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Delimiting species is challenging in recently diverged species, and adaptive radiation is fundamental to understanding the evolutionary processes because it requires multiple ecological opportunities associated with adaptation to biotic and abiotic environments. The young Petunia genus (Solanaceae) is an excellent opportunity to study speciation because of its association with pollinators and unique microenvironments. This study evaluated the phylogenetic relationships among a Petunia clade species with different floral syndromes that inhabit several environments. We based our work on multiple individuals per lineage and employed nuclear and plastid phylogenetic markers and nuclear microsatellites. The phylogenetic tree revealed two main groups regarding the elevation of the distribution range, whereas microsatellites showed high polymorphism-sharing splitting lineages into three clusters. Isolation by distance, migration followed by new environment colonization, and shifts in floral syndrome were the motors for lineage differentiation, including infraspecific structuring, which suggests the need for taxonomic revision in the genus.
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BACKGROUND: In prostate cancer (PCa), well-established biomarkers such as MSI status, TMB high, and PDL1 expression serve as reliable indicators for favorable responses to immunotherapy. Recent studies have suggested a potential association between CDK12 mutations and immunotherapy response; however, the precise mechanisms through which CDK12 mutation may influence immune response remain unclear. A plausible explanation for immune evasion in this subset of CDK12-mutated PCa may be reduced MHC expression. RESULTS: Using genomic data of CDK12-mutated PCa from 48 primary and 10 metastatic public domain samples and a retrospective cohort of 53 low-intermediate risk primary PCa, we investigated how variation in the expression of the MHC genes affected associated downstream pathways. We classified the patients based on gene expression quartiles of MHC-related genes and categorized the tumors into "High" and "Low" expression levels. CDK12-mutated tumors with higher MHC-expressed pathways were associated with the immune system and elevated PD-L1, IDO1, and TIM3 expression. Consistent with an inflamed tumor microenvironment (TME) phenotype, digital cytometric analyses identified increased CD8 + T cells, B cells, γδ T cells, and M1 Macrophages in this group. In contrast, CDK12-mutated tumors with lower MHC expression exhibited features consistent with an immune cold TME phenotype and immunoediting. Significantly, low MHC expression was also associated with chromosome 6 loss of heterozygosity (LOH) affecting the entire HLA gene cluster. These LOH events were observed in both major clonal and minor subclonal populations of tumor cells. In our retrospective study of 53 primary PCa cases from this Institute, we found a 4% (2/53) prevalence of CDK12 mutations, with the confirmation of this defect in one tumor through Sanger sequencing. In keeping with our analysis of public domain data this tumor exhibited low MHC expression at the RNA level. More extensive studies will be required to determine whether reduced HLA expression is generally associated with primary tumors or is a specific feature of CDK12 mutated PCa. CONCLUSIONS: These data show that analysis of CDK12 alteration, in the context of MHC expression levels, and LOH status may offer improved predictive value for outcomes in this potentially actionable genomic subgroup of PCa. In addition, these findings highlight the need to explore novel therapeutic strategies to enhance MHC expression in CDK12-defective PCa to improve immunotherapy responses.
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O objetivo deste estudo foi avaliar o nível de variabilidade genética e a estrutura populacional do golfinho-nariz-degarrafa (Tursiops truncatus) das porções tropical e subtropical do Oceano Atlântico Sul Ocidental e comparar os resultados com análises morfológicas prévias. Para tanto, analisamos 109 amostras de golfinhos-nariz-de-garrafa, as quais foram sequenciadas para a região controle do DNAmt e genotipadas para sete loci de microssatélites polimórficos. Os resultados sugerem que a espécie nessa região pode ser separada em duas grandes unidades biológicas, norte e sul, com uma área de parapatria no sul do Brasil. A unidade norte parece ocorrer em uma faixa de profundidade ampla, incluindo águas oceânicas. Esta unidade é consistente com a morfologia canônica de T. truncatus e pode ser dividida em três unidades de manejo: i) Arquipélago de São Pedro e São Paulo; ii) Norte e Nordeste do Brasil; iii) Bacia de Campos e Santos (que se estende pelo menos até o extremo sul do Brasil). A unidade sul é costeira, ocorrendo exclusivamente em águas muito rasas (< 10 m) e estuários. Esta unidade é consistente com descrições anteriores para Tursiops gephyreus (putativo). Entretanto, uma decisão formal sobre o status taxonômico de T. gephyreus deve aguardar estudos mais integrativos e geograficamente abrangentes.
