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reading matters 12: food mysteries

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New Scientist 3292 July 25 2020

Jacinta: So this cover story reminds me of something I read or heard a few years back  – that if you were to list the chemical ingredients of a hen’s egg, you’d never come to the end, or something like that. 

Canto: Well you’re on the right track, the cover story is titled ‘the dark matter in your diet’, but instead of a hen’s egg it starts with garlic. Both of these commonly consumed edibles, like just about everything else we eat, contain ‘nutritional dark matter’ that scientists have only recently started to focus on, surprisingly considering that we are, to a fair degree, what we eat. 

Jacinta: Yes, so we all know that food components or nutrients are usually divided into fats, carbohydrates and proteins, though these three can be subdivided to a near-infinite degree, but there are also vitamins, minerals and other biochemical elements in various quantities, and with variously vital effects. Currently the US Dept of Agriculture (USDA) has a database of 188 nutritional components of food, under which some info is provided on many thousands of chemical elements. 

Canto: So garlic, the USDA reckons, is found in 58,055 foodstuffs, including, uhh, garlic. Raw garlic itself is described as containing 67 nutrients, both macro and micro, some of which can only be found in very minute quantities. And yet many components, such as allin, which helps to give garlic its particular odour and flavour, aren’t listed on the database. 

Jacinta: Allin is converted into allicin, through the enzyme allinase, when you crush or chop garlic. That’s when that lovely/notorious stink hits you. 

Canto: Right, and this is apparently a major problem across the whole database. They added a few dozen flavonoids – plant compounds that can lower the prevalence of cardiovascular disease – in 2003, but recent researchers have been frustrated by the many gaps, and are building their own more comprehensive database, based on their own chemical analyses. It’s called FooDB, which now lists almost 400 times the number of nutritional compounds as the USDA database. 2306 for garlic, for example, compared to the USDA’s 67. But there’s a lot of work still to be done, even on garlic. Only a tiny fraction of those compounds have been quantified – we don’t know the exact concentrations. And this is a problem for the whole of FooDB, with about 85% of compounds unquantified.

Jacinta: Sounds like we need an equivalent of the old human genome project – but for every single edible product? Nice, a few hundred lifetimes’ work, if you can get the funding. 

Canto: Well, it suggests that we’ve massively overlooked the complexity of our food – and not only the foods themselves, but their interaction with the microbes and enzymes in our body. But here’s the thing – brace yourself – some nutritionists disagree!

Jacinta: OMG! Scientists are disagreeing?

Canto: The counter-argument is that ‘dark matter’ in nutritional terms is a beat-up. That, though much research is still needed in nutritional epidemiology, in relation to particular conditions and so forth, we know what the essential nutrients are, so the ‘dark matter’, which tends to exist in ultra-minute quantities, would make little difference. But the researcher who coined the term ‘nutritional dark matter’, Albert-Laszlo Barabasi, begs to differ – of course. He points out, for example, that vitamin E, or its absence, can have adverse effects at minuscule quantities, and it may be that all the flip-flopping advice we’re given about nutrition may have much to do with the gaps in our knowledge. Taking garlic again, it was found that of the 67 compounds listed for it on the USDA database, 37 had health effects one way or another, but of the 2306 on FooDB, some 574 had what they called ‘potential’ health effects. In any case, it seems to me that a more complete knowledge of what’s in our food can’t be a bad thing, and will very likely be of benefit in the long run. 

Jacinta: That makes sense, but isn’t everything even more complicated, when you think of how all these nutrients interact with our individual microbiota, and the enzymes that break down our food more or less efficiently, depending on how numerous and healthy they are, which no doubt varies between individuals? 

Canto: Yes, Barabasi and others working on all this ‘dark matter’ are well aware of these complex interactions, but they reckon that doesn’t detract from the need to know much more about this particular component of the food-nutrient-digestion-health cycle. And Barabasi does in fact compare the current state of knowledge with the days before the human genome project, when much DNA was considered ‘junk’. It’s just not a good idea to assume that such a large proportion of nutrients are barely worth knowing about. Let’s return to garlic again. It features quite a lot in the Mediterranean diet, which seems protective against cardiovascular disease. Steak, on the other hand, can be problematic. Our gut bacteria breaks down red meat, in the process producing a compound, trimethylamine, which our liver converts into trimethylamine-N-oxide (TMAO). High levels of TMAO in the bloodstream are linked to heart and vascular problems. But allicin, from garlic, which we’ve mentioned before, and which wasn’t on the USDA database, is known to inhibit the production of trimethylamine, so a diet containing red meat – not too much mind you – can be rendered a wee bit safer, and tastier, with a nice garlic dressing. 

Jacinta: And allicin appears to be an anti-carcinogen too. And luteolin, another component of garlic not on the standard database, is also reported to protect against cardiovascular disease. We love garlic! But what about processed foods. Surely there are all sorts of ways of processing, that’s to say transforming, foods and their component nutrients that won’t show up on the list of ingredients. And how do we know if those ingredient lists are accurate in the first place?

