Normalization of the data of cDNA microarray is an obligatory step during microarray experiments due to the relatively frequent non-specific errors. Generally, normalization of microarray data is based on the null hypothesis and variance model. In the Yang's model (Yang et al., 2001), at least two types of noises are included. The one is additive noise and the other is multiplicative noise. Usually, background is considered as one of additive noise to the signal and the variation between the signal pixels is the representative multiplicative noise. In this study, the relation between the signal (spot intensity minus background intensity) and background was observed and the influence of background on normalization as a representative additive factor was investigated. Although the relation has not been considered as a factor affecting the normalization, it could improve the accuracy of microarray data when the normalization was carried out considering signal/background ratio. The background dependent normalization decreased the number of genes whose expression levels were changed significantly and it could make their distribution more consistent through the whole range of signal intensities. In this study, printing pin dependent normalization was also carried out regarding the printing pin as a representative multiplicative noise. It improved the distribution of spots in the Cy3-Cy5 scatter plot, but its effect was slight. These studies suggest that there are some influences of the signals on the local backgrounds and they must be considered for the normalization of cDNA microarray data.
Carbocyanines ; DNA, Complementary/*analysis/genetics ; Gene Expression Profiling/*methods/*standards ; Linear Models ; Oligonucleotide Array Sequence Analysis/*methods/*standards ; Reference Standards ; Reproducibility of Results ; Sensitivity and Specificity

Free Cy5.5 dye and Cy5.5-labeled thermally cross-linked superparamagnetic iron oxide nanoparticles (TCL-SPION) have been routinely used for in vivo optical imaging. However, there is little information about the distribution and accumulation of free Cy5.5 dye and Cy5.5-labeled TCL-SPION in the tissues of mice. Free Cy5.5 dye (0.1 mg/kg body weight) and Cy5.5-labeled TCL-SPION (15 mg/kg body weight) were intravenously injected into the tail vein of ICR mice. The biodistribution and accumulation of the TCL-SPION and Cy5.5 were observed by ex vivo optical imaging and fluorescence signal generation at various time points over 28 days. Cy5.5 dye fluorescence in various organs was rapidly eliminated from 0.5 to 24 h post-injection. Fluorescence intensity of Cy5.5 dye in the liver, lung, kidney, and stomach was fairly strong at the early time points within 1 day post-injection. Cy5.5-labeled TCL-SPION had the highest fluorescence density in the lung at 0.5 h post-injection and decreased rapidly over time. Fluorescence density in liver and spleen was maintained over 28 days. These results suggest that TCL-SPION can be useful as a carrier of therapeutic reagents to treat diseases by persisting for long periods of time in the body.
Animals ; Carbocyanines/*pharmacology ; Ferric Compounds/*pharmacology ; Fluorescent Dyes/*pharmacology ; Kinetics ; Male ; Mice ; Mice, Inbred ICR ; Nanoparticles/*metabolism ; Time Factors ; Tissue Distribution

PURPOSE: To investigate the chemotherapeutic effect of quercetin against cancer cells, signaling pathway of apoptosis was explored in human pancreatic cells. METHODS: Various anticancer drugs including adriamycin, cisplatin, 5-fluorouracil (5-FU) and gemcitabine were used. Cell viability was measured by 3-[4,5-dimethylthiazol-2-yl]-2,5-diphe-nyltetra zolium bromide assay. Apoptosis was determined by 4'-6-diamidino-2-phenylindole nuclei staining and flow cytometry in PANC-1 cells treated with 50 microg/mL quercetin for 24 hours. Expression of endoplas mic reticulum (ER) stress mediators including, Grp78/Bip, p-PERK, PERK, ATF4, ATF6 and GADD153/CHOP proteins were measured by Western blot analysis. Mitochondrial membrane potential was measured by fluorescence staining with JC-1, rhodamine 123. Quercetin induced the apoptosis of PANC-1, which was characterized as nucleic acid and genomic DNA fragmentation, chromatin condensation, and sub-G0/G1 fraction of cell cycle increase. But not adriamycin, cisplatin, gemcitabine, and 5-FU. PANC-1 cells were markedly sensitive to quercetin. RESULTS: Treatment with quercetin resulted in the increased accumulation of intracellular Ca2+ ion. Treatment with quercetin also increased the expression of Grp78/Bip and GADD153/CHOP protein and induced mitochondrial dysfunction. Quercetin exerted cytotoxicity against human pancreatic cancer cells via ER stress-mediated apoptotic signaling including reactive oxygen species production and mitochondrial dysfunction. CONCLUSION: These data suggest that quercetin may be an important modulator of chemosensitivity of cancer cells against anticancer chemotherapeutic agents.
Apoptosis* ; Benzimidazoles ; Blotting, Western ; Carbocyanines ; Cell Cycle ; Cell Survival ; Chromatin ; Cisplatin ; Deoxycytidine ; DNA Fragmentation ; Doxorubicin ; Drug Therapy ; Flow Cytometry ; Fluorescence ; Fluorouracil ; Humans ; Membrane Potential, Mitochondrial ; Pancreatic Neoplasms ; Quercetin* ; Reactive Oxygen Species ; Reticulum ; Rhodamine 123

