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Table of contents: 2021

Research Article

Staphylococcus aureus is one of the main pathogens of importance in health care. Distributed worldwide, it has considerable impact on community and nosocomial infections. This bacteria has the tst and lukS-F PV genes that code for the TSST-1 toxin and leucocidin. These pathogenic microorganisms have the ability to survive for long periods on inert surfaces such as mobile phone screens. Senior dentistry students work in clinics and use their cell phones often, which could potentially spread this pathogen. We looked for the tst and lukS-F PV genes in S. aureus isolated from mobile phone screens of final year dentistry students. This was a descriptive cross-sectional observational study using 92 samples from the mobile phone screens of dental students, among which 16 were positive for S. aureus. They were identified by means of culture methods and detection of the nuc, nucA and femB genes.  The DNA was extracted using the alkaline lysis method; PCR was used in the molecular identification of the tst and lukS-F PV genes. Nine of the 16 S. aureus isolates had the tst gene, and 1/16 the lukS-F PV gene. This study shows the high frequency of virulent S. aureus on the mobile phone screens of dental students, which may contribute to the spread of this important pathogen.

Genet. Mol. Res. 20(3): GMR18928
DOI: 10.4238/gmr18928
Research Article

Water stress triggers various cellular responses in plants, altering normal metabolic flow. Pyruvate, an important component of the glycolysis pathway, is directly involved in cell processes, triggering genes that influence drought tolerance. Research with Arabidopsis has shown that synthetic pyruvate relieves drought damage. We evaluated the effects of exogenous pyruvate at 100 and 50,000 µM on mitigation of drought stress in two peanut cultivars submitted to water restriction. The evaluations were based on growth, gas exchange, and photosynthesis rate analyses. In addition, superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX) enzymes, and free proline were also assayed. In general, exogenous application of pyruvate contributed to mitigate the effects of water stress in the cultivar IAC Caiapó (sensitive to drought), based on gas exchange and instantaneous efficiency of water use. Exogenous pyruvate contributed to restore the action of antioxidative enzymes in BR 1 (tolerant to drought), based on measures of SOD (45%), CAT (129%) and APX (60%) in stressed plants, and full recovery at 50,000 µM. When treated with proline, stress attenuation was found only at 100 µM in both cultivars; the excess seemed to have a negative effect on stressed plants, probably affecting the cell environment.

Genet. Mol. Res. 20(3): GMR18907
DOI: 10.4238/gmr18907
Research Article

Currently, the use of cell phones is booming within the health system. Since they are frequently used, they have become an important vehicle for nosocomial infections, with Staphylococcus aureus being the most commonly found pathogen. We tested for resistance to beta-lactams in S. aureus isolated from phone screens of senior dentistry students who were involved in pre-professional clinical practice. Out of a total of 220 students, 92 participated in the study, from which 16 S. aureus positive samples were obtained; these samples are relevant due to the fact that the participants were in contact with patients. The S. aureus genes were identified by means of a PCR and the antibiotic resistance by using the Kirby Bauer's diffusion technique. All 16 isolated strains contained the blaZ gene; in seven the mecA gene was identified. Phenotypic resistance to penicillin and oxacillin manifested in 12 and 7 strains, respectively. We conclude that dental professional cell phones have potential as a nosocomial risk for pathogenic bacterial contamination.

 

Genet. Mol. Res. 20(3): GMR18931
DOI: 10.4238/gmr18931
Research Article

Canine distemper is a highly infectious disease, distributed throughout the world. It is characterized by lymphotropism, neurotropism, and epitheliotropism, resulting in severe clinical changes and death. We report on the clinical and hematological findings of dogs with neurological distemper. Thirty-two mixed breed dogs of both sexes and of various age groups with clinical presentation suggestive of distemper with neurological involvement were evaluated. Blood and urine samples were collected for hematological and PCR analysis. Of the 32 animals evaluated by the RT-PCR technique, 22 were positive for the distemper virus. In the clinical presentation of distemper positive animals, neurological disorders stood out, with myoclonus being the most prevalent (18/22). In the hematological evaluation, erythrocytes and leukocytes were within the reference range; thrombocytopenia and lymphopenia were the most relevant findings in dogs with neurological involvement and could be used by veterinary clinicians as auxiliary diagnostic parameters.

