Monthly Archives: September 2018

SP-D diagrams

Electron microgaphs of lung, Science and art cover illustrations, surfactant proteins A and D

I have looked at literally dozens of diagrams of SP-A and they just are repeats of the initial diagrams put out by the labs that investigated surfactant proteins early on. I am assuming the earliest came from this institution, Whitsett’s lab, but I am not going to spend the time to check.  Owing to the basic premise, certainly not unique to anyone in this institution alone, that the diagrams don’t matter as much as the science… i think that the dimensionality of the SP-A bouquet has been lost, most likely due to the lack of care in the production of the “diagrams” which accompany papers.  In fact the angle of the neck – CRD portion of the bouquet trimers has two configurations, open and closed, according to some researchers.  I will post the mean+/-SEM of the angles typically used in diagrams, vs what is actually measured in transmission electron micrographs.

Just a word to those preparing scientific illustrations – one does a huge disservice to perpetrate erroneous diagrams.

While on the topic of diagrams, why on earth do people keep representing the CRD of SP-A and SP-D as ovals, arranged like little tulips. THis is just lazy.  The CRD of both proteins have been so well worked out that from a protein database one can actually provide the entire structure (that is the neck and the CRD) and it looks absolutely nothing like the typical tulip. See a couple tulips below.  They are just not representative of actual molecules.

Sometimes I laugh – SP-D

Health - opinions, Rants, Science and art cover illustrations, surfactant proteins A and D, Ultimate order, the cell

I am trying to write a comment page about innate immunity proteins and the possibility of nano-superballs being used to configure and distribute such immune proteins (which, by the way is a logical next step in that research since at least two of the C-type lectins that are important for innate immunity actually do have fuzzyball multimer structures. Those would be SP-D and SP-A. When I saw this cute dimer of surfactant protein D I just laughed to myself, such a happy dancer.  This particular image of a surfactant protein D dimer came from a portion of an AFM image published by Arroyo et al, JMB, 430:1495-1509, 2018. Thanks to them for the laugh, and the inspiration to keep up the exercise program for the sake of good health.  This guy (girl) is just about to cross the half-marathon finish line.

What is interesting is the light and airy feeling, arms outstretched, legs in the air and the perfectly positioned ball (likely a loose CRD, ha ha) for a head.

Just for fun

Good Grief!, Rants

Working on the possible usefulness of surfactant proteins in the construction of fullerene nanoparticles for immune purposes….i google images…many many images, hunting for electron microscopy, cryo-preservation microscopy, electron tomography, atomic force microscopy, etc, to see whether anyone has produced images of surfactant proteins A or D, or maybe MBL as well.  Many exist for SP-D, not that many for SP-A, and some of the other c-type lectins I have not seen TEM for at all.

But just for fun, when i google images of the names of highly oligomerized SP-A or D, i get the terms fuzzy balls, and for fullerenes, the name superballs.  But google brings up the cutest images for rounded protein and mineral and vitamin supplements at the same time..  ha ha…. just fun. And…so much for artificial intelligence in image identification (or naming).

Surfactant protein D fuzzyballs

Electron microgaphs of lung, Science and art cover illustrations, surfactant proteins A and D, Ultimate order, the cell

I have scoured the literature to find any images, and even diagrams, of rat native and recombinant surfactant protein D, hereafter called SP-D. There are some very nice images (perhaps the best) by Crouch et al, published in JBC, (also using recombinant SP-D) which I have cut and pasted into this video, counting all the trimeric arms with “attached” carbohydrate recognition domains. Crouch et al indicated that about 5% of the structures are multi-assemblies, that is something around 12 arms? or more is what they show. Actually two authors have commented on the fuzzyball rarity in shadowed images for microscopy. Other images came from google searches for SP-D diagrams, and many of these are from McCormack, and from others in the lab here at Cincinnati’s Childrens Hospital.

The three dimensional structure (multimers) of SP-A and SP-D have been shown to be important for function.  Vieira et al 2017“In conjunction, these data demonstrate the critical role of oligomeric  and tridimensional structure of surfactant protein A and surfactant protein D for proper function.” and also say “SP-A and D can target pathogens by simple aggregation, without a direct interaction with the cell. Similar to complement C1q, SP- A can function as an “activation-ligand” which facilitates particle uptake once it is coated by Immunoglobulin G”

SP-A and SP-D have distinct functions though both are quite easily given the “title” of multivalent innate immune proteins.  What is interesting is that under some circumstances and not others, they may adopt a more spherical  and highly oligomerized state, or they may remain trimers, hexadecamers, dodecamers and in lower oligomerization states. For some reason the bouquet for SP-A as an 18-mer is most frequently cited in the literature when in fact the electron microscopy might show full fuzzyballs of SP-A, and other forms (periodicity in flat sheets, under other circumstances.  In the same micrographs of type II alveolar cells, SP-D fuzzyballs really havn’t been encountered, but in vitro SP-D makes great fuzzyballs.

