Posts Tagged ‘immune system’
immunity 2: MIT lecture – more on immunity and auto-immunity
So we’re looking at cell-mediated and auto-immunity in this second lecture. We see an image of listeria, an intracellular bacterium, pushing out the edges of the cell, so that it can move between cells without entering the extracellular space. Listeria is a food-borne bacterium which can cause severe intestinal illness. So think of a host cell with an intracellular pathogen, bacterial or viral, taking advantage of these cells to reproduce and spread. This is not good.
B cells, as described before, have an antigen receptor, initially on the plasma membrane, and sometimes secreted into the intracellular space, while T cells only have the membrane-bound form. In any case these antibodies are directed outwardly. How can a listeria-like infection, within the cells, be dealt with? This involves a process called antigen presentation, in which peptides – short sequences of amino acids – are presented and displayed on the cell surface, so that T cells, in this case, can observe what is happening within the cell. This involves another molecule previously mentioned, the major histocompatibility complex (MHC). There are two classes of MHC. Class 1 has a heavy chain – a long polypeptide – and a light chain. So, two polypeptides encoded by different genes. It has two Ig domains proximal to the plasma membrane – and it’s all inserted into this membrane – an integral membrane protein. Then at the other end, distal to the plasma membrane, is another structure, which, looking at its crystal structure, is a ‘beta sheet with two alpha helices’, shaped somewhat like a cup [a beta sheet is a common secondary structure in proteins, formed by polypeptide strands (beta strands) connected laterally by hydrogen bonds, creating a pleated, twisted, sheet-like structure]. Inside the cup is a peptide which displays some of its amino acids, away from the MHC molecule, for T cells to observe.
So these Class 1 MHCs are membrane proteins displayed on all nucleated somatic cells, and the peptides held by these MHCs are derived from the cytoplasm within the cell. They are loaded on to the MHC molecule, which is translated (using ribosomes and types of RNA) on the endoplasmic reticulum (ER), and its extracellular domain is initially present in the lumen (internal space) of the ER. Its peptides come from proteins in the cytoplasm. What happens to these proteins – including unfolded proteins and those that might be ubiquitinated [refers to a protein that has had ubiquitin, a small protein, covalently attached to it, often marking the protein for degradation or influencing its function or localisation – thanks AI, and it has of course dawned on me that this MIT course has followed on from earlier biochemistry learnin] – is that they’re processed by the proteasome [a large, cylindrical protein complex that degrades proteins tagged with ubiquitin, a process essential for maintaining cellular homeostasis and regulating various processes like cell cycle and protein quality control], which this lecturer describes as ‘a kind of shredder-like function for protein’, which cuts the proteins into peptides which can then be pumped into the ER lumen via a transporter, TAP…
The transporter associated with antigen processing (TAP) is a heterodimeric protein complex (TAP1 and TAP2) that transports peptides from the cytosol into the endoplasmic reticulum (ER), where they bind to MHC class I molecules, a crucial step in antigen presentation to cytotoxic T cells.from AI overview
From there they are loaded onto the class 1 MHC molecule. The source of these peptides is from proteins in the cytoplasm, processed by the proteasome. So now that a peptide-MHC complex has been created, it can then be trafficked to the plasma membrane of the cell, where the peptide will be displayed for T cells to observe. The types of T cell that look at these class 1 molecules are known as CD8+ T cells.
There are also class 2 MHC molecules, which have fundamentally different properties. Both molecules display peptides on the cell surface (antigen presentation), but the structure of MHC class 2 is quite different. Instead of a heavy and light chain, there are two chains of roughly equal size, and they’re encoded by different genes than the class 1 MHC. There are two Ig domains proximal to the plasma membrane, and at the end of the MHC molecule there’s a groove or pocket that holds a peptide (aka a peptide-binding cleft).
The class 2 MHC is expressed on a more restricted set of cells. They’re expressed specifically on specialised antigen-presenting cells, such as B cells and phagocytic cells [also known as phagocytes, they are specialised cells of the immune system that engulf and destroy foreign substances, pathogens, and cellular debris through a process called phagocytosis].
Phagocytosis is the process by which a cell uses its plasma membrane to engulf a large particle, giving rise to an internal compartment called the phagosome. It is one type of endocytosis. A cell that performs phagocytosis is called a phagocyte.
Endocytosis is a cellular process where a cell engulfs extracellular material, forming an internal vesicle to transport substances into the cell. This process, which includes phagocytosis (cell eating) and pinocytosis (cell drinking), is essential for nutrient uptake, cell signalling, and defence against pathogens.
Dendritic cells (DCs) are crucial immune cells that act as sentinels, capturing antigens and presenting them to T cells to initiate adaptive immune responses, effectively bridging innate and adaptive immunity (from AI overview)
References
Immunology 2 – Memory, T cells & Autoimmunity, MIT OpenCourseWare, YouTube video
Mary Wortley Montagu and early immunology
Mary Wortley Montagu, aristocrat, writer, poet, traveller and advocate of variolation
The person I live with recently had a women’s lunch in which the Covid pandemic came up for discussion. One of the women, whom I know to be a white South African by origin, and a Christian (all of which may be irrelevant), said ‘Well I didn’t get Covid, because I wasn’t vaccinated’. Apparently everyone present politely ignored this remark, but it was obviously sufficiently egregious for Sarah to mention it to me afterwards.
The only other thing I know about this woman, whom I’ve met a few times, is that she’s very much an advocate for ‘organic’ produce, and so opposed to GMOs, a topic about which I’ve written in the now-distant past, but which has often come up in SGU podcasts, perhaps most recently in episode 1024’s ‘science or fiction’ segment, in which it was pointed out that the US produces and consumes far more GM food than any other nation, even though, typically for such a divided nation, it protests more vehemently that any other country about the whole GM thing.
Anyway, this woman remarked that she (and so presumably everyone else who survived) didn’t get Covid because she wasn’t vaccinated. So, since ‘because’ is clearly a causal word, in basic logic, she is saying that the vaccine caused Covid. That’s to say the pandemic was caused by immunologists and their vaccines. Ergo, immunologists have slaughtered over 7 million people. The virus itself, presumably, doesn’t exist.
It’s hard to know where to begin with such people, but let’s just kindly say that they can’t think straight. In any case, it reminded me of all the efforts I made to understand the virus, its mode of action, the ACE2 receptor, the ‘cytokine storm’ and so forth, much of which I’ve already forgotten.
And yet…
I often come back to the immune system and its incalculable intricacies, because… well, just because. It’s just fascinating. As are our historical attempts to understand it and manipulate it to our benefit.
So I’ve begun to watch a set of lectures on immunology from MIT, delivered in 2018 – just in time to ready all those students for the SARS-CoV-2 outbreak! The first lecture began with the story of Edward Jenner, cowpox and the first vaccination, back in 1796, and I hadn’t made the connection between vaccine and vacca, the Latin word for cow, and of course vache in French. Silly me. But, even more interesting, on recounting this to my closest friend, she reminded me… who was that aristocrat, Lady Mary Whatsername, who was really the first…
So in the interests of feminist fairness and all, here’s her story.
In 1721, Lady Mary Wortley Montagu brought smallpox inoculation to Europe, by asking that her two daughters be inoculated against smallpox as she had observed practice in Turkey.
That’s from the WHO Brief History of Vaccines, referenced below. But as you can see from that site, it didn’t start with Lady Mary. Variolation, from ‘la variole’, a name for smallpox, goes back many centuries, and involves exposing people to ‘mild’ doses of smallpox to confer immunity. I’m not sure of the ‘how’ of that process – apparently one method was blowing old smallpox scabs into people’s noses, causing them to contract a mild form of the disease. I mean, what could go wrong?
In any case, as with Jenner decades later, this was clever thinking about the inducing of immunity, long before anything much was known about our super-complex two-pronged immune system.
So all of this is introductory to another attempt to get my head around that system, via the glorious magic of the internet. Who needs to pay for a university education nowadays? Well, I suppose I’m lucky I got to learn the world’s biggest international language from babyhood.
So I’ll start my dive into the deeps of our extraordinary immune system in my next post.
