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Biomedical subjects

Song Li

Publications and source records attributed to Song Li.

At least 91 records · Page 5Linked to original sources
PubMed2004

LUCY2: an interactive DNA sequence quality trimming and vector removal tool.

UNLABELLED: Lucy2 is a raw DNA sequence trimming and visualization tool based on the popular command-line Lucy1. Users can change parameters, trim multiple sequences and visualize the results within an integrated, easy-to-use graphical user interface. Lucy2 is designed specifically for non-programmers to use, and is currently available on Windows, Linux and MacOS X. Source code is also available for porting to the other platforms. AVAILABILITY: Lucy2 is distributed under the GNU General Public License and can be downloaded from www.complex.iastate.edu

Algorithms↗
PubMed2004

Microarray-based method for genotyping of functional single nucleotide polymorphisms using dual-color fluorescence hybridization.

Screening disease-related single nucleotide polymorphism (SNP) markers in the whole genome has great potential in complex disease genetics and pharmacogenetics researches. It has led to a requirement for high-throughput genotyping platforms that can maximize the efficient screening functional SNPs with respect to accuracy, speed and cost. In this study, we attempted to develop a microarray-based method for scoring a number of genomic DNA in parallel for one or more molecular markers on a glass slide. Two SNP markers localized to the methylenetetrahydrofolate reductase gene (MTHFR) were selected as the investigated targets. Amplified PCR products from nine genomic DNA specimens were spotted and immobilized onto a poly-l-lysine coated glass slide to fabricate a microarray, then interrogated by hybridization with dual-color probes to determine the SNP genotype of each sample. The results indicated that the microarray-based method could determine the genotype of 677 and 1298 MTHFR polymorphisms. Sequencing was performed to validate these results. Our experiments successfully demonstrate that PCR products subjected to dual-color hybridization on a microarray could be applied as a useful and a high-throughput tool to analyze molecular markers.

Fluorescent Dyes↗
PubMed2004

Targeted delivery of antisense oligodeoxynucleotides to folate receptor-overexpressing tumor cells.

A major problem in exploring the full potential of antisense ODN is the lack of a safe and efficient delivery system. In this study a new method has been developed that is highly efficient in encapsulating ODN inside folate receptor (FR)-targeted lipid vesicles. ODN formulated in these vesicles were efficiently protected from degradation by nucleases compared to free ODN. Folate efficiently mediated intracellular delivery of ODN to KB tumor cells that overexpress FR. Delivery of EGFR antisense ODN via FR-targeted lipid vesicles resulted in a significant down-regulation of EGFR expression in KB cells and cell growth inhibition, far more efficient than that with free ODN or ODN encapsulated in ligand-free lipid vesicles. Intracellular delivery of EGFR antisense ODN also sensitized KB cells to doxorubicin (DOX) treatment. Thus targeted delivery of ODN via this novel lipid vector may have potential in treating tumors that overexpress FR.

Blotting, Western↗
PubMed2004

PKHD1 protein encoded by the gene for autosomal recessive polycystic kidney disease associates with basal bodies and primary cilia in renal epithelial cells.

Mutations of the polycystic kidney and hepatic disease 1 (PKHD1) gene have been shown to cause autosomal recessive polycystic kidney disease (ARPKD), but the cellular functions of the gene product (PKHD1) remain uncharacterized. To illuminate its properties, the spatial and temporal expression patterns of PKHD1 were determined in mouse, rat, and human tissues by using polyclonal Abs and mAbs recognizing various specific regions of the gene product. During embryogenesis, PKHD1 is widely expressed in epithelial derivatives, including neural tubules, gut, pulmonary bronchi, and hepatic cells. In the kidneys of the pck rats, the rat model of which is genetically homologous to human ARPKD, the level of PKHD1 was significantly reduced but not completely absent. In cultured renal cells, the PKHD1 gene product colocalized with polycystin-2, the gene product of autosomal dominant polycystic disease type 2, at the basal bodies of primary cilia. Immunoreactive PKHD1 localized predominantly at the apical domain of polarized epithelial cells, suggesting it may be involved in the tubulogenesis and/or maintenance of duct-lumen architecture. Reduced PKHD1 levels in pck rat kidneys and its colocalization with polycystins may underlie the pathogenic basis for cystogenesis in polycystic kidney diseases.

Adult↗
PubMed2004

Poly(ethylene glycol) as solvent for transition metal mediated living radical polymerisation.

The use of poly(ethylene glycol)(PEG) with low molecular weights as a novel solvent for the transition metal mediated radical polymerisation of methyl methacrylate and styrene is reported. The utilisation of PEG leads to polymerisation kinetics that differ from those observed with more traditional organic solvents. Moreover, the amount of residual copper catalyst in the product is greatly reduced by precipitation of the polymer in ethanol.