Canto: Well, baby steps I suppose. Cooking, of course, has vital transformative effects upon many foods. And I recall that when you whisk an egg it becomes ‘denatured’ – how transformative does that sound! The more you think about the interaction of foods, with all their barely recognised components, with transformative processes occurring both outside and within our bodies, the more it makes your head spin, and the more you realise that dietary science has a long long way to go. 

garlic cultivars from the Phillippines

Written by stewart henderson

September 30, 2020 at 7:33 pm

covid19: corticosteroids, male susceptibility, evaluating health, remdesivir, coagulation factors

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from The Lancet, ‘the four horsemen of a viral apocalpse’


Canto: So short-course use of some steroids was being advocated in the medcram update 88, though without thorough RCT evidence. 

Jacinta: Well, data was presented from the Oxford RCT on those on oxygen or on ventilators showing a statistically significant reduction of mortality from short-course (up to 10 days) low dosage of dexamethasone, a freely-available steroid medication. The study involved some 2000 patients, but only those severely afflicted were helped by the medication. 

Canto: An interesting aside to the data is that in the study males outnumbered females by almost 2 to 1, and that accords with the overall ratio of male to female covid19 patients Dr Seheult is finding, which rather shocked me. Why would more males be coming down with the disease? Presumably that’s not the infection rate, but the rate at which they need to be hospitalised. 

Jacinta: Yes, you’re right, according to this Australian site (unfortunately undated):

Reports continue to emerge that men are significantly more vulnerable to COVID-19 than women. The commonly held perception that more men smoke and this makes them more susceptible along with other lifestyle factors does not tell the whole picture. White House COVID-19 Task Force director Dr Deborah Birx highlighted a “concerning trend” that men in all age brackets were becoming seriously ill from the virus at a higher rate than women, including younger males.

They’re suggesting more research needs to be done on this gender difference, for health issues in general. Some are claiming that estrogen makes a difference. In any case I think cardiovascular problems are more common in males – but maybe not so much in younger males. 

Canto: So update 89 is fairly short, and deals with US data about cases and deaths, most of it out of date now, and more on corticosteroids and the dangers of unsupervised use. Update 90 introduces us to a tool I’ve never heard of called ‘Discern’. Very useful for we autodidacts in helping us, for example, to enlighten our doctors as to our condition. Discern is a tool for evaluating internet health info, such as medcram’s updates on youtube, or anything else on youtube. The instrument asks you to evaluate the material according to 16 different criteria. Interestingly, this tool has been tested on covid19 material by a study out of Poland done in March. The results weren’t so good, especially for news channels. 

Jacinta: Yes, physicians’ information did best – but of course we don’t go to news channels for health information, and we’d advise against anyone else doing so. The study evaluated the Discern tool itself and found it excellent, then used the tool to evaluate health information, specifically on youtube. Of course know that there’s ‘viral misinformation’ from various news outlets that gets posted on youtube. And good to see that the medcram updates were some of the most highly rated using the Discern tool. 

Canto: So we’re now into reporting from early July with update 91. It starts by looking at a ‘covid risk calculator’ in which you can type in your age, gender, BMI, underlying conditions, waist circumference, and other data which you might need a full medical checkup to find out about (and that’s overdue for me), including, for example, %FMD, a measure I’ve never heard of, but which has to do with endothelial function. 

Jacinta: FMD stands for fibromuscular dysplasia. The Johns Hopkins medicine site describes it as a rare blood vessel disease in which the cells of some arteries become more stiff and fibrous and less flexible. This leads to weakness and damage. Not sure how it relates to covid19 but surely any pre-existing blood vessel damage is a danger for those contracting the virus. 

Canto: Right, so it’s unlikely anyone will know offhand their percentage of FMD. I don’t even know my HDL and LDL levels, never mind my HbA1c or lipids. I’d love to be able to take measures of all these myself, without visiting a doctor.

Jacinta: Typical male control freak. So all of this is to measure your risk of covid19 hospitalisation, ICU admission or mortality. Fun times. So next the update looks at Gilead, the makers of the antiviral remdesivir, who donated all their supplies of the drug to the USA in early May. But of course they kept manufacturing the drug and have to recoup the money they spent researching, developing and trialling it etc. The Wall Street Journal reports that a typical course of the drug will cost over $3000 per patient. Interestingly the Trump administration is wanting the drug to stay in the USA as much as possible, rather than be available overseas, and is spending money to that effect. 

Canto: Hmm. Is that protectionism? 

Jacinta: Yes I suppose. It’s not surprising that a country wants to look after its own first, especially via a product produced within its own borders. But I suspect this government would’t be interested in helping any other country – unless there was a quid pro quo. And there’s another antiviral, favipiravir, currently being trialled in Japan and the USA (I mean as of early July), and a vaccine, developed in China, is being used on the Chinese military in what seems a rather rushed and somewhat secretive fashion – we don’t know if they got the soldiers’ permission on this seemingly untried vaccine. At least at the phase 3 level.

Canto: Very CCP. 