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Abstract Genotypes of 10 microsatellite loci of 420 humpback whales from the Southwestern Atlantic Ocean population were used to estimate for the first time its contemporary effective (Ne) and census (Nc) population sizes and to test the genetic effect of commercial whaling. The results are in agreement with our previous studies that found high genetic diversity for this breeding population. Using an approximate Bayesian computation approach, the scenario of constant Ne was significantly supported over scenarios with moderate to strong size changes during the commercial whaling period. The previous generation Nc (Ne multiplied by 3.6), which should corresponds to the years between around 1980 and 1990, was estimated between ~2,600 and 6,800 whales (point estimate ~4,000), and is broadly compatible with the recent abundance surveys extrapolated to the past using a growth rate of 7.4% per annum. The long-term Nc in the constant scenario (point estimate ~15,000) was broadly compatible (considering the confidence interval) with pre-whaling catch records estimates (point estimate ~25,000). Overall, our results shown that the Southwestern Atlantic Ocean humpback whale population is genetically very diverse and resisted well to the strong population reduction during commercial whaling.
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Abstract In spite of many genetic studies that contributed for a deep knowledge about the peopling of the Americas, no consensus has emerged about important parameters such as the effective size of the Native Americans founder population. Previous estimates based on genomic datasets may have been biased by the use of admixed individuals from Latino populations, while other recent studies using samples from Native American individuals relied on approximated analytical approaches. In this study we use resequencing data for nine independent regions in a set of Native American and Siberian individuals and a full-likelihood approach based on isolation-with-migration scenarios accounting for recent flow between Asian and Native American populations. Our results suggest that, in agreement with previous studies, the effective size of the Native American population was small, most likely in the order of a few hundred individuals, with point estimates close to 250 individuals, even though credible intervals include a number as large as ~4,000 individuals. Recognizing the size of the genetic bottleneck during the peopling of the Americas is important for determining the extent of genetic markers needed to characterize Native American populations in genome-wide studies and to evaluate the adaptive potential of genetic variants in this population.
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Abstract Recently, it has been suggested that internal transcribed spacer (ITS) sequences are under selective constraints to preserve their secondary structure. Here, we investigate the patterns of the ITS nucleotide and secondary structure conservation across the Passiflora L. genus to evaluate the potential use of secondary structure data as a helpful tool for the alignment in taxonomically complex genera. Considering the frequent use of ITS, this study also presents a perspective on future analyses in other plant groups. The ITS1 and ITS2 sequences presented significant differences for mean values of the lowest energy state (LES) and for number of hairpins in different Passiflora subgenera. Statistical analyses for the subgenera separately support significant differences between the LES values and the total number of secondary structures for ITS. In order to evaluate whether the LES values of ITS secondary structures were related to selective constraints, we compared these results among 120 ITS sequences from Passiflora species and 120 randomly generated sequences. These analyses indicated that Passiflora ITS sequences present characteristics of a region under selective constraint to maintain the secondary structure showing to be a promising tool to improve the alignments and identify sites with non-neutral substitutions or those correlated evolutionary steps.
