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What is ICP27 trying to tell us? One of you could get a PhD if you figure it out !

It wouldn’t be the first time a viral protein led us to an important cellular mechanism. Consider what the polio virus taught us about the translation of mRNA into protein. It cleaves two components of eIF-4F (eukaryotic Initiation (of ribosome translation of mRNA into protein) Factor 4F totally shutting down synthesis of mRNAs with a cap on their 5′ end (which is most of them). Poliovirus proteins don’t have these caps so their proteins continue to be made.

Well this brings us to ICP27 (Infected Cell Protein 27) a product of the Herpes Simplex virus. You can read all about it in [ Proc. Natl. Acad. Sci. vol. 113 pp. 12256 – 12261 ’16 ]. ICP27 is essential for herpes virus infection. This work shows that it inhibits intron splicing (but in under 1% of cellular genes) and also promotes the use of alternative 5′ splice sites.

It also induces the expression of pre-mRNAS prematurely cleaved and polyAdenylated from cryptic polyAdenylation signals located in intron 1 or intron 2 of an amazing 1% of all cellular genes. These prematurely cleaved and polyAdenylated mRNA sometimes contain novel open reading frames (ORFs). They are typically intronless (they should be) and under 2 kiloBases long. They are expressed early during viral infection and efficiently exported to cytoplasm. The ICP27 targeted genes are GC rich (as are all Herpes simplex genes), contain cytosine rich sequences near the 5′ splice site.

The paper also showed that optimization of splice site sequences, or mutation of nearby cytosines eliminated ICP27 mediated splicing inhibition. Introduction of cytosine rich sequences to an ICP27 INsensitive splicing reporter conferred susceptibility to ICP27.

How is this going to help you get a PhD? Ask yourself. What are cryptic polyAdenylation signals doing in the first two introns in so many genes? It seems obvious (to me) that as well as the virus the cell is using them for some purpose. It isn’t hard to mutate something to the signal for polyadenylation AAUAAA. Interestingly cleavage doesn’t occur here, but 30 nucleotides or so downstream. The sequence occurs every 4^6 == 4096 nucleotides (if they’re random). I’m not sure what the total length of introns #1 and #2 are of our 20,000 or so protein coding genes, but someone should be able to find out and see if 200 occurrences of this sequence is more than would be expected by chance.

The plot thickens when the paper notes that “Over 200 genes are affected by ICP27. Over 30 (including PML, STING, TRAF6, PPP6C, MAP3K7, FBXw11, IFNAR2, NKFB1, RELA and CREBP are related to the immune pathway). Do you think the cell doesn’t use this pathway as well?

What about the existence of other viral (and cellular) proteins doing the same sort of thing (but on different introns perhaps). What are those novel open reading frames in the alternatively spliced mRNAs doing?

Fascinating stuff. Time to get busy if you’re an enterprising grad student, or young faculty member.

Vacation — no posts for a while

Off to Maine (and perhaps Prince Edward Island) and perhaps to see a dying friend (that’s what happens when you reach my age — 78 ). I’ve found that the best way to get back in the swing of things on return is just start with the latest journals, skipping what you missed. Trying to double up on your reading when you get back is unpleasant and makes you wish you never went away. If you missed something important, eventually you will hear about it.

So I stopped reading 26 August, and next evening bumped into a friend who wanted to discuss something in that day’s Science magazine.

Leave a comment on this post, if there’s anything you’d like to hear about.

The plural of anecdote is NOT data (in medicine at least)

The previous post (https://luysii.wordpress.com/2016/08/22/the-plural-of-anecdote-is-data/) showed that collecting a bunch of small studies (anecdotes) was extremely helpful in seeing the larger picture.

In medicine exactly the opposite occurs. The only way to find out if something works is to do a controlled study. [ Science vol. 297 p 325 ’02 ] There were over 50 observational studies showing benefits for hormone replacement in menopausal women.. Observational studies are basically anecdotes. During the planning study for the Women’s Health Initiative (WHI), some argued that it was unethical to deny some women hormones and give them a placebo. The reason HERS (Heart and Estrogen/Progesterone Replacement Study) was even done was that Wyeth couldn’t get the FDA to approve hormone replacement therapy as a treatment to prevent cardiovascular disease, so they funded HERS to prove their case. Most readers of this have probably read all sorts of bitching about the slowness of the FDA in approving drugs but in this case they did the female populace a huge favor.

As you probably know, the results of hormone replacement in both studies were a disaster (the HERS trial was stopped at 5.2 years after because of increased breast cancer in the treated group). There was also an increased risk of coronary heart disease by 30%, stroke by 41%. At least hip fracture was reduced. Fortunately, even though these were bad outcomes, they were infrequent,(but more frequent in the treated group).

