Research Article

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

Displaying 31 - 45 of 361
Research Article

Varroa destructor mites pose an increasing global threat to the apicultural industry and agricultural ecology; however, the issue of whether certain environmental factors reflect the level of mite infection is far from resolved. Here, a wireless sensor network (WSN) system was used to examine how V. destructor, which has vital impacts on honeybee (Apis mellifera) health and survival, affects the temperature and humidity of honeybee hives in a field experiment. This approach may facilitate early identification of V. destructor in hives, and thus enable timely remedial action. Using quantitative PCR, we also evaluated the expression of two genes, adipokinetic hormone (AKH) and adipokinetic hormone receptor (AKHR).The results showed that temperature in highly infested broods was higher than that in broods with low infestation. Moreover, mite infection in honeybee colonies was positively correlated with temperature but negatively correlated with humidity (P Varroa infection not only causes changes in temperature inside honeybee colonies, but also affects the expression of honeybee energy metabolism genes.

Genet. Mol. Res. 15(3): gmr8997
DOI: 10.4238/gmr.15038997
Research Article

Saponins are naturally-occurring units with broad diversity and are usually recognized as phytoanticipins. In order to develop new saponin chemical entities with high activity against Magnaporthe oryzae, we selected oleanolic acid (OA), which has wide natural distribution and rich content in plants. We used the ability of OA to act as an aglycone for glycosylation to obtain information on the structure-activity relationship (SAR) for rational molecular pesticide design. Oleanolic mono- or di-glycosides were synthesized at either the C3-hydroxy and/or C28-carboxyl position, using trichloroacetimidate or glycosyl bromide donors, respectively. Structures were confirmed by [1H]-,[13C]-NMR. Furthermore, the activity of the synthesized glycosides against M. oryzae was assessed in vitro, based on the mycelium growth rate. The twenty five oleanolic mono- or di-glycosides comprised fourteen saponins with 3-monosaccharide residue 1a-1n, six saponins with 28-monosaccharide residue 2a-2f, and five saponins with 3, 28-monosaccharide residue 3a-3e; all showed different activities against M. oryzae according to their different structures. We concluded that the optimal oleanolic mono- and di-glycoside structure for activity against M. oryzae is a C3 connection of a hexose such as mannose, galactose, or glucose, in combination with a C28 connection to a small group such as allyl or a C3 connection to a pentose accompanied by a larger group such as another pentose or heptenyl at C28.

Genet. Mol. Res. 15(3): gmr8998
DOI: 10.4238/gmr.15038998
Research Article

Epilepsy refers to a clinical syndrome generated by spontaneous seizures in the central nervous system. Epilepsy triggers a complex pathological process including inflammatory response and aquaporin 4 (AQP4) increase. It has been reported that AQP4 helps to enhance the immunological function of the central nervous system in pathological conditions, but the relationship between AQP4 and inflammatory cytokines is poorly understood in chronic epilepsy processes. As an inhibitor of sulfonamide carbonic anhydrase (CA), acetazolamide (AZA) may inhibit water infiltration through AQP4. In this context, pentylenetetrazole (PTZ) is used to induce the chronic epilepsy model in rats to study the chronic epilepsy effects of AQP4 inhibition on proinflammatory cytokine expression in the hippocampus and proinflammatory cytokine quantification analysis of the plasma. Based on the assumption that AQP4 regulates proinflammatory cytokine expression, this article aims to demonstrate this effect in chronic epilepsy of rats. Rats were divided into four groups and were treated with different drugs: saline (Control), acetazolamide (AZA), pentylenetetrazole (PTZ), and pentylenetetrazole plus acetazolamide (PTZ+AZA). The data showed that seizures increased proinflammatory cytokine expression and that AZA significantly inhibited AQP4 expression. Overall, the results suggested that AQP4 inhibition could weaken excitotoxicity in epileptogenesis by reducing proinflammatory cytokines in the hippocampus. The findings provide a new insight into the involvement of cerebral edema insult and proinflammatory cytokines in the process of chronic epilepsy.

Genet. Mol. Res. 15(3): gmr9012
DOI: 10.4238/gmr.15039012
Research Article

A basic problem of proteomics is identifying the subcellular locations of a protein. One factor making the problem more complicated is that some proteins may simultaneously exist in two or more than two subcellular locations. To improve multisite prediction quality, it is necessary to use effective feature extraction methods. Here, we developed a new feature extraction method based on the pK value and frequencies of amino acids to represent a protein as a real values vector. Using this novel feature extraction method, the multi-label k-nearest neighbors (ML-KNN) algorithm and setting different weights into different attributes’ ML-KNN, known as wML-KNN, were employed to predict multiplex protein subcellular locations. The best overall accuracy rate on dataset S1 from the predictor of Virus-mPLoc was 59.92 and 86.04% on dataset S2 from Gpos-mPLoc, respectively.

