Research Article

Table of Contents | Genet. Mol. Res. 2016 (3)

Displaying 76 - 90 of 361
Research Article

The dwarf and narrow-leaf rice (Oryza sativa L.) mutant dnl3 was isolated from the Japonica cultivar Zhonghua 11 (wild-type). dnl3 exhibited pleiotropic developmental defects. The narrow-leaf phenotype resulted from a marked reduction in the number of vascular bundles, while the dwarf stature was caused by the formation of foreshortened internodes and a reduced number of parenchyma cells. The suggestion that cell division is impaired in the mutant was consistent with the transcriptional behavior of various genes associated with cell division. The mutant was less responsive to exogenously supplied gibberellic acid than the wild-type, and profiling the transcription of genes involved in gibberellin synthesis and response revealed that a lesion in the mutant affected gibberellin signal transduction. The dnl3 phenotype was inherited as a single-dominant gene, mapping within a 19.1-kb region of chromosome 12, which was found to harbor three open reading frames. Resequencing the open reading frames revealed that the mutant carried an allele at one of the three genes that differed from the wild-type sequence by 2-bp deletions; this gene encoded a cellulose synthase-like D4 (CSLD4) protein. Therefore, OsCSLD4 is a candidate gene for DNL3. DNL3 was expressed in all of the rice organs tested at the heading stage, particularly in the leaves, roots, and culms. These results suggest that DNL3 plays important roles in rice leaf morphogenesis and vegetative development.

Genet. Mol. Res. 15(3): gmr8731
DOI: 10.4238/gmr.15038731
Research Article

Pecan (Carya illinoensis) has been introduced to East China for over one hundred years, but its planting is still only occurring at a small scale. The key limiting factor is its low yield. To enhance the yield pecan in East China, two pecan cultivars, Mahan and Western, were examined. Twenty traits describing phasic development, yield, nut quality, and cultural practice were investigated. We found that pecan cultivar Mahan gives a higher yield and nut quality than cultivar Western. We recommend interplanting of cultivar Pawnee to act as a pollinator tree. Appropriate cultivation practices that can be implemented to enhance fruit yield of cultivars Mahan and Western include soil-applied paclobutrazol (PBZ) at certain concentrations, pinching, and supplementary pollination. For example, the addition of 1.25 g/m2 of PBZ inhibits pecan branch growth and stimulates short bearing branches, which promotes fruit yield. We found that soil-applied PBZ reached optimal performance 82 days after application. A pinching length of 40 cm resulted in a fruit yield increase. In addition, grafting and transplantation may promote male flowering, but delays female flowering. These cultural practices may provide insights that can be used to improve pecan cultivation in East China.

Genet. Mol. Res. 15(3): gmr8732
DOI: 10.4238/gmr.15038732
Research Article

Fucosidosis is a rare lysosomal storage disorder inherited in an autosomal recessive manner. Its estimated frequency is below 1 in 200,000 live births. Its clinical phenotypes include progressive neurological and mental deterioration, coarse facial features, growth retardation, visceromegaly, angiokeratomas, and seizures. The disease is caused by mutations in the FUCA1 gene that lead to deficiency of a-L-fucosidase. Here, we describe the clinical and molecular features of a Thai boy with fucosidosis. Whole exome sequencing and array-based comparative genomic hybridization analysis revealed that the patient was compound heterozygous for a single base-pair deletion (c.670delC; p.P224LfsX2) inherited from his father, and a 3281-base-pair deletion covering exon 3 inherited from his mother. Neither mutation has been reported before so the FUCA1 mutational spectrum is herein expanded.

Genet. Mol. Res. 15(3): gmr8733
DOI: 10.4238/gmr.15038733
Research Article

The aim of this study was to examine the effect of polymorphisms in the cytochrome P450 (CYP) 2C19 gene (CYP2C19) on the Helicobacter pylori eradication rate in Brazilian patients with functional dyspepsia. Adults diagnosed with functional dyspepsia based on the ROME III criteria and infected with H. pylori were recruited to this study. The patients were subjected to gastrointestinal endoscopy and the H. pylori status was defined when both urease test and histopathology results were negative or positive. The patients were treated with proton pump inhibitor-based triple therapy (omeprazole, amoxicillin, and clarithromycin). CYP2C19*2 and CYP2C19*3 were genotyped by polymerase chain reaction-restriction fragment length polymorphism. One hundred and forty-eight patients (81.8% women) with a mean (± SD) age of 46.1 (12.2) years were included in this study. Based on the CYP2C19 genotypes, the patients were classified as homozygous extensive metabolizer (HomEM; 67.6%), heterozygous extensive metabolizer (HetEM; 26.3%), or poor metabolizer (PM; 6.1%). The H. pylori eradication rates in patients with HomEM, HetEM, and PM were 85.0, 89.7, and 100.0% (P = 0.376), respectively. The included study population comprised a high frequency of patients carrying the HomEM genotype. Although the genotypes of CYP2C19 variants were not statistically significant, the results of this study suggest a possible effect of the PM genotype on the efficacy of H. pylori eradication.

