231 registros encontrados - material ARTIGO E unidade Centro de Biologia Molecular e Engenharia Genética
"Association of APOE gene polymorphisms with primary open angle glaucoma in Brazilian patients"
ARTIGO - Inglês
Assunto: Apolipoproteínas E
Abstract: Background: Primary open-angle glaucoma (POAG) is a multifactorial disease that affects 65.5 million people worldwide. In addition to the...
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Abstract: Background: Primary open-angle glaucoma (POAG) is a multifactorial disease that affects 65.5 million people worldwide. In addition to the genetic variants already established as indicators of greater risk for POAG, the apolipoprotein (APOE) gene has been studied in some populations, with controversial results. The aim of this study is to investigate the frequency of the genetic variants of APOE in the Brazilian population, and to evaluate the association between these polymorphisms and the risk of POAG. APOE variants (rs429358; rs7412) were genotyped in 402 POAG patients and 401 controls. We evaluated the association between APOE genetic variants and the risk for POAG, as well as the correlation between the requirement of glaucoma surgery and the APOE polymorphisms. Among the three APOE gene isoforms, we found a low frequency of APOE alleles e2 (7.34%) and e4 (11.76%), but a high frequency of e3 (80.88%) in our population. When compared to e3e3 reference genotype, e2
allele-carriers (OR = 1.516; p-value = 0.04) and e2e3 genotype (OR = 1.655; p-value = 0.02) were associated with a greater risk for POAG. An additive genetic model confirmed the influence of the e2 allele in the risk of POAG in this sample of the Brazilian population (OR = 1.502; p-value = 0.04). There was no significant association between the analyzed genotypes and the requirement or number of glaucoma surgeries (p > .05). Brazilian individuals carrying the APOEe2 allele may be at an increased risk for the development of POAG
allele-carriers (OR = 1.516; p-value = 0.04) and e2e3 genotype (OR = 1.655; p-value = 0.02) were associated with a greater risk for POAG. An additive genetic model confirmed the influence of the e2 allele in the risk of POAG in this sample of the Brazilian population (OR = 1.502; p-value = 0.04). There was no significant association between the analyzed genotypes and the requirement or number of glaucoma surgeries (p > .05). Brazilian individuals carrying the APOEe2 allele may be at an increased risk for the development of POAG
ARTIGO - Inglês
Assunto: Artigo original
Abstract: Unveiling fungal genome structure and function reveals the potential biotechnological use of fungi. Trichoderma harzianum is a powerful...
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Abstract: Unveiling fungal genome structure and function reveals the potential biotechnological use of fungi. Trichoderma harzianum is a powerful CAZyme-producing fungus. We studied the genomic regions in T. harzianum IOC3844 containing CAZyme genes, transcription factors and transporters. We used bioinformatics tools to mine the T. harzianum genome for potential genomics, transcriptomics, and exoproteomics data and coexpression networks. The DNA was sequenced by PacBio SMRT technology for multiomics data analysis and integration. In total, 1676 genes were annotated in the genomic regions analyzed; 222 were identified as CAZymes in T. harzianum IOC3844. When comparing transcriptome data under cellulose or glucose conditions, 114 genes were differentially expressed in cellulose, with 51 being CAZymes. CLR2, a transcription factor physically and phylogenetically conserved in Trichoderma spp., was differentially expressed under cellulose conditions. The genes induced/repressed under cellulose conditions included those important for plant biomass degradation, including CIP2 of the CE15 family and a copper-dependent LPMO of the AA9 family. Our results provide new insights into the relationship between genomic organization and hydrolytic enzyme expression and regulation in T. harzianum IOC3844. Our results can improve plant biomass degradation, which is fundamental for developing more efficient strains and/or enzymatic cocktails to produce hydrolytic enzymes
3D cell-SELEX : development of RNA aptamers as molecular probes for PC-3 tumor cell line
ARTIGO - Inglês
Assunto: Neoplasias da próstata
Human prostate cancer (PCa) is a highly heterogeneous and multifactorial disease. Current clinical biomarkers are not sufficiently accurate, thus...
