Six dodecamers: SP-D – an analysis of shape, peaks and size, AFM images – hexamer length

surfactant proteins A and D

It has been a while since i posted results of my attempt to determine the shape of the SP-D dodecamer (hexamer and trimer) using AFM images (mostly from Arroyo et al). Plotting and finding signal processing programs to do this without bias (of course that was naive, as there is choice in the paramaters of each programs algorithms) took a couple years… but adding two new dodecamers (hexamers, trimers) to the dataset took just a couple months. The data can be compared, the first four, vs the first 6, that is the original four reduced to more or less similar numbers of plots and similar numbers of signal processing programs with two new added.  The latter two will provide the format used for all others.  That is: one image, six different processing methods, the first of which is “without signal and without image processing” the other five using signal processing programs (those selected have been stated before). So these data are the first four fact finding, but trimmed, datasets, and the data from the last two images are provided from what will be the methods for all future plots.

Just trying to figure out how to make these plots tell a story….

Most preliminary numbers are of the hexamer width.  See below: top image was the original set of four. Image below that (six individual dodecamers, listed separately, and with two means for the whole – 1) which includes all plots in a single number (n=1 big dataset), and 2) the data for each of the six molecules individually (n=6). You can compare the initial results with the more refined results… pretty similar.

Free Weather Call, Cincinnati, NOT FREE, you are paying with your privacy

Rants

Free Weather Call, Cincinnati.

Last week (the -6 degree week end of december 2022) i called free weather call about 10 times, in one morning, trying to watch the temperature to determine whether i could safely let my cats outside for a little while. It was a perfectly innocent event for me to monitor the temperature hourly.  Little did i expect what happened.

Interestingly, after 10 calls i got blocked. I could not understand why for a minute, and then knew this wasn’t free weather call at all, it was an advertising money making deal… and each time i called the free weather call must receive a sum of money from each advertiser and a “fail safe” number of clicks from each caller was part of their algorithm.  screw them.

I will not click to listen to viagra being advertised….  or any other of their advertisements, and it is a fake news item that they call it free weather call…. ha ha…. dont you just love how people scam us for our “minds” “money” “personal data”  free weather call is not free, they are monitoring you….  they must subscribe to the trumpian idea that “if i say it enough, it becomes real, whether it is real or not”

SP-D new way to show ridge plot and grayscale peaks

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

Still working on the peak height, width, valley measurements on surfactant protein D dodecamer grayscale values using AFM images.  Just thought this was an interesting way to show both the signal processing divisions for peaks, as well as the more subjective estimation (also from peak counts of image and signal processing peak numbers) division into sections. N peak center, either side, glycosylation peak(s), next is a long lumpy section (dark green), a reasonably consistent tiny low peak (pink), and a broader peak before the presumed neck coiled section (white), the likely neck domain (yellow) and the CRD (orange).  These measurements are taken from the N term outwards in two directions to the respective CRD of hexamers.  Two hexamers are measured separately, though mirrored and identical (theoretically) in all for trimeric arms.

This particular ridge plot is from molecule 80 (my designation number, as collected mostly from images found in Arroyo et al), and light gray lines along the plot lengths for each of the two hexamers are the divisions found by octave’s ipeak.m program using M80 as the amplitude and smoothing settings (unbiased).  These come close in this randomly selected image to fitting the 15 peak per hexamer consensus found previously. Color divisions are mine (educated bias), made to approximate the 15 peak per hexamer findings as well as my observations on the AFM images.

An obvious deviation is the unusually tall (bright) peak on the left side of the top hexamer at the domain of the CRD, and just as unusual is the low (less bright peak) on the left side of the bottom hexamer.  In other respects this molecjule (number 80) is very close to the means found for the first four dodecamers posted on this site.

Virtual run challenge: Pluto – King of the Kuiper Belt

Health - opinions

Cute logo, almost over, no where near was the 31million miles reached, run or walked by over 700 people who signed up.  I did finish more than my goal of 1,000 miles (beginning in May 2022 as I remember). I saw some pretty interesting posts….  one single entry of over 4,000 miles…. one gets a little nervous when posts are like this… LOL.  Mine were daily, and mostly earned jogging inside, and in the neighborhood with the dogs.  I will check on the 31st of Dec, but I hope to be in the top 10% of participants (and next oldest of the participants) 1202 miles logged with four days before the end….. I loved the logo which below.  I guess they didn’t shut this down on the first of jan 2023 after all….

so i keep adding miles (walking miles now, as i am running the year 2023 with RunTheEdge, so all miles added to this event are walking miles (per my fitbit). 1327.69 miles 01-22-2023.

