by Burkholderia cepacia using squid pen as the sole carbon and nitrogen source

[[abstract]]Reports of tyrosinase inhibitors from microorganisms are rare. A tyrosinase inhibitor- and insecticidal materials-producing bacterium, strain TKU026, was isolated from Taiwanese soil and identified as Burkholderia cepacia. Among the tested chitin-containing materials, squid pen best enhanced the production of tyrosinase inhibitors and insecticidal materials. The tyrosinase inhibitory activity (5000 U/mL) and insecticidal activity (81%) against Drosophila larvae was maximised after cultivation on 1% squid-pen containing medium for three days. The tyrosinase inhibitory activity persisted even when the culture was treated with acidic or alkaline conditions of pH 3 or 11. The activities of both tyrosinase inhibitors and insecticide remained at 100%, even after treatment at 100℃ for 30 min. The culture supernatant after three days of cultivation also showed antifungal activity against Aspergillus fumigatus and Fusarium oxysporum with maximal activities of 100% and 80%, respectively, but no antibacterial activity against Escherichia coli was observed. The tyrosinase inhibitors were assumed to be polyphenolic compounds according to the results of chromatography.[[notice]]補正完畢[[journaltype]]國外[[incitationindex]]SCI[[booktype]]紙本[[booktype]]電子版[[countrycodes]]NL

Significance of Aurora B overexpression in hepatocellular carcinoma. Aurora B Overexpression in HCC

<p>Abstract</p> <p>Background</p> <p>To investigate the significance of Aurora B expression in hepatocellular carcinoma (HCC).</p> <p>Methods</p> <p>The <it>Aurora B </it>and <it>Aurora A </it>mRNA level was measured in 160 HCCs and the paired nontumorous liver tissues by reverse transcription-polymerase chain reaction. Mutations of the <it>p53 </it>and <it>β-catenin </it>genes were analyzed in 134 and 150 tumors, respectively, by direct sequencing of exon 2 to exon 11 of <it>p53 </it>and exon 3 of <it>β-catenin</it>. Anticancer effects of AZD1152-HQPA, an Aurora B kinase selective inhibitor, were examined in Huh-7 and Hep3B cell lines.</p> <p>Results</p> <p><it>Aurora B </it>was overexpressed in 98 (61%) of 160 HCCs and in all 7 HCC cell lines examined. The overexpression of <it>Aurora B </it>was associated with <it>Aurora A </it>overexpression (<it>P </it>= 0.0003) and <it>p53 </it>mutation (<it>P </it>= 0.002) and was inversely associated with <it>β</it>-<it>catenin </it>mutation (<it>P </it>= 0.002). <it>Aurora B </it>overexpression correlated with worse clinicopathologic characteristics. Multivariate analysis confirmed that <it>Aurora B </it>overexpression was an independent poor prognostic factor, despite its interaction with Aurora A overexpression and mutations of <it>p53 </it>and <it>β</it>-<it>catenin</it>. In Huh-7 and Hep3B cells, AZD1152-HQPA induced proliferation blockade, histone H3 (Ser10) dephosphorylation, cell cycle disturbance, and apoptosis.</p> <p>Conclusion</p> <p><it>Aurora B </it>overexpression is an independent molecular marker predicting tumor invasiveness and poor prognosis of HCC. Aurora B kinase selective inhibitors are potential therapeutic agents for HCC treatment.</p

Ναυτικό μουσείο στο δέλτα του Φαλήρου

Σημείωση: το κυρίως κείμενο και το συνοδευτικό υλικό του διατίθεται σε ξεχωριστό ενιαίο αρχείο

Anticancer drugs for the modulation of endoplasmic reticulum stress and oxidative stress

Prior research has demonstrated how the endoplasmic reticulum (ER) functions as a multifunctional organelle and as a well-orchestrated protein-folding unit. It consists of sensors which detect stress-induced unfolded/misfolded proteins and it is the place where protein folding is catalyzed with chaperones. During this folding process, an immaculate disulfide bond formation requires an oxidized environment provided by the ER. Protein folding and the generation of reactive oxygen species (ROS) as a protein oxidative byproduct in ER are crosslinked. An ER stress-induced response also mediates the expression of the apoptosis-associated gene C/EBP-homologous protein (CHOP) and death receptor 5 (DR5). ER stress induces the upregulation of tumor necrosis factor-related apoptosis inducing ligand (TRAIL) receptor and opening new horizons for therapeutic research. These findings can be used to maximize TRAIL-induced apoptosis in xenografted mice. This review summarizes the current understanding of the interplay between ER stress and ROS. We also discuss how damage-associated molecular patterns (DAMPs) function as modulators of immunogenic cell death and how natural products and drugs have shown potential in regulating ER stress and ROS in different cancer cell lines. Drugs as inducers and inhibitors of ROS modulation may respectively exert inducible and inhibitory effects on ER stress and unfolded protein response (UPR). Reconceptualization of the molecular crosstalk among ROS modulating effectors, ER stress, and DAMPs will lead to advances in anticancer therapy