Research Article

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

Displaying 106 - 120 of 361
Research Article

The present study clearly showed that chronic exposure to polychlorinated biphenyls (PCBs) at environmentally relevant concentrations can damage juvenile tilapia livers by modulating antioxidant enzyme activities and gene transcription, which affects toxic bioaccumulation and histological congestion. The results suggest that PCBs caused a decrease in the activity of some hepatic antioxidative and biotransformation enzymes (SOD, CAT, GST, T-GSH, and MDA) in tilapia at 7 days, as well as transcriptional changes (sod, cat, and gst). Except for some antioxidant parameters (T-GSH, GSH/GSSG, T-AOC, and MDA), significant declines and increases occurred at 14 and 21 days, respectively. Most of the antioxidant enzymatic signatures and genotoxicity significantly increased at 14 and 21 days. This study presented evidence that PCBs could result in hepatic toxicity through oxidative stress in the early growth stages of tilapia, and we speculated that oxidative stress plays an important role in embryonic developmental toxicity induced by PCBs.

Genet. Mol. Res. 15(3): gmr8613
DOI: 10.4238/gmr.15038613
Research Article

Brazil is considered one of the domestication centers of cassava (Manihot esculenta), containing a large part of the biological diversity and traditional knowledge of the species. The aim of the present study was to evaluate the genetic diversity of cassava landraces grown by farmers in the north of Mato Grosso State, Brazil, using inter simple sequence repeat (ISSR) molecular markers. The study was carried out in the municipality of Alta Floresta, MT, on farms located in two rural areas. Seventeen cassava landraces were selected. The DNA was extracted and polymerase chain reaction amplifications were performed using 15 ISSR primers. Genetic similarity estimates were calculated using Jaccard’s index and the generated matrix was used for clustering the genotypes by using UPGMA and Tocher’s methods. The 15 ISSR primers amplified 120 fragments, revealing 61.67% polymorphism. The polymorphism information content ranged from 0.04 to 0.61, averaging 0.39. The most similar genotypes were AF5 and AF8, whereas the least similar were AF1 and AF16. The UPGMA clustering method formed five groups. Group I included twelve landraces, Group II contained two, and the other groups contained one landrace each. Tocher’s method resulted in six groups: 12 landraces clustered in one group, and the other groups each contained one landrace. The ISSR markers proved efficient in revealing genetic diversity among the cassava landraces. The landraces grown by farmers in the two rural areas of Alta Floresta have a great variability and, thus, can be exploited in programs for breeding and preservation of the species.

Genet. Mol. Res. 15(3): gmr8615
DOI: 10.4238/gmr.15038615
Research Article

In the present study, GIFT tilapia Oreochromis niloticus were exposed to polychlorinated biphenyls (PCBs) for 7, 14, and 21 days. Over the duration of the exposure, genotoxicity and the activity of Na+/K+-ATPase (NKA) and Ca+/Mg+-ATPase (CMA) were measured in the gill, kidney, and intestine, to evaluate changes in osmoregulatory response in O. niloticus. Our results showed significant decreases in organic NKA (except in gill tissues after 0.5 mg/L PCB-exposure) and CMA activity. The results of the genotoxicity assay showed significant increases in atp1a1a, nkcc2 (only in gill tissue), and fxyd7 (except after 21 days of 5 mg/L PCB exposure). We found significant increases in caspase proteins in the liver in the 5-mg/L PCB exposure group, and the transcripts showed dose-dependent increases between treatment groups over the exposure duration. This study presents evidence that chronic exposure to PCB could result in organic osmoregulatory response and hepatic apoptosis in GIFT tilapia.

