Category Archives: Neurology & Psychiatry

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 — https://en.wikipedia.org/wiki/University_of_Texas_tower_shooting.

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.

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.

Musical dyslexia

Back in the day, we were all shocked that the worst reader in our class, a girl who’d been left back, picked up a spelling mistake in our high school yearbook “The Lighththouse”.

Which brings me to the Ravel Piano Trio where I’m having the same problem she did. It’s probably one of the hardest works for piano trio in existence, and even with an hour a day on the first two movements I’m only making slow headway at best.  Even the violinist, a conservatory graduate, finds it difficult.

Normally when a pianist  looks at a score, chords and scales leap out, and you don’t have to look at every note in a Beethoven sonata to know what key he’s writing in.  Not so with Ravel.

In the second movement there is a sequence of 15 chords in which the right hand plays 4 notes, the left 2 or 3.  Here’s the first chord

left hand f double sharp, c sharp e – right hand f double sharp, a sharp, dsharp fsharp (the fsharp is about an octave higher than the the lower f double sharp).

You can’t look at that and know what to play — you’ve got to finger every note in order and hope that your brain will remember it the second time around.

All 15 of these chords like this must be played in about 10 seconds or less.

This is what life must have been like for the dyslexic girl back then (the diagnosis didn’t exist in the 50’s).  No wonder she was left back, if she had to figure out every word had letter by letter.

Like me probably after figuring out what one word (chord) was, she probably forgot what the multiple words of the sentence were trying to say (the music in the chord sequence).

You did notice the misspelling didn’t you? If not here it is — lightHThouse.  Most readers just look at the first few letters, recognize the word and move on, just like a pianist playing Mozart or Beethoven.  Not the poor girl back then or me with the Ravel.

How can it be like that?

The following quote is from an old book on LISP programming (Let’s Talk LISP) by Laurent Siklossy.“Remember, if you don’t understand it right away, don’t worry. You never learn anything, you only get used to it.”

Unlike quantum mechanics, where Feynman warned never to ask ‘how can it be like that’, those of us in any area of biology should always  be asking ourselves that question.  Despite studying the brain and its neurons for years and years and years, here’s a question I should have asked myself (but didn’t, and as far as I can tell no one has until this paper [ Proc. Natl. Acad. Sci. vol. 117 pp. 4368 – 4374 ’20 ] ).

It’s a simple enough question.  How does a neuron know what receptor to put at a given synapse, given that all neurons in the CNS have both excitatory and inhibitory synapses on them. Had you ever thought about that?  I hadn’t.

Remember many synapses are far away from the cell body.  Putting a GABA receptor at a glutamic acid synapse would be less than useful.

The paper used a rather bizarre system to at least try to answer the question.  Vertebrate muscle cells respond to acetyl choline.  The authors bathed embryonic skeletal muscle cells (before innervation) with glutamic acid, and sure enough glutamic acid receptors appeared.

There’s a lot in the paper about transcription factors and mechanism, which is probably irrelevant to the CNS (muscle nuclei underly the neuromuscular junction).   Even if you send receptors for many different neurotransmitters everywhere in a neuron, how is the correct one inserted and the rest not at a given synapse.

I’d never thought of this.  Had you?

 

Amyloid

Amyloid goes way back, and scientific writing about has had various zigs and zags starting with Virchow (1821 – 1902) who named it because he thought it was made out of sugar.  For a long time it was defined by the way it looks under the microscope being birefringent when stained with Congo red (which came out 100 years ago,  long before we knew much about protein structure (Pauling didn’t propose the alpha helix until 1951).

Birefringence itself is interesting.  Light moves at different speeds as it moves through materials — which is why your legs look funny when you stand in shallow water.  This is called the refractive index.   Birefringent materials have two different refractive indexes depending on the orientation (polarization) of the light looking at it.  So when amyloid present in fixed tissue on a slide, you see beautiful colors — for pictures and much more please see — https://onlinelibrary.wiley.com/doi/full/10.1111/iep.12330

So there has been a lot of confusion about what amyloid is and isn’t and even the exemplary Derek Lowe got it wrong in a recent post of his

“It needs to be noted that tau is not amyloid, and the TauRx’s drug has failed in the clinic in an Alzheimer’s trial.”

