The agar plate was used because it allows us to foster M.Smeg bacteria growth because the agar solidifies shortly after it is poured onto the plate and creates a solid surface for the M.Smeg bacteria to grow. Since the Bacteria is grown on a solid surface the clearing of the agar confirms the presence of phage.
The PET tool allows us to compare the cutting patterns made on our phages DNA in a restriction digest, based on the cutting patterns made by each enzyme we can compare them to other phages cutting patterns when reacted with these enzymes. The Phage Enzyme Tool is a data base which contains the data we need to compare the cutting patterns. Our phage had similarities with the cutting patterns of other phages that belong to the F-Cluster, so we were able to hypothesize our phage is a member of that cluster as well. The cluster can be confirmed through a PCR, but the PET allows us to hypothesize on a cluster to run a PCR reaction with.
Unfortunately we weren’t able to confirm that our phage was a member of the F-Cluster. Confirming the cluster of our phage allows us to get a better idea of the bacteria it can target, based on the type of bacteria other phages in the F cluster can lyse, we can hypothesize what type of bacteria our phage could lyse upon confirming. Phages in the same cluster contain about 50% of the same DNA so we can expect similarities with bacteria infection.
Hi Kaylee! Good job on your presentation. Do you think identifying the cluster and sub-cluster of your phage will help determine whether or not it will be effective in phage therapy? Basically, is there a relationship between the classification of the phage and its efficiency of infection?
Kind of, so our phage was confirmed to be a temperate phage, which is not the ideal lifecycle used for phage therapy as the lifecycle is typically lytic as it can clear the entire infection. Our phage could be switched to a lytic lifecycle if we are able to identify and remove the repressor protein. If we are able to confirm our phage cluster we can better understand the types of bacteria our phage can infect based on how other phages in the cluster lyse that bacteria. Phages in the same cluster contain about 50% of the same DNA, and subcluster contain 70% so we can expect to see similarities with the types of bacteria our phage can lyse, which can be applied to phage therapy based on the type of bacteria that causes the infection.
Yes, so it separates DNA and RNA samples by running an electrical current through the gel. The gel allows us to see if we have a good DNA sample because it separates the DNA from the RNA. If we saw bright bands at the bottom of the well, it would be concluded that our DNA was contaminated with RNA. Bright bands at the top demonstrate high quality and quantity DNA was successfully isolated from our phage sample, and is able to be ran on future experiments such as restriction digest and PCR.
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Why was an agar plate used instead of another method to grow the bacteria?
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The agar plate was used because it allows us to foster M.Smeg bacteria growth because the agar solidifies shortly after it is poured onto the plate and creates a solid surface for the M.Smeg bacteria to grow. Since the Bacteria is grown on a solid surface the clearing of the agar confirms the presence of phage.
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Can you explain what the Phage enzyme tools is a little more?
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The PET tool allows us to compare the cutting patterns made on our phages DNA in a restriction digest, based on the cutting patterns made by each enzyme we can compare them to other phages cutting patterns when reacted with these enzymes. The Phage Enzyme Tool is a data base which contains the data we need to compare the cutting patterns. Our phage had similarities with the cutting patterns of other phages that belong to the F-Cluster, so we were able to hypothesize our phage is a member of that cluster as well. The cluster can be confirmed through a PCR, but the PET allows us to hypothesize on a cluster to run a PCR reaction with.
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do you know what bacteria your phage specifically targeted?
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Unfortunately we weren’t able to confirm that our phage was a member of the F-Cluster. Confirming the cluster of our phage allows us to get a better idea of the bacteria it can target, based on the type of bacteria other phages in the F cluster can lyse, we can hypothesize what type of bacteria our phage could lyse upon confirming. Phages in the same cluster contain about 50% of the same DNA so we can expect similarities with bacteria infection.
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Hi Kaylee! Good job on your presentation. Do you think identifying the cluster and sub-cluster of your phage will help determine whether or not it will be effective in phage therapy? Basically, is there a relationship between the classification of the phage and its efficiency of infection?
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Kind of, so our phage was confirmed to be a temperate phage, which is not the ideal lifecycle used for phage therapy as the lifecycle is typically lytic as it can clear the entire infection. Our phage could be switched to a lytic lifecycle if we are able to identify and remove the repressor protein. If we are able to confirm our phage cluster we can better understand the types of bacteria our phage can infect based on how other phages in the cluster lyse that bacteria. Phages in the same cluster contain about 50% of the same DNA, and subcluster contain 70% so we can expect to see similarities with the types of bacteria our phage can lyse, which can be applied to phage therapy based on the type of bacteria that causes the infection.
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can you explain how the argos gel works?
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Yes, so it separates DNA and RNA samples by running an electrical current through the gel. The gel allows us to see if we have a good DNA sample because it separates the DNA from the RNA. If we saw bright bands at the bottom of the well, it would be concluded that our DNA was contaminated with RNA. Bright bands at the top demonstrate high quality and quantity DNA was successfully isolated from our phage sample, and is able to be ran on future experiments such as restriction digest and PCR.
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