Scielo RSS <![CDATA[Genetics and Molecular Biology]]> vol. 42 num. 1 lang. en <![CDATA[SciELO Logo]]> <![CDATA[Oxidative stress assessment by glutathione peroxidase activity and glutathione levels in response to selenium supplementation in patients with Mucopolysaccharidosis I, II and VI]]> Abstract We assessed levels of plasma selenium (Se), selenoproteins and their change after Se supplementation in patients with mucopolysaccharidosis (MPS) types I, II and VI. This was done in a retrospective study of the medical records of 30 patients with MPS I (n=13), MPS II (n=9) and MPS VI (n=8) who were being treated with enzyme replacement therapy. As part of routine nutritional monitoring, Se levels were measured, revealing that 28 patients (93.3%) had values below the normal range. Therefore, they received supplementation for 12 months, and Se was measured after 6 and 12 months. Glutathione peroxidase (GPx) activity, total glutathione (GSHt), oxidized glutathione (GSSG) and reduced glutathione (GSH) were measured at baseline and 6 months after Se supplementation. The mean GSHt at baseline was 7.90 ± 2.36 μmol/g Hb, and after Se supplementation it was 5.76 ± 1.13 μmol/g Hb; GSH/GSSG was 2.3 ± 1.16 at baseline and 0.58 ± 0.38 after supplementation. GPx activity was 16.46 ± 3.31 U/g Hb at baseline and 4.53 ± 4.92 U/g Hb after Se supplementation. The difference was shown to be statistically significant by paired t-test. In conclusion, our study demonstrated that oxidative stress parameters were altered by Se supplementation in patients with MPS I, II and VI who were previously deficient in Se. <![CDATA[Mannose-Binding Lectin 2 (MBL2) combined genotypes deficiency is associated with susceptibility for Oral Lichen Planus]]> Abstract Oral Lichen Planus (OLP) is an oral inflammatory condition, mediated by host immune system reaction, presenting basal membrane damages with inflammatory lesions in the mouth and/or skin. In this study, the role of functional polymorphisms in the MBL2 gene, encoding for Mannose-Binding Protein C (MBP-C), a member of the innate immune response and an acute-phase protein able to activate the complement cascade, was investigated to assess a possible association with OLP susceptibility in Italian patients. Two variations at the promoter region (called H/L and X/Y) and three at the first exon (at codon 52, 54, and 57) of the MBL2 gene were analyzed in 69 OLP patients and 244 healthy controls from northeastern Italy. Considering the polymorphisms singularly, the MBL2 X allele and C/T genotype of the D allele (correlated with low MBP-C expression) were associated with susceptibility to develop OLP. Moreover, when taking into account MBL2 combined genotypes, more OLP patients were deficient MBP-C producers than not deficient, who were more represented among healthy controls. MBL2 combined genotypes, responsible for deficient MBP-C production, are associated with an increased risk of developing OLP. <![CDATA[Identification of novel mutations of Insulin Receptor Substrate 1 (IRS1) in tumor samples of non-small cell lung cancer (NSCLC): Implications for aberrant insulin signaling in development of cancer]]> Abstract Lung cancer is the leading cause of cancer-related death, and NSCLC constitutes nearly 85%–90% of all cases. The IRS proteins function as adaptors and transmit signals from multiple receptors. Upon binding of insulin to the insulin receptor (IR), IRS1 is phosphorylated at several YXXM motifs creating docking sites for the binding of PI3Kp85, which activates AKT kinase. Therefore, we thought that gain of function mutantions of IRS1 could be related to development of lung cancer. In line with this, we wanted determine whether the IRS1 gene was mutated in the coding regions surrounding YXXM motifs. We sequenced the coding regions surrounding YXXM motifs of IRS1 using tumor samples of 42 NSCLC patients and 40 matching controls and found heterozygote p.S668T mutation in nine of 42 samples and four of nine also had the p.D674H mutation. We generated IRS1 expression vectors harboring p.S668T, p.D674H and double mutants. Expression of the mutants differentially affected insulin-induced phosphorylation of IRS1, AKT, ERK, and STAT3. Also, our mutants induced proliferation, glucose uptake, inhibited the migration of 293T cells and affected the responsiveness of the cells to cisplatin and radiation. Our results suggest that these novel mutations play a role in the phenotype of lung cancer. <![CDATA[Association of <em>FOSL1</em> copy number alteration and triple negative breast tumors]]> Abstract Copy number alterations (CNAs) are a frequent feature in human breast cancer, and one of the hallmarks of genomic instability. The FOSL1, GSTP1 and CCND1 genes are located at 11q13, a cytoband commonly affected by CNA in