Biology subjects

Oliveira, R. S.

Publications and source records attributed to Oliveira, R. S..

9 recordsLinked to original sources

bioRxiv2026

Genomic Epidemiology of Canine Distemper Virus (CDV) in Neotropical Primates in Brazil Reveals Multiple Spillover Events and Convergent Evolution at Hemagglutinin Residue 519

Canine distemper virus (CDV; Morbillivirus canis) is a multi-host paramyxovirus primarily maintained in the order Carnivora. However, recent outbreaks in Neotropical primates suggest recurrent cross-species spillover into non-human primates. Between May and July 2022, seven marmosets (Callithrix penicillata) were found dead in urban and peri-urban areas of Montes Claros, Minas Gerais, Brazil. Viral metagenomic sequencing recovered two near complete CDV genomes directly from liver samples. Maximum likelihood and Bayesian phylogenetic analyses placed these genomes within the South American CDV lineage and supported at least three independent zoonotic introductions into Callithrix populations. Domestic dogs (Canis lupus familiaris) were inferred as the most likely source and the crab-eating fox (Cerdocyon thous) as a probable bridge host. Ancestral-state reconstruction identified a substitution at position 519 of the hemagglutinin (H) protein (R519I in the two primate clades and R519G in a singleton primate sequence). In silico modelling of the marmoset signaling lymphocytic activation molecule (SLAM) complex was consistent with a modest reorganisation of the receptor-binding head in the 519-substituted variants (ipTM = 0.82), generating a testable hypothesis that this residue may contribute to adaptation at the primate SLAM receptor interface and is associated with altered predicted docking orientation for the receptor. Together, these findings suggest that residue 519 is a candidate marker of CDV adaptation to Neotropical primates and emphasise the importance of integrating genomic surveillance with domestic dog vaccination efforts under a One Health framework to reduce the threat of CDV spillover to vulnerable wildlife populations.

genomics↗

bioRxiv2026

Isolation and Genomic Characterization of Myxococcus faecalis Strains from Mangroves in Southeastern Brazil

Myxococcus faecalis was recently described from human fecal isolates, although subsequent evidence indicates an environmental distribution for this lineage. Here, we report the isolation and genomic characterization of two M. faecalis strains (BRX-014 and BRX-032) recovered from mangrove ecosystems along the southeastern coast of Brazil, representing the first record of the species in a marine-coastal biome. Phylogenomic reconstruction based on 120 conserved bacterial marker genes, together with Average Nucleotide Identity (ANI >97.6%) and digital DNA-DNA hybridization (dDDH 77.7-90.4%) analyses, confirmed their assignment to M. faecalis and demonstrated high genomic relatedness to strains previously recovered from soil and human feces samples. Pangenome analysis of five available genomes revealed a total repertoire of 9,827 genes, with a large core genome comprising 7,499 genes (76.3%), consistent with a highly conserved and nearly closed pangenome structure. Functional classification based on COG categories showed uniform distributions across all isolates. Comparative analysis of the degradome further revealed strong conservation of proteolytic and carbohydrate-active enzyme repertoires, dominated by serine and metallopeptidases and diverse glycoside hydrolases. The extensive genomic and functional similarity among isolates from geographically distant and ecologically distinct environments supports a broad ecological distribution of M. faecalis and suggests that its large and conserved genomic repertoire underpins its persistence across contrasting habitats. These findings expand the known ecological range of the species and provide a comparative genomic framework for future investigations into its distribution and functional potential across different habitats.

bioinformatics↗

bioRxiv2025

MonoAlg3D: Enabling Cardiac Electrophysiology Digital Twins with an Efficient Open Source Scalable Solver on GPU Clusters

Modelling and simulation are essential in biomedicine, and specifically in computational cardiology. Reliable, efficient and accurate solvers are critical. This study presents an open source, GPU-based cardiac electrophysiology solver for scalable digital twin multiscale simulations (MO_SCPLOWONOC_SCPLOWAO_SCPLOWLGC_SCPLOW3D), incorporating conduction system calibration and performance optimization. The solver employs the monodomain equation coupled with the Purkinje network, solved via the finite volume method, featuring a GPU-based linear solver and concurrent simulation dispatch with MPI. We demonstrate a 10.94x speedup over a CPU-based solution and scalability by running 512 simulations on 128 compute nodes, completing all coarse-mesh simulations in less than 24 minutes and fine-mesh simulations in 303 minutes. We also demonstrate integration into a cardiac digital twin pipeline for personalisation based on clinical data. The proposed open source solver enhances computational efficiency and physiological fidelity, enabling large-scale, high-speed cardiac simulations. This work marks a significant step toward fast and scalable cardiac simulations on GPU architectures, with integration in a Digital Twin personalisation pipeline including the conduction system.

bioengineering↗

bioRxiv2025

Genomic resources for curimba Prochilodus lineatus reveal a fractal pattern of hierarchical genetic population structure in mixed stocks across fish segregated by dams.