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Human prostate cancer (PCa) is a highly heterogeneous and multifactorial disease. Current clinical biomarkers are not sufficiently accurate, thus being unable to predict the clinical outcome. Therefore, searching for new biomarkers aiming to improve diagnosis, prognosis and therapy is still required. In this study, we performed 3D Cell-SELEX against PC-3 prostate cancer cell line, a novel strategy to select specific nucleic acid ligands against spheroid cells in 3D cell culture. This original system combines Cell-SELEX, a process that exploits the cellular structure to generate specific ligands, and 3D cell culture, an approach that mimics the tissue microenvironment in vitro. In the first round of 3D Cell-SELEX, a negative selection against RWPE-1, non-tumor cell line, was performed to subtract non-tumor specific aptamers. The supernatant was used in eight additional rounds of selection, which were performed against PC-3 cell line. After nine selection cycles, eight PC-3 specific RNA aptamers were selected and sequenced. The aptamers presented sizes between 20 and 50 nucleotides-long, with low free energy (∆G<−13.6), which contributed for their spontaneous folding and high stability. Furthermore, our results showed the aptamer A4 as a specific ligand to prostate tumor cells, with dissociation constant in the nanomolar scale. Therefore, the novel 3D Cell-SELEX procedure improved the selection of PCa cell-surface ligands and the aptamer A4 has shown potential for the identification of prostate tumor cells, suggesting the application of this molecule in further screening assays for PCa
A case of 46,XY DSD due to a novel mutation in the HSD17B3 gene
ARTIGO - Inglês
Assunto: Transtorno 46,XY do desenvolvimento sexual
Texto completo: https://www.karger.com/Article/Abstract/451040
A de novo mutation in CYP21A2 gene in a case of in vitro fertilization
ARTIGO - Inglês
Assunto: Proteína CYP21A2 humana
Abstract: Congenital adrenal hyperplasia, one of the most frequent autosome recessive disorders, is caused by defects in steroidogenic enzymes...
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Abstract: Congenital adrenal hyperplasia, one of the most frequent autosome recessive disorders, is caused by defects in steroidogenic enzymes involved in the cortisol biosynthesis. Approximately 95% of the cases are caused by abnormal function of the 21-hydroxylase enzyme. This deficiency leads to androgen excess, consequently, to virilization and rapid somatic growth with accelerated skeletal maturation. Mutations in CYP21A2 are responsible for different forms of 21-hydroxylase deficiency. Mild impairment in the enzymatic activity causes the non-classic or late-onset congenital adrenal hyperplasia that is observed with a prevalence of 1 in 1000 subjects in different populations. The present paper describes a de novo mutation that occurred in the paternal meiosis. The child, who was conceived by in vitro fertilization, presented with precocious puberty and diagnosed with non-classical 21-hydroxylase deficiency. DNA sequencing showed the compound heterozygosis for a de novo CYP21A1P/A2 chimeric gene and the p.Val281Leu mutation inherited from her mother, who was heterozygous for the mutation. The chimeric gene showed pseudogene-derived sequence from 5'-end to intron 3 and CYP21A2 sequences from intron 3 to 3'-end of the gene. Sequencing analysis of the father did not show any mutation. The multiplex ligation-dependent probe amplification (MLPA) assay did not indicate loss of DNA discarding gene deletion but confirmed the chimeric gene. In addition, supernumerary copies of CYP21A1P were observed for both parents and for the affect child. Since paternity has been confirmed, those results suggest that a de novo large gene conversion in the paternal meiosis could have occurred by misalignment of alleles bearing different copy numbers of genes in CYP21 locus
A joint learning approach for genomic prediction in polyploid grasses
ARTIGO - Inglês
Assunto: Artigo original
Abstract: Poaceae, among the most abundant plant families, includes many economically important polyploid species, such as forage grasses and...
