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In this manuscript, we isolate and characterize a phage that displays what we call anti-bacterial hyper-aggressive behavior. This behavior appears ideal for phage therapy of bacterial disease. It includes (1) formation of semi-turbid zones that subsequently clear, (2) formation of miniature satellite plaques, which probably constitute the foundation of the semi-turbid zones, (3) multi-day enlargement of both circular plaques and cleared semi-turbid zones, and (4) non-formation of phage-resistant host colonies. We emphasize the following key details in our response. (1) The semi-turbid zones are asymmetric and occupy an area much larger (2–10x) than the area of circular plaques formed on the same Petri plate (unlike semi-turbid plaques associated with other phenomena, such as lysis inhibition and lysogeny). (2) In the manuscript’s Figure 9d, we note that phage 0524phi7-1 destroys mature colonies of the host (unlike the behavior of other aggressive phages). (3) The asymmetry of semi-turbid zones is a point that we should have emphasized (because it implies non-diffusive, energy-requiring phage transport). (4) The input of energy for phage motion can be physical (to which we add some details for two physical effects); our mentioning of phage swimming is a hypothesis (that is, however, still viable). 

Viruses that infect bacteria (bacteriophages or phages) have a history of use in both biomedicine and basic molecular biology. Here, I briefly outline the pre-1940 use of phages in biomedicine and then more comprehensively outline the subsequent use of phages in determining the basics of molecular biology. Finally, I outline work that appears to form the foundation for a future, phage-enhanced biomedicine that generally extends medicine in the areas of anti-bacterial therapy (including vaccinology), anti-tumor therapy, and understanding the basic process of amyloid-associated neurodegenerative diseases. The following are general conclusions. (1) In the future, the discipline of phage-based biomedicine will be enhanced by more extensive merging with the discipline of basic phage biology (including molecular biology) and evolution. These two disciplines have been separated post-1940. (2) Biomedicine, in general, will be assisted if the focus is on key problems and key observations, thereby leaving details to later work. (3) Simplicity of strategy is a virtue that can be implemented and should be pursued with phages. (4) Capacity for directed evolution provides phages with generative (artificial intelligence-like) means for increasing biomedical effectiveness without using human design. Two related quotes set the stage (references at the end of the text). “But see that the imagination of nature is far, far greater than the imagination of man” (physicist Richard Feynman). “Nature, in all its variations and seeming paradoxes, speaks to those who pay attention and gives hints and clues to basic facts” (a thought attributed to Felix d’Herelle, a self-trained biologist who developed biological phage isolation and characterization). The integration of natural phenomenon-focused basic science and medical practice is an underlying theme. 

The ideal bacteriophages (phages) for the treatment of bacterial disease (phage therapy) would bypass bacterial evolution to phage resistance. However, this feature (called a hyper-aggression feature) has never been observed to our knowledge. Here, we microbiologically characterize, fractionate, genomically classify, and perform electron microscopy of the newly isolated Bacillus thuringiensis phage 0524phi7-1, which we find to have this hyper-aggression feature. Even visible bacterial colonies are cleared. Phage 0524phi7-1 also has three other features classified under hyper-aggression (four-feature-hyper-aggressive phage). (1) Phage 0524phi7-1 forms plaques that, although sometimes beginning as semi-turbid, eventually clear. (2) Clear plaques continue to enlarge for days. No phage-resistant bacteria are detected in cleared zones. (3) Plaques sometimes have smaller satellite plaques, even in gels so concentrated that the implied satellite-generating phage motion is not bacterial host generated. In addition, electron microscopy reveals that phage 0524phi7-1 (1) is a myophage with an isometric, 91 nm-head (diameter) and 210 nm-long contractile tail, and (2) undergoes extensive aggregation, which inhibits typical studies of phage physiology. The genome is linear double-stranded DNA, which, by sequencing, is 157.103 Kb long: family, Herelleviridae; genus, tsarbombavirus. The data suggest the hypothesis that phage 0524phi7-1 undergoes both swimming and hibernation. Techniques are implied for isolating better phages for phage therapy. 

Molecular dynamics techniques provide numerous strategies for investigating biomolecular energetics, though quantitative analysis is often only accessible for relatively small (frequently monomeric) systems. To address this limit, we use simulations in combination with a simplified energetic model to study complex rearrangements in a large assembly. We use cryo-EM reconstructions to simulate the DNA packaging-associated 3 nm expansion of the protein shell of an initially assembled phage T7 capsid (called procapsid or capsid I). This is accompanied by a disorder–order transition and expansion-associated externalization displacement of the 420 N-terminal tails of the shell proteins. For the simulations, we use an all-atom structure-based model (1.07 million atoms), which is specifically designed to probe the influence of molecular sterics on dynamics. We find that the rate at which the N-terminal tails undergo translocation depends heavily on their position within hexons and pentons. Specifically, trans-shell displacements of the hexon E subunits are the most frequent and hexon A subunits are the least frequent. The simulations also implicate numerous tail translocation intermediates during tail translocation that involve topological traps, as well as sterically induced barriers. The presented study establishes a foundation for understanding the precise relationship between molecular structure and phage maturation.