Welcome to the world of the physician

In a sense, the uncertainty about hematologic complications of the pandemic vaccines is good in that it is a real teaching moment for the public about what docs confront every day — balancing risk vs. reward. 

No drug is without side effects.  No surgery is without complications.  It is good to see the public  wrestle with these things.  

For a very good explanation of what those complications are and the risks and rewards of taking the vaccines please see — 

https://blogs.sciencemag.org/pipeline/archives/2021/04/14/vaccine-side-effects-q-and-a

Even more interesting are the 139 comments found at the end of  the article.  Some are from experts, some are from frightened lay people; as always there are people with an ax to grind.  As is usually the case in medicine, the data are not clear cut and sometimes contradictory.  As is always the case more data would be helpful, is desired and rarely available.  What is particularly interesting to me is the way some very knowledgable people wrestle with the data, interpreting the same data differently.  Welcome to the real world. 

On a more positive note, a friend who teaches at Hopkins sent me the a copy of the eMail below, with permission to share it.  This provides lots of excellent data on the protective effects of vaccination in a  group of people with a fairly high risk of exposure to the virus,  working at a major medical center where lots of very sick COVID-19 patients are being treated. 

35,000 were vaccinated.  Nonetheless 51 became infected at a time of maximum protection (5 weeks or more after the first shot), demonstrating that the vaccine isn’t 100% protective.  But no one ever claimed that it was.

 But only 2 of the 51 required hospitalization.  So the vaccine is effective in preventing serious illness from the virus (2/35,000).  So who cares if the other 49 had the symptoms of the flu.  They don’t and you shouldn’t.  The number of hematologic complications wasn’t stated. There were two at most, as they always result in hospitalization.  

To the Johns Hopkins Medicine community   Dear Colleagues,   As we continue to monitor COVID-19 infection and vaccination trends at Johns Hopkins Medicine (JHM), we want to share some data about the incidence of infection among JHM personnel following partial and full vaccination.   You are considered fully vaccinated, per the Centers for Disease Control and Prevention, two weeks or more after receiving the second dose of a two-dose COVID-19 vaccine regimen and two weeks or more after receiving a one-dose COVID-19 vaccine regimen. This is when the body has had a chance to produce the antibodies and immune response that protect against infection. Before this time, if you have started the vaccination series, you are considered partially vaccinated and you do not yet have the full amount of protection the vaccination provides against infection. While full vaccination has been found to be highly effective at preventing COVID-19, infection (the incidence is very low) is still possible even after being fully vaccinated.   We are monitoring the situation to determine how often infection seems to occur after partial or full vaccination, and the severity of those infections.   As of April 12, 2021, of the nearly 35,000 employees who were fully vaccinated (14 days or more after a second dose), 51 employees (0.14% of those who have been fully vaccinated) had tested positive for COVID-19. This demonstrates that SARS-CoV-2 infection is possible even after full vaccination, and it highlights the importance of continuing to practice basic infection prevention precautions after full vaccination. The good news is that acquiring COVID-19 after full vaccination appears to be relatively rare and, among these 51 cases, only two were severe enough to require hospitalization. This shows that the COVID-19 vaccine is highly protective against severe disease, hospitalization and death. If you have not yet been vaccinated, please schedule your appointment as soon as you can to protect yourself and others.

Some very disturbing pictures

Granted that these pictures look like microscope slides containing colored blobs, but once you understand what they show, the implications are quite frightening.

These images are biopsies of various portions of the gastrointestinal tract in a person who had become  symptomatic  three months earlier with COVID-19 from which the person  has now recovered).The green blobs represent fluorescent antibodies binding to the nucleocapsid protein of the pandemic virus (SARS-CoV-2).  They are found in the enterocyte cells which line the inside of the gut.  These are the enterocyte which live for just 5 days before they are shed.  

This is my first shot at getting pictures into my blog, and they do appear blurry (apologies !).  I will try to correct this. All you need view is in the first and second columns of rows a, c, and e as most  of the rest are controls. The pictures are from a Nature paper — here’s a link — https://www.nature.com/articles/s41586-021-03207-w.pdf

 

Why is this disturbing?  Because their presence implies that they have been made continually for the whole three months, as enterocytes are born and die. 

