Biology subjects

Brito, A. D.

Publications and source records attributed to Brito, A. D..

3 recordsLinked to original sources

bioRxiv2023

NanoPyx: super-fast bioimage analysis powered by adaptive machine learning

To overcome the challenges posed by large and complex microscopy datasets, we have developed NanoPyx, an adaptive bioimage analysis framework designed for high-speed processing. At the core of NanoPyx is the Liquid Engine, an agent-based machine-learning system that predicts acceleration strategies for image analysis tasks. Unlike traditional single-algorithm methods, the Liquid Engine generates multiple CPU and GPU code variations using a meta-programming system, creating a competitive environment where different algorithms are benchmarked against each other to achieve optimal performance under the user"s computational environment. In initial experiments focusing on super-resolution analysis methods, the Liquid Engine demonstrated an over 10-fold computational speed improvement by accurately predicting the ideal scenarios to switch between algorithmic implementations. NanoPyx is accessible to users through a Python library, code-free Jupyter notebooks, and a napari plugin, making it suitable for individuals regardless of their coding proficiency. Furthermore, the optimisation principles embodied by the Liquid Engine have broader implications, extending their applicability to various high-performance computing fields.

bioinformatics↗

bioRxiv2023

Processive movement of Staphylococcus aureus essential septal peptidoglycan synthases is independent of FtsZ treadmilling and drives cell constriction

Bacterial cell division is mediated by the tubulin-homolog FtsZ, which recruits peptidoglycan (PG) synthesis enzymes to the division site. Septal PG synthases promote inward growth of the division septum, but the mechanisms governing the spatiotemporal regulation of these enzymes are poorly understood. Recent studies on various organisms have proposed different models for the relationship between the movement and activity of septum-specific PG synthases and FtsZ treadmilling. Here, we studied the movement dynamics of conserved cell division proteins relative to the rates of septum constriction and FtsZ treadmilling in the Gram-positive pathogen Staphylococcus aureus. The septal PG synthesis enzyme complex FtsW/PBP1 and its putative activator protein, DivIB, moved processively, around the division site, with the same velocity. Impairing FtsZ treadmilling did not affect FtsW and DivIB velocities or septum constriction rates. Contrarily, inhibition of PG synthesis slowed down or completely stopped both septum constriction and the directional movement of FtsW/PBP1 and DivIB. Our findings support a model for S. aureus in which a single population of processively moving FtsW/PBP1 remains associated with DivIB to drive cell constriction independently of treadmilling FtsZ filaments.

microbiology↗

bioRxiv2023

The role of GpsB in cell morphogenesis of Staphylococcus aureus

For decades, cells of the gram-positive bacterial pathogen Staphylococcus aureus were thought to lack a dedicated elongation machinery. However, S. aureus cells were recently shown to elongate before division, in a process that requires a SEDS (Shape Elongation Division and Sporulation) / PBP (Penicillin Binding Protein) pair for peptidoglycan synthesis, consisting of the glycosyltransferase RodA and the transpeptidase PBP3. In ovococci and rod-shaped bacteria the elongation machinery, known as elongasome, is composed of various proteins besides a dedicated SEDS/PBP pair. To identify proteins involved in the elongation of S. aureus, we screened the Nebraska Transposon Mutant Library, which contains transposon mutants in virtually all non-essential staphylococcal genes, for mutants with modified cell shape. We confirmed the roles of RodA/PBP3 in S. aureus elongation and identified GpsB, SsaA, and RodZ as additional proteins involved in this process. The gpsB mutant showed the strongest phenotype, mediated by the partial delocalization from the division septum of PBP2, the only bifunctional PBP in S. aureus, with both glycosyltransferase and transpeptidase activity, and of the PBP4 transpeptidase. Increased levels of these PBPs at the cell periphery result in higher levels of peptidoglycan insertion throughout the entire cell, overriding the RodA/PBP3-mediated peptidoglycan synthesis at the outer edge of the septum, which leads to cell elongation. As a consequence, in the absence of GpsB, S. aureus cells become more spherical.

microbiology↗