Nezhad, P. E. | Search bioRxiv

bioRxiv2026

A Course-Undergraduate Research Experience (CURE) to explore the effect of structural variants on gene expression in C. elegans balancers

Bioinformatics, a discipline at the crossroads of Biology and Computational Sciences, also referred to as Computational Biology, is nowadays widely spread in research programs. However, implementing any Bioinformatics projects requires the ability to comprehend biological concepts and apply computational approaches, and rare are the undergraduate programs offering such multi-disciplinary training. In addition, understanding the dynamic between Biology research projects and Bioinformatics analyses is challenging with no real-life experience. Course-based undergraduate research experience (CURE) courses are innovative programs that allow more students to acquire research experience and provide the perfect setting to introduce students to applied bioinformatics. As a part of the Bachelor of Health Sciences of the Cumming School of Medicine at the University of Calgary (Canada), a CURE applied bioinformatics was implemented in the Winter of 2023 to 2025. Students investigated the effect of structural variants (SVs, genetic variants larger than 50 bp) on gene expression in the model organism Caenorhabditis elegans (a hermaphrodite 1-mm long roundworm). The students detected and characterized SVs by analyzing genome and transcriptome sequencing data of C. elegans strains called balancers, as they are known to carry large genomic variations balancing regions of the genome by limiting recombination and allowing maintenance of lethal mutations. They used Galaxy, a public web-based supercomputing resource, but also a local High-Performance computing system, and R, to report different effects of SVs on gene expression and splicing. Students research explained the molecular mechanism behind the uncoordinated phenotype caused by the reciprocal translocation eT1(III;V) and uncovered unexpected effects on gene expression on an understudied gene. We evaluated the courses impact on student learning journeys and showed that the CURE favored students understanding of the Bioinformatics field and fostered their research interest. We provide here guidelines to facilitate the CURE implementations to improve access for undergraduate students to bioinformatics research experiences.

bioinformatics↗

bioRxiv2025

Aging-enhanced accumulation of fibroblasts excludes oligodendrocytes in demyelinated lesions

Fibroblast dysregulation contributes to pathological fibrosis and aberrant repair. Emerging evidence suggest that fibroblasts accumulate in lesions following central nervous system injury, but whether and how they influence oligodendrocyte repair responses, including in aging, is uncertain. Here we report that fibroblasts accumulate in the parenchyma of spinal cord white matter lesions of 6 - 10 week old young mice after lysolecithin-induced demyelination. This was first observed through immunofluorescence microscopy that employed several markers attributed to fibroblasts, including platelet-derived growth factor-{beta}, collagen type 11, -smooth muscle actin, periostin and fibronectin; and by the use of platelet-derived growth factor-{beta} TdTomato reporter transgenic mice. Single-nucleus and spatial transcriptomics of lysolecithin lesions established the presence of fibroblasts in lysolecithin lesions and delineated them from closely related pericytes. CellChat ligand - receptor analyses highlight fibroblasts in the lysolecithin environment as a major source of input of signals for microglia/macrophages and oligodendrocyte precursor cells, with numerous reciprocal interactions. The infiltration of fibroblasts was promoted by microglia/macrophages, as anticipated by their temporal representation in lysolecithin lesions, and by tissue culture experiments where the migration of fibroblasts was enhanced by macrophages. Of particular relevance to spontaneous regenerative events in lysolecithin demyelination, areas of fibroblast accumulation were devoid of oligodendrocyte precursor cells. In tissue culture, oligodendrocyte precursor cells were excluded from fibroblast domains. Moreover, fibroblast accumulation after lysolecithin injury was enhanced with increasing age, a known detriment to the capacity to remyelinate after injury, and exclusion of oligodendrocyte precursor cells from fibroblast areas of 48 - 52 week mice exceeds that occurring in younger 6 - 10 weeks animals. Finally, by mining a publicly available single-nucleus RNA database of multiple sclerosis, we found fibroblasts in the edge of chronic active and chronic inactive lesions and in lesion core, and fewer in periplaque or normal white matter. We identified several communication networks between fibroblasts, microglia/macrophages and oligodendrocyte precursor cells in these MS lesions. Our collective results demonstrate a role of fibroblasts in demyelination-associated neuropathology, which is exacerbated by aging, and highlight the importance of regulating fibroblasts to promote effective CNS repair.

neuroscience↗