Circulation of Dengue virus serotype 1 genotype V and Dengue virus serotype 2 genotype III in Tocantins state, Northern Brazil, 2021–2022

In Brazil, the state of Tocantins, located in north-central Brazil, has experienced a significant number of cases of arboviral disease, particularly Dengue virus (DENV). This study aimed to deepen the knowledge on DENV circulation within that state by conducting full genome sequencing of viral genomes recovered from 61 patients between June 2021 and July 2022. There were a total of 8807 and 20,692 cases in 2021 and 2022, respectively, as reported by the state’s Secretary of Health. Nucleotide sequencing confirmed the circulation of DENV serotype 1, genotype V and DENV serotype 2, genotype III in the State. Younger age groups (4 to 43 years old) were mostly affected; however, no significant differences were detected regarding the gender distribution of cases in humans. Phylogenetic analysis revealed that the circulating viruses belong to DENV-1 genotype V American and DENV-2 genotype III Southeast Asian/American. The Bayesian analysis of DENV-1 genotype V genomes sequenced here are closely related to genomes previously sequenced in the state of São Paulo. Regarding the DENV-2 genotype III genomes, these clustered in a distinct, well-supported subclade, along with previously reported isolates from the states of Goiás and São Paulo. The findings reported here suggest that multiple introductions of these genotypes occurred in the Tocantins state. This observation highlights the importance of major population centers in Brazil on virus dispersion, such as those observed in other Latin American and North American countries. In the SNP analysis, DENV-1 displayed 122 distinct missense mutations, while DENV-2 had 44, with significant mutations predominantly occurring in the envelope and NS5 proteins. The analyses performed here highlight the concomitant circulation of distinct DENV-1 and -2 genotypes in some Brazilian states, underscoring the dynamic evolution of DENV and the relevance of surveillance efforts in supporting public health policies

Genomic epidemiology reveals the circulation of the Chikungunya virus east/central/south african lineage in Tocantins State, north Brazil

The chikungunya virus (CHIKV) is a mosquito-borne virus of the family Togaviridae transmitted to humans by Aedes spp. mosquitoes. In Brazil, imported cases have been reported since June 2014 through two independent introductions, one caused by Asian Lineage in Oiapoque, Amapá state, North Region, and another caused by East/Central/South African (ECSA) in Feira de Santana, Bahia state, Northeast Region. Moreover, there is still limited information about the genomic epidemiology of the CHIKV from surveillance studies. The Tocantins state, located in Northern Brazil, reported an increase in the number of CHIKV cases at the end of 2021 and the beginning of 2022. Thus, to better understand the dispersion dynamics of this viral pathogen in the state, we generated 27 near-complete CHIKV genome sequences from four cities, obtained from clinical samples. Our results showed that the newly CHIKV genomes from Tocantins belonged to the ECSA lineage. Phylogenetic reconstruction revealed that Tocantins’ strains formed a single well-supported clade, which appear to be closely related to isolates from the Rio Grande do Norte state (Northeast Brazil) and the Rio de Janeiro state (Southeast Brazil), that experienced an explosive ECSA epidemic between 2016–2019. Mutation analyses showed eleven frequent non-synonymous mutations in the structural and non-structural proteins, indicating the autochthonous transmission of the CHIKV in the state. None of the genomes recovered within the Tocantins samples carry the A226V mutation in the E1 protein associated with increased transmission in A. albopictus. The study presented here highlights the importance of continued genomic surveillance to provide information not only on recording mutations along the viral genome but as a molecular surveillance tool to trace virus spread within the country, to predict events of likely occurrence of new infections, and, as such, contribute to an improved public health service

Genetic variability in cerrado plant species populations. scientometric and meta-analytic evaluation

