Research Article

Table of Contents | Genet. Mol. Res. 2017 (1)

Displaying 1 - 15 of 159
Research Article

This study aimed to evaluate the immunomodulatory and neuroprotective effects of allogeneic and cryopreserved mesenchymal stem cells (MSCs) on spinal cord injury. A total of 120 rats were distributed into the following groups: negative control (NC) - without injury, positive control (PC) - with injury without treatment, and group treated with MSC (GMSC) - with injury and treated. Motor function was evaluated by the BBB test at 24, 48, and 72 h and at 8 and 21 postoperative days. Spinal cords were evaluated by histopathology and immunohistochemistry to determine the expression of CD68, NeuN, and GFAP. IL-10, TNF-α, IL-1β, TGF-β, BDNF, GDNF, and VEGF expression was quantified by RT-PCR. The GMSC presented higher scores for motor function at 72 h and 8 and 21 days after injury, lower expression of CD68 at 8 days, and lower expression of GFAP at 21 days compared to the PC. In addition, higher expression of NeuN and lower degeneration of the white matter occurred at 21 days. The GMSC also showed higher expression of IL-10 24 h after injury, GDNF at 48 h and 8 days, and VEGF at 21 days. Moreover, lower expression of TNF-α was observed at 8 and 21 days and TGF-β at 24 h and 21 days. There were no differences in the expression of IL-1β and BDNF between the GMSC and PC. Thus, cryopreserved MSCs promote immunomodulatory and neuroprotective effects in rats with spinal cord injury by increasing IL-10, GDNF, and VEGF expression and reducing TNF-α and TGF-β expression.

Genet. Mol. Res. 16(1):
DOI: 10.4238/gmr16019555
Research Article

In order to evaluate the milk yield, milk quality, and health of dairy cows fed a high-concentrate (HC) diet, eight lactating Holstein dairy cattle were randomly assigned to HC or low-concentrate (LC) diet groups and fed for 50 days, and the auto-control studying before and after treatment with the two diets was used. During the experiment, plasma and milk samples were collected and measured. With regard to milk component, HC feeding led to higher milk production (P < 0.05), but significantly lower milk protein percentage (P < 0.05), milk protein yield (P < 0.05), and milk fat percentage (P < 0.05) throughout the five periods than LC feeding. Milk somatic cell count and N-acetyl-D-glucosaminidase activity (P < 0.01) were higher than those observed under LC feeding. mRNA expression levels of interleukin-8 (IL-8), C-C motif chemokine ligand (CCL5), and lactalbumin alpha (α-LA) were investigated by qPCR and found to be significantly lower (P < 0.01) in cattle fed the HC diet. The amino acid content was analyzed by high performance liquid chromatography (HPLC), and the content of Asp (P < 0.01), Gln (P < 0.01), Ala (P < 0.05), Leu (P < 0.05), Lys (P < 0.05), and Ile (P < 0.01) was significantly lower in the HC group, whereas the content of Arg (P < 0.05) and Phe (P < 0.01) was significantly higher. These results suggest that the HC diet might have an important influence on mammary health. The amino acid content was lower, suggesting that depletion of amino acids, resulting in depleted milk protein, affects milk quality.

Genet. Mol. Res. 16(1): gmr16019204
DOI: 10.4238/gmr16019204
Research Article

We investigated the paracrine effects of bone marrow mesenchymal stem cells (BMSCs) on the proliferation, apoptosis, and alpha-actin-2 (ACTA2) expression of hepatic stellate cells (HSCs), and explored the possible mechanisms of hepatocyte growth factor (HGF). We established a co-culture system by culturing BMSCs on the upper layer and HSCs on the lower layer of a 6-well Transwell plate. Normal HSCs were cultured alone as a control. Cell apoptosis was determined by flow cytometry. We detected the expression of ACTA2 mRNA and ACTA2 protein in HSC using quantitative reverse transcription polymerase chain reaction (qRT-PCR) and western blotting, respectively. ACTA2 in HSCs was detected by fluorescent staining, and HGF in the co-culture supernatant was detected by enzyme-linked immunosorbent assay (ELISA). The apoptotic rate of HSCs in the experiment group was 2.6 times that in the control group (P < 0.05). The expression levels of ACTA2 mRNA and ACTA2 protein were significantly inhibited in HSCs compared with the control group (P < 0.05). HGF concentration in the co-culture supernatant was 0.43 ± 0.47 mM in the experimental group, which was significantly higher than in the control group (0.16 ± 0.43 mM) (P < 0.05). The paracrine effect of BMSCs, which was caused by the suppression of ACTA2 and HGF expression, induced HSC apoptosis.

