Monthly Archives: August 2020

Finding common peaks along the arms of a circular multimer: this is NOT surfactant protein D

Ultimate order, the cell

Finding ways to quantify shape, peak heights, widths, and patterns in a molecule which has long arms (100nm+) and lots of flexibility therein has its challenges. PLEASE READ< THIS IS NOT SURFACTANT PROTEIN D and I was NOT prepared by me, but will remain anonymous for the time being.   BUT, here is a section of a molecule which has approximately 30 arms with very definite “beads on a string” appearance.  Not all of the arms could be traced with sufficient (squinting and mental debating) could be deciphered (in fact relatively few remain untangled enough to produce a LUT plot with any kind of predictability. Here is a stack, which facilitates looking at the arm, the actual ImageJ tracing and the plot of luminance (brighness,  — i havn’t figured out which name is the best yet). Cropped and rotated (so that the bright peak is always at the left — and this was the beginning point of the traces, thus the biggest peak is also always at the left) arms are aligned in a column and are all the same magnification and enlargement. The plots at the right are given in the same height as ImageJ scale measured them, but were aligned by nm (100nm) which was a mean length of a trace of several of the straightest and most easily traced arms. No other alignment of the individual peaks or plots was made but picking a “last” peak that is commonly occurring and normalizing that with the beginning of the first peak cold make the interim peaks more easily seen. Hopefully the technique here will prove helpful looking at SP-D fuzzyballs.

There is pretty much a vertical line for a very wide and prominent ‘First peak’ (blue) followed by a regular less prominent peak of lesser height (gray).  Many of the arms showed four peaks before a rise to the second tallest middle peak (yellow).  Two subsequent peaks show up consistently (green and purple) moving to the right. (TOP IMAGE). Five of the easiest arms to plot also have peaks that line up well (BOTTOM IMAGE panel of 5 arms). (the image used was processed as 2DFFT in gwyddion then opened in ImageJ, and traced with a segmented line)

And before the 2016 election one of the most brilliant minds in our century said “Trump bad man. Real bad man.” — to clarify his more learned remark. What would he have said before the 2020 election?

Political - thoughts, Rants

LONDON (The Borowitz Report)—The theoretical physicist Stephen Hawking angered supporters of Donald J. Trump on Monday by responding to a question about the billionaire with a baffling array of long words.

Speaking to a television interviewer in London, Hawking called Trump “a demagogue who seems to appeal to the lowest common denominator,” a statement that many Trump supporters believed was intentionally designed to confuse them.

Moments after Hawking made the remark, Google reported a sharp increase in searches for the terms “demagogue,” “denominator,” and “Stephen Hawking.”

“For a so-called genius, this was an epic fail,” Trump’s campaign manager, Corey Lewandowski, said. “If Professor Hawking wants to do some damage, maybe he should try talking in English next time.”

Later in the day, Hawking attempted to clarify his remark about the presumptive Republican Presidential nominee, telling a reporter, “Trump bad man. Real bad man.”

SP-D multimer – shadowed image, deconvolve, photoshop eraser tool

surfactant proteins A and D

recombinant human SP-D multimer, tungsten shadowed image (see credits for SP-D and image in previous posts) that I used gwyddion to deconvolve, then the photoshop eraser tool to highlight and corelDRAW to shadow, brighten and increase contrast in the multimer itself, and corelDRAW to organize this figure.  Original shadowed multimer left, gwyddion – deconvolved image center, photoshop eraser and shadowed layer of just the multimer, right. I would really like to see more defined CRD and perhaps a glycosylation peak – if the latter exists which would look like a bright concentric ring around the center N terminals of these arms. Using the original bar marker and a circle to measure the size of  this particular multimer, diameter = 127.16nm.