Research Article

Table of Contents | Genet. Mol. Res. 2016 (2)

Displaying 91 - 105 of 482
Research Article

Recombinant human anti-tumor necrosis factor (TNF)-α scFv-Fc was expressed in TKO mutant Arabidopsis thaliana seeds using plant-specific codons. Immunoblotting using a human IgG1 antibody detected the expression of anti-TNF-α proteins in plants. Results from qRT-PCR analysis demonstrated that the time of harvest significantly affected the protein yield and quality. Our results indicate that the Phaseolus vulgaris β-phaseolin promoter directed anti-TNF-α scFv-Fc expression in A. thaliana seeds, with a maximum yield obtained at 20-days of development. Although the yield of anti-TNF-α scFv-Fc protein was not very high, accumulation of recombinant proteins in seeds is an attractive and simple method that can be used to purify biologically active anti-TNF-α scFv-Fc.

Genet. Mol. Res. 2016
DOI: 10.4238/gmr.15027726
Research Article

The aim of this study was to investigate the association between a functional variant of the basigin (BSG) gene, caused by a polymorphism (rs11473) at the miR-483-5p binding site, and the risk of esophageal squamous cell carcinoma (ESCC) in the Chinese population. The rs11473 polymorphism was genotyped in 624 esophageal cancer patients and 636 cancer-free age- and gender-matched controls using polymerase chain reaction restriction and direct sequencing. The functional variants resulting from the BSG rs11473 SNP were investigated using a luciferase activity assay and validated by immunoblotting. We discovered that ESCC patients carrying the rs11473 AA genotype or A allele were at a significantly higher risk of esophageal cancer [odds ratio (OR) = 1.560, 95% confidence interval  (CI) = 1.031-2.358, P = 0.037; OR = 1.231, 95%CI = 1.038-1.459, P = 0.017, respectively] than those carrying the GG genotype and G allele. Moreover, the rs11473 polymorphism modifies the binding of miR-483- 5p to basigin, as well as the basigin protein levels in esophageal cancer patients. Our data suggested that the rs11473 polymorphism at the miR- 483-5p binding site in the 3'-UTR of basigin gene may play a key role in the development of esophageal cancer in a Chinese population.

Genet. Mol. Res. 2016
DOI: 10.4238/gmr.15027735
Research Article

Glycine betaine is an important quaternary ammonium compound that is produced in response to several abiotic stresses in many organisms. The synthesis of glycine betaine requires the catalysis of betaine aldehyde dehydrogenase (BADH), which can convert betaine aldehyde into glycine betaine in plants, especially in halotolerant plants. In this study, we isolated the full-length cDNA of BADH from Suaeda corniculata (ScBADH) using reverse transcriptase-polymerase chain reaction and rapid amplification of cDNA ends. Next, we analyzed the expression profile of ScBADH using real-time PCR. The results showed that ScBADH expression was induced in the roots, stems, and leaves of S. corniculata seedlings under salt and drought stress. Next, ScBADH was overexpressed in Arabidopsis, resulting in the transgenic plants exhibiting enhanced tolerance over wild-type plants under salt and drought stress. We then analyzed the levels of glycine betaine and proline, as well as superoxide dismutase (SOD) activity, during salt stress in WT and transgenic Arabidopsis. The results indicated that overexpression of ScBADH produced more glycine betaine and proline, and increased SOD activity under NaCl treatment. Our results suggest that ScBADH might be a positive regulator in plants during the response to NaCl.

Genet. Mol. Res. 2016
DOI: 10.4238/gmr.15027848
Research Article

Using classic morphometric techniques to examine the head and thorax of Triatoma specimens, researchers identified a possible taxonomic problem involving T. arthurneivai (Lent & Martins) and T. wygodzinskyi (Lent). A recent geometric morphometric study indicated that the insects captured outside the Serra do Cipó region, State of Minas Gerais, Brazil, were T. wygodzinskyi. The misidentification of T. arthurneivai as T. wygodzinskyi could result in several problems associated with entoepidemiological lifting, the biological characterization of the species, and phylogenetic reconstruction. For the first time, we describe the use of cytogenetic analysis as a tool for differentiation between T. arthurneivai and T. wygodzinskyi. The results indicated that both species had the same number of chromosomes 2n = 22 (20A + XY). However, analyses of spermatocytes during early prophase indicated that it was possible to differentiate T. arthurneivai and T. wygodzinskyi, because only T. arthurneivai exhibited heteropycnotic blocks distributed in the chromatin. Therefore, we highlight the analysis of spermatocytes as a taxonomic tool for the characterization of T. arthurneivai and T. wygodzinskyi, and suggest that the technique can be used for entoepidemiological lifting in vector control programs. Thus, the results presented here, in conjunction with morphometric analyses, are of utmost taxonomic and epidemiological importance for the identification of T. arthurneivai and T. wygodzinskyi specimens.

