Monthly Archives: July 2022

Temporary Lobulation in Cartilagenous Models of Long Bones

The first rhythm and order I think i found as a graduate student in anatomy (light microscopy of cartilege) was the order of the beginning of long bone development in mice.  Back then, (as in 50 years ago) many journals didn’t have cover images. At this time, dissolving all my records, publications, micrographs from the finite universe, I made this cover for one very lovely design in nature. I attach a very bad phone phot of the publication (not even I, its author, was willing to spend the highway robbery that some journal websites ask for an almost equally fuzzy scanned image of the original).

Here is my suggested cover, half century down the pike, and a free link to a terrible scanned pdf of the paper. cartilagenous models of long bones


“In truth lives hope”, not in science

There has been something on my mind for a couple years, i would like to get UC to change its sineage. …it is a sign that i see when driving north on I75 on a medical building that is an extension of the university. This seems trivial, yet it is a deep moral dilemma. The sign says “In science lives hope.” After 50+ years in research, I know this is not a fair statement.

If i knew a contact person at UC with whom i could speak…. I would suggest that they change this “also somewhat simplistic, often erroneous, misplaced egotistical” claim…. and maybe change it to “In truth lives hope”

We would all be better off if we recognized there are no institutions, organizations, businesses that can claim to be any sort of “hope”…particularly not big institutions, whether religious or academic or for-profit. If the sineage gets changed to “truth” then we are not inclined to whitewash, praise, or criticize academia for mistakes,  amorality, and fallen hypotheses, but perhaps, move on to being hopeful for “truth” after lots of work, and discovering something that has merit beyond and greater than the scientific profession as it currently exists, not always, but often, in a ragged state self-serving state. The “truth” is actually the same in science, politics, religion, culture.

N, tiny peak, and glycosylation peak(s) proximity in some SP-D dodecamers

AFM images (from rhSP-D at pH 7.4 Arroyo et al) of SP-D are informative and numerous and during a careful analysis of them it seems pretty obvious that there are a significant number of occasions where there is a close “sticking” together of the strands of the trimer from the N termini junction, through the tiny peak on either side of the N peak and up to the glycosylation (often including it) peak(s)(plural here because there are a significant number of imaging and signal processing applications that count more than one peak in the area considered the glycosylation peak).
Here are two images (labels on each show the number of nm diameter, the length in nm of each of the hexamers, and arrows that show where the trimers from two hexamers are in close association. I scanned 83 images from the images of Arroyo et al, and found that such an association (which in order to be visualized with any confidence requires that the dodecamer to be lying such that the rest of the trimer-arms are separated, thus not just overlapping — overlapping trimer arms were not included in the count of closely associated N, tiny peak, and glycosylation peak associations.
I have also given a number (my reference number for the set of thumbnail images, and the set of dodecamers to which some measurements have been applied.
Any reason for such a close association between trimers in that specific location is not known by me, comments welcome. 100 nm bar is given for your “enjoyment”,  green nm measurements correspond to green segmented tracing through the center of the hexamer to which it refers, same for red segmented line and nm values.  Diameter values (orange) are made in ImageJ, and requires that three of the four carbohydrate recognition domains be touched.  It is easy to see that once past the glycosylation peaks, the arms of each trimer are separate. On the bottom image, the trimers are close on the top half of the micrograph, but not the bottom half, as the glycosylation peaks are separate. (42 dodecamers, of 86 total, show N, tiny peak, glycosylation peak closeness on one or both sides of the dodecamer.)

Four SP-D molecules: peak 7 width and subpeaks

This is an often hidden portion of the SP-D trimer, as it can be hidden under the CRD domain which can flop around and lie in different positions during processing.  It seems that this peak will be something around 5 nm (top figure) depending upon how the CRD domains have obscured it.  It might not have any subpeaks (the mode for this peak is 1 and it seems reasonable for this relatively tightly wound helical neck portion of the trimers (bottom figure).