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Abstract: Poaceae, among the most abundant plant families, includes many economically important polyploid species, such as forage grasses and sugarcane (Saccharum spp.). These species have elevated genomic complexities and limited genetic resources, hindering the application of marker-assisted selection strategies. Currently, the most promising approach for increasing genetic gains in plant breeding is genomic selection. However, due to the polyploidy nature of these polyploid species, more accurate models for incorporating genomic selection into breeding schemes are needed. This study aims to develop a machine learning method by using a joint learning approach to predict complex traits from genotypic data. Biparental populations of sugarcane and two species of forage grasses (Urochloa decumbens, Megathyrsus maximus) were genotyped, and several quantitative traits were measured. High-quality markers were used to predict several traits in different cross-validation scenarios. By combining classification and regression strategies, we developed a predictive system with promising results. Compared with traditional genomic prediction methods, the proposed strategy achieved accuracy improvements exceeding 50%. Our results suggest that the developed methodology could be implemented in breeding programs, helping reduce breeding cycles and increase genetic gains
A mixed model QTL analysis for sugarcane multiple-harvest-location trial data
ARTIGO - Inglês
Assunto: Cana-de-açúcar
Sugarcane-breeding programs take at least 12 years to develop new commercial cultivars. Molecular markers offer a possibility to study the genetic...
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Sugarcane-breeding programs take at least 12 years to develop new commercial cultivars. Molecular markers offer a possibility to study the genetic architecture of quantitative traits in sugarcane, and they may be used in marker-assisted selection to speed up artificial selection. Although the performance of sugarcane progenies in breeding programs are commonly evaluated across a range of locations and harvest years, many of the QTL detection methods ignore two- and three-way interactions between QTL, harvest, and location. In this work, a strategy for QTL detection in multi-harvest-location trial data, based on interval mapping and mixed models, is proposed and applied to map QTL effects on a segregating progeny from a biparental cross of pre-commercial Brazilian cultivars, evaluated at two locations and three consecutive harvest years for cane yield (tonnes per hectare), sugar yield (tonnes per hectare), fiber percent, and sucrose content. In the mixed model, we have included appropriate (co)variance structures for modeling heterogeneity and correlation of genetic effects and non-genetic residual effects. Forty-six QTLs were found: 13 QTLs for cane yield, 14 for sugar yield, 11 for fiber percent, and 8 for sucrose content. In addition, QTL by harvest, QTL by location, and QTL by harvest by location interaction effects were significant for all evaluated traits (30 QTLs showed some interaction, and 16 none). Our results contribute to a better understanding of the genetic architecture of complex traits related to biomass production and sucrose content in sugarcane
ARTIGO - Inglês
Assunto: Diabetes Mellitus neonatal permanente
Background: Permanent neonatal diabetes mellitus (PNDM) is a rare disorder, characterized by uncontrolled hyperglycemia diagnosed during the first 6...
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Background: Permanent neonatal diabetes mellitus (PNDM) is a rare disorder, characterized by uncontrolled hyperglycemia diagnosed during the first 6 months of life. In general, PNDM has a genetic origin and most frequently it results from heterozygous mutations in KCNJ11, INS and ABCC8 genes. Homozygous or compound heterozygous inactivating mutations in GCK gene as cause of PNDM are rare. In contrast, heterozygosis for GCK inactivating mutations is frequent and results in the maturity-onset diabetes of young (MODY), manifested by a mild fasting hyperglycemia usually detected later in life. Therefore, as an autosomal recessive disorder, GCK-PNDM should be considered in families with history of glucose intolerance or MODY in first relatives, especially when consanguinity is suspected.