Genet. Mol. Res. 20(3): GMR18884
DOI: 10.4238/gmr18884
Research Article

The study of genetic diversity of a population is one of the pillars to make selection in a breeding program successful. There are several techniques capable of estimating genetic divergence. Among them, those based on multivariate statistics deserve attention. Recently, methodologies based on Artificial Neural Networks (ANN) have been used to study the genetic diversity of a population. One of the strategies within ANN is Kohonen’s self-organizing maps (SOMs), which allows the organization of genetic diversity.  We estimated and organized the genetic divergence of pepper and chili genotypes Capsicum annum) for selection of diallel crosses. The experiment was conducted in a greenhouse in a completely randomized design with four replications. Nine commercially important genotypes of C. annum were evaluated, based on seven quantitative characters of the fruit. Univariate analysis was performed by analysis of variance and cluster mean. Multivariate [unweighted pair group method with arithmetic means (UPGMA) and Tocher)] and machine-learning techniques [SOMs] were employed. The genotypes showed high genetic variability for all traits. The traits total mass of raw fruit and fresh fruit length contributed the most to genetic diversity. UPGMA and Tocher classified the genotypes into two and four clusters, respectively. Through SOMs, it was observed that the neighborhood pattern between chili and pepper was obtained in only seven of the 12 neurons previously established. Overall, the use of SOM allowed the organization of genetic diversity among the genotypes. Specifically, SOM did not recommend crossing genotypes from the Cascadura Ikeda chili x Giant Ruby chili, Spicy for Pot pepper x Yellow Jamaica pepper, and Volcano pepper x Peter Pepper for variability exploration.

Genet. Mol. Res. 20(3): GMR18888
DOI: 10.4238/gmr18888
Research Article

Colombian creole breeds Blanco Orejinegro (BON) and Sanmartinero (SM) are widely used as pure breeds and in crossbreeding programs due to their excellent performance in the double ability of milk and meat production. We examined genomic regions and genes that from generation to generation have been selected by positive natural selection in favor of the adaptability and reproductive performance of these two Colombian creole breeds. Natural selection of genomics region and genes is one of the main evolutive changes resulting in phenotypic adaptations. The selected genomic regions can be detected by comparing differences in regional linkage disequilibrium (LD) between cattle populations with potential adaptations for economic traits. In this study, we used 58,868 single nucleotide polymorphisms (SNPs) from BON and 57482 SNPs from SM, using genotyping data from 1262 BON and 742 SM animals to estimate the variation of genome-wide LD between populations using the VARLD program. The top 0.1 and 0.01th percentiles of standardized VarLD scores were used as a criterion for all comparisons. A total of 10 selection signatures on chromosomes 3, 5, 11, 15, 18, 21, 22, 23, 25 and 29 were identified in all populations. These signatures overlapped with quantitative trait loci for adaptability and reproductive performance in both breeds. Within the signature located between 23,903,882 and 23,955,588 bp on chromosome 18, we identified the SLC6A2 gene involved in the response to high stress. Also, we identified the genes CTDSP2, CES1, CFAP161, CLEC14A, HIPK1, RBM4, SSTR involved in the expressions of economic traits (meat and milk production), KDMID, OLFML3 genes involved in reproductive traits (age at first calving and calving interval), and ATP23, LRRTM1, SLC6A2, DEK, SYT6, KDMID genes involved in cellular stress response and response to important environmental changes such as high temperature. We conclude that these genomic regions seem to point toward a recent selection in BON and SM populations. These regions can be used in selection and conservation programs.

Genet. Mol. Res. 20(3): GMR18882
DOI: 10.4238/gmr18882
Research Article

The Colombian Creole bovine breeds Blanco Orejinegro (BON) and Sanmartinero (SM) are the most important of the Creole breeds in Colombia because they are the most numerous, the most widely used in their pure form or in crosses with foreign breeds, and because they are dual-purpose producers of milk and meat. We estimated heritability for adaptability (coefficient of adaptability-CA and heat tolerance coefficient-HTC), and reproductive traits (age at first calving-AFC and calving interval-CI) using genomic and genealogical records. Variance components were estimated using the AIREMLF90 program under a mixed single-trait model to calculate genealogical and genomic heritability, based on genealogical, phenotypic, and genomic information.  Genomic information was obtained for 1,262 BON and 742 SM genotyped animals, with a total of 58,868 single nucleotide polymorphisms-SNPs in BON, and 57,482 SNPs in SM. Genealogical heritability values in BON for CA and HTC were 0.05 and 0.13, and 0.06 and 0.13 for AFC and CI, respectively. For the SM breed, genealogical heritability values ​​for CA and HTC were 0.08 and 0.09, and 0.20 and 0.07 for AFC and CI, respectively. Genomic heritability values in the BON breed ​​for CA and HTC were 0.06 and 0.16, and 0.07 and 0.14 for AFC and CI, respectively. For the SM breed, genomic heritability values ​​for CA and HTC were 0.10 and 0.11, and 0.20 and 0.07 for AFC and CI, respectively. Heritabilities for adaptability traits in both BON and SM were of medium to low magnitude, indicating the possibility of using these variables in selection schemes for adaptation-related characteristics.

