Biomedical subjects

Yan Xu

Publications and source records attributed to Yan Xu.

At least 55 records · Page 3Linked to original sources

PubMed2006

Photochemical approach to probing different DNA structures.

The various conformations of DNA--the A, B, and Z forms, the protein-induced DNA kink, and the G-quartet form--are thought to play important biological roles in processes such as DNA replication, gene expression and regulation, and the repair of DNA damage. The investigation of local DNA conformational changes associated with biological events is therefore essential for understanding the function of DNA. In this Minireview, we discuss the use of photochemical dehalogenation of 5-halouracil-containing DNA to probe the structure of DNA. Hydrogen abstraction by the resultant uracil-5-yl radicals is atom-specific and highly dependent on the structure of the DNA, suggesting that this photochemical approach could be applied as a probe of DNA conformations in living cells.

Crystallography, X-Ray↗

PubMed2006

C/EBPalpha is required for lung maturation at birth.

Epithelial cells lining the peripheral lung synthesize pulmonary surfactant that reduces surface tension at the air-liquid interface. Lack of surfactant lipids and proteins in the lungs causes respiratory distress syndrome, a common cause of morbidity and mortality in preterm infants. We show that C/EBPalpha plays a crucial role in the maturation of the respiratory epithelium in late gestation, being required for the production of surfactant lipids and proteins necessary for lung function. Deletion of the Cebpa gene in respiratory epithelial cells in fetal mice caused respiratory failure at birth. Structural and biochemical maturation of the lung was delayed. Normal synthesis of surfactant lipids and proteins, including SP-A, SP-B, SP-C, SP-D, ABCA3 (a lamellar body associated protein) and FAS (precursor of fatty acid synthesis) were dependent upon expression of the C/EBPalpha in respiratory epithelial cells. Deletion of the Cebpa gene caused increased expression of Tgfb2, a growth factor that inhibits lung epithelial cell proliferation and differentiation. Normal expression of C/EBPalpha required Titf1 and Foxa2, transcription factors that also play an important role in perinatal lung differentiation. C/EBPalpha participates in a transcriptional network that is required for the regulation of genes mediating perinatal lung maturation and surfactant homeostasis that is necessary for adaptation to air breathing at birth.

Animals↗

PubMed2006

Formation of the G-quadruplex and i-motif structures in retinoblastoma susceptibility genes (Rb).

The formation of G-quadruplex and i-motif structures in the 5' end of the retinoblastoma (Rb) gene was examined using chemical modifications, circular dichroism (CD) and fluorescence spectroscopy. It was found that substitutions of 8-methylguanine at positions that show syn conformations in antiparallel G-quadruplexes stabilize the structure in the G-rich strand. The complementary C-rich 18mer forms an i-motif structure, as suggested by CD spectroscopy. Based on the C to T mutation experiments, C bases participated in the C-C+ base pair of the i-motif structure were determined. Experiments of 2-aminopurine (2-AP) substitution reveal that an increase of fluorescence in the G-quadruplex relative to duplex is attributed to unstacked 2-AP within the loop of G-quadruplex. The fluorescence experiments suggest that formation of the G-quadruplex and i-motif can compete with duplex formation. Furthermore, a polymerase arrest assay indicated that formation the G-quadruplex structure in the Rb gene acts as a barrier in DNA synthesis.

5' Flanking Region↗

PubMed2006

Functional genomic responses to cystic fibrosis transmembrane conductance regulator (CFTR) and CFTR(delta508) in the lung.

