Genetic polymorphism sharing between closely related and sympatric plant species could result from common ancestry, ancient or recent hybridization. Here we analyzed four Petunia species from the ...subtropical highland grasslands in southern South America based on nuclear diversity to disentangle the causes of high polymorphism sharing between them. We genotyped microsatellite loci, employed population genetic methods to estimate variability, species limits, and ancient and recent gene flow, and assigned individuals to genetic and taxonomic groups. Finally, we modeled evolutionary processes to determine the impact of Quaternary climate changes on species phylogenetic relationships. Our results indicated that genetic diversity was strongly influenced by expansion and habitat fragmentation during the Quaternary cycles. The extensive polymorphism sharing is mainly due to species' common ancestry, and we did not discard ancient hybridization. Nowadays, niche differentiation is the primary driver for maintaining genetic and morphological limits between the four analysed Petunia species and there is no recent gene flow between them.
Abstract
Climate changes and associated glacial and interglacial cycles during the Quaternary strongly influenced the evolutionary history of countless number of species. Subtropical highland ...grasslands (SHG) in southern South America constitute a distinct vegetation type with high diversity and endemism rates. The most recent common ancestor of the genus Petunia (Solanaceae) originated in lowland grasslands, and some lineages secondarily migrated to SHG. Here, we describe the evolutionary history of an SHG species, P. altiplana, distributed throughout a wide area in a river-fragmented landscape. We used plastid and nuclear markers to evaluate the role of the Pelotas River and Quaternary climate cycles over the genetic structure and historical demography of this species based on a phylogeographical approach. We found moderate population expansions during the last 25 kyr, with a more recent (c. 1.6 kya) divergence between two groups of populations from opposite river margins, possibly caused by the expansion of the Araucaria Forest along the river valley, effectively isolating distinct grassland patches.
Abstract Closely related and young species often show high morphological similarity, challenging their identification and correct assignment. Molecular markers and integrative approaches have ...contributed to solving many taxonomic uncertainties. In this study, we evaluated the genetic variability and ecological features of Petunia guarapuavensis and Petunia scheideana, over which there is a taxonomic debate. Both species are endemic and rare, distributed in the subtropical highland grasslands in southern South America. We based our analyses on nuclear microsatellite and plastid sequences, aiming to disentangle the taxonomic ambiguities that made some consider these entities synonymous despite occupying different clades in the genus phylogenetic tree. Our findings support that there is genetic differentiation between these species, suggesting that they are independent taxonomic entities despite sharing floral traits and a few molecular polymorphisms. The low genetic sharing between the species is likely due to a common ancestor and recent divergence time. In contrast, their morphological similarity can be attributed to the absence of selective pressure, as both grow under similar ecological conditions. This study emphasizes that adding more than one sequence per species, combining data with dissimilar inheritance patterns, and exploring data through different methodologies help to disentangle taxonomic incongruences and reveal diversity that might otherwise remain hidden.
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•Active tuberculosis patients have increased plasma levels of IL-6, IP-10, TNF-α, sCD163 and sCD14.•Simultaneous detection of plasma sCD14 and IL-6 can identify active tuberculosis ...with an accuracy of 83%.•Plasma levels of sCD163 and TNF-α in APTB patients can classify the degree of disease progression.
Although much research has been done related to biomarker discovery for tuberculosis infection, a set of biomarkers that can discriminate between active and latent TB diseases remains elusive. In the current study we correlate clinical aspects of TB disease with changes in the immune response as determined by biomarkers detected in plasma. Our study measured 18 molecules in human plasma in 17 patients with active disease (APTB), 14 individuals with latent tuberculosis infection (LTBI) and 16 uninfected controls (CTRL). We found that active tuberculosis patients have increased plasma levels of IL-6, IP-10, TNF-α, sCD163 and sCD14. Statistical analysis of these biomarkers indicated that simultaneous measurement of sCD14 and IL-6 was able to diagnose active tuberculosis infection with 83% accuracy. We also demonstrated that TNF-α and sCD163 were correlated with tuberculosis severity. We showed that the simultaneous detection of both plasma sCD14 and IL-6 is a promising diagnostic approach to identify APTB, and further, measurement of TNF-α and sCD163 can identify the most severe cases of tuberculosis.