Well maybe it’s an artifact confined to one patient.  Unfortunately similar findings were present in 5/14 cases recovered COVID-19 patients who received GI tract biopsies for clinical reasons unrelated to COVID-19.  The 14 are from a larger series of recovered COVID19 patients (see the copy of the previous post below). Like Reverend Paley’s found watch, the presence of the viral nucleocapsid protein demands an explanation of what had to be present to put it there.

There are a series of requirement for this to happen.  The messenger RNA for the protein had to be made and present, which, in turn means at the least that the viral gene from which the mRNA for the nucleocapsid protein was made must also be present.  What mades nucleocapsid mRNA? The viral RNA dependent polymerase. So the polymerase must be present as well, along with the 3 genes coding for the 3 proteins making up the polymerase.  Not only that but all of the above must have been present in longer lived cells  than the enterocytes.

Defective viruses certainly appear during the course of viral infection (particularly as in AIDS), but it is very scary to realize just how much of the virus must be present and functioning to produce just these findings. Perhaps the fluorescent antibody was really binding to another protein, not from the virus at all.  After all, antibodies aren’t always as specific as we’d like them to be.  

However, the authors did something else which makes this much less likely. They wrote, “In addition, viral RNA was detected by in situ hybridization in biopsy samples from the two participants who were tested for it”

Further scariness:  Pictures e and f show the nucleocapsid protein is present at the far end of the terminal ileum (small intestine) a part of our GI tract which is 22 feet long. 

So this person although well, was literally crawling with both the viral protein and the machinery necessary to make it. 

Are many more, or all such people who are clinically recovered from clinical COVID-19 excreting infectious virus?  I’m sure people have looked, and if they haven’t they should be. 

I’m going to now insert the previous post on the subject.  It contains a link to the Nature paper, so feel free to follow it and look for yourself.  It contains a lot more detail. 

Is the virus still within you? Will it cause trouble?

Let’s say you’ve recovered from a bout with COVID-19. Is the virus still with you? Could it come back and cause trouble? Given the data in a recent paper [ Nature vol. 591 pp. 639 – 644 ’21 ] — https://www.nature.com/articles/s41586-021-03207-w.pdf, it’s quite possible.

But first a story about my grandmother.  She was born somewhere around the Baltic Sea in 1880 and came to America in 1893.  She died of undiagnosed (hence untreated) miliary Tuberculosis in a University Hospital in 1967.  Just about everyone in Europe in the 1880s was exposed to TB and just like SARS-CoV-2 many if not most were asymptomatic.  Their lungs walled off the organism in something called a Gohn complex — https://en.wikipedia.org/wiki/Ghon%27s_complex.  The organism didn’t die — and probably broke out of the complex as my grandmother aged and her immune system got weaker and weaker.  It is very unlikely that she picked it up by exposure in the 1960’s.  As they say TB is forgotten but not gone.  

Which brings me to the Nature paper.  At first I thought it was great and very optimistic.  Some 87 people from New York City who had symptomatic SARS-CoV-2 infection (proven by finding the viral genome using RT-PCR technique).  The authors studied the antibody responses at an average of 1.3 and 6.2 months after infection.  Although the antibody levels dropped (which always happens) they changed so they bound the virus more tightly.  This is called affinity maturation — https://en.wikipedia.org/wiki/Affinity_maturation.  

So that’s good? 

No that’s bad because it implies that the protein stimulating affinity maturation is still around. The authors note the persistent antigenic stimulation of the immune system is possible because an “antigen trapped in the form of immune complexes on follicular dendritic cells .. . . . can be long-lived, because follicular dendritic cells do not internalize immune complexes”.  

Well maybe, but the paper gives evidence for another mechanism of antigen persistence (which I find more persuasive). 14 of the people had intestinal biopsies for appropriate clinical indications (see Table 7 in the supplementary information of the article). In some of the biopsies they detect viral antigen in some of the enterocytes (cells which line the inside of the gut) — I’m assuming the antigen is the viral spike protein, but it’s hard to find exactly what it is. 

This is quite bad, as the lifetime of the enterocyte is 5 days.  This means that the antigen is being continually produced, which means that the mRNA for the antigen is being continually produced, which in turn means that the viral genome is still around.  The mean lifetime of cellular mRNAs is 10 hours although some hang around for days, however I doubt that the mRNA responsible for the viral antigen had lasted for 2.8 to 5.7 months which is the time after clinical infection when the biopsies were done. 

So it is possible, that like TB in the Gohn complex, the immune system has fought the virus to a draw, but that the intact organism could be still present.  As in my grandmother, it is possible that the virus will reappear as the immune system weakens with age (something that happens in all of us). 

