Genetics and Molecular Biology, Volume: 43, Issue: 2, Published: 2020
  • -866G/A and Ins/Del polymorphisms in the UCP2 gene and diabetic kidney disease: case-control study and meta-analysis Human And Medical Genetics

    Dieter, Cristine; Assmann, Taís Silveira; Lemos, Natália Emerim; Massignam, Eloísa Toscan; Souza, Bianca Marmontel de; Bauer, Andrea Carla; Crispim, Daisy

    Abstract in English:

    Abstract Uncoupling protein 2 (UCP2) decreases reactive oxygen species (ROS). ROS overproduction is a key contributor to the pathogenesis of diabetic kidney disease (DKD). Thus, UCP2 polymorphisms are candidate risk factors for DKD; however, their associations with this complication are still inconclusive. Here, we describe a case-control study and a meta-analysis conducted to investigate the association between UCP2 -866G/A and Ins/Del polymorphisms and DKD. The case-control study comprised 385 patients with type 1 diabetes mellitus (T1DM): 223 patients without DKD and 162 with DKD. UCP2 -866G/A (rs659366) and Ins/Del polymorphisms were genotyped by real-time PCR and conventional PCR, respectively. For the meta-analysis, a literature search was conducted to identify all studies that investigated associations between UCP2 polymorphisms and DKD in patients with T1DM or type 2 diabetes mellitus. Pooled odds ratios were calculated for different inheritance models. Allele and genotype frequencies of -866G/A and Ins/Del polymorphisms did not differ between T1DM case and control groups. Haplotype frequencies were also similar between groups. Four studies plus the present one were eligible for inclusion in the meta-analysis. In agreement with case-control data, the meta-analysis results showed that the -866G/A and Ins/Del polymorphisms were not associated with DKD. In conclusion, our case-control and meta-analysis studies did not indicate an association between the analyzed UCP2 polymorphisms and DKD.
  • Epistasis of polymorphisms related to the articular cartilage extracellular matrix in knee osteoarthritis: Analysis-based multifactor dimensionality reduction Human And Medical Genetics

    Fernández-Torres, Javier; Martínez-Nava, Gabriela Angélica; Zamudio-Cuevas, Yessica; Lozada, Carlos; Garrido-Rodríguez, Daniela; Martínez-Flores, Karina

    Abstract in English:

    Abstract Osteoarthritis (OA) is a complex disease with a multifactorial etiology. The genetic component is one of the main associated factors, resulting from interactions between genes and environmental factors. The aim of this study was to identify gene-gene interactions (epistasis) of the articular cartilage extracellular matrix (ECM) in knee OA. Ninety-two knee OA patients and 147 healthy individuals were included. Participants were genotyped in order to evaluate nine variants of eight genes associated with ECM metabolism using the OpenArray technology. Epistasis was analyzed using the multifactor dimensionality reduction (MDR) method. The MDR analysis showed significant gene-gene interactions between MMP3 (rs679620) and COL3A1 (rs1800255), and between COL3A1 (rs1800255) and VEGFA (rs699947) polymorphisms, with information gain values of 3.21% and 2.34%, respectively. Furthermore, in our study we found interactions in high-risk genotypes of the HIF1AN, MMP3 and COL3A1 genes; the most representative were [AA+CC+GA], [AA+CT+GA] and [AA+CT+GG], respectively; and low-risk genotypes [AA+CC+GG], [GG+TT+GA] and [AA+TT+GA], respectively. Knowing the interactions of these polymorphisms involved in articular cartilage ECM metabolism could provide a new tool to identify individuals at high risk of developing knee OA.
  • Genetic variants in the G gamma-globin promoter modulate fetal hemoglobin expression in the Colombian population Human And Medical Genetics

    Fong, Cristian; Mendoza, Yesica; Barreto, Guillermo

    Abstract in English:

    Abstract Fetal hemoglobin (HbF) is a determining factor for the development of sickle cell anemia. High HbF levels lower the intensity of symptoms of this disease. HbF levels can vary in patients with sickle cell anemia and individuals without the disease. The purpose of this study was to identify the genetic variants in the G gamma-globin gene promoter that can modulate HbF expression in patients with sickle cell anemia and healthy individuals from Colombia. In total, 413 bp of the G gamma-globin gene promoter were sequenced in 60 patients with sickle cell anemia and 113 healthy individuals. The allelic and genotype frequencies of the identified variants were compared between individuals with low and high HbF for both patients and healthy individuals. In total, we identified 15 variants in both groups, only three of which were shared between patients and healthy individuals. In healthy individuals, sites -16 and -309 (rs112479156) exhibited differences in allele frequencies. The mutant allele of -16 lowered the production of HbF, whereas the mutant allele of -309 increased its production. These results reveal the presence of different mechanisms of HbF regulation between patients with sickle cell and healthy individuals.
  • Cancer-related worry and risk perception in Brazilian individuals seeking genetic counseling for hereditary breast cancer Human And Medical Genetics

    Palmero, Edenir Inêz; Campacci, Natalia; Schüler-Faccini, Lavinia; Giugliani, Roberto; Rocha, José Claudio Casali da; Vargas, Fernando Regla; Ashton-Prolla, Patricia

    Abstract in English:

    Abstract In Brazil, the population in general has little knowledge about genetic risks, as well as regarding the role and importance of the Cancer Genetic Counseling (CGC). The goal of this study was to evaluate cancer-related worry and cancer risk perception during CGC sessions in Brazilian women at-risk for hereditary breast cancer. This study was performed in 264 individuals seeking CGC for hereditary breast cancer. Both cancer-affected and unaffected individuals were included. As results, individuals with and without cancer reported different motivations for seeking CGC and undergoing genetic testing. A correlation was observed between age at the first CGC session and age at which the closest relative was diagnosed with cancer. Multivariate analysis showed that educational level, cancer risk discussion within the family, and number of deaths by cancer among first-degree relatives influenced positively the cancer risk perception. In conclusion, the results of this study indicate that cancer-related worry and cancer risk perception are significant aspects of morbidity in individuals seeking CGC, whether they are cancer-affected or unaffected. CGC has an important role in health education and cancer prevention for its potential of promoting an accurate perception of the risk.
  • Screening of BRCA1 variants c.190T>C, 1307delT, g.5331G>A and c.2612C>T in breast cancer patients from North India Human And Medical Genetics

    Kour, Akeen; Sambyal, Vasudha; Guleria, Kamlesh; Singh, Neeti Rajan; Uppal, Manjit Singh; Manjari, Mridu; Sudan, Meena

    Abstract in English:

    Abstract The polymorphic variants of BRCA1, which lead to amino acid substitutions, have a known pathogenic role in breast cancer. The present study investigated in North Indian breast cancer patients the association of risk with four reported pathogenic variants of BRCA1: c.190T>C (p.Cys64Arg), 1307delT, g.5331G>A (p.G1738R) and c.2612C>T (p.Pro871Leu). Genotyping was done by PCR-RFLP method in 255 clinically confirmed breast cancer patients and 255 age and gender matched healthy individuals. For c.190T>C, 1307delT and g.5331G>A, all the patients and controls had the wild-type genotype indicating no association with breast cancer risk. For c.2612C>T polymorphism, the frequency of the CC, CT, and TT genotypes was 14.5 vs 15.7%, 59.6 vs 53.7% and 25.9 vs 30.6% in breast cancer patients and controls respectively. The frequency of heterozygotes (CT genotype) was higher in cases than controls but the difference was not statistically significant. Genetic model analysis showed no association of the four analyzed BRCA1 variants with breast cancer risk with any model. The studied variants were not associated with the risk of breast cancer in Punjab, North west India, suggesting a need for further screening of other BRCA1 variants. It is the first reported study on these 4 variants from India.
  • Haplotypic characterization of BRCA1 c.5266dupC, the prevailing mutation in Brazilian hereditary breast/ovarian cancer Human And Medical Genetics

    Gomes, Renan; Soares, Barbara Luisa; Felicio, Paula Silva; Michelli, Rodrigo; Netto, Cristina B. O.; Alemar, Barbara; Ashton-Prolla, Patrícia; Palmero, Edenir Inêz; Moreira, Miguel Ângelo Martins

    Abstract in English:

    Abstract Specific pathogenic mutations associated with breast cancer development can vary between ethnical groups. One example is BRCA1 c.5266dupC that was first described as a founder mutation in the Ashkenazi Jewish population, but was later also found in other populations. In Brazil, this mutation corresponds to 20% of pathogenic BRCA1 variants reported. Our objective was to investigate the haplotype component of a group of Brazilian families who inherited c.5266dupC in the BRCA1 gene and to verify the ancestry contribution from European, African, and Amerindian origins. Fourteen probands carrying c.5266dupC and 16 relatives (carriers and non-carriers) were investigated. The same haplotype was observed segregating within all the families analyzed, revealing no recombinants in a region of 0.68 Mb. Ancestry analysis demonstrated that the European component was predominant among probands. The BRCA1 c.5266dupC analysis indicates that there was a founder effect in the Brazilian population.
  • Newborn screening for lysosomal disorders in Brazil: A pilot study using customized fluorimetric assays Human And Medical Genetics

    Bender, Fernanda; Burin, Maira G.; Tirelli, Kristiane M.; Medeiros, Fernanda; Bitencourt, Fernanda Hendges de; Civallero, Gabriel; Kubaski, Francyne; Bravo, Heydy; Daher, Antoine; Carnier, Vanessa; Franco, José F. S.; Giugliani, Roberto