These weren’t lab animals, but someone’s wife and/or mother.

How could they have been so far off? Before all this started, estrogen users were different from nonUsers in several respects — first they were doing something about their health, and clearly had more medical supervision. In addition they were better educated, smoked less and of a higher social class, all of which tend to diminish morbidity and mortality.

Something very similar happened in my field of neurology (not that vascular disease doesn’t severely impact the nervous system). There was a very logical operation to improve cerebral circulation — the pulse just in front of your ear is the superficial temporal artery, a branch of the common carotid after it splits in the internal carotid which goes into the skull and supplies blood to the brain, and the external carotid. If the internal carotid is blocked and the common carotid artery is open, then open the skull and hook (anastomose) the superficial temporal artery to a vessel on the surface of the brain, bypassing the blockage. If you want to know how it is done see — http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1150876/.

There was all sorts of anecdotal evidence of miraculous recovery from stroke. The neurosurgeons and vascular surgeons mounted a wonderful controlled study of the surgery even though many thought it was unnecessary — so 1377 patients were prospectively randomized to have the surgery or medical management. The surgery wasn’t better than medical management N Engl J Med 1985; 313:1191-1200November 7, 1985DOI: 10.1056/NEJM198511073131904, so the procedure was abandoned.

A lump of coal to the authors

The following sentence appeared in a paper in the Proceedings of The National Academy of Sciences USA this year. The names of the authors have been withheld to protect the guilty. The following is an exact quote

These languages were selected because they provide contrasts of transparent vs. opaque orthographies with alphabetic vs. logographic writing systems, which map into monomorphemic and monosyllabic words vs. morphologically complex and multisyllabic words, having concatenated linear morphology vs. nonconcatenated nonlinear morphology, with visually simple vs. complex print, which map into tonal vs. nontonal spoken forms.

A post which may actually be of some use to Safari users

This post may actually be of some use (to those of you using Safari on a Mac anyway). Yesterday, I had the awful experience of a pop-up that I couldn’t get rid of. It said that I had to call a number right away to protect my identity etc. etc. I’d heard about malware that got on your computer encrypting everything so you couldn’t use it, except to pay them a ransom.

So I tried quitting Safari and restarting. No luck. There it was along with sites I always go to on Safari (PNAS, Nature, Science, Cell and Neuron).

So I tried to shut down (which wasn’t possible because I got a note that Safari was busy).

Then I used Force Quit to shut down Safari and was then able to shut down.

Rebooting was of no help whatsoever, as the pop-up appeared along with all 5 sites I usually have open whenever I opened Safari. This happened several times, yours truly being bull headed enough to try it again and again against all hope.

Time to call Applecare — they fixed it immediately. Apparently Safari has a some sore of cache which reopens everything you’ve opened on your last visit. This is what brought up my favored sites and the annoying popup.

The trick is to Open Safari from the Dock (and you must do it this way, not from recently used items) with the shift key held down — this flushed the cache (and the pop-up along with it).

Applecare said this pop-up wasn’t malware, just a scam which charged money to get rid of it (which you can now do free of charge).

Taking a break

No posts for a while. Off to Maine for some R & R after an intense two months of our daughter in law’s pregnancy complicated by pre-eclampsia followed by an emergency delivery at 34 weeks gestation of a 3.5 pound infant who had to spend 3 weeks in the neonatal ICU. Mother and daughter doing well presently. Sometimes you can really know too much. As a neurologist I saw everything which could go wrong in this situation (and plenty did).

There is a lot of very interesting material to post about which I’ve not had time for
l. A thermodynamic (rather than a chemical) explanation of temperature sensitivity of ion channels
2. The importance of a long terminal repeat of an endogenous retrovirus in our genome for the production of induced pluripotent stem cells (IPSCs)
3. A serious attack on the validity of some work which I posted on earlier https://luysii.wordpress.com/2014/02/23/are-memories-stored-outside-of-neurons/

Perhaps when we get back

Physics to the rescue

It’s enough to drive a medicinal chemist nuts. General anesthetics are an extremely wide ranging class of chemicals, ranging from Xenon (which has essentially no chemistry) to the steroid alfaxalone which has 56 carbons. How can they possibly have a similar mechanism of action? It’s long been noted that anesthetic potency is proportional to lipid solubility, so that’s at least something to hang your hat on.