Cystic fibrosis (CF), a common lethal pulmonary disorder in Caucasians, is caused by mutations in the cystic fibrosis transmembrane conductance regulator gene (CFTR) that disturbs fluid homeostasis and host defense in target organs. The effects of CFTR and delta508-CFTR were assessed in transgenic mice that 1) lack CFTR expression (Cftr-/-); 2) express the human delta508 CFTR (CFTR(delta508)); 3) overexpress the normal human CFTR (CFTR(tg)) in respiratory epithelial cells. Genes were selected from Affymetrix Murine Gene-Chips analysis and subjected to functional classification, k-means clustering, promoter cis-elements/modules searching, literature mining, and pathway exploring. Genomic responses to Cftr-/- were not corrected by expression of CFTR(delta508). Genes regulating host defense, inflammation, fluid and electrolyte transport were similarly altered in Cftr-/- and CFTR(delta508) mice. CFTR(delta508) induced a primary disturbance in expression of genes regulating redox and antioxidant systems. Genomic responses to CFTR(tg) were modest and were not associated with lung pathology. CFTR(tg) and CFTR(delta508) induced genes encoding heat shock proteins and other chaperones but did not activate the endoplasmic reticulum-associated degradation pathway. RNAs encoding proteins that directly interact with CFTR were identified in each of the CFTR mouse models, supporting the hypothesis that CFTR functions within a multiprotein complex whose members interact at the level of protein-protein interactions and gene expression. Promoters of genes influenced by CFTR shared common regulatory elements, suggesting that their co-expression may be mediated by shared regulatory mechanisms. Genes and pathways involved in the response to CFTR may be of interest as modifiers of CF.

Animals↗

PubMed2006

Adaptation and increased susceptibility to infection associated with constitutive expression of misfolded SP-C.

Mutations in the gene encoding SP-C (surfactant protein C; SFTPC) have been linked to interstitial lung disease (ILD) in children and adults. Expression of the index mutation, SP-C(Deltaexon4), in transiently transfected cells and type II cells of transgenic mice resulted in misfolding of the proprotein, activation of endoplasmic reticulum (ER) stress pathways, and cytotoxicity. In this study, we show that stably transfected cells adapted to chronic ER stress imposed by the constitutive expression of SP-C(Deltaexon4) via an NF-kappaB-dependent pathway. However, the infection of cells expressing SP-C(Deltaexon4) with respiratory syncytial virus resulted in significantly enhanced cytotoxicity associated with accumulation of the mutant proprotein, pronounced activation of the unfolded protein response, and cell death. Adaptation to chronic ER stress imposed by misfolded SP-C was associated with increased susceptibility to viral-induced cell death. The wide variability in the age of onset of ILD in patients with SFTPC mutations may be related to environmental insults that ultimately overwhelm the homeostatic cytoprotective response.

Animals↗

PubMed2006

Effect of surface hydrophobicity/hydrophilicity of mesoporous supports on the activity of immobilized lipase.

Taking advantage of the virtue of hydrophilic surface, lipase was firstly immobilized on SBA-15 as a support. Then the surface of the SBA-15 with enzyme entrapped inside the channels was modified by grafting with organic moieties. It has been found that the silylation with n-decyltrimethoxysilane (DE) and 3-(trimethoxysilyl)propyl methacrylate (MA) following the lipase immobilization increases the surface hydrophobicity. But the surface modified by MA shows more hydrophilicity than that modified by DE. The activity assay indicates that the hydrolytic activity for the hydrolysis of insoluble or partly soluble substrates increases with enhanced surface hydrophobicity.

Animals↗

PubMed2006

Production of galacto-oligosaccharides by immobilized recombinant beta-galactosidase from Aspergillus candidus.

The preparation of galacto-oligosaccharides (GOSs) was studied using the immobilized recombinant beta-galactosidase from Aspergillus candidus CGMCC3.2919. The optimal pH and temperature for the immobilized enzyme were observed at pH 6.5 and 40 degrees C, respectively. Increasing the initial lactose concentration increased the yield of GOSs. The dilution rate was found to be a key factor during the continuous production of GOSs. The maximum productivity, 87 g/L.h was reached when 400 g/L lactose was fed at dilution rate of 0.8/h. The maximum GOS yield reached 37% at dilution rate of 0.5/h. Continuous operation was maintained for 20 days in a packed-bed reactor without apparent decrease in GOS production. The average yield of GOSs was 32%, corresponding to the average productivity of 64 g/L.h, which implied that the immobilized recombinant beta-galactosidase has potential application for GOS production.

Aspergillus↗

PubMed2006

Carbon nanotube-enhanced separation of DNA fragments by a portable capillary electrophoresis system with contactless conductivity detection.

