Biology subjects

Bono, E.

Publications and source records attributed to Bono, E..

6 recordsLinked to original sources

bioRxiv2026

Graph Lens Lite: An interactive biological network viewer for displaying, exploring, and sharing disease pathobiology and drug mechanism of action models

Biological network visualization together with graph-based analyses are key techniques in systems biology and network medicine to detect patterns and generate hypotheses regarding disease pathobiology, drug target identification, biomarker prioritization, and digital drug discovery. Network representations provide an intuitive way to communicate and share research findings. We have developed Graph Lens Lite, a browser-based tool that combines rich visualization with a streamlined interface for exploring and sharing biological networks. It offers an expressive query language, topological network analysis, interactive filtering, visual grouping, customizable layouts, a data editor, fine-grained property-based styling, animated edge-flow visualization, community detection, and a context-aware locally powered AI assistant particularly suited for exploring molecular models of disease pathobiology or drug mechanism of action. We demonstrate its utility on a curated network model of autosomal dominant polycystic kidney disease. Graph Lens Lite is open source, with a live web version available at https://delta4ai.github.io/GraphLensLite/.

bioinformatics↗

bioRxiv2026

systematic evaluation and benchmarking of text summarization methods for biomedical literature: From word-frequency methods to language models

The rapid expansion of biomedical literature demands automated summarization tools that reliably condense research articles into concise, accurate summaries. We benchmarked 62 summarization methods, ranging from frequency-based and TextRank extractors to encoder-decoder models (EDMs) and large language models (LLMs), on 1,000 biomedical abstracts from 20 journals across ScienceDirect and Cell Press, using author-written highlights as reference summaries. Models were evaluated with a composite suite of lexical, semantic, and factual metrics, including ROUGE, BLEU, METEOR, embedding-based similarity, and factuality scores. General-purpose models (e.g., Mistral, GPT, Llama) achieved the highest overall performance across lexical and semantic dimensions, outperforming reasoning-oriented (e.g., DeepSeek, Magistral) and domain-specific (e.g., BioGPT, BioMistral) models. Notably, medium-sized models outperformed large-scale models, suggesting an optimal balance between model capacity and efficiency, while classical extractive methods lagged behind neural approaches. These findings provide a systematic reference for selecting biomedical summarization tools and highlight that broad pretraining outperforms narrow domain adaptation.

bioinformatics↗

bioRxiv2025

Acoustofluidic patterning for improved microtissue histology

Microtissues (such as organoids or spheroids) are useful to model healthy or diseased human tissues and organs, with application in drug testing, tissue engineering, and personalized medicine. To characterize their morphology and phenotype, microtissues are often monitored using histology and high-resolution imaging. While this technique is well-established and standard for macroscopic tissue sections, it remains challenging to execute and has low throughput in the context of these sub-millimeter structures, mainly due to the fact that their size makes them difficult to locate within the embedding medium. To enhance the efficiency of microtissue histology, we developed an acoustofluidic device that arranges microtissues in a coplanar arrangement within HistoGel, a widely used embedding medium. Pre-patterning microtissues within HistoGel streamlines downstream processing by positioning the centers of mass of the microtissues at a pre-defined plan in the sample, simplifying sectioning, labeling, and imaging. We validated the method using differently sized HepG2 microtissues and tumor microtissues from osteosarcoma cells (Saos-2, MG-63, HOS), demonstrating that this method can be applied to different microtissue shapes, sizes, and types, without modifying established post-processing techniques. Our approach substantially enhances the microtissue histology workflow and broadens possibilities for microtissue analysis.

bioengineering↗

bioRxiv2022

Nirmatrelvir treatment blunts the development of antiviral adaptive immune responses in SARS-CoV-2 infected mice

Alongside vaccines, antiviral drugs are becoming an integral part of our response to the SARS-CoV-2 pandemic. Nirmatrelvir - an orally available inhibitor of the 3-chymotrypsin-like cysteine protease - has been shown to reduce the risk of progression to severe COVID-19. However, the impact of nirmatrelvir treatment on the development of SARS-CoV-2-specific adaptive immune responses is unknown. Here, by using a mouse model of SARS-CoV-2 infection, we show that nirmatrelvir administration early after infection blunts the development of SARS-CoV-2-specific antibody and T cell responses. Accordingly, upon secondary challenge, nirmatrelvir-treated mice recruited significantly fewer memory T and B cells to the infected lungs and to mediastinal lymph nodes, respectively. Together, the data highlight a potential negative impact of nirmatrelvir treatment with important implications for clinical management and might help explain the virological and/or symptomatic relapse after treatment completion reported in some individuals.

immunology↗

bioRxiv2021

Controlled administration of aerosolized SARS-CoV-2 to K18-hACE2 transgenic mice uncouples respiratory infection and anosmia from fatal neuroinvasion

The development of a tractable small animal model faithfully reproducing human COVID-19 pathogenesis would arguably meet a pressing need in biomedical research. Thus far, most investigators have used transgenic mice expressing the human ACE2 in epithelial cells (K18-hACE2 transgenic mice) that are intranasally instilled with a liquid SARS-CoV-2 suspension under deep anesthesia. Unfortunately, this experimental approach results in disproportionate high CNS infection leading to fatal encephalitis, which is rarely observed in humans and severely limits this models usefulness. Here, we describe the use of an inhalation tower system that allows exposure of unanesthetized mice to aerosolized virus under controlled conditions. Aerosol exposure of K18-hACE2 transgenic mice to SARS-CoV-2 resulted in robust viral replication in the respiratory tract, anosmia, and airway obstruction, but did not lead to fatal viral neuroinvasion. When compared to intranasal inoculation, aerosol infection resulted in a more pronounced lung pathology including increased immune infiltration, fibrin deposition and a transcriptional signature comparable to that observed in SARS-CoV-2- infected patients. This model may prove useful for studies of viral transmission, disease pathogenesis (including long-term consequences of SARS-CoV-2 infection) and therapeutic interventions.

immunology↗

bioRxiv2021

COVID-eVax, an electroporated plasmid DNA vaccine candidate encoding the SARS-CoV-2 Receptor Binding Domain, elicits protective immune responses in animal models of COVID-19

The COVID-19 pandemic caused by the {beta}-coronavirus SARS-CoV-2 has made the development of safe and effective vaccines a critical global priority. To date, four vaccines have already been approved by European and American authorities for preventing COVID-19 but the development of additional vaccine platforms with improved supply and logistics profiles remains a pressing need. Here we report the preclinical evaluation of a novel COVID-19 vaccine candidate based on the electroporation of engineered, synthetic cDNA encoding a viral antigen in the skeletal muscle, a technology previously utilized for cancer vaccines. We constructed a set of prototype DNA vaccines expressing various forms of the SARS-CoV-2 Spike (S) protein and assessed their immunogenicity in animal models. Among them, COVID-eVax - a DNA plasmid encoding a secreted monomeric form of SARS-CoV-2 S protein RBD - induced the most potent anti-SARS-CoV-2 neutralizing antibody responses (including against the current most common variants of concern) and a robust T cell response. Upon challenge with SARS-CoV-2, immunized K18-hACE2 transgenic mice showed reduced weight loss, improved pulmonary function and significantly lower viral replication in the lungs and brain. COVID-eVax conferred significant protection to ferrets upon SARS-CoV-2 challenge. In summary, this study identifies COVID-eVax as an ideal COVID-19 vaccine candidate suitable for clinical development. Accordingly, a combined phase I-II trial has recently started in Italy.

immunology↗