Genet. Mol. Res. 16(1): gmr16019201
DOI: 10.4238/gmr16019201
Research Article

Association of signal-induced proliferation-associated 1 (SIPA) gene and protein expression with gastric cancer development was examined. SIPA1 mRNA and protein levels were determined by real-time quantitative polymerase chain reaction and western blot, respectively, in 40 gastric tumor and tumor-adjacent normal tissues. SIPA1, VEGF-A, and FVIII levels in 60 gastric tumor and 40 tumor-adjacent normal tissues were examined by immunohistochemical staining. Correlations between SIPA1, VEGF-A, and microvessel density (MVD) were analyzed. SIPA1 mRNA levels were significantly lower in tumor tissues than in tumor-adjacent normal tissues (P 0.05). Significantly higher MVD (57.4 ± 9.3) was observed in tumor tissues displaying positive SIPA1 staining than in tumor-adjacent normal tissues (41.2 ± 5.7, P

Genet. Mol. Res. 16(1): gmr16019271
DOI: 10.4238/gmr16019271
Research Article

The efficacy of bone marrow mesenchymal stem cell (BMSC) on liver fibrosis in animal has been proven, but a few studies have been made in human body and few such researches in China. This study was designed to investigate the effect of BMSC treatment on hepatic fibrosis induced by hepatolenticular degeneration and the influence on serological indicators. Sixty patients with liver fibrosis induced by hepatolenticular degeneration were randomly divided into two groups, a penicillamine group and a BMSCs plus penicillamine group, with 30 patients in each. The therapeutic effects on hepatic fibrosis, liver function, and serological indicators were recorded before and after the treatment, and the data were compared. After treatment, serum levels of HA, PCIII, LN, CIV, TIMP-1, and MMP-1 were reduced in both groups (P < 0.05). However, cytokine levels in the BMSCs plus penicillamine group were significantly lower than those in the penicillamine group (P < 0.05). Combination therapy with BMSCs and penicillamine had a significant positive effect on liver fibrosis induced by hepatolenticular degeneration.

Genet. Mol. Res. 16(1): gmr16019352
DOI: 10.4238/gmr16019352
Research Article

In vitro studies have shown that multidrug resistance protein 1 (MDR1) has an affinity for cortisol; however, in vivo association studies on the relationship between MDR1 gene polymorphisms and blood cortisol levels have produced inconsistent results. Therefore, we examined the effects of the C3435T polymorphism of the MDR1 gene on blood levels of hypothalamus-pituitary-adrenal (HPA) axis hormones such as cortisol and adrenocorticotropic hormone (ACTH) in healthy subjects. The subjects comprised 30 healthy Japanese males. Ten subjects were recruited for each of the C3435T MDR1 genotypes: C/C, C/T, and T/T. Blood samples were taken at 6:00 pm on two occasions with an interval of 2 weeks. Blood levels of cortisol and ACTH were determined by an electrochemiluminescence immunoassay. There were no significant differences in the blood levels of the HPA axis hormones among the MDR1 genotypes. The present study suggests that the C3435T MDR1 polymorphism does not affect blood levels of HPA axis hormones in healthy Japanese males.

Genet. Mol. Res. 16(1): gmr16019447
DOI: 10.4238/gmr16019447
Research Article

Zidovudine, the antiretroviral drug used to treat HIV infection, commonly causes adverse effects, such as systemic fever and gastrointestinal alterations. In the present study, the potential role of inosine triphosphate pyrophosphatase (ITPA) gene variant on the incidence of adverse events during antiretroviral therapy (ART) of HIV with zidovudine was discussed. Individuals from Northeastern Brazil (N = 204) receiving treatment for HIV-1 infection were recruited. Zidovudine-related adverse effects developed during the treatment were registered. The rs1127354 polymorphism in the ITPA gene was genotyped using real-time PCR to assess whether this single nucleotide polymorphism was associated with the occurrence of zidovudine-related adverse effects. We observed a significant association between the ITPA variant genotype and the reported systemic fever (odds ratio = 7.17, 95% confidence interval = 1.19-43.15; P = 0.032). Zidovudine use could indirectly lead to an increase in the levels of inosine monophosphate in an antimetabolite-like manner, which is converted to inosine triphosphate (ITP). The rs1127354 variant caused a decrease in ITPA activity, thereby leading to ITP accumulation. This in turn resulted in cytotoxicity, which was manifested by neutropenia and fever. Therefore, we hypothesized a pharmacogenetic model involving the ITPA variant genotype in multifactorial components that act together to determine the onset of zidovudine-related adverse effects.