ObjectiveTo explore the feasibility of inducing human umbilical cord mesenchymal stem cells (HUMSCs) to differentiate into Leydig cells in the interstitial tissue of the rat testis.

METHODSHUMSCs were obtained by tissue blocks culture attachment and their purity and multi-lineage differentiation ability were verified by flow cytometry and chondrogenic/adipogenic/osteogenic differentiation. Then the HUMSCs were marked by CM-Dil and transplanted into the interstitial tissue of the rat testis. At 4 and 8 weeks after transplantation, the survival and differentiation status of the HUMSCs were observed by immunofluorescence staining and flow cytometry. The suspension of the rat Leydig cells was obtained at 8 weeks for determining the expression of the Leydig cell marker 3β-HSD in the HUMSCs, the cells labeled with CM-Dil were sorted and cultured, and the medium collected after 3 days of culture for measurement of the testosterone level.

RESULTSThe expression of the Leydig cell marker CYPllal was not observed in the HUMSCs at 4 weeks but found at 8 weeks after transplantation and the differentiation rate of 3β-HSD was about 14.5% at 8 weeks. CM-Dil labeled cells survived after sorting and testosterone was detected in the medium.

CONCLUSIONSHUMSCs are likely to differentiate into Leydig cells in the interstitium of the rat testis.

Animals ; Biomarkers ; metabolism ; Carbocyanines ; Cell Differentiation ; Cholesterol Side-Chain Cleavage Enzyme ; metabolism ; Feasibility Studies ; Humans ; Leydig Cells ; cytology ; metabolism ; Male ; Mesenchymal Stromal Cells ; cytology ; Rats ; Testis ; cytology ; Time Factors ; Umbilical Cord ; cytology

Bone and Bones ; Carbocyanines ; Cell Culture Techniques ; Coculture Techniques ; Collagen ; Collagenases ; Drug Combinations ; Durapatite ; Endothelial Cells ; Laminin ; Lipoproteins ; Magnetics ; Magnets ; Mandible ; Mesenchymal Stromal Cells ; Molar, Third ; Nylons ; Osteoblasts ; Osteogenesis ; Perchloric Acid ; Periosteum ; Proteoglycans

OBJECTIVETo investigate the effect of Angelica polysaccharide (APS), platelet-derived growth factor (PDGF) and thrombopoietin (TPO) on the proliferation and apoptosis of human megakaryocytic cell line M-07e.

METHODSCell count and the viability testing of M-07e cells (trypan blue exclusion assay) were performed at 24 hours, 48 hours and 72 hours after treatment with APS, PDGF or TPO. Three apoptosis related flow cytometric assays including Annexin V, Caspase-3 and JC-1 were performed to determine apoptotic rate of each group at 72 hours after the treatment.

RESULTSAfter the incubation, the number of M-07e cells in the APS, PDGF and TPO group increased and the viabilities of the three groups were significantly higher than the control group (P < 0.05). The dead cells in the APS, PDGF and TPO group were (19.41 +/- 7.59)%, (21.38 +/- 7.25)% and (18.77 +/- 8.00)%, respectively by flow cytometry using Annexin V method, which were significantly lower compared to the control group (34.33 +/- 5.46)%. The expression of the activated caspase-3 in the group of APS, PDGF and TPO were (12.27 +/- 5.18)%, (12.39 +/- 6.26)% and (13.75 +/- 8.25)%, the APS and PDGF group decreased significantly compared to the control group (18.92 +/- 6.09)%. The ratio of total cell deaths in the APS, PDGF and TPO group were (23.64 +/- 6.69)%, (28.00 +/- 10.05)% and (27.99 +/- 8.99)%, the ratio in APS group decreased significantly compared to the control group (39.48 +/- 11.86)% by JC-1 method. Differences between APS and PDGF groups and between APS and TPO groups were not statistically significant.