breast cancer, with relevant function in progression and invasion. Our main goal was to analyze CNAs of these genes and determine their association with breast cancer subtypes. Seventy-three cases of invasive breast tumors [52 Luminal, 7 HER2+ and 14 triple negative (TNBC) subtypes] were analyzed by TaqMan assays. CNAs were observed for all genes, with gains more frequently observed. Gains of the FOSL1 gene were observed in 71% of the cases. This gene was the only one with a statistically significant difference (p&lt;0.001) among tumor subtypes, with increased copy number in TNBC compared to luminal and HER2+. No significant association of CNA and clinical and histopathological parameters from the patients was observed. Additional studies in larger breast cancer patient cohorts based on more refined molecular subtypes are necessary to confirm the observed association of FOSL1 gain with aggressive breast tumors phenotypes. <![CDATA[Does the expression of the <em>ACVR2A</em> gene affect the development of colorectal cancer?]]> Abstract Colorectal cancer has become a serious problem, especially in highly developed countries. As reported by the World Health Organization, the number of colon cancer cases in the world in 2012 amounted to 1.36 million. It is the second most common cancer in females (614,000 cases, 9.2% of the total) and the third in males (746,000 cases, 10.0% of the total) worldwide. It is believed that TGFβ pathway elements are involved in the pathogenesis of colorectal cancer. This study assessed one of these elements, the ACVR2A gene. Qualitative and quantitative analyses of the ACVR2A gene in 84 patients with colorectal cancer was performed. There was no statistically significant association between ACVR2A gene expression and age, gender, histological type, grading of tumor, vascular invasion, and presence of lymphocytes in tumor tissue. No association was observed between the ACVR2A gene expression level and the presence of metastases in regional lymph nodes and distant metastases. In this study, larger tumors (T3 and T4) were characterized by higher ACVR2A expression compared to smaller tumors (T1 and T2). This may indicate an association between ACVR2A expression and the severity of pathological changes in the tumor growth process. <![CDATA[Increased expression levels of Syntaxin 1A and Synaptobrevin 2/Vesicle-Associated Membrane Protein-2 are associated with the progression of bladder cancer]]> Abstract Gene expression is tightly regulated in time and space through a multitude of factors consisting of signaling molecules. Soluble N-ethylmaleimide-sensitive-factor attachment protein receptors (SNARE) are membrane proteins responsible for the intercellular trafficking of signals through endocytosis and exocytosis of vesicles. Altered expression of SNARE proteins in cellular communication is the major hallmark of cancer phenotypes as indicated in recent studies. SNAREs play an important role in maintaining cell growth and epithelial membrane permeability of the bladder and are not only involved in cancer progression but also metastatic cell invasion through SNARE-mediated trafficking. Synaptobrevin2/Vesicle associated membrane protein-2 (v-SNARE) and Syntaxin (t-SNARE) form a vesicular docking complex during endocytosis. Some earlier studies have shown a critical role of SNARE in colon, lungs, and breast cancer progression and metastasis. In this study, we analyzed the relative expression of the STX1A and VAMP2 (SYB2) for their possible association in the progression and metastasis of bladder cancer. The profiling of the genes showed a significant increase in STX1A and VAMP2 expression (p &lt; 0.001) in high-grade tumor cells compared to normal and low-grade tumors. These findings suggest that elevated expression of STX1A and VAMP2 might have caused the abnormal progression and invasion of cancer cells leading to the transformation of cells into high-grade tumor in bladder cancer. <![CDATA[<em>GJB2</em> c.235delC variant associated with autosomal recessive nonsyndromic hearing loss and auditory neuropathy spectrum disorder]]> Abstract Autosomal recessive nonsyndromic hearing loss (ARNSHL) is a genetically heterogeneous neurosensory disorder, usually characterized by congenital or prelingual hearing loss. We report a Han Chinese male, born to consanguineous parents, presenting with nonsyndromic sensorineural hearing loss, whose clinical phenotype was also consistent with auditory neuropathy spectrum disorder (ANSD). After exome sequencing, a gap junction protein beta 2 gene (GJB2) c.235delC variant in the homozygous state was detected in the patient. Both parents were heterozygous for this variant, as documented by Sanger sequencing. The known pathogenic GJB2 c.235delC variant was not detected in 200 healthy controls. It is predicted to be a disease-causing alteration by generating a truncated protein p.