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DNA methylation plays a key role in the development and plant responses to biotic and abiotic stresses. This work aimed to evaluate the DNA methylation in contrasting cassava genotypes for water deficit tolerance. The varieties BRS Formosa (bitter) and BRS Dourada (sweet) were grown under greenhouse conditions for 50 days, and afterwards, irrigation was suspended. The stressed (water deficit) and non-stressed plants (negative control) consisted the treatments with five plants per variety. The DNA samples of each variety and treatment provided 12 MethylRAD-Seq libraries (two cassava varieties, two treatments, and three replicates). The sequenced data revealed methylated sites covering 18 to 21% of the Manihot esculenta Crantz genome, depending on the variety and the treatment. The CCGG methylated sites mapped mostly in intergenic regions, exons, and introns, while the CCNGG sites mapped mostly intergenic, upstream, introns, and exons regions. In both cases, methylated sites in UTRs were less detected. The differentially methylated sites analysis indicated distinct methylation profiles since only 12% of the sites (CCGG and CCNGG) were methylated in both varieties. Enriched gene ontology terms highlighted the immediate response of the bitter variety to stress, while the sweet variety appears to suffer more potential stress-damages. The predicted protein-protein interaction networks reinforced such profiles. Additionally, the genomes of the BRS varieties uncovered SNPs/INDELs events covering genes stood out by the interactomes. Our data can be useful in deciphering the roles of DNA methylation in cassava drought-tolerance responses and adaptation to abiotic stresses.

Visceral leishmaniasis (VL) is a life-threatening disease caused by the protozoa Leishmania donovani and L. infantum . Likely, L. infantum was introduced in the New World by the Iberic colonizers. Due to recent introduction, the genetic diversity is low. Access to genomic information through the sequencing of Leishmania isolates allows the characterization of populations through the identification and analysis of variations. Population structure information may reveal important data on disease dynamics. Aiming to describe the genetic diversity of L. infantum from the Middle-North, Brazil, next generation sequencing of 30 Leishmania isolates obtained in the city of Teresina, from where the disease dispersed, was performed. The variations were categorized accordingly to the genome region and impact and provided the basis for chromosomal ploidy and population structure analysis. The results showed low diversity between the isolates and the Iberic reference genome JPCM5. Most variations were seen in non-coding regions, with modifying impact. The ploidy number analysis showed aneuploid profile. The population structure analysis revealed the presence of two L. infantum populations identified in Teresina. Further population genetics studies with a larger number of isolates should be performed in order to identify the genetic background associated with virulence and parasite ecology.

Elevated levels of IL-6 in plasma are associated with the severity of visceral leishmaniasis (VL). The clinical manifestations of VL vary among patients, influenced by host factors and the virulence of the Leishmania infantum parasite. Considering that severe VL may result from an exaggerated inflammatory response, this study investigated whether IL-6 could serve as a biomarker to identify pro-inflammatory virulence factors. We conducted a genome-wide association study (GWAS) analysis on L. infantum isolates from patients with VL, whose IL-6 concentrations were measured. The analysis revealed that the relationship between IL-6 levels and clinical outcomes (survival vs mortality) had an area under the curve (AUC) of 0.67 (95% CI 0.52–0.81). A cut-off of 391.7 pg mL −1 for IL-6 was established to conduct a logistic regression analysis. We identified 10 029 single nucleotide variants (SNVs) across 62 genomes, resulting in 6,948 SNVs after filtering, of which 6,341 are located in protein-coding regions. The association analysis with PLINK identified 722 variants, of which 35 showed significant associations, with odds ratios ≥3.3, primarily in coding regions. These findings demonstrate that IL-6 levels tended to be associated with the fatal outcome of VL and highlight 35 novel genetic variants that could serve as potential biomarkers for prognosis. Further research into the biological role of these variants may lead to new therapeutic targets and improve the clinical management of VL, especially in identifying high-risk patients.