Genet. Mol. Res. 15(3): gmr8734
DOI: 10.4238/gmr.15038734
Research Article

Tumor necrosis factor-α (TNF-α) stimulates osteoclast differentiation and suppresses osteoblast differentiation, leading to bone loss and decreased bone mass in local inflammation areas in patients with rheumatoid arthritis. The growth factor progranulin (PGRN) is expressed in various types of cells and play crucial roles in the pathogenesis of atherosclerosis and arthritis by blocking TNF-α. Here, we investigated the role of PGRN in blocking TNF-α-mediated inhibition of osteoblast differentiation and the regulatory mechanism. C2C12 stem cell was induced by bone morphogenetic protein-2 (BMP-2) for osteoblast differentiation. A significant increase in ALP activity (P ColI, Ocn, and Bsp in the induced cells (P ColI, Ocn, and Bsp (P Runx2 (P Osx (P ATF4 (P

Genet. Mol. Res. 15(3): gmr8126
DOI: 10.4238/gmr.15038126
Research Article

We carried out a hospital-based case-control study to investigate the role of XRCC1 gene Arg399Gln, Arg280His, and Arg194Trp polymorphisms in susceptibility to gastric cancer. A total of 214 gastric cancer patients and 247 control subjects were recruited between March 2013 and March 2015, and polymorphism genotype frequencies were determined by polymerase chain reaction-restriction fragment length polymorphism. Using the chi-square test, we detected statistically significant differences in age (chi-square = 22.25, P XRCC1 Arg194Trp TT genotype conferred increased susceptibility to gastric cancer compared to the CC genotype [odds ratio (OR) = 2.38, 95% confidence interval (CI) = 1.28-4.49]. Moreover, individuals carrying the T allele of this variant were found to be at moderately increased risk of this disease (OR = 1.56, 95%CI = 1.16-2.09). However, the XRCC1 Arg399Gln and Arg280His polymorphisms were shown to have no influence on the development of gastric cancer. In conclusion, we suggest that the XRCC1 gene Arg194Trp polymorphism is associated with gastric cancer susceptibility in the Chinese population.

Genet. Mol. Res. 15(3): gmr8342
DOI: 10.4238/gmr.15038342
Research Article

Short tandem repeats (STRs) are commonly used as genetic markers. The detection and analysis of STRs can be used to gather information on polymorphisms of interest to forensic geneticists. Denaturing polyacrylamide gel electrophoresis (PAGE) is an affordable method for the detection of minor sequence changes in DNA, while capillary electrophoresis (CE) is the gold standard for genotyping analysis. This appears to be the first study to directly compare data obtained using the two electrophoretic techniques. We analyzed genomic DNA from 209 individuals to compare genotyping results from seven Combined DNA Index System (CODIS) STR markers obtained by both techniques. The automated electrophoresis was carried out using a MegaBACETM 1000 DNA analysis system. Full concordance was found in 1297 of 1308 STR allele calls. Kappa and McNemar-Bowker tests indicated that there were no statistically significant differences between the results from the two methods. There was no statistically significant difference in precision between denaturing PAGE followed by silver nitrate staining, despite a longer protocol, compared with CE when applied to population studies. STR allele frequency data from non-automated genotyping techniques seem to be just as reliable as from automated genotyping methods.

Genet. Mol. Res. 15(3): gmr8436
DOI: 10.4238/gmr.15038436
Research Article

Hepatocellular carcinoma is one of the most common malignant tumors worldwide; it is estimated that there were 782,000 new cases in 2012. MicroRNAs (miRNAs) play an important role in carcinogenesis by regulating oncogenes and tumor suppressors. We investigated the role of miR-146a, miR-196a2, and miR-499 polymorphisms in the risk of hepatocellular carcinoma in a Chinese population. Hepatocellular carcinoma patients (175) and healthy controls (302) were recruited between April 2013 and March 2015. Genotype analysis of miR-146a, miR-196a2, and miR-499 polymorphisms was carried out by polymerase chain reaction-restriction fragment length polymorphism. There was a significant difference between the genotype distribution of miR-196a2 in hepatocellular carcinoma patients and controls (X2 = 17.23, P

