Author Archives: luysii

see first post

Do not go gentle into that good night

Cells in the body dying of necroptosis obey Dylan Thomas — “Do not go gentle into that good night” all sorts of inflammation ensues around the cell, and systemically if enough die that way at once.

Cells dying from the first discovered form of programmed cell death e.g. apoptosis disobey.  They die very quietly producing no inflammation, and are quietly munched up by phagocytes.  Just how this happens has been a huge mystery.

Well one way to figure out what is going on looks at a phagocyte before it meets an apoptotic cell and afterwards.  Quite a bit it turns out.  The brute force technique looks at the changes in our 20,000 or so protein coding genes.  They found increased expression in 886 and decreased expression in 966, some 9% of our total.  How do you make sense of that.

This is typical of the brute force approach to any condition (e.g. cancer, infection, vascular disease), and shows you just how hard it is to figure out what is going on from the mass of data produced.

The authors of Nature vol. 580 pp. 130 – 135 ’20 ( were far cleverer than that.  What they did was cause a bunch of cells to go apoptotic at once and then the “supernatants and cell pellets from apoptotic cells and live cell controls were subjected to untargeted metabolomic profiling against a library of more than 3,000 biochemical features or compounds.”

Then by a huge amount of work they found 6 metabolites released by the apoptotic cell  which when given together which could switch macrophages (a type of phagocyte)to the non-inflammatory state (e.g. the one above producing all those gene changes).

Then they pared the number of metabolites doing this down to 3 (spermidine, guanosine monophosphate and inosine monophosphate). They call this cocktail of metabolites MEMIX-3.

They get out of the cell dying of apoptosis because the executioner (caspase) chops up a protein channel on the cell surface (pannexin1), allowing the 6 metabolites to escape.  A rather parsimonious suicide note wouldn’t you think.

It gets better. MEMIX-3 obviously is an anti-inflammatory agent, and they showed that it attenuates arthritic symptoms and prevents rejection of a lung transplant.

Brilliant work, and possibly one of great therapeutic import.

A way to end the pandemic

Could infecting people with the four or so coronaviruses that cause the common cold protect them against the new coronavirus causing the pandemic?   The official name for the new virus is SARS-CoV-2, the name for the disease is COVID-19.

“According to Marie-Louise Landry, MD, an infectious disease expert at Yale Medical School and the Director of the Yale Clinical Virology Laboratory, four common human coronaviruses cause 15-30% of common colds”

Now ask yourself how she could make a statement like this.  I’m going to try to get in touch with her tomorrow, but it is very likely that these cold causing coronaviruses are detected by measuring antibodies to them, carried in the blood of people who have been infected by them in the past.

Could one coronavirus (even a benign one) give partial immunity to others?  It’s possible and it’s time to find out.  We could know  in a few weeks.

Assume the test to measure the antibodies to cold coronaviruses exists.  Then measure them in our real, honest to God, modern day heroes on the front lines  — the nurses, docs, EMTs, orderlies, housekeeping, cops, etc. etc.  who are exposed every day to COVID-19.

Every hospital in the country could at least draw blood on them, look to see if antibodies are present and wait.   I doubt that many would refuse the test.

Sadly, it wouldn’t be long before some of them became infected with SARS-CoV-2.  Then investigators couldlook to see if those with the antibodies to the cold causing coronaviruses were protected.

If so, then make a cocktail of the 4 or so coronaviruses and give it to everyone.   It would be Edward Jenner and the cowpox all over again —

Even if the protection was only partial, decreasing the number of susceptible individuals would be enough to slow the pandemic and possibly even stop it.

Covid19 could be coming for you

A friend and his wife are getting 3 days of meals delivered to their room in their retirement home.  Clearly a great way to socially isolate themselves.  This will help ‘flatten the curve’.  What that means is that the peak won’t be as high, so we won’t run out of beds and respirators.

But look at the curve in this article —

Now integrate the area under the curve.  Looks like the number of cases is comparable (more actually under the flattened curve).