Genet. Mol. Res. 20(3): GMR18878
DOI: 10.4238/gmr18878
Research Article

The management of nitrogen in wheat based on biological and environmental indicators can ensure productivity with a reduction in environmental impact. The objective of the study was to develop a more sustainable management of nitrogen use in wheat, considering the dose as a fraction of the total supply based on an estimate of the maximum technical and economic efficiency, and expected grain yield, in systems of succession of high and reduced release of N-residual, during acceptable and unfavorable crop years. The study was conducted from 2012 to 2018, in Augusto Pestana, RS, Brazil. Two experiments were conducted in each agricultural year and in each rotation system (soybean/wheat and corn/wheat), one to quantify the biomass yield and the other to determine grain yield. The experimental design was a randomized block with four repetitions in a 5 x 3 factorial, for doses of N-fertilizer (0, 30, 60, 90, 120 kg ha-1) and ways of supplying the nutrient [full condition (100%) at the phenological stage V3 (third expanded leaf); fractionated (70%/30%) at phenological stage V3/V6 (third and sixth expanded leaf) and fractionated (70%/30%) at phenological stage V3/R1 (third expanded leaf and ear differentiation)], in the soybean/wheat and corn/wheat succession systems with high and reduced N-residual release, respectively. More efficient use of nitrogen was obtained based on wheat grain productivity when applied at the full dose at the third expanded leaf stage. The supply of the maximum dose of nitrogen with an expectation of 3 t ha-1 ensures satisfactory productivity with reduced nutrient losses to the environment, especially in unfavorable years for cultivation, regardless of the succession system.

Genet. Mol. Res. 20(3): GMR18903
DOI: 10.4238/gmr18903
Research Article

Avena sativa is the sixth most produced cereal in the world. It is widely used for human consumption. Due to the bromatological quality of its forage, it is used for direct grazing, hay and silage. Due to the large number of interesting characteristics of forage white oats, the selection of unique characteristics becomes difficult and expensive for breeders. In this sense, the use of analysis with multiple characteristics can facilitate the process. Therefore, the objective of this work was to estimate genetic parameters of morphological characteristics, productivity, and quality of forages, as well as to define multiple characteristics that assist in the selection of promising white oat genotypes with forage profile through factor analysis. Field trials were carried out during the agricultural year of 2013 in the municipality of Capão do Leão, RS. The experimental design was in randomized blocks, with treatments arranged in four replications. The treatments corresponded to the genotypes CHIARASUL (G1), FAEM006 (G2), BARBARASUL (G3), BRISASUL, (G4) CGF03006 (G5), CGF07023-1 (G6), CGF07-74 027-1 (G7), CGF07033 (G8), CGF07033-1 (G9), CGF07041 (G10), CGF0705-7 (G11), CGF07060-2 (G12) and CGF07060-3 (G13). The characteristics analyzed were: plant height, leaf area, weight of fresh plants, weight of dry plants, number of tillers and levels of nitrogen, crude protein, phosphorus, potassium, calcium, magnesium, copper, zinc, manganese and iron. The data were submitted to the normality test and to various components of variance. Statistical analyses were performed using Selegen®, SAS® and Genes® software. The white oat genotypes expressed high genetic variability and possibility of selection for leaf area, fresh forage mass, dry forage mass, number of tillers and calcium content. Simultaneously the magnesium content with multiple traits + zinc content, dry matter + fresh mass, nitrogen content + calcium content, crude protein + potassium content and number of tillers, showing potential to select genotypes of interest for genetic improvement.