CONCLUSIONAPS, PDGF and TPO have similar effect in stimulating proliferation and inhibiting serum-free-culture induced apoptosis of M-07e cells.

Angelica ; chemistry ; Apoptosis ; drug effects ; Benzimidazoles ; pharmacology ; Carbocyanines ; pharmacology ; Caspase 3 ; metabolism ; Cell Proliferation ; drug effects ; Flow Cytometry ; Fluorescent Dyes ; pharmacology ; Humans ; Megakaryocytes ; drug effects ; physiology ; Organic Chemicals ; pharmacology ; Platelet-Derived Growth Factor ; pharmacology ; Thrombopoiesis ; Thrombopoietin ; pharmacology

OBJECTIVETo establish a high-sensitivity, high-specificity and low-cost hydrogel chip platform for the clinical screening of Y chromosome microdeletions.

METHODSSite-specific extended primers with a common sequence at the 5' end were used for hybridizing with the target. The Cy5-dUTP was incorporated into the products by primer extension, and the products were labeled with fluorescence. Then the extended products were added to the chip for hybridizing with acrylamide-modified common probes immobilized on the chip. After removal of the free Cy5-dUTP by electrophoresis, the signals were obtained by fluorescence scanning. And the detecting conditions of this method were optimized.

RESULTSSY254 of 9 samples was successfully detected with the hydrogel chip. The results showed that 3 were normal and the other 6 with microdeletions (1 female sample as a negative control), which coincided with the results of conventional multiplex PCR-electrophoresis.

CONCLUSIONThe hydrogel chip platform we established has provided a new technique for the detection of Y chromosome microdeletions, and is beneficial to the diagnosis and treatment of male infertility.

Carbocyanines ; Chromosome Deletion ; Chromosomes, Human, Y ; genetics ; Deoxyuracil Nucleotides ; Humans ; Hydrogels ; Infertility, Male ; Male ; Oligonucleotide Array Sequence Analysis ; methods ; Sex Chromosome Aberrations ; Sex Chromosome Disorders of Sex Development ; diagnosis ; genetics

OBJECTIVE: To investigate the feasibility of a novel molecular probe of Zn-DPA-PSS794 to monitor the efficiency of doxorubicin to ovarian cancer and compare with Cy5.5-annexin V. METHODS: Efficiency of doxorubicin to OVCAR-8 cells in vitro was measured by MTT assay and flow cytometry. The in vivo studies were performed on an OVCAR-8 xenograft tumor model. Mice were divided into a control group and a treatment group. Each group was divided into 2 subgroups, DPA and annexin V. In the treatment group, the mice were treated with doxorubicin for 2 doses. All mice were performed optical imaging by Zn-DPA-PSS794 or Cy5.5-annexin V, respectively and then sacrificed. The tumor was separated and stained by HE. The expression of caspase-3 protein was measured by Western blot. RESULTS: The IC50 of doxorubicin to OVCAR-8 was 6 μmol/L. The percentage of apoptosis and dead cells was 35% after doxorubicin treatment. In the optical image, photons accumulated in the tumor either by Zn-DPA-PSS794 or Cy 5.5-annexin V in the treatment group. That was negative in the control group. The fluorescence intensity had significant difference between the 2 groups(P<0.001). The nuclei were big and stained with deep color after the cells were stained with HE. The caspase-3 expression was high in the treatment group, while it was low in the control group. CONCLUSION Zn-DPA-PSS794 as a probe used by optical imaging can monitor the efficiency of doxorubicin to OVCAR-8 xenograft tumor, which is similar to Cy5.5-annexin V.
Animals ; Apoptosis ; drug effects ; Carbocyanines ; Cell Line, Tumor ; Doxorubicin ; pharmacology ; Female ; Fluorescent Dyes ; Humans ; Infrared Rays ; Mice ; Mice, Nude ; Molecular Imaging ; Organometallic Compounds ; Ovarian Neoplasms ; pathology ; Picolines ; Spectroscopy, Near-Infrared ; methods

