Biology subjects

Devkota, P.

Publications and source records attributed to Devkota, P..

4 recordsLinked to original sources

bioRxiv2026

A Reproducible MFASS Benchmark of Splice-Disruption Predictors Reveals a Shared Exon-Interior Blind Spot

We benchmark four published splicing variant-effect predictors against a multiplexed experimental splicing assay. On 27,733 single-nucleotide variants in and around human exons from MFASS with measured exon-inclusion outcomes, Pangolin is the strongest predictor of splice-disrupting variants (AUROC 0.888, average precision 0.421), ahead of SpliceAI (0.819, 0.321) and SpliceTransformer (0.786, 0.317), with MMSplice fourth (0.758, 0.256); all four exceed the older SPANR model (0.748, 0.228). The ranking reproduces the relative performance reported by the Pangolin authors, a correctness check on the pipeline. A calibrated consensus of the three deep-learning sequence-window predictors, evaluated on an exon-grouped held-out split, does not meaningfully improve over Pangolin alone. Stratifying by distance to the splice site exposes a shared blind spot: all five tools detect disruptions within a few bases of the splice site well, but recall declines sharply in the exon interior, and 19% of disrupting variants are missed by every tool; these shared misses are enriched among variants away from splice sites, and are predominantly exon-interior. MMSplice, the one model built for modular exonic and intronic effects rather than splice-site recognition, shows the same distance-dependent decline, so the blind spot is not an artifact of splice-site-centric architectures. Every number is computed against fixed experimental ground truth and is reproducible from the public dataset and the released code.

bioinformatics↗

bioRxiv2025

The Impact of a Western Diet with High Salt on Metabolic Outcomes in Male C57bl/6J Mice

ObjectiveThe Western diet promotes obesity and metabolic disease by increasing caloric intake and systemic inflammation. The typical Western diet is high in saturated fats, sugars, and salt. In pre-clinical rodent studies, the "Western" diet (also called the high-fat high-sucrose diet (HFHS)) is high in saturated fats and sugars (typically sucrose) but low in salt (<1% salt). As such, we sought investigate the impact of a chronic 3% NaCl Western diet (high-fat, high-sucrose + high salt (HFHS + Salt)) diet on systemic organ metabolism, liver mitochondrial function, and adipose tissue. MethodsThirty-six 8 week-old C57Bl/6J male mice were fed either a low-fat diet (LFD), a HFHS, or a HFHS + Salt diet for 16 weeks. Body weight, body composition, and food intake were monitored weekly. Glucose tolerance tests (GTT) and insulin concentrations were measured after 8 weeks of diet intervention to assess glucose and insulin homeostasis. Mice were euthanized at 16 weeks for liver mitochondrial respiration and tissue analysis. ResultsOver 16 weeks, the HFHS fed group gained significantly more weight than the other diet groups. Liver weights were similar in LFD and HFHS + Salt groups but higher in the HFHS group. Liver triglycerides (TAGs) were also similar between LFD and HFHS + Salt groups, while HFHS had elevated liver TAGs. Inguinal and brown adipose tissue depots were larger in both HFHS and HFHS + Salt vs. LFD. Surprisingly, the gonadal adipose tissue was significantly larger in the HFHS + Salt compared to HFHS and LFD groups - suggesting that a HFHS + Salt exacerbates gonadal adipose expansion more than typical rodent HFHS. Paradoxically, the addition of salt appears to have dampened expression of inflammation related genes (Ccl2 & Adgre1) in adipose tissue compared to HFHS alone. Metabolically, the HFHS+ Salt fed mice showed the highest glucose intolerance, followed by HFHS and then LFD groups. Liver mitochondrial respiration, assessed by changing ATP/ADP ratios, showed the HFHS group with the highest oxygen consumption, followed by HFHS + Salt, then LFD groups, highlighting differences in respiration with additional salt (HFHS vs HFHS + Salt). ConclusionWhile the excess salt mitigated some HFHS effects on weight gain and hepatic lipid accumulation, it exacerbated gonadal adipose expansion and impaired glucose tolerance. HFHS increased mitochondrial respiration, but salt addition appeared to dampen this effect. Dietary salt, within a high-fat/high-sucrose context, has differential impacts on metabolic outcomes compared to HFHS alone, underscoring the need for further research to fully understand how Western diets (high-fat, high-sucrose, and high salt) impact all aspects of metabolic health.

physiology↗

bioRxiv2024

Structural and antigenic characterization of novel and diverse Henipavirus glycoproteins

Henipaviruses, a genus within the Paramyxoviridae family, include the highly virulent Nipah and Hendra viruses that cause reoccurring outbreaks of deadly disease. Recent discoveries of several new Paramyxoviridae species, including the zoonotic Langya virus, have revealed much higher antigenic diversity than currently characterized and prompted the reorganization of these viruses into the Henipavirus and Parahenipavirus genera. Here, to explore the limits of structural and antigenic variation in both genera, collectively referred to here as HNVs, we constructed an expanded, antigenically diverse panel of HNV fusion and attachment glycoproteins from 56 unique HNV strains that better reflects global HNV diversity. We expressed and purified the fusion protein ectodomains and the attachment protein head domains and studied their biochemical, biophysical and structural properties. We performed immunization experiments in mice leading to the elicitation of antibodies reactive to multiple HNV fusion proteins. Cryo-electron microscopy structures of diverse fusion proteins elucidated molecular determinants of differential pre-fusion state metastability and higher order contacts. A crystal structure of the Gamak virus attachment head domain revealed an additional domain appended to the conserved 6-bladed, {beta}-propeller fold. Taken together, these studies expand the known structural and antigenic limits of the HNVs, reveal new cross-reactive epitopes within both genera and provide foundational data for the development of broadly reactive countermeasures.

biochemistry↗

bioRxiv2020

Single-Cell Transcriptomic Analysis Reveals Molecular Diversity of Human Oligodendrocyte Progenitor Cells

Injury and loss of oligodendrocytes can cause demyelinating diseases such as multiple sclerosis. To improve our understanding of oligodendrocyte development, which could facilitate development of remyelination-based treatment strategies, we performed single-cell-transcriptomic-analysis of developing human oligodendrocyte-precursor-cells (hOPCs). We engineered knock-in hESC-reporter lines in which an Identification-and-Purification tag is expressed under control of the endogenous, OPC-specific, PDGFR promoter, and performed time-course single-cell-RNA-sequencing of purified hOPCs. Our analysis uncovered marked transcriptional heterogeneity of PDGFR+ hOPCs and identified regulatory genes and networks that control their differentiation and myelination competence. Pseudotime trajectory analysis revealed two distinct trajectories for the development of oligodendrocytes vs astrocytes from hOPCs. We also identified novel transcription factors and other genes that developing hOPCs potentially use to choose between oligodendrocyte vs astrocyte lineages. In addition, pathway enrichment analysis followed by pharmacological intervention of those pathways confirm that mTOR and cholesterol biosynthesis signaling pathways are involved in maturation of oligodendrocytes from hOPCs.

neuroscience↗