Biology subjects

Guevara, J.

Publications and source records attributed to Guevara, J..

4 recordsLinked to original sources

bioRxiv2026

Point mutations and complex variants impact gene expression and addiction-related behaviors in Heterogeneous Stock rats

While various variants, including single nucleotide polymorphisms (SNPs), small insertions/deletions, short tandem repeats and structural variants, drive individual genetic differences, their influence on gene expression and complex traits remains unclear. We used short- and long-read sequencing to generate a comprehensive variant catalog in Heterogeneous Stock (HS) rats and performed joint cis-expression quantitative trait loci (cis-eQTL) mapping across five brain regions. We found that non-SNP variants accounted for over 50% of lead regulatory associations, many of which were poorly tagged by nearby SNPs using linkage disequilibrium (LD). Comparison between joint and SNP-only analyses showed that over 46% of shared eQTL genes had a non-SNP lead cis-eQTL, and fewer than half were in strong LD with the corresponding lead eSNP. Linking joint cis-eQTLs to complex trait associations identified mechanisms missed by SNP-only approaches, highlighting the importance of incorporating diverse variant types into genetic studies and providing a foundational resource for the HS rat community.

genetics↗

bioRxiv2026

Urbanization effects are trait-specific and city-dependent across a widespread spider's global range

Urban environments impose strong selective pressures through biotic and abiotic factors, driving changes in behavior, physiology, and morphology. Yet, responses vary across taxa and cities, and it remains unclear which traits respond consistently and what factors moderate this variation. We addressed these questions using the widespread European garden spider (Araneus diadematus) as a model, measuring size, color, and web-building traits along urban-rural transects in 22 cities across its distribution range. Using a meta-analytic framework, we assessed how city-specific characteristics influenced trait variation. Urbanization consistently reduced relative abdomen surface area, a proxy for body condition. Exploratory meta-regressions suggest that web-building response was predicted by temperature: compared to their non-urban surroundings, urban webs are larger in colder regions and smaller in warmer regions. In contrast, body size and abdomen brightness varied among cities without clear environmental predictors. These findings show that urbanization effects are trait- and context-dependent, likely influenced by local factors such as heat island intensity, microclimate, or prey availability. Linking within- and between-city variation will improve understanding of species phenotypic responses to urban environments.

ecology↗

bioRxiv2021

Customized de novo mutation detection for any variant calling pipeline: SynthDNM

MotivationAs sequencing technologies and analysis pipelines evolve, DNM calling tools must be adapted. Therefore, a flexible approach is needed that can accurately identify de novo mutations from genome or exome sequences from a variety of datasets and variant calling pipelines. ResultsHere, we describe SynthDNM, a random-forest based classifier that can be readily adapted to new sequencing or variant-calling pipelines by applying a flexible approach to constructing simulated training examples from real data. The optimized SynthDNM classifiers predict de novo SNPs and indels with robust accuracy across multiple methods of variant calling. AvailabilitySynthDNM is freely available on Github (https://github.com/james-guevara/synthdnm) Contactjsebat@ucsd.edu Supplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗

bioRxiv2018

Systemically administered MSCs given 24hrs after osteotomy do not affect bone formation in rat distraction osteogenesis

Distraction osteogenesis is a unique postnatal bone formation employed by orthopaedic surgeons to treat many conditions, however, the overall time to external frame removal can be extensive. Any strategies that accelerate healing would improve patient care. Distraction osteogenesis research in the past decade has shown that direct stem cell implantation enhances new bone formation. Systemic implantation would be more clinically desirable. Systemically delivered stem cells have been shown to home to a mandibular distraction site; however, effects on bone formation have not been studied. Ten-week-old, male Sprague-Dawley rats underwent surgery to implant an external fixator-distractor and an osteotomy was performed. Twenty-four hours postoperatively, each rat received tail vein injections of either saline or 10^6 fluorescently labeled primary mesenchymal stem cells. Animals in the validation groups were euthanized two days after surgery and the femora processed for histology. Animals in the experimental groups were given five days of latency, then the femur was lengthened once daily for five days (0.75mm/day, 3.75mm total). Following four weeks of consolidation, the animals were euthanized and the femora were evaluated by microCT and histology to quantify new bone formation. Labeled stem cells were found at the distraction site in validation animals. However, there were no differences in any bone or soft tissue outcomes. Systemic stem cell administration 24 hours after surgery does not improve DO outcomes. It is possible that the animal model was not challenging enough to discriminate any augmentation provided by stem cells.

bioengineering↗