Submitted by JÚLIO HEBER SILVA ([email protected]) on 2016-11-11T16:19:16Z No. of bitstreams: 2 Dissertação - Ueric José Borges de Souza - 2014.pdf: 1743680 bytes, checksum: 86eb5e29880e6c81a1e92e5690f2ffc4 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5)Approved for entry into archive by Jaqueline Silva ([email protected]) on 2016-11-17T16:14:50Z (GMT) No. of bitstreams: 2 Dissertação - Ueric José Borges de Souza - 2014.pdf: 1743680 bytes, checksum: 86eb5e29880e6c81a1e92e5690f2ffc4 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5)Made available in DSpace on 2016-11-17T16:14:50Z (GMT). No. of bitstreams: 2 Dissertação - Ueric José Borges de Souza - 2014.pdf: 1743680 bytes, checksum: 86eb5e29880e6c81a1e92e5690f2ffc4 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2014-05-29Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPESThe Cerrado biome of Brazil originally occupied approximately 2 million km2 of the country. It is formed by a heterogeneous mosaic of distinct habitats and has the richest flora of the savanas of the world, with high diversity at level of genera and families. It is also currently classified as a priority for conservation because of its rich biodiversity and simultaneous high level on threat due to the destruction of natural habitats resulting from anthropogenic activities. The advent of molecular biology techniques has allowed direct access to the genetic variability of species and populations and made it possible to infer the genetic variability within and among populations, increasing the interest in studying genetic diversity and structure in plant species population of the Cerrado biome. It was conducted here an exhaustive survey of scientific platforms such as the Web of Science, Scopus, Scielo and Google Scholar, to carry out an analysis of published papers evaluating the genetic variability within and among populations in plant species from the Cerrado biome, and to quantify and describe aspects of scientific production in the field of population genetics to plant species from the Cerrado using a scientometric approach, and using a meta-analytic approach to evaluate genetic variability, it was collected some of the genetic parameters estimated in the studies (observed (HO) and expected (HE) heterozygosities and the F statistics of Wright (FIS; FST or analogs)) to test the effect of this genetic parameters in some life history and ecological traits of the species and in methodological characteristics of the article. It was obtained 176 publications from 45 journals through the period of 1999-2012 and the number of studies published has increased significantly through this period. The journal “Genetics and Molecular Research” published the highest number of papers. Ninety-six species from 32 plant families were studied, with highest numbers from the family Fabaceae. Although the species comprised a wide sample of plants with different characteristics, trees, shrubs and herbs were the main life forms and “Mata de galeria”, “cerrado” and “cerradão” were the main fitofisionomies studied. The molecular markers used included microsatellites, cpDNA, isoenzymes, RAPDs, AFLPs and ISSRs and the Microsatellites were the most popular marker used and also show the highest mean value from the genetic variability within populations when compared across studies. It was observed that population genetics parameters molecular derived from molecular markers are closely associated with some life history traits and ecological traits of the species and with methodological characteristics of the article. The analyses allows a better understanding of the current knowledge on plant population genetics in Cerrado biome and the association with the population genetics parameters and some ecological, life history and methodological traits has considerable importance and may be useful to guide future research programs in this system with potential to produce information with important implications in evolutionary biology and ecology as well as in conservation biologyO bioma Cerrado ocupa aproximadamente 2 milhões km2 do Brasil. É formado por um mosaico heterogêneo de tipos de vegetação e tem a mais rica flora entre as savanas do mundo, com alta diversidade em nível de gêneros e famílias. Atualmente tem sido classificado como prioridade em programas de conservação devido à sua rica biodiversidade e perda de habitats naturais resultantes das atividades antropogênicas. Com o advento de técnicas moleculares, tornou-se possível o acesso direto da variabilidade genética das espécies e do modo como essa variabilidade genética se encontra distribuida dentro e entre populações, aumentando assim o interesse em estudar a diversidade genética e estrutura populacional de espécies de plantas do bioma Cerrado. Foi conduzida uma busca usando as bases de dados “Web of Science”, “Scopus”, “Scielo” e “Google Scholar” com o objetivo de realizar uma análise dos artigos publicados que avaliaram a variabilidade genética dentro e entre populações de espécies de plantas do bioma Cerrado, de modo a quantificar e descrever aspectos da produção científica na área de genética de populacões para espécies de plantas do Cerrado utilizando uma abordagem cienciométrica, e utilizando uma abordagem meta-analítica foi coletado alguns dos parâmetros genéticos estimados nos estudos (heterozigosidade esperada (HE) e observada (HO) e as estatísticas F de Wright (FIS (coeficiente de endogamia); FST ou análogos)) para testar o efeito destes parâmetros genéticos em caracteristicas ecológicas e de história de vida das espécies, bem como para características metodológicas extraídas dos artigos. A busca na base de dados resultou em um total de 176 publicações de 45 periódicos durante o período de 1999-2012 e o número de estudos publicados tem aumentado significativamente durante este período. A revista Genetics and Molecular Research apresentou o maior número de artigos publicados. Noventa e seis espécies, envolvendo 32 famílias botânicas foram estudadas, sendo Fabaceae representada pelo maior número de espécies. Diferentes características entre as espécies estudadas foi observado, sendo árvores, arbusto e ervas as principais forma de vida e mata de galeria, cerrado e cerradão os principais tipos fitofisionômicos das espécies. Diferentes tipos de marcadores moleculares, incluindo microssatélites, cpDNA, isoenzimas, RAPDs, AFLPs e ISSRs foram utilizados, sendo os microssatélites o marcador mais frequentemente usado, e também o com o maior valor médio para os parâmetros de variabilidade genética dentro de populações quando comparados entre os estudos. Foi observado que os parâmetros estimados nos estudos de genética de populações obtidos via marcadores moleculares estão relacionados com características ecológicas e de história de vida das espécies e com características metodologicas das publicações. A análise permitiu uma melhor compreensão atual sobre a genética de populações de plantas do bioma Cerrado e a associação encontrada entre parâmetros genético-populacionais e diferentes características das espécies tem importância no sentido de orientar pesquisas futuras, com potencial para produzir informações com implicações importantes para ecologia, biologia evolutiva e biologia da conservação

