Comparative analysis of sediment quality indices using different reference values in an environmental protection area in Southeastern Brazil.

Contamination of aquatic ecosystems by potentially toxic elements (PTEs) is a concerning environmental issue, given their persistence, toxicity potential, and ability to accumulate in living organisms. Several studies have been conducted to assess the contamination of aquatic ecosystems by PTEs, using pollution and ecological risk indices that rely on the concentration of these elements in aquatic sediments. However, many of these studies use global reference values for calculating the indices, which can lead to misleading interpretations due to substantial variations in PTEs concentrations influenced by the geological characteristics of each region. Therefore, the use of regional reference values is more appropriate when available. This study aimed to investigate variations in the results of five indices, employing global, regional, and quality reference values, based on sediment samples collected from rivers in the Ipanema National Forest, a protected area in Brazil exposed to various anthropogenic pressures. The results revealed that elements such as Al, Fe, and Mn exceeded the limits allowed by legislation in water samples, while As and Cr surpassed the limits in sediment samples. Comparative analysis highlighted significant discrepancies in the results of the indices when global reference values were used compared to regional and quality reference values, especially for As and Ba. Thus, this study underscores the importance of establishing specific regional values for an accurate assessment of sediment quality and the risks associated with contamination by PTEs in different regions worldwide.

Eosinophils mediate SIgA production triggered by TLR2 and TLR4 to control Ascaris suum infection in mice.

Human ascariasis is the most prevalent but neglected tropical disease in the world, affecting approximately 450 million people. The initial phase of Ascaris infection is marked by larval migration from the host's organs, causing mechanical injuries followed by an intense local inflammatory response, which is characterized mainly by neutrophil and eosinophil infiltration, especially in the lungs. During the pulmonary phase, the lesions induced by larval migration and excessive immune responses contribute to tissue remodeling marked by fibrosis and lung dysfunction. In this study, we investigated the relationship between SIgA levels and eosinophils. We found that TLR2 and TLR4 signaling induces eosinophils and promotes SIgA production during Ascaris suum infection. Therefore, control of parasite burden during the pulmonary phase of ascariasis involves eosinophil influx and subsequent promotion of SIgA levels. In addition, we also demonstrate that eosinophils also participate in the process of tissue remodeling after lung injury caused by larval migration, contributing to pulmonary fibrosis and dysfunction in re-infected mice. In conclusion, we postulate that eosinophils play a central role in mediating host innate and humoral immune responses by controlling parasite burden, tissue inflammation, and remodeling during Ascaris suum infection. Furthermore, we suggest that the use of probiotics can induce eosinophilia and SIgA production and contribute to controlling parasite burden and morbidity of helminthic diseases with pulmonary cycles.

Quantitative global studies reveal differential translational control by start codon context across the fungal kingdom.

Eukaryotic protein synthesis generally initiates at a start codon defined by an AUG and its surrounding Kozak sequence context, but the quantitative importance of this context in different species is unclear. We tested this concept in two pathogenic Cryptococcus yeast species by genome-wide mapping of translation and of mRNA 5' and 3' ends. We observed thousands of AUG-initiated upstream open reading frames (uORFs) that are a major contributor to translation repression. uORF use depends on the Kozak sequence context of its start codon, and uORFs with strong contexts promote nonsense-mediated mRNA decay. Transcript leaders in Cryptococcus and other fungi are substantially longer and more AUG-dense than in Saccharomyces. Numerous Cryptococcus mRNAs encode predicted dual-localized proteins, including many aminoacyl-tRNA synthetases, in which a leaky AUG start codon is followed by a strong Kozak context in-frame AUG, separated by mitochondrial-targeting sequence. Analysis of other fungal species shows that such dual-localization is also predicted to be common in the ascomycete mould, Neurospora crassa. Kozak-controlled regulation is correlated with insertions in translational initiation factors in fidelity-determining regions that contact the initiator tRNA. Thus, start codon context is a signal that quantitatively programs both the expression and the structures of proteins in diverse fungi.

Structural studies of the eIF4E-VPg complex reveal a direct competition for capped RNA: Implications for translation.