Add this to the extreme likelihood that covid19 will become endemic in the population (given the number of cases out there).  This means that absent a vaccine or a treatment, you will meet it sooner or later with whatever biologic resources you have.

On the positive side, the amount of research into the way virus kills is only matched by the number of therapeutic trials underway (both enormous).  The way the journals have opened up so results are widely available gratis and freely shared is impressive.

An experiment of nature

Back in day genetic diseases were called experiments of nature, which I thought rather cruel, as it implied a conscious intent to set them up (to me at least).  Well, we’re in the middle of one presently, and it may tell us something about climate change.  The New York Times today has a pious article “What the Pandemic Means for Climate Change” full of treacle.

However, it is possible that the drop in carbon dioxide (CO2) emissions (25% in China in February) if it goes on long enough might tell us something about the effect of CO2 on climate.

Suppose global CO2 drops and the temperature along with it.  This should convince the hardiest climate skeptic (not denier) that CO2 and global temperature are related.

I’m far from knowing enough to even guess, if a mild decline in emissions would change global CO2 levels and with it global temperatures, but both are being continuously measured so we’ll soon have the data.

Probably nothing will happen to either as there is so much CO2 in the atmosphere, that a blip of a 25% decline (even worldwide) won’t do anything.

I’m posting this, because the article said nothing about the possibility.

Any thoughts, particularly from people more knowledgeable than me


hed oga tet hec atw hoa tet her atw hob ith erp aw

Say what?  It’s a simple sentence made of 3 letter words frameshifted by one

he dog ate the cat who ate the rat who bit her paw

Codons are read as groups of three nucleotides, and frameshifting has always been thought to totally destroy the meaning of a protein, as an entirely different protein is made.

Not so says PNAS vol. 117 pp. 5907 – 5912 ’20. Normally a frameshifted protein has only 7% sequence identity with the original.  This is about what one would expect given that there are 20 amino acids, and chance coincidence would argue for 5%.  But there are more ways for proteins to be similar rather than identical.  One can classify our amino acids in several ways, charged vs. uncharged, aromatic vs. nonaromatic, hydrophilic vs. hydrophobic etc. etc.

The authors looked at 2,900 human proteins, then they frameshifted the original by +1 and compared the hydrophobicity profiles of the two.  Amazingly there was a correlation of .7 between the two, despite sequence identity of 7%.  Similarly frameshifting didn’t disturb the chance of intrinsic disorder.  So frameshifting is embedded in the structure of the universal genetic code, and may have actually contributed to its shaping.  Frameshifting could be an evolutionary mechanism of generating proteins with similar attributes (hydrophobicity, intrinsic order vs. disorder, etc.) but with vastly different sequences.  The evolution, aka natural selection aka deus ex machine aka God could muck about the ready made protein and find something new for it to do.   A remarkable concept.

The gag-pol precursor p180 of the AIDS virus is derived from the gag-pol mRNA by translation involving ribosomal frameshifting within the gag-pol overlap region.  The overlap is 241 nucleotides with pol in the -1 phase with respect to gag (that’s an amazing 80 amino acids).  I was amazed at the efficiency of coding of two different proteins (one and enzyme and one structural), but perhaps they aren’t that different in terms of hydrophobicity (or something else).

I’d love to see the hydropathy profile of the overlap of the two proteins, but I don’t know how to get it.

Do glia think?

Do glia think Dr. Gonatas?  This was part of an exchange between G. Milton Shy, head of neurology at Penn, and Nick Gonatas a brilliant neuropathologist who worked with Shy as the two of them described new disease after new disease in the 60s ( myotubular (centronuclear) myopathy, nemaline myopathy, mitochondrial myopathy and oculopharyngeal muscular dystrophy).

Gonatas was claiming that a small glial tumor caused a marked behavioral disturbance, and Shy was demurring.  Just after I graduated, the Texas Tower shooting brought the question back up in force —

A recent paper [ Neuron vol. 105 pp. 954 – 956, 1036 – 1047 ’20] gives good evidence that glia are more than the janitors and the maintenance crew of the brain.