Jacinta: So onto update 92, and we revisit the electron transport chain, with four successive electron transfers converting molecular oxygen into water. Problems within this chain can produce reactive oxygen species (ROS) such as superoxide, hydrogen peroxide and hydroxy radicals, which are destructive in excess. We also look, yet again, at covid19’s impact on angiotensin and particularly the production of superoxide, which in turn causes endothelial dysfunction, increased von Willebrand factor activity, which leads to thrombosis. People were presenting as ‘happy hypoxics’, looking and feeling fine but with very low oxygen levels, and autopsies revealed ‘microthrombi in the interalveolar septa’ of victims’ lungs. All this leading to a paper published in The Lancet which looked at factors in this process of coagulation and thrombosis:

We assessed markers of endothelial cell and platelet activation, including VWF antigen, soluble thrombomodulin [a marker of endothelial cell activation], soluble P-selectin [a marker of endothelial cell and platelet activation], and soluble CD40 ligand [a marker of platelet and T-cell activation], as well as coagulation factors, endogenous anticoagulants, and fibrinolytic enzymes.

So this was about getting to the bottom of the increased clotting. And the results were hardly surprising, but the final discussion section is worth quoting at length, as it seems to capture much that we know about covid19’s effects (at least short-term effects) at the moment: 

We therefore propose that COVID-19-associated coagulopathy is an endotheliopathy that results in augmented VWF release, platelet activation, and hypercoagulability, leading to the clinical prothrombotic manifestations of COVID-19-associated coagulopathy, which can include venous, arterial, and microvascular thrombosis. The factors responsible for this endotheliopathy and platelet activation are uncertain but could include direct viral infection of endothelial cells, collateral damage to the tissue as a result of immune infiltration and activation, complement activation, or any number of inflammatory cytokines believed to play a role in COVID-19 disease.

They suggest anti-platelet therapy and endothelial cell modification treatments as well as anticoagulation treatments, and they suggest some agents ‘which might have therapeutic potential’.

Canto: Potential? You’d think they’d be onto all this by now. 

Jacinta: Well there’s also potential for untried medications – at least untried in this context – to go terribly wrong. And it’s also likely that some hospitals are already onto using the safer forms of treatment. Dr Seheult speaks of the antioxidant N-acetylcysteine (NAC) in this context, as it has been shown to be a thrombolytic when used intravenously. There are studies pending on the effects of NAC in treating covid19 patients. 

Canto: Now, I’ve just been watching something on monoclonal antibodies as perhaps the most promising treatment yet, short of a vaccine. Can you explain….

Jacinta: Yes I’ll try, maybe next time.


Coronavirus Pandemic Update 88: Dexamethasone History & Mortality Benefit Data Released From UK

Coronavirus Pandemic Update 89: COVID 19 Infections Rising in Many States; Dexamethasone Cautions

Coronavirus Pandemic Update 90: Assess The Quality of COVID-19 Info With A Validated Research Tool

Coronavirus Pandemic Update 91: Remdesivir Pricing & Disparities in Drug Availability

Coronavirus Pandemic Update 92: Blood Clots & COVID-19 – New Research & Potential Role of NAC


reading matters 7

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She has her mother’s laugh, by Carl Zimmer , science author and journalist, blogger, New York Times columnist, etc etc

content hints – inheritance and heredity, genetics and epigenetics, Darwin and Galton, the Hapsburg jaw, eugenics, Hugo de Vries, Theodor Boveri, Luther Burbank, Pearl and Carol Buck, Henry Goddard, The Kallikak Family, Hitler’s racial hygiene laws, morons, the five races etc, Frederick Douglass, Thomas Hunt Morgan, Emma Wolverton, PKU, chromosomal shuffling, meiosis, cultural inheritance, mitochondrial DNA, Mendel’s Law, August Weismann, germ and soma, twin studies, genetic predispositions, mongrels, Neanderthals, chimeras, exosomes, the Yandruwandha people, IVF, genomic engineering, Jennifer Doudna, CRISPR, ooplasm transfers, rogue experiments, gene drives, pluripotency, ethical battlegrounds.

Written by stewart henderson

July 28, 2020 at 12:22 pm

epigenetics and imprinting 7: more problems, and ICRs

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This image has an empty alt attribute; its file name is screen-shot-2020-02-02-at-10.11.35-pm-1.pngthe only image I can find that I really understand


In the previous post in this series I wrote about the connection between two serious disorders, Angelman syndrome and Prader-Willi syndrome, their connection to a missing small section of chromosome 15, and how they’re related to parental inheritance. These syndromes can sometimes also be traced back to uniparental disomy, in which the section of chromosome 15 is intact, but both copies are inherited from the mother (resulting in PWS) or the father (resulting in AS).

So the key here is that this small section of chromosome 15 needs to be inherited in the correct way because of the imprinting that comes with it. To take it to the genetic level, UBE3A is a gene which is only expressed from the maternal copy of chromosome 15. If that gene is missing in the maternal copy, or if, due to uniparental disomy, both copies of the chromosome are inherited from the father, UBE3A protein won’t be produced and symptoms of Angelman syndrome will appear. Similarly, PWS will develop if a certain imprinted gene or genes aren’t inherited from the father. Other imprinting disorders have been found, for example, one that leads to Beckwith-Wiedemann syndrome, though the mechanism of action is different, in that both copies of a gene on chromosome 11 are switched on when only the paternal copy should be expressed. This results in abnormal growth (too much growth) in the foetus. It too has an ‘opposite’ syndrome, Silver-Russell syndrome, in which the relevant protein expression is reduced, resulting in retarded growth and dwarfism. 