Genet. Mol. Res. 15(3): gmr9013
DOI: 10.4238/gmr.15039013
Short Communication

Fifteen microsatellite loci were identified in the tetraploid spined loach, Cobitis biwae (Teleostei: Cobitidae). Among these, 14 were polymorphic (5-31 alleles) and showed moderate to high cross-species amplification transferability in four related species, Cobitis matsubarai, Cobitis taenia, Misgurnus anguillicaudatus, and Misgurnus fossilis. The loci, described herein, will be useful for population genetics, phylogeny, parentage analysis, and detection of hybridization among Cobitis species.

Genet. Mol. Res. 15(3): gmr9027
DOI: 10.4238/gmr.15039027
Research Article

The genus Brachiaria contains species that have great economic importance in the Brazilian agricultural sector, as they enable cattle ranching on acid and poor soils with species that are resistant to spittlebugs and form crop-livestock-forest integration systems. The genus mainly consists of tetraploid (2n = 4x = 36) and apomictic species such as B. decumbens and B. brizantha. Sexuality is found in diploid species (2n = 2x = 18) such as B. ruziziensis. Interspecific hybridization between species of interest is possible by the artificial tetraploidization of B. ruziziensis and the subsequent hybridization with genotypes of B. brizantha and B. decumbens. Therefore, tetraploidized plants have to have normal meiosis or low rates of irregularities, as well as produce viable pollen grains. The objective of this study was to compare meiosis and pollen grain viability and morphology in artificially tetraploidized B. ruziziensis with that of descendants generated from crossing and selfing. The frequency of meiotic abnormalities ranged from 4.43 to 11%, and pollen viability ranged from 61 to 85%. Abnormalities were detected from prophase I to the tetrad stage with a variable frequency between the genotypes. The meiotic behavior of the artificially tetraploidized plants was little affected, and the pollen viability of the genotypes was high. Regarding pollen grain ultrastructure, there were no variations or morphological changes in the different genotypes. The genotypes have meiotic stability and high pollen viability, and can be incorporated into Brachiaria breeding programs.

Genet. Mol. Res. 15(3): gmr8737
DOI: 10.4238/gmr.15038737
Research Article

Melon (Cucumis melo L.) is an important vegetable crop that ranks second in salt tolerance among the Cucurbitaceae. Previous studies on the two muskmelon cultivars ‘Bing XueCui’ (BXC) and ‘Yu Lu’ (YL) revealed that they had different characteristics under salt stress, but the molecular basis underlying their different physiological responses is unclear. Here, we combined a physiological study with a genome-wide transcriptome analysis to understand the molecular basis of genetic variation that responds to salt stress in the melon. BXC performed better under salt stress than YL in terms of biomass and photosynthetic characteristics, because it exhibited less reduction in transpiration rate, net photosynthesis rate, and stomatal conductance under 150-mM NaCl stress than YL. A transcriptome comparison of the leaves of the cultivars revealed that 1171 genes responded to salt stress in BXC while 1487 genes were identified as salt-stress-responsive in YL. A real-time polymerase chain reaction analysis of 12 of the responsive genes revealed that there was a strong, positive correlation with RNA sequencing data. The genes were involved in several pathways, including photosynthesis, the biosynthesis of secondary metabolites, metabolism, and plant hormone signal transduction, and their expression levels differed between the two cultivars in response to salt stress. This study provides a molecular perspective of two melon cultivars in response to salt stress, and its results could be used to investigate the complex molecular mechanisms underlying salt tolerance in the melon.

Genet. Mol. Res. 15(3): gmr8738
DOI: 10.4238/gmr.15038738
Research Article

The Chinese hawthorn (Crataegus pinnatifida Bge. var. major N.E.Br.) is uniquely originated in northern China. The ecological and horticultural importance of Chinese hawthorn is considerable and some varieties are valued for their fruit or medicine extracts. Its taxonomy and phylogeny remain poorly understood. Apart from general plant morphological traits, pollen is an important trait for the classification of plants and their evolutionary origin. However, few studies have investigated the pollen of Chinese hawthorn. Here, an analysis of plant and pollen morphological characteristics was conducted in 57 cultivars from the Shenyang region. Thirty plant morphological characters and nine pollen grain characters were investigated. The plant morphological analysis revealed that the coefficient of variation for 13 traits was >20%, which indicates a high degree of variability. We also found that the pollen grains varied greatly in size, shape (from prolate to perprolate), and exine pattern (striate-perforate predominantly). The number of apertures was typically three. Based on these findings, we suggest that pollen morphology associated with plant morphological traits can be used for classification and phylogenetic analysis of Chinese hawthorn cultivars. In sum, our results provide new insights and constitute a scientific basis for future studies on the classification and evolution of Chinese hawthorn.

