Biology subjects

Kalina, J.

Publications and source records attributed to Kalina, J..

3 recordsLinked to original sources

bioRxiv2026

The Drosophila Secretome

Secreted proteins are synthesized within the cell and actively transported outside, where they contribute to development, physiology, immunity, and cellcell communication. In Drosophila melanogaster, many secreted signaling pathways are evolutionarily conserved, making this species a powerful model for studying human development, cancer, neurobiology, and immune regulation. To assemble the Drosophila secretome, we systematically analyzed all fly protein sequences with computational tools, integrating FlyBase, UniProt and Gene Ontology annotations, and incorporating large-scale proteomics datasets. We identified 4,831 genes encoding putative secreted proteins, assigned confidence scores based on the type and strength of supporting evidence, and generated an online resource (www.flyrnai.org/apps/fly_secretome/) for exploring these data. Comparison with the human secretome shows that 54% of Drosophila secretome genes are conserved in the human genome and of these, 83% are annotated as secreted in human. In addition, comparison with Drosophila single-cell transcriptomic data revealed that secreted proteins are more tissue-specific than other genes. Finally, we demonstrate the utility of this resource by analyzing changes in expression of genes encoding putative secreted proteins during aging based on snRNA-seq datasets from the Aging Fly Cell Atlas.

genetics↗

bioRxiv2025

A Multiresolution Hierarchical Approach to Peak Picking for High Resolution Mass Spectrometry Data Analysis

MotivationAccurate peak detection is a critical first step in high-resolution mass spectrometry (HRMS) data analysis. Most existing tools rely on centroiding and grid-based assumptions, which simplify the raw profile data at the cost of information loss and reduced detection accuracy. ResultsWe present MRH, a novel peak detection method that operates directly on raw HRMS data using a hierarchical, multi-resolution decomposition of the (RT, m/z) space. Peaks are identified within resolution-dependent regions of interest using image-processing techniques, and an ambiguity score is introduced to quantify detection confidence. Benchmarking against widely used methods (apLCMS, centWave, and gridmass) shows that MRH consistently achieves higher F1 scores across concentrations, particularly excelling at low concentrations where competing tools fail. MRH also provides accurate localization of peaks and low ambiguity in detections, highlighting both robustness and precision. AvailabilityA proof-of-concept implementation of MRH and the evaluation dataset are freely available at https://github.com/VojtechBarton/MRH.

bioinformatics↗

bioRxiv2024

Generation and initial characterization of in vivo knockout of tetherin/BST2 in chicken

Tetherin/BST2 is an antiviral restriction factor initially described in mammals. It is active against multiple enveloped viruses at the budding phase, where it is able to physically link the budding virions to the virus-producing cell. We and others have previously identified tetherin orthologs in birds, and characterized the antiviral activity and interferon-inducibility of chicken tetherin. In this work, we have generated an in vivo model of tetherin absence in chicken by CRISPR/Cas9 modification of chicken primordial germ cells (PGC). The modified PGCs were transplanted into roosters with suppressed endogenous spermatogenesis, and transgenic (tetherin knockout) progeny was obtained by further crosses. The viability and phenotype of tetherin knockout animals did not differ from wild type chicken. In more detailed investigation, flow cytometry based differential white blood cell count revealed an increased number of heterophils in tetherin knockouts. Upon challenge with avian sarcoma and leukosis virus (ASLV), a prototypic avian retrovirus, we detected increase in viremia at days 6 and 13 post infection in tetherin knockout animals. The increased virus susceptibility is consistent with absence of antiviral tetherin. In summary, we introduce a new in vivo knockout model of chicken antiviral gene tetherin. These animals can be used in further characterizations of avian antiviral defenses and also to define thus far unknown physiological effects of tetherin in birds.

molecular biology↗