But Tau fibrils are amyloid, and prions are amyloid and the Lewy body is made of amyloid too, if you subscribe to the current definition of amyloid as something that shows a cross-beta pattern on Xray diffraction — https://www.researchgate.net/figure/Schematic-representation-of-the-cross-b-X-ray-diffraction-pattern-typically-produced-by_fig3_293484229.

Take about 500 dishes and stack them on top of each other and that’s the rough dimension of an amyloid fibril.  Each dish is made of a beta sheet.  Xray diffraction was used to characterize amyloid because no one could dissolve it, and study it by Xray crystallography.

Now that we have cryoEM, we’re learning much more.  I have , gone on and on about how miraculous it is that proteins have one or a few shapes — https://luysii.wordpress.com/2010/08/04/why-should-a-protein-have-just-one-shape-or-any-shape-for-that-matter/

So prion strains and the fact that alpha-synuclein amyloid aggregates produce different clinical disease despite having the same amino acid sequence was no surprise to me.

But it gets better.  The prion strains etc. etc may not be due to different structure but different decorations of the same structure by protein modifications.

The same is true for the different diseases that tau amyloid fibrils produce — never mind that they’ve been called neurofibrillary tangles and not amyloid, they have the same cross-beta structure.

A great paper [ Cell vol. 180 pp. 633 – 644 ’20 ] shows how different the tau protofilament from one disease (corticobasal degeneration) is from another (Alzheimer’s disease).  Figure three shows the side chain as it meanders around forming one ‘dish’ in the model above.  The meander is quite different in corticobasal degeneration (CBD) and Alzheimers.

It’s all the stuff tacked on. Tau is modified on its lysines (some 15% of all amino acids in the beta sheet forming part) by ubiquitination, acetylation and trimethylation, and by phosphorylation on serine.

Figure 3 is worth more of a look because it shows how different the post-translational modifications are of the same amino acid stretch of the tau protein in the Alzheimer’s and CBD.  Why has this not been seen before — because the amyloid was treated with pronase and other enzymes to get better pictures on cryoEM.  Isn’t that amazing.  Someone is probably looking to see if this explains prion strains.

The question arises — is the chain structure in space different because of the modifications, or are the modifications there because the chain structure in space is different.  This could go either way we have 500+ enzymes (protein kinases) putting phosphate on serine and/or threonine, each looking at a particular protein conformation around the two so they don’t phosphorylate everything — ditto for the enzymes that put ubiquitin on proteins.

Fascinating times.  Imagine something as simple as pronase hiding all this beautiful structure.

 

 

4 Interesting papers

Here are brief summaries of 4 recent very interesting papers, each of which may be the subject of a future post (now that I’m not as worried about the effects of the Wuhan flu on family members over in Hong Kong).  They are likely behind a pay wall unfortunately

l. Watching an endoplasmic reticulum extruded tubule cut a P-body in half. Very significant as we begin to appreciate the phase transitions going on in our cells — for an overview of this see — https://luysii.wordpress.com/2018/12/16/bye-bye-stoichiometry/.