The CRISPR–Cas are adaptive immune systems found in archaea and bacteria, responsible for providing sequence-specific resistance against foreign DNA. Strains of Pseudomonas aeruginosa may carry CRISPR/Cas system types I-F, I-E and/or I-C; however, several aspects related to the epidemiology and functionality of these systems have not yet been revealed. Here, we report 13 genomes of clinical strains of P. aeruginosa from Brazil that were positive for CRISPR/Cas system types I-F and I-E, a rare feature in this species. The phylogenetic tree, which was constructed with 161 other publicly available genomes, suggested no direct relationship between positive strains, and the various types of CRISPR/Cas systems were spread throughout the tree. Comparative analysis of the genetic locations of type I-F and a specific orphan CRISPR array (without cas genes), named the LES locus, showed sequence similarities between this orphan locus and type I-F, but these LES loci were inserted in a different genomic location. We also report the presence of prophages, the presence of anti-CRISPR genes, and possibly the presence of self-targeting spacers. Here, we conclude that CRISPR/Cas is highly associated with certain lineages and is spread throughout the phylogenetic tree, showing no clear pattern of evolutionary distribution. Moreover, the LES locus might be a CRISPR1 locus related to type I-F that may have been misplaced and maintained over time. Furthermore, strains carrying I-F and I-E are rare, and not all of them are closely related. Further functional work is needed to better comprehend if aspects reported in this study are functional, including the LES locus, self-targeting spacers, anti-CRISPR protection, and I-F/I-E-carrying lineages.

Advances in diagnostic techniques, along with environmental changes driven by human activity, have intensified the surveillance and monitoring of virus and arbovirus circulation on the Amazon. These efforts have increased the detection of insect-specific viruses in field-collected hematophagous arthropods. This study reports the first isolation of the Aguas Brancas virus from mosquitoes collected in the Brazilian Amazon and in a rural area of Brasília, Federal District, Brazil. Arthropods of the family Culicidae, genus Limatus durhamii, were collected at ground level in forest fragments. Sample BEAR812610 originated from Ananindeua, Pará, within the Evandro Chagas Institute’s grounds, and sample BEAR839941 from a forest fragment in Brasília (Ceilândia—Núcleo Rural Boa Esperança, Site B4). Specimens were identified to the species/genus level, macerated, and the supernatant inoculated into C6/36 and Vero cell cultures for viral isolation. The presence of arboviruses was determined by indirect immunofluorescence using antibodies against major arbovirus groups. Positive samples were sequenced for nucleotide and amino acid identification, and phylogenetic analysis confirmed the virus as belonging to the genus Orthoflavivirus. This represents the first report of the isolation and characterization of the insect-specific Aguas Brancas virus.

Lanthanide hydrogels HGLn with iminodiacetic acid (Ln = Eu and Gd) and Na3[Ln(DPA)3]·9H2O complexes (DPA = dipicolininate) were successfully synthesized via hydrothermal microwave‐assisted and via precipitation, respectively. Incorporation of Ln(DPA)3 complexes into the HGLn hydrogels resulted in the improvement of the spectroscopic properties and mechanical behavior. Rheological studies of the europium hydrogels doped with Gd(DPA)3 complex (HGEu‐Gd) showed a significant increase in the stiffness of the material by increasing the concentration of the incorporated complex. This effect also influences the increase in luminescence intensity of the HGEu‐Gd hybrid. A computational modeling study of the interaction between the complex and hydrogel matrix suggests that this interaction does not affect the coordination symmetry of either Eu3+ or Gd3+. On the other hand, there were changes in the corresponding emission lifetimes, although not accompanied by changes in the emission spectral profile. The individual contributions to the luminescence of the hybrid gel were related to the maintenance of individual material characteristics and those resulting from hydrogel‐complex interactions. Lanthanide‐based hydrogels incorporating Ln(DPA)3 complexes are synthesized and exhibit enhanced mechanical and luminescent properties. Increased complex concentration improves stiffness and emission intensity without altering coordination symmetry. Computational insights reveal preserved structural features, while lifetime changes highlight hydrogel–complex interactions, offering tunable hybrid materials with improved performance and potential multifunctional applications.