 

https://thankuscience.com/wp-content/uploads/2018/09/SP-D.avi (cut and paste)  SP-D .avi link

I was curious whether there was a pattern to the number of trimers in any given fuzzyball and for SP-D there were numerous articles which actually had pictures of oligomers.  The number of arms (trimers) for each fuzzyball of SP-D, randomly encountered in publications (not to be confused with randomly photographed under the microscope… as i am quite sure there was selection bias in photographing these) is shown on x axis of this quick summary graph.  Incidence is on the Y axis. I could have counted more (and may do that) in some images where there was indication that perhaps there were arms and CRDs that had been displaced during collapse of the fuzzyball onto the grid. Image below is taken from Crouch et al mentioned above and used without permission.

Here is a short videoclip of SP-D fuzzyballs — you can see where I have counted the carbohydrate recognition domains, as I overlayed them on the existing micrograph with red dots. There are places where I might add or subtract one now and then from what is pictured, but in general you can see that top number is something around 26 arms (each a trimeric molecule) in some fuzzyballs. I think more than 32 (a multiple of 4 is likely) arms in any given fuzzyball is going to be pretty uncommon.  It is very apparent in some that groups of 4 arms persist.  While the orientation of SP-D arms is probably end to end in those groups of 4, I am thinking that SP-A fuzzyballs are going to be four groups of 18-mers. Whether such is found in the literature I will soon find out.

Pentraxin diagram: what… certainly not 5

Rants, Science and art cover illustrations

Here is why i wonder if scientists in general have much in the way of “visual capacity”.  Here is a terrific example of a diagram which i find totally confusing. Please determine if i am the confused one or if this author and/or their diagrammer? The figure is part of an chapter: Fundamentals of Immunology – which is really a nice chapter but this just is funny.  Figure below is cut and pasted from their pdf file, I added the red text and the arrows pointing to an attempt at perspective for 5 semi-spherical structures…. at the top, bottom and the two rows of 4, making 8 in the middle (which apparently should have been two rows of 5, with 10 total.  So this is not a dig at the chapter as there is lots of great information there and the molecular reconstructions sare very nice.  Its just this one, on pentraxin…  pent for five, shows four structures in the lower half of this diagram. Too cute.   I would have to call this a visual typo. I read this great article on the cost of typos….  it is nicely written and makes me wonder whether not capitalizing the letter I when i type is keeping my websites from doing well in google searches (not so LOL).  At any rate, most expensive typo blog is worth reading and it is kind of funny.  What is below though is something that doesn’t often get “proofed” sadly, I don’t know why.  Scientific publications get substantial review… but so many scientific diagrams go to press with blatant mistakes that it is alarming.  These have significant impact on understanding principles and concepts yet are not really even investigated as “typos”.  So i get that the side view might just show two bumps, but there is 3Dimensions to the lowest diagram below, and in this perspective, five round areas shojld have shown up somewhere. Again, what is a great name for a diagrammatic mistake? BTW i am not listing the authors of this chapter, that just isn’t the point.

Laundering money

Rants

I laundered money today….. a one dollar bill (haha), sent by an advertising – poll taking group hoping for my participation. I didn’t ask for it, but instead of just putting it in my purse, i laundered it….. thinking of all those things (small pox virus, anthrax, bug juice, etc) that could have been purposefully added to the enticement. 

Sears washing machine repair — wow, not good

Rants

UPDATE,  no wonder sears is going bankrupt….. i have called countless times over the last three months…. just today i spent an hour on the phone with sears people, and an hour wasted, only to find out that a case number was not assigned to my refund… what….  This is so discouraging, I think “no body is home” there, maybe bankruptcy is what the 7 people with whom i spoke today, only to be transfered at one point to Lawn and Garden (what, this is customer service, and repair parts)….  no one is home, no one is home. Sears has to be the worst customer service and repair service i have ever experienced, and this is the group near cincinnati…. i should post their ID numbers, and little Jess, who answers the phone, has hung up at least three times and knows me by name.  wow,   what i want is nothing spectacular, just what they wrote out on my refund slip.

I won my battle (sort of) with the sears today…

Wednesday I had a repair appointment for a washing machine that had stopped working… sounded like the pump was bad.
This turned into a sad saga, but a reasonably good ending.

A subcontractor repair service here in Cincinnati was sent out to repair a Sears washer for me… first off I couldn’t believe the high pressure sales and the blatant attempt to tell me i had to replace more parts than necessary. He used the typical tricks…. pushing down on the washing machine tub to test the shock-springs… yep those were bad according to him. Then he clicked the dial back and forth to bring up the repair codes. I asked for the sequence so i could check it myself if i needed… he refused to give it up, or explain the way the codes were coming up. He told me i needed a new lid switch, new spring-shocks and a new pump. 509 bucks to fix a machine….I kept asking why i needed a new lid switch, the one in the machine was just fine…. he said the computer codes would not work unless i changed the switch. I stood there the entire time… asking questions, i’m sure he was totally pissed off, but nothing seemed to be going well. but it turns out that everything about which i querried him…. he lied about or was fudging.