Genomic resources, new microsatellite markers and a novel observation of a fractal pattern of the genetic population structure are presented for curimba Prochilodus lineatus, a suitable model organism for freshwater migratory species in South America. Our main goals were to investigate the presence of mixed fish stocks, the effects of isolation by dams and broodstocking over the genetic diversity for this species. We focused on the upper segment of the extremely fragmented Grande River, MG, Brazil, from the megadiverse continental La Plata Basin. Two main co-occurring genetically admixed stocks were identified by maximum likelihood estimation and iteratively unfolded with two further steps, through a hierarchical analysis of genetic structure. It consistently unveiled two newly defined internal groups, from the previously resolved clusters (23). We suggest this stratified pattern of mixed stocks from the main river channel may be attributed to the existence of different, well defined breeding grounds, nested within differential scales throughout this basin, arranged according to fractal geometry (1st order river, 2nd and 3rd order tributaries, and so on). This would imply in homing behaviour for this species. Our work also provides massive molecular data for this fish, including its first draft genome assembly and a valuable panel for the rapid and low-cost development of new microsatellite DNA markers. These findings will likely benefit researchers and environmental managers in tackling challenging issues regarding the conservation of Neotropical migratory fishes, as they support the hypothesis of the isolating effects of dams and broodstocking over genetic variability. More importantly, the results presented here point to the potential role of tributaries of different orders in harbouring genetically diverse populations of migratory freshwater fishes.

genetics↗

bioRxiv2021

Fast surveillance response and genome sequencing reveals the circulation of a new Yellow Fever Virus sublineage in 2021, in Minas Gerais, Brazil

Yellow fever virus (YFV) exhibits a sylvatic cycle of transmission involving wild mosquitoes and non-human primates (NHP). In Brazil, YFV is endemic in the Amazon region, from where waves of epidemic expansion towards other Brazilian states eventually occur. During such waves, the virus usually follows the route from North to the Central-West and Southeast Brazilian regions. Amidst these journeys, outbreaks of Yellow Fever (YF) in NHPs, with spillovers to humans have been observed. In the present work, we describe a surveillance effort encompassing the technology of smartphone applications and the coordinated action of several research institutions and health services that succeeded in the first confirmation of YFV in NHPs in the state of Minas Gerais (MG), Southeast region, in 2021, followed by genome sequencing in an interval of only ten days. Samples from two NHPs (one of the species Alouatta caraya in the municipality of Icarai de Minas and the other of the species Callithrix penicillata in the municipality of Ubai) were collected and the presence of YFV was confirmed by RT-qPCR. We generated three near-complete by Nanopore sequencer MinION. Phylogenetic analysis revealed that all viral genomes recovered are equal and related to lineage South America 1, clustering with a genome detected in the Amazon region (Para state) in 2017. These findings reveal the occurrence of a new wave of viral expansion in MG, six years after the beginning of the major outbreak in the state, between 2015-2018. No human cases were reported to date, showing the importance of coordinated work between local surveillance based on available technologies and support laboratories to ensure a quick response and implementation of contingency measures towards avoiding the occurrence of YF cases in humans.

molecular biology↗

bioRxiv2021

Accuracy of the pneumatic method for estimating xylem vulnerability to embolism in temperate diffuse-porous tree species

O_LIThe increasing frequency of global change-type droughts has created a need for fast, accurate and widely applicable techniques for estimating xylem embolism resistance to improve forecasts of future forest changes. C_LIO_LIWe used data from 12 diffuse-porous temperate tree species covering a wide range of xylem safety to compare the pneumatic and flow-centrifuge method for constructing xylem vulnerability curves. We evaluated the agreement between parameters estimated with both methods and the sensitivity of pneumatic measurements to the measurement duration. C_LIO_LIThe agreement between xylem water potentials at 50% air discharged (PAD) estimated with the Pneumatron and 50% loss of hydraulic conductivity (PLC) estimated with the flow-centrifuge method was high (mean signed deviation: 0.12 MPa, Pearson correlation: 0.96 after 15 sec of gas extraction). However, the relation between the estimated slopes was more variable, resulting in lower agreement in xylem water potential at 12% and 88% PAD/PLC. All parameters were sensitive to the duration of the pneumatic measurement, with highest overall agreement between methods after 16 sec. C_LIO_LIWe conclude that, if applied correctly, the pneumatic method enables fast and inexpensive estimations of embolism resistance for a wide range of temperate, diffuse-porous species, which makes it attractive for predicting plant performance under climate change. C_LI

plant biology↗

bioRxiv2021

A user manual to measure gas diffusion kinetics in plants: Pneumatron construction, operation and data analysis