(L79Cfs*3), disturbing the appropriate folding and/or oligomerization of connexins and leading to defective gap junction channels. This study shows that the association of homozygosity of the GJB2 c.235delC variant with ARNSHL and ANSD in a patient. <![CDATA[Linkage disequilibrium and past effective population size in native Tunisian cattle]]> Abstract To carry out effective genome-wide association studies, information about linkage disequilibrium (LD) is essential. Here, we used medium-density SNP chips to provide estimates of LD in native Tunisian cattle. The two measures of LD that were used, mean r2 and D’, decreased from 0.26 to 0.05 and from 0.73 to 0.40, respectively, when the distance between markers increased from less than 20 Kb to 200 Kb. The decay in LD over physical distance occurred at a faster rate than that reported for European and other indigenous breeds, and reached background levels at less than 500 Kb distance. This is consistent with the absence of strong selective pressure within the Tunisian population and suggests that, in order to be effective, any potential genome-wide association mapping studies will need to use chips with higher marker density. An analysis of effective population size (Ne) based on LD data showed a decline in past Ne, with a sudden drop starting about eight generations ago. This finding, combined with the high levels of recent inbreeding revealed by runs of homozygosity (ROH) analysis, indicate that this population is endangered and may be in urgent need of a conservation plan that includes a well-designed genetic management program. <![CDATA[Polymorphism of Sooty-fronted Spinetail (<em>Synallaxis frontalis</em> Aves: Furnariidae): Evidence of chromosomal rearrangements by pericentric inversion in autosomal macrochromosomes]]> Abstract The Passeriformes is the most diverse and cytogenetically well-known clade of birds, comprising approximately 5,000 species. The sooty-fronted spinetail (Synallaxis frontalis Aves: Furnariidae) species, which belongs to the order Passeriformes, is typically found in South America, where it is widely distributed. Polymorphisms provide genetic variability, important for several evolutionary processes, including speciation and adaptation to the environment. The aim of this work was to analyze the possible cytotypes and systemic events involved in the species polymorphism. Of the sampled 19 individuals, two thirds were polymorphic, an event supposedly linked to mutations resulting from genomic evolution that can be transmitted hereditarily. A chromosomal polymorphism was detected between the 1st and 3rdpairs of autosomal macrochromosomes. This type of polymorphism is related to a pericentric inversion in regions involving chromosomal rearrangements. Differently from other polymorphism studies that report a link between polymorphic chromosomes and phenotypic changes, S. frontalis did not present any morphological variation in the sampled individuals. <![CDATA[<em>In silico</em> identification and characterization of novel microsatellite loci for the Blue-and-yellow Macaw <em>Ara ararauna</em> (Linnaeus, 1758) (Psittaciformes, Psittacidae)]]> Abstract The illegal trade is a major threat to many bird species, and parrots are common victims of this activity. Domestic and international pet markets are interested on different parrot species, such as the Blue-and-yellow Macaw (Ara ararauna). This South American macaw is not globally threatened, but is under protection from over-exploitation. This study aimed to identify and characterize novel microsatellite loci for population and parentage analysis of A. ararauna. Scaffold sequences of Ara macao available in the NCBI database were used for microsatellite searches using MsatCommander software. We tested a total of 28 loci, from which 25 were polymorphic, one was monomorphic, and two did not generated amplification products. For polymorphic loci, the mean number of alleles was 8.24 (4 – 15 alleles per locus), the observed heterozygosity ranged from 0.333 to 0.917, and the expected heterozygosity from 0.353 to 0.890. The paternity exclusion probability and identity probability were highly discriminatory. Thus, these novel microsatellite markers can be useful for population assignment and paternity tests, helping the authorities to manage macaws from the illegal trafficking and control commercial breeders. <![CDATA[Development and characterization of 20 polymorphic microsatellite markers for <em>Epinephelus marginatus</em> (Lowe, 1834) (Perciformes: Epinephelidae) using 454 pyrosequencing]]> Abstract The dusky grouper, Epinephelus marginatus, is a well-known and widespread marine fish assessed as endangered by