Other work has noted that enantiomers of some anesthetics vary in potency implying that they are interacting with something optically active (like proteins). However, you should note sphingosine which is part of many cell membrane lipids (gangliosides, sulfatides etc. etc.) contains two optically active carbons.

A great paper [ Proc. Natl. Acad. Sci. vol. 111 pp. E3524 – E3533 ’14 ] notes that although Xenon has no chemistry it does have physics. It facilitates electron transfer between conductors (clearly a physical effect). The present work does some quantum mechanical calculations purporting to show that Xenon can extend the highest occupied molecular orbital (HOMO) of an alpha helix so as to bridge the gap to another helix.

This paper shows that Xe, SF6, NO and chloroform cause rapid increases in the electron spin content of Drosophila (probably another physical effect). The changes are reversible. Anesthetic resistant mutant strains (in what protein) show a different pattern of spin responses to anesthetic.

So they think general anesthetics might work by perturbing the electronic structure of proteins. It’s certainly a fresh idea.

What is carrying the anesthetic induced increase in spin? Speculations are bruited about. They don’t think the spin changes are due to free radicals. They favor changes in the redox state of metals. Could it be due to electrons in melanin (the prevalent stable free radical in flies). Could it be changes in spin polarization? Electrons traversing chiral materials can become spin polarized.

Why this should affect neurons isn’t known, and further speculations are given (1) electron currents in mitochondria, (2) redox reactions where electrons are used to break a disulfide bond.

Fascinating paper, and Mark Twain said it the best “There is something fascinating about science. One gets such wholesale returns of conjecture out of such a trifling investment of fact.”

A Touching Mother’s Day Story

Yes, a touching mother’s day story for you all. It was 47 years ago, and I was an intern at a big city hospital on rotation in their emergency room. The ER entrance was half a block from an intersection with a bar on each corner. On a Saturday night, we knew better than to try to get some sleep before 2AM or until we’d put in 2 chest tubes (to drain blood from the lungs, which had been shot or stabbed). The bartenders were an intelligent lot — they had to be quick thinking to defuse situations, and we came to know them by name. So it was 3AM 47 years ago and Tyrone was trudging past on his way home, and I was just outside the ER getting some cool night air, things having quieted down.

“Happy Mother’s day, Tyrone” sayeth I

“Thanks Doc, but every day is Mother’s day with me”

“Why, Tyrone?”

“Because every day I get called a mother— “

The weirdness of gravity

We experience gravity every waking moment, so it’s hard to recognize just how strange the gravitational ‘force’ actually is. Push a toy sailboat, a rowboat, and a yacht with the same amount of force (effort). What happens?

The smaller the boat, the faster it moves. Physicists would say the acceleration (change in velocity over time e.g. from the boat not moving at all to moving somewhat) is inversely proportional to the mass of the boat. This is Newton’s famous second law force = mass * acceleration. This isn’t actually what he said which you’ll find at the end.

So in every force except gravity, the bigger the force the more the acceleration. In Galileo’s famous experiment (which Wikipedia says might actually not have occurred), he dropped 2 objects of different masses from the leaning tower of Pisa and found that they hit the ground at the same time, so the acceleration of both due to the ‘force’ of gravity is the for all objects regardless of their different masses.

This implies that gravity is a force that adjusts itself to the mass of the object it is pushing on to produce the same acceleration. Weird, but true.

General relativity says, that the motion must be considered not just in space and time, but in 4 dimensional space-time where space can become our conventional time and vice versa. Here all paths are as straight as possible — because the 4 dimensional space-time we inhabit has an intrinsic curvature, produced by the masses found within it.

What Newton said: “The change of motion is proportional to the motive force impressed and is made in the direction of the straight line in which that force is impressed” By motion Newton means what we call momentum — mass * velocity.

The change in momentum is of course a change in velocity — which is what acceleration actually is. Note that mass is assumed constant regardless of how fast the object is moving. This isn’t even true in special relativity (which doesn’t include gravity — that’s what general relativity is all about).

While reading the research literature is a joy, sometimes it isn’t

“In this sense, enhanced connectivity of an essential node [e.g., in this study, as suggested by the previous analysis by Wühle et al. (17), the secondary somatosensory cortex, S2; for the issue of whether S1 is an essential node, see ref. 22] to brain structures, which render information consciously accessible, constitute predefined or privileged pathways along which neural information can propagate when confronted with an appropriate stimulus.”

I won’t tell you where this is from, but it’s but one horrible sentence among many. Even worse, the paper, is about something quite interesting — how much of the brain (and which parts) have to be activated before a barely perceptible stimulus is reported (e.g. when and where does consciousness begin).