Results: Here we describe two patients born from non-consanguineous parents within a family. They presented low birth weight with persistent hyperglycemia during the first month of life. Molecular analyses for KCNJ11, INS, ABCC8 did not show any mutation. GCK gene sequencing, however, revealed that both patients were compound heterozygous for two missense combined in a novel GCK-PNDM genotype. The p.Asn254His and p.Arg447Gly mutations had been inherited from their mothers and fathers, respectively, as their mothers are sisters and their fathers are brothers. Parents had been later diagnosed as having GCK-MODY. Conclusions: Mutations' in silico analysis was carried out to elucidate the role of the amino acid changes on the enzyme structure. Both p.Asn254His and p.Arg447Gly mutations appeared to be quite damaging. This is the first report of GCK-PNDM in a Brazilian family
Results: Here we describe two patients born from non-consanguineous parents within a family. They presented low birth weight with persistent hyperglycemia during the first month of life. Molecular analyses for KCNJ11, INS, ABCC8 did not show any mutation. GCK gene sequencing, however, revealed that both patients were compound heterozygous for two missense combined in a novel GCK-PNDM genotype. The p.Asn254His and p.Arg447Gly mutations had been inherited from their mothers and fathers, respectively, as their mothers are sisters and their fathers are brothers. Parents had been later diagnosed as having GCK-MODY. Conclusions: Mutations' in silico analysis was carried out to elucidate the role of the amino acid changes on the enzyme structure. Both p.Asn254His and p.Arg447Gly mutations appeared to be quite damaging. This is the first report of GCK-PNDM in a Brazilian family
ARTIGO - Inglês
Assunto: Artigo original
Abstract: Here, we report a bioluminescence resonance energy transfer (BRET) assay as a novel way to investigate the binding of unlabeled ligands to...
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Abstract: Here, we report a bioluminescence resonance energy transfer (BRET) assay as a novel way to investigate the binding of unlabeled ligands to the human transient receptor potential mucolipin 1 (hTRPML1), a lysosomal ion channel involved in several genetic diseases and cancer progression. This novel BRET assay can be used to determine equilibrium and kinetic binding parameters of unlabeled compounds to hTRPML1 using intact human-derived cells, thus complementing the information obtained using functional assays based on ion channel activation. We expect this new BRET assay to expedite the identification and optimization of cell-permeable ligands that interact with hTRPML1 within the physiologically relevant environment of lysosomes
A novel CYP21A2 mutation identified a patient with classical 21-hydroxylase deficiency
ARTIGO - Inglês
Assunto: Mutação (Biologia)
Texto completo: https://www.karger.com/Article/Abstract/451040
A novel image-based approach for soybean seed phenotyping using machine learning techniques
ARTIGO - Inglês
Assunto: Artigo original
Abstract: Soybean is important for protein and oil worldwide, requiring investments in research and production technology, mainly breeding programs,...
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Abstract: Soybean is important for protein and oil worldwide, requiring investments in research and production technology, mainly breeding programs, to meet the increasing demand. Seed morphology, including area, perimeter, and circularity, significantly impacts soybean yield. However, the analysis of these factors has been hindered by the lack of efficient computational approaches that offer accuracy and flexibility to user preferences and needs. This study presents a soybean phenotyping system framework that includes: seed segmentation in soybean images, morphological evaluation, and image-based prediction of hundred-seed weight (HSW). We used genotypes from a partial diallel cross design and collected red-green-blue images of seeds from each plot. We developed an in-house image processing pipeline for seed segmentation, which enabled a full morphological evaluation of the seeds. For predicting the HSW, we compared machine learning algorithms using the obtained morphological characteristics as input and features from state-of-the-art convolutional neural network (CNN) architectures. Our image segmentation methodology correctly identified over 98% of the seeds in the images, even when they were in proximity. Our morphological phenotyping approach's adaptability to other plant species was verified, fully demonstrating the pipeline's generalizability. The morphological measurements were effective in predicting the HSW with an accuracy of 0.71 predictive ability and mean squared error (MSE) of 3.15 (mean HSW of 19.74). The same results were observed for CNN features, highlighting the efficiency of the morphological measurements. ResNet-50 had the most effective feature extraction, with a mean accuracy of 0.60 (MSE of 4.15). Our study can aid automated phenotyping tool development in research and industry. We introduce a novel high-throughput soybean seed phenotyping system. We demonstrate the possibility of predicting an important component of production for the soybean crop. We show the efficiency of morphological measures as extractors of image features. Our results indicate that ML techniques can be easily adapted to precision tasks in plant phenology
Texto completo: https://acsess.onlinelibrary.wiley.com/doi/10.1002/csc2.21032
ARTIGO - Inglês
Assunto: Aparelho genital feminino - Doenças
In 21-hydroxylase deficiency (21-OHD), there is an influence of genotype on the severity of external genitalia virilization. However, females carrying...