Genet. Mol. Res. 15(3): gmr8620
DOI: 10.4238/gmr.15038620
Research Article

Grain yield is strongly influenced by the environment, has polygenic and complex inheritance, and is a key trait in the selection and recommendation of cultivars. Breeding programs should efficiently explore the genetic variability resulting from crosses by selecting the most appropriate method for breeding in segregating populations. The goal of this study was to evaluate and compare the genetic potential of common bean progenies of carioca grain for grain yield, obtained by different breeding methods and evaluated in different environments. Progenies originating from crosses between lines and CNFC 7812 and CNFC 7829 were replanted up to the F7 generation using three breeding methods in segregating populations: population (bulk), bulk within F2 progenies, and single-seed descent (SSD). Fifteen F8 progenies per method, two controls (BRS Estilo and Perola), and the parents were evaluated in a 7 x 7 simple lattice design, with plots of two 4-m rows. The tests were conducted in 10 environments in four States of Brazil and in three growing seasons in 2009 and 2010. Genetic parameters including genetic variance, heritability, variance of interaction, and expected selection gain were estimated. Genetic variability among progenies and the effect of progeny-environment interactions were determined for the three methods. The breeding methods differed significantly due to the effects of sampling procedures on the progenies and due to natural selection, which mainly affected the bulk method. The SSD and bulk methods provided populations with better estimates of genetic parameters and more stable progenies that were less affected by interaction with the environment.

Genet. Mol. Res. 15(3): gmr8622
DOI: 10.4238/gmr.15038622
Research Article

Mesenchymal stem cells (MSCs) have pleiotropic immuno-modulatory effects and pro-angiogenic ability, leading to the presumption that MSCs may be involved in the pathogenesis of many inflammatory or autoimmune disorders, including psoriasis. In a previous study, we reported the specific gene expression profile of dermal MSCs from psoriasis. Inflammation- and angiogenesis-related genes, such as lipopolysaccharide-induced tumor necrosis factor-alpha transcription factor (LITAF), dual-specificity protein phosphatase 1 (DUSP1), vascular endothelial growth factor α (VEGFα), and insulin-like growth factor-binding protein-5 (IGFBP5), are abnormally expressed in psoriatic dermal MSCs. As a key regulator of gene expression, miRNA are involved in a wide variety of biological processes; in fact, several miRNAs have been implicated in the development and progression of inflammatory or autoimmune disorders. In this study, we compared the miRNA expression profiles of dermal MSCs from patients with psoriasis to those in MSCs from normal individuals by microarray, and found that the pro-inflammatory miRNA miR-155 was significantly overexpressed in psoriatic MSCs (2.44 fold, P TAB2 (8.47 ± 1.55 vs 6.38 ± 2.10, P iNOS (5.26 ± 2.58 vs 3.73 ± 1.89, P

Genet. Mol. Res. 15(3): gmr8631
DOI: 10.4238/gmr.15038631
Research Article

With high nutritional value in its fruits, Dangshan Su pear has been widely cultivated in China. The stone cell content in fruits is a key factor affecting fruit quality in pear, and the formation of stone cells has been associated with lignin biosynthesis. O-Methyltransferase (OMT) is a key enzyme involved in lignin metabolism within the phenylpropanoid pathway. Here, we screened 26 OMT genes from the Pyrus bretschneideri cv. Dangshan Su genome using the DNATOOLs software. To characterize the OMT gene family in pear, gene structure, chromosomal localization, and conserved motifs of PbOMTs were analyzed. PbOMTs were divided into two categories, type I (designated PbCCOMTs) and type II (designated PbCOMTs), indicating the differentiation of function during evolution. Based on the analysis of multiple sequence alignment, cis-element prediction, and phylogenetic relationships, two candidate genes, PbCCOMT1 and PbCCOMT3, were selected for the analysis of temporal and spatial gene expression in pear. The promoter regions of both PbCCOMT1 and PbCCOMT3 contain regulatory motifs for lignin synthesis. Moreover, the two genes show high similarity and close phylogenetic relationships with CCOMTs in other species. Expression analysis showed that transcript levels of two PbCCOMTs were positively associated with the contents of both stone cells and lignin during the development of pear fruit. These results suggest that PbCCOMT1 and PbCCOMT3 are closely associated with lignin biosynthesis. These findings will help clarify the function of PbOMTs in lignin metabolism and to elucidate the mechanisms underlying stone cell formation in pear.

