Monthly Archives: January 2021

WHO WAS MISSING?

Good Grief!, Health - opinions, Political - thoughts, Rants

I got my covid shot (first one) two days ago, and I was overcome with admiration for those many many many individuals who were working in a parking garage, taking tabs on who comes in who goes out, asking about health and concerns, getting papers signed, directing the flow of traffic, entering and checking data, making follow up appointments, giving shots, standing by for the first 20 minutes post vaccination.  WHO WERE THEY? young women and young men.  WHO WAS MISSING? middle aged white men.  Just an observation.

BTW I was vaccinated to protect YOU, you, the people I dont even know and have nothing in common with.  And I am grateful to all the young people who were committed to YOUR health.

UC Health, thank you!

More pixels? not always better analysis!

Methods to assess TEM and AFM images

Imaging in microscopy is fraught with places where a small change in digital images can make a big difference in results. Case in point, made simply with photoshop, is that having an image at 600 ppi doesn’t always give you more information than processing an image that is only 72ppi. It all depends upon the ratio of ppi to blur.

These three identical images, from a published article by Lu et al, on bovine surfactant protein D is what i am working on to determine what the differences in shadow cast images, AFM images, image processing and presence or absence of conserved peaks in the SP-D dodecamer structure.  Below, a very low res image from a publication was used to see what could be determined about size and structure using simple image processing (in this case Adobe photoshop).

The conclusion is that more pixels is not always better.  I think it is kind of cute that in this bovine SP_D the N terminal junctions of the dodecamer here are not quite like that of rhSP-D (shadowed images), and there is not a prominent dark area where one would like to see some indication of a glycosylation site. And also I find the three ends of the trimer carbohydrate recognition domains are very nicely shown right next to the three predictable peaks in the collagen like domain (as routinely seen with AFM images of rhSP-D) so thats just a nice treat.

Missing 10nm in measures of shadowed SP-D hexamers vs multimer

Methods to assess TEM and AFM images, surfactant proteins A and D

Missing 10nm in measures of shadowed SP-D hexamers vs multimer —
If using just one (so far) multimer, shadowed with tungsten (in the technique of J. Griffith’s lab), shows that the N terminus of SP-D to the CRD is about N=7 Mean=63.9, SD=4.02 for a single arm (trimer), and closer to N=3, Mean=138.69nm, SD=5.19nm which leaves a difference of about 10nm between 2x the trimer and the full width (diameter) of SP-D. This difference and the look of the bunch of N termini in the center of the multimer lead credence to the side to side (at least occasionally if not always) of the N termini between (among) hexamers of SP_D.
Just a good look at the center of this multimer causes one to believe that these N termini are arranged in a ring, not end to end, and just mechanically, how would end to end work anyway.

Light yellow line show the course of the plot (made in ImageJ) in each of the images. (Images are shown in inverted contrast). Trimer plots are N terminus on the left side, hexamer plots are shown with the N termini in the center (both are marked with a red N and also in the multimer, a red arrow).  Counting the peaks in shadowed images is problematic,  but in fact comes up just proud of what shows up for AFM images,  background peaks can be used to reduce the noise, but image processing has not been used here.

Verge of a Dream: Want

Prose and Poems

I seem to want
What’s impossible
Not wishing to
Go to the sand
But have the beach
Come to me.

I don’t seem to
Want what is possible
That you’ll be
Happy In the life
Of another.

I seem to see what
Is not visible
Reading your lips
Despite hearing
And being less
Than foreverness.

Time, the sense
Most personal,
It started in
Your arms
And ended with
Leaving them.

RLB 1/5/2021

Verge of a Dream: Nothing I know about

Prose and Poems
The blues have had me
Without doubt and
Yours are yours and
Nothing I know about
Nothing I know about
There’s been pain
In my heart, without doubt
yours is yours
and nothing I know about
Nothing I know about
I’ve feared the wait
On the court steps
No doubt
Your fears are yours
And nothing I know about
Nothing I know about
I’ll stand alone when judged
As in my dreaded dreams
No doubt
Your nights are yours
And nothing
I know about.
I’ve turned my
Back without mercy
No doubt
Your loneliness
Has said that.
And what is yours
Is mine, so indelible
Is the exile

RLB 1/3/2021

Just for fun: color gradient of AFM of multimer

Science and art cover illustrations

This is just arts and crafts, but it does have a great definition of the arms of a multimer (the image itself i did not take but it is part of an ongoing effort to see what types of image processing provide the best data on number of peaks along the length of each arm.  So this is more science illustration with just  a tad of science. The original had some label in it which i patched with photoshop, then flattened, then exported as tiff, imported into CorelDRAW 19 where i did “texture sculpture”, relief at 10o and detail 100, smoothness 100, and depth 100.  This image was saved as a tif, opened in photoshop and a custom color gradient applied.   The ring multimer is pink.