The paper(s) itself [ Science vol. 367 pp. 507 – 508, 537, eaay7108 ’20 ]

2. Watching microglia caress the cell body (soma) of neurons [ Science vol. 367 pp. 510 – 511, 528 – 537 ’20 ].  They’re actually rather creepy, extending processes and feeling up neurons, removing synapses from processes.  They use receptors for ATP and ADP to detect when a neuron is in trouble.  A new cellular specialization is described — Somatic Purinergic Junctions — a combination of mitochondria, reticular membrane structures, vesicle-like membrane structures and clusters of a particular voltage gated potassium channel (Kv2.1)

3. The ubiquitin wars inside a macrophage invaded by TB [ Nature vol. 577 pp. 682 – 688 ’20 ]  Ubiquitin initially was thought to be a tag marking a protein for destruction.  It’s much more complicated than that.  A host E3 ubiquitin ligase (ANAPC2, a core subunit of the anaphase promoting complex/cyclosome) promotes the attachment of lysine #11 linked ubiquitin chains to lysine #76 of the TB protein Rv0222.  In some way this helps Rv022 to suppress the expression of proinflammatory cytokines.

4. FACT (FAcilitates Chromatin Transcription)  is a heterodimer of two proteins which form a heterodimer [ Nature vol. 577 pp. 426 – 431 ’20 ].  If you’ve ever wondered how the monstrously large holoenzyme of RNA polymerase II, manages to work its way around the nucleosome copying one strand, you need to know about FACT, which basically grabs the disclike nucleosome with DNA wrapped around it twice, grabs both H2A-H2B dimers and holds them outside while pol II passes.  You have to wonder which came first the nucleosome or FACT. Neither would be of much use by themselves.  Probably they both grew up together, but it’s hard to envision the intermediate stages.

Should your teen use marihuana?

Is marihuana bad for teen brain development?  The short answer is no one knows.  The long answer can be found here — https://www.pnas.org/content/117/1/7.  It’s probably the best thing out there on the question [ Proc. Natl. Acad. Sci. vol. 117 pp. 7 – 11 ’20 ].  The article basically says we don’t know, but lays out the cons (of which there are many) and the pros (of which there are equally many).

If you’re not a doc, reading the article with its conflicting arguments harmful vs. nonharmful, and then deciding what to tell your kid is very close to what practicing medicine is like.  Important decisions are to be made, based on very conflicting data, and yet the decisions can’t be put off.  Rote memory is of no use and it’s time to think and think hard.

Assuming you don’t have a PNAS subscription, or you can’t follow the link here are a few points the article makes.

It starts off with work on rats. “Tseng, based at the University of Illinois in Chicago, investigates how rats respond to THC (tetrahydrocannabinol), the main psychoactive ingredient in cannabis. He’s found that exposure to THC or similar molecules during a specific window of adolescence delays maturation of the prefrontal cortex (PFC), a region involved in complex behaviors and decision making”

Pretty impressive, but not if you’ve spent decades watching various treatments for stroke which worked in rodents crash and burn when applied to people (there are at least 50 such studies).  What separates us from rodents physically (if not morally) is our brains.  Animal studies, with all their defects of applicability to man is one of the two approaches we have — no one is going to randomize a bunch of 13 year olds to receive marihuana or not and watch what happens.

== Addendum 9 Jan ’20 — too good to pass up — Science vol. 367 pp. 83 – 87  ’20 shows just how different we are from rodents.  In addition to our cerebral cortex being 3 times thicker, human cortical neurons show something not found in any other mammal — These are graded action potentials in apical dendrites, important because they allow single neurons to calculate XORs (either a or b but not both and not none), something previously only thought possible for neuron ensembles.  XORs are important in Boolean algebra, hence in computation. ==

The other approach is observational studies on people which have led us down the garden path many times– see the disaster the women’s health study avoided here — https://luysii.wordpress.com/2016/08/23/the-plural-of-anecdote-is-not-data-in-medicine-at-least/.

45,000 Swedish military conscripts examined at conscription (age 19) and 15 years later.  Those who had used cannabis over 50 times before conscription were 6 times as likely to be diagnosed with schizophrenia.

Against that, is the fact that cannabis use has exploded since the 60s but schizophrenia has not (remaining at a very unfortunate 1% of the population).

In the Dunedin study, cannabis use by 15 was associated with a fourfold risk of schizophrenia at 26 (but not if they started using cannabis after 16 years of age. — https://en.wikipedia.org/wiki/Dunedin_Multidisciplinary_Health_and_Development_Study.