It was demonstrated that separation of DNA fragments by a CE-contactless conductivity detection system (CE-CCD) could be enhanced with multiple-wall carbon nanotubes (MWCNs) as buffer additive. For HaeIII digest of PhiX174 DNA, optimized MWCN concentration was obtained when the MWCN was above its threshold concentration, at which MWCN could form a network in the buffer as pseudostationary phase to provide additional interaction sites. In the case of larger DNA, MWCN near or below its threshold concentration was enough to provide great improvement of the resolution, which was shown by the separation of the 2-Log DNA ladder. Furthermore, the buffer containing MWCN could provide a more stable baseline in the CE-CCD system, owing to less fluctuation of its conductivity. Compared with CE-UV, CE-CCD with MWCN could provide lower LODs as well as better resolution.

Bacteriophage phi X 174↗

PubMed2006

Effects of Kanlijian on exercise tolerance, quality of life, and frequency of heart failure aggravation in patients with chronic heart failure.

OBJECTIVE: To observe the effects of conventional therapy combined with Kanlijian (KLJ) on exercise tolerance, quality of life and frequency of heart failure aggravation in patients with chronic heart failure (CHF). METHODS: Sixty CHF patients differentiated as sufferring from the syndrome of Xin-Shen Yang deficiency were included in the study and randomly assigned at the ratio of 2:1 into the KLJ group (n = 39) and the control group (n = 21). All the patients were treated with conventional therapy of Western medicine, but to those in the KLJ group, KLJ was medicated additionally one dose daily with 24 wks as one therapeutic course. The efficacy on TCM syndrome and changes of scores on TCM syndrome were observed after treatment. The indexes, including 6-minute walking distance (6MWD), quality of life (QOL, accessed by LHFQ scoring), NYHA grade, hemodynamic indexes and reducing/withdrawal rate of diuretic and digoxin before and after treatment were recorded and compared. Also the frequency of re-admission due to aggravation of heart failure in one year's time were observed. RESULTS: (1) The efficacy on TCM syndrome, improvement on scores of TCM syndrome, therapeutic effects on 6MWD, QOL, and NYHA grade in the KLJ group were superior to those in the control group. (2) Hemodynamic indexes after treatment, left ventricular fractional shortening (LVFS) and E peak/A peak (E/A), between the two groups had no significant difference, while left ventricular ejection fraction (LVEF) was increased significantly in the KLJ group, but with no obvious change in the control group. (3) The reducing/withdrawal rate of diuretic and digoxin in the KLJ group was significantly higher than that in the control group. (4) The 1-year frequency of re-admission significantly decreased in the KLJ group. CONCLUSION: The adjuvant treatment of KLJ on the basis of Western conventional therapy can significantly improve CHF patients' exercise tolerance, quality of life and cardiac function, reduce the dosage of diuretic and digoxin needed, and decrease the re-admission frequency due to aggravation of heart failure.

Digoxin↗

PubMed2006

Effect of antisense FosB and CREB on the expression of prodynorphin gene in rats with levodopa-induced dyskinesias.

The effects of antisense FosB and CREB intra-striatum injection on the expression of prodynorphin (PDyn) gene in striatal neurons of Levodopa-induced dyskinesias (LID) rats with Parkinson disease (PD) were explored. PD model in rats was established by 6-OHDA microinjection stereotaxically. The rats were treated with chronic intermittent Levodopa celiac injection for 28 days to get the LID rats. Antisense FosB and cAMP response element-binding protein (CREB) were injected into striatum of all rats respectively. In situ hybridization was used to measure the changes in the expression of PDyn mRNA in striatum and behavior changes were observed. The results showed after administration of antisense FosB, abnormal involuntary movement (AIM) was decreased and the expression of PDyn mRNA in striatum was increased in LID rats as compared with sense FosB group (P<0.01, respectively). As compared with the control group, the expression of PDyn mRNA in striatum was decreased by antisense CREB-treated LID group (P<0.01) and compared with sense CREB treated LID group, antisense CREB-treated LID group showed no changes in AIM scores and the expressions of PDyn mRNA (both P>0.05). In conclusion, FosB protein, which replaced the CREG, could regulate the expression of PDyn mRNA and play critical role in the pathogenesis of LID.