Journal Article↗
PubMed2004

Colorimetric silver detection of methylation using DNA microarray coupled with linker-PCR.

BACKGROUND: Aberrant DNA methylation of CpG site is among the earliest and most frequent alterations in cancer. Detection of promoter hypermethylation of cancer-related genes may be useful for cancer diagnosis or the detection of recurrence. Recently, several DNA microarray methods have been developed to detect the methylation status of the multiple genes. However, the microarrays are currently detected in fluorescence using a sophisticated laser-based scanner. These methods are limited by their lower sensitivity. METHODS: We present a sensitive colorimetric silver method coupled with linker-PCR to detect methylation status of four genes, including p16, E-cadherin, VHL, and hMLH1. The signal generated with this method results from the precipitation of silver onto nanogold particles bound to streptavidin used to detect biotinylated DNA. RESULTS: We show that p16, E-cadherin, VHL, and hMLH1 were all methylated in the positive control. However, no methylation was found in these genes for the negative control. P16 gene was only methylated in the sample, whereas others were not methylated. Furthermore, as little as 0.1 fmol of target DNA amplicons could be detected on the arrays. The results were further validated by methylation-specific PCR (MSP) and bisulfite DNA sequencing. CONCLUSIONS: The colorimetric silver detection of DNA microarray could be used as an inexpensive, useful, and sensitive tool to detect methylation status of the multiple genes in the future.

Adaptor Proteins, Signal Transducing↗
PubMed2004

Rho mediates the shear-enhancement of endothelial cell migration and traction force generation.

The migration of vascular endothelial cells in vivo occurs in a fluid dynamic environment due to blood flow, but the role of hemodynamic forces in cell migration is not yet completely understood. Here we investigated the effect of shear stress, the frictional drag of blood flowing over the cell surface, on the migration speed of individual endothelial cells on fibronectin-coated surfaces, as well as the biochemical and biophysical bases underlying this shear effect. Under static conditions, cell migration speed had a bell-shaped relationship with fibronectin concentration. Shear stress significantly increased the migration speed at all fibronectin concentrations tested and shifted the bell-shaped curve upwards. Shear stress also induced the activation of Rho GTPase and increased the traction force exerted by endothelial cells on the underlying substrate, both at the leading edge and the rear, suggesting that shear stress enhances both the frontal forward-pulling force and tail retraction. The inhibition of a Rho-associated kinase, p160ROCK, decreased the traction force and migration speed under both static and shear conditions and eliminated the shear-enhancement of migration speed. Our results indicate that shear stress enhances the migration speed of endothelial cells by modulating the biophysical force of tractions through the biochemical pathway of Rho-p160ROCK.

Animals↗
PubMed2004

Effects of the Trp64Arg polymorphism in the beta3-adrenergic receptor gene on insulin sensitivity in small for gestational age neonates.

To evaluate whether the Trp64Arg polymorphism in the beta3-adrenergic receptor (AR) gene is associated with decreased birth weight and might account for some of the association between birth weight and impaired insulin sensitivity, the beta3-AR genotype was assessed in 296 neonates of singleton pregnancies, including 76 neonates classified as small for gestational age (SGA) and 220 neonate classified as appropriate for gestational age (AGA). Fasting glucose and insulin levels were measured on d 3 after birth. The insulin levels and insulin-to-glucose ratio were significantly higher in the SGA group than in the AGA group. Frequency of the Trp64Arg allele was similar in the AGA and SGA groups (0.15 and 0.17, respectively). Moreover, when we adjusted for sex and gestational age, there was no significant difference in birth weight, fasting glucose, insulin levels, or insulin-to-glucose ratio between those with and without the mutation. However, in the SGA group, carriers of the Trp64Arg allele had significantly higher fasting insulin levels and insulin-to-glucose ratios than noncarriers (17.54 +/- 2.11 vs. 13.18 +/- 1.47 microIU/ml, P < 0.05; and 4.89 +/- 0.60 vs. 3.14 +/- 0.42, P < 0.05, respectively), whereas no association was detected for this polymorphism in the AGA group.SGA is an important factor that predisposes to insulin resistance, and the Trp64Arg beta3-AR gene polymorphism may contribute to insulin resistance associated with reduced fetal growth.

Diabetes Mellitus, Type 2↗
PubMed2004

The changing tails of a novel short interspersed element in Aedes aegypti: genomic evidence for slippage retrotransposition and the relationship between 3' tandem repeats and the poly(dA) tail.