You can take the position that all drugs we use to alter mental state (coffee, cigarettes, booze, marihuana, cocaine, heroin) are medicating underly conditions which we don’t like.  Perhaps marihuana use is just a marker for people susceptible to schizophrenia.  Mol. Psychiat. vol. 19 pp. 1201 – 1204 ’14 — 2,000 healthy adults were studied looking a genome variants known to increase the risk of schizophrenia.  Those with high risk variants were ‘more likely’ to use marihuana — not having read the actual paper i don’t know how much more.

There is a lot more in the article about the effects of cannabis on cognition and cognitive development — the authors note that ‘they have not replicated well’.  You’ll have to read the text (which you can get by following the link) for this.

One hope for the future is the ABCD study (Adolescent Brain Cognitive Development Study) — aka the ABCD study.  By 2018 it reached its goal of  accumulating 10,000 kids between the ages of 9 and 10.  They will be followed for a decade (probably longer if the results are interesting).  It’s the hope for the future — but that doesn’t tell you what to say to your kid now.  Read the article, use your best judgement and welcome to the world of the physician.

What is sad, is how little the field has advanced, since I wrote the (rather technical) post on marihuana in 2014.

Here it is below

Why marihuana scares me

There’s an editorial in the current Science concerning how very little we know about the effects of marihuana on the developing adolescent brain [ Science vol. 344 p. 557 ’14 ]. We know all sorts of wonderful neuropharmacology and neurophysiology about delta-9 tetrahydrocannabinol (d9-THC) — http://en.wikipedia.org/wiki/Tetrahydrocannabinol The point of the authors (the current head of the Amnerican Psychiatric Association, and the first director of the National (US) Institute of Drug Abuse), is that there are no significant studies of what happens to adolescent humans (as opposed to rodents) taking the stuff.

Marihuana would the first mind-alteraing substance NOT to have serious side effects in a subpopulation of people using the drug — or just about any drug in medical use for that matter.

Any organic chemist looking at the structure of d9-THC (see the link) has to be impressed with what a lipid it is — 21 carbons, only 1 hydroxyl group, and an ether moiety. Everything else is hydrogen. Like most neuroactive drugs produced by plants, it is quite potent. A joint has only 9 milliGrams, and smoking undoubtedly destroys some of it. Consider alcohol, another lipid soluble drug. A 12 ounce beer with 3.2% alcohol content has 12 * 28.3 *.032 10.8 grams of alcohol — molecular mass 62 grams — so the dose is 11/62 moles. To get drunk you need more than one beer. Compare that to a dose of .009/300 moles of d9-THC.

As we’ve found out — d9-THC is so potent because it binds to receptors for it. Unlike ethanol which can be a product of intermediary metabolism, there aren’t enzymes specifically devoted to breaking down d9-THC. In contrast, fatty acid amide hydrolase (FAAH) is devoted to breaking down anandamide, one of the endogenous compounds d9-THC is mimicking.

What really concerns me about this class of drugs, is how long they must hang around. Teaching neuropharmacology in the 70s and 80s was great fun. Every year a new receptor for neurotransmitters seemed to be found. In some cases mind benders bound to them (e.g. LSD and a serotonin receptor). In other cases the endogenous transmitters being mimicked by a plant substance were found (the endogenous opiates and their receptors). Years passed, but the receptor for d9-thc wasn’t found. The reason it wasn’t is exactly why I’m scared of the drug.

How were the various receptors for mind benders found? You throw a radioactively labelled drug (say morphine) at a brain homogenate, and purify what it is binding to. That’s how the opiate receptors etc. etc. were found. Why did it take so long to find the cannabinoid receptors? Because they bind strongly to all the fats in the brain being so incredibly lipid soluble. So the vast majority of stuff bound wasn’t protein at all, but fat. The brain has the highest percentage of fat of any organ in the body — 60%, unless you considered dispersed fatty tissue an organ (which it actually is from an endocrine point of view).