But now to the question of exactly how genes are switched on and off, or expressed and repressed. DNA methylation, briefly explained in my first post on this topic, is essential to this. Methyl groups are carbon-hydrogen compounds which can be bound to a gene to switch it off, but here’s where I start to get confused. I’ll quote Carey and try to make sense of it:

… it may be surprising to learn that it is often not the gene body that is methylated. The part of the gene that codes for protein is epigenetically broadly the same when we compare the maternal and paternal copies of the chromosome. It’s the region of the chromosome that controls the expression of the gene that is differently methylated between the two genomes.

N Carey, The epigenetics revolution, 2011 p140

The idea, I now realise, is that there’s a section of the chromosome that controls the part of the gene that codes for the protein and it’s this region that’s differently methylated. Such regions are called imprinting control regions (ICRs). Sometimes this is straightforward, but it can get extremely complicated, with whole clusters of imprinted genes on a stretch of chromosome, being expressed from the maternally or paternally derived chromosomes, and not simply through methylation. An ICR may operate over a large region, creating ‘roadblocks’, keeping different sets of genes apart, and affecting thousands of base-pairs, not always in the same way. Repressed genes may come together in a ‘chromatin knot’, while other, activated genes from the same region form separate bundles.

Imprinting is a feature of brain cells – something which, as of the writing of Carey’s book (2011), is a bit of a mystery. Not so surprising is the number of expressed imprinted genes in the placenta, a place where competing paternal-maternal demands are played out. As to what is going on in the brain, Carey writes this:

Professor Gudrun Moore of University College London has made an intriguing suggestion. She has proposed that the high levels of imprinting in the brain represents a post-natal continuation of the war of the sexes. She has speculated that some brain imprints are an attempt by the paternal genome to promote behaviour in young offspring that will stimulate the mother to continue to drain her own resources, for example by prolonged breastfeeding.

N Carey, The epigenetics revolution, 2011. pp141-2

This sounds pretty amazing, but it’s a new epigenetic world we’re exploring. I’ll explore more of it next time.


The epigenetics revolution, by Nessa Carey, 2011

Epigenetics, video: SciShow

Written by stewart henderson

February 2, 2020 at 10:33 pm

a DNA dialogue 4: purines, mostly

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Canto: So what’s a pyrimidine, molecularly speaking, and why does it differ from a purine, and why does it matter?

Jacinta: They’re two different types of nitrogenous bases, dummy, which are a subset, maybe, of nucleotide bases. All of which is largely gobbledygook at present.

Canto: Ok, we know there are four different nitrogenous bases in DNA.  Two of them, A & G, adenine and guanine, are purines, which structurally are two-carbon nitrogen ring bases. The other two, thymine and cytosine, T & C, are pyrimidines, which are one-carbon nitrogen ring bases. Uracil, in RNA, is also a pyrimidine. It replaces the thymine used in DNA.

Jacinta: That’s right, now we know that in DNA these nitrogenous bases are connected across the double helix, in pairs, in a particular way. A (a purine) always connects with T (a pyrimidine), and similarly C is always bonded to G. So why is this?

Canto: Why is it so? Well, put simply, the molecular structure of purines, which you’ll note have a two-carbon ring structure and so are larger than pyrimidines, doesn’t allow them to bond within the group, that’s to say with other purines, and the same goes with pyrimidines. It’s essentially due to the difference between hydrogen bond donors and acceptors for these groups.

Jacinta: So, looking at purines first, considering that they’re one of the building blocks of life, it’s not surprising that we find them in lots of the food we eat, especially in meat, mostly in organs like kidneys or liver. Structurally they’re heterocyclic aromatic organic compounds – as are pyrimidines. Heterocyclic simply means they have a ring structure composed of more than one element – in this case carbon and nitrogen. An aromatic compound isn’t quite what you think – structurally it means that it’s strong and stable, due to resonance bonds, which we won’t go into here. Below is a model of a purine molecule, which has the chemical formula C5H4N4 – the black globes are carbon atoms, the nitrogens are blue and the hydrogens white.

Purines and pyrimidines are both self-inhibiting and activating, so they actively bond with each other but inhibit self-bonding, so that they maintain a more or less equal amount as each other within the cell.

Canto: So that’s purines in general, but in DNA there are two purines, adenine and guanine, which must differ structurally – and are there any others?

Jacinta: Oh yes, caffeine is a purine, as well as uric acid…

Canto: Definitely aromatic.

Jacinta: And there are many others. Purines are very important molecules, used throughout the body for a variety of purposes, as components of ATP, cyclic AMP, NADH and coenzyme A, for example.

Canto: I’ve heard of some of those…

Jacinta: As to the difference between adenine and guanine, here’s how it’s described in this Research Gate article, which I’m sure is reliable:

The main difference between adenine and guanine is that adenine contains an amine group on C-6, and an additional double bond between N-1 and C-6 in its pyrimidine ring, whereas guanine contains an amine group on C-2 and a carbonyl group on C-6 in its pyrimidine ring

Canto: Shit, that explanation needs to be explained, please.

