Biology subjects

Ribeiro, T.

Publications and source records attributed to Ribeiro, T..

4 recordsLinked to original sources

bioRxiv2025

Genomics insights reveal multi-year maintenance of a new Deltacoronavirus infecting Seabirds from the Cagarras Island Archipelago Natural Monument, Brazil

Previous studies have identified various pathogens in seabirds, notably coronaviruses (CoVs) and influenza A viruses (IAVs), due to their potential to cause significant morbidity and mortality. The Cagarras Island Archipelago Natural Monument, located near Rio de Janeiro, Brazil, serves as nesting site for two species, the magnificent frigatebird (Fregata magnificens) and the brown booby (Sula leucogaster). Despite its ecological importance, no prior studies have investigated viral infections in these species, which share habitat interfaces with densely populated human areas. To address this gap, we sampled and tested seabirds for CoVs and IAVs from January 2022 to April 2024. Birds were captured and identified by species, age, and sex. Oropharyngeal and cloacal swabs, as well as blood samples, were collected. Viral RNA was extracted using the QIAamp Viral RNA Mini Kit, and the presence of IAVs was screened via real-time RT-PCR, while CoVs were screened using semi-nested RT-PCR. Sanger and metatranscriptomic sequencing were performed to identify viral strains and assess phylogenetic relationships. Of the 153 seabirds sampled, CoVs were detected in 6 individuals (9.1%) of F. magnificens and 16 individuals (18.4%) of S. leucogaster. No IAVs were found in either oropharyngeal or cloacal swabs, and all serum samples were negative for the presence of antibodies against the virus. We recovered two full deltacoronavirus genomes and eight additional draft genomes from S. leucogaster samples obtained from distinct sampling expeditions and additional enteroviruses, passeriviruses, and picornaviruses. Phylogenetic analysis revealed that the detected CoVs are closely related to avian deltacoronaviruses from environmental samples of S. leucogaster in the Sao Pedro and Sao Paulo Archipelago, indicating potential viral exchange between these seabird populations living at these distant islands. Moreover, multiple detections in different individuals at different time points are associated with specific Spike NTD deletions that have been shown to accumulate in immune escape lineages, supporting the long-term maintenance through new infections and reinfection of this virus in these bird populations. This is the first detection of CoVs in F. magnificens, highlighting their circulation in marine ecosystems. Further research is needed to understand the ecological and epidemiological implications, including potential cross-species transmission.

microbiology↗

bioRxiv2025

A deeper study on propionic acid-related inhibition during anaerobic digestion: insights on methane production and identification of biomarker candidates for an early warning

Propionic acid (HPr) accumulation is a major indicator of anaerobic digestion (AD) dysfunction, yet the relative contributions of acidity, undissociated HPr, and propionate ions (Pr-) to process inhibition remain poorly understood. We investigated these effects in mesophilic batch AD microcosms fed with municipal sewage sludge, using a comparative design involving HPr, sodium propionate (NaPr), NaCl, and HCl treatments across two series of experiments. While 20 mM HPr caused a 22% reduction in the maximal methane production rate, 81 mM HPr led to complete inhibition, with the initial pH dropping to 5.1. By contrast, 81 mM NaPr reduced methane production rate by only 40%, and 81 mM NaCl caused no inhibition, demonstrating that acidity is the dominant inhibitory factor, with Pr- exerting a secondary concentration-dependent effect. 16S rRNA gene amplicon sequencing revealed strong, compound-specific shifts in microbial community composition, affecting key functional groups including syntrophs and methanogenic archaea. The proportion of methanogens dropped from 2-3% in control reactors to less than 0.2% under 81 mM HPr, consistent with the observed methane production inhibition. Under HPr81, over 100 ASVs were differentially abundant compared to controls, a pattern largely shared with HCl-treated reactors, further confirming the predominant role of acidity. The number of differentially abundant ASVs was negatively correlated with methane production rates (R{superscript 2} = 0.97), underscoring the link between community reshaping and process impairment. These results provide a unifying framework for propionate inhibition in AD and suggest that microbial community profiling could serve as an early warning tool for process imbalance detection.

bioengineering↗

bioRxiv2024

A leaf-expressed TERMINAL FLOWER1 ortholog from coffee with alternate splice forms alters flowering time and inflorescence branching in Arabidopsis

Perennial, polycarpic species, such as Coffea sp L. (coffee), exhibit asynchronous flowering while maintaining concomitant vegetative growth. This growth dichotomy is associated directly with fruit development and maturation time. To identify molecular components that underlie asynchronous flowering, we isolated phosphatidylethanolamine binding protein (PEBP) homologs expressed in coffee and identified a gene with high similarity to Arabidopsis TERMINAL FLOWER1-like. In Arabidopsis, interaction of TFL1 (AtTFL1) with bZIP transcription factor floral regulator FD (AtFD) forms a floral repressor complex that maintains inflorescence meristems in an indeterminate state. Unlike AtTFL1, which is expressed only in the shoot apical meristem, CaTFL1 transcript was detected exclusively in coffee leaves. Moreover, this transcript retained an intron, which was not reported for AtTFL1. CaTFL1 was characterized through heterologous expression in Arabidopsis and protein interaction analysis. Ectopic overexpression of CaTFL1 in transgenic Arabidopsis plants caused extreme late flowering or prevented flowering. However, the most severe floral repressive activity occurred in transgenic plants that spliced out the extra intron from CaTFL1. Yeast two hybrid assay revealed that CaTFL1 protein encoded by the spliced mRNA interacts with AtFD, as well as Arabidopsis 14-3-3 protein. These findings suggest that CaTFL1 acts as a leaf-expressed floral repressor, whose activity is controlled by alternate splicing, and may contribute to asynchronous flowering in coffee.

plant biology↗

bioRxiv2024

Molecular control of dormancy transitions throughout the year in the monoecious cork oak

Bud dormancy plays a vital role in flowering regulation and fruit production, being highly regulated by endogenous and environmental cues. Deployment of epigenetic modifications and differential gene expression control bud dormancy/break cycles. Information on how these genetic and epigenetic mechanisms are regulated throughout the year is still scarce for temperate trees, such as Quercus suber. Here, the expression levels of QsCENL and QsDYL1 during different seasonal cycles of bud development suggest that QsCENL may be implicated in the establishment of growth cessation in Q. suber and that QsDYL1 is a good dormancy marker. Moreover, the analysis of the profiles of epigenetic marks and the expression of modifiers, in dormant versus non-dormant bud meristems, indicate that epigenetic regulation is implicated in how bud development progresses in Q. suber. The identification of bud specific mechanisms opens new possibilities to understand how trees respond to challenging environmental signals derived from climate change.

plant biology↗