Table of Contents | Genet. Mol. Res. 2020 (2)
Atherosclerosis is a multifactorial chronic-inflammatory disease related to endothelial aggression to the intima layer of medium and large caliber arteries. Hyperlipidemia and atherosclerosis cause eNOS to lose its function, producing superoxide and leading to endothelial dysfunction. The nitric oxide derived from eNOS is anti-atherogenic. Single nucleotide polymorphisms in the promoter region reduce its activity and predispose individuals to cardiovascular disease. We analyzed the T786C polymorphism of eNOS in atherosclerotic patients under statin treatment, to determine the clinical importance of this type of genetic variation. The study of this polymorphism in atherosclerotic patients with stents could help predict the probability of restenosis. We collected 79 peripheral blood samples from patients diagnosed with atherosclerosis undergoing statin treatment. These included 35 stent patients and 44 patients without stents. The TC genotype was prevalent in stent patients who smoke but there was no significant relation between the T786C polymorphism and restenosis. Based on an in silico approach through molecular modeling and molecular docking, we found that statins stabilize the eNOS protein. Seven amino acid residues in the eNOS binding pocket interact with the statin molecule; this family of drugs acts by stabilizing the eNOS protein. Thus, the use of such drugs may help reduce the risk of restenosis.
Ginger (Zingiber officinale Roscoe) is a self-incompatible plant and has high rates of infertility; its genetic diversity only occurs via processes of mutation and natural selection. Since ginger is important as a condiment and as an herbal medicine, understanding its diversity to a greater degree can contribute both to its conservation and to its use in breeding programs. Considering the importance of the species and the characterization of material from on-farm conservation, this study aimed to evaluate, by means of ISSRs (Inter Simple Sequence Repeats) molecular markers of genetic diversity among individuals obtained in 19 urban and rural backyards in Alta Floresta, Mato Grosso state, Brazil. For the extraction of total DNA, the CTAB method was used and the amplifications were performed using nine ISSR primers. The UPGMA clustering method, when compared with the Ward and Nearest Neighbor methods, best showed genetic diversity, and the Bayesian analysis defined two distinct groups in the Z. officinale germplasm that was evaluated. The ISSR primers amplified a total of 78 fragments and revealed 88% polymorphism. The PIC varied between 0.40 and 0.87, with an average of 0.70, and was classified as median in the detection of polymorphism. The most dissimilar individuals were AF06 and AF12, while the least dissimilar were AF06 and AF04. The Nei (He) and Shannon (I) diversity indices demonstrated genetic variability within the two groups formed from the Bayesian analysis, and AMOVA indicated that the genetic diversity was greater within the groups (53.06%) than among them (46.94%). The absence of duplicates among the individuals analyzed indicates that they can be used to form an active germplasm collection with the aim of conserving and maintaining the genetic diversity of the species.
The soybean stem fly (Melanagromyza sojae) is a widely distributed and highly damaging soybean pest, recently introduced to Brazil and neighboring countries. The bioecology of this pest under South American growing conditions is largely unknown, including how infesting populations survive throughout the winter. Fly larvae collected in August 2019 from Persian clover Trifolium resupinatum in Santa Maria, southern Brazil, were identified as M. sojae via molecular characterization. Persian clover is commonly grown as a cattle forage crop in this region. This is the first report of M. sojae occurring on T. resupinatum, and of any overwintering host available to the pest in the New World. This finding will help understand the bioecology of M. sojae populations in Brazil, so that adequate pest management strategies can be planned for this invasive pest.
The Asteraceae have high ecological importance in the threatened Atlantic Forest biome, as most species are pioneers and nectar-producing plants. Using population genetic data could help develop adequate conservation strategies for species and biomes. However, no genetic data or microsatellite markers are available for most Atlantic Forest native Asteraceae species. In their absence, heterologous microsatellite markers could help conduct population genetic studies of less studied species. We evaluated the transferability and utility for population studies of 15 anonymous microsatellite primers pairs developed from other Asteraceae to four others, three of which are important in folk medicine (Baccharis milleflora, Baccharis articulata, Baccharis dracunculifolia) and a toxic species of veterinary importance (Senecio brasiliensis). We found that the microsatellite primers had high transferability to phylogenetically close Asteraceae species. Transferability rates were below those reported for other plant families. The transferred microsatellite primers gave low polymorphism frequencies and high null allele frequencies in the populations. A major factor contributing to this low transferability and high frequency of null alleles is probably the high genetic variation of tropical Asteraceae.