Partial characterization and genome size of Stryphnodendron adstringens (Leguminosae)

Submitted by Franciele Moreira ([email protected]) on 2019-07-30T15:32:25Z No. of bitstreams: 2 Tese - Ueric José Borges de Souza - 2019.pdf: 8266207 bytes, checksum: 449b756007335607808f1c9691360d73 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5)Approved for entry into archive by Luciana Ferreira ([email protected]) on 2019-08-02T11:35:13Z (GMT) No. of bitstreams: 2 Tese - Ueric José Borges de Souza - 2019.pdf: 8266207 bytes, checksum: 449b756007335607808f1c9691360d73 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5)Made available in DSpace on 2019-08-02T11:35:13Z (GMT). No. of bitstreams: 2 Tese - Ueric José Borges de Souza - 2019.pdf: 8266207 bytes, checksum: 449b756007335607808f1c9691360d73 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2019-01-25Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPESUsing the massively parallel sequencing data generate from two individuals of the Stryphnodendron adstringens, it was possible to structure this thesis in two chapters. The first describes the assembly and annotation of the S. adstringens chloroplast genome and their comparison between species belonging to the mimosoid clade from Caesalpinoideae-Leguminosae subfamily. The second chapter describes the estimate genome size, assembly and annotation of repetitive elements and genes in the nuclear genome of the S. adstringens. Genomic libraries were sequenced using the Illumina HiSeq 2500 platform. Approximately 10 million reads were filtered and used to assemble the chloroplast genome using a combination of de novo and reference-guided strategies. The complete chloroplast genome of S. adstringens was assembled in a single circular molecule containing 162,169 base pairs, contained 111 different genes, with 77 protein-coding genes, 30 transfer tRNA and 4 ribosomal rRNA. A total of 137 microsatellites and 42 repeats structures were identified, with the highest proportion in the LSC (Large Single Copy) region. The average nucleotide variability among the five chloroplast genomes of Mimosoid species was estimated to be 0.01771. The Ka/Ks ratio indicated positive selection for three genes analyzed, rps16, psbH and clpP. The comparison of the structural characteristics in chloroplast genome among Mimosoid species demonstrated that gene coding regions are highly conserved. The phylogenetic reconstruction based on 73 protein-coding genes indicated that the Leguminosae- Caesalpinoideae subfamily was paraphyletic. The size of the nuclear genome of S. adstringens was estimated as 1C = 0.684 pg, which corresponds to a haploid genome of 669 Mpb. The nuclear genome was made of 63.320 contigs with a total size of approximately 495 Mbp. A total of 20.124 microsatellite regions were identified in the nuclear genome, with AT/TA repeats being the most frequent (44.16%). It was possible to identify that 44.58% of the nuclear genome of S. adstringens is composed of transposable elements. The most common class were retroelements, among these, the long terminal repeats (LTR) the most abundant family. 