Biology subjects

Robak, D.

Publications and source records attributed to Robak, D..

3 recordsLinked to original sources

bioRxiv2025

piRAT: piRNA Annotation Tool for annotating, analyzing, and visualizing piRNAs

MotivationIn recent years, Piwi-interacting RNAs (piRNAs) have been found to be involved in different biological roles beyond their initially identified role of protecting the germline genome. However, there is a lack of robust computational tools that facilitate their accurate annotation, analysis, and visualization, which would allow large-scale analysis of piRNAs across samples and species. ResultsWe present piRAT, a piRNA Annotation Tool for annotating both primary piRNAs from piRNA clusters and secondary piRNAs generated via the ping-pong cycle, using small RNA-seq data mapped to a genome. piRAT also performs descriptive analyses and generates comprehensive reports with visualizations to support annotations and provide further insights. Availability and ImplementationpiRAT is available on GitHub (https://github.com/ylla-lab/piRAT), implemented in Python 3, and released under MIT license. It is also installable through pip, conda, and available as Docker container (https://hub.docker.com/u/domrob). The Python implementation runs natively on Linux and in WSL in Windows, and the Docker image can run on Linux, Windows, and MacOS.

bioinformatics↗

bioRxiv2024

The Septin Cytoskeleton is a Novel Regulator of Intestinal Epithelial Barrier Integrity and Mucosal Inflammation

Background and AimsIntestinal epithelial barrier-integrity is essential for human health, and its disruption induces and exacerbates intestinal inflammatory disorders. While the cytoskeleton is critical for maintaining gut barrier-integrity, the role of the septins- the newest family of cytoskeletal proteins- is unknown. To address this knowledge gap, we evaluate the role of SEPT9- a critical component of the septin-cytoskeleton- in intestinal epithelial cell (IEC) barrier permeability and inflammation. MethodsWe developed SEPT9-NeonGreen knockin mice, inducible intestinal epithelial cell (IEC)-specific SEPT9 knockout (KO) mice, and SEPT9-KO human IEC lines. SEPT9 localization was analyzed using super-resolution microscopy. Barrier-integrity was assessed via transepithelial electrical resistance, FITC-dextran flux, and visualization of tight junction (TJ) and adherens junction (AJ) proteins. Dextran sodium sulfate-induced experimental colitis was evaluated in control and KO mice through measuring cytokine expression, immune cell infiltration, and IEC death. SEPT9 expression was examined in intestinal tissue of IBD patients. ResultsSEPT9 overlapped with TJs and AJs at IEC apical junctions. SEPT9 loss resulted in a leaky epithelial barrier due to mislocalization of junctional proteins. SEPT9 interacted with non-muscle myosin IIC (NMIIC) at the IEC apical-junctional actomyosin belt, and its ablation displaced NMIIC from IEC junctions. Loss of NMIIC also caused barrier disruption. SEPT9 KO mice exhibited increased susceptibility to experimental-colitis. SEPT9 expression was significantly reduced in intestinal mucosa of IBD patients. ConclusionSEPT9 regulates intestinal barrier integrity, supporting TJ and AJ assembly through NMIIC recruitment to the actomyosin belt. SEPT9 safeguards the intestinal mucosa during acute inflammation, and its reduced expression in IBD suggests a loss of this protective function. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=126 SRC="FIGDIR/small/629767v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@5141dcorg.highwire.dtl.DTLVardef@bae524org.highwire.dtl.DTLVardef@19c8eaorg.highwire.dtl.DTLVardef@d5b218_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

bioRxiv2024

Tear secretion via a paracellular pathway in lacrimal gland is regulated by myosin-mediated modulation of tight junction permeability

"Dry eye", characterized by symptoms of ocular discomfort and visual disturbances due to decreased tear secretion, affects 16 million Americans. Yet, there is currently no cure for dry eye as the mechanistic details of water secretion in the tear-producing lacrimal gland have not been fully elucidated. While a transcellular water secretion pathway via water channels like AQP5 has been reported, the existence and function of a paracellular pathway via tight junctions between epithelial cells remains controversial. The actomyosin cytoskeleton localizes to the apical junctions of epithelial cells across organs and regulates tight junction integrity. Here, we report that non-muscle myosin IIC (NMIIC) is enriched at apical junctions of ductal epithelial cells in the lacrimal gland, leading us to hypothesize that NMIIC regulates tear secretion through modulation of tight junction permeability. Consistent with this hypothesis, we found that tear volume after carbachol stimulation was significantly increased in mice lacking NMIIC, and levels of the tight junction protein ZO-1 were significantly reduced. Furthermore, pharmacological activation of NMIIC by 4-Hydroxyacetophenone in wildtype mice significantly inhibited tear secretion. In summary, our findings reveal a paracellular water secretion pathway in the lacrimal gland, which is regulated by NMIIC-mediated modulation of ductal cell tight junctional permeability, and can be targeted by small molecules. Significance StatementWhile dry eye affects more than 16 million Americans, there is currently no cure as the mechanisms underlying tear secretion are incompletely understood. Here, we report first evidence for the existence and function of a paracellular water pathway, in which water flows between cells, in the lacrimal gland. We also show that this pathway is directly regulated by the modulation of tight junction permeability by non-muscle myosin IIC (NMIIC). This study thus identifies a new mechanism for exocrine secretion, which can be targeted towards developing treatments for dry eye/mouth syndrome.

physiology↗