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In 21-hydroxylase deficiency (21-OHD), there is an influence of genotype on the severity of external genitalia virilization. However, females carrying mutations predicting a similar impairment of enzymatic activity present a wide variability of genital phenotypes. In such cases, interindividual variability in genes related to the sex steroid hormone pathway could play a role. To evaluate the influence of POR, HSD17B5 and SRD5A2 variants on the severity of external genitalia virilization in 21-OHD females. Prader stages were evaluated in 178 females with 21-OHD from a multicenter study. The 21-OHD genotypes were divided into two groups according to their severity: severe and moderate. The influences of the POR p.A503V, HSD17B5 c.-71A>G, HSD17B5 c.-210A>C, and SRD5A2 p.A49T and p.V89L variants on the degree of external genitalia virilization were analyzed. The POR p.A503V, HSD17B5 c.-71A>G, HSD17B5 c.-210A>C, and SRD5A2 p.A49T and p.V89L variants were found in 25, 33, 17, 1, and 31% of the alleles, respectively. In uni- and multilinear regression, HSD17B5 c.-210A>C has a significant influence on the degree of external genitalia virilization. This variant was also identified with a higher frequency in the most severely virilized females. We demonstrated that a variant in the promoter region of HSD17B5 related to fetal androgen synthesis influences the genital phenotype in 21-OHD females
DOI: https://doi.org/10.1159/000445684
Texto completo: https://www.karger.com/Article/FullText/445684
A target engagement assay to assess uptake, potency, and retention of antibiotics in living bacteria
ARTIGO - Inglês
Assunto: Artigo original
Abstract: New antibiotics are urgently needed to counter the emergence of antimicrobial-resistant pathogenic bacteria. A major challenge in antibiotic...
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Abstract: New antibiotics are urgently needed to counter the emergence of antimicrobial-resistant pathogenic bacteria. A major challenge in antibiotic drug discovery is to turn potent biochemical inhibitors of essential bacterial components into effective antimicrobials. This difficulty is underpinned by a lack of methods to investigate the physicochemical properties needed for candidate antibiotics to permeate the bacterial cell envelope and avoid clearance by the action of bacterial efflux pumps. To address these issues, here we used a target engagement assay to measure the equilibrium and kinetic binding parameters of antibiotics targeting dihydrofolate reductase (DHFR) in live bacteria. We also used this assay to identify novel DHFR ligands having antimicrobial activity. We validated this approach using the Gram-negative bacteria Escherichia coli and the emerging human pathogen Mycobacterium abscessus. We expect the use of target engagement assays in bacteria to expedite the discovery and progression of novel, cell-permeable antibiotics with on-target activity
ARTIGO - Inglês
Assunto: Placenta
Sickle cell disease (SCD) is a complex disease that is characterized by the polymerization of deoxyhemoglobin S, altered red blood cell membrane...
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Sickle cell disease (SCD) is a complex disease that is characterized by the polymerization of deoxyhemoglobin S, altered red blood cell membrane biology, endothelial activation, hemolysis, a procoagulant state, acute and chronic inflammation, and vaso-occlusion. Among the physiological changes that occur during pregnancy, oxygen is consumed by fetal growth, and pregnant women with SCD are more frequently exposed to low oxygen levels. This might lead to red blood cells sickling, and, consequently, to vaso-occlusion. The mechanisms by which SCD affects placental physiology are largely unknown, and chronic inflammation might be involved in this process. This study aimed to evaluate the gene expression profile of inflammatory response mediators in the placentas of pregnant women with sickle cell cell anemia (HbSS) and hemoglobinopathy SC (HbSC). Our results show differences in a number of these genes. For the HbSS group, when compared to the control group, the following genes showed differential expression: IL1RAP (2.76-fold), BCL6 (4.49-fold), CXCL10 (-2.12-fold), CXCR1 (-3.66-fold), and C3 (-2.0-fold). On the other hand, the HbSC group presented differential expressions of the following genes, when compared to the control group: IL1RAP (4.33-fold), CXCL1 (3.05-fold), BCL6 (4.13-fold), CXCL10 (-3.32-fold), C3 (-2.0-fold), and TLR3 (2.38-fold). Taken together, these data strongly suggest a differential expression of several inflammatory genes in both SCD (HbSS and HbSC), indicating that the placenta might become an environment with hypoxia, and increased inflammation, which could lead to improper placental development
ARTIGO - Inglês
Assunto: Urochloa humidicola
Abstract: We present the highest-density genetic map for the hexaploid Urochloa humidicola. SNP markers expose genetic organization, reproduction, and...