The study of microorganisms that inhabit the interior of plants (endophytes) has acquired great importance because of their potential to produce bioactive metabolites. Acmella ciliata (known in Brazil as jambu) is a native herb of South America, used in regional gastronomy and folk medicine in Amazonas - Brazil, has antibacterial properties, and may be a useful host for bioactive endophytes. We isolated endophytic microorganisms from A. ciliata and evaluated their ability to inhibit pathogenic fungi. We isolated 56 fungi and 39 endophytic bacteria, most of them from the leaves. The endophyte isolates were then tested in antagonism assays against the phytopathogens Fusarium decemcellulare and Colletotrichum gloeosporioides. The best antagonism index values against C. gloeosporioides were obtained with the endophytic fungus UEA-253 (40%), and the endophytic bacterium UEA-135 (46.3%). The highest antagonism index values were obtained against F. decemcellulare with the fungus UEA-234 (47.2%), and the bacterium UEA-135 (44.8%). The endophytic fungi with inhibitory bioactivity belong to the genera Curvularia, Colletotrichum, Plectosphaerella and Sordariomycetes, while the endophytic bacteria belong to the genera Bacillus, Pseudomonas and Enterobacter. We conclude that the endophytic fungi and bacteria isolated from A. ciliata have potential for use in the biocontrol of F. decemcellulare and C. gloeosporioides.
Cross-pollination and gametophytic self-incompatibility reduce the stability of Coffea canephora genotypes. This is an important crop for Brazil, the largest producer of this type of coffee and also a major exporter. The study of biometric characteristics is essential to assist in the selection of promising plant materials. We examined the diversity of morpho-agronomic traits of genotypes of C. canephora cv. Conilon through the evaluation of branch and leaf parameters. Assessments included plagiotropic branch length, number of nodes in plagiotropic branches, distance between nodes in plagiotropic branches, orthotropic branch length, number of nodes in orthotropic branch, distance between nodes in orthotropic branch, plant height, canopy diameter, leaf length, leaf width, and leaf area in two periods. The data from the 43 coffee genotypes were tested by multivariate and cluster analyses. Six groups were formed by the Tocher optimization method, and five groups by the unweighted pair group method with arithmetic mean (UPGMA) hierarchical method, suggesting an important genetic variability among plant materials. Both Tocher optimization and UPGMA hierarchical methods were consistent for clustering the genotypes, ordering them in six and five dissimilar groups, respectively, with genotypes 25 and 37 standing out with the greatest dissimilarity, constituting isolated groups by both methods. Pearson’s correlation ranged from very weak to very strong, positive and negative, among the characteristics, as also shown by principal component analyses. These analyses indicated the morpho-agronomic traits with a greater degree of correlation, assisting in the choice of promising plant materials. The genetic parameters estimates demonstrate genetic variability and thus breeding potential within the Conilon coffee genotypes studied. These results emphasize the usefulness of biometric evaluations as a tool for the identification and breeding of genotypes to compose new Conilon coffee cultivars.
Due to the increasing popularity of consuming only plant products, including vegetarianism and more recently veganism, vegetables and fruits have gradually become an increasingly important component of the human diet, worldwide. The large diversity of Brazilian tropical fruits, such as murici, Byrsonima crassifolia, (Malpighiaceae), associated with a dearth of information concerning this and other exotic species, has stimulated research on techniques to obtain increases in productivity, inserting these fruit species into regional and national agribusiness. We evaluated the variability of B. crassifolia genotypes and quantified the relative contribution of 12 morphological traits of its fruits and seeds. Ripe fruits were collected from 20 different genotypes (trees. The fruits were collected during the harvest season from December 2017 to January 2018. Twenty fruits of each genotype were selected; that were visually appealing, whole and without deformation, totaling 400 samples. We measured the length, width, thickness, weight, and volume of the fruits, the length, width, thickness and weight of the seed and the thickness and weight of the pulp. The data were obtained with a digital caliper and the degrees brix measured with a refractometer. Multivariate analyses were made with UPGMA hierarchical methods and Tocher optimization, using the standardized average Euclidean distance as a measure of dissimilarity, and principal components analysis (PCA). Four distinct groups were formed based on the data. The first three principal components explained 87.51% of the total variation. The brix measurement was the trait with the greatest contribution to the differentiation of the genotypes.
