Mardi Gras will always be here....

For the most part this week in lab involved recording data from experiments and tests that we set up in previous classes.

On Monday we counted the colonies on the countable plates from the serial dilution plating of soils that had been exposed to 5 kGy of gamma irradiation. We calculated the cfu/g values for each soil after 5 kGy radiation exposure and the surviving fraction. The surviving fraction was determined by comparing the cfu/g value before and after irradiation for each soil. Dr. Rainey discussed the results with us and we talked about the age of the soils, the locations of the soils sampled and the idea of competition on serial dilution plates. We found differences between the levels of survival between the soils and these data can be found at our AirSet site.
In addition we streaked out the remainder of our strains on starch agar plates (which Eugene had prepared for us). Monday was also 20 days since we inoculated our liquid cultures to determine growth in liquid media so we recorded these data. This test is a complicated one to both read and interpret. The liquid culture tubes were incubated without shaking and so after 20 days the majority of growth was in the bottom of the tubes. Before recording the growth we vortexed the tubes and scored them 0 to ++++. The majority of the strains seem to grow in liquid culture although some seem rather hydrophobic and clump.

On Monday Dr. Rainey also reaffirmed the importance of the BLOG in regards to how much effort we put into it and the fact that some in the class had not been reading or commenting on the BLOG. There is a good part of our grade involved in the BLOG and so it would be best to take it serious. It is also a wonderful way to recap on the week and learn about what we have been doing and what others in the class perspective is of what we are doing.

Recording growth at various temperatures and NaCl concentrations was the main activity on Wednesday. We found that some strains grew at all NaCl concentrations as was the case with the temperature range. A number of strains grew at the extremes tested (10C and 42C). The 10C results do in some ways have to be taken with a pinch of salt at this point as the 10C incubator went down (or up as the case was) and so they may have been at RT for a day or two before Dr. Rainey moved them to a new 10C incubator. We are going to repeat the 10C test again. For those strains growing at 10C we will try to grow then at 4C and for those growing at 42C we will try to grow them at 45 and 50C. When we set up these plates we will streak them from plates grown at 25C and not from the 10C or 42C plates as this could result in the selection or training the strain to grow at the extremes. It would seem that a lot of the strains do well at 30C. For the NaCl results we discussed the fact that those growing at the higher NaCl concentrations may have come from sample sites at which the soils have higher salt concentrations. We will compare these data between sites and with soil sample salinity in another class. The last task Wednesday was to streak a new stock plate and incubate it at 25C. Next week we will use this stock plate to streak other tests at various pH and to test the ability of the strains to degrade polysaccharides like xylan and cellulose.

At the end of class on Wednesday Dr. Rainey went over the plan for the midterm (which is on 4th March). He told us there will be 20 short questions involving a line or two of writing and 4 long questions that will have up to a page of space to write our answers. We need to know everything we have done in class and technical details of all our experiments as well as why we did what we did. We need to know what results we obtained and what they might mean and how they will be used in the overall aim of our class which is to characterize and describe new species of the genera we are working with. The BLOG and the comments will also be a valuable resource for eth midterm along with our lab notebooks. The worst part is that we need to read the papers he put up on AirSet but he did tell us which ones. In addition to the Eppard et al paper we need to read the papers that actually describe the genera and the new species. The paper Dr. Rainey published in AEM 2005 about the nine new Deinococcus species and the ecological evidence for a link between radiation and desiccation tolerance is also a MUST read! Dr. Rainey clearly does not like Mardi Gras or as he puts it “I DON’T do Mardi Gras” since he told us that Mardi Gras will be here for ever and will come every year (“even Katrina failed to get rid of it”) while the midterm in BIOL 4126 only comes once in your lifetime and so it might be better to spend the time studying for our midterm than going to Mardi Gras everyday.…..