Genet. Mol. Res. 16(1): gmr16019373
DOI: 10.4238/gmr16019373
Research Article

Phosphorylation is an important part of post-translational modifications of proteins, and is essential for many biological activities. Phosphorylation and dephosphorylation can regulate signal transduction, gene expression, and cell cycle regulation in many cellular processes. Phosphorylation is extremely important for both basic research and drug discovery to rapidly and correctly identify the attributes of a new protein phosphorylation sites. Moreover, abnormal phosphorylation can be used as a key medical feature related to a disease in some cases. The using of computational methods could improve the accuracy of detection of phosphorylation sites, which can provide predictive guidance for the prevention of the occurrence and/or the best course of treatment for certain diseases. Furthermore, this approach can effectively reduce the costs of biological experiments. In this study, a flexible neural tree (FNT), particle swarm optimization, and support vector machine algorithms were used to classify data with secondary encoding according to the physical and chemical properties of amino acids for feature extraction. Comparison of the classification results obtained from the three classifiers showed that the classification of the FNT was the best. The three classifiers were then integrated in the form of a minority subordinate to the majority vote to obtain the results. The performance of the integrated model showed improvement in sensitivity (87.41%), specificity (87.60%), and accuracy (87.50%).

Genet. Mol. Res. 16(1): gmr16019354
DOI: 10.4238/gmr16019354
Research Article

Interleukin-8 (IL-8) is a mediator of inflammation and plays an important role in regulating immune responses. To date, several studies have tested the association between IL-8 gene polymorphisms and development of coronary artery disease (CAD), but their results have proved to be inconsistent. We conducted an investigation to assess the relationship between the IL-8 -251A/T (rs4073) sequence variant and CAD in a Chinese population. Between April 2013 and January 2015, 217 patients with coronary angiography-confirmed CAD were enrolled in our study, along with 245 control subjects. IL-8 -251A/T genotyping was performed using a polymerase chain reaction-restriction fragment length polymorphism assay. A chi-square test revealed that IL-8 -251A/T genotype distributions significantly differed between CAD patients and control subjects (chi-square = 8.29, P < 0.02). Moreover, multiple-logistic regression analysis showed that individuals carrying TA [odds ratio (OR) = 1.59, 95% confidence interval (CI) = 1.01-2.57] and AA (OR = 2.06, 95%CI = 1.21-3.52) genotypes were at increased risk of CAD compared to those with the TT genotype. Under dominant (OR = 1.75, 95%CI = 1.13-2.73) and recessive (OR = 1.54, 95%CI = 1.02-2.37) genetic models, the IL-8 -251A/T polymorphism also significantly correlated with CAD. In conclusion, our results suggest that this variant is an independent risk factor for CAD development under codominant, dominant, and recessive models.

Genet. Mol. Res. 16(1): gmr16018224
DOI: 10.4238/gmr16018224
Research Article

Recent innovations in the genomic understanding of medulloblastomas have provided new ways to explore this highly invasive malignant brain cancer arising from the cerebellum. Among the four different medulloblastoma subgroups described to date, the sonic hedgehog (SHH) genetic pathway is the pathway activated in the tumorigenesis of medulloblastoma. SHH-related medulloblastomas are usually of nodular/desmoplastic histology and frequently occur in children under the age of three, an age group highly susceptible to the acute and long-term effects of treatment. Several new drugs aimed at SHH modulation are currently under development. This review focuses on the role of arsenic trioxide, a drug well established in clinical practice and probably an under-explored agent in medulloblastoma management, in the SHH pathway.

Genet. Mol. Res. 16(1): gmr16019412
DOI: 10.4238/gmr16019412
Research Article

We attempted to identify significant pathway cross-talk in rheumatoid arthritis (RA) by the Monte Carlo cross-validation (MCCV) method. We therefore obtained and preprocessed the gene expression profile of RA. MCCV involves identifying differentially expressed genes (DEGs), identifying differential pathways (DPs), calculating the discriminating score (DS) of the pathway cross-talk, and random forest (RF) classification. We carried out 50 bootstrap iterations of MCCV to identify the key instances of pathway cross-talk involved in RA. We identified a total of 17 significant DEGs and 15 significant DPs by comparing RA samples and normal controls. We found the most significant difference between RA and the normal controls in the eIF4 and p70S6K signaling regulation pathway. Furthermore, we identified 10 instances of pathway cross-talk with the best classification performance for RA and normal controls, using the RF classification model. All of the top 10 pathway pairs involved cross-talk with eIF4 and p70S6K signaling regulation, and the other 10 pathways were immune-related. By MCCV, we identified one critical DP and 10 significant instances of pathway cross-talk in RA. We propose that the eIF4 and p70S6K signaling regulation pathway and the other significant instances of pathway cross-talk play key roles in the occurrence and development of RA, and are potential predictive and prognostic markers for RA.

