Biology subjects

Sanchez, V.

Publications and source records attributed to Sanchez, V..

8 recordsLinked to original sources

bioRxiv2026

EphA3 couples attractive guidance to persistent retinal axon growth through modulation of EphA4 forward signaling in a plasma membrane cholesterol-dependent manner

Topographic mapping requires retinal axons not only to avoid inappropriate targets but also to advance directionally through permissive and attractive territories. Using chick retinal ganglion cells in stripe and Dunn chamber gradient assays, we investigated how extracellular EphA3 coordinates the directional guidance and growth dynamics of nasal axons. Nasal axons preferentially grew on EphA3-containing stripes and turned toward increasing concentrations of EphA3 in soluble gradients. EphA3 also increased axonal growth velocity, primarily by prolonging extension phases and reducing growth interruptions rather than by increasing maximal extension-phase velocity. Pharmacological inhibition of EphA4 enhanced axonal extension but abolished EphA3-dependent attraction, indicating that basal EphA4 activity is required for spatial guidance even though EphA4 signaling can constrain axonal advance. Plasma membrane cholesterol depletion altered basal growth dynamics and attenuated EphA3-dependent turning and extension persistence. Together, these findings identify EphA3 as a noncanonical attractive cue that coordinates directional guidance with persistent nasal axon growth through mechanisms dependent on EphA4 activity and membrane cholesterol. They also suggest that sustained EphA4 inhibition may promote axonal growth while compromising topographic targeting.

developmental biology↗

bioRxiv2025

Insights into global antimicrobial resistance dynamics through the sequencing of enteric bacteria from U.S. international travelers

Antimicrobial resistance (AMR) is an urgent threat to public health, but gaps in surveillance limit the detection of emergent novel threats and knowledge about the global distribution of AMR genes. International travelers frequently acquire AMR organisms, and thus may provide a window into AMR dynamics in otherwise poorly monitored regions and environments. To assess the utility of travelers as global AMR sentinels, we collected pre- and post-travel stool samples from 608 travelers, which were screened for the presence of extended-spectrum beta-lactamase producing Enterobacterales, carbapenem-resistant Enterobacterales, and mcr-mediated colistin-resistant Enterobacterales. A total of 307 distinct AMR organisms were sequenced in order to determine genotypic patterns and their association with travel region and behavior. Travel-associated AMR organisms were overwhelmingly E. coli, which exhibited considerable phylogenetic diversity regardless of travel region. However, the prevalence of resistance genes varied by region, with blaCTX-M-55 and blaCTX-M-27 significantly more common in travelers returning from South America and South-Eastern Asia, respectively. Hybrid assembly and plasmid reconstruction revealed the genomic neighborhood of blaCTX-M-55 frequently matched a motif previously linked to animal populations. Contact with animals was also associated with virulence factors in acquired AMR organisms, including carriage of the ColV plasmid, a driver of avian pathogenic E. coli. We identified novel variants of the mcr-1 gene in strains acquired from Western Africa, highlighting the potential for traveler surveillance to detect emerging clinical threats. Ongoing efforts to track travel-acquired organisms could complement existing global AMR surveillance frameworks. ImportanceWe collected pre- and post-travel stool samples from 608 U.S. international travelers, which were screened for the presence of three clinically relevant antimicrobial-resistant organisms, with the goal of understanding the utility of travelers as sentinels for emerging AMR and identifying regional resistance patterns. We sequenced 307 organisms and uncovered significant diversity and geographic heterogeneity in AMR organisms. We found significant differences in certain resistance gene alleles of travelers returning from South America and South-Eastern Asia, traveler contact with animals associated with virulence factors, including a plasmid that is a known driver of avian pathogenic E. coli, and novel variants of the colistin resistance mcr-1 gene in strains acquired from Western Africa. This work emphasizes the value of monitoring international travelers as a proxy for understanding AMR patterns globally and could be an important addition to existing global AMR surveillance frameworks.

genomics↗

bioRxiv2023

Structural Optimization of siRNA Conjugates for Albumin Binding Achieves Effective MCL1-Targeted Cancer Therapy