Even though dengue remains a major threat in Malaysia, information on insecticide resistance of vectors, along with the underlying genetic basis of such resistance, and the impact of a natural flooding disaster remains sparse. Kelantan was one of the states of Malaysia severely affected by monsoon flooding in December 2014. We examined the resistance profile of Aedes mosquitoes in after the big flood, comparing the susceptibility of Ae. aegypti and Ae. albopictus from flooded and unflooded areas. We also sought to validate a simple molecular assay for detecting knockdown resistance (kdr) mutations in the voltage-gated sodium channel (VGSC) gene of the mosquitoes. Mosquito immatures were collected by using ovitraps in Kampung Baru, Pasir Pekan, Tumpat (flooded area), and Bandar Baru Kubang Kerian, Kubang Kerian (unflooded area) five months after the flood disaster. The samples were reared to adult mosquitoes and bio-assayed following World Health Organization (WHO) protocol against deltamethrin (0.05%) and pirimiphos-methyl (0.25%) to evaluate their susceptibility. The DNA molecular assays focused on amino acid substitution in domain II (S989, I1011, L1014, and V1016) and domain III (F1534C) in segment 6 of the VGSC gene. Aedes aegypti and Ae. albopictus from both locations were found to be susceptible to pirimiphos-methyl (mortality >98%). A high level of resistance to deltamethrin was detected in Ae. Aegypti; the unflooded area mosquitoes had significantly lower mortality (17%) than the flooded area (74%). Investigation of kdr mutation showed F1534C substitution in the VGSC gene of Ae. aegypti from the flooded and unflooded areas, with an insignificant difference in frequency of 83 and 75% (P > 0.05). This mutation was not detected in Ae. albopictus.
Psidium guajava (guava) is a fruit tree of the Myrtaceae family of nutritional and economic importance and wide edaphoclimatic adaptation. For commercial orchard purposes, guava trees are derived from clonal propagation and the production cycle begins with drastic pruning. During its development the guava tree displays varied characteristics that may involve epigenetic mechanisms, such as DNA methylation, revealed by the formation of 5-methylcytosine (5-mC). In order to understand the variability of this mechanism, the %5-mC was evaluated in 22 guava genotypes from a working collection, in an experimental orchard, over five development stages – post-pruning, flowering, fructification, harvest and post-harvest – and subsequently in different tissues. Wide variation in DNA methylation was detected among the genotypes. Hypermethylation was found in one, whereas methylation and demethylation mechanisms were observed in 10 genotypes. Greater variability in DNA methylation among genotypes was found during the vegetative phase, mainly after pruning. On the other hand, uniformity was observed among the genotypes with regards to global DNA methylation during flowering, indicating that this mechanism is conserved in this specific phase. No differences in global DNA methylation was detected in the different plant tissues. In this study, the global epigenetic mechanisms of P. guajava were detected more frequently in vegetative than in reproductive phases. Important Brazilian cultivars such as Paluma, Pedro Sato, Sassaoka and Cortibel SLG exhibit changes in their methylation profiles during their production cycle. Others show greater stability, for instance Século XXI and six Cortibel cultivars, suggesting the possibility of selection for this characteristic. Furthermore, the methylation and demethylation mechanisms of adult guava plants indicate the relevance of epigenetics for the wide edaphoclimatic adaptation of the species. In addition, the clonal propagation of guava may provide an opportunity for the development of this crop through epibreeding approaches.
Dipteryx alata (Fabaceae), locally known as Baru, is a non-model, native tree species endemic to the Brazilian Savanna (Cerrado), with economic potential due to its use as food, medicine, animal forage, lumber, and in recovery of degraded areas and landscaping. Although D. alata is recognized as an important Brazilian resource, currently there is no genomic information for this species. We generated 22 Gb raw reads from the genomes of D. alata trees using the Illumina MiSeq platform. These were assembled in 275,707 nuclear genomic sequences (N50 = 1598 bp) with a total of 355 Mb, which corresponds to 44% of the whole genome. We detected 21,981 microsatellite regions, of which 49.3% were dinucleotides and 42.7% trinucleotides. We found 421,701 transposable elements (TEs) in 39.29% of the sequences. Long terminal repeat retrotransposons were the most abundant TEs. This is one of the first genomic scale studies for a native Cerrado species. The results can be used for the development of molecular markers for studies on evolution, population genetics and conservation of D. alata.
Meningiomas are the most common primary tumors of the central nervous system, accounting for 35.5% of cases, considering all age groups. Despite progress made in recent decades, tumorigenesis of meningiomas still remains a challenge. There is a consensus of a need for molecular tools to assist in diagnosis and prognosis of meningiomas. In this context, some studies demonstrate the importance of the role of estrogen and progesterone receptors, as well as the understanding of alterations in microRNA (miRNAs) expression levels in the tumorigenesis of meningiomas. The serum expression profile of miRNAs has been shown to correlate with tumor classification and clinical evolution. Investigation of such miRNAs as biomarkers is of great interest because it would be a non-invasive procedure. We evaluated the tissue and serum expression profile of miRNAs associated with estrogen and progesterone receptor pathways in grade I, II and III meningiomas. Tissue and blood samples from 40 patients with grade I, II and III meningiomas were investigated using real-time PCR to analyze the expression of the miRNAs miR-34a, miR-143, miR-145 and miR-335. The miRNAs miR-34a and miR-145 had significantly lower expression in the tumor tissue samples of grade II meningiomas when compared to grades I and III. We did not observe significant differences in miRNA expression in the blood samples. We concluded that the expression of these miRNAs is not correlated with tumor progression in meningiomas.