This has to mean that the stuff hangs around for a long time, without any specific enzymes to clear it.

It’s obvious to all that cognitive capacity changes from childhood to adult life. All sorts of studies with large numbers of people have done serial MRIs children and adolescents as the develop and age. Here are a few references to get you started [ Neuron vol. 72 pp. 873 – 884, 11, Proc. Natl. Acad. Sci. vol. 107 pp. 16988 – 16993 ’10, vol. 111 pp. 6774 -= 6779 ’14 ]. If you don’t know the answer, think about the change thickness of the cerebral cortex from age 9 to 20. Surprisingly, it get thinner, not thicker. The effect happens later in the association areas thought to be important in higher cognitive function, than the primary motor or sensory areas. Paradoxical isn’t it? Based on animal work this is thought to be due pruning of synapses.

So throw a long-lasting retrograde neurotransmitter mimic like d9-THC at the dynamically changing adolescent brain and hope for the best. That’s what the cited editorialists are concerned about. We simply don’t know and we should.

Having been in Cambridge when Leary was just getting started in the early 60’s, I must say that the idea of tune in turn on and drop out never appealed to me. Most of the heavy marihuana users I’ve known (and treated for other things) were happy, but rather vague and frankly rather dull.

Unfortunately as a neurologist, I had to evaluate physician colleagues who got in trouble with drugs (mostly with alcohol). One very intelligent polydrug user MD, put it to me this way — “The problem is that you like reality, and I don’t”.

Null hacking — Reproducibility and its Discontents — take II

Most scientific types have heard about p hacking, but not null hacking.

Start with p hacking.  It’s just running statistical test after statistical test on your data until you find something unlikely to occur by chance more than 5% of the time (a p of .05) making it worthy of publication (or at least discussion).

It’s not that hard to do, and I faced it day after day as a doc and had to give worried patients a quick lesson in statistics.  The culprit was something called a chem-20, which measured 20 different things (sodium, potassium, cholesterol, kidney tests, liver tests, you name it).  Each of the 20 items had a normal range in which 95% of the values from a bunch of (presumably) normal people would fall.  This of course means that 2.5% of all results would be outside the range on the low side, and 2.5% would be outside the range on the upside.

Before I tell you, how often would you expect to get a test where all 20 tests were normal?

The chance of a single test being normal is .95, two tests .95 * .95 = .90, 4 tests .90 * .90 = .81, 8 tests .81 * .81 = .65, 16 tests .65 *.65 = .42, 20 tests .42 * .81 = .32.

Less than 1/3 of the time.

That’s p hacking.  It has been vigorously investigated in the past few years in psychology, because a lot of widely cited results in supposedly high quality journals couldn’t be reproduced.  See the post of 6/16 at the end for the initial work.

It arose because negative results don’t win you fame and fortune and don’t get published as easily.

So there has been a very welcome and salutary effort to see if results could be confirmed — only 39% were — see the copy of the old post at the end.

So all is sweetness and light with the newly found rigor.  Not so fast says Proc. Natl. Acad. Sci. vol. 116 pp. 25535 – 25545 ’19.  The same pressures that lead investigators to p hack their result to get something significant and publishable, leads the replicators to null hack their results to win fame and fortune by toppling a psychological statue.

At this point it’s time for a Feynman quote “The first principle is that you must not fool yourself and you are the easiest person to fool.”

The paper talks about degrees of freedom available to the replicator, which in normal language just means how closely do you have to match the conditions of the study you are trying to replicate.

Obviously this is impossible for one of the studies and its replication they discuss — whether the choice of language used in a mailing  to urge people to vote in an election had any effect on whether they actually voted.  Obviously you can’t arrange to have the two hard fought elections in which there was a lot of interest of the initial study run again.  But the replicators choose a bunch of primaries in which interest and turnout was low, casting doubt on their failure to replicate the original results (which was that language DID make a difference in voter turnout).