In that case we wouldl have recrudescence not reinfection. 

PS:  My grandmother came to this country at age 13 alone and speaking no English.  Every time I feel sad at what the pandemic has put us all through, I think of that generation.  

PPS: When she got sick, I wanted to put her in the hospital where I was an intern, but our family GP (Dr. Richard A. Gove) told me taking care of my own family was a very bad idea and put her elsewhere.  I doubt that I’d have made the diagnosis, or that anyone at our hospital would have. 

PPPS:  I don’t know if they still do autopsies, but I was always able to get one after I’d tell families of the deceased about my grandmother.  It meant that my wife and I and our two little kids were all screened for TB. 

PPPPS — a friend brought up the following — Eleanor Roosevelt, who was thought to have aplastic anemia, was treated with prednisone and later found to have died of military tuberculous, probably the recurrence of tb acquired some 4 decades earlier.

 

 

Is the virus still within you? Will it cause trouble?

Let’s say you’ve recovered from a bout with COVID-19. Is the virus still with you? Could it come back and cause trouble? Given the data in a recent paper [ Nature vol. 591 pp. 639 – 644 ’21 ] — https://www.nature.com/articles/s41586-021-03207-w.pdf, it’s quite possible.

But first a story about my grandmother.  She was born somewhere around the Baltic Sea in 1880 and came to America in 1893.  She died of undiagnosed (hence untreated) miliary Tuberculosis in a University Hospital in 1967.  Just about everyone in Europe in the 1880s was exposed to TB and just like SARS-CoV-2 many if not most were asymptomatic.  Their lungs walled off the organism in something called a Gohn complex — https://en.wikipedia.org/wiki/Ghon%27s_complex.  The organism didn’t die — and probably broke out of the complex as my grandmother aged and her immune system got weaker and weaker.  It is very unlikely that she picked it up by exposure in the 1960’s.  As they say TB is forgotten but not gone.  

Which brings me to the Nature paper.  At first I thought it was great and very optimistic.  Some 87 people from New York City who had symptomatic SARS-CoV-2 infection (proven by finding the viral genome using RT-PCR technique).  The authors studied the antibody responses at an average of 1.3 and 6.2 months after infection.  Although the antibody levels dropped (which always happens) they changed so they bound the virus more tightly.  This is called affinity maturation — https://en.wikipedia.org/wiki/Affinity_maturation.  

So that’s good? 

No that’s bad because it implies that the protein stimulating affinity maturation is still around. The authors note the persistent antigenic stimulation of the immune system is possible because an “antigen trapped in the form of immune complexes on follicular dendritic cells .. . . . can be long-lived, because follicular dendritic cells do not internalize immune complexes”.  

Well maybe, but the paper gives evidence for another mechanism of antigen persistence (which I find more persuasive). 14 of the people had intestinal biopsies for appropriate clinical indications (see Table 7 in the supplementary information of the article). In some of the biopsies they detect viral antigen in some of the enterocytes (cells which line the inside of the gut) — I’m assuming the antigen is the viral spike protein, but it’s hard to find exactly what it is. 

This is quite bad, as the lifetime of the enterocyte is 5 days.  This means that the antigen is being continually produced, which means that the mRNA for the antigen is being continually produced, which in turn means that the viral genome is still around.  The mean lifetime of cellular mRNAs is 10 hours although some hang around for days, however I doubt that the mRNA responsible for the viral antigen had lasted for 2.8 to 5.7 months which is the time after clinical infection when the biopsies were done. 

So it is possible, that like TB in the Gohn complex, the immune system has fought the virus to a draw, but that the intact organism could be still present.  As in my grandmother, it is possible that the virus will reappear as the immune system weakens with age (something that happens in all of us). 

In that case we wouldl have recrudescence not reinfection. 

PS:  My grandmother came to this country at age 13 alone and speaking no English.  Every time I feel sad at what the pandemic has put us all through, I think of that generation.  

PPS: When she got sick, I wanted to put her in the hospital where I was an intern, but our family GP (Dr. Richard A. Gove) told me taking care of my own family was a very bad idea and put her elsewhere.  I doubt that I’d have made the diagnosis, or that anyone at our hospital would have. 

PPPS:  I don’t know if they still do autopsies, but I was always able to get one after I’d tell families of the deceased about my grandmother.  It meant that my wife and I and our two little kids were all screened for TB. 