Successful highly active antiretroviral therapy (HAART) has changed the outcome of AIDS patients worldwide because the complete suppression of viremia improves health and prolongs life expectancy of ...HIV-1+ patients. However, little attention has been given to the immunological profile of patients under distinct HAART regimens. This work aimed to investigate the differences in the immunological pattern of HIV-1+ patients under the first- or second-line HAART in Brazil.
CD4+ T cell counts, Viral load, and plasma concentration of sCD14, sCD163, MCP-1, RANTES, IP-10, IL-1β, IL-6, TNF-α, IL-12, IFN-α, IFN-γ, IL-4, IL-5, and IL-10 were assessed for immunological characterization of the following clinical groups: Non-infected individuals (NI; n = 66), HIV-1+ untreated (HIV; n = 46), HIV-1+ treated with first-line HAART (HAART 1; n = 15); and HIV-1+ treated with second-line HAART (HAART 2; n = 15).
We found that the immunological biosignature pattern of HAART 1 is similar to that of NI individuals, especially in patients presenting slow progression of the disease, while patients under HAART 2 remain in a moderate inflammatory state, which is similar to that of untreated HIV patients pattern. Network correlations revealed that differences in IP-10, TNF-α, IL-6, IFN-α, and IL-10 interactions were primordial in HIV disease and treatment. Heat map and decision tree analysis identified that IP-10>TNF-α>IFN-α were the best respective HAART segregation biomarkers.
HIV patients in different HAART regimens develop distinct immunological biosignature, introducing a novel perspective into disease outcome and potential new therapies that consider HAART patients as a heterogeneous group.
The successful establishment of HIV-1 infection is related to inflammasome blocking or inactivation, which can result in the viral evasion of the immune responses and formation of reservoirs in ...several tissues. In this sense, we aimed to evaluate the viral and cellular mechanisms activated during HIV-1 infection in human primary macrophages that allow an effective viral replication in these cells. We found that resting HIV-1-infected macrophages, but not those activated in classical or alternative patterns, released IL-1β and other pro-inflammatory cytokines, and showed increased CXCL10 expression, without changes in the NLRP3, AIM2 or RIG-I inflammasome pathways. Also, similar levels of Casp-1, phosphorylated NF-κB (p65) and NLRP3 proteins were found in uninfected and HIV-1-infected macrophages. Likewise, no alterations were detected in ASC specks released in the culture supernatant after HIV-1 infection, suggesting that macrophages remain viable after infection. Using in silico prediction studies, we found that the HIV-1 proteins Gag and Vpr interact with several host proteins. Comparable levels of trans-LTB4 were found in the supernatants of uninfected and HIV-1-infected macrophages, whereas ROS production was impaired in infected cells, which was not reversed after the PMA stimulus. Immunofluorescence analysis showed structural alterations in the mitochondrial architecture and an increase of BIM in the cytoplasm of infected cells. Our data suggest that HIV-1 proteins Gag and Vpr, through interacting with cellular proteins in the early steps of infection, preclude the inflammasome activation and the development of effective immune responses, thus allowing the establishment of the infection.
•HIV infects macrophages from several tissues and can harbor viral proliferation, representing an important reservoir.•The macrophage inflammasome is activated during viral recognition to control the infection and may result in cellular death.•Resting HIV-1-infected macrophages release IL-1b and increased CXCL10 expression, without changing the inflammasome pathways.•Our results suggest that proteins HIV-1 Gag and Vpr may subvert the inflammasome activation and allow viral replication.
Several technological approaches have been used to develop vaccines against COVID-19, including those based on inactivated viruses, viral vectors, and mRNA. This study aimed to monitor the ...maintenance of anti-SARS-CoV-2 antibodies in individuals from Brazil according to the primary vaccination regimen, as follows: BNT162b2 (group 1; 22) and ChAdOx1 (group 2; 18). Everyone received BNT162b2 in the first booster while in the second booster CoronaVac, Ad26.COV2.S, or BNT162b2. Blood samples were collected from 2021 to 2023 to analyze specific RBD (ELISA) and neutralizing antibodies (PRNT50). We observed a progressive increase in anti-RBD and neutralizing antibodies in each subsequent dose, remaining at high titers until the end of follow-up. Group 1 had higher anti-RBD antibody titers than group 2 after beginning the primary regimen, with significant differences after the 2nd and 3rd doses. Group 2 showed a more expressive increase after the first booster with BNT162B2 (heterologous booster). Group 2 also presented high levels of neutralizing antibodies against the Gamma and Delta variants until five months after the second booster. In conclusion, the circulating levels of anti-RBD and neutralizing antibodies against the two variants of SARS-CoV-2 were durable even five months after the 4th dose, suggesting that periodic booster vaccinations (homologous or heterologous) induced long-lasting immunity.