Genet. Mol. Res. 2016
DOI: 10.4238/gmr.15027869
Research Article

The aim of this study was to provide comprehensive insights into the genetic background of sturgeon by transcriptome study. We performed a de novo assembly of the Amur sturgeon Acipenser schrenckii transcriptome using Illumina Hiseq 2000 sequencing. A total of 148,817 non-redundant unigenes with base length of approximately 121,698,536 bp and ranges from 201 to 26,789 bp were obtained. All the unigenes were classified into 3368 distinct categories and 145,449 singletons by homologous transcript cluster analysis. In all, 46,865 (31.49%) unigenes showed homologous matches with Nr database and 32,214 (21.65%) unigenes were matched to Nt database. In total, 24,862 unigenes were categorized into significantly enriched 52 function groups by GO analysis, and 38,436 unigenes were classified into 25 groups by KOG prediction, as well as 128 enriched KEGG pathways were identified by 45,598 unigenes (P < 0.05). Subsequently, a total of 19,860 SSRs markers were identified with the abundant di-nucleotide type (10,658; 53.67%) and the most AT/TA motif repeats (2689; 13.54%). A total of 1341 conserved lncRNAs were identified by a customized pipeline. Our study provides new sequence and function information for A. schrenckii, which will be the basis for further genetic studies on sturgeon species. The huge number of potential SSRs and putatively conserved lncRNAs isolated by the transcriptome also shed light on research in many fields, including the evolution, conservation management, and biological processes in sturgeon.

Genet. Mol. Res. 2016
DOI: 10.4238/gmr.15027999
Research Article

The Neotropical Heliconia genus contains highly diversified plants and up to 220 species have been reported from the north of Mexico to the South of Brazil. Heliconia are cultivated as ornamental garden plants and as cut flowers. All species can be propagated by seeds or vegetatively, through rhizomes. Depending on the species, an individual plant can spread and form large clonal populations. H. bihai L., H. chartacea Lane ex Barreiros, and H. wagneriana Petersen are among the most cultivated Heliconia species. However, they still have undesirable characteristics that could be improved for the international market. This study aimed to characterize 15 half-sib families originating from commercial cultivations, by morphological and molecular markers. The genetic diversity (ĤE), considering all individuals of the three species was 0.103. For H. bihai half-sib families, the value of ĤE was 0.242, showing high genetic diversity. The ĤE value for H. chartacea was 0.068, indicating low genetic diversity. All individuals of H. wagneriana showed the same band patterns, suggesting that the two parental plants were propagated vegetatively from the same plant and may have undergone some endogamic crossings. These results showed that molecular characterization can differentiate individuals closely related as half-siblings for H. bihai and H. chartacea, despite the low variation observed with morphological descriptors. The high genetic diversity observed in H. bihai half-sibling genotypes can provide valuable resources for breeding programs.

Genet. Mol. Res. 2016
DOI: 10.4238/gmr.15028003
Research Article

This paper reports on the first occurrence of Psammolestes tertius in the Chapada Diamantina region, located in the city of Seabra, Bahia State, in northeastern Brazil. Following an active search, 24 P. tertius specimens were collected from Phacellodomus rufifrons (rufous-fronted thornbird) nests. The insects did not present any symptoms of infection by Trypanosoma cruzi. P. tertius males were cytogenetically analyzed, and the results were compared with those of other specimens from the Brazilian State of Ceará. Triatomines from both locations presented the same cytogenetic characteristics: 22 chromosomes, little variation in the size of the autosomes, Y chromosomes that were larger than the X chromosomes, a chromocenter formed only by the sex chromosomes during prophase, and autosomes lacking constitutive heterochromatin. However, it is important to note that this species shows intraspecific chromosomal variation. In light of the results obtained, it is recommended that more studies be performed to characterize P. tertius. These studies will be particularly helpful in understanding this species in ecological, biological, biogeographical, and phylogenetic terms.