Viruses have transformed our understanding of mammalian RNA processing, including facilitating the discovery of the methyl-7-guanosine (m7G) cap on the 5' end of RNAs. The m7G cap is required for RNAs to bind the eukaryotic translation initiation factor eIF4E and associate with the translation machinery across plant and animal kingdoms. The potyvirus-derived viral genome-linked protein (VPg) is covalently bound to the 5' end of viral genomic RNA (gRNA) and associates with host eIF4E for successful infection. Divergent models to explain these observations proposed either an unknown mode of eIF4E engagement or a competition of VPg for the m7G cap-binding site. To dissect these possibilities, we resolved the structure of VPg, revealing a previously unknown 3-dimensional (3D) fold, and characterized the VPg-eIF4E complex using NMR and biophysical techniques. VPg directly bound the cap-binding site of eIF4E and competed for m7G cap analog binding. In human cells, VPg inhibited eIF4E-dependent RNA export, translation, and oncogenic transformation. Moreover, VPg formed trimeric complexes with eIF4E-eIF4G, eIF4E bound VPg-luciferase RNA conjugates, and these VPg-RNA conjugates were templates for translation. Informatic analyses revealed structural similarities between VPg and the human kinesin EG5. Consistently, EG5 directly bound eIF4E in a similar manner to VPg, demonstrating that this form of engagement is relevant beyond potyviruses. In all, we revealed an unprecedented modality for control and engagement of eIF4E and show that VPg-RNA conjugates functionally engage eIF4E. As such, potyvirus VPg provides a unique model system to interrogate eIF4E.

Anatomical, behavioural and physiological analyses of craniofacial development by cineradiographic imaging in marmosets.

BACKGROUND: Non-human primates are the closest animal models to humans regarding genetics, physiology and behaviour. Marmoset monkeys in particular are one of the most versatile species for biomedical research. OBJECTIVE: To assess the craniofacial growth and development of the masticatory function in the common marmoset (Callithrix jacchus), from birth to the fourth month of life through minimally invasive cineradiographic imaging. METHODS: Ten individuals were followed-up from 0 to 4 months of age regarding craniofacial growth and masticatory function assessed by cineradiography. For the experimental procedure, we used a microfocal X-ray source apparatus and a beryllium fast-response image-intensifier. RESULTS: The duration of the masticatory cycles was stable across age groups. Chewing a very soft Castella cake or the slightly harder Marshmallow did not change the masticatory cycle in the time domain. On the other hand, linear and angular measurements of the jaw-opening movement showed a tendency for bigger movements at the latter stages of craniofacial growth. Qualitative analysis showed that marmosets had a small preference for Castella over Marshmallow, that they most often bit off pieces of food to chew with their posterior teeth, that they manipulated the food with their hands, and that they chewed the food continuously. CONCLUSION: We observed critical developmental events during the first 3 months of life in marmosets. Cineradiographic imaging in marmosets may provide valuable information on craniofacial form and function for basic and preclinical research models.

Leafy vegetables marketed as organic and conventional: assessment of essential and non-essential elements' content.

Trace and potentially toxic elements represent one class of food contaminants that has stimulated research. In markets, two main methods of growing vegetables are generally available: conventional and organic. Conventional farming has been the target of some concerns about the use of agrochemicals, especially the excessive use of pesticides, whereas organic agriculture minimizes the use of agrochemicals. As the main route for potentially toxic elements' absorption by humans is by food intake, it is important to evaluate if the method of cultivation influences their concentrations. This study evaluated the levels of potentially toxic elements and nutrients on four leafy vegetables: curly lettuce, collard greens, escarole, and rocket, cultivated by conventional and organic farming. We found that Al, Ba, Fe, and Sr levels were higher in conventional samples, whereas K, Pb, and Zn were higher in organic. Amongst the elements analysed, values of Fe, Al, and K were around 0.2, 0.3, and 70 g kg-1, respectively, except in collard greens, in which the values were lower. On the other hand, Ba, Sr, and Mn presented higher concentration in collard greens compared to the other vegetables in conventional cultivation (~ 35, 80, and 120 mg kg-1, respectively). The principal component analysis result shows that the samples were grouped according to the type of vegetable, regardless of the type of cultivation. Despite this, the evaluation of the cultivation by different types of farming is important in order to choose the healthiest option.

Prognostic factors in patients with advanced cancer and COVID-19: a cohort from the Palliative Care Unit of the Brazilian National Cancer Institute.

