Posts Tagged ‘early life’
epigenetics at the very beginning of life – my explorations
So let me see if I can understand epigenetics through other sources, and through what I’ve read so far. First, it’s essential for the very first cell divisions in human – or shall we say mammalian – life, at least for placental mammals. Their lives begin with a fertilised egg, a sperm cell and an egg cell (both known as gametes), each with its complement of DNA (but the egg cell contains much more, and there’s a difference between an ovum and an oocyte, which I won’t go into, as if I could). This cell, also known as a zygote, is the ultimate totipotent stem cell, potentially able to form every type of somatic (diploid) cell. So what causes this cell to divide and multiply, and become, in a few days, a blastocyst?
A blastocyst is already quite a complex collection of cells, with an outer layer, the trophectoderm, an inner cell mass, and a blastocoel, which is a fluid-filled cavity. So, already quite a jump from a zygote, so I need to know how that happens. But even before that, I need to know how a zygote comes into being. Wikipedia puts it this way:
The formation of a totipotent zygote with the potential to produce a whole organism depends on epigenetic reprogramming. DNA demethylation of the paternal genome in the zygote appears to be an important part of epigenetic reprogramming.
That doesn’t help too much, but I’m guessing that this ‘epigenetic reprogramming’ thing is what creates cell diversity – but this description tells us that the formation of the zygote is itself an epigenetic product. Here’s another description of the first steps:
The four stages of embryonic development include fertilization (zygote formation), cleavage (rapid cell division), blastocyst formation, and finally, implantation into the uterine lining.
Cleavage? The website I filched this from (ferty9.com, listed below) fails to elaborate, and looking up the word an sich just takes me to female breasts, which is pleasant but distracting. AI (never lies) gives more detail, claiming four cleavage stages, 1. the zygote stage, 2. the 2 to 8 cell stage, 3. the morula stage, and 4. blastocyst formation. And presumably epigenetics plays a role in the move from one stage to the next?
So, I’ve tracked down a most sciencey article, from ScienceDirect, entitled ‘Epigenetic regulation of early human embryo development’, which I hope to make sense of. Its opening paragraph is a bit daunting though:
Epigenomes undergo profound change during the first few days of embryonic development. The resetting and establishment of epigenomes are coordinated within and contribute to the wider processes of embryogenesis. As a consequence, faithful epigenetic regulation is required to safeguard development and to establish long-lived epigenetic states that have effects on genome function throughout the life course.
So now we have epigenomes, and here’s a definition:
Epigenome: The epigenome consists of all the chemical modifications of DNA and histones of a cell/organism that contribute to regulate gene expression independently of DNA sequence.
Histone modification involves the post-translational modification of specific amino acids that influence the overall structure of histone proteins. Changes in histone structure may then influence their function, resulting in incomplete DNA unwinding that may also effect transcription activity. Major histone modifications include acetylation, methylation, phosphorylation, ubiquitylation, and, less frequently, ribosylation, sumoylation, and citrullination
References
https://pmc.ncbi.nlm.nih.gov/articles/PMC4783933/
https://www.sciencedirect.com/science/article/pii/S153458072101042
https://embryology.med.unsw.edu.au/embryology/index.php/Blastocyst_Development#Introduction
https://www.sciencedirect.com/science/article/pii/S1934590923003314
Kangaroo Island – return to Emu Bay
Canto: I wanted to find out more about Emu Bay’s famous fossils so I decided to return and take the trek round the bay to the eastern extremity, photographing any rocky scenario I could find. The good thing was that, again, the weather was perfect for a long walk, and my thoroughly salubrious saunter helped me to break the record for most daily steps recorded on my iphone since I bought one eighteen months ago. The bad thing was that I really had no idea what I was looking for – Emu Bay shale, Burgess shale, WTF is shale? Is it a kind of rock? What colour and texture does it have and how is it formed? I should have researched the matter before proceeding, perhaps.
No matter, I took plenty of photos and now it’s a matter of mapping what I’ve found onto the descriptions in the literature.
shale – typically exhibits varying degrees of fissility, breaking into thin layers, often splintery and usually parallel to the otherwise indistinguishable bedding plane because of the parallel orientation of clay mineral flakes.[1] Non-fissile rocks of similar composition but made of particles smaller than 0.06 mm are described as mudstones (1/3 to 2/3 silt particles) or claystones (less than 1/3 silt). Rocks with similar particle sizes but with less clay (greater than 2/3 silt) and therefore grittier are siltstones.[1] Shale is the most common sedimentary rock. (Wikipedia)
This description doesn’t really help me. Fissility means the tendency of rocks to splinter along lines of weakness, which doesn’t help me either. I tried google images, but the variety of shale presented, and the near-complete lack of any connecting factors, didn’t help me either.
However, when I tried images for Emu Bay shale in particular, I felt some definite progress. Some of the shale was copper-brown, some was slate-grey, some dull yellow, some penicillin green. But I recognised some of the colours and textures in the rocks I photographed.
A trilobite in Emu Bay shale. Trilobites are the most long-lived class of complex creatures – in this case arthropods – of all time, I think, having inhabited the planet for about 270 million years: more than a thousand times longer than Homo sapiens (so far). Some 50 species of trilobite have been found at Emu Bay
Like many, of my generation at least, I learned at school that there were three kinds of rock – igneous, metamorphic and sedimentary. As Wikipedia informs us, shale is sedimentary, and that makes sense as it’s in sediment that fossils are found. Volcanic rock is extruded igneous rock, and there appears to be quite a bit of it at Emu Bay.
volcanic (extruded igneous) rock – I think – at Emu Bay. Lots of it about. Spongy and low density
A lot of this rock sits in gigantic chunks on the sand, but elsewhere they form craggy, small cliff-like structures.
One small area had what I suppose were sedimentary rocks with a coloration completely different from the rest – and of course the more you pay attention to rocks (and everything else) the more variety you find. They were a sulphurous yellow…
an anomalous bunch of yellowish rocks at the eastern end of Emu Bay
Other rocks looked like granite – intrusive igneous rocks – but another prevalent type I saw, forming ridges high above me, was a rock type I can’t easily identify, though no doubt it’s common enough.
Slate-like rock forming small cliffs, visible along much of the eastern side of Emu Bay
But it’s only through reading that I’ve found the type of rocks I’m after, and the more precise location of the fossil-rich shale. The colour is a dark coffee brown, as shown in the photo of the trilobite above, and these rocks only crop up (or crop out, to write technically) at the easternmost tip of the bay. In fact the onshore location of the fossil-rich shale is further still, a few hundred metres east of the bay proper, with a further site a few hundred metres inland. I would’ve had to clamber over the rocks photographed below, and get a bit wet, to find myself on-site.
the end of the road for me – but these are precisely the kind of rocks I was looking for, without knowing it. They’re only at the easternmost tip of the bay, and beyond
No matter. Hopefully the sites themselves are well-protected. I’m mindful of the concern about looters and trophy hunters, and the preciousness of such places as minefields of info about the extraordinary variety of the first highly successful complex life forms after the initial experiments of the Ediacaran biota a few million years before.
More about that in my next post.