    Abstract in English:

    Abstract Lysosomal storage disorders (LSDs) are a group of genetic disorders characterized by deficiency of specific lysosomal enzymes. In general, patients are clinically normal at birth, and progressively develop severe signs and symptoms. Diagnosis is usually made several years after onset of manifestations, preventing patients to have the benefits of the early treatment. Newborn screening programs are being considered for LSDs to allow early diagnosis and treatment. The present study evaluated the feasibility of a customized screening approach based on modified fluorometric assays with reduced amounts of reagents, substrates and samples for: mucopolysaccharidosis (MPS) type I (MPS I), MPS VI, Fabry, Gaucher, and Pompe diseases. We also evaluated the advantages of including blood chitotriosidase and urinary glycosaminoglycans in the protocol. By the measurement of the specific disease-associated enzymes (plus blood chitotriosidase and urinary glycosaminoglycans) we analyzed 834 de-identified DBS of unselected newborns. No positive case was detected, and the false-positive rates were low. Taking into consideration the limitations of this methodology, we believe that, after defining proper cutoffs, it could be a viable alternative to provide NBS for LSDs by laboratories that may not be able to afford the commercial methods available.
  • Integrated analysis of lncRNA-associated ceRNA network identified potential regulatory interactions in osteosarcoma Human And Medical Genetics

    Wang, Yongwei; Gao, Yaxian; Guo, Sen; Chen, Zhihong

    Abstract in English:

    Abstract This study aimed to identify potential therapeutic targets in osteosarcoma (OS) through the network analysis of competing endogenous RNAs (ceRNAs). The differentially expressed miRNAs (DEMIs) and mRNAs (DEMs) were identified between OS cell lines and human mesenchymal stem cells (hMSCs) from the data deposited under GSE70415 using limma package. Functional analysis of DEMs was performed using DAVID and clusterProfiler to identify significantly enriched Gene Ontology biological processes and KEGG pathways, respectively. The DEMI-DEM interaction network was constructed using Cytoscape. LncRNA–miRNA interactions were predicted using starBase database. The ceRNA regulatory network was constructed by integrating mRNAs, miRNAs, and lncRNAs, and functional enrichment analysis was performed for the genes involved. The analysis revealed a total of 326 DEMs and 54 DEMIs between OS cells and hMSCs. We identified several novel therapeutic targets involved in the progression and metastasis of OS, such as CBX7, RAD9A, SNHG7 and miR-34a-5p. The miRNA, miR-543 (target gene: CBX7) was found to be associated with the pathway Mucin type O-glycan biosynthesis. Using the ceRNA network, we established the following regulatory interactions: NEAT1/miR-543/CBX7, SNHG7/miR-34a-5p/RAD9A, and XIST/miR-34a-5p/RAD9A. CBX7, RAD9A, lncRNA SNHG7, miR-543, and miR-34a-5p may be explored as novel therapeutic targets for treatment of OS.
  • Leigh syndrome in a patient with a novel C12orf65 pathogenic variant: case report and literature review Human And Medical Genetics

    Perrone, Eduardo; Cavole, Thiago R.; Oliveira, Manuella G.; Virmond, Luiza do A.; Silva, Marina de França B.; Soares, Maria de Fatima F.; Iglesias, Simone Brasil de O.; Falconi, Ariane; Silva, Juliana S.; Nakano, Viviane; Milanezi, Maria Fernanda; Mendes, Carmen Silvia C.; Curiati, Marco Antonio; Micheletti, Cecília

    Abstract in English:

    Abstract Leigh syndrome is an early onset progressive disorder caused by defects in mitochondrial oxidative phosphorylation. Pathogenic variants in nuclear and mitochondrial genes are associated with the syndrome. Homozygous pathogenic variants in the C12orf65 gene impair the mitochondrial oxidative phosphorylation system. We describe a new case of Leigh syndrome caused by a novel pathogenic variant of the C12orf65 gene resulting in the lack of the Gly-Gly-Gln (GGQ) domain in the predicted protein, and review clinical and molecular data from previously reported patients. Our study supports that the phenotype caused by C12orf65 gene variants is heterogeneous and varies from spastic paraparesis to Leigh syndrome. Loss-of-function variants are more likely to cause the disease, and variants affecting the GGQ domain tend to be associated with more severe phenotypes, reinforcing a possible genotype-phenotype correlation.
  • Genetic variability of blood groups in southern Brazil Human And Medical Genetics

    Waskow, Gabriela; Rodrigues, Mirelen Moura de Oliveira; Höher, Gabriela; Onsten, Tor; Lindenau, Juliana Dal-Ri; Fiegenbaum, Marilu; Almeida, Silvana

    Abstract in English:

    Abstract We evaluated genetic variability among the blood groups Kell (c.578C > T and c.1790T > C), Kidd (c.838A > G), Duffy (c.125A > G, c.265C > T and c.1-67T > C), Diego (c.2561C > T), MNS (c.143T > C) and Rh (c.676G > C) in Rio Grande do Sul in southern Brazil. Genetic profiling from 382 volunteer blood donors was performed through allelic discrimination assays using a hydrolysis probe (TaqMan®) with a real-time PCR system. The sample was divided into two groups: Euro-Brazilian and Afro-Brazilian. A comparison with studies from other regions of Brazil and the 1000 Genomes Database showed significant differences for almost all polymorphisms evaluated in our population. Population differentiation between the Euro- and Afro-Brazilian groups was low (FST value 0.055). However, when each locus was evaluated individually, KEL*06 and FY*02N.01 allele frequencies were significantly higher in the Afro-Brazilian group than in the Euro-Brazilian group. Ethnic classification that uses phenotypic criteria to find blood units with rare antigens may be important when there is a need to detect blood units with an absence of Duffy antigens. There is also a greater probability of finding donors in the Afro-Brazilian group. Taken together, the data indicate strong European and African contributions to the gene pool, with intense admixture.
  • Diagnostic value of miR-145 and its regulatory role in macrophage immune response in tuberculosis Human And Medical Genetics

    Fu, Yinghui; Yang, Xue; Chen, Hongyan; Lu, Yugang

    Abstract in English:

    Abstract Tuberculosis (TB) induced by Mycobacterium tuberculosis (Mtb) is a serious global health burden. This study sought to investigate the expression and diagnostic value of serum miR-145 in TB patients and explore the biological function of miR-145 using macrophages. Serum expression levels of miR-145 were estimated by quantitative real-time PCR. A receiver operating characteristic curve was plotted to evaluate the diagnostic accuracy of miR-145. This study further focused on the effects of miR-145 on cell viability and inflammation in macrophages upon Mtb infection, and explored the potential target gene of miR-145. Serum expression levels of miR-145 were decreased in TB patients, and the upregulated inflammatory cytokines in TB patients were negatively correlated with the serum expression levels of miR-145. miR-145 had considerable diagnostic accuracy in distinguishing of TB patients from healthy individuals and differentiating between active TB cases and latent TB cases. Mtb infection induced an increase in cell viability and inflammatory responses in macrophages, but these promoting effects were rescued by the overexpression of miR-145. CXCL16 was determined as a target gene of miR-145 in macrophages. Overall, this study demonstrated that the decreased serum miR-145 expression serves a candidate diagnostic biomarker in TB patients. The overexpression of miR-145 in macrophages upon Mtb infection can suppress cell viability and infection-induced inflammation via regulating CXCL16, indicating the potential of miR-145 as a therapeutic target of TB.
  • DNA damage, oxidative stress, and inflammation in children with celiac disease Human And Medical Genetics

    Maluf, Sharbel Weidner; Wilhelm Filho, Danilo; Parisotto, Eduardo Benedetti; Medeiros, Guilherme da Silva de; Pereira, Carolina Hilgert Jacobsen; Maraslis, Flora Troina; Dornelles Schoeller, Carlos C.; Rosa, Julia Savan da; Fröde, Tânia Silvia

    Abstract in English:

    Abstract The objective of this study was to evaluate the level of genomic instability in patients with celiac disease and to establish a relationship between inflammation, oxidative stress, and DNA damage in these patients. Myeloperoxidase (MPO) activity, adenosine deaminase, nitric oxide (NOx), thiobarbituric acid, catalase (CAT), superoxide dismutase (SOD), glutathione peroxidase (GPx), and DNA damage were evaluated in peripheral blood samples from 47 celiac disease patients and 31 controls. Patients with celiac disease presented higher levels of DNA damage in comparison to controls (p=0.023). This difference was also observed for markers of oxidative stress, such as CAT (p=0.011) and SOD (p=0.013), and inflammatory markers such as MPO (p < 0.001) and NOx (p=0.009). Positive correlations were found between DNA damage levels and the values of CAT (r=0.405; p=0.009) and SOD (r=0.516; p < 0.001). Positive correlations were also found between GPx and NOx (r=0.349; p=0.030) and MPO and NOx (r=0.239; p=0.039). CAT and NOx showed a negative correlation (r= −0.315; p=0.042). In conclusion, intestinal inflammation can have systemic effects, causing an imbalance between oxidant and antioxidant markers, which may promote increased levels of DNA damage.
  • Molecular identification of Mazama species (Cervidae: Artiodactyla) from natural history collections Animal Genetics

