A cluster is a way of grouping up phages who have greater than 50% similarity within its genome. If we can determine Reiner’s cluster, we will be better able to predict its gene order and function! Also, to answer your second question, clusters are not directly associated with the infection rate of a phage.
Temperate phages are phages that undergo both the lytic cycle and the lysogenic cycle. When the phage goes under a lysogenic cycle, it will integrate a prophage into the bacteria’s genome, and does not kill the bacteria. This only happens a small percentage of the time, and turbid plaques are representative of this. The clear center of the turbid plaques indicates complete bacterial death/lysis, while the cloudy edges indicate a mixture of dead bacteria and alive bacteria who have embedded prophages. In clear plaques, it would indicate a lytic phage because there are no cloudy edges to indicate any bacterial survival!
Our use of SybrSafe during our restriction digest analyses allowed us to visualize the bands of the cut DNA fragments under UV light. However, if you were talking about fluorescent labeled prophages, that was not used in this research. It would actually be a viable option for a future experiment with Reiner! Its ability to integrate prophages within the genome allow it to participate in fluorescent tagging in the future.
What kind of bacterias would this phage protect you from?
Reiner is a mycobacteriophage, which means that it is able to infect Mycobacterium smegmatis!
Could you explain what a Cluster is and how this is specific to your experiment with Reiner? Does this Cluster help you determine the infection rate?
A cluster is a way of grouping up phages who have greater than 50% similarity within its genome. If we can determine Reiner’s cluster, we will be better able to predict its gene order and function! Also, to answer your second question, clusters are not directly associated with the infection rate of a phage.
Why do turbid plaques indicate a temperate phage?
Temperate phages are phages that undergo both the lytic cycle and the lysogenic cycle. When the phage goes under a lysogenic cycle, it will integrate a prophage into the bacteria’s genome, and does not kill the bacteria. This only happens a small percentage of the time, and turbid plaques are representative of this. The clear center of the turbid plaques indicates complete bacterial death/lysis, while the cloudy edges indicate a mixture of dead bacteria and alive bacteria who have embedded prophages. In clear plaques, it would indicate a lytic phage because there are no cloudy edges to indicate any bacterial survival!
How was the fluorescent labeling used in this research?
Our use of SybrSafe during our restriction digest analyses allowed us to visualize the bands of the cut DNA fragments under UV light. However, if you were talking about fluorescent labeled prophages, that was not used in this research. It would actually be a viable option for a future experiment with Reiner! Its ability to integrate prophages within the genome allow it to participate in fluorescent tagging in the future.