The high potential for therapeutic application of siRNAs to silence traditionally undruggable oncogenic drivers remains largely untapped due to the challenges of tumor cell delivery. Here, siRNAs were optimized for in situ binding to albumin through C18 lipid modifications to improve pharmacokinetics and tumor delivery. Systematic variation of siRNA conjugates revealed a lead structure with divalent C18 lipids each linked through three repeats of hexaethylene glycol connected by phosphorothioate bonds. Importantly, we discovered that locating the branch site of the divalent lipid structure proximally (adjacent to the RNA) rather than at a more distal site (after the linker segment) promotes association with albumin, while minimizing self-assembly and lipoprotein association. Comparison to higher albumin affinity (diacid) lipid variants and siRNA directly conjugated to albumin underscored the importance of conjugate hydrophobicity and reversibility of albumin binding for siRNA delivery and bioactivity in tumors. The lead conjugate increased tumor siRNA accumulation 12-fold in orthotopic mouse models of triple negative breast cancer over the parent siRNA. When applied for silencing of the anti-apoptotic oncogene MCL-1, this structure achieved approximately 80% MCL1 silencing in orthotopic breast tumors. Furthermore, application of the lead conjugate structure to target MCL1 yielded better survival outcomes in three independent, orthotopic, triple negative breast cancer models than an MCL1 small molecule inhibitor. These studies provide new structure-function insights on optimally leveraging siRNA-lipid conjugate structures that associate in situ with plasma albumin for molecular-targeted cancer therapy.

bioengineering↗

bioRxiv2022

Cytomegalovirus infection in newborn mice alters cerebellar development by lengthening G1/S phases of cerebellar granule cell precursors during postnatal cerebellar development

Human cytomegalovirus (HCMV) infection of the developing central nervous system (CNS) in infants infected in utero can lead to a variety of neurodevelopmental disorders. Although the link between HCMV infection and neurodevelopmental deficits is widely recognized, underlying mechanisms leading to altered neurodevelopment remain poorly understood. We have previously described a murine model of congenital HCMV infection in which murine CMV (MCMV) spreads hematogenously and establishes a focal infection in the brain of newborn mice. Infection results in the disruption of cerebellar cortical development characterized by reduced cerebellar size, but paradoxically, an increase in the number of cerebellar granule cell precursors (GCPs) in the external granular layer (EGL) of the cerebellar cortex. This increased number of GCPs in the EGL is associated with abnormal cell cycle progression and decreased GCP migration from EGL and IGL. In the current study, we demonstrated that MCMV infection led to prolonged G1- and S-phases of the GCP cell cycle and increased cell cycle exit. Treatment with TNF neutralizing antibody partially normalized the cell cycle progression of GCPs. Collectively, our results argue that inflammation can alter GCP proliferation and lead to premature exit from the cell cycle resulting in reduced cerebellar size in MCMV-infected mice. These findings provide insight into mechanisms of altered brain development of fetuses infected with HCMV and possibly, other infectious agents that induce inflammation during neurodevelopment.

developmental biology↗

bioRxiv2022

An Analysis of Protein Language Model Embeddings for Fold Prediction

The identification of the protein fold class is a challenging problem in structural biology. Recent computational methods for fold prediction leverage deep learning techniques to extract protein fold-representative embeddings mainly using evolutionary information in the form of multiple sequence alignment (MSA) as input source. In contrast, protein language models (LM) have reshaped the field thanks to their ability to learn efficient protein representations (protein-LM embeddings) from purely sequential information in a self-supervised manner. In this paper, we analyze a framework for protein fold prediction using pre-trained protein-LM embeddings as input to several fine-tuning neural network models which are supervisedly trained with fold labels. In particular, we compare the performance of six protein-LM embeddings: the LSTM-based UniRep and SeqVec, and the transformer-based ESM-1b, ESM-MSA, ProtBERT, and ProtT5; as well as three neural networks: Multi-Layer Perceptron (MLP), ResCNN-BGRU (RBG), and Light-Attention (LAT). We separately evaluated the pairwise fold recognition (PFR) and direct fold classification (DFC) tasks on well-known benchmark datasets. The results indicate that the combination of transformer-based embeddings, particularly those obtained at amino acid-level, with the RBG and LAT fine-tuning models performs remarkably well in both tasks. To further increase prediction accuracy, we propose several ensemble strategies for PFR and DFC, which provide a significant performance boost over the current state-of-the-art results. All this suggests that moving from traditional protein representations to protein-LM embeddings is a very promising approach to protein fold-related tasks.