Genet. Mol. Res. 15(3): gmr8739
DOI: 10.4238/gmr.15038739
Case Report

Albinism is a diverse group of hypopigmentary disorders caused by multiple-genetic defects. The genetic diagnosis of patients affected with albinism by Sanger sequencing is often complex, expensive, and time-consuming. In this study, we performed targeted next-generation sequencing to screen for 16 genes in a patient with albinism, and identified 21 genetic variants, including 19 known single nucleotide polymorphisms, one novel missense mutation (c.1456 G>A), and one disease-causing mutation (c.478 G>C). The novel mutation was not observed in 100 controls, and was predicted to be a damaging mutation by SIFT and Polyphen. Thus, we identified a novel mutation in SLC45A2 in a Chinese family, expanding the mutational spectrum of albinism. Our results also demonstrate that targeted next-generation sequencing is an effective genetic test for albinism.

Genet. Mol. Res. 15(3): gmr8743
DOI: 10.4238/gmr.15038743
Research Article

The fragrance gene, betaine aldehyde dehydrogenase 2 (Badh2), has been well studied in many plant species. The objectives of this study were to clone Badh2 and compare the sequences between aromatic and non-aromatic coconuts. The complete coding region was cloned from cDNA of both aromatic and non-aromatic coconuts. The nucleotide sequences were highly homologous to Badh2 genes of other plants. Badh2 consisted of a 1512-bp open reading frame encoding 503 amino acids. A single nucleotide difference between aromatic and non-aromatic coconuts resulted in the conversion of alanine (non-aromatic) to proline (aromatic) at position 442, which was the substrate binding site of BADH2. The ring side chain of proline could destabilize the structure leading to a non-functional enzyme. Badh2 genomic DNA was cloned from exon 1 to 4, and from exon 5 to 15 from the two coconut types, except for intron 4 that was very long. The intron sequences of the two coconut groups were highly homologous. No differences in Badh2 expression were found among the tissues of aromatic coconut or between aromatic and non-aromatic coconuts. The amino acid sequences of BADH2 from coconut and other plants were compared and the genetic relationship was analyzed using MEGA 7.0. The phylogenetic tree reconstructed by the Bayesian information criterion consisted of two distinct groups of monocots and dicots. Among the monocots, coconut (Cocos nucifera) and oil palm (Elaeis guineensis) were the most closely related species. A marker for coconut differentiation was developed from one-base substitution site and could be successfully used.

Genet. Mol. Res. 15(3): gmr8748
DOI: 10.4238/gmr.15038748
Research Article

The correlation between the -104C/T polymorphism in the peptidyl arginine deiminase 4 (PADI4) gene and rheumatoid arthritis (RA) risk has been analyzed in several studies. However, the results are inconclusive and remain to be confirmed in several ethnic groups. The effect of the PADI4-104C/T polymorphism on RA risk in the Chinese population was evaluated in a meta-analysis. Studies with dates of publication up to July 2015 conforming to the inclusion criteria were retrieved from PubMed and Chinese databases. The associations were assessed with pooled odds ratios (ORs) and 95% confidence intervals (CIs). Ten studies, including 2119 RA cases and 1962 controls, that conformed to the study criteria were included in this analysis. The overall analysis indicated a significant association between the PADI4-104C/T polymorphism and RA risk in the Chinese population (T vs C: OR = 1.45, 95%CI = 1.18-1.78; TT vs CC: OR = 1.49, 95%CI = 1.24-1.80; TT vs CC+CT: OR = 1.28, 95%CI = 1.08-1.51; TT+CT vs CC: OR = 1.75, 95%CI = 1.30-2.37). Analysis of data stratified by the geographic area and source of controls revealed that the PADI4-104C/T polymorphism was significantly associated with RA risk in a North Chinese population. In conclusion, the results of this meta-analysis indicated that the PADI4-104C/T variants could influence the risk of RA in the Chinese population; further studies in other ethnic groups are required to draw definite conclusions.