Genet. Mol. Res. 15(3): gmr8582
DOI: 10.4238/gmr.15038582
Research Article

Arachis pintoi and A. repens are legumes with a high forage value that are used to feed ruminants in consortium systems. Not only do they increase the persistence and quality of pastures, they are also used for ornamental and green cover. The objective of this study was to analyze microsatellite markers in order to access the genetic diversity of 65 forage peanut germplasm accessions in the section Caulorrhizae of the genus Arachis in the Jequitinhonha, São Francisco and Paranã River valleys of Brazil. Fifty-seven accessions of A. pintoi and eight of A. repens were analyzed using 17 microsatellites, and the observed heterozygosity (HO), expected heterozygosity (HE), number of alleles per locus, discriminatory power, and polymorphism information content were all estimated. Ten loci (58.8%) were polymorphic, and 125 alleles were found in total. The HE ranged from 0.30 to 0.94, and HO values ranged from 0.03 to 0.88. By using Bayesian analysis, the accessions were genetically differentiated into three gene pools. Neither the unweighted pair group method with arithmetic mean nor a neighbor-joining analysis clustered samples into species, origin, or collection area. These results reveal a very weak genetic structure that does not form defined clusters, and that there is a high degree of similarity between the two species.

Genet. Mol. Res. 15(3): gmr8601
DOI: 10.4238/gmr.15038601
Research Article

In this study, we investigated the correlation between serum chemokine (C-C motif) ligand 18 (CCL-18) and the prognosis as well as clinical characteristics of breast cancer. Blood samples from 207 breast cancer patients, 126 individuals with benign breast tumors, and 93 healthy women were collected. Serum CCL-18 expression was detected by enzyme-linked immunosorbent assay. Mann-Whitney’s U tests were carried out to analyze the relationship between serum CCL-18 and clinicopathological variables. The Kaplan-Meier method was used to evaluate the overall survival (OS), whereas differences between groups were analyzed by log-rank tests. The COX proportional hazard regression model was used to determine the association between clinicopathological characteristics and survival. We found that serum CCL-18 was significantly higher in breast cancer patients (290.06 ± 89.52 pg/mL) as compared to that in individuals with benign tumors (170.14 ± 26.57 pg/mL) or healthy women (119.36 ± 38.77 pg/mL) (P

Genet. Mol. Res. 15(3): gmr8632
DOI: 10.4238/gmr.15038632
Research Article

The aim of this study was to identify the possible correlation between polymorphisms in matrix metalloproteinase (MMP)-1 and MMP-3 and their corresponding protein levels in disc tissues obtained from patients with lumbar disc herniation (LDH) using biochemical and immunohistochemical analyses. Blood and disc samples were obtained from 100 patients with LDH who underwent a lumbar microdiscectomy. Based on the radiological degeneration, the patients were diagnosed with grade 2, 3, or 4 LDH. MMP-1 -1607 1G/2G and MMP-3 -1171 5A/6A were analyzed by real-time polymerase chain reaction. The expressions of MMP-1 and MMP- 3 were detected by biochemical and immunohistochemical analyses. We found no association between the MMP-1 polymorphism and disc degeneration and MMP-1 expression. However, patients expressing the 6A/6A and 5A/6A alleles of MMP-3 -11715A/6A showed higher MMP-3 expression, compared to those expressing the 5A/5A genotype. Additionally, the radiological degeneration grades were correlated with the histological degeneration scoring. Protein levels and immunopositive cell rates of MMP-1 and MMP-3 were associated with disc degeneration grades. Moreover, the MMP-1 and MMP-3 expression and the histological and radiological scores were positively correlated and the MMP-3 -11715A/6A polymorphism was associated with MMP-3 expression in herniated disc tissues. This study is the first to investigate polymorphisms in MMP-1 and MMP-3, as well as their corresponding protein expressions. We also quantified an association between the radiological degeneration grades and MMP-1 and MMP- 3 expression. Further genomic studies on MMPs could focus on the utilization of MMP-1 and MMP-3 as markers for the prevention and treatment of this disease.