References
https://www.sgutranscripts.org/wiki/SGU_Episode_1024
Natural selection – how far does it go?
you don’t control this variability
So let me try to understand something completely different, to do with genetics, neurology and selection theory. I’m reading a rather complex, demanding and ambitious book, published back in 1992, by Michael Gazzaniga, called Nature’s Mind, and sub-titled ‘The biological roots of thinking, emotions, sexuality, language and intelligence’. Selection theory gets a regular mention, and I’m assuming what is meant is the Darwinian theory of natural selection. That’s to say, the idea or finding that phenotypic traits that enable individuals in a species to more effectively survive, thrive and reproduce in their particular environment will be ‘naturally selected’ as against other less favourable traits. And so the species will ‘evolve’, that’s to say change, because individuals with the better-adapted traits for a particular environment will out-compete those without those traits and, crucially, pass on those traits to their offspring. Darwin, of course, could only speculate about how those traits were passed down to the next generation, as the whole story of genetic inheritance and DNA wasn’t fully established until well into the 20th century.
Anyway, Gazzaniga seems to be writing about selection theory as some kind of controversial issue, which surprises me and makes me wonder whether I’m reading him right. So let me focus on Chapter 2, ‘The plastic brain and selection theory’, to help my understanding. Here’s the opening sentence:
Although there is little argument that the selection process is at work at both the molecular and the evolutionary levels in whole organisms, there are major questions about whether the brain develops and functions in accordance with the concept of selection.
I don’t understand what Gazzaniga means by these separate ‘molecular’ and ‘evolutionary’ levels. After all, evolution just means change of a certain type – that’s to say, changes in organisms. And organisms are, of course, made up of molecules, coded for by genes. So the organisational structure of the brain, down to the molecular level (or upwards from the molecular level), has everything to do with our genetic inheritance. So what, then, are these major questions? Gazzaniga puts it this way:
…if, as I argue… the majority of our psychological capacities are the result of natural selection, the developing and static adult brain, which houses the neural circuits that enable the human’s high-powered psychological mechanisms to exist, must develop in a surefire, genetically determined way. At the level of behaviour, for example, we want to see whether or not a baby learns to identify a face, or whether there exist in the brain specific circuits enabling facial recognition, circuits laid down by prior genetic forces arrived at through selection pressure.
So, as I conceive it, Gazzaniga is exploring facial recognition (presumably that of other humans, but ‘face’ isn’t of course restricted to humans) in terms of learning and distinguishing, but also in terms of genes and circuitry that have evolved to render such recognition as vitally important. He cites the Nobel Prize-winning immunologist Niels Jerne’s view that selection operates at the cellular level, even though ‘it might look like instruction occurred at a higher level of organisation’. A ‘signal’ of recognition will prompt a response, once described as ‘unconscious’ (but it seems most scientists today dismiss this as a ‘woo’ word), that has been selected for on the most basic, molecular level.
So this takes us into a bit of immunology. Jerne used three analogies, as described by Gazzaniga: first, ‘the immune system is forever changed by the appearance of each new antigen, just as the brain is somehow changed by each new experience’, second, ‘each system – brain and immune system, appears to have a memory: when the same antigen presents itself a second time to an organism, the latter produces more and better antibodies’, and third ‘the experience one organism has developed for its immune system is not transferable to its progeny, just as my skiing ability is not necessarily transferred to my offspring’.
So, to antibodies, and the kappa light chain, which is present in the antibodies of humans and other animals. In all creatures who have these molecules, there is a variable and a constant part of the chain. They’re made up of amino acids, and the constant section is constant for all humans (and presumably for other species), while the variable part varies individually, or ontogenetically.
It seems that Jerne, and Gazzaniga, have taken this as some kind of analogy for the brain, the plasticity of which has both an ontogenetic (individual) and phylogenetic (species-specific) element. That’s to say, there’s a great deal of ontogenetic plasticity within the brain’s overall phylogenetic structure. I’m not sure if I’m getting this right, though. Here’s more from Jerne, comparing the immune system and the central nervous system:
In the immune system, the constant part of the light chain is obviously laid down in the DNA of the zygote, and it is equally clear that there is DNA in the zygote that represents the variable part of the light chain, although, ontogenetically, this DNA may exhibit an immense plasticity.
In the central nervous system, instincts are also obviously encoded in the zygote, most probably in the DNA. But if DNA acts only through transcription into RNA and translation into protein, and if the phenotypic expression of instincts is based on particular arrangements of neuronal synapses, the DNA through RNA and protein must govern the synaptic network in the central nervous system.
Niels Jerne, ‘Antibodies and learning: selection versus instruction’, 1967
So what to make of this ‘magnificent analysis’ (according to Gazzaniga)? You could say that it’s another brick in the deterministic wall, that ontogenetic plasticity, that which makes me different from you, starts with ‘particular arrangement of neuronal synapses’, or the particular sets of proteins that bring about those arrangements, or, before that…
I’m no doubt being influenced right now by some very recent discussions/arguments I’ve had on the subject of determinism, so I’m probably going further than Gazzaniga intended with his thinking. Or not. I shall continue reading the book to see if he comes to any definite determinist conclusions, or if he even touches on such a touchy subject.
References
M Gazzaniga, Nature’s Mind, 1992
on the lymphatic system and its clever cells, mostly
Activation of macrophage or B cell by T helper cell
Jacinta: So we’re focussing now on the lymphatic system, ‘clear water’ remember. A most misleading definition. So there’s this network of vessels, nodes and ducts….
Canto: What’s a node?
Jacinta: It’s a point of connection, or connections. In plants, a node is a point of branching, like with leaves.
Canto: Yeah I knew that. What’s a duct?
Jacinta: Don’t kid kid. It’s like a vessel, only, somehow different. Maybe bigger? Anyway, nodes go with lymph. There are over 500 of these lymph nodes throughout our bodies. The system does a lot of clean-up work, preserving fluid balance. It’s also much implicated in the immune system of course, and it’s involved in other stuff that’s quite hard to summarise, as you know.
Canto: Something from a reliable enough website:
The lymphatic system plays a key role in intestinal function. It assists in transporting fat, fighting infections, and removing excess fluid. Part of the gut membrane in the small intestine contains tiny finger-like protrusions called villi. Each villus contains tiny lymph capillaries, known as lacteals. These absorb fats and fat-soluble vitamins to form a milky white fluid called chyle. This fluid contains lymph and emulsified fats, or free fatty acids. It delivers nutrients indirectly when it reaches the venous blood circulation. Blood capillaries take up other nutrients directly.
Jacinta: Never heard of lacteals. Have heard of chyle, but don’t know much about it. So chyle contains lymph. But what’s lymph?
Canto: It’s a not-so-clear beige-coloured milky fluid containing lots of WBCs, especially lymphocytes, of course, and fatty stuff. Well, actually, that’s not lymph, that’s chyle. Or both… So there’s this lacteal system of the small intestine, capillaries for absorbing fats – well, actually transporting them… but we need to know what bile is, and emulsification, and lipase, and glycerides and esters, and no doubt much much more.
Jacinta: Well we’ve committed ourselves to learning about the immune system and associated processes for some ineffable effing reason, so let’s soldier on.
Canto: Okay, so bile has nothing to do with Trump, at least not in this context. Bile ducts are this network of tubes inside the liver – well actually there are intrahepatic and extrahepatic bile ducts. Bile itself is a fluid made and released by the liver, for breaking fat down into fatty acids. For ‘digesting’ fat, sort of. Not particularly relevant to the immune system, but it’s all interesting en it? And it can cause problems, such as chronic bile reflux. I suspect I’ve experienced bile reflux, though not chronically. I think it’s also called acid reflux, suggesting bile is a kind of acid.
Jacinta: Or maybe not. Here’s another one of those websites that know more than us:
Bile is composed of ingredients designed to digest fat. While it isn’t an acidic formula, it’s harsh on the sensitive linings of your stomach and esophagus. Chronic bile reflux can erode these protective linings, causing painful inflammation and, eventually, tissue damage (esophagitis).