Human bocavirus (HBoV) is a DNA virus that is mostly associated with respiratory infections. However, because it has been found in stool samples, it has been suggested that it may be a causative ...agent for human enteric conditions. This underpins the continuous search for HBoVs, especially after the introduction of the rotavirus vaccine due to acute gastroenteritis cases related to emergent viruses, as HBoVs are more likely to be found in this post-vaccine scenario. Therefore, the aim of this study is to demonstrate the prevalence of HBoV in children aged less than 10 years with acute gastroenteritis in Brazil from November 2011 to November 2012.
Stool samples from hospitalized children ≤10 years old who presented symptoms of acute gastroenteritis were analysed for the presence of rotavirus A (RVA) by an enzyme-linked immunosorbent assay (ELISA), and for HBoV DNA by nested PCR.
HBoV positivity was detected in 24.0 % (54/225) of samples. Two peaks of HBoV detection were observed in November 2011 and from July to September 2012. Co-infections between HBoV and rotavirus A were identified in 50.0 % (27/54) of specimens. Phylogenetic analysis identified the presence of HBoV-1 (94.8 %), HBoV-2 (2.6 %) and HBoV-3 (2.6 %) species, with only minor variations among them.
Our findings provide evidence for the circulation of most HBoV genotypes (except HBoV-4) in the North Region of Brazil at a considerable rate and further investigations are necessary to improve our knowledge in the context of HBoV infections and their role in gastrointestinal diseases.
Acute gastroenteritis (AG) is responsible for 525,000 deaths worldwide in children under-5-years and is caused by the Human Cosavirus (HCoSV; family Picornaviridae, Genus Cosavirus). Although its ...health importance, a significant percentage of diarrhea cases (≈ 40 %) still of unknown etiology. In Brazil, few studies have reported HCoSV-A sequences analyzing partial 5' UTR. This study characterized the first near-complete genome of a Cosavirus A (strain AM326) from a child hospitalized with AG in Amazonas state, Northern Brazil. High throughput sequencing (HTS) was performed using the HiSeq™ 2500 platform (Illumina) in one fecal specimen collected from the Surveillance of Rotavirus Network of the Evandro Chagas Institute collected in 2017. Sequence reads were assembled by the De Novo approach using three distinct algorithmic (IDBA-UD, Spades, and MegaHit). The final contig was recovered from the HCoSV-AM326 sample revealing 7,735 nt in length (SRA number SRR12535029; GenBank MT023104) and the genetic characterization, as well as phylogenetic analysis demonstrated a new variant strain from Brazil, highlighting the association of HCoSV-A as a possible causative agent of AG. This finding demonstrates the importance of the metagenomic approach to elucidate cases of diarrhea without a defined etiology, as well as providing a better understanding about the virus genetics, evolution and epidemiology.
•First near-complete genome of HCoSV-A in Brazil and detection a new variant strain of HCoSV-A;•Potential association of HCoSV-A with acute gastroenteritis;•The use of viral metagenomic approach to elucidate cases of diarrhea with no defined etiology.
To perform a molecular analysis of rotavirus A (RVA) G3P6 strains detected in 2012 and 2017 in the Amazon region of Brazil.
Eighteen RVA G3P6 strains were collected from children aged under 10 years ...hospitalized with acute gastroenteritis, and partial sequencing of each segment genome was performed using Sanger sequencing.
Phylogenetic analysis showed that all G3P6 strains had a DS-1-like genotype constellation. Two strains had the highest nucleotide identities with equine-like G3P6/G3P8 genotypes. Several amino acid alterations in VP4 and VP7 neutralizing epitopes of equine-like RVA G3P6 strains were observed in comparison with vaccine strains.
These findings suggest that equine-like RVA G3P6 strains have been circulating in the Amazon region of Brazil as a result of direct importation, and support natural RVA evolutionary mechanisms.
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