Genet. Mol. Res. 20(3): GMR18451
DOI: 10.4238/gmr18451
Research Article

Many research areas have datasets that face the challenges of high dimensionality and multilinearity. Although existing methods are efficient for constructing a complete model, it is often necessary to select the most important explanatory variables to obtain more parsimonious models. We evaluated and built models using three methods of selection of variables applied to data of single nucleotide polymorphism (SNP) markers and near-infrared spectroscopy (NIR), in addition to assessing the improvement in prediction quality when compared to the use of complete data. These included ordered predictors selection associated with partial least squares regression (PLS-OPS), sparse partial least squares regression (SPLS), and Supervised BLasso, the latter being an adaptation of the Bayesian Lasso (BLasso) method for variables selection. We used simulated data sets evaluated in two scenarios, and three real data sets, composed of one set of SNPs and two sets of NIR data. The predictive quality of each model was evaluated based on the mean correlation coefficient between predicted and actual values, and the square root mean squared error. In the set of simulated data evaluated in the first scenario, in terms of predictive capacity, the models after variables selection were similar when compared to the use of the complete data model, whereas in the second scenario, on average, the models performed better after the selection of variables, with SPLS being superior to the other methods. In the real SNPs dataset, the PLS-OPS had a good performance, attesting the usefulness of this method for this kind of data. In the NIR datasets, the predictive quality of models after variable selection were close to those obtained with the complete data. In general, when using the selection methods, the models maintained a good predictive capacity and became simpler due to the considerable reduction in the number of variables.

Genet. Mol. Res. 20(3): GMR18909
DOI: 10.4238/gmr18909
Research Article

There are over 7,000 components in cigarette smoke, 70 of which are considered genotoxic and carcinogenic. N-Nitrosamine 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) is one of these components. When treated with NNK at concentrations of as low as 0.1 nM, breast and lung cells are known to acquire malignant properties. The liver plays an important role in toxin metabolization, yet little is known about the cytotoxic effects of NNK on hepatocytes. Therefore, we assessed the effects of NNK on immortalized murine hepatocytes (AML12 cell line) using a repeated exposure approach. AML12 cells were subjected to either short- (single exposure for up to 72 h) or long-term (cumulative exposure for 90 days) testing, at various NNK concentrations (0.1, 10, and 1000 nM). DNA damage was analyzed using the comet assay, a gold-standard technique to assess DNA strand breaks in eukaryotic cells. The cells subjected to short-term exposure had a significantly increased proliferation rate in the 0.1 and 10 nM groups when compared to controls. Furthermore, the cells from the 10 nM group exhibited increased migration rate after cumulative exposure to NNK. The clastogenic effect of NNK increased in a concentration-dependent manner up to 10 nM. We conclude that NNK is genotoxic and significantly alters cell viability and migration, contributing to malignant transformation of hepatocytes.

Genet. Mol. Res. 20(3): GMR18832
DOI: 10.4238/gmr18832
Research Article

Helicobacter pylori is a gram-negative bacterium associated with the development of severe gastric pathologies, such as atrophy, metaplasia, and gastric adenocarcinoma. This microorganism is considered a class I carcinogen by the International Agency for Research on Cancer. The virulence genes in the strain causing infection influence the clinical outcome and can be used as specific markers for the severity of gastric diseases. We evaluated H. pylori infection and associations of cagA, vacA and dupA virulence genes with gastric pathologies. Antral and gastric body biopsies of 117 patients with dyspepsia were analyzed by histological and molecular techniques. Screening for H. pylori infection was performed using the hpx gene (16S rRNA). Positive samples were evaluated for vacA, cagA, and dupA virulence genes. The clinical outcomes presented by the patients were stratified according to severity, being considered severe lesions atrophy, metaplasia and adenocarcinoma. Gastritis, duodenitis, esophagitis, ulcer, and xanthelasma were considered non-severe pathologies. The prevalence of infection was 64.1%, with a high frequency of strains positive for cagA (80.0%), dupA (70.7%), and vacA (56.0%). The cagA gene was detected in all isolates from patients with severe pathologies, whereas the vacA gene was not detected in this group. Simultaneous detection of the three genes was observed in 14.3% and 35.8% of the isolates from individuals with severe and non-severe pathologies, respectively. Furthermore, fewer virulence genes were detected in isolates from patients with severe disease (0.7) than in isolates from non-severe cases (1.4). Patients with severe diseases had a higher mean age and greater number of gastric diseases than patients with non-severe pathologies. The circulating H. pylori strains in the Brazilian Midwest exhibit high heterogeneity in the frequencies of virulence genes. Individual virulence factors and their combinations may influence clinical outcomes.