Anyway, I’m not sure how we got from chyle to bile.
Canto: Right, back to chyle and lymph. Have you heard of lymphoedema? That’s a blockage of the lymphatic system, which causes tissue swelling, mostly in the arms and legs but possibly just about everywhere.
Jacinta: Yes, and things fall apart, the centre doesn’t hold. So let’s get back to lymph nodes and the cells they contain. Within lymph nodes there are germinal centres containing a lot of B cells, or B lymphocytes. These have receptors (B cell receptors) on their membranes which are IgD antibodies, all of which have different binding domains, due to genetic recombination, which allows them to deal with differently structured antigens. Once binding occurs, signals are sent to the lymphocyte’s nucleus, resulting in what’s called receptor-mediated endocytosis. The signalling response creates pseudopods and/or clathrins which pull the membrane inside.
Canto: Ok, sorry to be boringly predicable, what are clathrins?
Jacinta: They’re proteins, very ‘clever’ proteins, as so many of them are. They mediate endocytosis, which is essentially the surrounding and cutting off of extracellular material within the cell, creating a vesicle, called an endosome I think, which might be transported to further action sites. So this is happening within the B lymphocyte. We have this B cell receptor bound to a foreign antigen, and chromosome 6 of this cell then can produce a molecule (MHC2) to ‘fit’ the antigen and fuse it to the cell membrane. This has the effect of activating the B cell, carrying an MHC2 antigen-carrying molecule on its surface, and IgD antibodies. Of course I haven’t explained how the clathrins actually carry out this transformation, because I can’t but I believe it’s all been worked out.
Canto: Yes of course, and now our lymphocyte is an antigen-presenting cell. There are three types of such cells – B lymphocytes, macrophages and dendritic cells. However, the lymphocytes still need to proliferate to be effective, and this requires a stimulus. And so enter the macrophages. These have MHC2 molecules on their surface, bound to a specific foreign antigen, and they also have MHC1 surface molecules bound to a self antigen (as do all nucleated cells). The macrophage presents this MHC2 molecule with its antigen to a type of T cell, described as a’naive’ (i.e. non-specific) T helper cell. These helper cells will have, somewhere on their surface, specific protein molecules, called CD4, that ‘fit’ with the MHC2 molecules, and other specific molecules (T cell receptors) that fit with the foreign antigen. Specific TCRs fit with specific antigens. It’s all a matter of geometry, sort of.
Jacinta: These different types of TCRs are a product of genetic recombination, which involves RAG1 and RAG2 genes, and I can only guess that the R stands for recombination… Now these helper cells have CD3 signalling molecules inside (they send signals to the nucleus), and a molecule called CD28 on their surface. The macrophage has a protein, B7, which interacts with the CD28, and this protein interaction, called a co-stimulation reaction, sends a secondary signal to the nucleus – as opposed to the first, primary signal. This is known as co-stimulation.
Canto: So next, the macrophage starts secreting a molecule called interleukin-1, which binds to a specific receptor on the T helper cell, which results in a third signal to the nucleus, and activation of the T cell. The cell’s genes now produce interleukin-2, which can be secreted and will then bind to a receptor, as an ‘autocrine’, resulting in genes secreting another cytocrine, interleukin-4, and then interleukin-5. With all this, the T helper cell moves to another stage, becoming either a T helper 1 cell (stimulated by interleukin 12) or a T helper 2 cell (stimulated by interleukin 4). So, focussing on the T helper 2, it has activated interleukins 2,4 and 5, the latter two of which are especially important, after these cells have started dividing. That’s when those cytokines are produced.
Jacinta: We might be learning something. Now to the proliferation of the B lymphocyte. Interleukin 4 activates the B lymphocyte to start turning on genes for its proliferation – called clonal expansion. And they will have receptors (BCRs) specific to the foreign antigen. They’ll also have MHC2 surface molecules with exposed foreign antigens. They’re now ‘immuno-competent’ cells, and then, through the medium of interleukin 5, they will start differentiating. Some of these new types of cells are called plasma cells, which have a very prominent rough endoplasmic reticulum (RER), others are called memory B cells. Interleukin 5 and 6 stimulate plasma cells to produce and secrete antibodies specific to particular foreign antigens – or, rather, having variable regions that can adapt to and bind to those antigens.
Canto: And these antigens might be on the surface of bacteria, or not as the case may be. If they can bind to all the antigens on the bacterial (or viral) surface they can render it ineffective (neutralisation). Binding to freely circulating antigens can, however, cause problems. Such binding creates a precipitation reaction and this can be deposited in tissue resulting in a type 3 hypersensitivity. Don’t ask.
Jacinta: This is what United Staters call getting into the weeds, maybe. So that’s surely enough for now.
more baffling immune system stuff
1RH2 Recombinant Human Interferon Alpha 2b – evidemment
Jacinta: We’ve been mostly educating ourselves via the NinjaNerd YouTube series on immunology, which seems very comprehensive and yet comprehensible, for beginners, and then going to other websites for details. Now getting back to cluster differentiation (CD), a commonly used immunological term. Here’s a useful definition:
The cluster of differentiation (CD) is a protocol used for the identification and investigation of cell surface molecules present on leukocytes. CD molecules often act as receptors or ligands important to the function of immune cells.
Canto: That’s useful indeed. Each CD – 4 or 8 or 25 – represents a cluster of differentiation. Differentiated from other clusters. So back to T regulatory cells, which would be differentiated into those cells that predominantly have CD4 or CD8 molecules, as well as TCRs. All to help suppress auto-immune diseases in particular.
Jacinta: So we have these T regulatory cells, as well as helper and cytotoxic T cells, all created in the thymus essentially, and then they’re distributed to the lymphoid organs – the lymph node locations include ‘the groin, armpit, behind the ears, back of the head, sides of the neck and under the jaw and chin‘. There’s also the spleen and its sinusoidal capillaries, where T cells form a surrounding layer known as the ‘periarteriolar lymphoid sheath’ (PALS), more commonly known as white pulp. A large number of T regulatory cells however remain in a thymus region known as the thymic (Hassal’s) corpuscles. They’re also distributed throughout the body – the tonsils, the respiratory tract and so on. All originating from the red bone marrow.
Canto: Well I’m still a little confused about the difference between the innate and adaptive immune systems and whether there really is any clear distinction between them (I suspect not). My own distinction so far is that the innate system is quick and not very specific and well-attuned, and the adaptive is – everything else.
Jacinta: Well, a bacterial antigen releases endotoxins which causes a massive release of inflammatory cytokines, got that?
Canto: Not particularly. Get this:
Endotoxins (lipopolysaccharides, LPS) are agents of pathogenicity of Gram-negative bacteria, implicated in the development of Gram-negative shock. Endotoxin reacts with lipopolysaccharide-sensitive cells producing endogenous mediators such as tumour necrosis factor alpha (TNFα).
That was my first stop in trying to find out what endotoxins are. Needless to say, it’s meaningless to me. Though I know that ‘endo’ means ‘from within’ as opposed to ‘exo’… I think.
Jacinta; If you look that up you’ll find it’s horribly complex. Okay the bacteria release toxins which release cytokines in reaction. There are many different kinds of cytokines, including histamines, prostaglandins and leukotrienes. Amongst other things these cytokines will impact smooth muscle cells causing vasodilation, increasing blood flow causing heat and redness. Cytokines will also contract endothelial cells, causing fluid leakage and permeability, affecting pain receptors. Bradykinins are also involved in vasodilation and increased blood flow. All this induces swelling and pain. Broadly, the four signs of inflammation are: swelling, pain, heat and redness. That answers a basic exam question. Joint immobility is a fifth sign in some extreme cases.
Canto: I’m looking at a different video, “introduction to the immune system”, because I think we need to stay on the ground floor for a while. I also think looking at language might help. For example, ‘cytokines’ feature heavily, and I was thinking that they were like some kinds of proteins or enzymes, something sub-cellular that could whizz about the body, but then I noticed that white blood cells were called leukocytes, and there were lymphocytes and phagocytes… cells! Like, complex organisms. And ‘kine’, apart from being about cattle, is where our word ‘kind’ came from, as in Kinds of Minds. So ‘cytokines’, methinks, are just the vast array of cells relating to the immune system.
