Thank you for the question! So in general, all of the bacteriophages which could infect the bacteria we were using “behave” in similar ways as far as the way they infect bacteria. The mechanisms they use can differ a little bit (Myoviridae contract their tails while Siphoviridae don’t) but as far as use research goes the most important difference is the comparison between temperate phages and lytic phages since that makes the difference between immediate lysis and genetic integration. Ultimately with mycobacteriophages like the one’s our lab used, the families and the clusters are more ways of organizing the phages as opposed to completely differentiating how they act. The changes in behavior would start to appear when you start looking at different orders of viruses.
Wonderful and engaging presentation! Is there an initial recommendation that you have as to a specific proposed method of “designing” or causing direct phage evolution? This is a very interesting suggested proposal.
Great question! At this point the most efficient way to design phages seems to be by letting them reproduce and evolve on their own under controlled conditions. We could control conditions by changing the buffers, the temperatures, or even by slightly changing the bacteria which they use as a host. Phages tend to be hyper-selective as to which bacteria they infect, but by slowly changing the bacteria, which we could do using decades old recombinant engineering techniques, it seems like it should be possible to expedite beneficial evolution in a lab setting. Research has been done of using the recombinant techniques on the phages directly however it seems to be less efficient than letting the phages “figure out” the best way for themselves. I had a similar question below and I will introduce one other experiment which I would like to see done there. Thank you.
When you are speaking about the DNA being good. What exactly does that mean? If the DNA is bad what type of after effect would that create for your experiment.
When I say good DNA I am referring to DNA which is undamaged and well representative of the DNA which is naturally found in the active phages. Bad DNA in our case would generally mean DNA which had denatured or broken down somewhere in the process of its isolation. “Bad” DNA would be useless in our later experiments because it would not give accurate results about which cuts were made by which enzymes. It would also show an incomplete picture if we tried to map the phages genome. Thank you for the question!
Within the mycobacteriophage group, there are currently 20 recognized clusters named A through T. Some of the larger clusters such as the A cluster are broken further into sub-clusters. There have also been 9 isolated phages which were not found to belong to any of these clusters; they are known as singletons.
Awesome presentation! You mentioned testing to see if phage evolution could be “directed” in the future; what kind of future experiments might you use to do so?
I appreciate this question! I talked a little bit about this in a reply to a similar question above if you’d like a bit more insight into the idea. Anyway, I would be very interested in doing an experiment where we first produce a phage sample like the one we already had which uses M. smegmatis as its host and slowly, over many generations, start to introduce some of a similar but pathogenic bacteria such as M. tuberculosis. I think it would be interesting to see whether the phage starts being able to use the other bacteria along with the original host. If we believe that both bacteria can act as a host, we could then slowly move toward a pure host solution of the pathogenic bacteria in hopes that we can develop a phage that is especially good at killing the pathogen from the starting phage that used a harmless bacteria.
curesymposium.org 
What does the classification of the phage (temperate, siphoviridae, cluster A) implicate about it’s behavior compared to other phages?
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Thank you for the question! So in general, all of the bacteriophages which could infect the bacteria we were using “behave” in similar ways as far as the way they infect bacteria. The mechanisms they use can differ a little bit (Myoviridae contract their tails while Siphoviridae don’t) but as far as use research goes the most important difference is the comparison between temperate phages and lytic phages since that makes the difference between immediate lysis and genetic integration. Ultimately with mycobacteriophages like the one’s our lab used, the families and the clusters are more ways of organizing the phages as opposed to completely differentiating how they act. The changes in behavior would start to appear when you start looking at different orders of viruses.
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Wonderful and engaging presentation! Is there an initial recommendation that you have as to a specific proposed method of “designing” or causing direct phage evolution? This is a very interesting suggested proposal.
LikeLike
Great question! At this point the most efficient way to design phages seems to be by letting them reproduce and evolve on their own under controlled conditions. We could control conditions by changing the buffers, the temperatures, or even by slightly changing the bacteria which they use as a host. Phages tend to be hyper-selective as to which bacteria they infect, but by slowly changing the bacteria, which we could do using decades old recombinant engineering techniques, it seems like it should be possible to expedite beneficial evolution in a lab setting. Research has been done of using the recombinant techniques on the phages directly however it seems to be less efficient than letting the phages “figure out” the best way for themselves. I had a similar question below and I will introduce one other experiment which I would like to see done there. Thank you.
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When you are speaking about the DNA being good. What exactly does that mean? If the DNA is bad what type of after effect would that create for your experiment.
LikeLike
When I say good DNA I am referring to DNA which is undamaged and well representative of the DNA which is naturally found in the active phages. Bad DNA in our case would generally mean DNA which had denatured or broken down somewhere in the process of its isolation. “Bad” DNA would be useless in our later experiments because it would not give accurate results about which cuts were made by which enzymes. It would also show an incomplete picture if we tried to map the phages genome. Thank you for the question!
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How many phage clusters exist?
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Within the mycobacteriophage group, there are currently 20 recognized clusters named A through T. Some of the larger clusters such as the A cluster are broken further into sub-clusters. There have also been 9 isolated phages which were not found to belong to any of these clusters; they are known as singletons.
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Awesome presentation! You mentioned testing to see if phage evolution could be “directed” in the future; what kind of future experiments might you use to do so?
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I appreciate this question! I talked a little bit about this in a reply to a similar question above if you’d like a bit more insight into the idea. Anyway, I would be very interested in doing an experiment where we first produce a phage sample like the one we already had which uses M. smegmatis as its host and slowly, over many generations, start to introduce some of a similar but pathogenic bacteria such as M. tuberculosis. I think it would be interesting to see whether the phage starts being able to use the other bacteria along with the original host. If we believe that both bacteria can act as a host, we could then slowly move toward a pure host solution of the pathogenic bacteria in hopes that we can develop a phage that is especially good at killing the pathogen from the starting phage that used a harmless bacteria.
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