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Mathematical comparison of protocols for adapting a bacteriophage to a new host.
Virus Evol
November 2024
Institute for Modeling Collaboration and Innovation, University of Idaho, 875 Perimeter drive, Moscow, ID 83844, United States.
Interest in phage therapy-the use of bacterial viruses to treat infections-has increased recently because of the rise of infections with antibiotic-resistant bacteria and the failure to develop new antibiotics to treat those infections. Phages have shown therapeutic promise in recent work, and successful treatment minimally requires giving the patient a phage that will grow on their infecting bacterium. Although nature offers a bountiful and diverse supply of phages, there have been a surprising number of patient infections that could not be treated with phages because no suitable phage was found to kill the patient's bacterium.
View Article and Find Full Text PDFEfficient Simulation of Viral Transduction and Propagation for Biomanufacturing.
ACS Synth Biol
October 2024
Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.
The design of biomanufacturing platforms based on viral transduction and/or propagation poses significant challenges at the intersection between synthetic biology and process engineering. This paper introduces vitraPro, a software toolkit composed of a multiscale model and an efficient numeric technique that can be leveraged for determining genetic and process designs that optimize transduction-based biomanufacturing platforms and viral amplification processes. Viral infection and propagation for up to two viruses simultaneously can be simulated through the model, considering viruses in either the lytic or lysogenic stage, during batch, perfusion, or continuous operation.
View Article and Find Full Text PDFCharacterizing behavioural differentiation in gene regulatory networks with representation graphs.
NAR Genom Bioinform
September 2024
Institute of Mathematics and Computer Science, University of Latvia, Raina bulvaris 29, Riga LV1459, Latvia.
We introduce the formal notion of representation graphs, encapsulating the state space structure of gene regulatory network models in a compact and concise form that highlights the most significant features of stable states and differentiation processes leading to distinct stability regions. The concept has been developed in the context of a hybrid system-based gene network modelling framework; however, we anticipate that it can also be adapted to other approaches of modelling gene networks in discrete terms. We describe a practical algorithm for representation graph computation as well as two case studies demonstrating their real-world application and utility.
View Article and Find Full Text PDFHorizontal transfer of probable chicken-pathogenicity chromosomal islands between Staphylococcus aureus and Staphylococcus agnetis.
PLoS One
July 2023
Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, AR, United States of America.
Staphylococcus agnetis is an emerging pathogen in chickens but has been most commonly isolated from sub-clinical mastitis in bovines. Previous whole-genome analyses for known virulence genes failed to identify determinants for the switch from mild ductal infections in cattle to severe infections in poultry. We now report identification of a family of 15 kbp, 17-19 gene mobile genetic elements (MGEs) specific to chicken osteomyelitis and dermatitis isolates of S.
View Article and Find Full Text PDFSynergistic Interactions among Complex-Targeting Phages Reveal a Novel Therapeutic Role for Lysogenization-Capable Phages.
Microbiol Spectr
June 2023
Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada.
Antimicrobial resistance is a danger to global public health and threatens many aspects of modern medicine. Bacterial species such as those of the Burkholderia cepacia complex (Bcc) cause life-threatening respiratory infections and are highly resistant to antibiotics. One promising alternative being explored to combat Bcc infections is phage therapy (PT): the use of phages to treat bacterial infections.
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