Biology subjects

Amaral, M.

Publications and source records attributed to Amaral, M..

3 recordsLinked to original sources

bioRxiv2025

Rotiferometer: an automated system for quantification of rotifer cultures

Accurate quantification and continuous monitoring of Brachionus plicatilis L. rotifer cultures are essential for aquaculture and aquatic animal research laboratories. Manual counting methods are labor-intensive, error-prone, and inefficient for large-scale operations, necessitating automated solutions. This study presents the Rotiferometer, an automated and cost-effective system that integrates mechanical design, deep learning, and automation for precise rotifer detection, classification and counting. Using a YOLOv8 model, the system achieves a mean average precision (mAP@0.5) of 94.7% in distinguishing gravid and non-gravid rotifers. It proceeds by scanning a 1 mL Sedgewick Rafter slide under 3 minutes, ensuring rapid and accurate enumeration. A strong correlation was observed between manual and Rotiferometer counts, (with R2 values of 0.9729 and 0.9868 for gravid and non-gravid rotifers, respectively), confirming the system s accuracy. Additionally, the analysis of operator variability using the Rotiferometer delivered consistent results regardless of the user, minimizing the need for specialized expertise. Finally, a 45-day monitoring experiment with the Rotiferometer effectively tracked rotifer population changes, identifying key phases of growth, decline, and recovery. These results highlight the device s potential to enhance rotifer culture management by providing real-time, reliable, and automated monitoring, thereby optimizing aquaculture productivity and research efficiency.

bioengineering↗

bioRxiv2024

Stability vs flexibility: reshaping monolayer and bilayer archaeal membranes in silico

Cellular membranes differ across the tree of life. In most bacteria and eukaryotes, single-headed lipids self-assemble into flexible bilayer membranes. By contrast, thermophilic archaea tend to possess bilayer lipids together with double-headed, monolayer spanning bolalipids, which are thought to enable cells to survive in harsh environments. Here, using a minimal computational model for bolalipid membranes, we explore the trade-offs at play when forming membranes. We find that flexible bolalipids form membranes that resemble bilayer membranes because they are able to assume a U-shaped conformation. Conversely, rigid bolalipids, which resemble the bolalipids with cyclic groups found in thermophilic archaea, take on a straight conformation and form membranes that are stiff and prone to pore formation when they undergo changes in shape. Strikingly, however, the inclusion of small amounts of bilayer lipids in a bolalipid membrane is enough to achieve fluid bolalipid membranes that are both stable and flexible - resolving this trade-off. Our study suggests a mechanism by which archaea can tune the material properties of their membranes as and when required to enable them to survive in harsh environments and to undergo essential membrane remodelling events like cell division.

biophysics↗

bioRxiv2017

A Mathematical Model of the Phosphoinositide Pathway

Phosphoinositides are signaling lipids that constitute a complex network regulating many cellular processes. We propose a computational model that accounts for all known species of phosphoinositides in the plasma membrane of mammalian cells. The model replicates the steady-state of the phosphoinositide pathway and most known dynamic phenomena. Furthermore, sensitivity analysis demonstrates model robustness to moderate alterations in any of the parameters. Model analysis suggest that the greatest contributor to PI(4,5)P2 production is a flux representing the direct transformation of PI into PI(4,5)P2 and is also responsible for the maintenance of this pool when PI(4)P is decreased. PI(5)P is also shown to be a significant source for PI(4,5)P2 production. The model was validated with data from siRNA screens that knocked down the expression of several enzymes in the pathway. The screen monitored the activity of the epithelium sodium channel, ENaC, which is activated by PI(4,5)P2. Moderating ENaC activity can have a therapeutic effect in Cystic Fibrosis (CF) patients. Our model suggests control strategies where the activities of the enzyme PIP5KI or the PI4K+PIP5KI+DVL protein complex are decreased and cause an efficacious reduction in PI(4,5)P2 levels while avoiding undesirable alterations in other phosphoinositide pools.\n\nAbbreviations

systems biology↗