the International Union for the Conservation of Nature. Analyzing the genetic diversity of this species is, therefore, of utmost importance and necessary for conservation purposes. Microsatellites are molecular tools with advantages that are ideal for population analyses. This study provides the first set of species-specific microsatellite loci for E. marginatus that can be applied when assessing both intra- and interpopulation genetic variation. Twenty microsatellite loci were isolated and characterized for the dusky grouper by genotyping 20 individuals obtained from the North Eastern Atlantic Ocean (n = 4) and from the South Western Atlantic Ocean (n = 16). The number of alleles per locus varied from 2 to 11, while the observed and expected heterozygosities ranged from 0.25 to 0.94 and 0.34 to 0.89, respectively. The polymorphic information content varied from moderately to highly informative. This suite of markers provides the first specific nuclear tools for E. marginatus and, thus, allows to assess with more specificity different populations’ structures. <![CDATA[Overexpression of <em>salt-induced protein</em> (<em>salT</em>) delays leaf senescence in rice]]> Abstract Senescence, a highly programmed process, largely determines yield and quality of crops. However, knowledge about the onset and progression of leaf senescence in crop plants is still limited. Here, we report that salt-induced protein (salT), a new gene, may be involved in leaf senescence. Overexpressing salT could prolong the duration of leaves with higher concentrations of chlorophyll compared with the wild type. Moreover, overexpression of salT could delay the senescence of rice leaves though the inhibition of senescence associated genes (SAGs). Overall, the characterization of salT suggested that it is a new gene affecting the leaf senescence induced by natural and dark conditions. <![CDATA[Cross-genera SSR transferability in cacti revealed by a case study using <em>Cereus</em> (Cereeae, Cactaceae)]]> Abstract The study of transferability of simple sequence repeats (SSR) among closely related species is a well-known strategy in population genetics, however transferability among distinct genera is less common. We tested cross-genera SSR amplification in the family Cactaceae using a total of 20 heterologous primers previously developed for the genera Ariocarpus, Echinocactus, Polaskia and Pilosocereus, in four taxa of the genus Cereus: C. fernambucensis subsp. fernambucensis, C. fernambucensis subsp. sericifer, C. jamacaru and C. insularis. Nine microsatellite loci were amplified in Cereus resulting in 35.2% of success in transferability, which is higher than the average rate of 10% reported in the literature for cross-genera transferability in eudicots. The genetic variation in the transferred markers was sufficient to perform standard clustering analysis, indicating each population as a cohesive genetic cluster. Overall, the amount of genetic variation found indicates that the transferred SSR markers might be useful in large-scale population studies within the genus Cereus. <![CDATA[In silico characterization of microRNAs-like sequences in the genome of Paracoccidioides brasiliensis]]> Abstract Eukaryotic cells have different mechanisms of post-transcriptional regulation. Among these mechanisms, microRNAs promote regulation of targets by cleavage or degradation of the mRNA. Fungi of the Paracoccidioides complex are the etiological agents of the main systemic mycosis of Latin America. These fungi present a plasticity to adapt and survive in different conditions, and the presence of microRNAs-like molecules could be part of the mechanisms that provide such plasticity. MicroRNAs produced by the host influence the progression of this mycosis in the lungs besides regulating targets involved in apoptosis in macrophage, activation of T and B cells and the production of cytokines. Therefore, this work analyzed the presence of regions in the genome of this fungus with a potential to encode microRNAs-like molecules. Here we show by analysis of sequence similarity the presence of 18 regions, putatively coding for microRNAs-like molecules in the Paracoccidioides brasiliensis genome. We also described the conservation of dicer and argonaut proteins and the cognate transcripts induced in the yeast parasitic phase. This work represents a starting point for the analysis of the presence of those molecules in the morphological stages of the fungus and their role in fungal development. <![CDATA[Genetic diversity and population structure of naturally rare <em>Calibrachoa</em> species with small distribution in southern Brazil]]> Abstract Calibrachoa is a South-American genus comprising 27 species, several considered endemic or rare; few were subjects in genetic studies. We