Biology subjects

Pop, C.

Publications and source records attributed to Pop, C..

5 recordsLinked to original sources

bioRxiv2026

The Impact of Small-group Education on Student Wellbeing in Undergraduate Biology: a Student Perspective on Self-Determination Theory

Alarming reports about mental health have raised awareness of student wellbeing in STEM Education. Self-Determination Theory (SDT) implies that wellbeing can be improved by fulfilling the needs for autonomy, competence and relatedness. Educational design elements such as small-group teaching, peer feedback and offering a low-stakes practice environment can help fulfill these SDT needs. These elements were applied in a new academic skills course in our undergraduate Biology program. Here, we investigated how this affected the students sense of autonomy, competence and relatedness, and whether this was related to wellbeing. First, a survey among 48 students confirmed that student wellbeing is positively correlated to SDT fulfillment. Next, group interviews with students revealed that wellbeing is mostly dependent on relatedness, which is facilitated through small-group teaching in the first semester. Furthermore, students reported that (1) relatedness evolves through bonding with peers over the shared experience of struggle, (2) competence requires (peer) feedback and opportunities for growth, especially in laboratory coursework and (3) a structured, low-stakes environment supports competence, but without optimal challenge, also undermines a sense of autonomy. This illustrates how students perceive the effects of small-group educational activities on their wellbeing through the lens of Self-Determination Theory.

scientific communication and education↗

bioRxiv2026

A novel IL-1β reporter assay identifies tolcapone as a caspase-1 suppressor targeting pyroptosis in endotoxemia

Unconventional protein secretion mediated by gasdermin D (GSDMD) pores is essential for the release of pro-inflammatory cytokines such as interleukin-1{beta} (IL-1{beta}), a major driver of many inflammatory pathologies. Despite extensive investigation over the years, discovery of IL-1{beta} secretion modulators has been hindered by the lack of robust, scalable experimental platforms. To date, IL-1{beta} related studies largely rely on primary cells and animal models, suitable for mechanistic studies but not readily scalable for high-throughput applications. Here, we engineered a CRISPR-based reporter cell line that allows quantitative monitoring of endogenous IL-1{beta} secretion while preserving the physiologically relevant inflammasome signaling. This platform faithfully recapitulated the response of primary macrophages to pathogen-associated molecular pattern (PAMPs) stimulation and supported the screening of an FDA-approved drug library comprising 1,398 compounds. Form this screen, we identified tolcapone as a potent inhibitor of IL-1{beta} secretion, reducing cytokine release by more than 80% across the screening pipeline. Mechanistically, tolcapone suppressed caspase-1 activation, thereby limiting GSDMD cleavage, pore formation, and the downstream maturation and secretion of IL-1{beta} and IL-18 in vitro. In vivo, tolcapone administration attenuated the acute inflammatory response in a lipopolysaccharide-induced endotoxemia model. Together, these findings establish our reporter platform as a robust tool for discovery of endogenous IL-1{beta} secretion modulators and identify tolcapone as a promising inhibitor of inflammasome-driven immune pathology.

immunology↗

bioRxiv2024

PopGenPlayground: a population genomics analysis pipeline

BackgroundPopulation genomic projects are essential in the current drive to map the genome diversity of human populations across the globe. Various barriers persist hindering these efforts, and the lack of bioinformatic expertise and reproducible standardized population-scale analysis is one of the major challenges limiting their discovery potential. Scalable, automated, user-friendly pipelines can help researchers with minimum programming skills to tackle these issues without extensive training. ResultsPopGenPlayground (PGP), is a streamlined, single-command computation pipeline designed for human population genomics analysis based on Snakemake workflow management system. Developed to automate secondary analysis of a previously published national genome project, it leverages the publicly available genomic databases for comparative analysis and annotation of variant calls. ConclusionsPGP presents a multi-platform robust population analysis pipeline, that reduces the time and the expertise levels to perform the main core of population analysis for a national genome project. PGP provides a comprehensive secondary analysis tool and can be used to perform analysis on a personal computer or using a remote high-performance computing platform.

bioinformatics↗

bioRxiv2024

ROUA Database: 300 Human Genomes from the border of Ukraine and Romania

We present a multi-layered data source (ROUA Database) providing the results of Whole Genome Sequencing of two human populations in the Carpathian Mountains region, specifically Ukraines Transcarpathia and Romanias Satu Mare and Baia Mare provinces, areas previously underexplored in population genomics. The database contains the raw and annotated files of the whole genome sequences from 300 individuals from these regions, including annotations of common and unique genetic variants following a sampling protocol designed to capture the genetic diversity of Ukrainians and Romanians, including minority groups like Wallachians and Roma. The data is hosted on a dedicated web resource. We provide information on how to access to results of primary and secondary analysis of the data, including comparative analysis with previously published populations from Ukraine, and populations from International Genome Sample Resource and Human Genome Diversity Project. The free research access to this database is contributing to growing understanding of human genetic diversity in Central Europe. This effort emphasizes the potential for reuse of the generated data, advocating for open access to support future research in genomics, bioinformatics, and personalized medicine.

genomics↗

bioRxiv2017

Learning RNA secondary structure (only) from structure probing data

1. Introduction 1. Introduction 2. Methods 3. Experiments 4. Discussion References The structure of an RNA molecule is critical to its function. Structured regions in an RNA molecule permit or impede the binding of proteins and small molecules, resulting in downstream effects on gene expression [24, 16]. However, accurate determination of RNA structure is an involved process, requiring tedious experimentation [8, 1, 10] or careful analysis of evolutionary constraints [9]. As such, several computational methods have been developed to determine RNA structure in silico. In this work, we focus on methods that predict an RNAs secondary structure - the set of complementary Watson-Crick basepairs. These methods may be broadly ...

bioinformatics↗