Jacinta: Haha well let’s look at more diagrammatic structures, but first – an amine group, also called an amino group, is a derivative of  NH3 (ammonia), consisting of a nitrogen atom bonded to hydrogen atoms, at its simplest. This gives adenine the formula ‎C5H5N5. Guanine has, in addition to the amine group, a carbonyl group, which is a carbon double bonded to an oxygen, C=O. This gives guanine the formula C5H5N5O. Anyway, it’ll all become clear over the next dozen or so years…



Written by stewart henderson

January 26, 2020 at 5:26 pm

A DNA dialogue 2: the double helix

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Canto: Ok we talked about base pairs at the end of dialogue 1. A (nucleo)base pair is, duh, a pairing of nucleobases. There are four types of base in DNA – adenine and thymine, which always pair together, and the other pairing, cytosine and guanine.

Jacinta: Please explain – what’s a nucleobase, what do they do, and why do they come in pairs?

Canto: Well, let’s see, how do we begin… DNA stands for deoxyribonucleic acid…

Jacinta: So it’s an acid. But bases are like the opposite of acids aren’t they? So how can an acid be constructed of its opposite?

Canto: Look, I can’t answer that right now – I haven’t a clue – but let’s keep investigating the structure and function, and the answers might come. So, you’ll know that there was a battle in the 1950s to elucidate the structure of DNA, and it was found to form a double helix two strands of – I don’t know what – connected to each other in a twisted sort of way by, I think, those base pairs connected by hydrogen bonds. Anyway, here’s a fairly typical explanation, from Nature Education, which we’ll try to make sense of:

The double helix describes the appearance of double-stranded DNA, which is composed of two linear strands that run opposite to each other, or anti-parallel, and twist together. Each DNA strand within the double helix is a long, linear molecule made of smaller units called nucleotides that form a chain. The chemical backbones of the double helix are made up of sugar and phosphate molecules that are connected by chemical bonds, known as sugar-phosphate backbones. The two helical strands are connected through interactions between pairs of nucleotides, also called base pairs. Two types of base pairing occur: nucleotide A pairs with T, and nucleotide C pairs with G.

Jacinta: So I think I have a problem with this description. I think I need a picture, fully labelled. So the two strands themselves are made up of nucleotides, and the connections between them are made up of bonded sugar and phosphate molecules? But the strands are connected, via sugar and phosphate, in particular ways – ‘through interactions’ – which only allow A to pair with T, and C to pair with G?.

Canto: I think that’s right. Maybe we can find a picture.

Jacinta: Ok, so we got it completely wrong. The backbone, of sugar-phosphate, is the outer, twisted strand, or two of them, like the vertical bars of a twisted ladder, or the toprails of a spiral staircase, and the base pairs are like the stairs themselves, made of two separate parts, the bases, bonded together by hydrogen…

Canto: Forget the description, the picture above is worth all our words. It also tells us that the DNA molecule is around 2 nanometres wide. That’s two billionths of a metre. And 3.4 nanometres long for a full twist of the double helix, I think.

Jacinta: Whateva. There’s also this claim that the two strands are ‘anti-parallel’. It looks to me as if they’re simply parallel, but twisted. What does this mean? Is it significant?

Canto: I don’t know – maybe we’ll find out next time. I’m already exhausted.

Jacinta: …….

Written by stewart henderson

January 16, 2020 at 5:13 pm

Posted in biochemistry, DNA, science

Tagged with , ,

epigenetics and imprinting 4: the male-female thing

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Gametes are gametes because of epigenetic modifications in their pro-nuclei, but they have to lose these modifications, or transform them, when they come together to form zygotes. The male pro-nucleus DNA methylation is stripped away immediately after sperm penetrates egg. The egg pronucleus undergoes the same process, but more gradually. It’s like a wiping away of epigenetic memory, creating totipotency, which becomes a more limited pluripotency as the blastocyst, with its inner cell mass (ICM), forms. 

The ICM cells begin differentiating through the regulation of some key genes. For example, a gene codes for a protein that switches on a set of genes, which code for proteins in a cascading effect. But it’s not quite a matter of switching genes on or off, it’s rather more complex. The process is called gene reprogramming, and it’s of course done effortlessly during every reproductive cycle. Artificial reprogramming of the kind carried out by Yamanaka and others, an essential part of cloning, hasn’t come close to this natural process that goes on in mammals and other species every day.

Clearly, though the epigenetic reprogramming for the female pronucleus is different from that carried out more swiftly in the male. As Carey puts it, ‘the pattern of epigenetic modifications in sperm is one that allows the male pronucleus to be reprogrammed relatively easily.’ Human researchers haven’t been particularly successful in reprogramming an adult nucleus by various methods, such as transferring it to a fertilised egg or treating it with the four genes isolated by Yamanaka. The natural process of gene reprogramming eliminates most of the epigenetic effects accumulated in the parent genes, but as the reprogramming is a different process in the male and female pro-nucleus, this shows that they aren’t functionally equivalent. There is a ‘parent-of-origin effect’. Experiments done on mice to explore this effect found that DNA methylation, an important form of chromatin modification (and the first one discovered), was passed on to offspring by the female parent. That’s to say, DNA from the female was more heavily methylated than that from the male. Carey describes the DNA as ‘bar-coded’ as coming from the male or the female. The common term for this is imprinting, and it’s entirely epigenetic.

Imprinting has been cast by Carey, and no doubt others, as an aspect of the ‘battle of the sexes’. This battle may well be imprinted in the pronuclei of the fertilised egg. Here’s how Carey puts the two opposing positions:

Male: This pregnant female is carrying my genes in the form of this foetus. I may never mate with her again. I want my foetus to get as big as possible so that it has the greatest chance of passing on my genes.

