Biology subjects

Colinas, N.

Publications and source records attributed to Colinas, N..

2 recordsLinked to original sources

bioRxiv2025

Specifind: A Natural Language Processing Tool for Automating Species Occurrence (Re-)Discovery from Scientific Literature

A vast amount of valuable information on species occurrences remains embedded within the unstructured and continuously expanding body of ecological literature written in natural language. When effectively extracted, such dispersed knowledge has the potential to significantly improve understanding of species distributions and ecological patterns, thereby enabling more targeted and informed conservation actions. To address this challenge, Specifind is introduced as a tool designed to facilitate the extraction of species occurrence data through the identification of scientific species names, geographic references, and the relationships between them while ensuring traceability. At its core lies a newly developed and expertly annotated dataset comprising over one thousand open-access abstracts drawn from five domains: biogeography, botany, entomology, mycology, and zoology. A suite of Natural Language Processing components has been integrated, including Document Layout Analysis, Optical Character Recognition, Named Entity Recognition, Coreference Resolution, and Relation Extraction. These components enable the accurate identification and contextual linking of species and geographic entities, even when references are distributed throughout the text. As a result, Specifind enhances the discoverability and usability of species occurrence information embedded within unstructured scientific texts. It is expected to reduce the substantial effort required for manual literature review, thereby supporting biodiversity research, informing conservation planning, and facilitating ecological analysis.

bioinformatics↗

bioRxiv2021

Zooplankton as a transitional host for Escherichia coli in freshwater

This study shows that Escherichia coli can be temporarily enriched in zooplankton in natural conditions and that these bacteria can belong to different phylogroups and sequence types including environmental as well as clinical and animal isolates. We isolated 10 E. coli strains and sequenced the genomes of two of them. Phylogenetically the two isolates were closer to strains isolated from poultry meat than with freshwater E. coli, albeit their genomes were smaller than those from poultry. After isolation and fluorescent protein tagging of strains ED1 and ED157 we show that Daphnia sp. can take up these strains and release them alive again, thus forming a temporary host for E. coli. In a chemostat experiment we show that the association does not prolong the bacterial long-term survival, but that at low abundances it does also not significantly reduce the bacterial numbers. We demonstrate that E. coli does not belong to the core microbiota of Daphnia, suffers from competition by the natural microbiota of Daphnia, but can profit from its carapax to survive in water. All in all, this study suggests that the association of E. coli to Daphnia is only temporary but that the cells are viable therein and this might allow encounters with other bacteria for genetic exchange and potential genomic adaptations to the freshwater environment. ImportanceThe contamination of freshwaters with faecal derived bacteria is of major concern regarding drinking water acquisition and recreational activities. Ecological interactions promoting their persistence are still very scarcely studied. This study, which analyses the survival of E. coli in the presence of zooplankton, is thus of ecological as well as water safety relevance.

ecology↗