Biomedical subjects

H-C Yang

Publications and source records attributed to H-C Yang.

4 recordsLinked to original sources

PubMed2006

A genome-wide study of preferential amplification/hybridization in microarray-based pooled DNA experiments.

Microarray-based pooled DNA methods overcome the cost bottleneck of simultaneously genotyping more than 100 000 markers for numerous study individuals. The success of such methods relies on the proper adjustment of preferential amplification/hybridization to ensure accurate and reliable allele frequency estimation. We performed a hybridization-based genome-wide single nucleotide polymorphisms (SNPs) genotyping analysis to dissect preferential amplification/hybridization. The majority of SNPs had less than 2-fold signal amplification or suppression, and the lognormal distributions adequately modeled preferential amplification/hybridization across the human genome. Comparative analyses suggested that the distributions of preferential amplification/hybridization differed among genotypes and the GC content. Patterns among different ethnic populations were similar; nevertheless, there were striking differences for a small proportion of SNPs, and a slight ethnic heterogeneity was observed. To fulfill appropriate and gratuitous adjustments, databases of preferential amplification/hybridization for African Americans, Caucasians and Asians were constructed based on the Affymetrix GeneChip Human Mapping 100 K Set. The robustness of allele frequency estimation using this database was validated by a pooled DNA experiment. This study provides a genome-wide investigation of preferential amplification/hybridization and suggests guidance for the reliable use of the database. Our results constitute an objective foundation for theoretical development of preferential amplification/hybridization and provide important information for future pooled DNA analyses.

Databases, Nucleic Acid↗

PubMed2006

Effects of hydrogen peroxide (H2O2) on alkaline phosphatase activity and matrix mineralization of odontoblast and osteoblast cell lines.

Hydrogen peroxide (H(2)O(2)), an oxidizing agent, has been widely used as a disinfectant. Recently, because of its reactive properties, H(2)O(2) has also been used as a tooth bleaching agent in dental care. This is a cause for concern because of adverse biological effects on the soft and hard tissues of the oral environment. To investigate the influence of H(2)O(2) on odontoblasts, the cells producing dentin in the pulp, we assessed cellular viability, generation of reactive oxygen species (ROS), alkaline phosphatase (ALP) activity, and nodule formation of an odontoblastic cell line (MDPC-23) after treatment with H(2)O(2), and compared those with the effects on preosteoblastic MC3T3-E1 cells. Cytotoxic effects of H(2)O(2) began to appear at 0.3 mmol/L in both MDPC-23 and MC3T3-E1 cells. At that concentration, the accumulation of intracellular ROS was confirmed by a fluorescent probe, DCFH-DA. Although more ROS were detected in MDPC-23, the increasing pattern and rate are similar between the two cells. When the cells were treated with H(2)O(2) at concentrations below 0.3 mmol/L, MDPC-23 displayed a significant increase in ALP activity and mineralized bone matrix, while MC3T3-E1 cells showed adverse effects of H(2)O(2). It is known that ROS are generally harmful by-products of aerobic life and represent the primary cause of aging and numerous diseases. These data, however, suggest that ROS can induce in vitro cell differentiation, and that they play a more complex role in cell physiology than simply causing oxidative damage.

Alkaline Phosphatase↗

PubMed2006

Peroxisome proliferator-activated receptor-gamma agonist is protective in podocyte injury-associated sclerosis.

We have previously observed increased expression of peroxisome proliferator-activated receptor gamma (PPARgamma) in podocytes in both rat and human sclerotic conditions. The aim of the present study was to investigate whether activation of PPARgamma can attenuate podocyte injury-associated glomerulosclerosis in vivo. Puromycin aminonucleoside nephropathy was induced in Sprague-Dawley rats. The animals then either received no further treatment (control group (CONT)); or the PPARgamma agonist, pioglitazone (Pio) starting at week 0 (P0); or Pio starting at week 6 (P6), with sacrifice at week 12. At week 12, urinary protein excretion and systolic blood pressure were similar in the three groups. Glomerular filtration rate and glomerulosclerosis were decreased in CONT and P0 at week 12, but preserved in P6 rats. PPARgamma expression in CONT at 12 weeks was increased in podocytes and in mesangial WT-1 cells in segmentally sclerotic glomeruli, with less Wilms' tumor 1 (WT-1) staining. In P6 rats, mesangial WT-1 staining was lessened, but podocyte staining was strongly accentuated. Delayed treatment with Pio partially restored podocyte staining and tended to decrease the ratio of proliferating cell nuclear antigen-positive to apoptotic cells in glomeruli. Both treatment groups showed significantly reduced infiltrating glomerular macrophages and plasminogen activator inhibitor-1 mRNA expression in cortex, with no change in transforming growth factor-beta1 and tissue inhibitor of metalloproteinase-1 mRNA. Pio also decreased renal cortical angiopoietin-like protein 4 expression to almost 20% of CONT group, associated with increased vascular endothelial-derived growth factor expression in glomeruli. We conclude that treatment with PPARgamma agonist has protective effects on progression of glomerulosclerosis.

Angiopoietin-Like Protein 4↗

PubMed2006

A comparison of individual genotyping and pooled DNA analysis for polymorphism validation prior to large-scale genetic studies.

Polymorphism validation is an important issue in genetic studies because only polymorphic markers provide useful information. We analyzed genetic data for 180 SNPs in the human major histocompatibility complex region in Caucasian and Taiwanese populations, and evaluated ethnic heterogeneity between these populations to illustrate the importance of polymorphism validation. An initial individual genotyping experiment (IGE) with 95 samples was compared with a DNA pooling allele-typing experiment (PAE) of 630 individuals for polymorphism validation based on authentic data sets. Afterwards, all samples were genotyped individually in a confirmation study. Under narrow (broad) polymorphism criteria, 24 (41) polymorphic SNPs in Caucasians could not be validated in the Taiwanese population, suggesting a 13% (23%) inconsistency rate and revealing a strong discrepancy between genetic backgrounds, probably due to ethnic heterogeneity. IGE yielded high sensitivity and specificity for polymorphism validation, but may be sensitive to sampling variation. PAE showed high sensitivity (97%) and specificity (100%) using a narrow polymorphism criterion, but reduced specificity (83%) using a broad criterion. Public domain polymorphism databases should therefore be used with caution and polymorphism validation should be performed routinely prior to conducting large-scale genetic studies. PAE is a cost-saving, reliable alternative to IGE for polymorphism validation, especially for a stringent polymorphism criterion.

Asian People↗