So.. he told me i needed a new lid switch — that the switch came up on the error codes… also the new switch part looked different, but he put it in… he told me i need the new spring-shock things….but when he opened the new package all four of them were bigger than the parts he took out…. i mentioned it twice…. at one point he said “dont touch that” while i was measuring the springs… (and i can understand him not wanting me to mess with stuff) i just replied i wasn’t touching them, just sizing them up. They were at least 3 inches too long. He did not explain, nor did he go to his truck to get the right parts….so he put the spring in and the tub now hung at least 3 inches below the rim of the lid, clearly not an adequate repair…. i said… i don’t like that, there is so much room that things will spillover the tub inbetween the sides of the washing machine. To that he replied, don’t overfill the tub. I said those were the wrong springs and i mentioned it to you twice…. he did not remove and replace them with the right springs. He did put in a pump, which turns out to have been the only real problem.

Then he would NOT stop trying to sell me the maintenance package which would take 250 off my bill…. and the monthly charge would only be 50 dollars for one year… I declined, and i asked him if he got a kickback…. he said NO. Then he told me when i apologized for getting in his business, “he was a christian and he would not take it personally” ha ha.. I wasnt really happy with the whole job..or his excape clause of “being christian” that was supposed to couch his deceit.

So the next morning i got the repair person scheduling lady on the line and asked for her supervisor (which she did not provide me with) and i had a VISA employee on the other line asking them to cancel (challenge) the payment.

So sears agreed to send out a “different” (as i specified) repair person. What i had in my mind to tell him was…. Wednesday you did it your way, but Friday (today) we will do it my way. First thing we did per my request, was to put my old switch back in…. of course it worked just fine….. second thing i asked him was to check the part number on the pump…. to make sure it was the right pump for this machine….since i had no confidence that the old repair guy put the right pump in. But according to the new tech that was an OK part… but i felt it necessary to have the new guy check since everything else the first repair person told me was false.

Next thing we talked about was whether i really needed new spring-shock things…. he opened the right part number (which by the way had four springs the same length as the my originals)… I did try to test the old springs before agreeing to new ones, to see if they were weak or broken or not stiff anymore….. i could probably have had him put the old ones back in but instead chose to get the new ones…. because this machine does take a beating when i wash bedspreads and rugs…. so i did opt in for that. However the tub now sits just half an inch or so under the lid like it should.

Anyway Sears did not (and better not have) charged me for the new service call to swap out the springs and lid switch –but it wasted four hours of waiting for them to arrive.  BUT the young tech did remove the $$ for the unnecessary part and tax and labor for the lid switch….and he confirmed for me it was NOT true that the timer needed to be changed even though it worked OK just because of an error code, he also told me too that there IS a kick back to the repairman for getting  customers to sign up for the repair plan (i knew that, the first guy just lied), whats more, there IS an additional bonus if you get a certain number of people to sign up…. all in all… the first guy was a joke.

i did tell the young kid this morning he would do well, he was honest, that is the most important attribute a person can have. What i would like to tell the veteran repair person who mentioned he was getting ready to retire, is that he may profess to being “christian” but he was a dishonest “christian”…. we as followers of the red letters dont need that kind of publicity…and Sears doesnt either, ha ha.

Travesty: when unsubscribe doesn’t work

Rants

Travesty: when unsubscribe doesn’t work what options do you have.  So i get an email from Alibaba — i am not sure why, but had to hunt high and low to find their faded grey “unsubscribe” link, and when I get to the link — haha — this is what I see.  Now that’s pretty sneaky….. not letting people unsubscribe — under pretense.  Fake truth – out and out lying – attempts to upsel and deceive – pretty ugly world sometimes, and this is just the small stuff.

alibaba has a fake unsubscribe link

Micrographs and mosaics

Science and art cover illustrations

I have used this technique before, maybe decades (more than 3) ago when faced with the very real necessity of pitching my beloved black and white prints from the microscopes I have used in the past, that is light microscopes, electron microscopes, and dissecting microscopes.  The tesserae in this picture (which was made expressly for one of my two grandsons) are made from a combination of TEM and LM micrographs.  The big-“eyed” structures are keratinocyte nuclei with one or two nucleoli, and one in particular has an apoptotic keratinocyte nearby. There is mouse back skin, and thin layers of keratin present, and some wacked-out cristae formation in mitochondria from liver of genetically engineered mice, and/or rats exposed to toxins for the sake of determining whether we are poisoning ourselves with chemicals and stuff, and whatever else I have saved in the box of potential cut-ups.  One mitochondrion in the center has peripheral parallel cristae and the one below that has a collection of protein in the intracristae space.  If you look closely you can see the little pale KODAK letters which were on the sides of prints that we used to make of film strips…. that was indeed a long time ago.  I actually have saved enough of the extra prints to make a large abstract…. maybe someday I will get to it.  In the meantime, identify all the structures that you can.

fun mosaic picture with transmission and light micrographs left over from research projects