Biology subjects

Lopez, Y.

Publications and source records attributed to Lopez, Y..

5 recordsLinked to original sources

bioRxiv2025

The magnitude of cryptic insect diversity in one tropical rainforest

O_LICryptic species represent significant entities in conservation planning and are common among tropical insects. Many studies focusing on cryptic species have been restricted to a narrow taxon and it is not clear whether some insect clades or assemblages may have a greater propensity for cryptic speciation than others. Here, we contrast cryptic diversity among 22 insect assemblages surveyed on Barro Colorado Island (BCI), a tropical rainforest in Panama. C_LIO_LICryptic species were defined as externally indistinguishable from their sister species but with a different barcode index number. We detected 214 cryptic species out of a total of 2,006 species studied (10.6%). The percentage of cryptic species varied greatly among assemblages (0-19%), with half of assemblages devoid of cryptic species, and the highest proportions of cryptics in Pieridae and Formicidae. C_LIO_LIThe percentage of cryptic species was weakly influenced by phylogeny and it was best explained by the local number of species and an index of taxonomic knowledge. Cryptic species were distinguished by an average distance divergence in sequence of 9%, but their ecological characteristics remain unclear. C_LIO_LIAsymptotic estimates indicated that 11.4% of species studied on BCI may be cryptic. Since many of the species-rich insect assemblages occurring on BCI were not considered in this study, this estimate probably represents a lower bound to the true cryptic insect richness on BCI. C_LIO_LIThis significant contribution to biodiversity should not be ignored and, because of apparent low population levels, may be particularly vulnerable to land use and climate changes. C_LI

evolutionary biology↗

bioRxiv2024

Bats from the Colombian Caribbean Reveal a new subtype of Influenza A (H18N12)

Influenza viruses have an excellent capacity for mutation and adaptation in mammalian hosts, which makes them viruses of medical and veterinary importance. Influenzaviruses have been studied mainly in birds but minor in bats. It is unknown whether Chiroptera are reservoirs of influenza viruses. However, circulation in bats showed molecular divergence from H17N10 (Guatemala) and H18N11 (Peru), and they were designated as new subtypes. The study aimed to characterize the influenza A virus detected in the fishing bat Noctilio albiventris. A surveillance study of pathogens of public health interest was carried out; rectal samples were taken from four fishing bats (N. albiventris) captured in Talaigua Nuevo, Bolivar, Colombia. The samples were sequenced by NGS using DNBseq (MGI-G50(R)) and analyzed with bioinformatics tools. Eight viral contigs associated with the Orthomyxoviridae family were obtained. The identified segments showed around 90% similarity with H18N11, except for the neuraminidase (N). The phylogenetic analysis of the N protein showed the appearance of a basal branch to the N11 subtype, and the molecular clock indicates that it does not share a recent common ancestor. 3D modeling indicates that the N protein of N. albiventris presents three mutations (K363R, T242K, and I139V) near the hypothetical active site of the protein. These mutations potentially increase the interaction with the HLA-DR of bats, which could have significant implications for the viruss behavior. The phylogenetic, evolutionary, and antigenic divergence of the N protein of N. albiventris suggests a new subtype called H18N12. Its role as a pathogen must be studied.

bioinformatics↗

bioRxiv2023

CCR3 inhibition suppresses inflammation-driven recruitment of peripheral immune cells to the eye

C-C chemokine receptor type 3 (CCR3) has been linked with age-related macular degeneration (AMD) pathologies. Specifically, its function as an immune modulator in AMD remains unclear. To address this question, we investigated the impact of CCR3 inhibition on inflammation, a key driver of AMD pathologies, by assessing inflammatory cytokines and infiltrating immune cells in two models of ocular inflammation. Mice were orally dosed twice a day with AKST4290, a CCR3 small molecular inhibitor, in the sodium iodate (NaIO3) and myelin oligodendrocyte glycoprotein (MOG) models. A combination of autoradiography and analytical chemistry techniques were used to assess drug concentration and distribution. Bead-based multiplexing technology was used to determine cytokine concentrations, and flow cytometry and immunohistochemistry was used to ascertain ocular immune-cell composition. CCR3 expression was detected in the retinal pigment epithelium (RPE)/choroid complex where AKST4290 was found to preferentially accumulate at sustained levels. In the NaIO3 model, inhibition of CCR3 with AKST4290 significantly decreased both the concentration of specific chemokines and the number of multiple populations of infiltrating peripheral immune cell. Furthermore, effects of CCR3 inhibition on immune cell infiltration were confirmed in the MOG model. These data demonstrate that CCR3 inhibition strongly modulates local inflammation by impacting both cytokine concentrations and immune cell composition in ocular diseases. Moreover, these findings together with the known role of CCR3 in promoting pathologic angiogenesis implicate a pleiotropic role for CCR3 in AMD.

cell biology↗

bioRxiv2023

Multi-representation DeepInsight: an improvement on tabular data analysis

Tabular data analysis is a critical task in various domains, enabling us to uncover valuable insights from structured datasets. While traditional machine learning methods have been employed for feature engineering and dimensionality reduction, they often struggle to capture the intricate relationships and dependencies within real-world datasets. In this paper, we present Multi-representation DeepInsight (abbreviated as MRep-DeepInsight), an innovative extension of the DeepInsight method, specifically designed to enhance the analysis of tabular data. By generating multiple representations of samples using diverse feature extraction techniques, our approach aims to capture a broader range of features and reveal deeper insights. We demonstrate the effectiveness of MRep-DeepInsight on single-cell datasets, Alzheimers data, and artificial data, showcasing an improved accuracy over the original DeepInsight approach and machine learning methods like random forest and L2-regularized logistic regression. Our results highlight the value of incorporating multiple representations for robust and accurate tabular data analysis. By embracing the power of diverse representations, MRep-DeepInsight offers a promising avenue for advancing decision-making and scientific discovery across a wide range of fields.

bioinformatics↗

bioRxiv2019

Somatodendritic HCN channels in hippocampal OLM cells revealed by a convergence of computational models and experiments

Determining details of spatially extended neurons is a challenge that needs to be overcome. The oriens-lacunosum/moleculare (OLM) interneuron has been implicated as a critical controller of hippocampal memory making it essential to understand how its biophysical properties contribute to function. We previously used computational models to show that OLM cells exhibit theta spiking resonance frequencies that depend on their dendrites having hyperpolarization-activated cation channels (h-channels). However, whether OLM cells have dendritic h-channels is unknown. We performed a set of whole-cell recordings of OLM cells from mouse hippocampus and constructed multi-compartment models using morphological and electrophysiological parameters extracted from the same cell. The models matched experiments only when dendritic h-channels were present. Immunohistochemical localization of the HCN2 subunit confirmed dendritic expression. These models can be used to obtain insight into hippocampal function. Our work shows that a tight integration of model and experiment tackles the challenge of characterizing spatially extended neurons.

neuroscience↗