Akshay Mody, Week 4 +5, continuing experiments and analyzing data
I have been thoroughly enjoying my time in the Turner Lab at Yale University. Weeks 4 and 5 have been extremely productive as I conduct research under my graduate student named Katie. My research has been focusing on different strains of the shigella bacterium, including a few strains that have outer membrane proteins knocked out. The eventual goal of the research I am conducting is to find bacteriophages, or viruses that infect bacteria, that use specific receptors to infect and kill bacteria. The shigella bacterium is involved in human gut problems. Big picture, if we find bacteriophages that use the outer membrane protein C or A of the shigella bacterium as a receptor, and we push evolutionary processes to alter the membrane, the bacterial strain will become less virulent.
The last two weeks, we have been spotting and titering a library of over thirty phages to see if any use OMP A or C as the receptor to enter the bacterial membrane. This process is very slow and consists of making plates, amplifying the phage, making top layer, and other techniques learned earlier in the lab experience. In addition, we will be conducting a live/ dead assay to see if anything more can be done to make the results more conclusive.
I have been coming to the lab around 8:30 every morning and leave at around 3. Afterwards, I run for about 1 hour and than have driving school twice a week. I have learned that patience is key when working in the lab, as well as the importance of being punctual and understanding when dealing with situations in the lab.
I will post some of the data here when it becomes more coherent.
7 phages did not spot on the OMP A/ C knockout. This made us believe that these phages could use these proteins as receptors to infect the bacteria. We did further titer tests to explore the density and PFU of the phages and hopefully will put selective pressures on the bacteria in the near future.
The last two weeks, we have been spotting and titering a library of over thirty phages to see if any use OMP A or C as the receptor to enter the bacterial membrane. This process is very slow and consists of making plates, amplifying the phage, making top layer, and other techniques learned earlier in the lab experience. In addition, we will be conducting a live/ dead assay to see if anything more can be done to make the results more conclusive.
I have been coming to the lab around 8:30 every morning and leave at around 3. Afterwards, I run for about 1 hour and than have driving school twice a week. I have learned that patience is key when working in the lab, as well as the importance of being punctual and understanding when dealing with situations in the lab.
I will post some of the data here when it becomes more coherent.
7 phages did not spot on the OMP A/ C knockout. This made us believe that these phages could use these proteins as receptors to infect the bacteria. We did further titer tests to explore the density and PFU of the phages and hopefully will put selective pressures on the bacteria in the near future.
| Spot Test | ||||||
| Phage Name | Titer on SF | SF | ompA- | ompC- | ompA-/C- | |
| 31C | 2800000000 | 1 | 1 | 1 | 1 | |
| 34B | 59000000000 | 1 | 1 | 1 | 1 | |
| 28B | 16300000000 | 1 | 1 | 1 | 1 | |
| 31B | 7100000000 | 1 | 1 | 1 | 1 | |
| 30S | 1900000000 | 1 | 1 | 1 | 1 | |
| 5S | 2700000000 | 1 | 0 | 0 | 0 | |
| KETA | 29000000 | 1 | 1 | 1 | 1 | |
| HC | 89000000000 | 1 | 1 | 1 | 1 | |
| A1-1 | 5100000000 | 1 | 1 | 1 | 0 | |
| A1-2 | 1.08E+11 | 1 | 1 | 1 | 1 | |
| KCC | 500000000 | 1 | 1 | 1 | 1 | |
| D3 | 0 | 0 | 0 | 0 | ||
| CCCB-A | 13100000000 | 1 | 1 | 1 | 1 | |
| CCCB-B | 1.3E+11 | 1 | 1 | 1 | 1 | |
| CCCS-C | 1 | 0 | 1 | 0 | ||
| 39S | 2800000000 | 1 | 1 | 1 | ||
| 38B | 6500000000 | 1 | 1 | 1 | ||
| 37B | 5700000000 | 1 | 1 | 0 | ||
| 53 | 170000000 | 1 | 0 | 1 | ||
| 37S | 360000000 | 1 | 1 | 0 | ||
| 38S | 27000000 | 1 | 1 | 1 | ||
| 50 | 1 | 1 | 1 | |||
| 44 | 1 | 1 | 1 | |||
| 52 | 1 | 1 | 1 | |||
| 39B | 710000000 | 1 | 1 | 1 | ||
| 70 | 91000000 | 1 | 1 | 0 | ||
| 67 | 75000000 | 1 | 1 | 0 | ||
| 60B | 1810000000 | 1 | 1 | 1 | ||
| 60S | 1100000000 | 1 | 1 | 1 | ||
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