S-STEM Scholar Micheal Dockham's Blog

Monday - 11/25/24 This week was bit different, as the semester is coming to an end, and our focus of research is changing. With ANAS slowly approaching next semester, we are looking to ideas for what my project and presentation could be on. Originally, I thought of contributing to the pH research of Deinococcus by do a pH analysis on D. grandis, one of the closest strains to D. ficus. However, this was considered "descriptive science" and another approach was suggested.  As stated previously, I could not confirm d. ficus ability to grow in the large range of pHs like stated on Bacdive.com. More test and analysis will be needed to confirm this strains ability to survive in a wide range of pH levels.  Now we are looking at a bioinformatic project, looking into say the catalase cycle in d. ficus.  This has proven to be challenging as I am still very new at bioinformatic research and pathway analysis, so this idea is more of a scaffolding to a greater idea. The upcoming break...

 Monday 11.18           14 flask, 2 for each pH level were inoculated with WT d. ficus and left in the shaking incubator at      37C for 24 hours. Tuesday 11.19 Inoculated flasks were checked upon arrival of lab, most media showed minimal to zero growth so far. Left to incubate for another 24 hours.  Wednesday 11.20     Flask were removed from incubator after 48hr of growth.  OD Values of flask were then quantified. Growth was seen at pH 7, 7.23(c) and 8. Growth was not detected at pH 5,6,9 and 10. OD values were highest at the pH of 8 with an OD value of 3.21.  Control media, pH 7.23 had an OD of 2.94 and the grwoth in pH 7 measured an OD of 2.58      Thursday 11.21 Day was spent helping Madi calculate and plan for her pH experiment. We decided to use 3 pH levels to start, 6, 7 and 8, with the possibility of going father in both directions in the future. We discussed the avenues of this research a...

 Monday 11-11           Tuesday 11-12              After compiling a list of materials and receiving them, I got to work making my pH controlled media. At first, the proper amount of each acid and base was added, then dissolved in 80mL of di H2O This was done for every pH level, using the appropriate amount of materials, then dialed in using HCl and NaOH, then filled to 100mL total. Each flask had a concentration of 12mM. These were then covered and put together with the rest of the autoclave items. Wednesday 11-13 Received all 7 flask (pH level each) from autoclave and divided them out into 3x 30mL flask each, with 10mls left for testing. Autoclave showed to have minimal effect on most buffer solutions, while pH 9 and 10, sodium carbonate/bicarbonate, showed significant color change. They also showed the most change in pH between pre and post-autoclave testing,  Thursday 11-14 Sick Friday 11-15 Sick

  Monday 10.28.24     Prepped cultures for the week. Making 6 total.           2x D. Ficus WT - 20ml          2x D. Ficus (transformed) + CMR - 20ml          2x E. coli + prad1 + AMP - 20ml Discussed plan for tomorrow and rest of the week. The goal is to perform plasmid extractions on the 6 cultures made today. We are testing WT and Transformed Ficus against both primers to confirm the presence of pRAD1 in our transformed d. ficus. We will be comparing this to how the primers behave with the actually pRAD1 extraction as well.  The goal overall is to finally confirm the presence of our pRAD1 vector in our transformed d. ficus cells. This has proven to be challenging. Both for ficus and for deinococcus in general. . Tuesday 10.29.24 Both WT and "Transformed" ficus cells didn't appear grown enough, so they were left to incubate for another 24 hours.  In the meantime, a Zyppy Plasmid Ext...

 Monday 10.21.24 With current complications in PCR reaction results. We have decided to run PCR on our wild-type strain of D. ficus, using both cmr+ and amp primers to verify if contamination of species, both transformed and wild-type strain has happened.  Plates made on Friday were observed, with wild-type strain having normal growth, while our transformed strain grew on one plate somewhat well, and was left in the incubator to grow at temperature of 37C. Primers for PCR were located and the proper request emails were sent out.  Along with this transformation confirmation attempts we have decided to also explore D. ficus ability to survive and possibly thrive in higher pH environments. Apparently and according to research ficus should be able to grow in high alkalinity environments up to a pH of 10. We want to explore and confirm this, make observations and try and understand how these strain can survive in such a high alkaline environment.  We have decided to use m...

 With the electroporation machine shock pod down, and the funds lacking to replace it we changed our focus to chemical transformation. The goal, similar to the electroporation goal, is to insert the pRAD1 vector into D. Ficus via chemical transformation Here we attempt what I am calling the Tuohy Transformation protocol, a method described by Dr. Tuohy that uses simple chemical transformation methods to perform the procedure.  This involves incubating our cells in R2B media for 24 hours at 30C, this should have been 37C. Cells were pelleted and resuspended in fresh R2B(100ul) 40uL of CaCl2 in added and mixed This is then incubated for 15 minutes on ice. With delays in the lab, such as lines to the stations, the cells sat for around 45 minutes in ice 8ul of pRAD1(368ng) elution was added to 30ul of culture mix This was then incubated at 37C for 90 minutes. 1.5ml of R2B was not added tho, as the protocol called for. instead more cells were added. This was then placed back on ice...