Jacinta: Yes, this is good – a phagocyte is an ‘eating cell’. A lymphocyte is a type of WBC that’s involved in the immune system. T cells are lymphocytes, as are B cells. So, yes, they’re complex, gene-containing thingumies, all of them, and lymphocytes are so called because the lymph system is full of them. But note that ‘cyte’ just means ‘cell’, not necessarily of the white or immune kind.
Canto: So starting again at the beginning, with the innate and adaptive systems. So the innate system is what often causes pains and fevers, that redness and itchiness and raised temperature mentioned before – inflammation. Because of the release of cytokines, as you’ve explained.
Jacinta: Ah but here’s where it becomes confusing and unhelpful. On a website designed, I think, for high school biology students I found this:
Cytokines…. are a broad category of small proteins that are important in cell signaling. They are released by cells and affect the behavior of other cells. Cytokines include interferons, interleukins, lymphokines, and tumor necrosis factor.
So it looks like you were right in the first place. It is confusing though. Interferons are proteins, as are interleukins, and ScienceDirect, which is generally reliable, says this:
Cytokines, chemokines, and lymphokines are multifunctional immunoregulatory proteins secreted by cells of the immune system.
So we’ve both been confused, and maybe looking at language origins might confuse us more. Best just to accept what the biochemists say.
Canto: So, are we starting again, again? Let’s look at some of the cytokine types. Interferons are as mentioned, signalling proteins. But what, exactly, is meant by signalling, and what exactly is a protein? A chain of amino acids, je crois. So, signalling – that’s about sending and receiving and responding to signs of change:
Individual cells often receive many signals simultaneously, and they then integrate the information they receive into a unified action plan. But cells aren’t just targets. They also send out messages to other cells both near and far.
So far, so obvious. These signals are essentially chemical. Even neurotransmission reduces down to the chemical level. But we’ll stick with pathogens and immunity. Receivers of signals are generally called receptors, and immune-system cells often, but not always, have receptors within or sticking out of the cell membrane.
Jacinta: Interferons are so-called because they interfere with viruses and such. We’ve actually been able to create them in the lab since the 80s for treating some cancers:
Interferons are the frontline defenders in your body. A variety of cells, including white blood cells, produce interferons in response to infection and other stimuli, like cancer cells. They initiate signaling cascades by stimulating the infected cells and those nearby to produce cytokines.
Canto: But are they the frontline defenders? And they’re cytokines themselves, as aforementioned. Cytokine seems a pretty broad term.
Jacinta: Our refined or not-so-refined new definition – cytokines are types of stuff created by a variety of cells as an immune response to pathogens. As to interferons, don’t worry about it.
Canto: Too late, I’m worried. Here’s another quote:
More than twenty distinct IFN [interferon] genes and proteins have been identified in animals, including humans. They are typically divided among three classes: Type I IFN, Type II IFN, and Type III IFN. IFNs belonging to all three classes are important for fighting viral infections and for the regulation of the immune system.
Should we just devote the rest of our lives to interferons and forget the rest?
Jacinta: Everything’s connected to everything else. And we shouldn’t despair – we’ve learned much about the lymphatic system, for example, that we didn’t know before.
Canto: We didn’t know anything before. But yes I’m encouraged. And getting back to language, lymph is apparently Latin for ‘clear water’, which is a good start for thinking about lymphatic fluid, even if it’s anything but clear.
Jacinta: Like sea or river water I suppose. The more you look… Blame all those pesky microscopes and such. Anyway, one video describes the lymphatic system as having three main functions: 1) returning fluid to the heart: 2) helping large molecules (hormones and lipids) enter the blood: 3) immune surveillance.
Canto: Okay let’s look at all that in a bit more detail next time.
stuff on the immune system 2: T cells, mostly
It’s still early days, but gene-therapy modifications of bone marrow stem cells may be the solution to many haematological malignancies
Peter Doherty, An insider’s plague year
something like…
Canto: So we’re going to try and educate ourselves with the help of all these videos out there on the immune system, with hopefully occasional references to the SARS-Cov2 coronavirus. And we’re not going to reference all these videos and websites because it’s just too time consuming and nobody else is going to read this stuff, it’s just for ourselves, mostly much.
Jacinta So in a vid about T-cell development (and they’re a product of the adaptive immune system) we hear that T-cells are produced in the red bone marrow. Why red?
Canto: Bone marrow comes in 2 types:
Red bone marrow contains blood stem cells that can become red blood cells, white blood cells, or platelets. Yellow bone marrow is made mostly of fat and contains stem cells that can become cartilage, fat, or bone cells.
Jacinta: So it’s not about red bones. So stem cells are like stems, green shoots that can develop into all sorts of different plants?
Canto: Yes and so you can imagine the potential, if we can induce them to specialise in ways that we want. Homo deus and all that. My brief research tells me that they’re found all around the body, not just the marrow. But it doesn’t tell me how they came into being. And there are apparently different types, as in ‘blood stem cells’. So these particular cells are pushed out into the world via sinusoidal capillaries…
Jacinta: Capillaries are the narrowest of blood vessels, I know that much…
Sinusoid capillaries allow for the exchange of large molecules, even cells. They’re able to do this because they have many larger gaps in their capillary wall, in addition to pores and small gaps. The surrounding basement membrane is also incomplete with openings in many places.
Canto: I must say that the number of high-quality, comprehensive videos on immunology, e.g. on YouTube, is such a boon. The comments say it all, ‘if only I had this info available when I was doing my PhD’ etc etc. So back to T cells. They move, I think as precursor T cells, to the thymus, via those capillaries. The thymus is a small gland near the top of the lungs (in the thoracic cavity) which is an essential component of the lymphatic system, itself a part of our general immune system.
Jacinta: It’s described as a primary lymphoid organ – at last I’m going to find out more about lymph! I hope. So the thymus is where T cells develop, and the red bone marrow, another primary lymphoid organ, is where B cells develop.
Canto: And B cells are a ‘type of white blood cell that makes infection-fighting proteins called antibodies’. Whereas T cells fight infections more directly as well as doing a lot of signalling…
Jacinta: Interesting thing about the thymus – it functions mostly through early childhood and adolescence, after which it atrophies, its tissues becoming fibrous and non-functional. So its role in T cell maturation occurs in our early years.
Canto: The thymus secretes different types of chemokines, or chemotactic agents (thymosin, thymotaxin, thymopoetin and thymic factors) which are somehow able to pull these undeveloped T cells in the right direction. This process is called chemotaxis.
Jacinta: A chemical taxi system, how cute. So we mentioned the two primary lymphoid organs, and there are secondary lymphoid organs – the lymph nodes (found in a number of bodily locations) and the spleen (on your left side, just around the bottom of your rib-cage). Just on chemokines – we’ve heard of cytokines, and the worrisome ‘cytokine storm’ that was oft-mentioned during the Covid period. Chemokines are a subset of these cytokines, which are –
‘an exceptionally large and diverse group of pro- or anti-inflammatory factors that are grouped into families based upon their structural homology or that of their receptors. Chemokines are a group of secreted proteins within the cytokine family whose generic function is to induce cell migration’.
Canto: So now we’re looking at these precursor T cells arriving at the thymus. So the thymus has a heap of thymic, epithelial cells which secrete the above-mentioned chemokines, which stimulate certain genes within the T cells to produce two enzymes (proteins), RAG1 and RAG2 (RAG stands for recombination activating gene – the genes encode the proteins). These are types of recombinase…
Jacinta: Think of genetic recombination, or mixing:
Recombinases are a family of enzymes having functional roles in homologous and site-specific recombination. It’s an event in organisms that involves DNA breakage, strand exchange between homologous segments, and ligation of DNA segments using DNA ligase.
Canto: So in this T cell context the gene ‘shuffling’, as it might be called, produces different protein types to deal with different antigen types. For example they produce T cell receptors (TCRs) designed to recognise and ‘receive’ differently-shaped antigens.