OBJECTIVE: To evaluate the potential and correlation between near-infrared fluorescence (NIRF) imaging using cyanine 5.5 conjugated with hydrophobically modified glycol chitosan nanoparticles (HGC-Cy5.5) and 18F-fluorodeoxyglucose-positron emission tomography (18F-FDG-PET) imaging of collagen-induced arthritis (CIA). MATERIALS AND METHODS: We used 10 CIA and 3 normal mice. Nine days after the injecting collagen twice, microPET imaging was performed 40 minutes after the intravenous injection of 9.3 MBq 18F-FDG in 200 microL PBS. One day later, NIRF imaging was performed two hours after the intravenous injection of HGC-cy5.5 (5 mg/kg). We assessed the correlation between these two modalities in the knees and ankles of CIA mice. RESULTS: The mean standardized uptake values of 18F-FDG for knees and ankles were 1.68 +/- 0.76 and 0.79 +/- 0.71, respectively, for CIA mice; and 0.57 +/- 0.17 and 0.54 +/- 0.20 respectively for control mice. From the NIRF images, the total photon counts per 30 mm2 for knees and ankles were 2.32 +/- 1.54 x 10(5) and 2.75 +/- 1.51 x 10(5), respectively, for CIA mice, and 1.22 +/- 0.27 x 10(5) and 0.88 +/- 0.24 x 10(5), respectively, for control mice. These two modalities showed a moderate correlation for knees (r = 0.604, p = 0.005) and ankles (r = 0.464, p = 0.039). Moreover, both HGC-Cy5.5 (p = 0.002) and 18F-FDG-PET (p = 0.005) imaging also showed statistically significant differences between CIA and normal mice. CONCLUSION: NIRF imaging using HGC-Cy5.5 was moderately correlated with 18F-FDG-PET imaging in the CIA model. As such, HGC-Cy5.5 imaging can be used for the early detection of rheumatoid arthritis.
Animals ; Ankle Joint/radionuclide imaging ; Arthritis, Experimental/*radionuclide imaging ; Carbocyanines/administration & dosage/*diagnostic use ; Chitosan/administration & dosage/*diagnostic use ; Fluorodeoxyglucose F18/administration & dosage/diagnostic use ; Injections, Intravenous ; Knee Joint/radionuclide imaging ; Male ; Mice ; Microscopy, Confocal ; Nanoparticles ; Positron-Emission Tomography/*methods ; Radiopharmaceuticals/administration & dosage/diagnostic use ; Statistics, Nonparametric

OBJECTIVETo detect the differentially expressed genes in human polycystic kidney by cDNA microarray.

METHODSThe PCR products of 8398 genes were spotted onto a chip in array. Both mRNAs isolated from polycystic kidney tissue and normal kidney tissue were reversely transcribed to cDNAs with the incorporation of fluorescent dUTP (Cy5-dUTP and Cy3-dUTP) for preparing the hybridization probes. The mixed probes were hybridized to the cDNA microarray. Then the cDNA microarray was scanned for the fluorescent signals and the display of differences between the 2 tissues. IGF1 mRNA, one of the up regulated genes was detected by in situ hybridization technique in the two tissues to validate the result from cDNA microarray.

RESULTSThe result indicated that the expressions of 263 genes were up regulated while the expressions of 94 genes were down regulated in the polycystic kidney tissue among the 8398 target genes. Bioinformatical analysis of those genes had been performed. The up-regulated genes were mainly the ones of oncogene, cellular skeleton and movement, apoptosis related protein, cell signal transduction protein, and cytokine. The down regulated genes were mainly the ones of anti-oncogene, DNA binding and transcription factors, cell signal transduction protein, and metabolism protein. The IGF1 mRNA expression detected by in situ hybridization was consequently consistent with the cDNA microarray.

CONCLUSIONcDNA microarray is an effective and quick method for studying differential expressed genes. Three hundred and fifty-seven differentially expressed genes with different functions were revealed in the polycystic kidney tissue, which may play some roles in the progression of polycystic kidney.

Carbocyanines ; chemistry ; Computational Biology ; DNA, Complementary ; chemistry ; genetics ; Fluorescent Dyes ; chemistry ; Gene Expression Profiling ; Humans ; In Situ Hybridization ; Insulin-Like Growth Factor I ; genetics ; Oligonucleotide Array Sequence Analysis ; methods ; Polycystic Kidney, Autosomal Dominant ; genetics ; Reproducibility of Results ; Reverse Transcriptase Polymerase Chain Reaction ; methods