Female: I want this foetus to pass on my genes. But I don’t want it to be at the cost of draining me so much that I never reproduce again. I want more than this one chance to pass on my genes.

So there’s a kind of balance that has developed in we eutherian mammals, in a battle to ensure that neither sex gains the upper hand. Further experiments on mice in recent times have explored how this battle is played out epigenetically. I’ll look at them in the next post in this series.


The Epigenetics Revolution, by Nessa Carey, 2011

Written by stewart henderson

January 9, 2020 at 10:50 am

epigenetics and imprinting 3: at the beginning

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stuff that can be done with iPS cells

A zygote is the union of two gametes (haploid cells), the sperm and the egg. It’s the first diploid cell, from which all the other diploid cells – scores of trillions of them – are formed via mitosis.

What’s interesting about this from an epigenetic perspective is that gametes are specialised cells, but zygotes are essentially totipotent – the least specialised cells imaginable – and all this has to do with epigenetics.

I’m not entirely clear about what happens to turn specialist gametes into totipotent zygotes, and that’s what I’m trying to find out. I’m not sure yet whether zygotes immediately start differentiating as they divide and multiply or whether the first divisions – in what is called the zygote phase, which eventually forms the blastocyst – form an identical set of zygotes. 

The two-week period of these first divisions is called the germinal phase. During this phase zygotes divide mitotically while at the same time moving, I’m not sure how, from the fallopian tube to the uterus. Apparently, after the first few divisions, differentiation starts to occur. The cells also divide into two layers, the inner embryo and the outer placenta. The growing group of cells is called a blastocyst. The outer layer burrows into the lining of the uterus and continues to create a web of membranes and blood vessels, a fully developed placenta.

But, as Nessa Carey would say, this is a description not an explanation. How does this initial cell differentiation – into the outer layer (trophectoderm), which becomes the placenta and other extra-embryonic tissues, and the inner cell mass (ICM) – come about? Understanding these mechanisms, and the difference between totipotent cells (zygotes) and pluripotent cells (embryonic stem cells) is clearly essential for comprehending, and so creating, particular forms of life. This PMC article, which examines how the trophectoderm is formed in mice, demonstrates the complexity of all this, and raises questions about when the ‘information’ that gives rise to differentiation becomes established in these initial cells. Note for example this passage from the article, which dates to 2003:

It is now generally accepted that trophectoderm is formed from the outer cell layer of the morula, while the inner cells give rise to the ICM, which subsequently forms the epiblast and primitive endoderm lineages. What remains controversial, however, is whether there is pre-existing information accounting for these cell fate decisions earlier than the 8-cell stage of development, perhaps even as early as the oocyte itself. 

The morula is the early-stage embryo, consisting of 16 totipotent cells. The epiblast is a slightly later differentiation within the ICM. An oocyte is a cytoplasm-rich, immature egg cell.

Molecular biologists have been trying to understand cell differentiation by working backwards, trying to turn specialised cells into pluripotent stem cells, mostly through manipulating their nuclei. You can imagine the benefits, considering the furore created a while back about the use of embryonic stem (ES) cells in medical treatments. To be able to somehow transform a liver or skin cell into this pluripotential multi-dimensional tool would surely be a tremendous breakthrough. Most in the field, however, considered such a transformation to be little more than a pipe-dream.

Carey describes how this breakthrough occurred. Based on previous research, Shinya Yamanaka and his junior associate Kazutoshi Takahashi started with a list of 24 genes already found to be ‘pluripotency genes’, essential to ES cells. If these genes are switched off experimentally, ES cells begin to differentiate. The 24 genes were tested in mouse embryonic fibroblasts, and, to massively over-simplify, they eventually found that only 4 genes, acting together, could transform the fibroblasts into ES-type cells. Further research confirmed this finding, and the method was later found to work with non-embryonic cells. The new cells thus created were given the name ‘induced pluripotent stem cells’, or iPS cells, and the breakthrough has inspired a lot of research since then.

So what exactly does this have to do with epigenetics? The story continues.

Written by stewart henderson

January 6, 2020 at 5:28 pm

epigenetics and imprinting 2: identical genes and non-identical phenotypes

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I’ve now listened to a talk given by Nessa Carey (author of The epigenetic revolution) at the Royal Institution, but I don’t think she even mentioned imprinting, so I may not mention it again in this post, but I’ll get back to it. 

The talk was of course easier to follow than the book, and it didn’t really teach me anything new, but it did hammer home some points that I should’ve mentioned at the outset, and that is that it’s obvious that genetics isn’t the whole story of our inheritance and development because it doesn’t begin to explain how, from one fertilised egg – the union of, or pairing of, two sets of chromosomes – we get, via divisions upon divisions upon divisions, a complex being with brain cells, blood cells, skin cells, liver cells and so forth, all with identical DNA. It also doesn’t explain how a maggot becomes a fly with the same set of genes (or a caterpillar becomes a butterfly, to be a little more uplifting). These transformations, which maintain genetic inheritance while involving massive change, must be instigated and shaped by something over and above genetics but intimately related to it – hence epigenetics. Other examples include whether a crocodile hatchling will turn out male or female – determined epigenetically via the temperature during development, rather than genetically via the Y chromosome in mammals.   