A novel family of tRNA-related SINEs named gecko was discovered in the yellow fever mosquito, Aedes aegypti. Approximately 7200 copies of gecko were distributed in the A. aegypti genome with a significant bias toward A + T-rich regions. The 3' end of gecko is similar in sequence and identical in secondary structure to the 3' end of MosquI, a non-LTR retrotransposon in A. aegypti. Nine conserved substitutions and a deletion separate gecko into two groups. Group I includes all gecko that end with poly(dA) and a copy that ends with AGAT repeats. Group II comprises gecko elements that end with CCAA or CAAT repeats. Members within each group cannot be differentiated when the 3' repeats are excluded in phylogenetic and sequence analyses, suggesting that the alterations of 3' tails are recent. Imperfect poly(dA) tail was recorded in group I and partial replication of the 3' tandem repeats was frequently observed in group II. Genomic evidence underscores the importance of slippage retrotransposition in the alteration and expansion of the tandem repeat during the evolution of gecko sequences, although we do not rule out postinsertion mechanisms that were previously invoked to explain the evolution of Alu-associated microsatellites. We propose that the 3' tandem repeats and the poly(dA) tail may be generated by similar mechanisms during retrotransposition of both SINEs and non-LTR retrotransposons and thus the distinction between poly(dA) retrotransposons such as L1 and non-poly(dA) retrotransposons such as I factor may not be informative.

Aedes↗
PubMed2004

[The expression of TGF-beta 1 mRNA in pubescent rhesus monkeys' condyle under Class III intermaxillary functional orthopedic force].

OBJECTIVE: To investigate the expression of TGF-beta 1 mRNA in pubescent Rhesus monkeys' condylar under Class III intermaxillary functional orthopedic force for different lengths of time. METHODS: Six pubescent Rhesus monkey were divided into two test groups and a control group. Monkeys in the test groups were TMAIII while the control groups did not. Histological method (HE staining) and in situ hybridization were employed in this study. RESULTS: 1. The histological results showed that, compared with the control group, the anterior part of the condyle became thicker while the median part and the posterior part became thinner in 3 months group. However, in 6 months group, the change was similar to 3 months group. 2. The results of in situ hybridization showed that, in control group, TGF-beta 1 mRNA mildly expressed in the anterior part of the condyle while extensively in the median and posterior parts. In 3 months group, TGF-beta 1 mRNA expressed in all parts of condyle; the most intensive expression was in the anterior part. Compared with 3 months group, the expression of TGF-beta 1 mRNA decreased in 6 months group, but the expression in anterior part was stronger than in median and posterior parts. CONCLUSION: Under Class III Orthopedic therapy, TGF-beta 1 mRNA probably participated in the endochrondral bone remodeling in the condyle, and the expression was closely related to loading time. In 3 months group, the expression of TGF-beta 1 mRNA was stronger than that in 6 months group. It was inferred that the remodeling of endochrondral bone was more active in 3 months group.

Animals↗
PubMed2004

A model of 3D-structure of H+, K+-ATPase catalytic subunit derived by homology modeling.

AIM: To build a model of 3D-structure of H(+), K(+)-ATPase catalytic subunit for theoretical study and anti-ulcer drug design. METHODS: The model was built on the basis of structural data from the Ca(2+)-ATPase. Structurally conserved regions were defined by amino acid sequence comparisons, optimum interconnecting loops were selected from the protein databank, and amino (N)- and carboxyl (C)-terminal ends were generated as random coil structures. Applying molecular mechanics method then minimized the model energy. Molecular dynamics technique was used to do further structural optimization. RESULTS: The model of 3D-structure of H(+), K(+)-ATPase was derived. The model is reasonable according to several validation criteria. There were ten transmembrane helices (TM1-TM10) in the model and inhibitor-binding site was identified on the TM5-8 riched negatively charged residues. CONCLUSION: The 3D-structure model from our study is informative to guide future molecular biology study about H(+), K(+)-ATPase and drug design based on database searching.

Amino Acid Sequence↗
PubMed2004

Effects of a fatty acid synthase inhibitor on adipocyte differentiation of mouse 3T3-L1 cells.

AIM: To investigate the influence of C75, a fatty acid synthase inhibitor, on adipocyte differentiation. METHODS: Mouse 3T3-L1 preadipocytes were induced to differentiation by insulin, isobutylmethylxanthine, and dexamethasone. Oil red O staining was performed and activity of glycerol-3-phosphate dehydrogenase (GPDH) was measured. The level of peroxisome proliferators-activated receptor gamma (PPARgamma) mRNA was assayed by semi-quantitative reverse transcription PCR. RESULTS: C75 blocked the adipogenic conversion in a dose-dependent manner and the inhibitory effects occurred both in the early phases (48 h) and in the latter phases (8 d) of the process. Treatment with C75 for 8 d induced more decrease in lipid content than 48 h (P<0.01). Treatment with C75 50 mg/L for 48 h or 8 d decreased GPDH activity by 52.8 % and 31.2 % of Vehicle, respectively. Treatment with C75 10-50 mg/L for 48 h or 8 d down-regulated PPARgamma mRNA expression compared with control (P<0.01). CONCLUSION: C75 blocked the adipocyte differentiation, which was related with down-regulation of PPARgamma mRNA.