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Luehea divaricata (Malvaceae) is a plant widely used for treatment of various inflammatory and infectious conditions; however few reports discuss its biological properties. The aim of this study was to evaluate the anti-inflammatory and analgesic effects as well as the macrophage activity in mice treated with the hydroalcoholic crude extract of L. divaricata (CLD). Thin layer chromatography revealed presence of epicathequin, stigmasterol, lupeol and α,β-amyrin in the extract. To evaluate the anti-inflammatory and analgesic activities, animals were subjected to paw edema induced by carrageenan test, writhing, formalin and capsaicin tests. Immunomodulatory activity was evaluated by adhesion and phagocytic capacity, lysosomal volume, and reactive oxygen species (ROS) production by peritoneal macrophages, after daily treatment with CLD for 15 days. CLD promoted reduction in paw edema (36.8% and 50.2%; p<0.05 at doses of 100 and 300 mg/kg, respectively), inhibited writhing behavior at the higher dose (64.4%, p<0.05), reduced formalin reactivity (81.2% and 91.6% at doses of 100 and 300 mg/kg, respectively, p<0.05), and reduced capsaicin reactivity by 63.9% (300 mg/kg). CLD (200 mg• kg-1• day-1) increased phagocytosis capacity of macrophages (~3 fold, p<0.05), neutral red uptake (~50%, p<0.001), and ROS production (~90%, p<0.001). These data suggest that CLD possesses anti-inflammatory, analgesic and immunostimulatory properties.
Luehea divaricata (Malvaceae) é utilizada para o tratamento de várias condições patológicas, entretanto, há poucos relatos sobre sua bioatividade. O objetivo deste estudo foi avaliar o efeito anti-inflamatório e analgésico, bem como a atividade de macrófagos em camundongos tratados com extrato bruto hidroalcoólico (CLD) da planta. Cromatografia em camada delgada revelou a presença de epicatequina, estigmasterol, lupeol e α,β-amirina no material. Para avaliar a atividade anti-inflamatória e analgésica, animais foram submetidos a teste de edema de pata induzido por carragenana, teste de contorções, da formalina e da capsaicina. A atividade imunomodulatória foi avaliada pela capacidade de adesão e de fagocitose dos macrófagos, volume lisossômico e produção de espécies reativas de oxigênio (ROS), após tratamento diário com CLD por 15 dias. CLD promoveu redução do edema de pata (36,8% e 50,2%; 100 e 300 mg/kg, respectivamente; p<0,05), redução do número de contorções (64,4%; 300 mg/kg; p<0,05), redução da reatividade no teste da formalina (81,2% e 91,6%; 100 e 300 mg/kg, respectivamente; p<0,05), e no teste da capsaicina em 63,9% (300 mg/kg). CLD (200 mg• kg-1• day-1) aumentou capacidade de fagocitose dos macrófagos (~3 vezes, p<0,05), volume lisossômico (~50%, p<0,001) e produção de ROS (~90%, p<0,001). Estes dados sugerem que o CLD possui propriedades anti-inflamatórias, analgésicas e imunoestimulatórias.
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Camundongos , Adjuvantes Imunológicos/classificação , Malvaceae , Analgésicos/classificação , Anti-Inflamatórios/classificação , Espécies Reativas de OxigênioRESUMO
The discovery and characterization of informative intraspecific genetic markers is fundamental for evolutionary and conservation genetics studies. Here, we used nuclear ribosomal ITS sequences to access intraspecific genetic diversity in 23 species of the genus Passiflora L. Some degree of variation was detected in 21 of these. The Passiflora and Decaloba (DC.) Rchb. subgenera showed significant differences in the sizes of the two ITS regions and in GC content, which can be related to reproductive characteristics of species in these subgenera. Furthermore, clear geographical patterns in the spatial distribution of sequence types were identified in six species. The results indicate that ITS may be a useful tool for the evaluation of intraspecific genetic variation in Passiflora.
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The genus Ixinandria was described in 1979 to include I. steinbachi from the upper río Juramento in northern Argentina and I. montebelloi from the upper río Bermejo in southern Bolivia. We used a multivariate morphometric analysis (Principal Components Analysis) and a molecular comparison of the Cytochrome Oxidase I gene to investigate variation among distinct populations from the known distribution range of both species. We conclude that the populations are not significantly distinct and do not deserve separate species recognition, and we place I. montebelloi in the synonymy of I. steinbachi.