Genet. Mol. Res. 15(3): gmr8669
DOI: 10.4238/gmr.15038669
Research Article

In this research, compound Maqin decoction (CMD) has been shown to positively affect in airway inflammation of asthma models. We evaluated the effects of CMD on the expression of transforming growth factor (TGF)-β1/Smad proteins, interleukin (IL)-17, and IL-10 in lung tissue of asthmatic rats. Asthma was induced in a rat model using ovalbumin. After a 4-week treatment with CMD, rats were killed to evaluate the expression of TGF-β1 and Smad proteins in lung tissue. IL-10 and IL-17 levels in lung tissue homogenates were determined by ELISA. The expression of TGF-β1 and Smad3 protein increased, whereas expression of Smad7 protein decreased upon high-dose or low-dose treatment with CMD or by intervention with dexamethasone, compared to the control. There was a significant difference between treatment with a high dose CMD and the control treatment, but no significant difference was found between high-dose CMD treatment and dexamethasone intervention. The expression of TGF-β1 and Smad7 protein increased, whereas the expression of Smad3 protein decreased in the model group compared to other groups. In the CMD high-dose group, low-dose group, and dexamethasone intervention group, the IL-17 concentrations in lung tissue homogenates were decreased, while IL-10 levels were increased. Again, there was a significant difference between CMD high-dose and control treatment, but not between CMD high-dose treatment and dexamethasone intervention. Thus, positive effects of CMD against asthmatic airway remodeling may be due to its regulatory effect on TGF-β1, Smad3, and Smad7 protein levels and on cytokines such as IL-10 and IL-17.

Genet. Mol. Res. 15(3): gmr7539
DOI: 10.4238/gmr.15037539
Research Article

Biliary atresia (BA) is a destructive bile duct disease occurring in newborn children within a few weeks after birth. In this study, the effect of miR-29c and miR-129-5p on epithelial-mesenchymal transition (EMT) in experimental BA was explored by constructing BA mouse models via Rhesus rotavirus vaccine infection. miR-29c and miR-129-5p expression was analyzed by real-time quantitative polymerase chain reaction. EMT was established by induction with transforming growth factor (TGF)-β1. miR-29c and miR-129-5p were overexpressed and inhibited, respectively, by Lipofectamine transfection. EMT-related protein (formin-like 2, FMNL2; E-cadherin; vimentin; and cytokeratin-19, CK-19) expression was analyzed by western blot and immunofluorescent assay. The results indicated that miR-29c and miR-129-5p were downregulated and upregulated in BA mice. TGF-β1 induction caused a time-dependent decrease and increase in miR-29c and miR-129-5p, respectively. Additionally, TGF-β1 induced an increase in FMNL2 and vimentin expression and a decrease in E-cadherin and CK-19 expression (P 0.05). Thus, miR-29c upregulation or miR-129-5p downregulation effectively prevented EMT in BA by regulating the expression of EMT pathway-related proteins. Therefore, miR-29c and miR-129-5p could be utilized as therapeutic targets for BA in the future.

Genet. Mol. Res. 15(3): gmr7753
DOI: 10.4238/gmr.15037753
Research Article

The aim of this study was to investigate the expression of T-cell immunoglobulin mucin domain molecule-3 (Tim-3) in osteosarcoma tissues, and analyze its effect on cell proliferation and metastasis in an osteosarcoma cell line. Tim-3 mRNA and protein expression in osteosarcoma tissue was detected by reverse transcriptase-polymerase chain reaction and immunohistochemistry, respectively. Additionally, the cell viability, apoptosis rate, and invasive ability of the osteosarcoma cell line MG-63 were tested using the methyl thiazolyl tetrazolium assay, Annexin V-propidium iodide flow cytometry, and a Transwell assay, respectively, following Tim-3 interference using small interfering RNA (siRNA). We also analyzed the expression of Snail, E-cadherin, vimentin, and nuclear factor (NF)-kB in the cells by western blot. We observed that Tim-3 mRNA and protein was significantly overexpressed in osteosarcoma tissues, compared to the adjacent normal tissue (P

Genet. Mol. Res. 15(3): gmr7844
DOI: 10.4238/gmr.15037844
Research Article

The aim of this study was to determine the association between two SNPs (rs2235371 and rs2013162) in the interferon regulatory factor 6 (IRF6) gene and non-syndromic cleft palate (NSCP) in northeast China. We genotyped these two SNPs in 104 NSCP cases, as well as in 178 parents and 300 controls. Case-control and case-parent analyses were performed using χ2 tests and family-based association tests (FBAT). Results indicated that there were significant differences in both genotypic and allelic distributions between patients and controls at rs2235371 and rs2013162 in the IRF6 gene. Case-parent analysis revealed over-transmission of the C allele in rs2235371 and the A allele in rs2013162. Lastly, FBAT showed over-transmission of the CA haplotype. This study demonstrated that the two SNPs, rs2235371 and rs2013162, are strongly associated with NSCP in the northeast Chinese population.

Genet. Mol. Res. 15(3): gmr8210
DOI: 10.4238/gmr.15038210