Glia cover most synapses (so neurotransmitter there doesn’t leak out, I thought) giving rise to the term tripartite synapse (presynaptic terminal + postsynaptic membrane + glial covering).

Here’s what they studied.  The cerebral cortex projects some of its axons (which use glutamic acid as a neurotransmitter) to a much studied nucleus in animals (the nucleus accumbens).  This is synapse #1. The same nucleus gets a projection of axons from the brainstem ventral tegmental area (VTA) which uses dopamine as a neurotransmitter.  However, the astrocytes (a type of glia) covering synapse #1 have the D1 dopamine receptor (there are 5 different dopamine receptors) on them.  It isn’t clear if the dopamine neurons actually synapse (synapse #2) on the astrocytes, or whether the dopamine  just leaks out of the synaptic cleft to the covering glia.

Optogenetic stimulation of the VTA dopamine neurons results in an elevation of calcium in the astrocytes (a sign of stimulation). Chemogenetic activation of these astrocytes depresses the presynaptic  terminals of the neurons projecting the nucleus accumbens  from the cerebral cortex .  How does this work?  Stimulated astrocytes release ATP or its produce adenosine.  This binds to the A1 purinergic receptor on the presynaptic terminal of the cortical projection.

So what?

The following sure sounds like the astrocyte here is critical to brain function.  Activation of the astrocyte D1 receptor contributes to the locomotor hyperactivity seen after an injection of amphetamine.

Dopamine is intimately involved in reward, psychosis, learning and other processes (antipsychotics and drugs for hyperactivity manipulate it).  That the humble astrocyte is involved in dopamine action takes it out of the maintenance crew and puts it in to management.

A final note about Dr. Shy.  He was a brilliant and compelling teacher, and instead of the usual 1% of a medical school class going into neurology, some 5% of ours did.  In 1967 he ascended to the chair of the pinnacle of American Neurology at the time, Columbia University.  Sadly, he died the month he assumed the chair.  Scuttlebut has it that he misdiagnosed his own heart attack as ‘indigestion’ and was found dead in his chair.

Decoys and the Strategic Defense Initiative (SDI)

It will take a detour through history to understand how lung cells try to defeat MRSA (Methicillin Resistant Staph. Aureus), a very nasty bug.

Back in 1983 President Reagan proposed building an antiMissile defense system, which would shoot down Russian InterContinental Ballistic Missiles (ICBMs) aimed at us.  Almost every scientist of note said it was impossible technically, because even if you could shoot down one (which they didn’t think you could), the Russians would send multiple decoy ICBMs without warheads.  It was an enormously expensive project and one the Russians had no hope of matching.  People still argue whether their attempt to match the US caused the Russians  to collapse — — although collapse they did being overextended in Afghanistan (as we’ve been for 20 years).

But that’s exactly what A549 cells (derived from lung epithelium) do to fake out MRSA according to Nature vol. 579 pp. 260 – 264 ’20.  One of the reasons MRSA is so nasty is that it secretes a protein (alpha toxin) which forms holes in cells it binds to.  Well alpha toxin has a target it must bind to cause trouble, otherwise it would form holes in everything including itself.  The target is an enzyme on the surface of the cell called ADAM10, which is a protease found on the cell membrane.

You may not have thought of it, but when you diet, your cells eat themselves, rather than just sloughing of the cells in the fat you don’t like (love handles, double chin etc. etc.).  Wouldn’t that be nice though.  The process is called autophagy, in which membranes appear, surround small bits of each cell and them fuse with the lysosome, which breaks the contents down into metabolically useful material (sugars, fats, amino acids).  Some 41 different proteins are involved called ATG’s (for AuTophagy Gene).