It will be interesting what adding four more measurements to this dataset will confirm or refute. It is nice that the small N of four (composed of 50 to 100 separate grayscale plots of trimers (from a tracing of the hexamer) after image and signal processing, show some consensus.

Four SP-D molecules: Sixth peak(s) and sub-peaks

Same process  for determining peak width, and sub peak number…. as before. peak 6 i expected to show up a little wider (here it is about 7.5nm+0.12).  in previous plots that are colored one can see it as that peak(s) which are white.

summary plot from months ago,  below to remind one what the scheme of the bilateral symmetry was/is.

PEAKS PER TRIMER (trimer=about 74 nm including the full N term peak with each plot)
Peak 1=N term peak (full) (peach) @20nm
Peak 2=Tiny peak (purple) @2.5nm
Peak 3=glycosylation peak(s) light green @8nm
Peak 4= unnamed (darker green) @12nm
Peak 5= unnamed (pink) @4nm
Peak 6- unnamed (white) @7.5nm
Peak 7= Neck (yellow) @4.5nm
Peak 8=carbohydrate recognition domain peaks (orange) @ 17nm

Four SP-D molecules: Fifth peaks – lateral to the fourth peak(s) which are lateral to the glycosylation peaks in this bilaterally symmetrical hexamer

This is a small peak by comparison to the glycosylation peak(s) and to the fourth peak just lateral (in a bilaterally symmetrical hexamer) which is @12nm in width, this very narrow and lower peak is only 4nm wide (at the valleys).  In previous ridge (Joy) plots it is colored in a bright pink just in case you want to look up its position and relative height and width.

After finding width and number of sub-peaks for each of the 7 peaks on either side of the N, i will make a diagram with the dimensions (width, height, and sub-peaks) found for each of the four dodecamers in this short list of test molecules.
There is a peak 5 in 74% of the trimers, less than 1 per trimer, and no sub-peaks noted.



Four SP-D molecules: Fourth peaks – lateral to the glycosylation peaks

Here is a peak series that I think occurrs with a frequency that legitimizes it as being thought of as a distinct entity.  The peak number in grayscale plots for SP-D hexamers has been calculated by numerous signal and image programs but the pattern itself is the result of observing countless images and the patterns within each hexamer mirrored as two trimers.  (N being central (peak 1), tiny peak lateral to N (peak 2), glycosylation peak being (3), and this peak (4) with unknown function or quality is consistently as wide, with a lower peak height than the glycosylation peak.  The divisions are mine.  It appears (looking at four dodecamers of SP-D (as individual trimers) to be about 11 nm in width.  It does show subpeaks just like the N and the glycosylation peak.  It would be amazing if the subpeaks were indicators of the “twisting” together at a subtle distance the three individual SP-D molecules.  Thats not too far fetched.  This conjecture might hold up until the CRD are reached which becomes rather random positioning of the globular part of the protein.

It helps to visualize this peak (deep green in the ridge plots link to one here). The “tiny peak” (purple) can be viewer towards the top of this ridge plot, but not at the base of the plot.

The number of sub-peaks (tabulated without bias within the five signal processing peak finding algorithms, and the hand counts are consistent with this peak being one for sure but maybe with a smaller element or subpeak. I am defining sub-peaks as smaller peaks which visually appear to be part of a single wider taller peak.

Four SP-D molecules: 13, 14, 15, 16, 17? peaks per hexamer

n=4 dodecamers, with many different signal and image processing filters, giving rise to about 114 different plots and peak numbers; the peak number summary of each dodecamer provides: n=4, 17.25 total peaks per hexamer+2.48. This is still just four molecules.

1) N term peak = @20nm which is divided into two sub peaks about 50% of the time.
2) Tiny peak of @3nm either side of the N term peak
3) Glycosylation peak @9nm, either side of N term peak, and consistently composed of two parts (two peaks)