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Biology subjects

Ferenc, K.

Publications and source records attributed to Ferenc, K..

2 recordsLinked to original sources

Proliferative Capacity and Neural Lineage Commitment of Muller Glia in the Adult Human Retina

BackgroundThe mammalian retina lacks meaningful regenerative capacity, and degeneration usually leads to irreversible vision loss. Although lower vertebrates regenerate retinal neurons through Muller glia, this capacity has generally been considered absent in humans. This study investigated whether defined humoral cues alone are sufficient to unlock a latent neurogenic program in human Muller cells. MethodsLong-term organotypic retinal cultures were established from 39 adult donors. Cultures were treated with FGF-2 and GSK-3 inhibition to assess proliferation across the peripheral and central retina. Cellular responses were evaluated using single-cell transcriptomics and immunohistochemistry. ResultsFGF-2 treatment and GSK-3 inhibition induced robust proliferation across both peripheral and central retina, with 79.09 {+/-} 6.32% of dividing cells identified as Muller glia, some completing multiple cell cycles. Single-cell transcriptomics revealed activation of progenitor-like and neuronal differentiation pathways, whereas immunohistochemistry demonstrated expression of early and late neuronal markers spanning all major retinal lineages. Newly generated cells expressed markers of cone, rod, bipolar, horizontal, amacrine, and ganglion cell identities, together with evidence of early synaptogenesis. ConclusionsThese findings reveal an intrinsic regenerative potential in adult human Muller glia and show that defined humoral cues can activate a latent neurogenic program in these cells. This may have implications for future vision-restoration strategies in degenerative retinal disease.

neuroscience↗

Empirical study on software and process quality in bioinformatics tools

Software quality in computational tools impacts research output in a variety of scientific disciplines. Biology is one of these fields, especially for High Throughput Sequencing (HTS) data, such tools play an important role. This study therefore characterises the overall quality of a selection of tools which are frequently part of HTS pipelines, as well as analyses the maintainability and process quality of a selection of HTS alignment tools. Our findings highlight the most pressing issues, and point to software engineering best practices developed for the improvement of maintenance and process quality. To help future research, we share the tooling for the static code analysis with SonarCloud which we used to collect data on the maintainability of different alignment tools. The results of the analysis show that the maintainability level is generally high but trends towards increasing technical debt over time. We also observed that the development activities on alignment tools are generally driven by very few developers and are not utilising modern tooling to their advantage. Based on these observations, we recommend actions to improve both maintainability and process quality in open source alignment tools. Those actions include improvements in tooling like the use of linters as well as better documentation of architecture and features. We encourage developers to use these tools in order to ease future maintenance efforts, increase user experience, support reproducibility, and ultimately increase the quality of research through increasing the quality of research software tools.

bioinformatics↗