Genet. Mol. Res. 15(3): gmr8664
DOI: 10.4238/gmr.15038664
Research Article

Osteogenesis imperfecta (OI) is a heterogeneous disorder that causes fragility, deformity, and fractures in bones. A large number of genes that are associated with the disease have been identified in the last decade; this makes the genetic diagnosis of OI more difficult. To improve our knowledge of the genetic mutation profile in OI we used single-stranded conformation polymorphism screening and automated sequencing to investigate the SERPINH1, FKBP10, and SERPINF1 genes, which are related to recessive OI, in 23 unrelated Brazilian patients. Nine rare changes and four common polymorphisms were detected. Most changes were benign genetic variants. In general, changes in the SERPINH1 and SERPINF1 genes were synonymous polymorphisms or missense changes located in non-coding regions. A pathogenic change was found in the FKBP10 gene. The characterization of mutations related to OI in distinct populations can improve our knowledge of the genetic aspects of OI and help us develop molecular strategies for the diagnosis of the disease.

Genet. Mol. Res. 15(3): gmr8665
DOI: 10.4238/gmr.15038665
Research Article

Ramulosis is one of the most aggressive diseases in cotton, and understanding the genetic control of its resistance is imperative for selecting superior cotton genotypes in breeding programs. This study analyzed the inheritance pattern of this resistance using chi-square goodness-of-fit tests to determine the phenotypic proportions of the F2 generation, and a mixed inheritance approach to jointly model major gene and polygenes effects. F1, F2, Rc1, and Rc2 generations were obtained by crossing resistant (BRS Facual, CNPA 2984, or CNPA 2043) and susceptible (Delta Opal, CNPA 999, or CNPA 2161) genotypes, and were assessed under field conditions with artificial inoculation of the pathogen (Colletotrichum gossypii var. cephalosporioides). Genetic control of the trait varied among the crossings. For Delta Opal x BRS Facual and CNPA 2161 x BRS Facual, phenotypic segregations in the F2 generation did not differ from the expected proportions for the hypothesis of duplicate genes (15:1). For Delta Opal x CNPA 2043, the segregation did not differ from the expected proportions for dominant recessive epistasis (13:3). The hypothesis of genetic control by one major gene was supported only for the Delta Opal x CNPA 2043 crossing. Three other crossings showed evidence of polygenes in the inheritance of the trait. In conclusion, major genes and polygenes are likely involved in the genetic control of ramulosis resistance in cotton.

Genet. Mol. Res. 15(3): gmr8667
DOI: 10.4238/gmr.15038667
Research Article

Resistance to metronidazole (Mtz) in Helicobacter pylori is a major problem worldwide, especially in developing countries. Alterations in Mtz nitroreductase enzymes, such as oxygen-insensitive NADPH nitroreductase (RdxA) and NADPH flavin oxidoreductase (FrxA), are the major contributing factors for this resistance. In this study, rdxA and frxA were amplified, sequenced, and analyzed in 34 Mtz-resistant H. pylori isolates (MIC ≥ 8 μg/mL) using multiple allele-specific polymerase chain reaction (MAS-PCR); this method was developed to target the most common genotypes of rdxA in H. pylori. In this study, the rdxA and frxA genes in Mtz-resistant H. pylori strains displayed a large number of point mutations. The rdxA and frxA genes of Mtz-resistant clinical isolates showed a higher percentage of missense mutations (97.1 and 78.6%, respectively) compared to 26695 reference strains; additionally, missense mutations were more common than frameshift (20.6 and 32.1%) and nonsense mutations (8.8 and 10.7%, respectively) in these genes. The most common missense mutations in rdxA were D 59 N (94.1%), T 31 E (88.2%), and R 131 K (85.3%). The most common missense mutations in frxA were F 72 S (57.1%), G 73 S (57.1%), and C 193 S (53.6%). The developed MAS primers, specific to position 175 and 392 of rdxA, successfully amplified the common alleles and distinguished the variants. MAS-PCR could be a useful tool for epidemiological studies of H. pylori, associated with Mtz resistance. rdxA variants must be screened in order to ensure the effectiveness of Mtz-based H. pylori therapies in developing countries.