Genet. Mol. Res. 20(3): GMR18883
DOI: 10.4238/gmr18883
Research Article

Neurodegenerative diseases affect nerve cells, causing impairment in mobility and cognitive abilities, characteristics present in two highly relevant neuropathologies, amyotrophic lateral sclerosis (ALS), and multiple sclerosis (MS). The pathogenesis of these diseases, although distinct, share common neurodegenerative mechanisms. Several studies suggest that miRNAs, small molecules of endogenous non-coding RNA, may assume an important regulatory role in neurodegeneration where their differential expression enables the elucidation of the molecular basis of this process, in addition to offering possible therapeutic targets. We performed a systematic review of the literature through a search in Web of Science, Pubmed/NCBI, and virtual health library (BVS) databases, applying terms indexed in MeSH and DeCS, such as “microRNA”, “amyotrophic lateral sclerosis” and “multiple sclerosis”. We included studies in English, Portuguese, or Spanish, published in the last five years, relating miRNAs associated with pathophysiological pathways of ALS and MS. We excluded studies on non-humans or with polymorphisms in pre-miR genes, duplicated data, or with unavailable data, resulting in a final number of 70 studies included. According to systematic review findings, the families miR-9, miR-23, miR-26, miR-125, miR-133, miR-146, miR-181, miR-206, miR-320, and miR-326 are frequently dysregulated in ALS and MS. The miR-155 and let-7 families are commonly associated with both diseases, regulating genes involved in mechanisms such as neuroinflammation, neurogenesis, and cell differentiation. The elucidation of the newest miRNAs and their main pathways may assist in the characterization of the molecular basis of these diseases, mainly involving those associated with pro-inflammatory processes, microglia activation, and neuronal death, mechanisms associated with ALS. They also can involve myelin breakdown mechanisms, astrocyte damage, and neuronal death, which are related to MS. These molecular markers may help determine biomarkers for amyotrophic lateral sclerosis and multiple sclerosis.

Genet. Mol. Res. 20(3): GMR18843
DOI: 10.4238/gmr18843
Research Article

Gaucher Disease (GD) is an autosomal recessive genetic disorder, caused by a deficiency of the enzyme B-glucocerebrosidase (GBA). In Colombia, despite considerable research on GD, the frequency of the GBA gene variants in the population is unknown, making it difficult to determine the risk of occurrence based on carriers. To identify the variants of the GBA gene, a transversal, descriptive, non-experimental study was carried out with the results obtained from the sequencing of the complete exome of 320 patients with complex disease, without clinical suspicion of GD. Bioinformatics software was used to analyze the clinical significance of the different variants. The population frequency of each variant was calculated, and a network of interaction of the GBA gene was developed. As a result, 41 variants associated with the GBA gene were found; 21/41 of the variants reported have a benign significance, 5/41 of the variants reported were classified as pathogenic or probably pathogenic and 7/41 of the variants reported presented uncertain significance. The gene interaction network showed close associations between GBA and genes PSAP, SCARB2, LAMP2, all of them focused on functions of vacuolar locations, lysosomal and vacuolar lumen instructions, vacuolar and lysosomal membranes. We conclude that the impact on the phenotype highly depends on the pathogenicity of the variants. In our sample, a high frequency of benign variants was found; however, pathogenic variants were detected, which should be the object of study in precision medicine associated with GD.

Genet. Mol. Res. 20(2): GMR18818
DOI: 10.4238/gmr18818
Research Article

Aspergillus flavus produces carcinogenic aflatoxins. This species is divided based on the type of sclerotia produced, designated as “S” for numerous small and “L” for fewer and large. “L” strains are concerning since they are prevalent in corn, peanut, rice, and soil samples. Nearly all “S” strains and approximately 70% of “L” strains produce aflatoxins. Host specificity within isolates is not well understood and needs to be better characterized. We isolated A. flavus from commercial peanut samples from Southern Brazil and investigated their genetic variability and their genetic correlation with four A. flavus isolates previously obtained from commercial bulgur wheat in the same region. We also evaluated the antifungal activity of essential oils on some of the isolates. Eleven “L” type A. flavus strains were isolated from peanut kernels. Eight of these isolates were considered aflatoxigenic, based on thin-layer chromatography and culture techniques. The genetic biodiversity of the A. flavus isolates was analyzed using Random Amplified Polymorphic DNA (RAPD) and Inter Simple Sequence Repeat (ISSR) analyses, which indicated differences according to host, however, did not regarding aflatoxin production. Essential oils of oregano, thyme, cinnamon, lavender, and fennel inhibited the isolate’s growth. In conclusion, A. flavus isolates differ according to host and essential oils have potential to control this fungus.

Genet. Mol. Res. 20(2): GMR18787
DOI: 10.4238/gmr18787

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