So, to add to the description I gave last time, the histone proteins that the DNA wraps itself round come in batches or clusters of eight. The DNA wraps around one cluster, then another, and so on with millions of these histone clusters (which have much-studied ‘tails’ sticking out of them). And I should also remind myself that our DNA comes in a four-letter code strung together, out of which is constructed 3 billion or so letters.

The detailed description here is important (I hope). One gene will be wrapped around multiple histone clusters. Carey, in her talk, gave the example of a gene that breaks down alcohol faster in response to consumption over time. As Carey says, ‘[the body] has switched on higher expression of the gene that breaks down alcohol’. The response to this higher alcohol consumption is that signals are generated in the liver which induce modifications in the histone tails, which drive up gene expression. If you then reduce your alcohol consumption over time, further modifications will inhibit gene expression. And it won’t necessarily be a matter of off or on, but more like less or more, and the modifications may relate to perhaps an endless variety of other stimuli, so that it can get very complicated. We’re talking about modifications to proteins but there can also be modifications to DNA itself. These modifications are more permanent, generally. This is what creates specialised cells – it’s what prevents brain cells from creating haemoglobin, etc. Those genes are ‘tightened up’ or compacted in neurons by the modifying agents, so that, for example, they’re permanently unable to express the haemoglobin-creating function.

All of this is extremely fascinating and complex, of course, but the most fascinating – the most controversial and headline-creating stuff – has to do with carrying epigenetic changes to the next generation. The inheritance of acquired characteristics, no less. Next time.


What is epigenetics? with Nessa Carey – The Royal Institution (video)

The Epigenetics Revolution, by Nessa Carey, 2011

Written by stewart henderson

January 3, 2020 at 3:58 pm

how statins work 3: the beginnings of cholesterol, from Acetyl-CoA

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Coenzyme A – an acetyl group attaches to the -SH shown in red

So how is cholesterol made in the body? We need to know this in order to understand how statins inhibit or interfere with this process.

I’ve shown the actual structure of cholesterol in part 1 of this series, but remember it’s a sterol, which is a steroid – four carbon rings with hydrogen atoms attached – in which one of the hydrogens is replaced by an alcohol group. The particular form of sterol called cholesterol, with a 7-carbon chain attached to the end-carbon ring (the D ring), and three methyl groups attached to specific carbons in the rings and chain (it’s better to look at the skeletal structure in part 1). There are precisely 27 carbon atoms specifically placed within the molecule.

I’m using a set of videos to understand how cholesterol is synthesised – it might be best to look at them yourself, but I’m writing it all down to improve my own understanding. So we start by understanding something about acids and their conjugate bases. Apparently an acid is a molecule which is capable of donating protons into solution. Take pyruvic acid and its conjugate base pyruvate. Here’s what Wikipedia says about them:

Pyruvic acid (CH3COCOOH) is the simplest of the alpha-keto acids, with a carboxylic acid and a ketone functional group. Pyruvate, the conjugate base, CH3COCOO, is a key intermediate in several metabolic pathways throughout the cell.

I don’t understand the first sentence, but no matter, pyruvic acid is a 3-carbon molecule with a carboxylic acid at one end and a ketone group in the middle of the molecule (according to Britannica, a ketone is ‘any of a class of organic compounds characterized by the presence of a carbonyl group in which the carbon atom is covalently bonded to an oxygen atom. The remaining two bonds are to other carbon atoms or hydrocarbon radicals)’. The proton that comes off the oxygen of the alcohol group of the pyruvic acid can be donated into the surrounding solution, increasing its acidity. The pyruvic acid is thus transformed into its negatively charged conjugate base (it’s no longer capable of donating protons but it can receive them). This is the case with all acids in the cytoplasm of cells. As inferred in the quote above, conjugate bases are vital components of biosynthetic pathways. Most of the molecules in the cytoplasm will exist as pyruvate at a physiological pH of around 7.5.

Next – and hopefully this will become clear eventually – we’re going to look at two molecules, NAD+ (nicotinamide adenine dinucleotide) and NADP+ (nicotinamide adenine dinucleotide phosphate). They transport electrons, and are capable of accepting a hydride anion, which is a hydrogen atom with a negative charge. The normal hydrogen atom, called protium, has a proton and an electron only. When it donates away its electron it becomes a hydrogen cation, and when it gains an electron it becomes a hydride anion.

NAD+ is an adenine organic base bound to a ribose sugar. Then there are two phosphate groups coming off the ribose sugar, the second of which attaches to another ribose sugar. This second ribose sugar has nicotinamide attached to it (see below),

in which the phosphate groups are magenta-coloured circles. To explain something about ribose sugars, here’s something from Pearson Education:

The 5-carbon sugars ribose and deoxyribose are important components of nucleotides, and are found in RNA and DNA, respectively. The sugars found in nucleic acids are pentose sugars; a pentose sugar has five carbon atoms. A combination of a base and a sugar is called a nucleoside. Ribose, found in RNA, is a “normal” sugar, with one oxygen atom attached to each carbon atom. Deoxyribose, found in DNA, is a modified sugar, lacking one oxygen atom (hence the name “deoxy”). This difference of one oxygen atom is important for the enzymes that recognize DNA and RNA, because it allows these two molecules to be easily distinguished inside organisms.