Then the authors of the PNAS paper reanalyzed the data of the replicators a different way, and found that the original study was replicated.  This is the second large degree of freedom, the choice of the way to analyze the raw data — the same as the original authors or differently — “reasonable people may differ” about these matters.

There’s a lot more in the paper including something called the Bayesian Causal Forest which is a new method of data analysis which the authors favor (which I confess I don’t understand).

Here’s the old post  of 6/16

Reproducibility and its discontents

“Since the launch of the clinicaltrials.gov registry in 2000, which forced researchers to preregister their methods and outcome measures, the percentage of large heart-disease clinical trials reporting significant positive results plummeted from 57% to a mere 8%”. I leave it to you to speculate why this happened, but my guess is that probably the data were sliced and diced until something of significance was found. I’d love to know what the comparable data is on anti-depressant trials. The above direct quote is from Proc. Natl. Acad. Sci. vol. 113 pp. 6454 – 6459 ’16. The article looked at the 100 papers published in ‘top’ psychology journals, about which much has been written — here’s the reference to the actual paper — Open Science Collaboration (2015) Psychology. Estimating the reproducibility of psychological science. Science 349(6251):aac4716.

The sad news is that only 39% of these studies were reproducible. So why beat a dead horse? The authors came up with something quite useful — they looked at how sensitive to context each of the 100 studies actually was. By context they mean the time of the study (e.g., pre- vs. post-Recession), culture (e.g., individualistic vs. collectivistic culture), the location (e.g., rural vs. urban setting), or the population (e.g., a racially diverse population vs. a predominantly White or Black or Latino population). Their conclusions were that the contextual sensitivity of the research topic was associated with replication success (e.g. the more context sensitive, the less likely it was that the study could be reproduced). This was even after statistically adjusting for several methodological characteristics (e.g., statistical power, effect size, etc. etc). The association between contextual sensitivity and replication success did not differ across psychological subdisciplines.

Addendum 15 June ’16 — Sadly, the best way to say this is — The more likely a study is to be true (replicable) the more likely it is to be not generally applicable (e.g. useful).

So this is good. Up to now the results of psychology studies have been reported in the press as of general applicability (particularly those which enforce the writer’s preferred narrative). Caveat emptor is two millenia old. Carl Sagan said it best — “Extraordinary claims require extraordinary evidence.”

For an example data slicing and dicing, please see — https://luysii.wordpress.com/2009/10/05/low-socioeconomic-status-in-the-first-5-years-of-life-doubles-your-chance-of-coronary-artery-disease-at-50-even-if-you-became-a-doc-or-why-i-hated-reading-the-medical-literature-when-i-had-to/

 

The neuropharmacological brilliance of the meningococcus

The meningococcus can kill you within 12 hours after the spots appear — https://en.wikipedia.org/wiki/Waterhouse–Friderichsen_syndrome.  Who would have thought that it would be teaching us neuropharmacology.   But it is —  showing us how to make a new class of drugs, that no one has ever thought of.

One of the most important ways that the outside of a cell tells the inside what’s going on and what to do is the GPCR (acronym for G Protein Coupled Receptor).  Our 20,000 protein coding genome contains 826 of them. 108 G-protein-coupled receptors (GPCRs) are the targets of 475 Food and Drug Administration (FDA)-approved drugs (slightly over 1/3).   GPCRs are embedded in the outer membrane of the cell, with the protein going back and forth through the membrane 7 times (transmembrane segment 1 to 7 (TM1 – TM7). As the GPCR sits there usually the 7 TMs cluster together, and signaling molecules such as norepinephrine, dopamine, serotonin etc. etc. bind to the center of the cluster.   This is where the 475 drugs try to modify things.