    Mantellatto, Aline Meira Bonfim; González, Susana; Duarte, José Maurício Barbanti

    Abstract in English:

    Abstract Natural history museum collections constitute an invaluable patrimony of biological diversity for analysing the taxa distribution and evolution. However, it is very common to discover taxonomic misidentification in museum collections based on incorrect data. The aim of this research was to identify brocket deer species (Mazama genus) using molecular markers. We collected 199 samples, performed DNA extraction and species identification using a specific mitochondrial marker based on a fragment of cytochrome b (Cytb) for Neotropical deer. We achieved the amplification and sequencing of 77 specimens and verified that 26% of the skulls were wrongly identified. Moreover, in the museum collections 57% of the specimens were only identified as Mazama sp, and we were able to identify them by molecular methods to the species level. Our findings clearly demonstrate the importance of integrating molecular analyses to identify Mazama species, since using only external morphology can result in a high probability of errors. We recommend the selection of non-convergent morphological characters, which together with the use of DNA collected from museum specimens should contribute to more accurate taxonomic identifications.
  • Extinction and emergence of genomic haplotypes during the evolution of Avian coronavirus in chicken embryos Animal Genetics

    Brandão, Paulo E.; Hora, Aline S.; Silva, Sheila O. S.; Taniwaki, Sueli A.; Berg, Mikael

    Abstract in English:

    Abstract Avian coronavirus (AvCoV) is ubiquitously present on poultry as a multitude of virus lineages. Studies on AvCoV phenotypic traits are dependent on the isolation of field strains in chicken embryonated eggs, but the mutant spectrum on each isolate is not considered. This manuscript reports the previously unknown HTS (high throughput sequencing)-based complete genome haplotyping of AvCoV isolates after passages of two field strains in chicken embryonated eggs. For the first and third passages of strain 23/2013, virus loads were 6.699 log copies/ μL and 6 log copies/ μL and, for 38/2013, 5.699 log copies/μL and 2.699 log copies/μL of reaction, respectively. The first passage of strain 23/2013 contained no variant haplotype, while, for the third passage, five putative variant haplotypes were found, with > 99.9% full genome identity with each other and with the dominant genome. Regarding strain 38/2013, five variant haplotypes were found for the first passage, with > 99.9% full genome identity with each other and with the dominant genome, and a single variant haplotype was found. Extinction and emergence of haplotypes with polymorphisms in genes involved in receptor binding and regulation of RNA synthesis were observed, suggesting that phenotypic traits of AvCoV isolates are a result of their mutant spectrum.
  • Chromosome comparison among five species of Neotropical cichlids of Cichlasoma and Gymnogeophagus (Perciformes) Animal Genetics

    Pires, Larissa Bettin; Usso, Mariana Campaner; Giuliano-Caetano, Lucia; Dias, Ana Lúcia

    Abstract in English:

    Abstract The genera Cichlasoma and Gymnogeophagus belong to the subfamily Cichlinae, the only one in Neotropical cichlids. Cichlasoma dimerus, C. paranaense, C. portalegrense, Gymnogeophagus rhabdotus, and G. lacustris were collected at different points in the Paranapanema and Paraguay basins and the Lagoon of Patos hydrographic system. In addition to conventional analysis, CMA3 fluorochrome staining, and FISH with 18S rDNA probe were performed. All species had a diploid number equal to 48, with interand intraspecific differences in karyotype formulae. All species presented a single AgNOR site, except G. rhabdotus and the C. paranaense population of the Paranapanema River, which revealed more than one pair of nucleolar chromosomes. AgNORs were coincident to 18S rDNA and CMA3. Heterochromatin was distributed in the pericentromeric chromosomal regions and coincident with NORs. For the first time, this work shows cytogenetic data for C. portalegrense, G. lacustris, and G. rhabdotus. Although some results reinforce the idea of conservative chromosome evolution of 2n in Cichlinae, interspecific and populational variations observed confirm that chromosomal rearrangements affect the microstructural karyotype diversification in this group of fish.
  • Importance of naturalized breeds as a base for the formation of exotic sheep (Ovis aries) breeds in tropical altitude regions Animal Genetics

    Oliveira, Joyce Azambuja de; Egito, Andrea Alves do; Crispim, Bruno do Amaral; Vargas Junior, Fernando Miranda de; Seno, Leonardo de Oliveira; Barufatti, Alexeia

    Abstract in English:

    Abstract Recent molecular tools and technologies have marked the discovery of the origin and domestication processes of a wide variety of species, using either genomic or mitochondrial molecular markers to provide input for selection programs, as well as the management and conservation of animal breeds. This study aimed to analyze genes of mitochondrial DNA of the following sheep (Ovis aries) breeds: Pantaneira, Bergamácia, Dorper, White Dorper, Ile de France and Hampshire Down, to obtain their population genetic parameters and investigate the origin of these sheep populations reared in the State of Mato Grosso do Sul. The analysis of mitochondrial DNA allowed to infer their phylogenetic relationships and revealed significant differences among them when compared with each other and with sequences obtained from GenBank. Through the formation of haplotypes, it was noted that the Pantaneira breed served as the maternal basis for the formation of the other breeds reared in the region, and it was possible to suggest a European origin for the sheep populations studied.
  • Comparison of the heterochromatin and telomeric sequences distribuition in chromosomes of 11 species of Amazonian marsupials (Didelphimorphia; Didelphidae) Animal Genetics

    Silva, Carlos Eduardo Faresin e; Souza, Érica Martinha Silva de; Eler, Eduardo Schmidt; Silva, Maria Nazareth Ferreira da; Feldberg, Eliana

    Abstract in English:

    Abstract In recent decades the diploid numbers recorded in the New World marsupials have been widely discussed in the context of the processes of karyotype evolution in these mammals. While Interstitial Telomeric Sequences (ITS) have long been interpreted as remnants of chromosomal fusion, the biological role of these features, together with their intraspecific variation, has raised a number of questions. In the present study, we analyzed the karyotype of 11 species of Amazonian didelphids, comparing the distribution of the heterochromatin with that of the telomeric signals, and found that, in six species, the ITS coincided with the blocks of heterochromatin. While ITS were found in the X chromosomes of all Marmosa murina individuals, they were variable in all the other species, representing a specific character of each lineage. Our results support the conclusion that ITS may not always be a consequence of chromosomal rearrangements, and that the mechanisms that produce them are still unclear.
  • Genetic diversity in populations of African mahogany (Khaya grandioliola C. DC.) introduced in Brazil Plant Genetics

    Soares, Sabrina Delgado; Bandeira, Ludmila Ferreira; Ribeiro, Stela Barros; Telles, Mariana Pires de Campos; Silva, João Augusto da; Borges, Canrobert Tormin; Coelho, Alexandre Siqueira Guedes; Novaes, Evandro

    Abstract in English:

    Abstract Given its high-valued wood, the African mahogany (Khaya grandifoliola) has been envisaged as a renewable source of tropical hardwoods in Brazil. However, there are concerns about the hypothesized low diversity among the few K. grandifoliola germplasm sources introduced in the country. Using eight microsatellite markers, we evaluated the genetic diversity and divergence among 53 superior trees selected from three provenances of K. grandifoliola located in the state of Para. These populations are among the oldest plantations (>15 years) in Brazil and, therefore, the country's main seed sources. The average number of alleles per locus was 5.9, expected heterozygosity was moderate (^=0.56) and lower than the high observed heterozygosity (HO=0.74). Therefore, the intrapopulation fixation index was negative (f=-0.31) indicating the possibility that selection of superior trees might have favored heterozygous plants with heterosis. No genetic structure was observed between provenances. The genetic diversity observed within selected trees, with an effective population size (Ne) of 30.4, is comparable to that of natural populations of African and Brazilian mahoganies. Therefore, our results contradict the idea that the genetic diversity of K. grandifoliola introduced in Brazil is low and show that our germplasm can be exploited for breeding purposes.
  • Functional analysis of 4-coumarate: CoA ligase from Dryopteris fragrans in transgenic tobacco enhances lignin and flavonoids Plant Genetics

    Li, Shan-Shan; Chang, Ying; Li, Bo; Shao, Shu-Li; Zhen-Zhu-Zhang,

    Abstract in English:

    Abstract 4-Coumaric acid: coenzyme A ligase (4CL) is a key enzyme in the phenylpropanoid metabolic pathway that regulates the biosynthesis of lignin and flavonoids. Therefore, the study of 4CL is important to explore the accumulation and regulation of metabolites. This study investigated the role that the 4CL2 gene from Dryopteris fragrans (Df4CL2) plays in the metabolite synthesis. Changes in gene expression, enzyme activity, and the content of lignin and flavonoids were measured in different tissues of tobacco as model plant that was successfully transferred with Df4CL2. Tobacco plants with Df4CL2 (transgenic tobacco, TT) were successfully obtained via the Agrobacterium-transformation method. This TT tended to be thicker and had an earlier flowering period than wild type tobacco (WT). The expression levels of Df4CL2 were higher in the stem, leaf, and root in TT compared to WT. In addition, compared to WT, TT had higher 4CL enzyme activity and higher lignin and flavonoids contents. This suggests that Df4CL2 is involved in the synthesis of lignin and flavonoids in D. fragrans. This research provides important evidence toward understanding the phenylpropanoid metabolic pathway in ferns.
  • Flower transcriptome dynamics during nectary development in pepper (Capsicum annuum L.) Plant Genetics

