Biology subjects

Betegon-Putze, I.

Publications and source records attributed to Betegon-Putze, I..

4 recordsLinked to original sources

bioRxiv2024

TOTEM: A web TOol for Tissue-EnrichMent analysis on gene lists

Analysis of spatiotemporal patterns of gene expression is crucial to decode biological systems responses. High-throughput sequencing allows in-depth transcriptome analyses and experimental designs, providing valuable reference expression atlases. Specifically, testing overrepresentations of tissue-specific genes based on these atlases can provide valuable insights; however, such an approach is not accessible to inexperienced users. Here, we introduce TOTEM (TOol for Tissue-EnrichMent), a web tool designed to calculate enrichment values per tissue by identifying tissue-specific genes from an organ/organism of interest given a user gene list. Results are visually represented, and users gene classified. The utility of TOTEM is manifest when using integrated single cell expression atlases, enabling the study of complicated tissues, with the maximum possible resolution. Its effectiveness is validated by the study of BRL3 role in stress specifically from the vascular tissues. Finally, TOTEMs modular design allows for continual integration of new experiments. TOTEM can be freely accessed at: https://totemwebtool.com.

plant biology↗

bioRxiv2021

Self-confined expression in the Arabidopsis root stem cell niche

Stem cell niches are local microenvironments that preserve their unique identity while communicating with adjacent tissues. In the primary root of Arabidopsis thaliana, the stem cell niche comprises the expression of two transcription factors, BRAVO and WOX5, among others. Intriguingly, these proteins confine their own gene expression to the niche, as evidenced in each mutant background. Here we propose through mathematical modeling that BRAVO confines its own expression domain to the stem cell niche by attenuating its WOX5-dependent diffusible activator. This negative feedback drives WOX5 action to be spatially restricted as well. The results show that WOX5 diffusion and sequestration by binding to BRAVO is sufficient to drive realistic confined BRAVO expression at the stem cell niche. We propose that attenuation of a diffusible activator can be a general mechanism to confine genetic activity to a small region while at the same time maintain signaling within it and with the surrounding cells.

systems biology↗

bioRxiv2020

Precise transcriptional control of cellular quiescence by BRAVO/WOX5 complex in Arabidopsis roots

Root growth and development are essential features for plant survival and the preservation of terrestrial ecosystems. In the Arabidopsis primary root apex, stem-cell specific transcription factors BRAVO and WOX5 co-localize at the Quiescent Center (QC) cells, where they repress cell division so that these cells can act as a reservoir to replenish surrounding stem cells, yet their molecular connection remains unknown. Here, by using empirical evidence and mathematical modeling, we establish the precise regulatory and molecular interactions between BRAVO and WOX5. We found that BRAVO and WOX5 regulate each other besides forming a transcription factor complex in the QC necessary to preserve overall root growth and architecture. Our results unveil the importance of transcriptional regulatory circuits at the quiescent and stem cells to the control of organ initiation and growth of plant tissues.

plant biology↗

bioRxiv2018

MyROOT: A novel method and software for the semi-automatic measurement of plant root length

Root analysis is essential for both academic and agricultural research. Despite the great advances in root phenotyping and imaging however, calculating root length is still performed manually and involves considerable amounts of labor and time. To overcome these limitations, we have developed MyROOT, a novel software for the semi-automatic quantification of root growth of seedlings growing directly in agar plates. Our method automatically determines the scale from the image of the plate, and subsequently measures the root length of the individual plants. To this aim, MyROOT combines a bottom-up root tracking approach with a hypocotyl detection algorithm. At the same time as providing accurate root measurements, MyROOT also significantly minimizes the user intervention required during the process. Using Arabidopsis, we tested MyROOT with seedlings from different growth stages. Upon comparing the data obtained using this software with that of manual root measurements, we found that there are no significant differences (t-test, p-value < 0.05). Thus, MyROOT will be of great aid to the plant science community by permitting high-throughput root length measurements while saving on both labor and time.

plant biology↗