Daily Archives: December 31, 2018

Fun and colorful plots of LUT tables in three SP-D dodecamers

surfactant proteins A and D, Ultimate order, the cell

Sometimes it is nice just to have fun. Here are some LUT plots for dimers of SP-D, colored differently and also aligned at the brightest N terminal associations and the peak lightness of the CRD. I picked out some areas where there appeared to be consensus in terms of peaks in the plots.  Certainly there are at least 5 peaks in each, and maybe 7 or 9.  More images analyzed will tell for sure. In this image below the yellow band is probably needs to be narrower, maybe it is some element before the neck and CRD.  Using these few plots it seems (as is noticed in the micrographs) that one can document  a distinct N terminal dimension but an additional light area which includes part of the collagen like domain.

The center (Nterm+?) in many images measured with different techniques works out to about 25nm, give or take. so this measure is a little on the small side. The CRD is on the small side as well (but not by much). This is likely due to the fact that there is “space” between the peaks here which is left out, where on the original micrographs, the measures are inclusive of the grey areas between bright spots.

This technique might actually be valuable across other TEMs of similar molecules

surfactant proteins A and D, Ultimate order, the cell

This process is easy now. I think it has broader applications. Can’t wait to find some other types (not just the c-type lectins but more complicated polymers).  Anyway, here is dodecamer I named d-80, with densities along the whole dodecamer noted in the two LUT plots below.  I see, also, the next step would be to analyze the multiple plots together. I think that requires stretching fixing the number of pixels analyzed in ImageJ so that the databases can be combined.

Better LUT tables for densities along SP-D dodecamers

Ultimate order, the cell

This set of figures makes it reasonably clear that cutting and centering horizontally 40 or 50 segments of an SP-D dodecamer destined to be analyzed for grey scale densities along its arm makes for a smoother plot. Compare the bottom red and orange plots, the orange one made without cutting but after orienting the arms more or less to allow for a horizontal line or rectangle to be drawn, and the red plot, where the cuts have been centered. The results show a smoother and more informative plot in the latter process.

It seems now that the procedure just uses CorelDRAW to produce the images and then imports an RGB (these were just 72ppi — and the input and output image size was not changed) into ImageJ to provide the LUT numbers and dataset to export to excel. It seems to work well and is easy.

This particular image (not mine) is AFM, and produces a smooth plot with about half the number of bright peaks as a shadowed molecule. Determining how many blips are present, and perhaps distances between them, from the N terminal to the carbohydrate recognition domains is a goal.

Top red plot superimposed upon the dimer arm of SP-D is shown (i named it d-81a) and the bottom red plot is the dimer of SP-D from the same dodecamer (i named d-81b). I am not sure how to combine plots.  ha ha.

New Health Sciences Building for faculty and students who have not yet learned to recycle? Why bother?

Ultimate order, the cell

Construction is well underway for a 64 million dollar  Health Sciences building at the University of Cincinnati. Is it supposed to make us better at living in our environment, preventing disease, helping the ecosystems of the planet?  Maybe some of this money would have been better spent on educating our current students (and faculty and department chairs, even in the Department of Environmental Health) that we are NOT alone in this world, and our actions have consequences millenia after we are dust.

Why, right in the middle of the Medical Campus and only one building away from the Department of Environmental Health, would the trash cans be filled with recyclable plastics and metal, and replete with empty cigarette packs and plastic bags?

Is no one at HOME here? Is no one educating the students how to be good stewards of the earth.  I have worked here for 50 years and have watched the decline in the last 20 years (yes — decline) of any semblance of concern over being leaders in saving the environment (NOTICE I AM NOT TALKING GLOBAL WARMING OR PETROLEUM PRODUCTION BUT JUST PERSONAL AWARENESS OF OUR FOOTPRINTS). This is just common sense awareness about which I am complaining — where is it.

Were I to rank this University (which I consider myself to be a pat of) on a scale of  5 stars for earth-awareness my ranking would be less than 1 star. Sorry UC, you get the raspberry buzzer.