Biology subjects

Barros, S.

Publications and source records attributed to Barros, S..

6 recordsLinked to original sources

bioRxiv2026

Genome-wide characterization of extant clonal diversity in Chilean Carmenere

Carmenere is a widely cultivated and internationally recognized grapevine cultivar in Chile, yet genetic variation among its clones remains poorly characterized. Early studies based on SSR and AFLP markers detected limited polymorphism, but these approaches interrogate only a small fraction of the genome, leaving the extent of clonal diversity unresolved. Here, we generated an improved chromosome-scale diploid genome assembly of Carmenere FPS clone 02 and characterized clonal genomic diversity by sequencing 36 biological replicates representing 12 clones maintained in Chile, including heritage selections rescued from old producer vineyards by Vina Santa Carolina as part of its Bloque Herencia conservation program, and commercial nursery-derived clones. Focusing on low-frequency variants and using replicate-aware consensus calling, we identified more than 9,000 private single nucleotide variants (SNVs) and small indels per clone, providing high-resolution markers for clonal identification. Although most variants were located in repetitive or intergenic regions, a subset affected coding sequences, with genes involved in plant-pathogen interactions, transport, and secondary metabolism most frequently impacted. While variant-affected genes associated with wine anthocyanin content, TA, pH, and alcohol percentage were identified, broader phenotypic characterization will be required to assess their biological significance. Overall, this study provides a genome-wide characterization of extant clonal diversity in Carmenere, with implications for clonal selection and genetic resource conservation.

genomics↗

bioRxiv2023

Validation of the in-house designed one-trial inhibitory avoidance test for two strains of adult zebrafish

Open-source validated tools are important for affordable high-quality science. Zebrafish model is often used in behavioral sciences, thus validated tools must be developed for this species. We aimed to implement the memory task one-trial inhibitory avoidance test in our laboratory by creating a custom-built 3D printed apparatus and custom-made hardware and software using microcontrollers; this decreases the costs and increases methodological flexibility. In this task, a mild electric shock (3.3 {+/-} 0.3V and 2A for 5sec) is used as an aversive stimulus for the one-trial inhibitory avoidance task based on classical conditioning. For this study we used 72-adult zebrafish from the AB and TU strain. The aversive stimulus caused a robust and long-lasting memory that was learned in one session. The apparatus consisted in one aquarium with two compartments (white and black) where, during the conditioning session, the shock was delivered in the preferred side (black), followed by 30min of immersion in 20M MK-801, a compound known for inducing amnesia (amnesic group, n= 20 for AB and 17 for TU), or in clean water (control, n= 20 for AB and 15 for TU). Both the AB and TU strain animals from the control group took more time to enter in the black compartment after conditioning (p[≤]0.039), indicating avoidance for the black side, while the latency was not altered in the MK-801 group, demonstrating impaired memory. In summary, this open-source apparatus is an affordable and validated option for memory assessment for the two most used strains of zebrafish in research.

animal behavior and cognition↗

bioRxiv2022

Metformin disrupts Danio rerio metabolism at environmentally relevant concentrations: A generational study

Metformin (MET) is an anti-diabetic pharmaceutical with a large-scale consumption, which is increasingly detected in surface waters. However, current knowledge on the generational effects of MET exposure in the metabolism of non-target organisms is limited. The present study aimed at investigating the effects of MET in the model freshwater teleost Danio rerio, following a generational exposure (from egg up to 9 months exposure) to environmentally relevant concentrations ranging from 361 ng/L to 13 000 ng/L. Biochemical markers were used to determine cholesterol and triglycerides levels, as well as mitochondrial complex I activity in males and females zebrafish liver. mRNA transcript changes were also assessed in the liver of both sexes by means of an exploratory RNA-seq analysis and expression levels of key genes involved in the energy metabolism and lipid homeostasis, i.e. acaca, acadm, cox5aa, idh3a, hmgcra, prkaa1, were determined using qRT-PCR analysis. The findings here reported revealed that MET was able to significantly disrupt critical biochemical and molecular processes involved in zebrafish metabolism, such as cholesterol and fatty acid biosynthesis, the mitochondrial electron transport chain and the tricarboxylic acid cycle, concomitantly to changes on the hepatosomatic index. Non-monotonic dose response curves were frequently detected in the gene expression profile, with higher effects observed for 361 ng/L and 2 166 ng/L concentrations. Collectively, the obtained results suggest that environmentally relevant concentrations of MET are able to severely disrupt D. rerio metabolism, with potential impacts at the ecological level, supporting the need to update the environmental quality standard (EQS) and predicted no-effect concentration (PNEC) for MET. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=85 SRC="FIGDIR/small/487223v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@e9baecorg.highwire.dtl.DTLVardef@eedd72org.highwire.dtl.DTLVardef@c87a5org.highwire.dtl.DTLVardef@9d7c55_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIDanio rerio was exposed to metformin for a full generation; C_LIO_LIMET affected COX I activity, as well as Chol and TGL content in zebrafish liver; C_LIO_LIMET altered mRNA levels of genes involved in energy metabolism and lipid content; C_LIO_LINon-monotonic dose-response curves were frequently detected; C_LIO_LIDue to the results obtained, MET PNEC should be reviewed. C_LI