The Pneumatron device presented measures gas diffusion kinetics in the xylem of plants. The device provides an easy, low-cost, and powerful tool for research on plant water relations. Here, we describe in detail how to construct and operate this device to estimate xylem vulnerability to embolism, and how to analyse pneumatic data. Simple and more elaborated ways of constructing a Pneumatron are shown, either using wires, a breadboard, or a printed circuit board. The instrument is based on an open-source hardware and software system, which allows users to operate it in an automated or semi-automated way. A step-by-step manual and a troubleshooting section are provided. An excel spreadsheet and an R-script are also presented for fast and easy data analysis. This manual should help new users to avoid common mistakes, especially regarding stable measurements of the minimum and maximum amount of gas that can be discharged from xylem tissue.

plant biology↗

bioRxiv2018

In-season internal and external training load quantification of an elite European soccer team

Elite soccer teams that participate in European competitions often have a difficult schedule, involving weeks in which they play up to three matches, which leads to acute and transient subjective, biochemical, metabolic and physical disturbances in players over the subsequent hours and days. Inadequate time recovery between matches can expose players to the risk of training and competing whilst not fully recovered. Controlling the level of effort and fatigue of players to reach higher performances during the matches is therefore critical. Therefore, the aim of the current study was to provide the first report of seasonal internal and external training load (TL) that included Hooper Index (HI) scores in elite soccer players during an in-season period. Sixteen elite soccer players were sampled, using global position system, session rating of perceived exertion (s-RPE) and HI scores during the daily training sessions throughout the 2015-2016 in-season period. Data were analysed across ten mesocycles (M: 1 to 10) and collected according to the number of days prior to a match. Total daily distance covered was higher at the start (M1 and M3) compared to the final mesocycle (M10) of the season. M1 (5589m) reached a greater distance than M5 (4473m) (ES = 9.33 [12.70, 5.95]) and M10 (4545m) (ES = 9.84 [13.39, 6.29]). M3 (5691m) reached a greater distance than M5 (ES = 9.07 [12.36, 5.78]), M7 (ES = 6.13 [8.48, 3.79]) and M10 (ES = 9.37 [12.76, 5.98]). High-speed running distance was greater in M1 (227m), than M5 (92m) (ES = 27.95 [37.68, 18.22]) and M10 (138m) (ES = 8.46 [11.55, 5.37]). Interestingly, the s-RPE response was higher in M1 (331au) in comparison to the last mesocycle (M10, 239au). HI showed minor variations across mesocycles and in days prior to the match. Every day prior to a match, all internal and external TL variables expressed significant lower values to other days prior to a match (p<0.01). In general, there were no differences between player positions.\n\nConclusionsOur results reveal that despite the existence of some significant differences between mesocycles, there were minor changes across the in-season period for the internal and external TL variables used. Furthermore, it was observed that MD-1 presented a reduction of external TL (regardless of mesocycle) while internal TL variables did not have the same record during in-season match-day-minus.

physiology↗

bioRxiv2018

Environment-driven genomic and trait divergence in a neotropical mangrove highlight differential sensitivities to climate change

Local adaptation is often a product of environmental variations in the geographical space and has implications for biodiversity conservation. We investigated the role of latitudinal heterogeneity in climate on the organization of genetic and phenotypic variation in the dominant coastal tree, Avicennia schaueriana. In a common garden experiment, samples from an equatorial region, marked by rainy/dry seasons, accumulated less biomass, showed lower stomatal conductance and transpiration, narrower xylem vessels, smaller leaves and higher reflectance of long wavelengths (red light) on the stem epidermis, than samples from a subtropical region, marked by warm/cold seasons. Transcriptome differences identified between trees sampled under field conditions at equatorial and subtropical sites, were enriched in functional categories as responses to temperature, solar radiation, water deficit, photosynthesis and cell wall biosynthesis. The diversity based on thousands of SNP loci revealed a north-south genetic structure. Remarkably, signatures of selection were identified in loci associated with photosynthesis, anthocyanin accumulation and the responses to osmotic and hypoxia stresses. Our results suggest the existence of divergence in key resource-use characteristics, likely driven by climate seasonality, based on water-deficit and solar radiation. These findings provide a basis for conservation plans and for predictions for coastal plant responses to climate change.

plant biology↗