attempted to generate new data about the phylogenetically related and rare species C. eglandulata, C. sendtneriana, C. serrulata, and C. spathulata concerning their genetic diversity and population structure, which, coupled with their known restricted distribution, could help access their conservation status and contribute to the study of the Brazilian biodiversity. We sequenced 88 individuals for plastid intergenic spacers and genotyped 186 individuals for five microsatellite loci. Compared among each other, C. sendtneriana and C. serrulata presented the highest values of genetic diversity [π% (sd) = 0.23 (0.14) and 0.43 (0.25), respectively], followed by C. spathulata [π% (sd) = 0.19 (0.12)] and C. eglandulata [π% (sd) = 0.02 (0.03)]. Population differentiation was evident for these latter species, whereas it was not significant for C. sendtneriana and C. serrulata. Factors such as habitat specificity and fragmentation, pollination syndrome, and life history could explain the observed patterns. Based on the new genetic data and the species’ biology, a conservation status was assigned for C. sendtneriana and the status of the other three species was reviewed. <![CDATA[Science and evolution]]> Abstract Evolution is both a fact and a theory. Evolution is widely observable in laboratory and natural populations as they change over time. The fact that we need annual flu vaccines is one example of observable evolution. At the same time, evolutionary theory explains more than observations, as the succession on the fossil record. Hence, evolution is also the scientific theory that embodies biology, including all organisms and their characteristics. In this paper, we emphasize why evolution is the most important theory in biology. Evolution explains every biological detail, similar to how history explains many aspects of a current political situation. Only evolution explains the patterns observed in the fossil record. Examples include the succession in the fossil record; we cannot find the easily fossilized mammals before 300 million years ago; after the extinction of the dinosaurs, the fossil record indicates that mammals and birds radiated throughout the planet. Additionally, the fact that we are able to construct fairly consistent phylogenetic trees using distinct genetic markers in the genome is only explained by evolutionary theory. Finally, we show that the processes that drive evolution, both on short and long time scales, are observable facts. <![CDATA[A re-annotation of the <em>Anopheles darlingi</em> mobilome]]> Abstract The mobilome, portion of the genome composed of transposable elements (TEs), of Anopheles darlingi was described together with the genome of this species. Here, this mobilome was revised using similarity and de novo search approaches. A total of 5.6% of the A. darlingi genome is derived of TEs. Class I gypsy and copia were the most abundant superfamilies, corresponding to 22.36% of the mobilome. Non-LTR elements of the R1 and Jockey superfamilies account for 11% of the TEs. Among Class II TEs, the mariner superfamily is the most abundant (16.01%). Approximately 87% of the A. darlingi mobilome consist of short, truncated and/or degenerated copies of TEs. Only three retrotransposons, two belonging to gypsy and one to copia superfamilies, are putatively active elements. Only one Class II element, belonging to the mariner superfamily, is putatively active, having 12 copies in the genome. The TE landscape of A. darlingi is formed primarily by degenerated elements and, therefore, somewhat stable. Future applications of TE-based vectors for genetic transformation of A. darlingi should take into consideration mariner and piggyBac transposons, because full length and putatively active copies of these elements are present in its genome. <![CDATA[The complete chloroplast genome sequences of three <em>Spondias</em> species reveal close relationship among the species]]> Abstract This study reports the complete chloroplast sequences of three Spondias species. The genome sequences were obtained for Spondias tuberosa, Spondias bahienses, and Spondias mombin using the Illumina sequencing technology by a combination of de novo methods and a reference-guided assembly using Sapindus mukorossi as reference. The genomes of S. tuberosa, S. bahiensis, and S. mombin had 162,036, 162,218, and 162,302 bp, respectively. The coding regions exhibited 130 genes, including 34–35 tRNAs and 4 rRNAs. The results revealed synteny among the genomes, with high conservation in the gene order and content and CG content. The inverted repeat regions (IRA and IRB) and the large and small single copies were very similar among the three genomes. The phylogenomic analysis reported similar topologies as that of previous studies, which used