Biology subjects

Machado, D. J.

Publications and source records attributed to Machado, D. J..

3 recordsLinked to original sources

bioRxiv2026

HP2NET: Empowering Efficient Phylogenetic Network Analysis through High-Performance Computing

Advances in High-Performance Computing (HPC) have enabled increasingly complex genomic analyses, including those in phylogenomics. These analyses contribute to understanding the evolution of viruses and pathogens, improving our knowledge of disease transmission, and supporting targeted public health strategies. However, due to the increasing number of tools and processing steps involved, executing these analyses manually, step by step, becomes error-prone and inefficient. To address this challenge, we present HP2NET, a robust framework for reproducible, efficient, and scalable phylogenetic network analysis. HP2NET integrates five workflows based on state-of-the-art tools such as PhyloNetworks and PhyloNet, allowing the analysis of multiple datasets and workflows in a single execution. The framework includes features such as task packaging and data reuse to improve performance and resource utilization in HPC environments. We perform a comprehensive performance evaluation of the software used within HP2NET, identifying bottlenecks and analyzing gains from parallel processing. Data reuse provided up to 15.35% time reduction, for a small dataset, in our experimental environment, while parallel execution of the five pipelines reduced total runtime by up to 90.96% compared to sequential runs. Finally, we validate HP2NET in a real-world case study by analyzing Dengue virus genomes, demonstrating its applicability value for large-scale phylogenetic analyses.

bioinformatics↗

bioRxiv2021

Heat efficiently inactivates coronaviruses inside vehicles

Heat is an established method to inactivate coronaviruses, and there is utility in using heat to reduce viral load on common touch points in vehicles exposed to a person shedding SARS-CoV-2. As SARS-CoV-2 is a Biosafety level (BSL)-3 pathogen, real world testing of heat as a sanitation method for public and private vehicles becomes a challenge, requiring a surrogate coronavirus that can be handled safely outside of a BSL-3 facility. In this study, we used Bovine Coronavirus (BCoV) as a surrogate for SARS-CoV-2 to test the efficacy of heat-based betacoronavirus inactivation. In vitro, a 30-minute exposure to 56{degrees}C completely inactivated BCoV in solution, and a 15-minute exposure reduced recovery of BCoV >1000-fold. When heated to 56{degrees}C for 15 minutes, the infectivity of BCoV spotted and dried on typical porous and non-porous automobile interior materials was reduced by 99 - 99.99%. When BCoV was spotted and dried on hard plastic (seat) material placed inside an out of service transit bus, 56{degrees}C heat for 30 minutes reduced BCoV infectivity 85 - 99.5%. Thus, 56{degrees}C is an accessible, rapid, and effective method to inactivate coronaviruses inside motor vehicles.

microbiology↗

bioRxiv2019

Active Notch Signaling is Required for Arm Regeneration in a Brittle Star

Cell signaling pathways play vital roles in coordinating cellular events in development. For example, the Notch signaling pathway is highly conserved across all multicellular animals and is known to coordinate a multitude of diverse cellular events, including proliferation, differentiation, fate specification, and cell death. Specific functions of the pathway are, however, highly context-dependent and are not well characterized in post-traumatic regeneration. Here, we use a small-molecule inhibitor of the pathway (DAPT) to demonstrate that Notch signaling is required for proper arm regeneration in the brittle star Ophioderma brevispina, a highly regenerative member of the phylum Echinodermata. We also employ a transcriptome-wide gene expression analysis to characterize the downstream genes controlled by the Notch pathway in the brittle star regeneration. We demonstrate that arm regeneration involves an extensive crosstalk between the Notch pathway and other cell signaling pathways. In the regrowing arm, Notch regulates the composition of the extracellular matrix, cell migration, proliferation, and apoptosis, as well as components of the innate immune response. We also show for the first time that Notch signaling regulates the activity of several transposable elements. Our data also suggests that one of the possible mechanisms through which Notch sustains its activity in the regenerating tissues is via suppression of Neuralized1.

developmental biology↗