31,636 genes and 95,811 transcripts were predicted with an average of 3.03 per gene. From the total number of predicted transcripts, 60,798 were classified functionally, according to Gene Ontology. Around 1,521 transcripts (1.58%) were similar with protein sequences involved in the tannin biosynthesis pathways. This work represents a great advance in the knowledge on the structure and organization of the nuclear and chloroplast genomes of S. adstringens. In addition, the results obtained provide genomic resources for future genetic and biotechnological investigations on the species.A partir da análise dos dados de sequenciamento paralelo massivo do genoma de dois indivíduos de Stryphnodendron adstringens foi possível estruturar a tese em dois capítulos. O primeiro descreve a montagem e anotação do genoma cloroplastidial da espécie S. adstringens e sua comparação com o genoma de espécies pertencentes ao clado mimosoide da subfamília Caesalpinoideae-Leguminosae. O segundo capítulo estimou o tamanho do genoma, a montagem e a anotação de elementos repetitivos e genes no genoma nuclear da espécie S. adstringens. As bibliotecas genômicas foram sequenciadas usando a plataforma de sequenciamento de nova geração Illumina Hiseq2500. Na montagem do genoma cloroplastidial, aproximadamente 10 milhões de pares de base foram filtrados e usados para a montagem por estratégias de novo e reference-guided. O genoma cloroplastidial de S. adstringens foi montado em uma única sequência contendo 162.169 bp, sendo identificados 77 genes codificadores de proteínas, 30 genes de tRNA e 4 genes de rRNA. Um total de 137 microssatélites e 42 estruturas de repetição foram identificadas, com a maior proporção na região LSC (Large Single Copy). A diversidade nucleotídica média estimada do genoma S. adstringens entre cinco espécies do clado mimosoide, foi de 0,0177. A razão Ka/Ks indicou seleção positiva em três genes rps16, psbH and clpP. A comparação da estrutura genoma cloroplastidial de S. adstringens com outras espécies do clado mimosoide demonstrou que regiões gênicas são altamente conservadas. A reconstrução filogenética usando 73 genes codificantes de proteínas sugere que a família Leguminosae-Caesalpinoideae é parafilética. Para a montagem do genoma nuclear os reads de sequenciamento foram trimados, produzindo um conjunto de dados contendo total de aproximadamente 100 bilhões de pares de base. O tamanho do genoma de S. adstringens foi estimado em 1C = 0.684 pg, o que corresponde a aproximadamente 669 Mpb. O genoma nuclear foi montado usando estratégias de novo em 63.320 contigs com um tamanho total de aproximadamente 495 Mbp. Um total de 20.124 regiões microssatélites foi identificado no genoma nuclear, sendo a repetição AT/TA mais frequente (44,16%). Foi possível identificar que 44,58% do genoma nuclear de S. adstringens é composto de elementos transponíveis. Os retroelementos foram a classe mais comum, dentre estes, as repetições terminais longas (LTR) a família mais abundante. Foram preditos 31.636 genes e 95.811 transcritos com um média de 3,03 por gene. Do total de transcritos preditos, 60.798 foram classificados funcionalmente, nos termos do Gene Ontology. Cerca de 1.521 transcritos (1,58%) foram similares com sequências de proteínas envolvidas nas vias de biossíntese de taninos. Este trabalho representa um grande avanço nos conhecimentos sobre a estrutura e a organização dos genomas nuclear e cloroplastidial de S. adstringens. Além disso, os resultados obtidos fornecem recursos genômicos para novas investigações genéticas e biotecnológicas para a espécie

