Identification of significantly different modules between permanent and deciduous teeth by network and pathway analyses.

The differences in genetic backgrounds between deciduous and permanent teeth might contribute to the differences in developmental processes, histological characteristics, and tooth life cycles. Here, we attempted to identify significantly different modules between permanent and deciduous teeth via network and pathway analyses. We identified 291 differentially expressed genes (DEGs) between permanent and deciduous teeth using significance analysis of microarray methods. Co-expression networks of DEGs were constructed by weighted gene co-expression network analysis (WGCNA). Three pathways with a significant number of DEGs and P value <0.01 were identified. Integrated co-expression network and pathway (pathway and adjacent gene) analyses were used to extract three pathway-related modules: the calcium signaling pathway-related, ECM-receptor interaction pathway-related, and neuroactive ligand-receptor interaction pathway-related modules. We also attempted to analyze the topological centralities (degree, closeness, stress, and betweenness) of co-expression networks and modules. Four genes (TMEM229A, PPAPDC1A, LEPREL1, and GAD1) and three pathway-related modules that were significantly different in the deciduous and permanent teeth showed similar properties and good centralities. The relative expression levels of key genes were validated, and the differential expression of TMEM229A, LEPREL1, and GAD1 was confirmed by reverse transcription-polymerase chain reaction (P < 0.05). In conclusion, the results of this study may provide a greater understanding of the molecular pathogenesis and potential biomarkers of the progression from deciduous to permanent teeth.

Analysis of gene expression patterns and levels in maize hybrids and their parents.

Heterosis has greatly contributed to conventional plant breeding and is widely used to increase crop plant productivity. However, although some studies have explored the mechanisms of heterosis at the genomic and transcriptome level, these mechanisms still remain unclear. The growth and development of maize seedlings and immature embryos have an important impact on subsequent production. This study investigated differentially expressed genes (DEGs) between parents and reciprocal hybrids in the seedling leaves, roots, and immature embryo 15 days after pollination using amplified fragment length polymorphism (AFLP)-based transcript profiling (cDNA-AFLP). We isolated 180, 170, and 108 genes from the leaves, roots, and immature embryos, respectively, that were differentially expressed between hybrids and parents. Sequencing and functional analysis revealed that 107 transcript-derived fragments in the roots and leaves and 90 in the immature embryos were involved in known functions, whereas many DEGs had roles in plant growth and development, photosynthesis, signal transduction, and seed germination. Quantitative reverse-transcription polymerase chain reaction analysis of relative expression levels between reciprocal hybrids and both parental genotypes of selected genes produced results that were consistent with cDNA-AFLP. We validated the expression patterns of 15 selected genes related to heterosis formation and revealed that most showed non-additive expression in one or both hybrids, including dominant, underdominant, and overdominant expression. This indicates that gene-regulatory interactions among parental alleles play an important role in heterosis during the early developmental stages of maize.

Correlation between serum YKL-40 levels and albuminuria in type 2 diabetes.

We explored the correlation between serum YKL-40 levels and albuminuria in type 2 diabetes mellitus (T2DM) and its clinical significance. This study used a cross-sectional survey method. According to the American Diabetes Association 2007 Clinical Practice Recommendations, 738 patients with T2DM were divided into three groups: a normoalbuminuria group [albumin-to-creatinine ratio (ACR) <30 µg/mg, N = 360], a microalbuminuria group (ACR 30-300 µg/mg, N = 246), and a macroalbuminuria group (ACR ≥ 300 µg/mg, N = 332). The serum YKL-40 levels were determined by a quantitative sandwich enzyme-linked immunosorbent assay in all the cases and in 210 control subjects. Serum YKL-40 levels were significantly higher in the T2DM group vs the control group (P < 0.05), the macroalbuminuria group vs the microalbuminuria group (P < 0.05), and the microalbuminuria group vs the normoalbuminuria group (P < 0.05). Serum YKL-40 levels correlated with ACR in all participants. Significant correlation of YKL-40 was found with ACR, 2-h plasma glucose, glycated hemoglobin, fasting blood glucose, homeostatic model assessment of insulin resistance index, systolic blood pressure, duration, diastolic blood pressure, age, triglycerides, and high-density lipoprotein cholesterol (r-values: 0.713, 0.524, 0.515, 0.467, 0.438, 0.409, 0.407, 0.374, 0.112, 0.097, and -0.123, respectively). ACR correlated with serum YKL-40 levels (Beta = 0.555, P < 0.001). YKL-40 may be involved in the occurrence and development of diabetic nephropathy and would be useful as a new marker for the disease.

Analysis of DNA methylation patterns and levels in maize hybrids and their parents.

Heterosis is the superior performance of heterozygous individuals and has been widely exploited in plant breeding, although the underlying regulatory mechanisms still remain largely elusive. To understand the molecular basis of heterosis in maize, in this study, roots and leaves at the seedling stage and embryos and endosperm tissues 15 days after fertilization of 2 elite hybrids and their parental lines were used to estimate the levels and patterns of cytosine methylation by the methylation-sensitive amplification polymorphism method. The relative total methylation levels were lower in all the tissues of all hybrids than their corresponding mid-parent values, and the number of demethylation events was higher in the hybrids. These results implied that the decreasing trend and demethylation in hybrids relative to their parents may enable the derepression and possibly expression of many genes that were associated with the phenotypic variation in hybrids. To further analyze the observed methylation pattern changes, a total of 63 differentially displayed DNA fragments were successfully sequenced. Basic Local Alignment Search Tool analysis showed that 11 fragments shared similarity with known functional proteins in maize or other plant species, including metabolism, transposon/retrotransposon, development, stress response, and signal transduction, which indicated that these genes might play a significant role in maize hybrid vigor.

Effect of CDH1 gene methylation on transforming growth factor (TGF-ß)-induced epithelial-mesenchymal transition in alveolar epithelial cell line A549.

The aim of this study was to investigate the specific molecular mechanism of the transforming growth factor ß (TGF-ß)-induced epithelial-mesenchymal transition in a lung cancer cell line, and to provide new ideas for targeting therapy of lung cancer. A549 cells were treated with different concentrations of TGF-ß and 5-aza-deoxycytidine (5-aza-dC). The morphological changes after the intervention were observed. The change in the expression of the epithelial marker E-cadherin (E-cad) was detected by Western blot. The proliferation of A549 cells was measured using the MTT assay. Cell movement and invasion capacity was evaluated with the cell scratch test and invasion test. TGF-ß induced A549 cells to transform to a mesenchymal cell morphology and downregulated the expression of E-cad, and 5-aza-dC inhibited this phenomenon. Compared with the control group, the number of transmembrane cells was higher and cell migration was markedly increased in the experimental group with continued culture in the presence of 10 ng/mL TGF-ß, showing significant differences (P < 0.05). CDH1 gene methylation is involved in TGF-ß-induced epithelial-mesenchymal transition in the alveolar epithelial cell line A549.