    Deng, Ming-hua; Zhao, Kai; Lv, Jun-heng; Huo, Jin-long; Zhang, Zhu-qing; Zhu, Hai-shan; Zou, Xue-xiao; Wen, Jin-fen

    Abstract in English:

    Abstract The measurement of gene expression can provide important information about gene function and the molecular basis for developmental processes. We analyzed the transcriptomes at three different developmental stages of pepper flower [sporogenous cell division, stage (B1); pollen mother cell meiosis, stage (B2); and open flower (B3)]. In the cDNA libraries for B1, B2, and B3: 82718, 77061, and 91491 unigenes were assembled, respectively. A total of 34,445 unigene sequences and 128 pathways were annotated by KEGG pathway analysis. Several genes associated with nectar biosynthesis and nectary development were identified, and 8,955, 12,182, and 23,667 DEGs were identified in the B2 vs B1, B3 vs B1, and B3 vs. B2 comparisons. DEGs were involved in various metabolic processes, including flower development, nectar biosynthesis, and nectary development. According to the RNA-seq data, all 13 selected DEGs showed similar expression patterns after q-PCR analysis. Sucrose-phosphatase, galactinol-sucrose galactosyltransferase, and sucrose synthase played very important roles in nectar biosynthesis, and CRABS CLAW could potentially be involved in mediating nectary development. A significant number of simple sequence repeat and single nucleotide polymorphism markers were predicted in the Capsicum annuum sequences. The new results provide valuable genetic information about flower development in pepper.
  • Differential gene expression in response to water deficit in leaf and root tissues of soybean genotypes with contrasting tolerance profiles Plant Genetics

    Reis, Rafaela Ribeiro; Mertz-Henning, Liliane Marcia; Marcolino-Gomes, Juliana; Rodrigues, Fabiana Aparecida; Rockenbach-Marin, Silvana; Fuganti-Pagliarini, Renata; Koltun, Alessandra; Gonçalves, Leandro Simões Azeredo; Nepomuceno, Alexandre Lima

    Abstract in English:

    Abstract Water deficit is one of the major limitations to soybean production worldwide, yet the genetic basis of drought-responsive mechanisms in crops remains poorly understood. In order to study the gene expression patterns in leaves and roots of soybean, two contrasting genotypes, Embrapa 48 (drought-tolerant) and BR 16 (drought-sensitive), were evaluated under moderate and severe water deficit. Transcription factors from the AP2/EREBP and WRKY families were investigated. Embrapa 48 showed 770 more up-regulated genes than BR 16, in eight categories. In general, leaves presented more differentially expressed genes (DEGs) than roots. Embrapa 48 responded to water deficit faster than BR 16, presenting a greater number of DEGs since the first signs of drought. Embrapa 48 exhibited initial modulation of genes associated with stress, while maintaining the level of the ones related to basic functions. The genes expressed exclusively in the drought-tolerant cultivar, belonging to the category of dehydration responsive genes, and the ones with a contrasting expression pattern between the genotypes are examples of important candidates to confer tolerance to plants. Finally, this study identified genes of the AP2/EREBP and WRKY families related to drought tolerance.
  • Transference of multiple resistance to peanut through the development of cross-compatible complex hybrids of wild Arachis Plant Genetics

    Fávero, Alessandra Pereira; Custodio, Adriana Regina; Dinato, Naiana Barbosa; Godoy, Ignácio José de; Seijo, José Guillermo; Michelotto, Marcos Doniseti

    Abstract in English:

    Abstract Peanut (Arachis hypogaea L.) is a tetraploid species with an A and B genome, while the majority of wild Arachis species are diploid with distinct genomes. In pre-breeding programs, one way to introgress interesting wild genes into peanut is by producing amphidiploids. This study aimed at the hybridization between distinct amphidiploids and their characterization, to combine high crossability with peanut, observed in some amphidiploids, with high pest and disease resistances observed in others. These new hybrids were called complex hybrids. Four amphidiploids previously obtained were crossed at four different combinations, and the derived complex hybrids were crossed with four peanut cultivars. Morphological, reproductive, chromosome complement, molecular markers for hybrid identification, phytopatological, and entomological characterizations were performed on the complex hybrids. All cross combinations resulted in complex hybrids. One complete complement of each diploid progenitor was confirmed in each hybrid. Plants of six distinct hybrid combinations were obtained between the complex hybrids and peanut. Based on morphological characterization, differences among progenies from distinct cross combinations were observed. Complex hybrids were considered more resistant to all diseases and pests than peanut cultivars. The simultaneous introgression of genes from four wild Arachis species into peanut was possible through the development of complex hybrids.
  • Expression Quantitative Trait Loci (eQTL) mapping for callose synthases in intergeneric hybrids of Citrus challenged with the bacteria Candidatus Liberibacter asiaticus Plant Genetics

    Curtolo, Maiara; Granato, Laís Moreira; Soratto, Tatiany Aparecida Teixeira; Curtolo, Maisa; Gazaffi, Rodrigo; Takita, Marco Aurélio; Cristofani-Yaly, Mariângela; Machado, Marcos Antonio

    Abstract in English:

    Abstract Citrus plants have been extremely affected by Huanglongbing (HLB) worldwide, causing economic losses. HLB disease causes disorders in citrus plants, leading to callose deposition in the phloem vessel sieve plates. Callose is synthesized by callose synthases, which are encoded by 12 genes (calS1– calS12)in Arabidopsis thaliana. We evaluated the expression of eight callose synthase genes from Citrus in hybrids between Citrus sunki and Poncirus trifoliata infected with HLB. The objective of this work was to identify possible tolerance loci combining the expression quantitative trait loci (eQTL) of different callose synthases and genetic Single-Nucleotide Polymorphism (SNP) maps of C. sunki and P. trifoliata. The expression data from all CscalS ranged widely among the hybrids. Furthermore, the data allowed the detection of 18 eQTL in the C. sunki map and 34 eQTL in the P. trifoliata map. In both maps, some eQTL for different CscalS were overlapped; thus, a single region could be associated with the regulation of more than one CscalS. The regions identified in this work can be interesting targets for future studies of Citrus breeding programs to manipulate callose synthesis during HLB infection.
  • CRZ1 regulator and calcium cooperatively modulate holocellulases gene expression in Trichoderma reesei QM6a Genetics Of Microorganisms

    Martins-Santana, Leonardo; Paula, Renato Graciano de; Silva, Adriano Gomes; Lopes, Douglas Christian Borges; Silva, Roberto do Nascimento; Silva-Rocha, Rafael

    Abstract in English:

    Abstract Trichoderma reesei is the main filamentous fungus used in industry to produce cellulases. Here we investigated the role of CRZ1 and Ca2+signaling in the fungus T. reesei QM6a concerning holocellulases production. For this, we first searched for potential CRZ1 binding sites in promoter regions of key genes coding holocellulases, as well as transcriptional regulators and sugar and calcium transporters. Using a nearly constructed T. reeseiAcrz1 strain, we demonstrated that most of the genes expected to be regulated by CRZ1 were affected in the mutant strain induced with sugarcane bagasse (SCB) and cellulose. In particular, our data demonstrate that Ca2+ acts synergistically with CRZ1 to modulate gene expression, but also exerts CRZ1-independent regulatory role in gene expression in T. reesei, highlighting the role of the major regulator Ca2+ on the signaling for holocellulases transcriptional control in the most part of cellulases genes here investigated. This work presents new evidence on the regulatory role of CRZ1 and Ca2+ sensing in the regulation of cellulolytic enzymes in T. reesei, evidencing significant and previously unknown function of this Ca2+sensing system in the control key transcriptional regulators (XYR1 and CRE1) and on the expression of genes related to sugar and Ca2+ transport.
  • Fusarium oxysporum f. sp. phaseoli genetic variability assessed by new developed microsatellites Genetics Of Microorganisms

    Sasseron, Graziéle R.; Benchimol-Reis, Luciana L.; Perseguini, Juliana M.K.C.; Paulino, Jean Fausto C.; Bajay, Miklos M.; Carbonell, Sérgio A.M.; Chiorato, Alisson F.