So, just for my own understanding, nucleotides include phosphate groups. NAD+ is a dinucleotide, with two nucleotides (ribose sugars with phosphate groups attached), attached to adenine and to nicotinamide molecules. Also, NAD+ has a positive charge around the nicotinamide – on its nitrogen atom.

NAD+ becomes neutralised by accepting a hydride anion (one proton and two electrons) and becomes NADH, or reduced NAD. Now, remembering NADP+, it has an extra phosphate group on the ribose sugar of the adenine nucleotide (also called an organic base, apparently). Like NAD+, NADP+ can accept a hydride anion (becoming reduced NADP) and then later exchange it in another reaction. Effectively these molecules are electron carriers, collecting electrons and transporting them to where they’re needed for other reactions.

Now to introduce something else completely new for me – Acetyl-CoA (acetyl coenzyme A). A quick grab again, this time from Wikipedia:

Acetyl-CoA is a molecule that participates in many biochemical reactions in protein, carbohydrate and lipid metabolism. Its main function is to deliver the acetyl group to the citric acid [Krebs] cycle to be oxidized for energy production

Acetyl-CoA is found, and presumably produced, in mitochondria, and as part of this cholesterol-synthesising pathway it needs to be removed from the ‘mitochondrial matrix’. What’s that, I ask. So here’s a bit about the mitochondrial matrix, from yet another source, this time

The mitochondrion consists of an outer membrane, an inner membrane, and a gel-like material called the matrix. This matrix is more viscous than the cell’s cytoplasm as it contains less water. The mitochondrial matrix has several functions.It is where the citric acid cycle takes place. This is an important step in cellular respiration, which produces energy molecules called ATP. It contains the mitochondrial DNA in a structure called a nucleoid. A mitochondrion contains its own DNA and reproduces on its own schedule, apart from the host cell’s cell cycle. It contains ribosomes that produce proteins used by the mitochondrion. It contains granules of ions that appear to be involved in the ionic balance of the mitochondrion.

So basically this matrix is like (or equivalent to) the cell’s cytoplasm, only more viscous, and contains ribosomes, one or more nucleoids and ionic granules, inter alia.

Acetyl-CoA is essential to the biosynthesis of cholesterol, and is found initially in the mitochondrial matrix, and we need to look at the pathway for its removal from that matrix into the cytoplasm, where all the action occurs.

Intruding into the mitochondrial matrix from the (quite impermeable) inner cell membrane are the cristae, which give the membrane more of a surface layer for interactions. This inner membrane is the site of oxidative phosphorylation. What’s that, I ask. Well, it’s key to the production of ATP, and at least I know that ATP is the ‘energy molecule’, and that it’s produced in mitochondria. Here’s something about the process from Khan Academy:

Oxidative phosphorylation is made up of two closely connected components: the electron transport chain and chemiosmosis. In the electron transport chain, electrons are passed from one molecule to another, and energy released in these electron transfers is used to form an electrochemical gradient. In chemiosmosis, the energy stored in the gradient is used to make ATP.

So a strong proton gradient is built up across the inner membrane of the mitochondrion. It’s a concentration gradient but also an ‘electrical potential difference’ gradient, so that the electrical potential within the matrix is lower, by some 160 millivolts, than that across the inter-membrane space. The protons within this space are unable to pass back into the matrix. The only way they can get back into the matrix is by means of ATP synthase which can harness the energy from the protons as they move down the chemical and electrical gradient, and use that energy to bind ADP to inorganic phosphate to create ATP.

I don’t fully understand all that, but the main point here is that the mitochondrial inner membrane is very ‘tight’, which makes it difficult to transfer Acetyl-CoA out of the matrix and into the inter-membrane space, from which it can more easily diffuse through the more permeable outer membrane into the cytoplasm.

The structure of Acetyl-CoA: it consists of an acetic acid molecule (CH3COOH) with a thioester link to the thiol group of a coenzyme A molecule. The importance for us here is this thiol (HS) group, which is similar structurally to an alcohol (HO) group, as sulphur has similar properties to its periodic table neighbour, oxygen. So thiol groups can be linked to carboxylic acid groups as alcohol groups can. Acetyl essentially means acetic acid with the alcohol removed. To get this Acetyl-CoA out of the matrix, it is first bound to oxaloacetate, a four-carbon molecule, to create citrate, the first molecule of the citric acid cycle. This citrate can be passed through the mitochondrial inner membrane and into the cytoplasm where it can be converted back into Acetyl-CoA.

So the conjugate base, oxaloacetate, has carboxylic acid groups, attached to the first and fourth carbon atoms, that have lost their protons into solution. An enzyme within the matrix is able to combine oxaloacetate with Acetyl-CoA and water to create citrate…

Okay, this is proving to be a much longer story than I might’ve hoped, but I like to be thorough – and in reality I’m still not being thorough enough. There’s a lot of rubbish on the internet about statins, much of it self-serving in one way or another, so I’ll just keep plodding along until I feel at least halfway informed about the matter. Meanwhile, you just keep getting on with your work, and don’t mind me.


Cholesterol biosynthesis part 1, by Ben1994, 2015

Cholesterol biosynthesis part 2, by Ben 1994, 2015

Written by stewart henderson

October 14, 2019 at 5:26 pm