OBJECTIVE: To describe overall survival (OS) in 90 days and to evaluate the prognostic factors in patients with advanced cancer and COVID-19. METHODS: This is a retrospective cohort study carried out at the Palliative Care Unit of the Brazilian National Cancer Institute. Patients with advanced cancer and COVID-19 confirmed by Reverse Transcription Polymerase Chain Reaction were included. Kaplan-Meier's curves, log-rank test, and Cox regression were performed. RESULTS: Eighty-three inpatients were selected. The average age was 61.4 (±12.6) years, with a higher proportion of women (73.4%). The most prevalent tumor type was breast (36.7%), followed by gastrointestinal tract (20.3%). The OS was 32 [interquartile range (IQR): 6-70] days, and at the end of the follow-up period, 17 patients (20.5%) were alive and 66 (79.5%) had died. Patients with advanced cancer and COVID-19 and who were 60-74 years old [hazard ratio (HR): 2.03; 95% confidence interval (CI): 1.09-3.78], with lung tumors (HR: 17.50; 95% CI: 1.70-28.34), with lung metastasis (HR: 4.21; 95% CI: 2.17-8.15), and with chronic obstructive pulmonary disease (HR: 4.92; 95% CI: 1.01-24.69) had higher risk of death in 90 days. CONCLUSION: The age of 60-74 years old, lung tumors (primary or metastases), and the presence of chronic obstructive pulmonary disease were considered independent prognostic factors in patients with advanced cancer and COVID-19.

The environmental importance of iron speciation in soils: evaluation of classic methodologies.

Iron is an essential mineral and one of the most abundant in soils, presenting itself in the environment as ferrous and ferric ions. As each oxidation state of iron has a different role in the environment, its speciation in environmental studies is important. The determination of ferrous iron received great attention from soil chemists because of its important role in agriculture, in redox processes, and as an electron acceptor in the catalysis of organic matter. Methodologies with the use of colorimetric reagents to determine ferrous iron are divergent and not very clear. In this study, we compared two colorimetric reagents (1,10-phenanthroline and ferrozine) to determine the total concentration of iron, ferrous and ferric ions in soil, using simple and low-cost methodologies. The determination of ferrous and total iron with 1,10-phenanthroline colorimetric reagent, following published instructions, did not correlate with ferrozine method, presenting an erroneous quantification. After neutralizing the extract of 1,10-phenanthroline with NaOH, both colorimetric methods allowed to quantify with precision and high yield the amount of ferrous and total iron extracted from the soil. The oxidation states of iron have a different contribution and importance to the environment. In this sense, the improvement of a widely used methodology is crucial for the better study of iron speciation in soil.

FISIK: Framework for the Inference of In Situ Interaction Kinetics from Single-Molecule Imaging Data.

Recent experimental and computational developments have been pushing the limits of live-cell single-molecule imaging, enabling the monitoring of intermolecular interactions in their native environment with high spatiotemporal resolution. However, interactions are captured only for the labeled subset of molecules, which tends to be a small fraction. As a result, it has remained a challenge to calculate molecular interaction kinetics, in particular association rates, from live-cell single-molecule tracking data. To overcome this challenge, we developed a mathematical modeling-based Framework for the Inference of in Situ Interaction Kinetics (FISIK) from single-molecule imaging data with substoichiometric labeling. FISIK consists of (I) devising a mathematical model of molecular movement and interactions, mimicking the biological system and data-acquisition setup, and (II) estimating the unknown model parameters, including molecular association and dissociation rates, by fitting the model to experimental single-molecule data. Due to the stochastic nature of the model and data, we adapted the method of indirect inference for model calibration. We validated FISIK using a series of tests in which we simulated trajectories of diffusing molecules that interact with each other, considering a wide range of model parameters, and including resolution limitations, tracking errors, and mismatches between the model and the biological system it mimics. We found that FISIK has the sensitivity to determine association and dissociation rates, with accuracy and precision depending on the labeled fraction of molecules and the extent of molecule tracking errors. For cases where the labeled fraction is too low (e.g., to afford accurate tracking), combining dynamic but sparse single-molecule imaging data with almost-whole population oligomer distribution data improves FISIK's performance. All in all, FISIK is a promising approach for the derivation of molecular interaction kinetics in their native environment from single-molecule imaging data with substoichiometric labeling.