But the autophagy genes can also be used to secrete stuff to the outside of the cell, and in fact that’s how the lung cells beat MRSA, they secrete zillions of little vesicles called exosomes (an entirely interesting newly discovered story, to be covered at another time), containing the target of alpha toxin — ADAM10.  Clever no?  The authors were so excited they invented a new word for it the defensosome. The ATG involved is called ATG16L1.  Previously the function of ATG16L1 appeared well defined, conjugating phosphatidylethanolamine to LC3, a ubiquitinLike molecule to form the autophagosome.  That’s probably nomenclature overload, but it’s worthwhile getting an appreciation of the complicated things going on inside our cells.


General relativity at last

I’ve finally arrived at the relativistic gravitational field equation which includes mass, doing ALL the math and understanding the huge amount of mathematical work it took to get there:  Chistoffel symbols (first and second kind), tensors, Fermi coordinates, the Minkowski metric, the Riemann curvature tensor ( geodesics, matrices, transformation laws, divergence of tensors, the list goes on.  It’s all covered in a tidy 379 pages of a wonderful book I used — “The Geometry of Spacetime” by James J. Callahan, professor emeritus of mathematics at Smith college.  Even better I got to ask him questions by eMail when I got stuck, and a few times we drank beer and listened to Irish music at a dive bar north of Amherst.

Why relativity? The following was written 8 years ago.  Relativity is something I’ve always wanted to understand at a deeper level than the popularizations of it (reading the sacred texts in the original so to speak).  I may have enough background in math, to understand how to study it.  Topology is something I started looking at years ago as a chief neurology resident, to get my mind off the ghastly cases I was seeing.

I’d forgotten about it, but a fellow ancient alum, mentioned our college president’s speech to us on opening day some 55 years ago.  All the high school guys were nervously looking at our neighbors and wondering if we really belonged there.  The prez told us that if they accepted us that they were sure we could do the work, and that although there were a few geniuses in the entering class, there were many more people in the class who thought they were.

Which brings me to our class relativist (Jim Hartle).  I knew a lot of the physics majors as an undergrad, but not this guy.  The index of the new book on Hawking by Ferguson has multiple entries about his work with Hawking (which is ongoing).  Another physicist (now a semi-famous historian) felt validated when the guy asked him for help with a problem.  He never tooted his own horn, and seemed quite modest at the 50th reunion.  As far as I know, one physics self-proclaimed genius (and class valedictorian) has done little work of any significance.  Maybe at the end of the year I’ll be able to read the relativist’s textbook on the subject.  Who knows?  It’s certainly a personal reason for studying relativity.  Maybe at the end of the year I’ll be able to ask him a sensible question.

Well that took 6 years or so.

Well as the years passed, Hartle was close enough to Hawking that he was chosen to speak at Hawking’s funeral.

We really don’t know why we like things and I’ve always like math.  As I went on in medicine, I liked math more and more because it could be completely understood (unlike medicine) –Why is the appendix on the right and the spleen on the left — dunno but you’d best remember it.

Coming to medicine from organic chemistry, the contrast was striking.  Experiments just refined our understanding, and one can look at organic synthesis as proving a theorem with the target compound as statement and the synthesis as proof.

Even now, wrestling with the final few pages of Callahan today took my mind off the Wuhan flu and my kids in Hong Kong just as topology took my mind off various neurologic disasters 50 years ago.

What’s next?  Well I’m just beginning to study the implications of the relativistic field equation, so it’s time to read other books about black holes, and gravity.  I’ve browsed in a few — Zee, Wheeler in particular are written in an extremely nonstuffy manner, unlike medical and molecular biological writing today (except the blogs). Hopefully the flu will blow over, and Jim and I will be at our 60th Princeton reunion at the end of May.  I better get started on his book “Gravity”

One point not clear presently.  If mass bends space which tells mass how to move, when mass moves it bends space — so it’s chicken and the egg.  Are the equations even soluble.