PPPPS — a friend brought up the following — Eleanor Roosevelt, who was thought to have aplastic anemia, was treated with prednisone and later found to have died of military tuberculous, probably the recurrence of tb acquired some 4 decades earlier.

 

 

 

More moonlighting

Well we used to think we understood what ion channels in the cell membrane did and how they worked. To a significant extent we do know how they conduct ions, permitting some and keeping others out in response to changes in membrane potential and neurotransmitters. It’s when they start doing other things that we begin to realize that we’re not in Kansas anymore.

Abnormal binding of one protein (filamin A) to one of the classic ion channels (the alpha7 nicotinic cholinergic receptor) may actually lead to a therapy for Alzheimer’s disease — for details please see — https://luysii.wordpress.com/2021/03/25/the-science-behind-cassava-sciences-sava/

The Kv3.3 voltage gating potassium channel is widely expressed in the brain.  Large amounts are found neurons concerned with sound, where firing rates are high.  Kv3.3 repolarizes them (and quickly) so they can fire again in response to high frequency stimuli (e.g. sound).  Kv3.3 is also found in the cerebellum and a mutation Glycine #529 –> Arginine is associated with a hereditary disease causing incoordination (type 13 spinocerebellar ataxia or SCA13 to be exact).

Amazingly the mutant conducts potassium ions quite normally.  The mutation (G529R) causes the channel not to bind to something called Arp2/3 with the result that actin (a muscle protein but found in just about every cell in the body) doesn’t form the network it usually does  at the synapse.  Synapses don’t work normally when this happens. 

Why abnormally functioning synapses isn’t lethal is anyone’s guess, as is why the mutation only affects the cerebellum.  So it’s another function of an ion channel, completely unrelated to its ability to conduct ions (e.g. moonlighting). 

To understand anything in the cell you need to understand nearly everything in the cell

Understanding how variants in one protein can either increase or decrease the risk of Parkinson’s disease requires understanding of the following: the lysosome, TMEM175, Protein kinase B, protein moonlighting, ion channel lysoK_GF, dopamine neurons among other things. So get ready for a deep dive into molecular and cellular biology.

It is now 50 years and 6 months since L-DOPA was released in the USA for Parkinson’s disease, and I was tasked as a resident by the chief with running the first L-DOPA clinic at the University of Colorado.  We are still learning about the disease as the following paper Nature vol. 591 pp. 431 – 437 ’21 will show. 

The paper describes an potassium conducting ion channel in the lysosomal membrane called LysoK_GF.  The channel is made from two proteins TMEM175 and protein kinase B (also known as AKT).

TMEM175 is an ion channel conducting potassium.  It is unlike any of the 80 or so known potassium channels.  It  contains two repeats of 6 transmembrane helices (rather than 4) and no pore loop containing the GYG potassium channel signature sequence. Lysosomes lacking it aren’t as acidic as they should be (enzymes inside the lysosome work best at acid pH).  Why loss of a potassium channel show affect lysosomal pH is a mystery (to me at least).

Genome Wide Association Studies (GWAS) have pointed to the genomic region containing TMEM175 as having risk factors for Parkinsonism.  Some variants in TMEM175 are associated with increased risk of the disease and others are associated with decreased risk — something fascinating as knowledge here should certainly tell us something about Parkinsonism.  

The other protein making up LysoK_GF is protein kinase B (also known as AKT). It is found inside the cell, sometimes associated with membranes, sometimes free in the cytoplasm. It is big containing 481 amino acids. Control of its activity is important, and Cell vol. 169 pp. 381 – 405 ’17 lists 21 separate amino acids which can be modified by such things as acetylation, phosphorylation, sumoylation, Nacetyl glucosamine, proline hydroxylation.  Well 2^21 is 2,097,152, so this should keep cell biologists busy for some time. Not only that some 100 different proteins AKT phosphorylates were known as 2017.  

TMEM175 is opened by conformational changes in AKT.  Normally the enzyme is inactive because the pleckstrin homology domain binds to the catalytic domain inhibiting enzyme activity as the substrate can’t get in.

Remarkably you can make a catalytically dead AKT, and it still works as a controller of TMEM175 activity — this is an example of a moonlighting molecule — for more please see — https://luysii.wordpress.com/2021/01/11/moonlighting-molecules/.