Genetic variants of VWF gene in type 2 von Willebrand disease.

INTRODUCTION: von Willebrand disease (VWD) is the most common inherited bleeding disorder. Few studies have explored the molecular basis of type 2 VWD. AIM: This study aimed to identify variants associated with type 2 VWD. METHODS: We collected clinical and laboratory data, as well as response to desmopressin and bleeding assessment tool (BAT) score in patients diagnosed with type 2 VWD. We sequenced exons 17, 18, 20 and 28 of the VWF gene. RESULTS: We identified 19 different variants in 40 unrelated patients (47.5%). Most of the variants (84.2%) were found in exon 28. A total of 10/19 variants (52.6%) were identified as "likely causative" in 17/40 patients (42.5%), according to the ISTH-SSC and EAHAD VWF gene mutations databases. Nine variants were initially identified as potentially benign. However, through analyses in silico, four of these variants were reclassified as "likely pathogenic" (Ile1380Val, Asn1435Ser, Ser1486Leu and Tyr1584Cys). Response to desmopressin was associated with three variants: Met740Ile, Arg1597Gln and Tyr1584Cys. Major bleeding was associated with variants related to VWD subtypes 2B and 2M. CONCLUSION: In conclusion, we identified 19 variants, of which 14 are "likely pathogenic" and therefore associated with VWD. We suggest a possible association of pathogenic variants with major bleeding, response to desmopressin and BAT score ≥10, although this requires further confirmation.

Spatial modeling applied to environmental monitoring: identifying sources of potentially toxic metals in aquatic system.

Aquatic contamination by potentially toxic metals is a problem that has been aggravated, especially due to the quantity and the diversity of sources. Locating these sources is not always an easy task, especially because of the wide variety of possibilities. In this context, the application of geostatistical methods may represent an excellent tool to find out sources of metal contaminants in aquatic systems. Thus, the objective of this work was to elaborate an approach to identify sources of potentially toxic metals (Zn, Ba, Pb, Cr, Mn and Fe), by relating their spatial-temporal variations with the local land use patterns, along a longitudinal profile of the Pirapora River, located in the State of Sao Paulo, Brazil. For this purpose, water samples were collected at different points, taking into consideration each specific land use pattern and quantifying the metals contents by microwave plasma atomic emission spectrometry. In this work, thirteen land use patterns have been identified: mining, forestry, abandoned pasture, water, urban area, human occupation, floodplain, bare soil, temporary crop, roads, forest, streets and pasture. The results revealed temporal variations for the metals Ba, Cr, Fe, and Pb and spatial for Zn and Mn, making possible to correlate the presence of these two latter metals with mining and forestry, the most proeminent activities in the region. Overall, this work proposes a model which brings together geoprocessing and analytical methods, in order to correlate spatial-temporal variations of potentially toxic metals with specific land use patterns of a determined region, aiming the environmental monitoring.

Extracts of Peels and Seeds of Five Varieties of Brazilian Jabuticaba Present High Capacity to Deactivate Reactive Species of Oxygen and Nitrogen.

Jabuticaba has a high concentration of phenolic compounds, which have a significant antioxidant capacity. Methodologies have been developed to evaluate the ability of plant extracts to fight free radicals such as H2O2, O2•-, HOCl, ONOO- and ROO•. Thus, the capacity of deactivation of reactive oxygen species (ROS) and reactive nitrogen species (RNS) in peel and seed extracts of five varieties of jabuticaba was evaluated. Sabará peel (SFP) deactivated HOCl with IC50 9.24 µg. mL-1; Paulista seed (PF) deactivated O2•- with IC50 16.15 µg. mL-1; Coroada seed (CFP) deactivated ONOO- with IC50 3.84 µg. mL-1; the peel of CFP deactivated ONOO- with IC50 5.88 µg. mL-1; the peel of SFP deactivated the ROO• at 918.16 µmol TE. g-1; and Sabará seed deactivated H2O2 with 49.11% inhibition at a concentration of 125 µg. mL-1 of extract. These results demonstrate the high antioxidant potential of this fruit, indicating that it could be extremely beneficial to human health.

Natural organic matter residue as a low cost adsorbent for aluminum.

