Sarah M Parker | PubMed Health

PubMed2026

Plotgardener App: a graphical interface for publication-ready genomic visualization.

SUMMARY: Plotgardener is an R package used for generating high-quality genomic visualizations. Despite its broad range of functions and versatility, its reliance on code presents a barrier for many potential users. To address this, we developed a macOS desktop application version of Plotgardener that enables users to create publication-ready genomic plots with no programming experience. The application employs a modular architecture comprising an Electron.js backend, a React frontend, and a Python parser that dynamically analyzes the Plotgardener package to ensure interface fields remain synchronized with package updates. By lowering the technical barrier to advanced genomic visualization, the Plotgardener desktop application broadens access to powerful visualization workflows for researchers and clinicians. AVAILABILITY: The current release of the Plotgardener App is an open source macOS desktop application built with Electron (Node.js), featuring a React frontend and a Python-based parser. The download link is available at https://phanstiellab.github.io/plotgardener/articles/guides/plotgardenerApp.html and on Zenodo (doi: https://doi.org/10.5281/zenodo.21684228). The source code is hosted on GitHub at https://github.com/rishabhsvemuri/ThePlotgardenerApp.

Genomics↗

PubMed2004

Adenoviral overexpression of the glutamylcysteine ligase catalytic subunit protects pancreatic islets against oxidative stress.

The catalytic subunit of glutamylcysteine ligase (GCLC) primarily regulates de novo synthesis of glutathione (GSH) in mammalian cells and is central to the antioxidant capacity of the cell. However, GCLC expression in pancreatic islets has not been previously examined. We designed experiments to ascertain whether GCLC is normally expressed in islets and whether it is up-regulated by interleukin-1 beta (IL-1 beta). GCLC expression levels were intermediate compared with other metabolic tissues (kidney, liver, muscle, fat, and lung). IL-1 beta up-regulated GCLC expression (10 ng/ml IL-1 beta, 3.76 +/- 0.86; 100 ng/ml IL-1 beta, 4.22 +/- 0.68-fold control) via the p38 form of mitogen-activated protein kinase and NF kappa B and also increased reactive oxygen species levels (10 ng/ml IL-1 beta, 5.41 +/- 1.8-fold control). This was accompanied by an increase in intraislet GSH/GSSG ratio (control, 7.1 +/- 0.1; 10 ng/ml IL-1 beta, 8.0 +/- 0.5; 100 ng/ml IL-1 beta, 8.2 +/- 0.5-fold control; p < 0.05). To determine whether overexpression of GCLC increases the antioxidant capacity of the islet and prevents the adverse effects of IL-1 beta on glucose-induced insulin secretion, islets were infected with an adenovirus encoding GCLC. IL-1 beta significantly decreased glucose-stimulated insulin secretion (control, 123.8 +/- 17.7; IL-1 beta, 40.2 +/- 3.9 microunits/ml insulin/islet). GCLC overexpression increased intraislet GSH levels and partially prevented the decrease in glucose-stimulated insulin secretion caused by IL-1 beta. These data provide the first report of GCLC expression in the islet and demonstrate that adenoviral overexpression of GCLC increases intracellular GSH levels and protects the beta cell from the adverse effects of IL-1 beta.

Adenoviridae↗