Normally the activity and conformation of AKT is controlled by the metabolic state of the cell (with 21 different molecular knob sites on the protein this shouldn’t be hard).  So the fact that AKT conformation controls TMEM175 conductivity which controls lysosome activity gives the metabolic state of the cell a way to control lysosomal function.  

Notice how to understand anything in the cell you must ask ‘what’s it for’, thinking that is inherently teleological. 

Now on to the two risk factors for Parkinsonism in TMEM175.  The methionine –> threonine mutation at amino acid #393 reduces the lysoK_GF current and is associated with an increased risk of parkinsonism, while the glutamine –> proline mutation at amino acid position #65 gives a channel which remains functional under conditions of nutrient starvation. 

The authors cultured dopamine neurons and found out that the full blooded channel LysoK_GF (TMEM175 + AKT) protected neurons against a variety of insults (MPTP — a known dopamine neuron toxin, hydrogen peroxide, nutrient starvation). 

TMEM175 knockout neurons accumulate more alpha-synuclein — the main constituent of the Lewy body of Parkinsonism.

So it’s all one glorious tangle, but it isn’t just molecular biological navel gazing, because it is getting close to one cause (and hopefully a treatment) of Parkinson’s disease.  

The pandemic virus as evolution professor

Like it or not, the pandemic virus (SARS-CoV-2) is giving us all lessons in evolution and natural selection. The latest is one of the clearest examples of natural selection you are likely to see.  It is very clear cut, but to leave almost no one behind, I’m going to put in a lot of background material which will bore the cognoscenti — they can skip all this and go to the meat of the issue after the ****

The genetic code is read in groups of 3.  Imagine a language in which all words must be 3 letters long. 

The dog ate the fat cat who bit the toe off one mad rat.   Call this the reading frame, in which the words all make sense to you

Any combination of 3 letters means something to the machinery inside the cell responsible for reading the code, so deleting the f in fat 

gives us 

The dog ate the atc atw hob itt het oeo ffo nem adr at.   So this is a shift of 1 from the reading frame.  While it may not make sense to you, it makes sense to the cellular machinery. 

Now let’s delete 2 letters (in a row)

The dog ate the fat cat who bit the tof fon ema dra t.  

Not much sense after the deletion is there?  Or at least a completely different message.  This is a shift of 2 from the reading frame.

Now 3 letters (in a row)

The dog ate the fat cat who bit the toe off one mad rat.  

This gives 

The dog ate the fat cat who bit the tff one mad rat.  

Which has a funny looking word (tff), but leaves the rest of the 3 letter words intact (one mad rat).  This is called an in frame deletion. It basically lops out a single 3 letter word.  

Lopping out 4, 5, 6, .. letters will just give you one of the 3 patterns (frame shift of 1, frame shift of 2 or no frameshift at all) shown above (but nothing new)

*****

Now the business end of the pandemic virus is the spike protein, and these are where the mutations everyone is worried about occur.  The spike protein binds to another protein (ACE2) on the surface of human cells and then the virus enters causing havoc.  All the vaccines we have are against the spike protein. 

The spike protein is big (1,273 different 3 letter words).  

Mutations occur randomly.  We now have something called GISAID (Global Initiative on Sharing All Influenza Data) which has well over 100,000 genome sequences of the virus.  

Other things being equal we should see as many 1,  4 (3+1), 7 (2*[3] + 1), 10 letter deletions as 2, 5 (3 + 2), 8 ( 2*[3] + 2) , as 3, 6, 9, 12, letter   deletions.

The set  1, 4, 7, 10, . . represents a shift of 1 from the original reading frame, the set 2, 5, 8, 11 … represents a frame shift of two and 3, 6, 9 .. represents a set of deletions producing no frameshift at all.

Since thousands on thousands of experiments show that mutations occur randomly, 1/3 of all deletion mutations should show a frameshift of 1, 1/3 of all deletion mutations should have a frame shift of 2, and 1/3 of all deletion mutations should produce no frameshift at all. 

Well the authors of Science vol. 371 pp. 1139 – 1142 ’21  looked at 146,795 viral sequences and found 1,108 deletions in the gene for the spike protein.

They did not find each of the 3 types of deletions occuring to the same extent (1/3 of the time).  Among all deletions, 93% were in frame.  

Why? Because out of frame deletions change everything that comes after them. 

Recall

The dog ate the atc atw hob itt het oeo ffo nem adr at.  

This means that a functional spike protein won’t be formed, and the virus won’t infect our  cells, and it certainly won’t be found in GISAID.  