pharmacology and toxicology↗

bioRxiv2021

Bagaza virus in wild birds, Portugal, 2021

Bagaza virus (BAGV) emerged in Spain, in 2010. Since then, BAGV was not reported in other European countries until September 2021, when BAGV was diagnosed by molecular methods in one corn bunting and several red-legged partridges, after abnormal mortality in Southern Portugal. Sequencing revealed high similarity with strains reported previously.

pathology↗

bioRxiv2020

The anti-lipidemic drug simvastatin modulates Epigenetic Biomarkers in the Amphipod Gammarus locusta

The adverse effects of certain environmental chemicals have been recently associated with epigenomes modulation. Although the changes in the epigenetic signature are still not integrated into hazard and risk assessment, they are interesting candidates for linking environmental exposures to altered phenotypes given that these changes may be passed across multiple non-exposed generations. Here, we addressed the effects of simvastatin (SIM), one of the most prescribed human pharmaceuticals, in epigenetic regulators of the amphipod Gammarus locusta, as a proxy to support its integration in hazard and environmental risk assessment. SIM is a known modulator of epigenome in mammalian cell lines, and has been reported to impact G. locusta ecological endpoints at environmentally relevant levels. G. locusta juveniles were exposed to three SIM concentrations (0.32, 1.6 and 8 {micro}g.L-1), for 15 days. The basal expression of selected epigenetic regulators was determined, along with the quantification of DNA methylation levels and the assessment of key ecological endpoints. Exposure to 0.32 and 8 {micro}g.L-1 SIM induced significant downregulation of DNA methyltransferase1 (dnmt1), concomitantly with Global DNA hypomethylation and impact on growth. Overall, this work is the first to validate the basal expression of key epigenetic regulators in a keystone marine crustacean, supporting the integration of epigenetic biomarkers into hazard assessment frameworks.

pharmacology and toxicology↗

bioRxiv2018

Chronic environmentally relevant levels of Simvastatin induces non-monotonic responses in Zebrafish (Danio rerio)

Simvastatin (SIM), a hypocholesterolaemic compound, is among the most prescribed pharmaceuticals for cardiovascular disease prevention worldwide. Several studies have shown that acute exposure to SIM is able to produce multiple adverse effects in aquatic organisms. However, uncertainties still remain regarding the chronic effects of SIM in aquatic ecosystems. Therefore, the present study aimed to investigate the effects of SIM in the model freshwater teleost zebrafish (Danio rerio) following a chronic exposure (90 days) to environmentally relevant concentrations ranging from 8 ng/L to 1000 ng/L. This study used a multi-parametric approach integrating distinct ecological-relevant endpoints, i.e. survival, growth, reproduction and embryonic development, with biochemical markers (cholesterol and triglycerides). Furthermore, Real Time PCR was used to analyse the transcription levels of key genes involved in the mevalonate pathway (hmgcra, cyp51, and dhcr7). Globally, SIM induced several non-monotonic dose-responses; embryonic development, biochemical and molecular markers, were significantly impacted in the low-intermediate concentrations, 40 ng/L and 200 ng/L, whereas no effects were recorded for the highest tested SIM levels (1000 ng/L). Taken together, these findings expand our understanding of statins effects in teleosts, demonstrating significant impacts at environmentally relevant concentrations. The findings highlight the importance of addressing the effects of chemicals under chronic low-level concentrations.\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=83 SRC=\"FIGDIR/small/289694v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (17K):\norg.highwire.dtl.DTLVardef@1922156org.highwire.dtl.DTLVardef@caad80org.highwire.dtl.DTLVardef@44c058org.highwire.dtl.DTLVardef@1afe60f_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LISeveral uncertainties exist regarding simvastatin mode of action in non-target organisms\nC_LIO_LIThis work integrates D. rerio multi-level responses after long-term exposure to simvastatin\nC_LIO_LISimvastatin impacted cholesterol/triglycerides levels and transcript levels of genes related to mevalonate pathway.\nC_LIO_LIParental exposure to simvastatin induced offspring embryonic malformations.\nC_LIO_LIEmbryonic abnormalities, biochemical and molecular data did follow a non-monotonic curve.\nC_LI

pharmacology and toxicology↗