Genet. Mol. Res. 16(1): gmr16029142
DOI: 10.4238/gmr16029142
Research Article

Pak choi is a highly nutritious vegetable that is widely grown in China, Southeast Asia, and other parts of the world. Because it reproduces by seed, it is very important to understand the mechanism of floral organ development. Therefore, using the Chinese cabbage genome as a reference, this study analyzed the expression profiles of shoot apex genes at flower bud differentiation stages 1 and 5, in order to identify genes related to floral organ development. The results showed that the proportion of mapped genes was high, with 84.25 and 83.80% of clean reads from the two sample saligned to the reference genome, respectively. A total of 525 differentially expressed genes (DEGs) were identified, 224 of which were upregulated and 301 were downregulated. The expression levels of genes homologous to Chinese cabbage flowering genes were also analyzed at stages 1 and 5; the expression levels of Bra012997 (ap1), Bra000393 (SOC1), and Bra004928 (SOC1) were significantly upregulated at stage 5, suggesting that these three genes positively regulate floral development in pak choi. DEGs involved in floral organ development were analyzed with homologous genes from Arabidopsis thaliana; the homologous genes Bra029281 (AGL42), Bra026577 (ARPN), Bra022954 (SPL3), Bra029293 (ARF2), Bra007978 (AtRLP12), Bra033221 (SPL8), Bra008037 (LOX4), Bra001598 (IAA19), Bra003892 (PATL1), Bra038778 (AT4G21323), Bra025315 (KLCR2), and Bra013906 (DTX35) are directly related to floral organ development in Arabidopsis, suggesting that these genes have corresponding functions during flower organ development in pak choi, and could be candidates for further genetic research. These results provide a foundation for research on the molecular mechanism of flower organ development in pak choi and other Brassica rapa vegetables.

Genet. Mol. Res. 16(1): gmr16019233
DOI: 10.4238/gmr16019233
Research Article

The Fluorescence Image Analyzer (FLIMA) software was developed for the quantitative analysis of images generated by fluorescence in situ hybridization (FISH). Currently, the images of FISH are examined without a coefficient that enables a comparison between them. Through GD Graphics Library, the FLIMA software calculates the amount of pixels on image and recognizes each present color. The coefficient generated by the algorithm shows the percentage of marks (probes) hybridized on the chromosomes. This software can be used for any type of image generated by a fluorescence microscope and is able to quantify digoxigenin probes exhibiting a red color, biotin probes exhibiting a green color, and double-FISH probes (digoxigenin and biotin used together), where the white color is displayed.

Genet. Mol. Res. 16(1): gmr16019658
DOI: 10.4238/gmr16019658
Research Article

Intramammary infections are one of the main causes of productivity loss in dairy cows. To better understand the immune system response and to avoid the use of live animals, we validated the use of isolated bovine udder as an ex situ model. Six mammary glands were collected from cows ready for culling. Three udders were perfused with Tyrode's solution and three were not-perfused. During six hours, we collected perfusate samples for biochemical analysis. We also collected alveolar and teat canal tissue to evaluate gene expression. The biochemical parameters indicated that the perfused udders remained viable for the entire period of the experiment. A real-time polymerase chain reaction showed an increase in 18S rRNA gene expression in the alveolar tissue at 3 and 4 h after perfusion. There was also an increase in the Ubiquitin gene in the teat canal from not-perfused udders at 1, 3, and 4 h after slaughter. In general, gene expression was stable during the experiment. Our results indicated that the isolated perfused bovine udder model is appropriate for genetic studies, opening a new perspective in animal experimentation methods.

Genet. Mol. Res. 16(1): gmr16019637
DOI: 10.4238/gmr16019637
Research Article

Multiflorous spikelets are found in several grass species of agricultural and economic interest. In oat, this morphological characteristic is associated with the production of naked grains. Although many genetic studies have been performed over the past century, the inheritance of the multiflorous spikelet trait is not fully understood in oat. The objectives of this study were to evaluate environmental effects on the multiflorous spikelet trait, to estimate the number of genes controlling the trait, and to clone and characterize sequences of the AP2 gene in oat. Two genetic populations of recombinant inbreed lines were screened for the multiflorous spikelet trait from different years and sowing dates under field experiments. Normal, multiflorous, and mosaic spikelets were analyzed in the whole panicle for both years and sowing dates. Specific primer pairs for the AP2 gene was utilized to amplify and clone oat sequences. The results demonstrate that under higher temperature and day-length conditions, the variable expressivity of the multiflorous spikelet trait was less pronounced in both populations. Genetic analyses indicated the action of one major gene and two or three modifying genes controlling the expression of the multiflorous spikelet trait in oat, depending on the genetic background. Sequences with similarity to the AP2 gene were isolated from the oat lines UFRGS 017004-2 and URS Taura, and genetic polymorphisms were identified, which are valuable to confirm the action of AP2 on the multiflorous spikelet trait. Our results provide information to assist in the development of future studies of the multiflorous spikelet trait in oat.

Genet. Mol. Res. 16(1): gmr16019588
DOI: 10.4238/gmr16019588