partial chloroplast, wherein S. mombin was the first diverging lineage, while S. tuberosa and S. bahiensis were derived, indicating that the phylogenetic analysis using partial or complete genome produces similar results. In summary, (1) we presented the first complete chloroplast genome for the genus Spondias, (2) phylogenies analyzed using the complete chloroplast genomes revealed a robust phylogenetic topology for Spondias, and (3) gene order, content, and orientation in Spondias are highly conserved. <![CDATA[Genome sequence of the H<sub>2</sub>-producing <em>Clostridium beijerinckii</em> strain Br21 isolated from a sugarcane vinasse treatment plant]]> Abstract We report on the nearly complete genome sequence of Clostridium beijerinckii strain Br21, formerly isolated from a sugarcarne vinasse wastewater treatment plant. The resulting genome is ca. 5.9 Mbp in length and resembles the size of previously published C. beijerinckii genomes. We annotated the genome sequence and predicted a total of 5323 genes. Strain Br21 has a genetic toolkit that allows it to exploit diverse sugars that are often found after lignocellulosic biomass pretreatment to yield products of commercial interest. Besides the whole set of genes encoding for enzymes underlying hydrogen production, the genome of the new strain includes genes that enable carbon sources conversion into butanol, ethanol, acetic acid, butyric acid, and the chemical block 1,3-propanediol, which is used to obtain polymers. Moreover, the genome of strain Br21 has a higher number of ORFs with predicted beta-glucosidase activity as compared to other C. beijerinckii strains described in the KEGG database. These characteristics make C. beijerinckii strain Br21 a remarkable candidate for direct use in biotechnological processes and attest that it is a potential biocatalyst supplier. <![CDATA[Draft genome of <em>Thermomonospora</em> sp. CIT 1 (Thermomonosporaceae) and <em>in silico</em> evidence of its functional role in filter cake biomass deconstruction]]> Abstract The filter cake from sugar cane processing is rich in organic matter and nutrients, which favors the proliferation of microorganisms with potential to deconstruct plant biomass. From the metagenomic data of this material, we assembled a draft genome that was phylogenetically related to Thermomonospora curvata DSM 43183, which shows the functional and ecological importance of this bacterium in the filter cake. Thermomonospora is a gram-positive bacterium that produces cellulases in compost, and it can survive temperatures of 60 ºC. We identified a complete set of biomass depolymerizing enzymes in the draft genome of Thermomonospora sp. CIT 1, such as α-amylase, catalase-peroxidases, β-mannanase, and arabinanase, demonstrating the potential of this bacterium to deconstruct the components of starch, lignin, and hemicellulose. In addition, the draft genome of Thermomonospora sp. CIT 1 contains 18 genes that do not share identity with five other species of Thermomonospora, suggesting that this bacterium has different genetic characteristics than those present in genomes reported so far for this genus. These findings add a new dimension to the current understanding of the functional profile of this microorganism that inhabits agro-industrial waste, which may boost new gene discoveries and be of importance for application in the production of bioethanol. <![CDATA[Erratum]]> Abstract The filter cake from sugar cane processing is rich in organic matter and nutrients, which favors the proliferation of microorganisms with potential to deconstruct plant biomass. From the metagenomic data of this material, we assembled a draft genome that was phylogenetically related to Thermomonospora curvata DSM 43183, which shows the functional and ecological importance of this bacterium in the filter cake. Thermomonospora is a gram-positive bacterium that produces cellulases in compost, and it can survive temperatures of 60 ºC. We identified a complete set of biomass depolymerizing enzymes in the draft genome of Thermomonospora sp. CIT 1, such as α-amylase, catalase-peroxidases, β-mannanase, and arabinanase, demonstrating the potential of this bacterium to deconstruct the components of starch, lignin, and hemicellulose. In addition, the draft genome of Thermomonospora sp. CIT 1 contains 18 genes that do not share identity with five other species of Thermomonospora, suggesting that this bacterium has different genetic characteristics than those present in genomes reported so far for this genus. These findings add a new dimension to the current understanding of the functional profile of this microorganism that inhabits agro-industrial waste, which may boost new gene discoveries and be of importance for application in the production of bioethanol.