We will be getting trapped in the filter like the DNA........

There seemed to be some mass hysteria in the first few days of the week and so Monday lab seemed a mix of asking Dr. Rainey questions on what might be or not be on the mid term with some serious lab work in between.

It is always good to be able to read the results of experiments set up some 3 weeks before. This not only shows that all our lab work was not in vain but we end up with actual results on our strains that brings us a step closer to describing new species of the genera we are studying.

Starch hydrolysis a test that has been done for all of the other described species of the genera we are studying proved rather straight forward and after flooding the plates with iodine gave us positive and negative results as well as a few strains showing a weakly positive result. These data allowed us to start and make some comparisons with the species described in the papers. One student noted that Geodermatophilus obscurus as described in 1968 is positive for starch hydrolysis but yet we have strains that on the basis of colony pigmentation we would predict to be members of this genus that are negative for starch hydrolysis. We need to compare all of our starch hydrolysis results with those in the papers describing the various species. As we have a large collection of strains some of which will surely belong to the same species we will be able to say if starch hydrolysis is a clear result (+ve or –ve or w) or if it varies for the strains that belong to the new species we hope to describe.

It was in the AEM paper of Rainey et al., 2005 (on AirSet) that members of the family Geodermatophilaceae were first reported to be resistant to gamma ionizing radiation. This trait has never been tested for the species already described in the literature. Considering a lot of the species of the family Geodermatophilaceae were isolated from arid environments and are considered to be desiccation resistant it is possible that they would also be ionizing radiation resistant. This week we got the first ionizing radiation resistance results for our 78 strains. Looking at the data and the comments provided in the BLOG entries above it is clear that many of our strains are resistant to a dose of at least 6 kGy (others only to 3 kGy) of gamma radiation. We have now tested the strains for resistance to an exposure to 10 kGy and will have the results in 3-4 weeks from now. These data are very interesting and will be useful for inclusion in the species descriptions as well as to make correlations between source and level of ionizing radiation resistance. The spot technique that we use is qualitative give a + or – value for a given radiation dose. To determine the D10 we would have to do a quantitative experiment in which we would determine actual cfu values and plot survival curves. This would be an amount of work beyond the time allowed for BIOL 4126 class.

We observed the plates of our isolates (20 in total) that we recovered from our serial dilution plates of the arid soils before and after radiation exposure. These isolates had been selected on the basis of their colony color and morphology that resembled those of the genera we are studying. After incubation we saw that some were not pure cultures and others had colors that probably exclude them from further study. From those that we considered pure and the target color we extracted DNA from them using the MOBIO kit. This DNA will be used in 16S rRNA gene sequence PCR in a future class with the aim of identifying these strains to the genus level before extensive characterization.

After the dreaded mid term that I think turned out to be “not that bad” we set up plates for the determination of growth of our strains at different pH values. We spotted 10ul from a suspension of each strain on plates of MA, PCA, 1/10, 1/100 and R2A at pH 4, 5, 6, 7, 8, 9, 10. We will read these results 3 weeks from now. The data from this experiment will provide us with information of the pH range over which growth occurs but also on the optimum pH for growth.

So we are making great progress on our research and actually have a plan of action. Unfortunately the government of the SSA does not have such a plan of action but rather they have the equivalent of a mixed culture (us and our fellow citizens) which is poured through a tax filter were the selection will be for those that worked hard and did well in life (they are caught in the filter and stripped of their assets) while those who did nothing and will do nothing until the end of their natural lives pass through to the medium rich in nutrients in the tube below, live the good life and wait for the assets of those trapped in the tax filter to be redistributed to them..……