Jacinta: So getting back to those chemokines, they’re inducing other genetic activity to produce CD (cluster differentiation) proteins, of which there are various conformations, such as CD4 and CD8. These proteins form on the outside of the T cells, where they, hopefully, bind to MHC (major histocompatibility complex) proteins on the thymic cells. And of course there’s always more complexity – ‘a human typically expresses six different MHC class I molecules and eight different MHC class II molecules on his or her cells’. For now just think MHC-1 and MHC-2. Recognition of the appropriate MHC molecules by the CD4 and 8 proteins is called ‘positive selection’. If positive selection doesn’t happen the T cells will die (apoptosis).
Canto: The next step, assuming T cell survival, has to do with the previously-mentioned TCRs. The MHC molecules on the thymic cells carry a ‘self peptide’, and just to show how complex and relatively recent our immunological knowledge is, here’s a quote from a Pub-Med abstract from late 2001:
Twenty years ago, antigenic and self peptides presented by MHC molecules were absent from the immunological scene. While foreign peptides could be assayed by immune reactions, self peptides, as elusive and invisible as they were at the time, were bound to have an immunological role. How self peptides are selected and presented by MHC molecules, and how self MHC-peptide complexes are seen or not seen by T cells raised multiple questions particularly related to MHC restriction, alloreactivity, positive and negative selection, the nature of tumor antigens and tolerance.
So, if we could imagine ourselves as upper-class kids who entered university in the late 70s, (instead of working in factories or bludging off the dole as we were doing), none of this would’ve been known to anyone and we could’ve helped make the breakthrough…
Jacinta: Woulda-coulda-shoulda. Back again to those T cell receptors (TCRs), which apparently are not supposed to recognise or connect with the thymic cells’ self or antigenic peptides, as that would lead to auto-immune complications. So they’re ‘designed’ for that purpose, so that they don’t recognise those peptides, and don’t connect with them. This is called negative selection. If for some reason recognition does occur, apoptosis will result. That process occurs by the release of FAS (aka APO-1 or CD95 – don’t ask) from the thymic cell to a receptor in the T cell.
Canto: So, up to this point, if the T cell has come through alive, it’s TCR-positive, CD4 positive and CD8 positive. Its CD4 molecule may interact fortuitously with the thymic cell’s MHC2 (but the CD8 doesn’t interact with MHC1). In that case, there will be gene up-regulation of the cell’s CD4 molecules and down-regulation of CD8. That’s to say, CD4s will increase and CD8s will reduce, and it will present other TCRs. This turns it into a ‘T helper cell’. On the other hand, if the cell’s CD8s connect with the MHC1, there will be up-regulation of CD8, down-regulation of CD4, converting it into a cytotoxic T cell. Some of these helper and cytotoxic T cells can further develop into T regulatory cells, aka T suppressor cells, important for auto-immune disease suppression. This is promoted by molecules such as CD25 and interleukin 2.
Jacinta: Ok that’s enough head-spinning for one post, except perhaps just to say that interleukin 2 is ‘a protein that regulates the activities of white blood cells (leukocytes, often lymphocytes) that are responsible for immunity’. And we might find out more about what ‘cluster differentiation’ actually means….
Reference
This almost all comes from one video:
stuff on the immune system and that recent pandemic: 1 – how to get lost in a single cell
got that?
Canto: So, looking way back to the Covid-19 year or two, which we survived (and I’m wondering if the virus has too), have we retained what we’ve learned from all those Medcram videos we watched, and from the various ‘vaccine hesitant’ characters we encountered…
Jacinta: One of whom was a nurse as I recall, but I must say, mind like a sieve, I don’t feel I’ve retained much, so we’re reading Nobel Prize-winning immunologist Peter Doherty’s An insider’s plague year, to help us set down some info and promote our lifelong learning.
Canto: So what’s the difference between a drug and a vaccine, Doherty asks, noting that even experienced journalists confuse the two. Drug of course is a broad term, for anything chemical used to treat people, by pill, injection, bottle, patch or suppository. At the beginning of his ‘plague journal’ Doherty mentions two drugs I recall from our Medcram viewings, hydroxychloraquine, an anti-malarial, and remdesivir, ‘an experimental anti-Ebola drug’.
Jacinta: Yes, hydroxychloraquine was touted early on in the year (2020) as being of some use. A USA site, Drugbank online, said this:
Chloroquine and hydroxychloroquine are both being investigated for the treatment of SARS-CoV-2
followed by this:
The FDA emergency use authorization for hydroxychloroquine and chloroquine in the treatment of COVID-19 was revoked on 15 June 2020.
Remdesivir seems to have been somewhat more effective in reducing symptoms, as was seen earlier in treating MERS-CoV sufferers. It received the FDA’s authorisation just a few weeks before the other drug’s authorisation was revoked.
Canto: The word drug features in the USA’s FDA (Food and Drug Administration), while in Australia we have the TGA (Therapeutic Goods Administration), and therapeutic is simply medicalese for drug. The first of these tended to be natural remedies such as quinine, a useful anti-malarial extracted from Cinchona tree bark. Tonic water has quinine in it, hence the name. Another natural anti-malarial is artemisinin, from sweet wormwood. These ingredients, extracted and purified, have been extremely important in combatting the biggest killer disease in the global south.
Jacinta: In treating SARS-CoV2, remdesivir was the only effective antiviral in the first 12 months, apart from – monoclonal antibodies. I’ve heard of them, now I’m going to try and explain them. I’ll start with this quote from the Mayo Clinic:
Monoclonal antibodies are laboratory-produced molecules engineered to serve as substitute antibodies that can restore, enhance, modify or mimic the immune system’s attack on cells that aren’t wanted, such as cancer cells.
Antibodies (aka immunoglobulin, of which there are 5 types) are Y-shaped proteins that can bind to specific antigens (the foreign nasties) via a lock-and-key mechanism. Monoclonal antibodies, as mentioned above, have been particularly effective in some cancer treatments.
Canto: Well, only this month our TGA has posted an update on the decreased effectiveness of monoclonal antibodies against emerging SARS-CoV2 variants:
emerging data show that anti-spike protein monoclonal antibodies demonstrate a significant decrease in their in-vitro neutralising activities against many newer circulating SARS-CoV-2 variants, particularly Omicron and its subvariants.
Jacinta: Mmm. So let’s go on with our very basic training in immunology. So it’s the organs of the lymphatic system – the lymph nodes, the thymus, the spleen and the bone marrow – that produce or harbour and further develop our immune cells. Now, these immune cells come in different types with different names, such as phagocytes, which are a type of white blood cell (WBC)…
Canto: Yes, this immune system stuff might require dozens or hundreds of posts. Phagocytes can be ‘professional’ or non-professional’ depending on effectiveness. The professionals include neutrophils, macrophages, mast cells, dendritic cells and monocytes – all WBCs. They’re all more or less good at detecting antigens. And I believe these WBCs form what’s called the innate, rather than adaptive, immune system.
Jacinta: So getting back to the SARS-CoV2 Betacoronavirus – we’ll be jumping around a lot in these posts, methinks – it has this thing called a spike protein on its outer coat, and this protein has a receptor-binding domain (RBD) with binds to the angiotensin-converting enzyme (ACE) receptor, or ACE2 receptor. ACE2 receptors exist throughout the body but the principal pathway for this virus involves the epithelial cells at the base of the lungs and in the blood vessels. So I’m reading a Nature article, referenced below, entitled ‘Mechanisms of SARS-CoV-2 entry into cells’, and I want to frame this stuff in my own words to understand it. Apparently ACE2 is the receptor for other Betacoronaviruses and Alphacoronaviruses, so immunologists and virologists are pretty familiar with it.
Canto: Yes, and there’s all this terminology – for example a virion is the whole viral particle – not just the DNA or RNA core and its proteins but the external envelope – everything that allows it to exist extra-cellularly. So a coronavirus virion is made up of nucleocapsid and other proteins, including the spike proteins that facilitate entry into potential host cells via the ACE2 receptors.