Genet. Mol. Res. 15(3): gmr8674
DOI: 10.4238/gmr.15038674
Research Article

This study evaluated the chemical and genetic diversity of high-seed-yield sorghum germplasms from Korea, the United States, and South Africa. We identified significant differences in the chemical contents of whole plants at the heading stage in all cultivars, including differences in crude protein, fat, fiber, ash, neutral detergent fiber, acid detergent fiber, mineral, and fatty acid contents. Our results suggest that Banwoldang is the most appropriate cultivar for roughage because of its high protein yield. We identified significant differences in the tannin, flavonoid, amylose, mineral, crude fat, fatty acid, and 3-deoxyanthocyanin contents in the whole grain from all cultivars, but not in the mineral or crude fat contents. Tannin levels were generally low. IS645 contained the highest levels of flavonoids and linolenic acid compounds, and Moktak had the highest amylose and deoxyanthocyanidin content in the grain. To assess genetic diversity, we used 10 simple sequence repeat (SSR) primer sets to identify 38 alleles with 3-8 alleles per locus. Based on phylogenetic analysis of the SSR markers, the sorghum cultivars were divided into three major groups. Comparison of clusters based on chemical compositions with those based on SSRs showed that the groups formed by the three native Korean cultivars clustered similarly in molecular dendrograms. Association analysis was conducted for the 10 SSR marker; 48 chemical and growth traits were present for two marker traits (seed color and whole plant fatty acid content) with significant marker-trait associations. These markers could be used to select sorghum cultivars for breeding programs.

Genet. Mol. Res. 15(3): gmr8677
DOI: 10.4238/gmr.15038677
Research Article

DIO3 gene encoding type 3 iodothyronine deiodinase is an imprinted gene, located in the DLK1-DIO3 (delta-like 1 homolog-type 3 iodothyronine deiodinase) imprinted domain, and is potentially involved in degrading excessive amounts of thyroid hormone to protect embryogenesis. However, the underlying regulatory mechanism of the imprinted DIO3 gene expression during fetal and neonatal development in goats has not been elucidated. In this study, we explored the DNA methylation patterns of the caprine DIO3 intragenic CpG island and quantified gene expression level in six tissues from Chinese Nanjiang Yellow 3-day old kids. The expression of the DIO3 gene was determined using quantitative reverse transcription-polymerase chain reactions (qRT-PCRs), while the identification of methylation patterns was determined using bisulfite-sequencing PCRs. Modest, and non-significant (P > 0.05), methylation patterns were noted for the DIO3 CpG island methylation in the brain, heart, liver, kidney, lung, and longissimus dorsi tissues (ranging from 26.48 to 34.92%). The expression level of the DIO3 mRNA was significantly higher (P 0.05), which indicated that the expression of the caprine DIO3 gene was likely modified by other regulatory elements. This study identified DNA methylation and expression patterns of the DIO3 gene in goats and provided insights into further regulatory mechanisms of expression and imprinting in the DLK1-DIO3 domain.

Genet. Mol. Res. 15(3): gmr8678
DOI: 10.4238/gmr.15038678
Research Article

Varronia curassavica Jacq. is a medicinal and aromatic plant from Brazil with significant economic importance. Studies on genetic diversity in active germplasm banks (AGB) are essential for conservation and breeding programs. The aim of this study was to analyze the genetic diversity of V. curassavica accessions of the AGB of Medicinal and Aromatic Plants of the Federal University of Sergipe (UFS), using inter-simple sequence repeat molecular markers. Twenty-four primers were tested, and 14 were polymorphic and informative, resulting in 149 bands with 97.98% polymorphism. The UPGMA dendrogram divided the accessions into Clusters I and II. Jaccard similarity coefficients for pair-wise comparisons of accessions ranged between 0.24 and 0.78. The pairs of accessions VCUR-001/VCUR-503, VCUR-001/VCUR-504, and VCUR-104/VCUR-501 showed relatively low similarity (0.24), and the pair of accessions VCUR-402/VCUR- 403 showed medium similarity (0.78). Twenty-eight accessions were divided into three distinct clusters, according to the STRUCTURE analysis. The genetic diversity of V. curassavica in the AGB of UFS is low to medium, and it requires expansion. Accession VCUR-802 is the most suitable for selection in breeding program of this species, since it clearly represents all of the diversity present in the AGB.