3T3 Cells↗
PubMed2004

[DSRAD gene mutations in three families with dyschromatosis symmetrica hereditaria].

OBJECTIVE: To identify the DSRAD gene; mutations in three Chinese families with dyschromatosis symmetrica hereditaria. METHODS: All exons of DSRAD gene were analyzed in each person of these families with PCR-DNA sequencing. DNA samples from 100 unrelated, normally pigmented adult individuals were also included as control. RESULTS: We identified a missense mutation of C3220T (R1074C) in DSRAD gene in family A, and another missense mutation of G3325T (D1109Y) in DSRAD gene in family B and C. No same mutation was found in unaffected individuals in the families and the controls. CONCLUSION: We found two special missense mutations in DSRAD gene in three families of dyschromatosis symmetrica hereditaria. These mutations may impair DSRAD protein function, and as a consequence, cause skin dyschromatosis.

Adenosine Deaminase↗
PubMed2004

[Acquisition of Mutans streptococci by children of 3-4 years with possible source of the pathogen from their mothers].

OBJECTIVE: The aim of this study was to investigate the prevalence of Mutans streptococci (MS) in children of 3-4 years and thus reveal the relationship between the children's acquisition of MS and their mothers' pathogen. METHODS: Fifty mother-child pairs were selected, examined and divided into three groups according to the children's caries. MS in plaque and mothers' salivary samples were detected by MSB medium. Then 200 MS strains from 20 mothers-children were analyzed by AP-PCR. RESULTS: Acquisition of MS was identified in 37 of 50 children (74%), including 11 of 24 caries-free children and all 26 children with caries. The difference was significant (P<0.01). Genotypes showed that 16 of 37 children (43.2%) had the same fingerprint as their mothers'. The level of MS identified in mothers' salivary sample was lower than that in mothers' plaque sample (32% and 56%). CONCLUSION: These results suggested that caries in children of 3-4 years are closely related with MS acquisition. Mothers are still their important source of MS. The sensitivity of mothers' salivery samples is much lower than that of plaque samples in studying the transmission of MS.

Adult↗
PubMed2003

Inhibition of LPS- and CpG DNA-induced TNF-alpha response by oxidized phospholipids.

Lipid oxidation is commonly seen in the innate immune response, in which reactive oxygen intermediates are generated to kill pathogenic microorganisms. Although oxidation products of phospholipids have generally been regarded to play a role in a number of chronic inflammatory processes, several studies have shown that oxidized phospholipids inhibit the LPS-induced acute proinflammatory response in cultured macrophages and endothelial cells. We report in this study that oxidized 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphorylcholine (PAPC), but not nonoxidized PAPC, significantly inhibits the LPS-induced TNF-alpha response in intact mice. Oxidized PAPC also inhibits the 2'-deoxyribo(cytidine-phosphate-guanosine) (CpG) DNA-induced TNF-alpha response in cultured macrophages and intact mice. To elucidate the mechanisms of action, we show that oxidized PAPC, but not nonoxidized PAPC, inhibits the LPS- and CpG-induced activation of p38 MAPK and the NF-kappaB cascade. These results suggest a role for oxidized lipids as a negative regulator in controlling the magnitude of the innate immune response. Further studies on the mechanisms of action may lead to development of a new type of anti-inflammatory drug for treatment of acute inflammatory diseases such as sepsis.

Animals↗
PubMed2003

Enhanced cell attachment and osteoblastic activity by P-15 peptide-coated matrix in hydrogels.

The cells in bone grow on a composite matrix made up of mineral and organic (mainly type-I collagen) components. In this study, anorganic bone mineral (ABM) particles were coated with a cell-binding domain of type-I collagen (P-15 peptide) to mimic the bone matrix components and suspended in injectable hyaluronate (Hy) hydrogels. The ABM/P-15/Hy was compared to ABM/Hy-the same matrix without P-15 peptide. Osteoblast-like HOS cells migrated through the hydrogels around ABM/P-15 or ABM particles; however, more cells adhered to ABM/P-15/Hy particles, and the cells formed better surface coverage and had more stress fibers on ABM/P-15/Hy. HOS cells cultured on ABM/P-15/Hy had increased osteogenic gene expression for alkaline phosphatase and bone morphogenetic proteins, and deposited more mineralized matrix. Studies with two different hydrogels (carboxymethylcellulose and sodium alginate) showed similar enhanced cell attachment and mineralization. The studies suggest that the ABM/P-15 in hydrogels can be used as an injectable biomimetic matrix to facilitate bone repair.

Biomimetic Materials↗