Jacinta: So let’s focus for now on the nucleocapsid (N) protein. Another Nature article, with multiple authors, has this title: ‘The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA’, which sounds ominous. And the article starts with a problem:
The SARS-CoV-2 nucleocapsid (N) protein is an abundant RNA-binding protein critical for viral genome packaging, yet the molecular details that underlie this process are poorly understood.
Yes, especially by me. I get that these N proteins bind and ‘package’ the RNA, but I don’t get ‘phase separation’…
Canto: Phase separation is a key biological concept, it seems, but complex, and probably something that requires lab work to fully comprehend. Here’s a quote from ScienceDirect that might help:
Many biological macromolecules, such as proteins and nucleic acids, exert their biological functions by forming phase-separated condensates, and phase separation is closely related to various human diseases. Gene transcriptional regulation is an indispensable part of gene expression and normal function in cells. Its abnormal regulation often causes the occurrence of different diseases. In recent years, the occurrence of phase separation during transcriptional regulation has become an area of intense research.
It sounds like problems with phase separation may lead to irregular transcription, or vice versa, resulting in variants, mutations and such, but I’m guessing.
Jacinta: So reading further into the ScienceDirect article, you’re right, it’s near impossible to understand this stuff just through reading – you surely need to see it happening in cells. And cells, such as our own, are effing complex. Here’s another (long) quote to prove it:
In cells, which are the basic unit of the structure and function of organisms, the need for various components to perform their corresponding functions at the correct time and space is a problem that cells continuously need to solve. To this end, cells have evolved a set of organelles, including membrane-encapsulated organelles (such as mitochondria, nuclei, lysosomes, the Golgi apparatus, and endoplasmic reticulum) and membrane-less organelles (such as nucleoli, Cajal bodies, stress granules, P bodies, U bodies, and signaling bodies) …. Membrane-encapsulated organelles enclose specific proteins, nucleic acids and other substances to perform their functions within a particular space. Still, how other types of membrane-less organelles form and exert their biological functions has eluded investigators for many years. In recent years, it has been discovered that different intracellular biological macromolecules assemble and separate from each other to form liquid-like structures called “biomolecular condensates”….
and it goes on. It’s dauntingly complex, but I must say I wish I was 40 years younger and working in this fascinating field. To work out more precisely the processes involved and then to be able to manipulate them…
Canto: Homo deus indeed.
Jacinta: Femo deus if you don’t mind, and that’s not even a recognised term. I just can’t wait for the 31st century.
Canto: Well let’s just stay in the shallows and say a few words about these membraned and unmembraned intracellular organelles. Mitochondria we know a bit about, the ATP-yielding (making?) organelles that existed separately eons ago as prokaryotes…
Jacinta: Thank the indefatigable iconoclast Lynn Margulis for presenting this argument, and endosymbiosis in general, against vociferous mostly male opposition…
Canto: Lysosomes are the ‘digestive system’ of the cell, containing enzymes that break down the polymeric structures of proteins, lipids, nucleic acids and carbohydrates. They vary greatly in size depending on the digestive tasks they work on. The Golgi apparatus or complex is, unsurprisingly, a complex organelle that packages proteins to be sent out into the intracellular or intercellular world – nuff said. The endoplasmic reticulum has two sub-units, rough and smooth. They’re kind of attached to the nuclear membrane of the cell, the smooth further out than the rough. It’s involved in transportation and protein folding, let’s say no more.
Jacinta: So now to the membrane-less organelles – but it looks like phase transition as a subject for analysis is about how these organelles transition from dormant to active states or how they transition from one task to another. Anyway, just a few words to introduce these organelles. Nucleoli are defined briefly as ‘small dense spherical structures in the nucleus of a cell during interphase’. They also appear to segregate in unexpected ways as cells divide – again something about phase transition. Cajal bodies are often associated with nucleoli and are involved in the processing of some RNA molecules. They appear to have other roles that aren’t yet fully understood. Stress granules are these changeable, dynamic, liquid-solid entities made from RNP (ribonucleoprotein). P bodies are somewhat similar, as are U bodies, named for being ‘uridine-rich’, whatever that may mean. In any case P and U bodies appear to act co-operatively. Signalling bodies, according to Khan Academy:
A signaling molecule is released by one cell, then travels through the bloodstream to bind to receptors on a distant target cell elsewhere in the body.
Canto: Okay, that’s enough terminology, and we won’t do all the references as nobody reads this stuff anyway.
Jacinta: Fine, we’re having fun, though it may take till doomsday to get our heads around this stuff. Wish I could afford a lab, and all its equipment….
References
Peter Doherty, An insider’s plague year, 2021
https://go.drugbank.com/drugs/DB01611
https://www.nejm.org/doi/full/10.1056/nejmoa2007764
https://www.tga.gov.au/news/news/update-effectiveness-monoclonal-antibodies-against-covid-variants
what is this thing called lymph? some more…
Canto: So we learned a lot about lymph recently, but strangely enough, it made us hungry for more. So, it has two functions, circulatory and immunological. I’d like get more detail on both those functions, and in particular I’d like to know more about lymphocytes, what they are, how they’re made and what they do.
Jacinta: Sounds like a plan. So first, lymph in the circulatory system. Here’s what I’ve gleaned from an online video. This system brings oxygen and nutrients to all our bodily tissues, as well as removing waste materials. Ultimately this feeding and removal process occurs in the smallest vessels, the capillaries, which penetrate into tissues and organs. Nutrient-rich blood plasma moves out of capillaries ‘at the arterial end of capillary beds, while tissue fluid containing wastes reabsorbs back in at the venous end’.
Canto: Okay, whoa. First, I have difficulty separating left from right, and east from west, what they call directional dyslexia. I also, in a probably related way, have problems with arteries and veins. One goes into the heart, the other goes out….
Jacinta: Haha, think arteries away (AA), and that’s all you need to know. I have the same problem, quelle surprise!
Canto: So I get that nutrient-rich ‘blood plasma’, presumably some kind of mixture of blood and plasma, moves out of arterial capillaries into tissues, to feed and energise and rejuvenate them and such, but I’ve never heard of capillary beds, and ’tissue fluid’ sounds a bit questionable…
Jacinta: These are all good issues to raise. Apparently there’s a whole capillary bed network. So, getting back to basics, our cardiovascular system is this super-complex network of veins, arteries and capillaries that move oxygen, nutrients, hormones and waste materials to and from our tissues and organs. It’s often analogised as something like a city road network, highways with off-ramps leading to main roads, side-roads and such. And capillary beds are the network of smaller vessels leading into and out of particular tissues. Anyway here’s a useful definition from a medical website:
Capillaries do not function independently. The capillary bed is an interwoven network of capillaries that supplies an organ. The more metabolically active the cells, the more capillaries required to supply nutrients and carry away waste products. A capillary bed can consist of two types of vessels: true capillaries, which branch mainly from arterioles and provide exchange between cells and the circulation, and vascular shunts, short vessels that directly connect arterioles and venules at opposite ends of the bed, allowing for bypass.
If all of the precapillary sphincters in a capillary bed are closed, blood will flow from the metarteriole directly into a thoroughfare channel and then into the venous circulation, bypassing the capillary bed entirely. This creates what is known as a vascular shunt.
And, since I know you’re wondering:
A metarteriole is a short microvessel in the microcirculation that links arterioles and capillaries. Instead of a continuous tunica media, they have individual smooth muscle cells placed a short distance apart, each forming a precapillary sphincter that encircles the entrance to that capillary bed.
And as for tunica media, I won’t quote, I’ll put it in my own words. Arteries and veins have three-layered linings called tunicae. The tunica media, as the name suggests, is the middle layer between the inner tunica intima and the outer tunica externa. The make-up and structure of this layer (and the others) varies in relation to the size of the artery. For example, there’s a lot more tissue in the layers of the aorta, the body’s largest artery.
