Light blog

Today sitting at the picnic table waiting the laundry I am warm. The sun is out, the breeze is energetic enough to freshen me up and also is carrying in the smell of mud. Perhaps it is low tide?

The light blog reflects a light week, as in easy lifting not intense inspiration. I spent most of the week at Philadelphia, part of a site visit team for the NSF, driving over to Providence for a train on Tuesday morning and getting back Friday night.

That did leave me Monday. I sub-cultured BY2 cells, with the ethanol burner, now filled with 100%, delivering a mighty flame as wonted, so much so that it was a challenge to snuff out (I am ok with that). I imaged day-7 cells for retardance, thereby completing the series I started the week before.

And, I had another session on the confocal fluorescence microscope, set up for imaging polarized fluorescence. I am slowly learning how to navigate through all the complex software panels. And even with Mai having patiently watched me set it all up, I soon realized that the system was not working correctly. Mai came up to troubleshoot and we discovered one tricky little setting was amiss. Once that was sorted, the macros worked. The polarized fluorescence from the stained cellulose looked remarkable. Alas, they are marooned on the confocal’s computer, I forgot to transfer them. Rhodos instead.

Figure 1. Rhodos blooming around the drive to the cottage here. This was two weeks ago, happy garlands for moving in.

Nevertheless, these images of polarized fluorescence require further steps to become usable. There is a huge amount of background. I mean that in areas of the image where there is little or no fluorescence (i.e., areas without staining), the algorithm calculates appreciable anisotropy. Probably this is happening because the algorithm takes ratios. Thus, fluorescent input that is vanishingly small can give rise to large calculated anisotropy. This week, I need to work with Rudolf to see if this anomalous background can be wrangled. Perhaps the final anisotropy can be scaled against the total intensity? or some such dodge.

Finally, today. To steal a march on a busy Monday, I went to the lab this morning. I discovered the shaker I use to grow BY2 cells was too warm. Uh oh. This had happened last summer when I was getting started. The shaker heats but cannot cool. Typically, people use it to grow bacteria at 37˚C, well above room temperature; BY2 need a balmy 26˚C. While that is a little warmer than room temperature, the shaker’s motor generates enough heat to warm the chamber up higher than 26˚C. Last summer, I cranked down the thermostat in the room where the shaker sits, making the room a little chilly but allowing the motor’s heat to dissipate. Two weeks ago when I arrived, the thermostat was still set low and the room was suitably cool; when I walked in today, the room had lost its cool. Using a hunk of Styrofoam, I wedged open the shaker’s lid about as far as it would go without forcing it to stop shaking, making an opening that allows air to circulate. The temperature settled down to 26˚C. I texted Rudolf, who told me that he had eased up on the thermostat, the room had been chilly after all. I nudged the dial back down and the room slowly started to cool. I will check later today after the laundry is folded. I hope the cells are ok. They are tough and the temperature would have risen fairly slowly, allowing them time to adjust. I hope…