Animals↗

PubMed2006

Blocking of N-acetylglucosaminyltransferase V induces cellular endoplasmic reticulum stress in human hepatocarcinoma 7,721 cells.

N-acetylglucosaminyltransferase V (GnT-V) is an important tumorigenesis and metastasis-associated enzyme. To study its biofunction, the GnT-V stably suppressed cell line (GnT-V-AS/7,721) was constructed from 7,721 hepatocarcinoma cells in previous study. In this study, cDNA array gene expression profiles were compared between GnT-V-AS/7,721 and parental 7,721 cells. The data indicated that GnT-V-AS/7,721 showed a characteristic expression pattern consistent with the ER stress. The molecular mechanism of the ER stress was explored in GnT-V-AS/7,721 by the analysis on key molecules in both two unfolded protein response (UPR) pathways. For ATF6 and Ire1/XBP-1 pathway, it was evidenced by the up-regulation of BIP at mRNA and protein level, and the appearance of the spliced form of XBP-1. As for PERK/eIF2alpha pathway, the activation of ER eIF2alpha kinase PERK was observed. To confirm the results from GnT-V-AS/7,721 cells, the key molecules in the UPR were examined again in 7,721 cells interfered with the GnT-V by the specific RNAi treatment. The results were similar with those from GnT-V-AS/7721, indicating that blocking of GnT-V can specifically activate ER stress in 7,721 cells. Rate of (3)H-Man incorporation corrected with rate of (3)H-Leu incorporation in GnT-V-AS/7,721 was down-regulated greatly compared with the control, which demonstrated the deficient function of the enzyme synthesizing N-glycans after GnT-V blocking. Moreover, the faster migrating form of chaperone GRP94 associated with the underglycosylation, and the extensively changed N-glycans structures of intracellular glycoproteins were also detected in GnT-V-AS/7,721. These results supported the mechanism that blocking of GnT-V expression impaired functions of chaperones and N-glycan-synthesizing enzymes, which caused UPR in vivo.

Carcinoma, Hepatocellular↗

PubMed2006

The new models of the human telomere DNA in K+ solution revealed by NMR analysis assisted by the incorporation of 8-bromoguanines.

The structure of human telomeric DNA has been controversial: the solution structure in the presence of Na(+) has been reported to be antiparallel basket-type quadruplex by NMR, while the crystal structure in the presence of K(+) has been reported to be parallel propeller-type quadruplex. The solution structure in the presence of K(+) has drawn intense interest, as the intracellular K(+) concentration is higher than that of Na(+), but the structure is still open to address. Recently Sugiyama et al. has suggested that the DNA exists as a mixture of mixed-parallel/antiparallel quadruplex and antiparallel chair-type quadruplex on the basis of the combination of a series of 8-bromoguanine mutations and CD analysis. Here, we have started NMR analysis of the DNAs with the mutations to evaluate the proposed model. So far, NMR analysis is qualitatively consistent with the proposal. The structure determination is in progress to evaluate the model at atomic resolution.

DNA↗

PubMed2006

The recognition of higher-order G-quadruplex by chiral cyclic-helicene molecules.

The G-quadruplex structures represent a new class of molecular targets for DNA-interactive compounds that might be useful for targeting telomeres. Here we describe a study on the structure-based design of cyclic helicenes displaying chiral and steric selection in binding to higher-order G-quadruplexes. We propose a new ligand-binding site for G-quadruplex-binding compounds. These results provide proof of concept for small molecule inhibitors of telomerase associated with higher-order G-quadruplex structures.

Binding Sites↗

PubMed2006

Methods for investigating placental fatty acid transport.