    Abstract in English:

    Abstract Fusarium oxysporum f. sp. phaseoli (Fop) J.B. Kendrich & W.C. Snyder is the causal agent of Fusarium wilt of common bean (Phaseolus vulgaris L.). The objective of this study was to develop microsatellite markers (SSRs) to characterize the genetic diversity of Fop. Two libraries enriched with SSRs were developed and a total of 40 pairs of SSRs were characterized. Out of these, 15 SSRs were polymorphic for 42 Fop isolates. The number of alleles varied from two to ten, with an average of four alleles per locus and an average PIC (Polymorphic Information Content) of 0.38. The genetic diversity assessed by microsatellites for Fop was low, as expected for an asexual fungus, and not associated with geographic origin, but they were able to detect enough genetic variability among isolates in order to differentiate them. Microsatellites are a robust tool widely used for genetic fingerprinting and population structure analyses. SSRs for Fop may be an efficient tool for a better understanding of the ecology, epidemiology and evolution of this pathogen.
  • Genetic differences among Moraxella bovis and Moraxella bovoculi isolates from infectious bovine keratoconjunctivitis (IBK) outbreaks in southern Brazil Genetics Of Microorganisms

    Comin, Helena Brocardo; Domingues, Robert; Gaspar, Emanuelle Baldo; Santos, João Rodrigo Gil De Los; Cardoso, Fernando Flores

    Abstract in English:

    Abstract The objective of this study was to evaluate the genetic diversity of Moraxella bovis and Moraxella bovoculi bacteria isolated from infectious bovine keratoconjunctivitis (IBK) outbreaks in the state of Rio Grande do Sul, Brazil. The genetic diversity among Moraxella spp. was evaluated by RAPD-PCR, JWP1-JWOPA07-PCR, ERIC-PCR and by sequencing the 16S-23S intergenic regions. Based on the dendrogram, two genetically differentiated clades were observed; 14 isolates were classified as M. bovis and 17 as M. bovoculi. Genetic distances between the M. bovis samples ranged from 0.0379 to 0.4285, while for M. bovoculi the dissimilarities ranged from zero to 0.7297. Alternatively, based on sequencing analyses of the 16S-23S intergenic region, M. bovis and M. bovoculi isolates were grouped into the same two different clades, but it was not possible to differentiate between isolates within clades. PCR techniques were demonstrated to be a satisfactory tool to unravel the genetic variability among Moraxella spp., while sequencing of the 16S-23S intergenic region was only able to differentiate two species of the Moraxella genus. Despite sampling geographically close regions, we demonstrate considerable genetic diversity in M. bovis and M. bovoculi strains and genetically distinct M. bovis strains co-infecting the same animal.
  • Cytotoxic and genotoxic evaluation of cotinine using human neuroblastoma cells (SH-SY5Y) Mutagenesis

    Dalberto, Daiana; Nicolau, Caroline Cardoso; Garcia, Ana Leticia Hilario; Nordin, Adriane Perachi; Grivicich, Ivana; Silva, Juliana da

    Abstract in English:

    Abstract Cotinine is the main metabolite of nicotine, which is metabolized in the liver through a cytochrome P450 enzyme. Different studies point to genetic instability caused by nicotine, such as single and double DNA strand breaks and micronuclei formation, but little is known about the effect of cotinine. Therefore, the present in vitro study assessed the effects of cotinine on cell viability and DNA damage in SH-SY5Y neuroblastoma cells, as well as genotoxicity related to oxidative stress mechanisms. Comparisons with nicotine were also performed. An alkaline comet assay modified by repair endonucleases (FPG, OGG1, and Endo III) was used to detect oxidized nucleobases. SH-SY5Y neuronal cells were cultured under standard conditions and exposed for 3 h to different concentrations of cotinine and nicotine. Cytotoxicity was observed at higher doses of cotinine and nicotine in the MTT assay. In the trypan blue assay, cells showed viability above 80% for both compounds. Alkaline comet assay results demonstrated a significant increase in damage index and frequency for cells treated with cotinine and nicotine, presenting genotoxicity. The results of the enzyme-modified comet assay suggest a DNA oxidative damage induced by nicotine. Unlike other studies, our results demonstrated genotoxicity induced by both cotinine and nicotine. The similar effects observed for these two pyridine alkaloids may be due to the similarity of their structures.
  • The distribution of 45S rDNA sites in bird chromosomes suggests multiple evolutionary histories Evolutionary Genetics

    Degrandi, Tiago Marafiga; Gunski, Ricardo José; Garnero, Analía del Valle; Oliveira, Edivaldo Herculano Correa de; Kretschmer, Rafael; Souza, Marcelo Santos de; Barcellos, Suziane Alves; Hass, Iris

    Abstract in English:

    Abstract The distribution of 45S rDNA cluster in avian karyotypes varies in different aspects, such as position, number of bearer chromosomes, and bearers being macro- or microchromosomes. The present study investigated the patterns of variation in the 45S rDNA-bearer chromosomes of birds in order to understand the evolutionary dynamics of the cluster configuration and its contribution to the evolution of bird karyotypes. A total of 73 bird species were analyzed, including both published data and species for which rDNA-FISH was conducted for the first time. In most birds, the 45S rDNA clusters were located in a single pair of microchromosomes. Hence, the location of 45S rDNA in macrochromosomes, observed only in Neognathae species, seems to be a derived state, probably the result of chromosomal fusion between microchromosomes and distinct macrochromosomes. Additionally, the 45S rDNA was observed in multiple microchromosomes in different branches of the bird phylogeny, suggesting recurrence of dispersion processeses, such as duplications and translocations. Overall, this study indicated that the redistribution of the 45S rDNA sites in bird chromosomes followed different evolutionary trajectories with respect to each lineage of the class Aves.
  • Phylogenetic niche conservatism and plant diversification in South American subtropical grasslands along multiple climatic dimensions Evolutionary Genetics

    Barros, Michel J.F.; Silva-Arias, Gustavo A.; Segatto, Ana Lúcia Anversa; Reck-Kortmann, Maikel; Fregonezi, Jeferson N.; Diniz-Filho, José Alexandre F.; Freitas, Loreta B.

    Abstract in English:

    Abstract Phylogenetic niche conservatism can be investigated at multiple scales on an explicit geographical context. Haplotype-based comparative analyses of lineages occupying the same region, and thus subjected to similar environmental factors, allow decoupling shared evolutionary and ecological patterns, as well as multiple dimensions of adaptive diversification. Here we aimed to assess the role of environmental drivers on diversification of subtropical grassland, based on haplotypic diversity of two plant genera. We sampled two closely related and co-distributed grassland plant genera, Petunia and Calibrachoa, across their entire distribution area. Eigenvectors extracted from pairwise distances based on chloroplast DNA haplotypes were used to fit Phylogenetic Signal-Representation (PSR) curves to estimate evolutionary patterns in 19 bioclimatic variables and altitude. The PSR curves showed that altitude, precipitation, and temperature variables changed at different rates with haplotype differentiation. Altitude and temperature traits evolved under conditions closer to a neutral dynamics, whereas precipitation traits differentiated following more complex models. Our results indicated that the diversification in the two genera was more limited by precipitation conditions. Based on these novel findings, we suggest that future studies should test the possible impact of precipitation variables on the process of ecological differentiation in these genera.
  • Tools for Evolutionary and Genetic Analysis (TEGA): A new platform for the management of molecular and environmental data Evolutionary Genetics

    Elias, Dario Ezequiel; Rueda, Eva Carolina Rueda

    Abstract in English:

    Abstract Population genetics studies the distributions and changes in population allele frequencies in response to processes, such as mutation, natural selection, gene flow, and genetic drift. Researchers daily manage genetic, biological, and environmental data of the samples, storing them in text files or spreadsheets, which makes it difficult to maintain consistency and traceability. Here we present TEGA, a WEB-based stand-alone software developed for the easy analysis and management of population genetics data. It was designed to: 1) facilitate data management, 2) provide a way to execute the analysis procedures, and 3) supply a means to publish data, procedures, and results. TEGA is distributed under the GNU AGPL v3 license. The documentation, source code, and screenshots are available at https://github.com/darioelias/TEGA. In addition, we present Rabid Fish, the first implementation of TEGA in the Genetics Labortory of the Faculty of Humanities and Sciences at the National University of the Litoral, where research focuses on population genetics studies applied to non-model organisms.
  • HW_TEST, a program for comprehensive HARDY-WEINBERG equilibrium testing Evolutionary Genetics

    Santos, Fernando Azenha Bautzer; Lemes, Renan Barbosa; Otto, Paulo Alberto

    Abstract in English:

    Abstract This article deals with a Windows (© Microsoft Inc.) executable, user-friendly program that tests the hypothesis of Hardy-Weinberg (HW) proportions from autosomal multiallelic data using different methods that include parametric, nonparametric and exact bootstrap tests, the latter obtained through computer simulations. The program can be obtained free of charge directly from the internet repository https://github.com/Lemes-RenanB/HardyWeinbergTesting.
  • Tracking a recent horizontal transfer event: The P-element reaches Brazilian populations of Drosophila simulans Evolutionary Genetics

    Nascimento, Ana M.L.; Silva, Bráulio S.M.L.; Svartman, Marta; Kuhn, Gustavo C.S.

    Abstract in English:

    Abstract The “cut-and-paste” P-element present in some Diptera illustrates two important transposable elements abilities: to move within genomes and to be transmitted between non-mating species, a phenomenon known as horizontal transposon transfer (HTT). Recent studies reported a HTT of the P-element from Drosophila melanogaster to D. simulans. P-elements first appeared in D. simulans European samples collected in 2006 and spread across several populations from Europe, Africa, North America and Japan within seven years. Nevertheless, no P-element was found in South American populations of D. simulans collected between 2002 and 2009. We investigated the presence of the P-element in D. simulans collected in five Brazilian localities between 2018 and 2019, using a combination of methodologies such as PCR, DNA sequencing and FISH on chromosomes. Our experiments revealed the presence of the P-element in all sampled individuals from the five localities. The number of P-elements per individual varied from 11 to 20 copies and truncated copies were also observed. Altogether, our results showed that P-element invasion in D. simulans is at an advanced stage in Brazil and, together with other recent studies, confirms the remarkable rapid invasion of P-elements across worldwide D. simulans populations.
  • What could be the fate of secondary contact zones between closely related plant species? Evolutionary Genetics

    Schnitzler, Carolina K.; Turchetto, Caroline; Teixeira, Marcelo C.; Freitas, Loreta B.

