Biology subjects

Espinoza, M.

Publications and source records attributed to Espinoza, M..

4 recordsLinked to original sources

bioRxiv2025

Selecting methods for draft GEM generation in multicellular eukaryotes: a comparative analysis

Motivated by multiple strategies that have successfully implemented genome-scale models (GEMs) into their pipeline, several approaches have been developed for automatic generation of draft GEMs. However, most of these methods are not optimized for their use for multicellular eukaryotes and their performance for this task is unclear. In this work we present a comparative analysis of seven automated reconstruction tools (AuReMe, carveMe, Merlin, modelSEED, Pathway tools, Raven and Reconstructor) applied to three multicellular eukaryotes: the mosquito Aedes aegypti, the CHO (Chinese Hamster Ovary) cell line from Cricetulus griseus and the brown algae Ectocarpus siliculosus. Evaluation of these tools was based on metrics for network size, functionality, consistency, representation of organelle-specific functions and organism-specific metabolites, annotation quality and execution time. Finding that similarity of obtained metabolic networks is highly influenced by databases in which these methods base their predictions over phylogeny. Our works aims at providing a practical resource to guide researchers in selecting methods for draft generation tailored to organism characteristics and research goals. Author summaryGenome-scale models (GEMs) represent all the potential biochemical transformations that a specific organism can carry out based on the information encoded in its genome. Although these models are a powerful tool for analyzing omics datasets and simulating the metabolic effects of genetic modifications or changing media composition, the process of manually reconstructing a genome-scale model is complex and time-consuming. Motivated by their potential applications, several tools have been developed for the automated generation of draft GEMs, however, most of them are oriented to simpler organisms such as bacteria or single-cell eukaryotes, while their relative performance for modeling multicellular eukaryotes is unclear. In this work, we compared seven tools for draft GEMs reconstruction of three organisms: for the mosquito Aedes aegypti, the brown algae Ectocarpus siliculosus and the CHO cell line from Cricetulus griseus. Our results showed that no tool systematically outperformed others, suggesting that method selection is influenced by several factors such as organism-specific data availability and their intended application.

systems biology↗

bioRxiv2025

Habitat use of juvenile green turtles along the North Pacific coast of Costa Rica

Understanding how threatened marine species use coastal areas and the extent of connectivity across different spatial and temporal scales is important for identifying critical habitats that can enhance conservation efforts in other regions of their distribution. In this study, we investigated the site fidelity and habitat use of juvenile yellow morphotype green sea turtles (Chelonia mydas) in the Gulf of Santa Elena, north Pacific coast of Costa Rica. Fifteen juvenile green sea turtles (49 - 83 cm curved carapace length; CCL) were monitored for 19 - 629 days with an array of 11 acoustic receivers placed within 5 main habitat types: muddy areas, reef patches, macroalgae, rocky reefs, and mangroves. Daily and seasonal locations of the turtles were estimated using a positioning estimation algorithm to determine the site fidelity and habitat use within the study area. Large juveniles ([≥] 65 CCL) were detected disproportionally in the macroalgae habitat during the upwelling season (43.9% detections) from December - April, and in the reef patch habitat during the non-upwelling season (36.0%) from May to November. Small juveniles (< 65 cm CCL) had more detections in the reef patch habitat during both seasons (Upwelling: 35.4%, non-upwelling: 45.4%) relative to other habitats sampled. More than half of the turtles monitored (67%) showed strong site fidelity to the study area, ranging from 68.9 to 100% from October 2020 to September 2022. Our results suggest that juvenile green sea turtles, particularly larger individuals, have a strong association with coral / rocky reef patches and macroalgae habitats, similar to adults. Our finding suggested that protecting similar habitats in other areas along the Central American coast will help rebuild the Eastern Pacific Ocean green sea turtle population.

ecology↗

bioRxiv2022

Population structure and genetic connectivity of the scalloped hammerhead shark (Sphyrna lewini) across nursery grounds from the Eastern Tropical Pacific: implications for management and conservation

Defining demographically independent units and understanding gene flow between them is essential for managing and conserving exploited populations. The scalloped hammerhead shark, Sphyrna lewini, is a coastal semi-oceanic species found worldwide in tropical and subtropical waters. Pregnant females give birth in shallow coastal estuarine habitats that serve as nursery grounds for neonates and small juveniles, and adults move offshore and become highly migratory. We evaluated the population structure and connectivity of S. lewini in coastal areas across the Eastern Tropical Pacific (ETP) using both sequences of the mitochondrial DNA control region (mtCR) and nuclear-encoded microsatellite loci. The mtCR defined two genetically discrete geographic groups: the Mexican Pacific and the central-southern Eastern Tropical Pacific (Guatemala, Costa Rica, Panama, and Colombia). Overall, the mtCR data showed low levels of haplotype diversity ranged from 0.000 to 0.608, while nucleotide diversity ranged from 0.000 to 0.0015. A more fine-grade population structure analysis was detected using microsatellite loci where Guatemala, Costa Rica, and Panama differed significantly. Genetic diversity analysis with nuclear markers revealed an observed heterozygosity ranging from 0.68 to 0.71 and an allelic richness from 5.89 to 7.00. Relatedness analysis revealed that individuals within nursery areas were more closely related than expected by chance, suggesting that S. lewini may exhibit reproductive philopatric behaviour within the ETP. Findings of at least two different management units, and evidence of philopatric behaviour call for intensive conservation actions for this critically endangered species in the ETP.

genetics↗

bioRxiv2020

A first assessment of the distribution and abundance of large pelagic species at Cocos Ridge seamounts (Eastern Tropical Pacific) using drifting pelagic baited remote cameras

Understanding the link between seamounts and large pelagic species (LPS) is critical for guiding management and conservation efforts in open water ecosystems. The seamounts along the Cocos Ridge in the Eastern Tropical Pacific (ETP) are thought to play a critical role for LPS moving between Cocos Island (Costa Rica) and Galapagos Islands (Ecuador). However, to date, research efforts to understand pelagic community structure beyond the borders of these oceanic Marine Protected Areas (MPAs) have been limited. This study used drifting-pelagic baited remote underwater video stations (BRUVS) to characterize the distribution and relative abundance of LPS at Cocos Ridge seamounts. Our drifting-pelagic BRUVS detected a total of 21 species including sharks, large teleosts, small teleosts, dolphins and one sea turtle, of which 4 are threatened species. Relative abundance and richness of LPS was significantly higher at shallow seamounts (<400m) compared to deeper ones (>400m) suggesting that seamount depth could be an important driver structuring LPS assemblages along the Cocos Ridge. Our cameras provided the first visual evidence of the schooling behaviour of S. lewini at two shallow seamounts outside the protection limits of Cocos and Galapagos Islands. However, further research is still needed to demonstrate a positive association between LPS and Cocos Ridge seamounts. Our findings showed that drifting pelagic BRUVS are an effective tool to survey LPS in fully pelagic ecosystems of the ETP. This study represents the first step towards the standardization of this technique throughout the region.

ecology↗