Genet. Mol. Res. 2016
DOI: 10.4238/gmr.15028004
Research Article

Several post-translational modifications (PTM) have been discussed in literature. Among a variety of oxidative stress-induced PTM, protein carbonylation is considered a biomarker of oxidative stress. Only certain proteins can be carbonylated because only four amino acid residues, namely lysine (K), arginine (R), threonine (T) and proline (P), are susceptible to carbonylation. The yeast proteome is an excellent model to explore oxidative stress, especially protein carbonylation. Current experimental approaches in identifying carbonylation sites are expensive, time-consuming and limited in their abilities to process proteins. Furthermore, there is no bioinformational method to predict carbonylation sites in yeast proteins. Therefore, we propose a computational method to predict yeast carbonylation sites. This method has total accuracies of 86.32, 85.89, 84.80, and 86.80% in predicting the carbonylation sites of K, R, T, and P, respectively. These results were confirmed by 10-fold cross-validation. The ability to identify carbonylation sites in different kinds of features was analyzed and the position-specific composition of the modification site-flanking residues was discussed. Additionally, a software tool has been developed to help with the calculations in this method. Datasets and the software are available at https://sourceforge.net/projects/hqlstudio/ files/CarSpred.Y/.

Genet. Mol. Res. 2016
DOI: 10.4238/gmr.15028006
Research Article

The aim of the current study was to investigate survivin expression in congenital choledochal cysts (CCCs), and its associations with clinical parameters of CCCs. In total, 121 children with CCCs were included in this study as the case group, and their cysts were staged according to the Todani classification system. Additionally, 49 normal gallbladder specimens from healthy children were included as the control group. Survivin detection was conducted using immunohistochemical staining. Associations between positive survivin expression and clinical parameters of CCCs were then analyzed. Positive survivin expression was observed in the cytoplasm, and was seen as granular with yellow or dark brown staining. In the case group, positive survivin expression was detected in most tissues. Specifically, compared to that of normal tissues, the cystic-shaped and fusiform-shaped CCC tissues had significantly higher positive survivin expression rates (all P < 0.05). Importantly, positive survivin expression was also shown to be significantly associated with gender and histological type (both P < 0.05). In conclusion, increased survivin expression was observed in CCC tissues, and was correlated with certain clinical parameters of CCCs, suggesting a possible prognostic value of survivin for CCC progression.

Genet. Mol. Res. 2016
DOI: 10.4238/gmr.15028032
Research Article

In this study, we aimed at finding the genetic regularity of grape maturation period. Early-maturing grapevine, “87-1”, was used as the female parent and late-maturing, “9-22”, as the male parent, to create an F1 hybrid population. A total of 149 individual plants and their parents were selected as the mapping population. Sequence-related amplified polymorphism and simple-sequence repeat analyses were performed. We performed a linkage analysis and constructed a molecular genetic map. In the obtained map, the female and male parents each covered 19 linkage groups containing 188 and 175 maker loci, respectively. The total map distances for the female and male parents were 1074.5 and 1100.2 cM, respectively, whereas the average genetic distances between each two loci were 5.7 and 7.8 cM, respectively. The interval-mapping method was used in a quantitative trait locus (QTL) analysis for fruit maturation period. A total of 12 QTLs associated with fruit maturation period were detected. These included four QTLs in the male parent genetic map that were located in linkage groups M5, M11, M14-1, and M16, with a 62.6-75.7% rate of contribution of each QTL. Another three QTLs were found in the female parent genetic map, located in linkage groups F6, F14-1, and F18, with a 72.7-77.7% rate of contribution of each QTL. Five more QTLs were detected in the consensus map, located in linkage groups LG11, LG14-1, LG16, LG17, and LG18, with 8.9-75.7% phenotypic variance explained by each QTL.

Genet. Mol. Res. 2016
DOI: 10.4238/gmr.15028040
Research Article

The aim of this study was to investigate the abilities of cartilage-derived morphogenetic protein 1 (CDMP1) transgenic cell sheets in repairing rabbit cartilage defects. Rabbit CDMP1 transgenic bone marrow mesenchymal stem cell (BMSC) sheets (CDMP1-BMSCs) were cultured on temperature-sensitive culture dishes, and CDMP1 expression and type II collagen protein in the cell sheets were detected. Tissue-engineered cell sheets were constructed and transplanted into defect rabbit thyroid cartilage, to investigate the expression of engineered cartilage collagen protein and proteoglycan (GAG). The experiment was divided into three groups; A) BMSC sheet, B) Ad-CMV-eGFP-transfected cell sheet, and C) Ad-CMV-hCDMP1-IRES-eGFP-transfected cell sheet. The expression of CDMP1 was detected in the transgenic cell sheets. The engineered cartilage exhibited positive immunohistochemical and Alcian blue staining. The expression levels of type II collagen protein and GAG in group A were positive, whereas those in group B and group C were negative (P < 0.05). The CDMP1-BMSC sheets had a good cartilage differentiation activity, and could effectively repair rabbit laryngeal cartilage defects.