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Abstract: We present the highest-density genetic map for the hexaploid Urochloa humidicola. SNP markers expose genetic organization, reproduction, and species origin, aiding polyploid and tropical forage research. Tropical forage grasses are an important food source for animal feeding, with Urochloa humidicola, also known as Koronivia grass, being one of the main pasture grasses for poorly drained soils in the tropics. However, genetic and genomic resources for this species are lacking due to its genomic complexity, including high heterozygosity, evidence of segmental allopolyploidy, and reproduction by apomixis. These complexities hinder the application of marker-assisted selection (MAS) in breeding programs. Here, we developed the highest-density linkage map currently available for the hexaploid tropical forage grass U. humidicola. This map was constructed using a biparental F1 population generated from a cross between the female parent H031 (CIAT 26146), the only known sexual genotype for the species, and the apomictic male parent H016 (BRS cv. Tupi). The linkage analysis included 4873 single nucleotide polymorphism (SNP) markers with allele dosage information. It allowed mapping of the ASGR locus and apospory phenotype to linkage group 3, in a region syntenic with chromosome 3 of Urochloa ruziziensis and chromosome 1 of Setaria italica. We also identified hexaploid haplotypes for all individuals, assessed the meiotic configuration, and estimated the level of preferential pairing in parents during the meiotic process, which revealed the autopolyploid origin of sexual H031 in contrast to apomictic H016, which presented allopolyploid behavior in preferential pairing analysis. These results provide new information regarding the genetic organization, mode of reproduction, and allopolyploid origin of U. humidicola, potential SNPs markers associated with apomixis for MAS and resources for research on polyploids and tropical forage grasses
An eye on sickle cell retinopathy
ARTIGO - Inglês
Assunto: Retinopatia falciforme
An open source plant kinase chemogenomics set
ARTIGO - Inglês
Assunto: Artigo original
Abstract: One hundred twenty-nine protein kinases, selected to represent the diversity of the rice (Oryza sativa) kinome, were cloned and tested for...
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Abstract: One hundred twenty-nine protein kinases, selected to represent the diversity of the rice (Oryza sativa) kinome, were cloned and tested for expression in Escherichia coli. Forty of these rice kinases were purified and screened using differential scanning fluorimetry (DSF) against 627 diverse kinase inhibitors, with a range of structures and activities targeting diverse human kinases. Thirty-seven active compounds were then tested for their ability to modify primary root development in Arabidopsis. Of these, 14 compounds caused a significant reduction of primary root length compared with control plants. Two of these inhibitory compounds bind to the predicted orthologue of Arabidopsis PSKR1, one of two receptors for PSK, a small sulfated peptide that positively controls root development. The reduced root length phenotype could not be rescued by the exogenous addition of the PSK peptide, suggesting that chemical treatment may inhibit both PSKR1 and its closely related receptor PSKR2. Six of the compounds acting as root growth inhibitors in Arabidopsis conferred the same effect in rice. Compound RAF265 (CHIR-265), previously shown to bind the human kinase BRAF (B-Raf proto-oncogene, serine/threonine kinase), also binds to nine highly conserved rice kinases tested. The binding of human and rice kinases to the same compound suggests that human kinase inhibitor sets will be useful for dissecting the function of plant kinases
DOI: https://doi.org/10.1002/pld3.460
Texto completo: https://onlinelibrary.wiley.com/doi/10.1002/pld3.460
ARTIGO - Inglês
Assunto: Fatores de risco
Age-related macular degeneration (AMD) is a progressive, mutifactorial condition that affects the central retina, and represents an important cause of...