The contamination of aquatic and terrestrial environments by potentially toxic metals is highlighted by the possible impacts that their high availability can have on the environment. Thus, the development of alternative absorbents that can be used in the remediation of contaminated areas is of great environmental interest. Humin, one of the fractions of natural organic matter, is a promising alternative in studies on the retention of different metals that are environmentally toxic. In this study, the influence of the organic and inorganic humin constituents that are involved in the retention of aluminum species was evaluated. After extraction and calcination to obtain the ashes (inorganic constituents), humin and ash samples were structurally characterized by Fourier transform infrared spectroscopy and scanning electron microscopy. Interaction studies between aluminum-humin and ash-humin were performed in the pH range of 4.0-8.0 and with various contact times. The results of the characterization of humin and ash showed different functional groups present in the structures of these materials. Based on the results of the interaction between humin-aluminum and ash-aluminum, it can be inferred that both the organic and inorganic components of humin are efficient at absorbing aluminum. However, the adsorption isotherms showed that humin and the ashes have different adsorption behaviors. Humin is the only fraction of natural organic matter with a significant inorganic constituent content; it is the fraction least used by researchers in this field and is often discarded as waste. In light of this, the results obtained in this work highlight the importance of humin as a natural adsorbent material. Humin may be promising for the removal of aluminum species in contaminated environments due to the presence of organic and inorganic constituents.

Isolation and chemical characterization of agelaiatoxin8 (AvTx8) from Agelaia vicina wasp venom and its biological effects on GABA neurotransmission.

Arthropod venoms are sources of molecules that may be useful tools to investigate molecular mechanisms of putative new medicines and laboratory drugs. Here we show the effects of the compound agelaiatoxin-8 (AVTx8), isolated from Agelaia vicina venom, on γ-aminobutyric acid (GABA) neurotransmission in rat brain synaptosomes. Analysis reveals that AvTx8 is composed by 14 amino acid residues with a molecular weight (MW) of 1567 Da. AvTx8 increased GABA release and inhibited GABA uptake in synaptosomes from rat cerebral cortex. AvTx8 inhibited GABA uptake and increased GABA release in the presence of Ca+ , Na+ , and K+ channel blockers, suggesting that it acts directly on GABA transporters. In addition, AvTx8 significantly decreases GABA binding in synaptic membranes from rat brain cortex, suggesting that it also modulates the activity of GABA receptors. Moreover, AvTx8 decreased GAT-1- and GAT-3-mediated GABA uptake in transfected COS-7 cells. Accordingly, we suggest that AvTx8 modulates GABA neurotransmission and might provide a novel entry point for identifying a new class of GABA-modulating neuroprotective drugs.

Identification and characterization of expressed retrotransposons in the genome of the Paracoccidioides species complex.

BACKGROUND: Species from the Paracoccidioides complex are thermally dimorphic fungi and the causative agents of paracoccidioidomycosis, a deep fungal infection that is the most prevalent systemic mycosis in Latin America and represents the most important cause of death in immunocompetent individuals with systemic mycosis in Brazil. We previously described the identification of eight new families of DNA transposons in Paracoccidioides genomes. In this work, we aimed to identify potentially active retrotransposons in Paracoccidioides genomes. RESULTS: We identified five different retrotransposon families (four LTR-like and one LINE-like element) in the genomes of three Paracoccidioides isolates. Retrotransposons were present in all of the genomes analyzed. P. brasiliensis and P. lutzii species harbored the same retrotransposon lineages but differed in their copy numbers. In the Pb01, Pb03 and Pb18 genomes, the number of LTR retrotransposons was higher than the number of LINE-like elements, and the LINE-like element RtPc5 was transcribed in Paracoccidioides lutzii (Pb01) but could not be detected in P. brasiliensis (Pb03 and Pb18) by semi-quantitative RT-PCR. CONCLUSION: Five new potentially active retrotransposons have been identified in the genomic assemblies of the Paracoccidioides species complex using a combined computational and experimental approach. The distribution across the two known species, P. brasiliensis and P. lutzii, and phylogenetics analysis indicate that these elements could have been acquired before speciation occurred. The presence of active retrotransposons in the genome may have implications regarding the evolution and genetic diversification of the Paracoccidioides genus.

Direct Protocol for Ambient Mass Spectrometry Imaging on Agar Culture.