Ladies and Gentlemen you have just witnessed natural selection in action. 

Actually it’s even more complicated and even more impressive than that.  The in frame deletions occurred in one of four areas, which happen to be where antibodies to the spike protein bind.  So the out of frame deletions were selected against, and the in frame deletions were selected for. 

The blind watchmaker in action.

Another way to see how improbable it is that random choice should choose one of 3 equally probable possibilities 97% of the time, imagine that you are throwing dice.  You throw a single dye 100 times, and 97 times you get either of two numbers (say 3 and 6) .  You know the dye is loaded.  The load being natural selection in the case of genome deletions. 

 

 

 

 

 

Answer to Friday’s homework problem

2 days ago you were tasked with the following homework problem: Design a protein to capture cholesterol and triglycerides and insert them between the two leaflets of the standard biological membrane similar but not identical to the plasma membrane.

Why not just tell you Nature/God/Evolution’s solution to the problem?  Because unless you’ve thought about how you’d do it, you won’t appreciate the elegance (and beauty to a chemist) of the solution. 

Lipid droplets are how your cells store cholesterol and triglycerides (neutral fats).  Cholesterol and most fats are made in the lumen of the endoplasmic reticulum.  Then they move through the homework protein and accumulate between the two leaflets of the endoplasmic reticulum membrane, growing into lens-like structures with diameters of 400 to 600 Angstroms before they leave to enter the cytoplasm.  

Well clearly to get them between the sheets so to speak a hole must be formed in the membrane leaflet closest to the lumen, and the hole must have open sides so the cholesterol and triglyceride can escape.  

The protein must also catch the lipids in the lumen.  This is accomplished by an 8 stranded beta sandwich.  The protein must also cross the endoplasmic reticulum membrane so the lipids its caught can escape the sides.  

Like a lot of pores in the membrane (such as ion channels), several copies of the protein must come together to form the hole.  In this case the protein contains two transmembrane alpha helices.  Its hard to count just how many monomers make up the power, but my guess is 11 or so. 

Here’s a picture

 

The transmembrane (TM)alpha helices are in purple, the beta sandwiches are in blue-greem.

8 nm is 8 nanoMeters or 800 angstroms.  The hole looks to be around 30 Angstroms across — plenty of room to allow cholesterol and triglycerides to enter.  When you look at the top view you see that there is plenty of room between the alpha helices within the membrane for the lipids to escape out the side.  

Here’s the reference https://www.pnas.org/content/pnas/118/10/e2017205118.full.pdf

and the citation Proc. Natl. Acad. Sci. vol. 118 pp. e2017205118 ’21.  It’s a beautiful paper

The protein itself is called seipin, and mutations cause a variety of lipodystrophies, some of which have mental retardation.  The paper has some nice molecular dynamics simulations of seipin in action (if you believe that sort of thing). 

Were you smart enough to figure all this out on your own.  Nature/God/Evolution was.  I wasn’t.

TDP43 and the anisosome

Neurologists have been interested in TDP43 (Tar Dna binding Protein of 43 kiloDaltons) for a long time. Mutants cause some cases of ALS (Amyotrophic Lateral Sclerosis — Lou Gehrig disease) and FTD (FrontoTemporal Dementia).  Some 50 different mutations in the protein have been found in cases of these two diseases.  Intracellular inclusions containing TDP are found in > 90% of sporadic ALS (no mutations) and 45% of FTD.

TDP43 contains 414 amino acids (as you might expect for a protein with a 43 kiloDalton mass).  There is an amino terminal ubiquitinlike fold, two RNA Recognition Motifs (RRMs) followed by a glycine rich low complexity sequence prion-like domain at the other (carboxy) end.  The disease causing mutations are found in the low complexity sequence. 

A  phase separated structure (the anisosome) never seen before involves  mutant TDP43 [ Science vol. 371 pp. 585, abb4309 pp. 1 –> 15 ’21 ].  It is a phase separated mass with liquid spherical shells and liquid cores.  The shells showed birefringence — evidence of a liquid crystal.  The cores show the HSP70 chaperone bound to TDP43 (which wasn’t binding RNA).

ATP is required to maintain the chaperone activity of HSP70. When ATP levels are reduced, the anisosome is converted into the protein aggregates seen in ALS and FTD.  So the anisosome is a protective mechanism. 