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Age-related macular degeneration (AMD) is a progressive, mutifactorial condition that affects the central retina, and represents an important cause of blindness in the elderly population worldwide. Its pathogenesis is complex, with genetics and environmental factors playing critical roles. The genetic component of AMD has been estimated at 45% to 70%, with at least 34 genomic loci implicated in its etiology. Different variants of complement pathway-associated genes have been associated with the disease, demonstrating the importance of immune pathology and inflammation in the mechanism of AMD. The purpose of this study was to evaluate the role of the variants CFB R32Q (rs641153) and CFH (rs1410996) in the risk of development of AMD in a Brazilian population. This was a case-control study, in which 443 unrelated AMD patients and 471 controls were evaluated for the rs641153 and 451 unrelated AMD patients and 435 controls were evaluated for the rs1410996 SNPs through PCR/direct sequencing. AMD patients were diagnosed according to the International Classification System and subdivided in subgroups: dry and wet; early and advanced disease.Genotype distributions were significantly different when cases and controls were compared. When analyzing rs641153, AG/AA genotypes were more frequent in controls than in cases when compared to GG genotype (p= 0.0008), OR: 0.548 (IC95% 0.385-0.780). When comparing early versus advanced forms, GG genotype was more frequent in patients with advanced AMD (p=0.0006), OR: 1.878 (IC95% 1.081-3.262). No association was observed for the comparison of wet versus dry forms. For rs1410996, GG/AG genotypes were more frequent in cases than controls when compared to AA genotype (p=0.0296), OR: 1.462 (IC95% 1.038-2.059). For the comparison of GG versus AA genotype, OR was 2.030 (IC95% 1.375-2.996) (p=0.0002). No association was observed for the comparisons early versus advanced and dry versus wet AMD.These results are in accordance with the literature and support the role of the A variant of the CFB gene in AMD susceptibility, as a protection factor for the disease and the G variant of the CFH gene as a risk factor for the disease. To our knowledge, this is the first report of the association of these variants with AMD in Brazilians, a highly admixed population
Texto completo: https://iovs.arvojournals.org/article.aspx?articleid=2767534
ARTIGO - Inglês
Assunto: Espectrometria de massa
Mutations in the mitochondrial DNA (mtDNA) have been associated with aminoglycoside-induced and nonsyndromic deafness in different populations. In the...
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Mutations in the mitochondrial DNA (mtDNA) have been associated with aminoglycoside-induced and nonsyndromic deafness in different populations. In the present study, we investigated the contribution of mutations in mitochondrial genes to the etiology of hearing loss in a Brazilian sample. Using mass spectrometry genotyping technology, combined with direct sequencing, 50 alterations previously described in 14 mitochondrial genes were screened in 152 patients with sensorineural hearing loss and in104 normal hearing controls. Fifteen known mitochondrial alterations were detected (G709A, A735G, A827G, G988A, A1555G, T4363C, T5628C, T5655C, G5821A, C7462T, G8363A, T10454C, G12236A, T1291C, G15927A). Pathogenic mutations in MT-RNR1 and MT-TK genes were detected in 3 % (5/152) of the patients with hearing loss. This study contributed to show the spectrum of mitochondrial variants in Brazilian patients with hearing loss. Frequency of A1555G was relatively high (2.6 %), indicating that this mutation is an important cause of hearing loss in our population. This work reports for the first time the investigation and the detection of the tRNALys G8363A mutation in Brazilian patients with maternally inherited sensorineural hearing loss.
ARTIGO - Inglês
Assunto: Cana-de-açúcar
Background: Sugarcane is an important crop worldwide for sugar production and increasingly, as a renewable energy source. Modern cultivars have...