Not so the meningococcus. It binds to the beta2 adrenergic receptor on the surface of brain endothelial cells lining cerebral blood vessels, turning on a signaling cascade which eventually promotes opening junctions of the brain endothelial cells with each other, so the bug can get into the brain.  All sorts of drugs are used to affect beta2 adrenergic receptors, in particular drugs for asthma which activate the receptor causing lung smooth muscle to relax.  All of them are small molecules which bind within the 7 TM cluster.

According to Nature Commun. vol 10 pp. 4752 –> ’19, the little hairs (pili) on the outside of the organism bind to sugars attached to the extracellular surface of the receptor, pulling on it activating the receptor.

This a completely new mechanism to alter GPCR function (which, after all,  is what our drugs are trying to do).  This means that we potentially have a whole new class of drugs, and 826 juicy targets to explore them with.

Here is one clinical experience I had with the meningococcus.  A middle aged man presented with headache, stiff neck and fever.  Normally spinal fluid is as clear as water.  This man’s was cloudy, a very bad sign as it usually means pus (lots of white blood cells).  I started the standard antibiotic (at the time)  for bacterial meningitis — because you don’t wait for the culture to come back which back then took two days.  The lab report showed no white cells, which I thought was screwy, so I went down to the lab to look for myself — there weren’t any.  The cloudiness was due to a huge number of meningococcal bacteria.  I though he was a goner, but amazingly he survived and went home. Unfortunately his immune system was quite abnormal, and the meningitis was the initial presentation of multiple myeloma.

Is the microtubule alive ??

When does inanimate matter become animate?  How about cilia — they beat and move around.  No one would call  the alpha/beta tubulin dimer from which they are formed alive.  The tubulin proteins contain 450 amino acids or so and form a globule 40 Angstroms (4 nanoMeters) in diameter.  The dimer is then 40 x 80 Angstroms and looks like an oil drum.  Then they form protofilaments stacked end to end — e.g. alpha beta alpha beta.  Then 13 protofilaments then align side by side to form the microtubule (which is 250 Angstroms in diameter, with a central hole about half that size.  Do you think you could design a protein to do this?

Lets make it a bit more complicated, and add another 10 protofilaments forming a second incomplete ring.  This is the microtubule doublet, and each cilium has 9 of them all arranged in a circle.

Hopefully you have access to the 31 October cell where the repeating unit of the microtubule doublet is shown in exquisite detail — https://www.cell.com/action/showPdf?pii=S0092-8674%2819%2931081-5. — Cell 179, 909–922 ’19

The structure is from the primitive eukaryote Chlamydomonas, the structure repeats every 960 Angstroms (e.g every 12 alpha/beta tubulin dimers).  So just for one repeating unit which is just under 1/10 of a micron (10,000 Angstroms) there are (13 + 10) * 12 = 276 dimers.  The cilium is 12 microns long so that’s 12 * 276 * 100 = 298,080 alpha tubulin dimers/microtubule doublet. The cilium has 9 of these + another doublet in the center, so thats 2,980,800 alpha tubulin dimers/cilium.

The cell article is far better than this, because it shows how the motor proteins which climb along the outside of the doublet (such as dynein) attach.The article also describes the molecular ruler (basically a 960 Angstrom coil coil which spans the repeat. They found some 38 different proteins associated with the microtubule repeat.  They repeat as well at 80, 160, 240, 480 and 960 Angstrom periodicity.  The proteins in the hole in the center of the microtubule (e.g. the lumen) are rich in a protein module called the EF hand which binds calcium, and which likely causes movement of the microtubule, at which point the damn thing (whose structure we now know) appears alive.

Because of the attachment of the partial ring (B ring) to the complete ring of protofilaments, each of the 23 protofilaments has a unique position in the doublet, and each of the proteins in the lumen is bound to a specific mitotubule profilament. There are 6 different coiled coil proteins inside the A ring, occupying  specific furrows between the protofilaments.

Staggering complexity built from a simple subunit, but then Monticello is only made of bricks.