Trends in the scientific literature on Stryphnodendron adstringens (Leguminosae): an important Brazilian medicinal tree

Stryphnodendron adstringens, commonly known as “barbatimão”, is a native Brazilian savannah tree that has been long used in folk medicine due to its phytotherapy properties. The aim of the present study was to perform a scientometric analysis based on articles published in journals indexed in Web of Science database. Seventy publications on barbatimão were found and included in this scientometric research, most of which were published in English. The temporal trend analysis in the number of publications showed that the number of scientific articles about S. adstringens had increased significantly over the years. The papers found were published in 51 scientific journals, most of which are international. The main knowledge gaps relating to S. adstringens were in the fields of environmental sciences, evolutionary biology and genetics. The mains trends in barbatimão studies involves pharmacology pharmacy, forestry and medicinal chemistry. Tannin and medicinal plant were the most frequent keywords, showing its importance as a phytotherapeutic resource. Brazil was responsible for 92.96% of the knowledge about this species, obtained through scientific production. The analysis of the publications found made it possible to understand the current knowledge about the species S. adstringens

Tendências da literatura científica sobre genética de populações de plantas do Cerrado

RESUMO O Cerrado é considerado um dos "hotspots" mundiais de biodiversidade, em função da grande extensão de vegetação natural que vem sendo continuamente perdida e do elevado número de espécies endêmicas de plantas, que muitas vezes têm sido listadas como prioridades em programas de conservação e para estudos de genética de populações. A fim de verificar tendências nos estudos de genética de populações das espécies de plantas deste bioma, uma avaliação cienciométrica dos artigos publicados e disponíveis em diferentes bases de dados foi realizada. Um total de 171 publicações provenientes de 48 periódicos foi encontrada, entre os anos de 1999 a 2014, com o número de publicações aumentando significativamente nesse período. Noventa e uma espécies com diferentes formas de vida foram estudadas, usando diferentes tipos de marcadores moleculares. A análise cienciometrica dos artigos encontrados permitiu uma melhor compreensão do conhecimento atual sobre a genética de populações de plantas do bioma Cerrado

The Complete Plastid Genome of Artocarpus camansi: A High Degree of Conservation of the Plastome Structure in the Family Moraceae

Understanding the plastid genome is extremely important for the interpretation of the genetic mechanisms associated with essential physiological and metabolic functions, the identification of possible marker regions for phylogenetic or phylogeographic analyses, and the elucidation of the modes through which natural selection operates in different regions of this genome. In the present study, we assembled the plastid genome of Artocarpus camansi, compared its repetitive structures with Artocarpus heterophyllus, and searched for evidence of synteny within the family Moraceae. We also constructed a phylogeny based on 56 chloroplast genes to assess the relationships among three families of the order Rosales, that is, the Moraceae, Rhamnaceae, and Cannabaceae. The plastid genome of A. camansi has 160,096 bp, and presents the typical circular quadripartite structure of the Angiosperms, comprising a large single copy (LSC) of 88,745 bp and a small single copy (SSC) of 19,883 bp, separated by a pair of inverted repeat (IR) regions each with a length of 25,734 bp. The total GC content was 36.0%, which is very similar to Artocarpus heterophyllus (36.1%) and other moraceous species. A total of 23,068 codons and 80 SSRs were identified in the A. camansi plastid genome, with the majority of the SSRs being mononucleotide (70.0%). A total of 50 repeat structures were observed in the A. camansi plastid genome, in contrast with 61 repeats in A. heterophyllus. A purifying selection signal was found in 70 of the 79 protein-coding genes, indicating that they have all been highly conserved throughout the evolutionary history of the genus. The comparative analysis of the structural characteristics of the chloroplast among different moraceous species found a high degree of similarity in the sequences, which indicates a highly conserved evolutionary model in these plastid genomes. The phylogenetic analysis also recovered a high degree of similarity between the chloroplast genes of A. camansi and A. heterophyllus, and reconfirmed the hypothesis of the intense conservation of the plastome in the family Moraceae