Canto: Great, and yes, intrinsically interesting, but let’s return to lymph. So the lymphatic system is a ‘cleaning up’ and drainage system among other things. There are some 700 lymph nodes throughout the body – armpits, groin, throat, and in the intestines where they’re involved in the absorption of fat. A node in this context is a bean-like structure which filters the lymph passing through it. It contains lots of lymphocytes for combating/consuming pathogens. If the system fails to function properly, oedema or lymphoedema results (a swelling or puffiness). As well as these numerous tiny nodes, there’s the spleen, a multifunctional lymphatic organ located on the left side of our bodies next to the stomach. It produces a range of cells including many types of white blood cells such as murderous macrophages and of course lymphocytes. The spleen is divided into a ‘red pulp’ and a smaller ‘white pulp’ section, and I could go into greater detail about T cell zones and B cell zones and the various functions of these cells and their subdivisions.
Jacinta: Yes I think we have a general sense in that the lymphatic system of nodes and spleen improves circulation through removal and replacement, and immunity through renewal of ageing cells and production of lymphocytes and other antibody-type cells. All of this started with our attempt to get a handle on CFS or ME/CFS or CFIDS and its relation to the immune system. It’s been an interesting little journey into an unknown land for us, and my impression is that there’s still a lot to be learned even by researchers steeped in lymph, so to speak.
Canto: Yes, and it’s given us some little background into immunology and the amazing complexity of the animal body…
References
https://www.betterhealth.vic.gov.au/health/conditionsandtreatments/lymphatic-system
https://en.wikipedia.org/wiki/Lymphatic_system
https://en.wikipedia.org/wiki/Metarteriole
SARS-Cov2 and oxidative stress
So I feel it’s time for me to get back to the epidemiology and immunology stuff that I know so little about, especially as it pertains to SARS-Cov2. Watching Dr Seheult’s Medcram updates again after a long hiatus, and catching up with them from the end of April, I note that he’s arguing – and I presume this is a mainstream view, as he clearly keeps an eye on the latest research – that the virus mostly does its damage in attacking the body’s endothelium, and that this in turn causes oxidative stress. The endothelium is a thin layer of cells, or a layer of thin cells, that form the inner lining of the blood and lymph vessels (one day I’ll find out what lymph actually is and does).
Oxidative stress is associated with an imbalance in the level of oxidants such as super-oxide anion and hydrogen peroxide, reduced forms of oxygen (with extra electrons). I don’t really understand this, so I’ll start from scratch. But just preliminary to that, the effects of oxidative stress are manifold. Here’s a summary from news-medical.net:
Oxidative stress leads to many pathophysiological conditions in the body. Some of these include neurodegenerative diseases such as Parkinson’s disease and Alzheimer’s disease, gene mutations and cancers, chronic fatigue syndrome, fragile X syndrome, heart and blood vessel disorders, atherosclerosis, heart failure, heart attack and inflammatory diseases.
It’s known that SARS-Cov2 enters via the lungs, and does damage there, but it’s now thought that most of the damage is done in the endothelium. To understand this, Dr Seheult is going to teach me some ‘basic’ stuff about metabolism, oxidation, energy production and such. So, we start with mitochondria, the energy-producing organelles inside our cells, which have their own DNA passed down the female line. Looking into a mitochondrion, we have the matrix inside, and around it, between the inner and outer membranes, is the inter-membrane space (IMS). Our food, broken down into its essential components, carbs, fats and proteins, is absorbed into the matrix, and somehow turned into ‘two-carbon units’ called acetyl coenzyme A. This is metabolism, apparently. These molecules go through a famous process called the Krebs cycle, of which I know nothing except that it’s about more metabolism… Although now I know that it produces electrons, tied up in two important molecules, NADH and FADH2. These electrons ‘love to be given up’, a way of saying they ‘want’ to be reduced. The molecule that gives up electrons is said to be oxidised, the receiving molecule is reduced. So think of a molecule being reduced as the opposite of losing, rather counter-intuitively. The oxidised molecule is the one that loses electrons. All this is about energy production within the matrix, and the aim is to end up with a molecule I’ve heard and forgotten much about, adenosine triphosphate (ATP). This molecule is the energy molecule, apparently, and the energy is produced by ‘knocking off’ one of the phosphates, according to Dr Seheult, leaving, apparently, adenosine diphosphate (ADP) plus ‘energy’ (clearly, this part needs a little more detail). So going from the diphosphate form to the triphosphate requires energy, going the other way releases energy – none of which really explains why ATP is the body’s energy source. Anyway…
Returning to the carbs, fats and proteins, they go through these mitochondrial processes to produce electrons which want to reduce stuff. So NADH goes to the membrane which separates the IMS from the matrix of the mitochondrion, where proteins can be found that are willing to accept electrons, i.e. to be reduced. The electrons are brought in ‘at the very top of the scale’ (?) and lose some of their reducing ability, so they go down to a lower state of reduction, and protons are pumped into the IMS. (I’m sure this is all true but making sense of it is another matter. It certainly makes me think of proton pump inhibitors, drugs that reduce gastric reflux, but that would be the subject of another set of posts). Then ‘it goes to another species’ by which I think Seheult means another protein, judging from the video, but what he means by ‘it’ I’ve no idea. The NADH? The wave/body of electrons? Anyway, things keep going down to a lower level, becoming more oxidised, and more and more protons are pumped out. So there comes to be a very high concentration of protons (H+) in the IMS, creating a very low PH (high acidity). Meanwhile, the electron transport chain has gone down so many levels that it can only reduce oxygen itself, which by accepting electrons turns finally into water. It’s apparently essential to have sufficient oxygen to keep this cycle going, and to keep the protons pumping, because the protons in the IMS want to move to a place of lower concentration, in the matrix. In doing this, they pass through a channel, which involves, somehow, a coupling of ADP to ATP. Without enough oxygen, this process is stymied, ATP can’t be supplied, leading to insufficient energy and cell death.
So, I think I understand this, as far as it goes. Now, if you over-eat, with lots of high-calorie fats and carbs entering the cells, you’ll likely end up with a surplus of electrons, tied up in NADH and FADH2, which can cause problems. This is where super-oxides come in.
Oxygen is the final electron acceptor in the electron transport chain, and when you add an electron to this final acceptor you get a super-oxide, an oxygen molecule with an additional electron, aka a radical. These are very reactive and dangerous. They can cause DNA damage and serious inflammation, and the body uses them to kill bacteria. If you add another electron, you get H2O2, hydrogen peroxide, and another one again produces a hydroxy radical, OH. Another electron gives water, so it’s these intermediate molecules that are called ‘dangerous species’. Cells such as neutrophils (a type of white blood cell) make these, via an enzyme called NADPH oxidase, as part of their defence against antigens, but an accumulation of these radicals is problematic and needs to be dealt with.
One enzyme the body uses to bring down these accumulating radicals is super-oxide dismutase (SOD), which takes two super-oxides and converts them into O2 and H2O2. SOD comes in three types, related to where they reside – in the mitochondria, the cytosol and the extracellular matrix. These enzymes are powered by zinc, copper and, in the mitochondria, manganese. So what happens to the extra hydrogen peroxide created? An enzyme called glutathione peroxidase (GPx) reduces H2O2 to water by giving it two electrons. Where do these electrons come from? According to Seheult, and this is presumably ‘basic’ microbiology, the antioxidant glutathione has two forms, oxidised and reduced. The reduced form is 2GS-H, with a hydrogen bonded to the sulphur group. The oxidised form is G-S-S-G, a disulphide bond replacing the hydrogen. With the reduced form, GPx donates its extra two electrons to H2O2, reducing it to water. The glutathione system is recharged by reducing it back with NADPH, which has two electrons which are converted to NADP+ (?) Glutathione reductase is the key enzyme in that process. It might take me a few lifetimes to get my head around just this much.
Meanwhile there’s another system… Catalase, an iron-boosted enzyme, can convert two molecules of H2O2 into O2 and H2O. This occurs in organelles called peroxisomes. The major point to remember in all this is that super-oxides are harmful species that can cause oxidative stress, and the major solutions come in the form of SOD and GPx. In fact the general name for these harmful molecules – super-oxides, hydrogen peroxide, and hydroxy radicals – is reactive oxygen species (ROS).