O gênero Ixinandria foi descrito em 1979 para incluir I. steinbachi do alto rio Juramento no norte da Argentina e I. montebelloi do alto rio Bermejo no sul da Bolívia. Utilizamos análise morfométrica multivarida (Análise de Componentes Principais) e uma comparação molecular do gene Citocromo Oxidase I para investigar a variação entre populações distintas da área de distribuição de ambas as espécies. Concluímos que as populações não são significativamente distintas e não merecem reconhecimento como espécies separadas, e colocamos Ixinandria montebelloi na sinonímia de I. steinbachi.
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Animais , Complexo IV da Cadeia de Transporte de Elétrons/genética , Especificidade da Espécie , Peixes-Gato/classificaçãoRESUMO
Several genomes of mycoplasmas have been sequenced and here we tried to retrieve the evolutionary relationships of nine species using a phylogenomic approach. Several methods were used to build phylogenetic trees based on protein sequence information, gene-order, and gene-content. We also utilized datasets composed of individual and concatenated sets of orthologous proteins, as well as with reduced unreliable alignment regions. Most of our results converge to a single topology, except for the trees built with both the maximum parsimony method and with the gene-order dataset. The gene-content dataset presented trees consistent with most nodes of the convergent tree, but in the gene-order dataset most internal branches were clearly saturated and unreliable. The topological difference between the trees obtained by the diverse methods could not be explained by regions with unreliable alignments or attributed to horizontal gene transfer among the genomes. It is possible that the incongruence between the methods could be associated with their differential sensibility in relation to certain evolutionary factors. Further analysis using other empirical genomic datasets would be necessary in order to better understand the basis of such conflicts.
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The phylum Placozoa, represented by its single species Trichoplax adhaerens, has always been considered one of the most basal animal clades due to its low morphological complexity. However, despite its importance, the phylogenetic position of the Placozoa remains uncertain, as does the relationships between the basal metazoans. We sequenced the nearly complete large subunit (LSU) of the T. adhaerens rRNA gene together with the small subunit (SSU) rRNA and used several methods to infer the phylogenetic position of Placozoa and the relationships between the basal animal phyla. The phylogenetic trees obtained from the LSU, SSU and SSU + LSU datasets support monophyly of all basal metazoan phyla, except the Porifera. However, the relationships between all these phyla were not consistently resolved due to a strong conflict between the LSU and SSU phylogenetic signals. The hypotheses that Placozoa is a derived Cnidaria or the most basal metazoan were not supported by our data. Moreover, our analyses suggests that Placozoa is most likely the sister group of Cnidaria and/or Bilateria.
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The genes encoding 13 classes of pathogenesis-related (PR) proteins were examined for positive selection using maximum-likelihood (ML) models of codon substitution. The study involved 194 sequences from 54 species belonging to 37 genera. Although the sizes of the sequences examined varied from 237 bp for PR12 to 1,110 bp for PR7, most classes (9 out of 13) contained sequences made up of more than 400 nucleotides. Signs of positive selection were obtained for sites in PR proteins 4, 6, 8, 9 and 15 using an ML-based Bayesian method and likelihood ratio tests. These results confirm the importance of positive selection in proteins related to defense mechanisms already observed in a wide array of organisms
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Evolução Molecular , Proteínas de Plantas , Variação Genética , Seleção Genética , VirulênciaRESUMO
O vírus linfotrópico de células T-humanas do tipo II (HTLV-II) é identificado em muitos grupos de ameríndios. No Brasil, tem sido encontrado em indivíduos da população urbana, bem como em índios oriundos da região Amazônica. Os Índios Guaraní, do Sul do país, foram investigados para infecção por HTLV-I/II. Três indivíduos, oriundos de uma amostra de 52 índios, demonstraram sororeatividade para HTLV-II (ensaio imunoenzimático e Western blot). Este estudo preliminar foi o primeiro a identificar a presença de infecção por HTLV-II em ameríndios do Sul do Brasil.