Biology is clearly leading chemistry around by the nose.  No chemist would ever have predicted something like this, or received a grant to mix all this stuff in a test tube not even thinking about stoichiometry and see what happened.  For more details on phase separation please see an old post — https://luysii.wordpress.com/2020/12/20/neuroscience-can-no-longer-ignore-phase-separation/

Here’s some stuff from that post to whet your appetite

Advances in cellular biology have largely come from chemistry.  Think DNA and protein structure, enzyme analysis.  However, cell biology is now beginning to return the favor and instruct chemistry by giving it new objects to study. Think phase transitions in the cell, liquid liquid phase separation, liquid droplets, and many other names (the field is in flux) as chemists begin to explore them.  Unlike most chemical objects, they are big, or they wouldn’t have been visible microscopically, so they contain many, many more molecules than chemists are used to dealing with.

These objects do not have any sort of definite stiochiometry and are made of RNA and the proteins which bind them (and sometimes DNA).  They go by any number of names (processing bodies, stress granules, nuclear speckles, Cajal bodies, Promyelocytic leukemia bodies, germline P granules.  Recent work has shown that DNA may be compacted similarly using the linker histone [ PNAS vol.  115 pp.11964 – 11969 ’18 ]

The objects are defined essentially by looking at them.  By golly they look like liquid drops, and they fuse and separate just like drops of water.  Once this is done they are analyzed chemically to see what’s in them.  I don’t think theory can predict them now, and they were never predicted a priori as far as I know.

No chemist in their right mind would have made them to study.  For one thing they contain tens to hundreds of different molecules.  Imagine trying to get a grant to see what would happen if you threw that many different RNAs and proteins together in varying concentrations.  Physicists have worked for years on phase transitions (but usually with a single molecule — think water).  So have chemists — think crystallization.

Proteins move in and out of these bodies in seconds.  Proteins found in them do have low complexity of amino acids (mostly made of only a few of the 20), and unlike enzymes, their sequences are intrinsically disordered, so forget the key and lock and induced fit concepts for enzymes.

Are they a new form of matter?  Is there any limit to how big they can be?  Are the pathologic precipitates of neurologic disease (neurofibrillary tangles, senile plaques, Lewy bodies) similar.  There certainly are plenty of distinct proteins in the senile plaque, but they don’t look like liquid droplets.

It’s a fascinating field to study.  Although made of organic molecules, there seems to be little for the organic chemist to say, since the interactions aren’t covalent.  Time for physical chemists and polymer chemists to step up to the plate.

 

The United States lost the battle with the virus by March of 2020

Two papers published this February show that the USA had lost the ability to contain the pandemic virus by early April 2020.  The first paper was submitted in July 2020, the second in August.  They would have changed our perception of what we were up against in late 2020.  Here are links to both — they are not behind a paywall, and a friend who subscribes to neither was able to access them through these links.

The Nature paper is the most damning.  10,000 blood samples from Mt. Sinai hospital in New York City accumulated from February through July 2020 were studied for antibodies to the pandemic virus (whose presence implies previous infection)

Figure 1 p. 147 shows it best, with weekly numbers of tests and cases, in two groups — people attending urgent care and (more representative of the general population) patients who visited the obstetrics and gynecology department and visits for labour and deliveries, oncology-related visits, as well as hospitalizations owing to elective surgeries, transplant surgeries, pre-operative medical assessments and related outpatient visits, cardiology office visits and other regular office and/or treatment visits.

As you might expect the ER patients had a higher percentage of antibodies.  The first PCR confirmed case in the city was 1 March, with 1000 cases by the 15th. 

It was no secret that NYC was in the middle of the pandemic.  What is quite shocking is the number of people with antibodies (hence previously infected with the virus) in the presumably healthy group.  By 5 April 33/326  (10%) of tests were antibody positive, by 19 April 46/241 (19%) where it essentially remained to the end of the study in July.  Game over. Containment impossible. 

The second paper is from Boston where the virus genomes were sequenced from March through May of 2020.  The sequence of the viral genome tells you where the virus was coming from.  There were 120 separate introductions of the virus into the Boston area.  Most were from North America.  But of those from elsewhere how many do you think were from Asia?  Amazingly only 3.  How many from Europe?  19.  It’s like Wile. E. Coyote  peering earnestly toward Asia to nab the roadrunner, while a pack of roadrunners from Europe passes him from behind without him noticing a thing. 

It isn’t the fault of the authors that this information has just come out this month.  It would have changed our perception of the epidemic and what to do about it Trump or no Trump.  