Herein we describe a new protocol that allows direct mass spectrometry imaging (IMS) of agar cultures. A simple sample dehydration leads to a thin solid agar, which enables the direct use of spray-based ambient mass spectrometry techniques. To demonstrate its applicability, metal scavengers siderophores were imaged directly from agar culture of S. wadayamensis, and well resolved and intense images were obtained using both desorption electrospray ionization (DESI) and easy ambient sonic-spray ionization (EASI) with well-defined selective spatial distributions for the free and the metal-bound molecules, providing clues for their roles in cellular metabolism.

Hydroxyurea increases plasma concentrations of microparticles and reduces coagulation activation and fibrinolysis in patients with sickle cell anemia.

Microparticles (MPs) are present in healthy subjects and their concentration increases in patients at high risk of thrombosis. We evaluated 10 patients with sickle cell anemia (SCA) treated with hydroxyurea (HU) and 13 SCA patients without this treatment. MP concentrations were determined by flow cytometry. Coagulation was evaluated using the thrombin-antithrombin complex (TAT) and D-dimers. Total MP concentrations were increased in the HU-treated group (265 × 10(6)/ml vs. 67.45 × 10(6)/ml; p = 0.0026), as well as MPs derived from RBC (67.83 × 10(6)/ml vs. 26.31 × 10(6)/ml; p = 0.05), monocytes (51.31 × 10(6)/ml vs. 9.03 × 10(6)/ml; p = 0.0084), monocytes with tissue factor (TF) expression (2.27 × 10(6)/ml vs. 0.27 × 10(6)/ml; p = 0.0058), endothelium (49.42 × 10(6)/ml vs. 7.23 × 10(6)/ml; p = 0.007) and endothelium with TF (1.42 × 10(6)/ml vs. 0.26 × 10(6)/ml; p = 0.0043). Furthermore, the concentrations of TAT (7.56 vs. 10.98 µg/l; p = 0.014) and D-dimers (0.65 vs. 1.29 µg/ml; p = 0.007) were reduced with HU. The MP elevation may suggest a direct cytotoxic effect of HU. Another explanation is a cell surface increase secondary to a megaloblastic process, resulting in increased vesicle release. In our opinion, the known benefits of HU on SCA patients, along with the reduction in coagulation activation, surpass its potential detrimental effect on MPs. Future studies should elucidate the role of MPs and demonstrate their significance in different contexts.

Effect of the competition of Cu(II) and Ni(II) on the kinetic and thermodynamic stabilities of Cr(III)-organic ligand complexes using competitive ligand exchange (EDTA).

The effect of competition of Cu(II) and Ni(II) on the kinetic stability of Cr(III) complexed with natural organic matter (NOM) was characterized using EDTA exchange with single-stage tangential-flow ultrafiltration. For a water sample from Serra de Itabaiana, 3% of spiked Cr(III) was exchanged, while for a sample from the Itapanhaú River, 7, 10, 10, and 21% was exchanged in experiments using Cr(III) alone and in combination with Cu(II), Ni(II), or Cu(II) + Ni(II), respectively. Times required to reach exchange equilibrium with EDTA were less than 360 min. The influence of competition from Ni(II) and Cu(II) on the availability of complexed Cr(III) was low, demonstrating preference of the ligand sites for Cr(III). This was correlated with sample humification, as confirmed by EPR and (13)C NMR analyses. Exchange efficiency was in the order Cu > Ni > Cr, and the process could be readily described by first order kinetics, with average rate constants of 0.35-0.37 h(-1).

Enzymology of Pyran Ring†A Formation in Salinomycin Biosynthesis.

Tetrahydropyran rings are a common feature of complex polyketide natural products, but much remains to be learned about the enzymology of their formation. The enzyme SalBIII from the salinomycin biosynthetic pathway resembles other polyether epoxide hydrolases/cyclases of the MonB family, but SalBIII plays no role in the conventional cascade of ring opening/closing. Mutation in the salBIII gene gave a metabolite in which ring A is not formed. Using this metabolite in vitro as a substrate analogue, SalBIII has been shown to form pyran ring A. We have determined the X-ray crystal structure of SalBIII, and structure-guided mutagenesis of putative active-site residues has identified Asp38 and Asp104 as an essential catalytic dyad. The demonstrated pyran synthase activity of SalBIII further extends the impressive catalytic versatility of α+ß barrel fold proteins.