bioinformatics↗

bioRxiv2020

Unsupervised protein embeddings outperform hand-crafted sequence and structure features at predicting molecular function

MotivationProtein function prediction is a difficult bioinformatics problem. Many recent methods use deep neural networks to learn complex sequence representations and predict function from these. Deep supervised models require a lot of labeled training data which are not available for this task. However, a very large amount of protein sequences without functional labels is available. ResultsWe applied an existing deep sequence model that had been pre-trained in an unsupervised setting on the supervised task of protein function prediction. We found that this complex feature representation is effective for this task, outperforming hand-crafted features such as one-hot encoding of amino acids, k-mer counts, secondary structure and backbone angles. Also, it partly negates the need for deep prediction models, as a two-layer perceptron was enough to achieve state-of-the-art performance in the third Critical Assessment of Functional Annotation benchmark. We also show that combining this sequence representation with protein 3D structure information does not lead to performance improvement, hinting that three-dimensional structure is also potentially learned during the unsupervised pre-training. AvailabilityImplementations of all used models can be found at https://github.com/stamakro/GCN-for-Structure-and-Function. Contactameliavm@ugr.es Supplementary informationSupplementary data are available online.

bioinformatics↗

bioRxiv2019

Viral manipulation of functionally distinct neurons from mice to humans

Recent success in identifying gene regulatory elements in the context of recombinant adeno-associated virus vectors have enabled cell type-restricted gene expression. However, within the cerebral cortex these tools are presently limited to broad classes of neurons. To overcome this limitation, we developed a strategy that led to the identification of multiple novel enhancers to target functionally distinct neuronal subtypes. By investigating the regulatory landscape of the disease gene Scn1a, we identified enhancers that target the breadth of its expression, including two that are selective for parvalbumin and vasoactive intestinal peptide cortical interneurons. Demonstrating the functional utility of these elements, we found that the PV-specific enhancer allowed for the selective targeting and manipulation of these neurons across species, from mice to humans. Finally, we demonstrate that our selection method is generalizable to other genes and characterize four additional PV-specific enhancers with exquisite specificity for distinct regions of the brain. Altogether, these viral tools can be used for cell-type specific circuit manipulation and hold considerable promise for use in therapeutic interventions.

neuroscience↗

bioRxiv2019

Ingested insecticide to control Aedes aegypti: Developing a novel dried attractive toxic sugar bait device for intra-domiciliary control

BackgroundIllnesses transmitted by Aedes aegypti (Linnaeus, 1762) such as dengue, chikungunya and Zika comprise a considerable global burden; mosquito control is the primary public health tool to reduce disease transmission. Current interventions are inadequate and insecticide resistance threatens the effectiveness of these options. Dried attractive bait stations (DABS) are a novel mechanism to deliver insecticide to Ae. aegypti. The DABS are a high-contrast 28 inch2 surface coated with dried sugar-boric acid solution. Ae. aegypti are attracted to DABS by visual cues only, and the dried sugar solution elicits an ingestion response from Ae. aegypti landing on the surface. The study presents the development of the DABS and tests of their impact on Ae. aegypti mortality in the laboratory and a series of semi-field trials. MethodsWe conducted multiple series of laboratory and semi-field trials to assess the survivability of Ae. aegypti mosquitoes exposed to the DABS. For laboratory experiments we assessed the lethality, the killing mechanism, and the shelf life of the device through controlled experiments. In the semi-field trials, we released laboratory-reared female Ae. aegypti into experimental houses typical of peri-urban tropical communities in South America in three trial series with six replicates each. Laboratory experiments were conducted in Quito, Ecuador, and semi-field experiments were conducted in Machala, Ecuador - an area with abundant wild populations of Ae. aegypti and endemic arboviral transmission. ResultsIn the laboratory, complete lethality was observed after 48 hours regardless of physiological status of the mosquito. The killing mechanism was determined to be through ingestion, as the boric acid disrupted the gut of the mosquito. In experimental houses, total mosquito mortality was greater in the treatment house for all series of experiments (p<0.0001). ConclusionsThe DABS devices were effective at killing female Ae. aegypti under a variety of laboratory and semi-field conditions. DABS are a promising intervention for interdomiciliary control of Ae. aegypti and arboviral disease prevention.

ecology↗