Genet. Mol. Res. 15(3): gmr8750
DOI: 10.4238/gmr.15038750
Research Article

Genetic parameters and associations between morpho-agronomic traits and nutritional efficiencies of arabica coffee cultivars were estimated to identify promising traits to assist in the selection of coffee genotypes efficient in potassium use, under limiting conditions of this nutrient. The experiment was conducted in a greenhouse with 20 arabica coffee cultivars grown in nutrient solution with a low potassium level (1.5 mM), using a randomized block design with three replicates. The traits evaluated were plant height, number of leaves, number of nodes, internode length, stem diameter, leaf area, rooting efficiency, potassium absorption efficiency, potassium translocation efficiency, biomass production efficiency, and potassium use efficiency. Genetic variability among coffee cultivars for all the evaluated traits was found. The phenotypic variance for all traits showed a higher contribution of genetic variance compared to environmental variance. Plant height, internode length, stem diameter, leaf area, biomass production efficiency, and potassium use efficiency had a genotypic determination coefficient (H2) above 80% and variation index greater than one. Leaf area and stem diameter had significant and positive genetic correlations with rooting, biomass production, and potassium use efficiencies. Stem diameter has great potential for use in breeding programs with a goal of indirect selection of cultivars that have greater potassium use efficiency in environments with restrictions of this nutrient.

Genet. Mol. Res. 15(3): gmr8753
DOI: 10.4238/gmr.15038753
Research Article

Colombian creole cattle have important adaptation traits related to heat tolerance and reproductive and productive efficiency. Romosinuano (ROMO) and Blanco Orejinegro (BON) are the most common breeds used by Colombian cattle breeders. Growth traits are of prime importance in these animals, which are mainly raised for beef production. Genes encoding growth hormone, growth hormone receptor, homeobox protein, insulin growth factor binding protein 3, leptin, and myostatin have been associated with physiological growth pathways in cattle and other species. We therefore aimed to identify single nucleotide polymorphisms (SNPs) within these genes in ROMO, BON, and Zebu cattle. DNA regions of these genes were sequenced in 386 animals; 47 new SNPs were found, of which 14 were located in the exonic regions, thereby changing the protein sequence. An association of SNPs with weaning weight (WW), daily weight gain at weaning (DWG), and weight at 16 months (W16M) traits was deduced. The genetic analysis revealed several SNPs related to these traits. The SNP GhRE06.2 had a significant association with WW and the SNP Lep03.4 was highly associated with DWG and W16M. Other polymorphisms were significantly associated with WW and DWG, although they did not surpass the Bonferroni significance threshold. The new mutations identified may indicate important points of genetic control in the DNA that could be responsible for changes in the expression of the analyzed traits. These SNPs might be used in future breeding programs to improve the productive performance of cattle in beef farms.

Genet. Mol. Res. 15(3): gmr8762
DOI: 10.4238/gmr.15038762
Research Article

The terrestrial snail Helix pomatia (Gastropoda: Stylommatophora: Helicidae) is one of the largest gastropod species in Europe. This species is strictly protected in some European Union countries; however, at the same time, it is also farmed and commercialized for human consumption. Here, we describe 11 microsatellite markers that are very useful in population genetic studies for assessing the status of both wild and farmed populations of this species of community interest. The microsatellites were isolated using 454 pyrosequencing technologies and 11 primer pairs were selected and used for genotyping an H. pomatia population and also checked for cross-species amplification on H. lucorum and H. lutescens specimens. The number of alleles per locus ranged from 3 to 13 and observed heterozygosity was between 0.458 and 0.917. Seven of these loci were polymorphic in H. lucorum, and four in H. lutescens. This set of nuclear markers provides a powerful tool for population genetic studies of this species of community interest, and also for closely related species. The described microsatellite markers should also facilitate the identification of populations of conservation concern.

Genet. Mol. Res. 15(3): gmr8817
DOI: 10.4238/gmr.15038817
Research Article

Endophytic microorganisms, mainly bacteria and fungi, have intrinsic relationships with the host plants, involving complex chemical and genetic communication networks. The relationship among these organisms involves the development of regulatory mechanisms of gene expression that control their development and response to different interactions. Although RNA molecules are already being used in studies of microorganism diversity and taxonomy, for example, using comparisons of rRNA regions, they may also be useful tools in the exploration of gene regulation and modeling of other molecules, such as the analysis of microRNA and small interfering RNAs. Transcriptional profile analyses are capable of providing robust information on biosynthetic pathways, genes involved in the interaction and differential production of metabolites by endophytes, using RNA-seq approaches. In-depth studies of RNA types and their functions in endophytes may provide valuable information that can be used for biotechnological manipulation of microorganisms to produce metabolites, bioremediation, biological control of pathogens, and decrease plant diseases, among other economically important applications. Our study highlights the present state of knowledge of studies involving endophytes, RNA molecules, and future perspectives.

Genet. Mol. Res. 15(3): gmr8879
DOI: 10.4238/gmr.15038879