I think this image shows pretty nicely how little, except for cosmetics, the image processing of a cropped portion of a multimer involved in immune defense and differentiation in epithelia shows here affects the raw data (LUT grayscale plots).  There are small variations in the length of the “arm” which are more likely due to that actual tracing in ImageJ than any difference due to processing. That said, gaussian blur tends to increase the dimensions slightly, highpass filtering increases the grayscale, and unsharp mask creates greater peak heights.  So the peak number and the smoothness of the plot can be improved with processing, and the peak height, but no real gain in information is obtained.

The greater task is to look carefully at the molecule, deciding whether tracings of the beginning and ending of close, twisted and overlapping arms (as plotted) (made by hand) make sense.

Images below show plots (color coded as to image processing filters used) and the actual images and trace-lines (screen print from ImageJ tracing). In this case: filters, each named,  were performed in photoshop; plots were made in excel as traced in ImageJ; calculator.net was used for determining means and SD of arm length and peak number;  corelDRAW was used to normalize the x axis (y axis remained unchanged from original plots) and to color code the plot lines.

Next task is to measure peak widths and heights. Unsharp mask (amount 300, 40px radius, 20 threshold) followed by a 10px gaussian blur provided the smoothest plot.  The High peak (left) and low peak height for the next three peaks, and a subsequent high peak seems to be a pretty prevalent pattern for arms in this molecule.

This is the plot for unsharp mask and gaussian blur. It is so remarkably like the very first plots I made on this protein.  Since 99.34 nm was close to 100 i used a 100 set of 1 nm dividers to mark out the valleys of these peaks.  Interesting features are the absolute regularity of the first five peaks, not in height, but in width, and the first and 4th peaks being higher, and the series of similar size peaks in the middle of the plot.

High pass filtering can help sort out background from data, especially microscopic data. Here is a summary about the high pass filter when used alone, and with gaussian blur. The subject matter is a segment of a multimer (either round or linear) and the brightest peak is where the tracing for gray scale LUT tables begins.  Each trace is shown, and along with that a plot of the peak height (and soon to be measured peak width (at mid height and at the base).   The plots of the arms shown at the bottom of the figure are color coded with the plots shown in the graph (graph made in image J, highpass filter and gaussian blur made with photoshop 6. Figure assembeled in CorelDRAW x5. THis is NOT surfactant protein A or D, but another multimer involved in innate immunity.

Has anyone else noticed a speech pattern from the previous president.  It is like a set of words become a mantra, perhaps a meditative experience, or a soothing mantra, maybe even a prayer list, a mandala, a rosary or prayer beads. The following quote made me think of this.

This is the quote “”The county has, for whatever reason, also refused to produce the network routers. We want the routers, Sonny, Wendy, we got to get those routers, please. The routers. Come on, Kelly, we can get those routers. Those routers. You know what? We’re so beyond the routers, there’s so many fraudulent votes without the routers. But if you got those routers, what that will show, and they don’t want to give up the routers. They don’t want to give them. They are fighting like hell. Why are these commissioners fighting not to give the routers?”

I think all will
again be well when
the garden begun
before unforcasted
change have you
Back again to then
connect
The dreams of your
Father and talents
of the family.
I think that the
direction can be changed
releasing in
centrifugal loss
that not needed,
to become more
like Saturn, in
a ring about the planet.
I think you will,
once the swirling air
settles, know
why you were called
then, for no more
than one clear minute.
And that moment
Is maybe more but
no less than
nights, than mornings
and in between,
spent in the
eye of the hurricane,
grasping for an
answer to
hold on to.

RLB 16/19/2021

Determining a beginning and an end creates a dilemma for measuring LUT plots. There are many variables playing on where to start the plot-line and where to end it. The total distance from one end of the CRD of a hexamer to the other CRD can be measured in at least these ways. 1. brightest spot to brightest spot, 2. straightest line (whether that means beginning or ending the line in a place where one of the three elements of the CRD are spread apart creating a darker and shorter line path.

DMBT1 is an interesting multimer and it according to a couple of images I have seen it can appear in two configurations: ring and linear.  One confusing issue is why, if the linear molecule has arms apparently extending in two directions along the spine, does the ring multimer not have arms extending toward the center of the ring?

There is a very simple explanation, which I am proposing, not as someone who knows much about DMBT1, but from the perspective of someone who has done lots of imaging, and microscopy and has found that there is an abundance of information in images, it just takes some serious concentration and visualization.

So for starters here are two diagrams (not to scale, not depicting the correct number of SRCR- like domains because I dont really know that number but suspect from looking at AFM images that it is more than 8) and not suggesting that there is a given number of arms in a ring or linear multimer (though the two images I have examined have about 30+ arms each), and I am not suggesting size of the individual proteins modeled nor the amount of space in the link regions (SIR) is accurate, but just making a suggestion about how the ring and linear multimers might actually NOT be so different.  At the same time, it eliminates the need for explaining why the linear multimer has arms on both sides and the ring multimer does not.

Below: ring multimer (left) linear multimer (right).  If one looks closely at the right image one sees that there is a red fill down the center of the line, which actually I am suggesting represents a collapse of the open circle on the left…. literally stuck together obliterating the space in the ring. This possibility originates from a shadowed image in a publication by Erica Crouch where she attributes the image to John Heuser. The spine of that linear multimer obviously (at least to me) is a junction of two rows.

I suspect that the SRCR domains have the ability to be closely bound, side to side, maybe two or three (judging by the height and width of brightness peaks seen with AFM).  If they bind side to side, then why not also bind to molecules across the diameter, more side to side associations, to close the circle. This would look a little more like the sideview of a lampshade with the spine only raised slightly.

Having the arms on either side of the ring multimer is visually untenable, my guess is that it is an easy leap to suggest that it is not tenable in the molecular sense either.  See diagram below. Flattening the ring is about the simplest explanation to explain the side to side arms extending in the linear multimer but not in the ring multimer.  See diagram below of the “not really plausible” ring multimer.

For these diagrams, the model for the individual arms was redrawn from a diagram in a publication by Martin P Reichhardt et al, Structures of SALSA/DMBT1 SRCR domains reveal the conserved ligand-binding mechanism of the ancient SRCR fold.http://doi.org/10.26508/lsa.201900502.

The diagram above (with questionmark) is about the length of each arm that I measured in ImageJ so to make it more or less a reasonable estimate, some of the SRCR domains are not shown (which is consistent with often occurring different numbers of repeats). It seems to me that the linear structure must have some kind of end to end, as well as side to side binding in SRCR domains at the N termini.  Just thinking outloud, suggestions are welcome.