OOPS, virtualrun pulled the plug on this one, LOL, feb 1 2023 (likely no longer making them money, likely too, not really interested in 31,000,000 miles as a goal.

Verge of a Dream: Teardrops

Prose and Poems

I don’t need
To fall down
Or try and win
Then fail again.
Thinking of
You not thinking
of me is
all it takes
to release the
teardrops in me.

I don’t need
to wake up
scared in the
middle of the
night.
Or give up like
I might do
from the toll
of years that
anyone can see
and I feel.
Thinking of
how forever
ends apart
is all it takes
to release the
teardrops
from my heart.

If I’ve hoped
for something
and it was
good and lost.
Or happiness comes
at so much
cost. It won’t
make me feel
let down. Because
having your
last kiss is
all there is
and in
their release
no more
the time
will be when
sweet teardrops
forget
to fall.

RLB 11-29-2022

FROM: Bobby Schuller – Hour of Power 11-22-2022

Quotes and Typos

I thought this was really good — pertaining to our individual worldviews (including those who view their own ideas as just and dictatoral -aka wars and opressions) and wanted to save it to read again and again.

Quote “Yesterday we introduced the thought that each of us as humans has our own little kingdom. To further that discussion, today, I want to talk about how every one of these kingdoms operates under a philosophy, which is known as a worldview. A worldview is a lens through which you view circumstances and situations; it’s sort of a mishmash of your religion, culture, background, family life, and education. Your worldview provides a framework in which you see and process tragedy, and victory and you perceive meaning and purpose in life. A worldview attempts to answer these four questions: Who am I? Where am I? What’s the problem? What’s the solution?

In Jesus’ day, there were two primary groups that attempted to answer those questions: the Jews and the Romans. The Romans taught that you were 100% what you did and what you achieved. On the other hand, the Pharisees taught that you were dirty and that the only way to achieve holiness was to separate from unclean people. Neither of these worldviews offered any hope for those with disabilities, the poor, or sinners.

So Jesus came into a world with neither helpful nor hopeful worldviews. This is why it was such a big deal when He got up on a mountain and began to speak to a bunch of outcasts — sick people, outsiders, and Samaritans — telling them that they were blessed because they were meek, poor in spirit, and sad. You see, friend, the Kingdom of God is for everyone and it alone offers hope to ALL of humanity! Isn’t that the best news?”  animation made from google earth pro and GIMP…  how fun

MY OPINION

Rants

Extremeism does not exist in all religion or all governing practices (it does certainly exist in a few)

Extreemists do exist in religions and governing practices (they certainly exist in all)

Perfluorophenanthrene: microscopic droplets in hepatocyte lysoso-peroxisomes

Legacy Perfluorocarbons

This is a negative I retrieved from storage (40 years past) which has a clear picture of the repartition of perfluorochemical emulsions (just some, dependent on the properties of each perfluorocarbon) within the lysososomes/perosisosomes of liver hepatocytes and interstitial cells.  This image is one I pseudocolored showing how within a membrane bound organelle, proteins coat small globules of perfluorophenanthrene (PFP – chemical image from ChemSpider, lined to name).

 

Image below neg 8946, plastic block 28373, mouse # 26, liver, 21 days after infusion with perfluorophenanthrene (i can look up the dose in mg/kg).  This type of intra-organellar, reemulsification of perfluorocarbon based blood substitute is very dependent on which perfluorochemical is infused). Please note that I have drawn around each lysosome/peroxisosome with sharpie (LOL) to define them.

Two mitochondria are present, many polysomes, and rough ER as well.  THe pink areas within mitochondria are “not identified as routine cristi, but something has changed there”.

Also note that during processing it is most likely that the actual PFP is no longer there and thus a “ghost” vacuole is present but clearly demarcated by the presence of the proteins fixed within.

 

Four dodecamers: CRD peak-valley grayscale values

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

same MO. See from bottom image that just one of the dodecamers (number 42a_aka_44)  had any missing values, and then just 1. So the separate sum (172 with and without that one missing value) is listed in the top image, along with the summary of just the means of the four dodecamers calculated separately) and the single dodecamer with one missing value is the very bottom set of valley parameters.