Fatty acids (FAs), especially essential fatty acids (EFAs) and their long chain polyunsaturated fatty acid (LCPUFAs) derivatives, are critical for proper fetal development. The fetus relies on the placental transfer of EFAs from the maternal circulation for development. In fact, fatty acid transfer is highly directional from the mother to the fetus. Significant changes in placental fatty acid transport and metabolism, the two primary processes that govern placental FA supply from mother to fetus, can subsequently result in aberrant fetal fatty acid/lipid homeostasis and dramatically increase the risk of abnormal fetal development. Besides passive diffusion, specific fatty acid transfer conferring proteins can actively mediate directional placental fatty acid uptake and transport. Enzymes for fatty acid beta-oxidation and synthesis and the ones participating PUFA metabolism, including cytochrome P450 (mainly CYP4A), cyclooxygenases (COXs), and lipooxygenases (LOXs), have also been identified in the placenta. Methods for studying functional placental fatty acid uptake/transport/metabolism are discussed, focusing on an in vitro placental trophoblast model and long chain unsaturated fatty acids. The relevant theory of FA transport pathways, kinetic data analysis (uptake rates, permeability, influx/efflux ratio, Km, and so on) and high-performance liquid chromatography identification are also discussed.

Animals↗

PubMed2006

[Establishment of murine cell line transfected with human CD14 gene].

This study was aimed to construct the CD14 eukaryotic expression vector, establish the transgeneic CD14 positive cell line in order to facilitate the establishment of a mouse model of antibody targeting therapy for human acute monocytic leukemia (AML-M(5)). Total RNA extracted from peripheral blood mononuclear cells was treated with RNAase-free DNAase, the human CD14 gene was cloned and sequenced through the RT-PCR and T-A clone techniques. Eukaryotic expressional vector pcDNA3.1(+)/CD14 was constructed by cleaving with double restriction endonuleases and ligating with T4 ligase. A murine melanoma cell line B16 was transfected with the pcDNA3.1(+)/CD14 recombinant with Superfect transfection reagent. Positive clones were selected by G418 and the expression of human CD14 on the transfectant was confirmed by flow cytometry (FCM). The results indicated that the sequence of the human CD14 cDNA cloned was exact to be same as the one from GenBank database. The recombinant pcDNA3.1(+)/CD14 was identified with double-enzyme cleaving. The expression of the human CD14 on the transfectant (B16/CD14) was confirmed by FCM. In conclusion, the murine cell line B16/CD14 fransfected with human CD14 gene has been established which can be used for the study of human AML-M(5) antibody targeting therapy with mouse model.

Animals↗

PubMed2006

[The effect of propyl gallate on the activity of various antifungal drugs against filamentous fungi in vitro].

OBJECTIVE: The influence of an antioxidant, propyl gallate (PG), on the activity of amphotericin B (AMB), terbinafine (TBF), butenafine (BTF) and ketoconazole (KCZ) against ocular pathogenic filamentous fungi in vitro was investigated to determine whether PG could increase the antifungal activity. METHODS: Susceptibility tests were performed against 6 isolates of ocular pathogenic filamentous fungi (Fusarium solanae, Fusarium moniliforme, Fusarium poae, Fusarium oxysporum, Aspergillus fumigatus and Aspergillus flavus) and 2 quality control strains (Candida krusei ATCC 6258 and Cadida parapsilosis ATCC 22019) by the NCCLS M38-P broth microdilution method (MIC). PG was added to the incubation media at a final concentration of 400 microg/ml. Antifungal agents were serially two-fold diluted and final dilutions were made in 1640 and PG-1640 culture media to a concentration ranging from 0.0313 to 16 microg/ml for AMB, TBF, BTF and KCZ. One hundred microl of the corresponding diluted inoculum suspension was added to each well of the microdilution tray. The MIC end-point of AMB was determined as 100% growth reduction and the MIC end-point of TBF, BTF, KCZ and PG was determined as 75% growth reduction as compared with the turbidity produced by the control well. RESULTS: At a concentration of 400 microg/ml, PG did not show any antifungal activity under these experimental conditions. The combination of PG (400 microg/ml) with amphotericin B revealed a remarkably increased activity against all of the isolates of ocular pathogenic filamentous fungi and quality control strains. In the combination of PG with terbinafine, a remarkably increased activity was observed against Fusarium solanae, Fusarium poae, Fusarium oxysporum, Aspergillus fumigatu and Aspergillus flavus. The combination of PG with butenafine had remarkably synergistic effect against Fusarium solanae, but did not synergistic or even showed antagonistic effect for other isolates. The combination of PG with ketaconazole was synergistic against Fusarium solanae, but was antagonistic against all other isolates. CONCLUSIONS: Combination of PG and amphotericin has remarkably synergistic effect against all tested ocular pathogenic filamentous fungi isolates. Combination of PG and terbinafine has remarkably synergistic effect against some isolates. The PG-amphotericin combination and the PG-terbinafine combination may have a role in future studies of antifungal eye drops.