Landscape and Climate Influence the Patterns of Genetic Diversity and Inbreeding in Cerrado Plant Species

The anthropization of the landscape of the Cerrado biome that has occurred over the past few decades has fragmented its natural environments, impacting the connectivity of the plant populations and altering their gene flow. Plant species may also reduce population size in response to sub-optimal climatic and environmental conditions, and observed distribution patterns may align with theoretical schemes, such as the center–periphery model, that is, it is possible that populations on the edge have lower genetic diversity than center populations, theoretically submitted to environmental conditions closer to the optimum. In this context, we evaluate whether the genetic diversity and inbreeding coefficients of Cerrado plant species are affected by landscape features and climate characteristics, and in particular, if the distribution of the genetic diversity of these plants is consistent with the center–periphery model. To do this, we conducted a literature search for genetic studies of Cerrado plant populations using Scopus, Web of Science, and Scielo databases and the species found were used as a proxy to explore patterns throughout the biome. The data were analyzed using generalized linear mixed models (GLMM) and multiple matrix regressions (MMRRs) to evaluate the effects of landscape features and climatic variables on the observed (HO) and expected heterozygosity (HE), allelic richness (AR) and inbreeding (Fis) patterns of the local populations. The landscape was evaluated in terms of the percentage land cover of agriculture (AG), forestry (FO), remnant vegetation (RV), urban areas (UA), pasture (PA), and water (WA) within buffers of 1 km, 3 km, and 5 km around the study populations. We analyzed 121 populations of 31 plant species. The GLMMs showed that HO was affected by FO regardless of buffer size, while HE was also affected by FO, but also by WA and UA. AR was affected by WA and UA in all three buffer zones while the Fis was affected by FO and AU. The MMRRs showed that WA may affect HO, HE, and Fis within the 1 km buffer, while FO affects HO and UA affects AR within the 5 km buffer. In the case of the 1 km and 3 km buffers, however, the geographic distance between populations was identified as a factor determining the genetic diversity and inbreeding indices, indicating that isolation by distance may be an important factor defining the breeding patterns of the Cerrado plant populations. The GLMMs and MMRRs also showed that the mean annual temperature (MAT) and, to a lesser extent, isothermality (ISO) can explain the variation in genetic diversity observed in the Cerrado plant populations. We also found that the center–periphery model fits the distribution pattern observed in most of the species evaluated, including Annona crassiflora,Annona coriacea, Copaifera langsdorffii, and Eugenia dysenterica. Our results indicate that changes in the climate and the landscape of Brazilian Cerrado must be considered carefully to guarantee minimizing the impacts of these processes on the genetic diversity of Cerrado plant species and ensuring the long-term conservation of these species in this biome

Biodiesel and Bioplastic Production from Waste-Cooking-Oil Transesterification: An Environmentally Friendly Approach

Alternative sources of fuel have been a concern in the last few decades. The growth of urbanization and industrialization will lead to the exhaustion of fossil fuels, attracting studies on alternative routes. The main aim of this study was to produce biodiesel from waste cooking oil (WCO) by methyl transesterification using sodium hydroxide as a catalyst. For this, the physicochemical parameters of biodiesel were studied in triplicate (density, acidity, saponification, viscosity, corrosiveness to copper, visual appearance, and cloud point). An analysis by thin layer chromatography and infrared spectrometry was also performed. The increase in yield (83.3%) was directly proportional to the increase in the catalyst (0.22 g of NaOH). The infrared absorption spectra of WCO and biodiesel showed the presence of common and singular bands of each material. Furthermore, a simple and low-cost mechanism was proposed for purifying glycerol. The spectra of glycerol versus purified glycerin showed that the glycerin produced was pure, being used in the formulation of bioplastic. The product was checked for biodegradation and photodegradation, with incredible soil-degradation times of 180 days and photodegradation of only 60 days. In this way, biodiesel production from WCO showed environmentally friendly proposals and applicability. As the next steps, it is necessary to test the biodiesel produced in combustion engines and improve the bioplastic production, including a spectroscopic characterization and extensive biodegradation testing