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Background: Sugarcane is an important crop worldwide for sugar production and increasingly, as a renewable energy source. Modern cultivars have polyploid, large complex genomes, with highly unequal contributions from ancestral genomes. Long Terminal Repeat retrotransposons (LTR-RTs) are the single largest components of most plant genomes and can substantially impact the genome in many ways. It is therefore crucial to understand their contribution to the genome and transcriptome, however a detailed study of LTR-RTs in sugarcane has not been previously carried out. Sixty complete LTR-RT elements were classified into 35 families within four Copia and three Gypsy lineages. Structurally, within lineages elements were similar, between lineages there were large size differences. FISH analysis resulted in the expected pattern of Gypsy/heterochromatin, Copia/euchromatin, but in two lineages there was localized clustering on some chromosomes. Analysis of related ESTs and RT-PCR showed transcriptional variation between tissues and families. Four distinct patterns were observed in sRNA mapping, the most unusual of which was that of Ale1, with very large numbers of 24nt sRNAs in the coding region. The results presented support the conclusion that distinct small RNA-regulated pathways in sugarcane target the lineages of LTR-RT elements. Individual LTR-RT sugarcane families have distinct structures, and transcriptional and regulatory signatures. Our results indicate that in sugarcane individual LTR-RT families have distinct behaviors and can potentially impact the genome in diverse ways. For instance, these transposable elements may affect nearby genes by generating a diverse set of small RNA's that trigger gene silencing mechanisms. There is also some evidence that ancestral genomes contribute significantly different element numbers from particular LTR-RT lineages to the modern sugarcane cultivar genome
ARTIGO - Inglês
Assunto: Cana-de-açúcar
Whole genome duplication has played an important role in plant evolution and diversification. Sugarcane is an important crop with a complex hybrid...
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Whole genome duplication has played an important role in plant evolution and diversification. Sugarcane is an important crop with a complex hybrid polyploid genome, for which the process of adaptation to polyploidy is still poorly understood. In order to improve our knowledge about sugarcane genome evolution and the homo/homeologous gene expression balance, we sequenced and analyzed 27 BACs (Bacterial Artificial Chromosome) of sugarcane R570 cultivar, containing the putative single-copy genes LFY (seven haplotypes), PHYC (four haplotypes), and TOR (seven haplotypes). Comparative genomic approaches showed that these sugarcane loci presented a high degree of conservation of gene content and collinearity (synteny) with sorghum and rice orthologous regions, but were invaded by transposable elements (TE). All the homo/homeologous haplotypesof LFY, PHYC, and TOR are likely tobe functional, because they are all under purifying selection (dN/dS << 1). However, they were found to participate in a nonequivalently manner to the overall expression of the corresponding gene. SNPs, indels, and amino acid substitutions allowed inferring the S. officinarum or S. spontaneum origin of the TOR haplotypes, which further led to the estimation that these two sugarcane ancestral species diverged between 2.5 and 3.5 Ma. In addition, analysis of shared TE insertions in TOR haplotypes suggested that two autopolyploidization may have occurred in the lineage that gave rise to S. officinarum, after its divergence from S. spontaneum
DOI: https://doi.org/10.1093/gbe/evw293
Texto completo: https://academic.oup.com/gbe/article/9/2/266/2895932
Ancient DNA sequence revealed by error-correcting codes
ARTIGO - Inglês
Assunto: DNA
A previously described DNA sequence generator algorithm (DNA-SGA) using error-correcting codes has been employed as a computational tool to address...
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A previously described DNA sequence generator algorithm (DNA-SGA) using error-correcting codes has been employed as a computational tool to address the evolutionary pathway of the genetic code. The code-generated sequence alignment demonstrated that a residue mutation revealed by the code can be found in the same position in sequences of distantly related taxa. Furthermore, the code-generated sequences do not promote amino acid changes in the deviant genomes through codon reassignment. A Bayesian evolutionary analysis of both code-generated and homologous sequences of the Arabidopsis thaliana malate dehydrogenase gene indicates an approximately 1 MYA divergence time from the MDH code-generated sequence node to its paralogous sequences. The DNA-SGA helps to determine the plesiomorphic state of DNA sequences because a single nucleotide alteration often occurs in distantly related taxa and can be found in the alternative codon patterns of noncanonical genetic codes. As a consequence, the algorithm may reveal an earlier stage of the evolution of the standard code
DOI: https://doi.org/10.1038/srep12051
Texto completo: https://www.nature.com/articles/srep12051