Genet. Mol. Res. 15(3): gmr8681
DOI: 10.4238/gmr.15038681
Research Article

Leishmaniasis is a disease caused by protozoa of the genus Leishmania. Two distinct forms are recognized: visceral leishmaniasis (VL) and cutaneous leishmaniasis (CL). In the Americas, the causative agent of VL is L. infantum chagasi, whereas L. braziliensis is principally responsible for CL. Domestic dogs constitute the main source of VL in urban environments, and have also been implicated in CL epidemiology. We carried out molecular and serological surveys to detect Leishmania infection in dogs from the municipality of Ituberá in Bahia, Brazil. Furthermore, we identified risk factors associated with illness in dogs from this locality. Blood samples were collected from 399 dogs and tested using an indirect immunofluorescence assay (IFA) and polymerase chain reaction (PCR) to detect Leishmania spp antibodies and L. infantum chagasi and L. braziliensis DNA, respectively. Dogs were clinically evaluated and tissue samples from those exhibiting skin lesions were examined for parasites. In addition, the dog owners completed an epidemiological questionnaire to identify factors associated with infection. Skin lesions consistent with CL were found on 37 (9.3%) of the evaluated animals, but parasitological examination was negative for all samples. The IFA returned positive results for 60 (15%) dogs. PCR identified DNA from L. braziliensis in 86 (21.6%) animals, where as all samples proved negative for L. infantum chagasi. The 134 dogs (33.6%) testing positive using IFA and/ or PCR were considered infected, and of these, only 13 demonstrated skin lesions. Animals from rural areas were 3.39-times more likely to be infected compared to those in urban environments.

Genet. Mol. Res. 15(3): gmr8684
DOI: 10.4238/gmr.15038684
Research Article

Several receptor proteins of Cry toxin have been previously identified, including cadherin-like, aminopeptidase N, and alkaline phosphatase. In the present work, a novel binding protein, V-ATPase subunit A (HpVAA), was identified in Holotricia parallela larvae and characterized. We performed reverse transcription-polymerase chain reaction and rapid amplification of cDNA ends technology to obtain the cDNA of the full-length hpvaa. Sequencing analysis showed that the open reading frame of hpvaa (GenBank accession No. KU497557) is 1845 bp long, encoding 614 amino acid residues. The predicted molecular weight and isoelectric point of HpVAA were 67.85 kDa and 4.9, respectively. The HpVAA protein, which includes two putative conserved domains, ATP-synt_ab_N and ATP-synt_ab_C, and a Walker A (GAFGCGKT) motif and a Walker B (SMMAD) motif, possesses the same structural characteristics as V-ATPase subunit A from other insects. The protein was successfully expressed in Escherichia coli, and a ligand blot assay showed binding of the protein with Cry8Ea3 toxin. Transcriptional analysis of hpvaa in different tissues of H. parallela larvae was performed by qRT-PCR, which showed that the relative expression of hpvaa in the Malpighian tubules is higher than that in other tissues.

Genet. Mol. Res. 15(3): gmr8994
DOI: 10.4238/gmr.15038994
Research Article

The complementary DNA (cDNA) of the giant panda (Ailuropoda melanoleuca) ferritin light polypeptide (FTL) gene was successfully cloned using reverse transcription-polymerase chain reaction technology. We constructed a recombinant expression vector containing FTL cDNA and overexpressed it in Escherichia coli using pET28a plasmids. The expressed protein was then purified by nickel chelate affinity chromatography. The cloned cDNA fragment was 580 bp long and contained an open reading frame of 525 bp. The deduced protein sequence was composed of 175 amino acids and had an estimated molecular weight of 19.90 kDa, with an isoelectric point of 5.53. Topology prediction revealed one N-glycosylation site, two casein kinase II phosphorylation sites, one N-myristoylation site, two protein kinase C phosphorylation sites, and one cell attachment sequence. Alignment indicated that the nucleotide and deduced amino acid sequences are highly conserved across several mammals, including Homo sapiens, Cavia porcellus, Equus caballus, and Felis catus, among others. The FTL gene was readily expressed in E. coli, which gave rise to the accumulation of a polypeptide of the expected size (25.50 kDa, including an N-terminal polyhistidine tag).

Genet. Mol. Res. 15(3): gmr8593
DOI: 10.4238/gmr.15038593