20/20 hindsight is a wonderful thing.  Here’s Dr. Fauci doing the best he could with what he knew at the time — he is NOT to be faulted to saying this — he changed quickly. 

In the clip, Dr Fauci says “There’s no reason to be walking around with a mask. When you’re in the middle of an outbreak, wearing a mask might make people feel a little bit better and it might even block a droplet, but it’s not providing the perfect protection that people think that it is. And, often, there are unintended consequences — people keep fiddling with the mask and they keep touching their face.”

Fauci made this comment on an interview with 60 Minutes on March 8, a time when NYC proven cases were surging from 1 to 1000. 

Our vaunted intelligence service and the ‘situation room’ either did  not know or did not tell Dr. Fauci about the fact that the dean of a Hong Kong medical school wrote an article in the South China Morning Post 27 January 2020 stating that  “research shows self-sustaining human-to-human transmission is already happening in all major mainland cities.”  For details please see https://luysii.wordpress.com/2020/01/27/what-to-do-about-the-wuhan-flu/

Here are the links to the two papers cited above  https://www.nature.com/articles/s41586-020-2912-6.pdf

and https://science.sciencemag.org/content/sci.371/6529/eabe3261.full.pdf

 

600,000 Pandemic deaths in the United Kingdom ! ! !

Yes, 600,000 pandemic deaths in the UK given their attack rate of 182/100,000 and a population the size of the USA (328 million) actually it’s even worse than that because their case fatality rate is 2.9 % and ours is 1.8% — so multiply the 600,000 deaths by 1.6 and you get a million deaths in the UK given their attack rate and case fatality rate (and scaling their population to match ours).

Where are these numbers coming from — the same place that those in the previous post came from — https://coronavirus.jhu.edu/data/mortality, Johns Hopkins. 

Here are the top ten attack rates per 100,000 population from the previous post

181.70, 180.83, 158.39, 155.25, 152.49, 143.61. 142.73, 140.98, 124.72, 118.50

You were asked to guess where the USA, and the UK were.  No the USA is not at the top, but in the middle (hardly great but not as bad as the 500,000 headline would imply).  The UK is at the top. 

Here are the 10 countries (alphabetized) from which these rates were drawn

Czech Republic, France, Italy, Mexico, Peru, Portugal, Slovakia, Spain, United Kingdom, USA

Here are the case fatality rates (in percent) from the same 10 countries

8.8, 3.5, 3.4, 2.9, 2.3, 2.2, 2.1, 2.0, 1.8, 1.7

The UK is 2.9 and the US among the lowest at 1.8  

Not what you’ve likely been led to believe.  

There are worse problems afoot for the USA.  Granted the following  are 3 small and nonrandomized samples, but the minorities who need it the most aren’t getting the vaccine (and not because it is being withheld from them).

Sample #1 Yrs Trly and wife second shot yesterday —

My wife and I received the booster dose of the Pfizer vaccine today. We live in a town that is 45% Latino (mostly Puerto Rican). Both times we were there, the vaccinees were almost all Caucasian, a disaster in the making. The nurse I spoke with said that what we’d seen about Latinos not getting vaccinated was typical in her experience. She also noted misinformation going around among them, such that vaccination would make you sterile.

Sample #2 a friend who was vaccinated elsewhere (but in the same metro area)- “That was my experience at the State Curative site at XXXXXXX. Large African-American population in that area; however, only caucasians getting the vaccines on both occasions. Puzzling.”

Sample #3 a college classmate and friend –Welcome to the club. I received my vaccine through Hopkins as a practicing clinician. My wife received hers as a DC resident through the DC Government in a Black neighborhood; all of the vaccinees there were whites from Foggy Bottom and Georgetown. the DC Government then got smart and has been allocating vaccine by specific neighborhood.

Now there was a giant article in the 4 January New Yorker by Lawrence Wright blaming the magnitude of the pandemic on Trump’s not pushing mask wearing. 

Well here’s our Vice President — https://abc7ny.com/vice-presidential-debate-vp-2020-kamala-harris/6852144/

Harris was asked if Americans should take the vaccine and if she would. Harris says that if doctors “tells us that we should take it, I’ll be the first in line to take it, absolutely. But if Donald Trump tells us that we should take it, I’m not taking it.”  Well he did tell us exactly that. 

Is it her fault that minorities aren’t taking the vaccine?  Don’t wait for the New Yorker to take up the issue.