So we have to relate all this to the effects of SARS-Cov2, which enters the body through the ACE-2 (angiotensin-converting enzyme-2) receptor. According to a 2008 research paper, ACE-2, the receptor for which is blocked by SARS-Cov2, ‘confers endothelial protection and attenuates atherosclerosis’. Quoting from the paper, we find a section called ‘ACE-2 modulates ANG II(angiotensin 2)-induced ROS production in endothelial cells’. The researchers’ essential finding was that ‘ACE-2 functions to improve endothelial homeostasis’, and it seems this function is being disrupted by SARS-Cov2. As Dr Seheult puts it, SARS-Cov2 inhibits the inhibitor, that is it inhibits ACE-2, which normally acts to regulate angiotensin 1,7 (not explained in this particular video), thus allowing NADPH oxidase to keep producing super-oxides, with the resultant oxidative stress. As Seheult concludes here, subjects with compromised systems caused by diabetes, cardiovascular disease or obesity, affecting the production or effectiveness of SOD and GPx, might be relying on ACE-2 and angiotensin 1,7 to maintain some semblance of health. Are these the subjects that are succumbing most to the virus? That’s to be explored in future videos, and future posts here.
Reference
Coronavirus Pandemic Update 63: Is COVID-19 a Disease of the Endothelium (Blood Vessels and Clots)? (video by Dr Roger Seheult – clearly a hero in this time)
Covid19: world progress, cytokine storms, our plans
Canto: So while we need to be worried about – and to know something about – the cytokine storm that the Covid19 infection can lead to (and we’ll learn about that soon), there’s also a storm of activity on the SARS-CoV-2-fighting front.
Jacinta: Yes, intravenous zinc was talked about in the Medcram series as an effective tool in fighting viral pneumonia, and a world-first trial is being conducted by Austin Health and Melbourne University to test its effectiveness for Covid-19 sufferers with respiratory problems. We’re still catching up on the Medcram series, and update 52 talks of the drug ivermectin, already on the WHO list of essential medicines. The WHO website, incidentally, is promoting a ‘solidarity’ clinical trial for Covid-19 treatments, involving, singly or in combination, remdesivir, hydroxychloraquine, lopinavir, ritonavir and interferon beta-1a. So that gives some idea of the work that’s going on to fight symptoms and reduce the death rate.
Canto: And, you know, I’ve been feeling guilty about singling out the USA as the worst-case scenario all round. It’s not actually so. It’s not fair to look at total figures and point out that the USA tops the list for Covid19 fatalities, and draw calamitous conclusions. You have to take into account its much larger population compared, for example, to number two on the list, Spain. The US has suffered about 2.5 times the fatalities of Spain, but it has about 7 times the population. In fact, if you look at fatalities as a proportion of population, there are many countries worse off than the USA – namely Spain, Italy, France, the UK, Belgium (the worst hit), the Netherlands, Switzerland, Ireland and Sweden. All European countries, notably.
Jacinta: Yes and I’m sure they’ll all have their particular stories to tell about why this is happening to them, and will be wanting to learn lessons from Taiwan, Hong Kong, South Korea, and even our big faraway island, but I really want to look at solutions, in terms of eradicating the virus, or blocking it, or building up our immunity. Having said that, flattening the curve, and reducing fatalities, is a primary focus, which means continuing the physical distancing and looking for ways to keep economies running while this goes on. In spite of patches of civil libertarian activity here and there, the vast majority of our global population is on the same page with this, I think.
Canto: Well I’m looking at an Axios article from the Johns Hopkins website. It compares global performance under Covid19 to a mock pandemic exercise, Event 201, conducted some six months ago. They’ve found some positives and some negatives in their analysis. Positives – a greater degree of compliance with physical distancing measures than expected, ‘the degree of surge capacity augmentation in the health care system which has been possible’, and the rapid growth of international collaboration among scientists, leading to a quickened progress of trials for possible treatments. Negative – disparate and often contradictory messages from authorities – mostly political authorities – leading to confusion and distrust of governments and other institutions. This is partially explained by the complexity of the virus itself, which has made it difficult to characterise to the general public, and to be fully understood by non-medical authorities, such as political leaders.
Jacinta: It’s a weird situation, as there’s no end in sight, everyone’s worried about ending restrictions too soon, yet everyone’s worried about the economy, and those countries, like Australia, that are heading towards winter, are bracing for heightened problems, while northern hemisphere countries are hoping for summer’s relief but worried about the autumn when it might be hard to cope with a second outbreak, should it come. And medicos are warning that expectations of a vaccine in eighteen months might be overly optimistic. But I want to be optimistic – I want to look at anything that’ll reduce symptoms and save lives. One treatment, among many others it should be noted, is hydroxychloraquine, which is being given so much of a bad press, because of its being over-hyped by a Trump administration intent on getting political points for a silver-bullet cure. There have already been a number of small, less-than-gold-standard studies, some in which the drug is combined with the antibiotic azithromycin, and the results appear to be all over the place. We’re still awaiting the results of randomised, placebo-controlled, double-blinded studies, which are under way.
Canto: I note that a couple of reports on chloraquine and hydroxychloraquine on the JAMA website have been taken down, I suspect because of all the politicising. That’s a shame. Anyway I mentioned the cytokine storm at the beginning of this post, so I’ll try to comprehend it. A clue to the meaning comes in this mid-March article on the Lancet website. In an early sentence it mentions ‘cytokine storm syndrome’, and in the following sentence refers to the treatment of ‘hyperinflammation’. It seems the two terms are interchangeable. Another term, in the very next sentence, is ‘a fulminant and fatal hypercytokinaemia’….
Jacinta: Sounds like they’re just showing off.
Canto: Please don’t say that about our frontline covidtroops. Okay, a better site for understanding cytokines and their storms is this from New Scientist. As we’ve guessed, it’s an over-reaction of the immune system, sometimes fatal. Cytokines are small proteins, produced throughout the body, which trigger inflammation as an immune response. Sometimes the intensity of the cytokine response results in hyperinflammation. So you might say the cytokine storm is the cause and hyperinflammation the effect.
Jacinta: So this raises questions. For example, why do some have what seems an over-production of these cytokines and others don’t, in response to SARS-CoV-2 in particular? And what do these cytokines actually do to cause inflammation?
Canto: You’re asking me? Well, it’s conjectured that younger people don’t have the developed immune system that produces all these cytokines, and that’s why you don’t see symptoms. But that raises the question – do others have over-developed immune systems, but maybe only for this particular virus? Is there a general goldilocks level?
Jacinta: And is there a way of distinguishing between those who succumb to the hyperinflammation, which in turn can cause acute respiratory distress syndrome (ARDS), and those who succumb to the virus itself? Or is it always the immune response that does people in?
Canto: I don’t think so. If the immune response doesn’t work at all, I suspect the virus will spread like a cancer to the rest of the body?
Jacinta: That can’t be right. That’d mean those kids who don’t suffer the cytokine storm, or any immune reaction, would remain infected until it spread through their bodies and they dropped dead. That definitely isn’t happening.
Canto: No, you’re right – they’re developing antibodies, presumably, (and that’s a whole other story), without going through much in the way of suffering. In fact, children’s apparent immunity to the virus is something of a mystery that demands further research. If everyone could develop that kind of immunity…
Jacinta: So many questions we can’t answer. I mean, not just the myriad questions we, as dilettantes and autodidacts, can’t answer, but the fewer but many questions epidemiologists, virologists and ICU workers can’t answer. But I propose that we continue to try and educate ourselves and explore, in our feeble but earnest way. I propose that we dedicate this blog, for the foreseeable, to exploring terms and conditions, so to speak, and treatments, such as ‘cytokine’, ‘ACE-2’, ‘hypoxia’ and ‘quercetin’ and how they relate to or are affected by the Covid-19 infection. Like putting pieces together in a jigsaw puzzle, sort of. It might help us being overwhelmed by the whole picture.
Canto: Okay, let’s try it.
References
Coronavirus pandemic update 52, Medcram youtube video
https://coronavirus.jhu.edu/news
https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(20)30628-0/fulltext
https://www.newscientist.com/term/cytokine-storm/
https://www.centerforhealthsecurity.org/event201/
https://jamanetwork.com/journals/jama/pages/coronavirus-alert