Chronic psychological stress alters the hypothalamic–pituitary–adrenal axis (HPA-axis), triggering chronic oxidative-inflammatory states that are associated with physical and psychiatric conditions. However, it is not clear if basal oxidative-inflammatory states triggered by genetic variation affect the HPA-axis by altering cortisol, adrenocorticotropic hormone (ACTH) and dehydroepiandrosterone sulfate (DHEA-S) levels. Humans have a single nucleotide polymorphism (SNP) found in manganese-dependent superoxide dismutase (Val16Ala-SOD2, rs4880), which has two alleles (V and A) which affect the basal efficacy of SOD2 antioxidant enzyme in the mitochondria. The VV-genotype, which presents low SOD2-efficacy, has been associated with chronic inflammatory states, as well as higher risk of depression and self-reported psychological stress. Therefore, basal oxidative imbalance could have some influence on modulation of HPA-axis physiology. We tested this hypothesis comparing morning blood levels of cortisol, ACTH and DHEA-S and other biochemical markers in 90 healthy adult university students previously genotyped for the SOD2-SNP (30 volunteers for each genotype, 26.5 ± 8.7 years old). Only volunteers who self-reported no perception of psychological stress were included in the study. The VV group had higher morning cortisol and ACTH, and lower DHEA-S and brain-derived neurotrophic factor (BDNF) than A-allele subjects. These results indicate some influence of S-imbalance on modulation of this molecule. Therefore, we suggest that genetically controlled pro-oxidative and inflammatory states could modulate physiological markers for stress and neurogenesis.
Probiotics are live nonpathogenic microorganisms extensively used in food, pharmaceutical and medicinal industries. Recently, attention has focused on specific features of probiotics and on the abilities of some long known and recently described species of this group. In general, desired features of probiotics include resistance to acid and bile salts to avoid dysbiosis and induction of immune system development. The advent of next-generation sequencing technology has propelled the genomic area, allowing a search for probiotic features in a wide range of probiotic species, especially bacteria. In this context, functional genomics analyses can help interpret big data, correlating the findings with comparative genomics analyses, in a search for direct applications. To select the articles in this review, we used the following indexing terms: (probiotics OR probiosis) AND (genomics OR transcriptomics OR proteomics OR metabolomics OR culturomics) AND bacteria. Proteomics and transcriptomics methodologies reveal important information about proteins and transcripts differentially expressed under specific conditions that mimic host environments in health and disease. In addition, new research approaches have been developed for probiotics, such as metabiotic and metagenomic analyses of host microbiota. Also, we examined probiotic related features, including bacterial safety aspects; tolerance towards digestive constraints, such as gastric juice and bile salts; bacterial pathogen exclusion mechanisms; adhesion-related genes; antimicrobial peptides; immune development and function; omics; metagenomics; culturomics; functional genomics; transcriptomics; proteomics; metabiotics and metabolomics. In summary, currently there is considerable interest in probiotic bacteria, and structural and functional genomics analyses have potential to help research in this area.
Genetic improvement of soybean involves various biometric techniques and genomic tools. Controlled hybridization is an indispensable tool of the researcher; however, considering the complexity of the process, floral sensitivity and a strong effect of environmental conditions, the procedure is difficult to control. The objective of this work was to define the optimal periods for artificial hybridization of soybean, in order to maximize the number of seeds formed, and to understand the relationships between the agronomic characteristics of the parents and progenies. The study was carried out in Campos Borges, Rio Grande do Sul, Brazil, during the agricultural years of 2013, 2014, 2015, 2016, 2017 and 2018. The crosses were made during the initial period of flowering of the culture in the greenhouse, totaling 498 directed crosses. There was considerable variability in the number of crosses successfully made, in seed number and viability, and in the crossing index. The efficiency of obtaining heterozygous soybean seeds was 13.8% using planned crosses under controlled conditions. The optimum period to maximize the number of seeds was from 8:15 to 9:45 AM, the number of seeds being inversely proportional to the advance in the day hours. The flower color and the growth habit of the parents express a similar tendency as the time of the cross is determinant for the success of this stage of breeding.
Cluster of differentiation 1 (CD1) is antigen-presenting molecule involved in the presentation of lipid and glycolipid antigens to specific T cells and natural killer T cells. They exhibit a low rate of polymorphism compared to classical major histocompatibility complex presenting molecules. In this case control study, we examined a possible association of genetic polymorphism in CD1A and CD1D genes with colorectal cancer (CRC) in a Saudi population consisting of 120 patients with CRC and 118 matched controls. They were genotyped for the CD1A T/C 622 and CD1D A/T 354 polymorphisms using PCR-SSP. An apparent protective effect of the C allele, heterozygous TC and additive TC + CC genotypes against CRC was observed. These associations were found only in individuals >57 years. No association was observed between the CD1D A/T 354 polymorphism and CRC.