Genet. Mol. Res. 2016
DOI: 10.4238/gmr.15028058
Research Article

Hagenia abyssinica (Bruce) J.F. Gmel is an endangered tree species endemic to the high mountains of tropical Africa. We used Illumina paired-end technology to sequence its nuclear genome, aiming at creating the first genomic data library and developing the first set of genomic microsatellites. Seventeen microsatellite markers were validated in 24 individuals. The average number of alleles per locus was 7.6, while the observed and expected heterozygosities ranged from 0.000 to 0.958 and from 0.354 to 0.883, respectively. These polymorphic markers will be used as tools for further molecular studies to facilitate formulation of appropriate conservation strategies for this species.

Genet. Mol. Res. 2016
DOI: 10.4238/gmr.15028168
Research Article

The Wnt signaling pathway plays a key role in insurgence and progression of many different forms of cancer. Some crucial components of the Wnt pathway have been proposed to be novel targets for cancer therapy. To date, the Wnt signaling pathway has not been studied in cutaneous squamous cell carcinoma (CSCC). This study was designed to investigate the expression of Wnt1 and SFRP1 from the Wnt pathway in CSCC. Tissue samples were obtained from 35 patients with CSCC and 30 controls admitted to the Xinjiang Uygur Autonomous Region People’s Hospital at Urumchi City, China. Gene and protein expressions of Wnt1 and SFRP1 were quantified by immunohistochemistry and western blotting. Wnt1 expression was significantly higher (P < 0.05) in CSCC samples than in normal skin cells of the control subjects; in contrast, SFRP1 expression was significantly lower in CSCC tissues than that in tissues of control subjects (P < 0.05). Moreover, Wnt1 expression (P < 0.05) was found to be correlated with histopathological differentiation in CSCC, and negatively correlated with SFRP1 expression in CSCC (rs = -0.473, P = 0.015). Therefore, we concluded that Wnt1 and SFRP1 play important roles in the development of CSCC and could be potent markers for diagnosis, prevention, and therapy of CSCC.

Genet. Mol. Res. 2016
DOI: 10.4238/gmr.15028187
Research Article
Authors:

This study aimed to predict pathogenic genes of childhood asthma based on molecular interaction networks and gene expression data. Known pathogenic genes identified from the human protein-protein interaction network were denoted as seed genes, and were included in network A. We extracted sub-network B (pathogenic network), which consisted of genes that interacted with at least two seed genes. We assigned a weight to select the pathogenic genes from this network according to its interactions and co-expressions with the seed genes. We also conducted ClusterONE analysis for the pathogenic network, and determined the statistical significance of the predicted clusters through a significance score (SS). Lastly, we investigated the biological pathways of the seed and candidate genes based on information obtained from the KEGG database. In network A, we identified 172 interactions and 125 genes that interacted with seed genes. In the pathogenic network, we found 51 genes and 102 interactions. The top 10 candidate genes with high weight scores were recorded. The SS of the predicted clusters demonstrated that 3 gene clusters were statistically relevant for childhood asthma. Pathway analysis showed that the seed genes and the top 10 candidate genes were significantly enriched in the same three biological processes. NFKBIA and BIRC3, which were involved in all three biological processes, may therefore be pathogenic genes. Using the network approach, we predicted that the pathogenic genes NFKBIA and BIRC3 are associated with childhood asthma. This information can provide guidelines for future experimental verification of childhood asthma.

Genet. Mol. Res. 2016
DOI: 10.4238/gmr.15028226
Research Article

We investigate the role of ERCC5 gene polymorphisms (rs17655 and rs751402) in the development of gastric cancer in a Chinese population. A total of 142 gastric cancer patients whose diagnoses were confirmed by pathology, and 274 control subjects were recruited from Tangshan Gongren Hospital between March 2013 and March 2015. Genotyping of ERCC5 rs17655 and rs751402 polymorphisms was performed by polymerase chain reaction-restriction fragment length polymorphism. Compared with the control subjects, we found that gastric cancer patients were more likely to be older, smoke tobacco, drink alcohol, and suffer from Helicobacter pylori infection. Using a chi-square test, a significant difference was observed in the distribution ofERCC5 rs751402 genotypes between patient and control groups (chi-square = 7.79, P = 0.02). In addition, unconditional multiple logistic regression analysis revealed that the AA genotype of rs751402 significantly increased gastric cancer risk compared to the GG genotype [odds ratio (OR) = 2.61, 95%CI = 1.23-5.49; P = 0.005]. Moreover, we found that the AA genotype correlated with elevated risk of gastric cancer when compared to the GG+AG genotype under a recessive model (OR = 2.21, 95%CI = 1.11-4.39; P = 0.01). In conclusion, we suggest that the ERCC5 rs751402 polymorphism is associated with development of gastric cancer.

Genet. Mol. Res. 2016
DOI: 10.4238/gmr.15027828

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