    Abstract in English:

    Abstract Interspecific hybridization has been fundamental in plant evolution. Nevertheless, the fate of hybrid zones throughout the generations remains poorly addressed. We analyzed a pair of recently diverged, interfertile, and sympatric Petunia species to ask what fate the interspecific hybrid population has met over time. We analyzed the genetic diversity in two generations from two contact sites and evaluated the effect of introgression. To do this, we collected all adult plants from the contact zones, including canonicals and intermediary colored individuals, and compared them with purebred representatives of both species based on seven highly informative microsatellite loci. We compared the genetic diversity observed in the contact zones with what is seen in isolated populations of each species, considering two generations of these annual species. Our results have confirmed the genetic differentiation between the species and the hybrid origin of the majority of the intermediary colored individuals. We also observed a differentiation related to genetic variability and inbreeding levels among the populations. Over time, there were no significant differences per site related to genetic diversity or phenotype composition. We found two stable populations kept by high inbreeding and backcross rates that influence the genetic diversity of their parental species through introgression.
  • ACE2 diversity in placental mammals reveals the evolutionary strategy of SARS-CoV-2 Evolutionary Genetics

    Fam, Bibiana S.O.; Vargas-Pinilla, Pedro; Amorim, Carlos Eduardo G.; Sortica, Vinicius A.; Bortolini, Maria Cátira

    Abstract in English:

    Abstract The recent emergence of SARS-CoV-2 is responsible for the current pandemic of COVID-19, which uses the human membrane protein ACE2 as a gateway to host-cell infection. We performed a comparative genomic analysis of 70 ACE2 placental mammal orthologues to identify variations and contribute to the understanding of evolutionary dynamics behind this successful adaptation to infect humans. Our results reveal that 4% of the ACE2 sites are under positive selection, all located in the catalytic domain, suggesting possibly taxon-specific adaptations related to the ACE2 function, such as cardiovascular physiology. Considering all variable sites, we selected 30 of them located at the critical ACE2 binding sites to the SARS-CoV-like viruses for analysis in more detail. Our results reveal a relatively high diversity of ACE2 between placental mammal species, while showing no polymorphism within human populations, at least considering the 30 inter-species variable sites. A perfect scenario for natural selection favored this opportunistic new coronavirus in its trajectory of infecting humans. We suggest that SARS-CoV-2 became a specialist coronavirus for human hosts. Differences in the rate of infection and mortality could be related to the innate immune responses, other unknown genetic factors, as well as non-biological factors.
  • Survey for positively selected coding regions in the genome of the hematophagous tsetse fly Glossina morsitans identifies candidate genes associated with feeding habits and embryonic development Evolutionary Genetics

    Freitas, Lucas; Mesquita, Rafael D.; Schrago, Carlos G.

    Abstract in English:

    Abstract Tsetse flies are responsible for the transmission of Trypanossoma sp. to vertebrate animals in Africa causing huge health issues and economic loss. The availability of the genome sequence of Glossina morsitans enabled the discovery of several genes related to medically important phenotypes and novel physiological features. However, a genome-wide scan for coding regions that underwent positive selection is still missing, which is surprising given the evolution of traits associated with the hematophagy in this lineage. In this study, we employed an experimental design that controlled for the rate of false positives and we performed a scan of 3,318 G. morsitans genes. We found 145 genes with significant historical signal of positive selection. These genes were categorized into 18 functional classes after careful manual annotation. Based on their attributed functions, we identified candidate genes related with feeding habits and embryonic development. When our results were contrasted with gene expression data, we confirmed that most genes that underwent adaptive molecular evolution were frequently expressed in organs associated with key physiological evolutionary innovations in the G. morsitans lineage, namely, the salivary gland, the midgut, fat body tissue, and in the spermatophore.
  • Global phylogeography of the critically endangered hawksbill turtle (Eretmochelys imbricata) Evolutionary Genetics

    Arantes, Larissa S.; Vargas, Sarah M.; Santos, Fabrício R.

    Abstract in English:

    Abstract The hawksbill turtle is a broadly distributed, highly migratory and critically endangered sea turtle species. The paucity of studies restricts the comprehension of its behavior and life history. In this work, we performed a global phylogeographic analysis using a compilation of previously published mitochondrial haplotype data to understand the dynamics and diversity of hawksbill populations worldwide. Our results revealed a complex demographic pattern associated to hawksbill phylogeography since the Pliocene. Isolation by distance is not enough to explain distinct demographic units of hawksbill turtles, which are also influenced by other factors as oceanic currents, coral reef distribution and nesting timing. The foraging aggregations are typically mixed stocks of individuals originating from multiple nesting areas, but there is also a trend of foragers coming from nearby natal beaches. Phylogenetic analysis indicates two highly divergent major lineages split between Atlantic and Indo-Pacific rookeries, but there is also a more recent Atlantic Ocean colonization from the Indo-Pacific Ocean. Long-distance dispersal events are likely responsible for homogenization between distant populations within oceans. Our findings provided new insights about population connectivity, identified gaps that should be prioritized in future research and highlighted the need for international efforts aiming at hawksbill's conservation.
  • Role of the MAPK pathway in human lung epithelial-like A549 cells apoptosis induced by paraquat Cellular, Molecular And Developmental Genetics

    Sun, Da-Zhuang; Song, Chun-Qing; Xu, Yong-Min; Dong, Xue-Song

    Abstract in English:

    Abstract This study aims to investigate the value of mitogen-activated protein kinases (MAPKs) for paraquat (PQ)-induced apoptosis in human lung epithelial-like A549 cells and the specific mechanism. A549 cell apoptosis were induced by PQ. These cells were divided into six groups: control group (cells were cultured in RPMI-1640 medium); SP600125 group (cells were preconditioned with SP600125); SB203580 group (cells were preconditioned with SB203580); PQ group (cells were treated with PQ); SP600125+PQ group (cells were preconditioned with SP600125 following PQ); SB203580+PQ group (cells were preconditioned with SB203580 following PQ). The cell survival rate, apoptosis rate, and activities of caspase-3 and -9 were detected. When compared with the control group, both SP600125 and SB203580 groups had no significant difference in the detected indicators. When compared with PQ group, the cells in both SP600125+PQ group and SB203580+PQ group had significantly increased viability and level of anti-apoptotic protein Bcl-2; and had decreased apoptotic rates, decreased levels of caspase-3 and -9, and decreased level of pro-apoptotic protein Bax. The ratio of p-JNK/JNK protein expression in the SP600125+PQ group significantly decreased, while the ratio of the p-P38/P38 protein expression in the SB203580+PQ group decreased. PQ induced A549 cell apoptosis through the MAPKs pathway.
  • PACT/PRKRA and p53 regulate transcriptional activity of DMRT1 Cellular, Molecular And Developmental Genetics

    Fujitani, Kazuko; Otomo, Asako; Nagayama, Yuto; Tachibana, Taro; Kato, Rika; Kawashima, Yusuke; Kodera, Yoshio; Kato, Tomoko; Takada, Shuji; Tamura, Kei; Takamatsu, Nobuhiko; Ito, Michihiko

    Abstract in English:

    Abstract The transcription factor DMRT1 (doublesex and mab-3 related transcription factor) has two distinct functions, somatic-cell masculinization and germ-cell development in some vertebrate species, including mouse and the African clawed frog Xenopus laevis. However, its transcriptional regulation remains unclear. We tried to identify DMRT1-interacting proteins from X. laevis testes by immunoprecipitation with an anti-DMRT1 antibody and MS/MS analysis, and selected three proteins, including PACT/PRKRA (Interferon-inducible double-stranded RNA dependent protein kinase activator A) derived from testes. Next, we examined the effects of PACT/PRKRA and/or p53 on the transcriptional activity of DMRT1. In transfected 293T cells, PACT/PRKRA and p53 significantly enhanced and repressed DMRT1-driven luciferase activity, respectively. We also observed that the enhanced activity by PACT/PRKRA was strongly attenuated by p53. Moreover, in situ hybridization analysis of Pact/Prkra mRNA in tadpole gonads indicated high expression in female and male germline stem cells. Taken together, these findings suggest that PACT/PRKRA and p53 might positively and negatively regulate the activity of DMRT1, respectively, for germline stem cell fate.
  • Comparative transcriptome analysis of the hippocampus from sleep-deprived and Alzheimer’s disease mice Cellular, Molecular And Developmental Genetics

    Wei, Yi

    Abstract in English:

    Abstract We did a comparative analysis of the gene expression profiles of the hippocampus from sleep deprivation and Alzheimer’s disease (AD) mice. Differentially expressed genes (DEGs) were identified by comparing the transcriptome profiles of the hippocampus of sleep deprivation or AD mouse models to matched controls. The common DEGs between sleep deprivation and AD were identified by the overlapping analysis, followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. The results showed that a total of 16 common DEGs showed similar change patterns in both sleep deprivation mice and AD mice. Sgk1, Ly6a, Atp6v0e, Hspb8, Htra1, Pdk4, Pfkfb3, Golm1, and Plin3 were up-regulated in the two disorders, whereas, Marcksl1, Fgd1, Scarb1, Mvd, Klhl13, Elovl2, and Vps29 were down-regulated. Acetyl-CoA metabolic process and lipid biosynthetic process were significantly enriched by those DEGs. The highly expressed DEGs and the two GO terms were associated with neuropathological changes according to the previous studies. As expected, sleep deprivation may contribute the AD development through these common DEGs.
  • Combined use of mitochondrial and nuclear genetic markers further reveal immature marine turtle hybrids along the South Western Atlantic Cellular, Molecular And Developmental Genetics

