Combating Infectious Diseases with Synthetic Biology

Khan, Anooshay; Ostaku, Julian; Aras, Ebru; Şeker, Urartu Özgür Şafak

doi:10.1021/acssynbio.1c00576

Cited by 7 publications

(2 citation statements)

References 85 publications

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“…Designing living therapeutics is another prospect, e.g. immune T-Cell therapies ( BBC_News 2022 ) or to counteract infectious diseases using commensal bacteria ( Khan et al 2022 ), especially with a multicellular histological simulation component related to our ongoing and past ( Matzko et al 2023 ) research. From the perspective of the Z-score based methods in GEP and the R statistics for the cell lineage classifier using Manhattan distance of feature vectors, diagnostics and therapeutics might be tailored regarding the healthy range of expression norms, or indeed cell lineage classification.…”

Section: Discussionmentioning

confidence: 99%

BioNexusSentinel: a visual tool for bioregulatory network and cytohistological RNA-seq genetic expression profiling within the context of multicellular simulation research using ChatGPT-augmented software engineering

Matzko,

Konur

2024

Bioinformatics Advances

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Motivated by the need to parameterize ongoing multicellular simulation research, this paper documents the culmination of a ChatGPT augmented software engineering cycle resulting in an integrated visual platform for efficient cytohistological RNA-seq and bioregulatory network exploration. As contrasted to other systems and synthetic biology tools, BioNexusSentinel was developed de novo to uniquely combine these features. Reactome served as the primary source of remotely accessible biological models, accessible using BioNexusSentinel’s novel search engine and REST API requests. The innovative, feature-rich gene expression profiler component was developed to enhance the exploratory experience for the researcher, culminating in the cytohistological RNA-seq explorer based on Human Protein Atlas data. A novel cytohistological classifier would be integrated via pre-processed analysis of the RNA-seq data via R statistical language, providing for useful analytical functionality and good performance for the end user. Implications of the work span prospects for model orthogonality evaluations, gap identification in network modelling, prototyped automatic kinetics parameterization, and downstream simulation and cellular biological state analysis. This unique computational biology software engineering collaboration with generative natural language processing artificial intelligence was shown to enhance worker productivity, with evident benefits in terms of accelerating coding and machine-human intelligence transfer. Availability BioNexusSentinel project releases, with corresponding data and installation instructions, are available at https://github.com/RichardMatzko/BioNexusSentinel.

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Section: Discussionmentioning

confidence: 99%

BioNexusSentinel: a visual tool for bioregulatory network and cytohistological RNA-seq genetic expression profiling within the context of multicellular simulation research using ChatGPT-augmented software engineering

Matzko,

Konur

2024

Bioinformatics Advances

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“…Engineered phages, designed to target specific pathogens, have demonstrated potential as a therapeutic option for treating infections that occur after lung transplant in patients with CF [ 82 ]. After undergoing a lung transplant, a patient with CF, who had a medical history of infections caused by P. aeruginosa and Mycobacterium abscessus received phage therapy; The treatment involved the i.v.…”

Section: Ltris and Different Respiratory Diseasesmentioning

confidence: 99%

Phage therapy: breathing new tactics into lower respiratory tract infection treatments

Vaezi,

Healy,

Ebrahimi

et al. 2024

Eur Respir Rev

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Lower respiratory tract infections (LRTIs) present a significant global health burden, exacerbated by the rise in antimicrobial resistance (AMR). The persistence and evolution of multidrug-resistant bacteria intensifies the urgency for alternative treatments. This review explores bacteriophage (phage) therapy as an innovative solution to combat bacterial LRTIs. Phages, abundant in nature, demonstrate specificity towards bacteria, minimal eukaryotic toxicity, and the ability to penetrate and disrupt bacterial biofilms, offering a targeted approach to infection control. The article synthesises evidence from systematic literature reviews spanning 2000–2023, in vitro and in vivo studies, case reports and ongoing clinical trials. It highlights the synergistic potential of phage therapy with antibiotics, the immunophage synergy in animal models, and the pharmacodynamics and pharmacokinetics critical for clinical application. Despite promising results, the article acknowledges that phage therapy is at a nascent stage in clinical settings, the challenges of phage-resistant bacteria, and the lack of comprehensive cost-effectiveness studies. It stresses the need for further research to optimise phage therapy protocols and navigate the complexities of phage–host interactions, particularly in vulnerable populations such as the elderly and immunocompromised. We call for regulatory adjustments to facilitate the exploration of the long-term effects of phage therapy, aiming to incorporate this old-yet-new therapy into mainstream clinical practice to tackle the looming AMR crisis.

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