Over the last several decades, extensive changes in land use and land cover (LULC) have caused substantial environmental impacts in the watersheds of southeastern Amazonia, such as the Verde River Watershed (VRW). The effects of anthropogenic activities on soil cover loss rates in the VRW were evaluated to estimate soil loss over time by applying the revised Universal Soil Loss Equation (RUSLE) in a geographic information system (GIS) environment via rainfall erosivity (R), soil erodibility (K), topography (LS), and LULC (CP) data. The VRW experiences strong seasonality, with the most significant R concentrated from January to April, which coincides with a relatively high rainfall index reaching approximately 42% of the annual total. Most of the VRW has gently undulating to flat relief (88.9%) and low LS values (0.02–0.025), but its upper course has a sandy soil texture with high K values (0.02–0.073). Pastureland has replaced forested areas during the past 40 years, dramatically changing the landscape with more significant changes in LULC rates in the upper VRW. Estimates of annual and average soil losses and areas at high and very high risk of erosion increased by more than 200% from 1984 to 2021. In conclusion, deforestation is the main factor influencing erosion patterns and volume in the VRW and has accelerated soil degradation, increasing the risks to human health and the maintenance of tropical rainforests. Additionally, simply stopping deforestation is insufficient to prevent the expansion of areas with high and very high erosion risk. It is crucial to implement reforestation projects to recover forested areas.

Yellow fever (YF) is an acute and potentially fatal hemorrhagic disease caused by the Yellow Fever virus (YFV), endemic to sub-Saharan Africa and several tropical countries, including Brazil. In Brazil, the Amazon region is considered the main endemic area. YFV is maintained in a sylvatic cycle involving Neotropical primates and mosquitoes of the genera Haemagogus and Sabethes, acting as primary and secondary vectors, respectively. In March 2024, entomovirological surveillance was conducted in Santa Bárbara do Pará, Pará, Brazil. A total of 286 mosquitoes were collected, classified into 13 species across nine genera, and grouped into 33 pools. Seventeen pools were tested by RT-qPCR for Orthoflavivirus (YFV, DENV, WNV, SLEV), Alphavirus (CHIKV, MAYV), and Orthobunyavirus (OROV). YFV was detected in four Haemagogus janthinomys pools, with Ct values ranging from 22.2 to 27.9. Metagenomic sequencing confirmed the presence of YFV with assigned reads and >99% protein identity. Notably, the detection occurred without human cases or primate deaths, enabling timely vaccination of the local population. These findings confirm YFV circulation in forested areas of the Belém metropolitan region and reaffirm Hg. janthinomys as a key vector. Our study reinforces the relevance of early entomovirological surveillance and preventive strategies, such as vaccination, to mitigate yellow fever reemergence.

Background Although penile cancer (PC) is uncommon in developed countries, it is widespread in developing countries. The state of Maranhão (Northeast, Brazil) has the highest global incidence recorded for PC, and, despite its socioeconomic vulnerability, it has been attributed to human papillomavirus (HPV) infection. This study aimed to determine the histopathological features, the prevalence of HPV infection, and the immunohistochemical profile of PC in Maranhão. Methods A retrospective cohort of 200 PC cases were evaluated. HPV detection was performed using nested-PCR followed by direct sequencing for genotyping. Immunohistochemistry (IHC) was performed using monoclonal antibodies anti-p16 INK4a , p53, and ki-67. Results Our data revealed a delay of 17 months in diagnosis, a high rate of penile amputation (96.5%), and HPV infection (80.5%) in patients from Maranhão (Molecular detection). We demonstrated the high rate of HPV in PC also by histopathological and IHC analysis. Most patients presented koilocytosis (75.5%), which was associated with those reporting more than 10 different sexual partners during their lifetime ( p  = 0.001). IHC revealed frequent p16 INK4a overexpression (26.0%) associated with basaloid ( p  < 0.001) and high-grade tumors ( p  = 0.008). Interestingly, p16 appears not to be a better prognostic factor in our disease-free survival analysis, as previously reported. We also demonstrated high ki-67 and p53 expression in a subset of cases, which was related to worse prognostic factors such as high-grade tumors, angiolymphatic and perineural invasion, and lymph node metastasis. We found a significant impact of high ki-67 ( p  = 0.002, log-rank) and p53 ( p  = 0.032, log-rank) expression on decreasing patients’ survival, as well as grade, pT, stage, pattern, and depth of invasion ( p  < 0.05, log-rank). Conclusions Our data reaffirmed the high incidence of HPV infection in PC cases from Maranhão and offer new insights into potential factors that may contribute to the high PC incidence in the region. We highlighted the possible association of HPV with worse clinical prognosis factors, differently from what was observed in other regions. Furthermore, our IHC analysis reinforces p16, ki-67, and p53 expression as important diagnosis and/or prognosis biomarkers, potentially used in the clinical setting in emerging countries such as Brazil.