Tag Archives: data

Feb 28 Yeast Growth

I’ve been scratching my head about this for the past two days. I could have sworn that I did a measurement of yeast growth after adaptation and it turns out I did. Here is the data:

I’ll graph this data and publish that when I’m done (after I defend).

Tobacco Seed Growth Rates

I got some awesome new data to show. The first is the compilation of all the Repeating Crumley experiments. And the second is some new data that I’ve been meaning to create and now have with the help of Koch.

Tobacco seed germination rates
Tobacco seed germination rates

The data above is the compilation of all the RC data. Each trial had different water types, but I combined the samples that were the same in every set (DDW, DI water, 33% D2O, 66% D2O, and 99% D2O). Steve adapted his R-code that applies binomial confidence intervals to a data set and used it on this data. If that makes no sense, then just know that the dotted lines are the most probable range of germination rates. For instance, in 66% D2O there is a ~70% likelihood that seeds will germinate at a rate within the dotted yellow lines.

Now it’s time for some brand new data:

tobacco seed root length
tobacco seed root length

Here we went through the pictures from Trial 5 and compared the growth rates of the roots. We calculated the lengths of various seeds in each image and tracked the changes from image to image. We chose DI, DDW, and 1% D2O, because the D2O concentrations are relatively similar and because we wanted to test a hypothesis from a while ago. It’s interesting that the seeds in DDW and D2O grow at the same rate, while seeds in DI water grow at roughly half the speed.

WT E. coli colony (on D2O LB agar) morphology

Yesterday I posted some pictures of E. coli colony morphologies. This was one of the colonies, but it wasn’t as developed, so today I’m adding the extra day’s growth image.

WT E. coli grown on DI LB agar
WT E. coli grown on DI LB agar

Looks great! It’s interesting to note that the colonies grown on D2O agar grow out. Instead of getting thick like it normally does, it grows in an outward direction. I guess I would attribute that to the stress induced by being in D2O.

Comparing the results from today to WT E. coli grown onĀ  DI media and D2O adapted E. coli grown on D2O media, it seems there is an interesting mix of morphological behavior. The adapted E. coli is very “brainy” and obviously the normal WT is “smooth,” but today’s specimen is in between smooth and brainy. Unfortunately I can’t make out the topographical features because the E. coli (as I mentioned above) is very flat. But the contour is very feature rich.

E. coli cells in D2O

I’m not going to make many comments about these cells. It seems that in D2O, E. coli is more likely to say fused but it’s not as obvious as it is with yeast. I make no other observations.

Last Arabidopsis Update

The media is dwindling and the plants will die shortly. I’ll be restarting this experiment in larger environments with more media. Hopefully the plants can do better.

Yesterday Koch noticed that the roots in 10% D2O were much longer than those of the plants in DDW. Something interesting.

E. Coli Colony Morphology in D2O

Here are the results of yesterday’s setup. Here I’m comparing 4 samples:

  1. Wild type (WT) E. coli grown on DI LB agar
  2. WT E. coli grown on D2O LB agar
  3. D2O adapted E. coli grown on DI LB agar
  4. D2O adapted E. coli grown on D2O LB agar

All 4 samples were incubated for the same amount of time, and taken from starter cultures of similar absorbance. The absorbances of the starter cultures are as follows:

  1. Wild type (WT) E. coli grown in DI LB – 0.641
  2. WT E. coli grown in D2O LB – 0.325
  3. D2O adapted E. coli grown in DI LB – 0.489
  4. D2O adapted E. coli grown in D2O LB – 0.112

The D2O adapted E. coli took over the DI LB plate! I’ve re-inoculated those cells from that plate to get a picture that would show a typical colony and compare that morphology to the rest. I’ve also allowed the two D2O media samples to incubate for another 24 hours.

It should also be said that the D2O adapted colonies grown on D2O media look distressed compared to the WT colonies on DI media. But compare the two D2O adapted colonies and it’s tough to discern. Whatever mechanism gives the colonies a distressed appearance on D2O media, seems to be completely uninhibited on DI media. It’s tough to tell if the cells are distressed or just out of control.

Still these results seem pretty comparable to the last time I did these experiments (except using YPD). I’ll update again tomorrow, and insert these results into my dissertation.

Preliminary Results of YPD deterioration

Absorbance of DI YPD (pink), D2O YPD (green), and blank (red)
Absorbance of DI YPD (pink), D2O YPD (green), and blank (red)

These are the results of the experiment I stated a couple weeks ago. I have been tracking the deterioration (previously called aggregation, but I’m not entirely sure aggregation is the correct terminology) of YPD in both solvents. Today they looked pretty well degraded so I thought I’d share the results. Between the two, the DI YPD is more absorbent than the D2O YPD at nearly every wavelength measure (major uncertainty below 350nm).
I’m associating degradation with absorbance since the blank (which is also DI YPD) has an absorbance of zero at all the same frequencies.

D2O YPD also records 0 for absorbance at 600nm, which is the wavelength used for cell count studies, so there would be no interference from the solution. Whether or not the media is still usable by cells is undetermined.

I’m beginning a second experiment that would track the absorbance every few days via the same mechanism. If you recall, I began this experiment taking pictures and eventually moved toward using the nanodrop. This probe seems to do a good job so its continued use is reasonable.

Man I’ve been writing my dissertation for too long…