Some sanity (and hope) about the Wuhan flu

There is an excellent article in the following link,

Epidemiology Professor Marc Lipsitch, head of the Center for Communicable Disease Dynamics at the Harvard T.H. Chan School of Public Health, called the pace of coronavirus testing in the U.S. “utterly inadequate” and “a debacle” that robs public health officials of information crucial to devising an effective response and protecting health care workers. Testing has been so slow that no one knows the extent of the U.S. epidemic, though scientists guess at somewhere between “tens of thousands and hundreds of thousands” of cases.

Let’s say that is true that 100,000 people in the USA have already been infected.  What does that mean?  It means that most people with it aren’t very sick (we don’t have 100K people in ICUs on respirators).  This is the hope anyway

The CDC monopolized testing for Corona virus for a while and then distributed faulty test kits (while you may not like Trump, this isn’t his fault). So we have no way of knowing what’s out there.

That’s information gap #1 — we don’t know how many people are actively infected with the virus

Information gap #2 is even worse, and very likely longer to be corrected.  We don’t know how many people are out there who have fought the infection off and are no longer sick.  This will require a test for the antibodies to the virus they’ve developed (something that doesn’t happen right away during the acute infection although that’s where it begins).  Such information  is not available now, and likely won’t be for a month or two.

Addendum: Not everyone reading this knows what an antibody is so this is in response to a few questions.  Antibodies are proteins made by your body in response to an invading organism (which kill it).  This is why your kids have measles, mumps and rubella vaccines — they give the kids proteins from the viruses (not the whole organism), and your kids react as if infected by the intact virus (which is why they often seem to have the flu after vaccination), producing antibodies to those proteins, so when the real thing comes sneaking around, your kid’s antibodies recognize it and fight it off.  Having an antibody to the Wuhan flu is perfect evidence that you’ve been infected with it (even if the virus is long gone).  They aren’t something you’d have normally.  It isn’t simple to develop and validate a test for anti-Wuhan antibodies which why I think it will be a while before we have a test we can trust.

This will tell us just how much to worry about the virus.  Most reading this are too young  to remember the polio epidemic (which also put people on respirators).  After antibody tests finally became available it was found that only one out of every one hundred people infected developed paralysis.


Do orphan G Protein Coupled Receptors self stimulate?

Self-stimulation is frowned on in the Bible — Genesis 38:8-10, but one important G Protein Coupled Receptor (GPCR) may actually do it.  At least 1/3 of the drugs in clinical use manipulate GPCRs, and we have lots of them (at least 826/20,000 protein coding genes according to PNAS 115 p. 12733 ’18).  However only 360 or so are not involved in smell, and in one third of them  we have no idea what the natural ligand for them actually is (Cell vol. 177 p. 1933 ’19).  These are the orphan GPCRs, and they make a juicy target for drug discovery (if only  we knew what they did)

One orphan GPCR goes by the name of GPR52. It is found on neurons carrying the D2 dopamine receptor.  GPR52 binds to G(s) family of G proteins stimulating the production of CAMP (which would antagonize dopamine signaling), enough to stimulate (if not self-stimulate) any neuropharmacologist.

Which brings us to the peculiar behavior of GPR52 as shown by Nature vol. 579 pp. 142 – 147 ’20.  The second extracellular loop (ECL2) folds into what would normally be the binding site for an exogenous ligand (the orthosteric site).  Well, it could be protecting the site from inappropriate ligands.  But it isn’t, as removing or mutating ECL2 decreases the activity of GPR52 (e.g. less CAMP is produced).  Pharmacologists have produced a synthetic GPR52 agonist (called c17).  However it binds to a side pocket, in the 7 transmembrane region of the GCPR.   This is interesting in itself, as no such site is known in any of the other GPCRs studied.

Most GPCRs have some basal (constitutive) activity where they spontaneously couple to their G proteins, but the constitutive activity of GPR52 is quite high, so c17 only slightly increases the rise in CAMP that GPR52 normally produces.

This might be an explanation for other orphan GPCRs — like a hermaphrodite they could be self-fertilizing.