    Brito, Cíntia; Vilaça, Sibelle Torres; Lacerda, Ana Luzia; Maggioni, Rodrigo; Marcovaldi, Maria Ângela; Vélez-Rubio, Gabriela; Proietti, Maíra Carneiro

    Abstract in English:

    Abstract Marine turtle hybridization is usually sporadic and involves reports of only a few individuals; however, Brazilian populations have high hybridization rates. Here we investigated the presence of hybrids in morphologically identified immature hawksbills (Eretmochelys imbricata) along the South Western Atlantic (SWA). We sequenced one mitochondrial (D-Loop) and three nuclear DNA (RAG1, RAG2, and CMOS) markers to better understand the patterns and characteristics of hybrids. We identified 22 hybrids (n = 270), 11 of them at the extreme South of the SWA. Uruguay had the highest hybrid frequency in the SWA (~37.5%) followed by southern Brazil with 30%. These are common areas for loggerheads (Caretta caretta) but uncommon for hawksbills, and these hybrids may be adopting the behavior of loggerheads. By analyzing nuclear markers, we can infer that 50% of the sampled hybrids are first generation (F1) and 36% are the result of backcrosses between hybrids and pure E. imbricata (> F1). We also report for the first time immature E. imbricata x Lepidochelys olivacea hybrids at the Brazilian coast. Considering the high frequency of hybrids in the SWA, continuous monitoring should be performed to assess the fitness, genetic integrity, and extent of changes in the gene pools of involved populations.
  • BAP1 functions as a tumor promoter in prostate cancer cells through EMT regulation Cellular, Molecular And Developmental Genetics

    Park, Chan Mi; Lee, Jae Eun; Kim, Jung Hwa

    Abstract in English:

    Abstract BRCA1-associated protein 1 (BAP1) is a deubiquitinating enzyme that has long been considered to be a tumor suppressor in various tumors, including renal cell carcinoma, uveal melanoma, mesothelioma, and cutaneous melanoma. However, the involvement of BAP1 in the progression of prostate cancer has not been studied until recently. Herein, we investigated the tumor promoting function of BAP1 in the context of prostate cancer. Analysis of The Cancer Genome Atlas (TCGA) data set showed that prostate cancer patients express high levels of BAP1 mRNA. High BAP1 expression is inversely correlated with disease-free survival in patients with prostate cancer. Among the prostate cell lines tested, BAP1 expression was high in tumorigenic and metastatic cell lines, but was low in normal prostate cell line. Knockdown of BAP1 in PC3 or DU145 cells induced mesenchymal-to-epithelial transition (MET). Further, BAP1-knockdown resulted in decreased migration and invasion of PC3 and DU145 cells. Conversely, overexpression of BAP1 in RWPE1, a normal prostate cell line, induced the migratory and invasive properties. Collectively, our findings identified that BAP1 has a tumor promoting function in prostate cancer cells, and suggest that BAP1 can serve as a potential therapeutic target for prostate cancer.
  • USP7 deubiquitinates and stabilizes EZH2 in prostate cancer cells Cellular, Molecular And Developmental Genetics

    Lee, Jae Eun; Park, Chan Mi; Kim, Jung Hwa

    Abstract in English:

    Abstract Regulation of target proteins by the ubiquitin-proteasome system (UPS) is common in a wide range of cellular events, including transcriptional regulation, cell cycle progression, differentiation, and tumorigenesis. Ubiquitin-specific protease 7 (USP7) has been implicated in tumor development and metastasis in various malignancies through the regulation of target protein stability. In this study, we found that the enhancer of zeste homolog 2 (EZH2), which catalyzes the methylation at lysine 27 of histone H3, is a target of USP7 and is stabilized by USP7-mediated deubiquitination. In prostate cancer cells, the transcriptional repression function of EZH2 was inhibited by USP7-knockdown. Furthermore, ectopic introduction of EZH2 restored the cell migration, invasion, and sphere-forming potential of prostate cancer cells, which had been decreased by USP7-knockdown. Moreover, combined treatment with the USP7-specific inhibitor P5091 and EZH2 inhibitors, such as GSK126, EPZ6438, and DZNep, induced synergistic inhibitory effects on cell migration, invasion, and sphere-forming potential in prostate cancer cells. Collectively, our findings revealed that the promotion of the malignancy-associated characteristics of prostate cancer cells by USP7 was in part due to EZH2 stabilization. Thus, we suggest that simultaneous treatment with a USP7 inhibitor and an EZH2 inhibitor could be a rational strategy for treating EZH2-dependent cancers.
  • Overexpression of klotho suppresses growth and pulmonary metastasis of osteosarcoma in vivo Cellular, Molecular And Developmental Genetics

    Li, Ying; Xiao, Hai-jun; Xue, Feng

    Abstract in English:

    Abstract Klotho is originally discovered as an anti-aging gene and knock-out of klotho accelerates aging in mice. Subsequent studies support the anti-carcinogenesis role of klotho in a variety of human malignancies. The present study investigated the role of klotho on growth and metastasis of osteosarcoma cells. The osteosarcoma cells were transduced with lentivirus particles encoding klotho or scramble control. The reconstructed osteosarcoma cells were injected into the femoral medullary cavity of nude mice to establish a xenograft animal model. The anti-tumor properties of klotho were evaluated in terms of tumor growth, apoptosis, glycogen production, and pulmonary metastasis. Lentivirus-mediated overexpression of klotho significantly decreased tumor volume and weight in osteosarcoma mice. Determination of PCNA and Ki67 expression revealed that overexpression of klotho inhibited cell proliferation in tumor tissues obtained from osteosarcoma xenografts. PAS staining also showed that overexpression of klotho significantly decreased the production of glycogen in osteosarcoma. Moreover, TUNEL positive cells were significantly increased after lentivirus-mediated overexpression of klotho. Furthermore, lentivirus-mediated upregulation of klotho reduced the number of pulmonary metastatic lesions in mice compared to control mice. These findings demonstrated that elevated klotho could inhibit osteosarcoma cell growth and pulmonary metastasis in vivo, suggesting that klotho may be a valuable therapeutic target for osteosarcoma.
  • Comparative analysis of the complete chloroplast genomes from six Neotropical species of Myrteae (Myrtaceae) Genomics And Bioinformatics

    Rodrigues, Nureyev F.; Balbinott, Natalia; Paim, Igor; Guzman, Frank; Margis, Rogerio

    Abstract in English:

    Abstract Myrteae is the largest and most diverse tribe within Myrtaceae and represents the majority of its diversity in the Neotropics. Members of Myrteae hold ecological importance in tropical biomes for the provision of food sources for many animal species. Thus, due to its several roles, a growing interest has been addressed to this group. In this study, we report the sequencing and de novo assembly of the complete chloroplast (cp) genomes of six Myrteae species: Eugenia brasiliensis, E. pyriformis, E. nitida, Myrcianthes pungens, Plinia edulis and Psidium cattleianum. We characterized genome structure, gene content, and identified SSRs to detect variation within Neotropical Myrteae. The six newly sequenced plastomes exhibit a typical quadripartite structure, gene content and organization highly conserved among Myrtaceae species. Some differences in genome length, protein-coding genes and non-coding regions were found. Besides, IR boundaries present structural changes among species. Increased sequence diversity was observed in some intergenic regions, suggesting their suitability for investigating intraand interspecific genetic diversity in populational studies. These data also contribute to the improvement of taxa sampling in further phylogenetic investigations to understand Myrtaceae evolution.
  • A comparison between SOLiD 5500XLand Ion Torrent PGM-derived miRNA expression profiles in two breast cell lines Genomics And Bioinformatics

    Branco, Gabriela Pereira; Valieris, Renan; Povoa, Lucas Venezian; Araújo, Luiza Ferreira de; Fernandes, Gustavo Ribeiro; Souza, Jorge Estefano Santana de; Amorim, Maria Galli de; Ferreira, Elisa Napolitano e; Silva, Israel Tojal da; Nunes, Diana Noronha; Dias-Neto, Emmanuel

    Abstract in English:

    Abstract Next-generation sequencing (NGS) platforms allow the analysis of hundreds of millions of molecules in a single sequencing run, revolutionizing many research areas. NGS-based microRNA studies enable expression quantification in unprecedented scale without the limitations of closed-platforms. Yet, whereas a massive amount of data produced by these platforms is available, comparisons of quantification/discovery capabilities between platforms are still lacking. Here we compare two NGS-platforms: SOLiD and PGM, by evaluating their microRNA identification/quantification capabilities using two breast-derived cell-lines. A high expression correlation (R2 > 0.9) was achieved, encompassing 97% of the miRNAs, and the few discrepancies in miRNA counts were attributable to molecules that have very low expression. Quantification divergences indicative of artefactual representation were seen for 14 miRNAs (higher in SOLiD-reads) and another 10 miRNAs more abundant in PGM-data. An inspection of these revealed an increased and statistically significant count of uracyls and uracyl-stretches for PGM-enriched miRNAs, compared to SOLiD and to the miRBase. In parallel, adenines and adenine-stretches were enriched for SOLiDderived miRNA reads. We conclude that, whereas both platforms are overall consistent and can be used interchangeably for microRNA expression studies, particular sequence features appear to be indicative of specific platform bias, and their presence in microRNAs should be considered for database-analyses.
  • Transcriptomics analysis of Psidium cattleyanum Sabine (Myrtaceae) unveil potential genes involved in fruit pigmentation Genomics And Bioinformatics

    Vetö, Nicole M.; Guzman, Frank; Kulcheski, Franceli R.; Segatto, Ana Lúcia A.; Lacerda, Maria Eduarda G.; Margis, Rogerio; Turchetto-Zolet, Andreia C.