Amphotericin B↗

PubMed2006

[Loss of heterozygosity at chromosome 8p21-p23 in adenocarcinoma of gastric cardia].

Chromosome 8p21-p23 harbors tumor suppressor gene(s) implicated in multiple types of cancers. To investigate the involvement of the gene(s) in the carcinogenesis of adenocarcinoma of gastric cardia, loss of heterozygosity (LOH) for microsatellite markers at chromosome 8p21-p23 was examined. Laser capture microdissection (LCM) was used to obtain homogeneous tumor cells from 19 surgical specimens. Subsequently, genomic DNA extracted from the LCM-captured cells was amplified by multiple displacement amplification. Each tumor was assessed for allelic loss using 13 microsatellite markers. An overall LOH frequency of 63.2% (12/19) was observed and the LOH frequency for individual markers varied from 25% to 55.6%. One common deleted region of about 1.2 Mb (8p22GGAA-8p22ATCT) was defined. Our data indicated that the tumor suppressor gene at chromosome 8p22 might play an important role in the development of adenocarcinoma of gastric cardia.

Adenocarcinoma↗

PubMed2006

[Effects of periosteum, synovium and cartilage tissues on genes for joint cartilage regeneration].

OBJECTIVE: To study the effects of the periosteum,synovium and cartilage tissues on the gene expressions of proteoglycan, collagen II, and nuclear factor kappa B (NF-kappaB) and to investigate the different effects of these tissues on cartilage regeneration. METHODS: In 20 New Zealand white rabbits, 20 cartilage explants were taken from the knee joints in each rabbit, the size of which was 4 mm x 4 mm x 4 mm. All the cartilages were divided into the following 4 groups and cultured for 7 days: Group A, with 5 pieces (2 mm x 2 mm) of the synovium of the knee joints in each dish; Group B, with 5 pieces (2 mm x 2 mm) of the periosteum in each dish; Group C, with 5 pieces (2 mm x 2 mm x 2 mm) of the cartilage in each dish; and Group D, with no addition of other tissues (control group). RNA was extracted from the cells of the cartilage explants (4 mm x 4 mm x 4 mm) in all the dishes. The gene expressions of proteoglycan, collagen II and NF-kappaB were defected by a reverse transcription-polymerase chain reaction (RT-PCR). RESULTS: In group A, the gene expression of proteoglycan was significantly decreased. The relative density of this gene expression had a significant difference when compared with that in group D (1.09 +/- 0.21 vs. 1.25 +/- 0.25, P < 0.05); the gene expressions of collagen I and NF-kappaB were also decreased, but they had no significant differences when compared with those in group D (P > 0.05). In group B, the gene expressions of proteoglycan, collagen II, and NF-kappaB were significantly increased. The relative densities of these gene expressions were 1.60 +/- 0.26, 1.57 +/- 0.24, and 4.20 +/- 2.22, respectively, which had significant differences when compared with those in group D (P < 0.05). In group C, the relative density of the gene expression of collagen II was 1.43 +/- 0.28, which had a significant difference when compared with that in group D (P < 0.05), but the relative densities of the gene expressions of proteoglycan and NF-kappaB had no significant differences when compared with those in group D (P > 0.05). CONCLUSION: The results indicate that the periosteum can up-regulate the gene expressions of proteoglycan, collagen II and NF-kappaB. The NF-kappaB is likely to be an important nuclear transcription factor related to cartilage regeneration. The results also suggest that the periosteum may be better in facilitating the cartilage repair and regeneration in clinical practice.

Animals↗