    Abstract in English:

    Abstract Psidium cattleyanum Sabine is an Atlantic Forest native species that presents some populations with red fruits and others with yellow fruits. This variation in fruit pigmentation in this species is an intriguing character that could be related to species evolution but still needs to be further explored. Our goal was to provide genomic information for these morphotypes to understand the molecular mechanisms of differences in fruit colour in this species. In this study, we performed a comparative transcriptome analysis of red and yellow morphotypes of P. cattleyanum, considering two stages of fruit ripening. The transcriptomic analysis performed encompassing leaves, unripe and ripe fruits, in triplicate for each morphotype. The transcriptome consensus from each morphotype showed 301,058 and 298,310 contigs from plants with yellow and red fruits, respectively. The differential expression revealed important genes that were involved in anthocyanins biosynthesis, such as the anthocyanidin synthase (ANS) and UDP-glucose:flavonoid-o-glucosyltransferase (UFGT) that were differentially regulated during fruit ripening. This study reveals stimulating data for the understanding of the pathways and mechanisms involved in the maturation and colouring of P. cattleyanum fruits and suggests that the ANS and UFGT genes are key factors involved in the synthase and pigmentation accumulation in red fruits.
  • Methodological differences can affect sequencing depth with a possible impact on the accuracy of genetic diagnosis Genomics And Bioinformatics

    Borges, Murilo G.; Rocha, Cristiane S.; Carvalho, Benilton S.; Lopes-Cendes, Iscia

    Abstract in English:

    Abstract For a better interpretation of variants, evidence-based databases, such as ClinVar, compile data on the presumed relationships between variants and phenotypes. In this study, we aimed to analyze the pattern of sequencing depth in variants from whole-exome sequencing data in the 1000 Genomes project phase 3, focusing on the variants present in the ClinVar database that were predicted to affect protein-coding regions. We demonstrate that the distribution of the sequencing depth varies across different sequencing centers (pair-wise comparison, p < 0.001). Most importantly, we found that the distribution pattern of sequencing depth is specific to each facility, making it possible to correctly assign 96.9% of the samples to their sequencing center. Thus, indicating the presence of a systematic bias, related to the methods used in the different facilities, which generates significant variations in breadth and depth in whole-exome sequencing data in clinically relevant regions. Our results show that methodological differences, leading to significant heterogeneity in sequencing depth, may potentially influence the accuracy of genetic diagnosis. Furthermore, our findings highlight how it is still challenging to integrate results from different sequencing centers, which may also have an impact on genomic research.
  • Characterization of a Paracoccidioides spp. strain from southeastern Brazil genotyped as Paracoccidioides restrepiensis (PS3) and review of this phylogenetic species Genomics And Bioinformatics

    Cocio, Tiago Alexandre; Nascimento, Erika; Kress, Marcia R. V. Z.; Bagagli, Eduardo; Martinez, Roberto

    Abstract in English:

    Abstract Phylogenetic species of Paracoccidioides brasiliensis complex (S1a and S1b, PS2, PS3, and PS4) and Paracoccidioides lutzii are agents of paracoccidioidomycosis, an endemic fungal disease in Latin America. P. restrepiensis (PS3 genotype) was classified as monophyletic and geographically restricted to Colombia and neighboring territories. BAT (or Pb-327B) was isolated from a patient living in the southeast region of Brazil but with genotype similar to Colombian Paracoccidioides spp. strains. This study aimed to define the phylogenetic species of BAT isolate by using additional genotyping methods, as well as reviewing the epidemiological and clinical studies related to P. restrepiensis isolates. Genomic DNA of BAT isolate and reference strains of P. brasiliensis sensu stricto (S1b), P. americana (PS2), P. restrepiensis (PS3), and P. lutzii were analyzed by conventional polymerase chain reaction (PCR) of partial gp43 exon 2 loci, by PCR-RFLP technique of tub1 gene, and by sequencing of the whole gp43 exon 2 loci. Here, we show that BAT isolate belongs to P. restrepiensis species, which is an unusual identification in southeastern Brazil, where P. brasiliensis sensu stricto is the prevalent genotype. This identification has relevance for geographical distribution and propagation of the genus Paracoccidioides in South America.
  • Comparative analysis of codon usage patterns in Rift Valley fever virus Genomics And Bioinformatics

    Kim, Hayeon; Cho, Myeongji; Son, Hyeon S.

    Abstract in English:

    Abstract Rift Valley fever virus (RVFV) is a vector-borne pathogen and is the most widely known virus in the genus Phlebovirus. Since it was first reported, RVFV has spread to western Africa, Egypt and Madagascar from its traditional endemic region, and infections continue to occur in new areas. In this study, we analyzed genomic patterns according to the infection properties of RVFV. Among the four segments of RVFV, the nucleotide composition, overall GC content and the difference of GC composition in the third position of the codons (%GC3) between groups were the largest in the S (NP) segment, showing that more diverse codons were used than in other segments. Furthermore, the results of CAI analysis of the S (NP) segment showed that viruses isolated from regions where no previous infections had been reported had the highest values, indicating greater adaptability to human hosts compared with other viruses. This result suggests that mutations in the S (NP) segment co-evolve with the infected hosts and may lead to expansion of the geographic range. The distinctive codon usage patterns observed in specific genomic regions of a group with similar infection properties may be related to the increasing likelihood of RVFV infections in new areas.
  • Complete chloroplast genome sequence of Caryocar brasiliense Camb. (Caryocaraceae) and comparative analysis brings new insights into the plastome evolution of Malpighiales Genomics And Bioinformatics

    Nunes, Rhewter; Souza, Ueric José Borges de; Targueta, Cintia Pelegrineti; Pinto, Rafael Barbosa; Soares, Thannya Nascimento; Diniz-Filho, José Alexandre Felizola; Telles, Mariana Pires de Campos

    Abstract in English:

    Abstract Caryocar brasiliense (Caryocaraceae) is a Neotropical tree species widely distributed in Brazilian Savannas. This species is very popular in central Brazil mainly by the use of its fruits in the local cuisine, and indeed it is one of the candidates, among Brazilian native plants, for fast track incorporation into cropping systems. Here we sequenced the complete chloroplast genome of C. brasiliense and used the data to access its genomic resources using high-throughput sequencing. The chloroplast exhibits a genome length of 165,793 bp and the typical angiosperm quadripartite structure with two copies of an inverted repeat sequence (IRa and IRb) of 34,902 bp each, separating a small single copy (SSC) region of 11,852 bp and a large single copy (LSC) region of 84,137 bp. The annotation analysis identified 136 genes being 87 protein-coding, eight rRNA and 37 tRNA genes. We identified 49 repetitive DNA elements and 85 microsatellites. A bayesian phylogenetic analysis helped to understand previously unresolved relationships in Malpighiales, placing Caryocaraceae as a separated group in the order, with high supported nodes. This study synthetizes valuable information for further studies allowing a better understanding of evolutionary patterns in the group and providing resources for future breeding programs.
  • Molecular relationships of Campomanesia xanthocarpa within Myrtaceae based on the complete plastome sequence and on the plastid ycf2 gene Genomics And Bioinformatics

    Machado, Lilian de Oliveira; Vieira, Leila do Nascimento; Stefenon, Valdir Marcos; Faoro, Helisson; Pedrosa, Fábio de Oliveira; Guerra, Miguel Pedro; Nodari, Rubens Onofre

    Abstract in English:

    Abstract Plastomes are very informative structures for comparative phylogenetic and evolutionary analyses. We sequenced and analyzed the complete plastome of Campomanesia xanthocarpa and compared its gene order, structure, and evolutionary characteristics within Myrtaceae. Analyzing 48 species of Myrtaceae, we identified six genes representing ‘hotspots’ of variability within the plastomes (ycf2, atpA, rpoC2, pcbE, ndhH and rps16), and performed phylogenetic analyses based on: (i) the ycf2 gene, (ii) all the six genes identified as ‘hotspots’ of variability, and (iii) the genes identified as ‘hotspots’ of variability, except the ycf2 gene. The structure, gene order, and gene content of the C. xanthocarpa plastome are similar to other Myrtaceae species. Phylogenetic analyses revealed the ycf2 gene as a promissing region for barcoding within this family, having also a robust phylogenetic signal. The synonymous and nonsynonymous substitution rates and the Ka/Ks ratio revealed low values for the ycf2 gene among C. xanthocarpa and the other 47 analyzed species of Myrtaceae, with moderate purifying selection acting on this gene. The average nucleotide identity (ANI) analysis of the whole plastomes produced phylogenetic trees supporting the monophyly of three Myrtaceae tribes. The findings of this study provide support for planning conservation, breeding, and biotechnological programs for this species.
  • [RETRACTION]: Expression of serum microRNA-378 and its clinical significance in renal cell carcinoma Retraction

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