#retroviruses

[xanananas]

With Subnautica 2 making rounds recentlyish, I think something worth mentioning is that viruses impacting evolution are not a thing of fiction. Maybe not as extreme, but still extremely remarkable.

Retroviruses are viruses able to insert their genetic code into animal genomes to later reproduce. A notable example is HIV, which without treatment impairs the immune system due to it targetting immune cells. Fortunately other retroviruses can be overcome with immune responses, though their genetic code still remains in the organism.

A consequence of this is actually a lot of retroviral DNA in animals, including us, built over time and a number of features, including really pivotal ones, actually are controlled by portions of our genome which came from retroviruses.

Myelin sheaths running along nerves are an adaptation almost exclusive to jawed vertebrates. By insulating nerves, myelin essentially reduces lost current and increases the speed of signals. It enables faster movements and transmission of information, and by extension is why we and other animals are able to think actively and quickly. More broadly a lot of complexity in vertebrates would not be possible without it.

Anyway it turns out that an ancient retroviral insert is actually necessary for their development and regulation. Essentially we owe our brains in part to prehistoric viral infections in early jawed fish ancestors.

Another thing of mention which has been known about a bit longer is the placenta. Not only is there also a genetic link between its development and ancient retroviral DNA, but the proteins in the placenta enabling the exchange of nutrients without inducing an immune response in of themselves seem to be similar to the proteins in viruses enabling infection to begin with or so I had skimmed (someone can correct me on the details of that).

I'm not sure if the Subnautica 2 developers deliberately drew from these discoveries or independently came to these concepts, but either way it's surprisingly well-reasoned speculative biology even though there are things maybe a bit out there like the proteavirus causing routine horizontal gene transfer between animal specied, never mind whether human infection should be possible.

[neurosciencenews]

Are the ‘viral’ agents of MS, ALS and schizophrenia buried in our genome?

Retroviruses may be a missing causal link in diseases like ALS, multiple sclerosis and schizophrenia.

[biochemistry-official]

The Central Dogma

What is it? The central dogma is a common way to refer to one of the most fundamental concepts in biology: how organisms store, transmit, and act upon information. It was coined by Francis Crick partially because he forgot the meaning of the word 'dogma.' (Really, he did).  Basically it goes like this:

Image Credit: Khan Academy, “Intro to gene expression”

Long term storage of information (like how to build a protein, or how often a cell should divide) is stored in DNA. When the cell needs that information, the DNA is transcribed into messenger RNA, or mRNA. Then, that mRNA is translated into a chain of amino acids, which folds into a protein that can do work within the cell. It could perform a chemical reaction, become part of a cellular structure, regulate transcription of specific genes, etc.

The DNA to RNA transition is called transcription because the mRNA is basically a copy of the DNA but with a slightly different molecule. It's pretty easy to look at an RNA sequence and figure out what portion of the DNA it was transcribed from. The RNA to protein transition is called translation because it's like the RNA is being translated into a completely different language. Every three bases of RNA (a codon) codes for a specific amino acid. But, since there are 64 possible combinations of RNA bases and only 20 amino acids, there is a lot of redundancy. If you know the exact sequence of amino acids in a protein, you can't figure out the exact RNA sequence that created it.

What are the exceptions to it? Although broad, simple theories are appealing, they almost never capture the true complexity of life. The central dogma is true for most processes in the cell. Genes make RNA, which makes protein. However, there are some exceptions.

Viruses lack the ability to replicate or reproduce by themselves, so they have to infect other cells to survive. Some viruses don't have a genome made of DNA, they have an RNA genome instead. One class of these is called retroviruses, because they move backwards against the usual flow of information described by the central dogma. When they invade the cell, they reverse transcribe their RNA genome into DNA, which gets inserted into the genome of the host. HIV (human immunodeficiency virus) is an example of a retrovirus.

Prions are another example of a process that defies the central dogma. They are proteins that can cause disease by triggering other proteins to switch into a misfolded state. They are infectious, but they don't have any RNA or DNA genomes, they're just a single protein. The first prion discovered was called Prion Protein, because scientists are very creative. Many animals have genes for prion proteins and have tons of normal, healthy prion protein in their bodies. However, these proteins can change shape (misfold) into an alternate, infectious state. Once one protein misfolds, it gets all the other prion protein around it to misfold as well. They clump up into giant, stable aggregates of proteins, which end up killing the cell they're in. Then, the prions find other cells to infect and kill. So, they act like pathogens, but they don't have any genome and don't even fit the definition of a living thing. Examples of prion diseases include mad cow disease, Creutzfeldt-Jakob disease, kuru, and possibly Alzheimer's (the research on this is still pretty new). There are no current treatments for prion diseases, but fortunately they are pretty rare.

[currentsinbiology]

Viruses in the Genome Important For the Brain

Over millions of years retroviruses have been incorporated into our human DNA, where they today make up almost 10 per cent of the total genome. A research group at Lund University in Sweden has now discovered a mechanism through which these retroviruses may have an impact on gene expression. This means that they may have played a significant role in the development of the human brain as well as in various neurological diseases.

“TRIM28 Controls a Gene Regulatory Network Based on Endogenous Retroviruses in Human Neural Progenitor Cells” by Per Ludvik Brattås, Marie E. Jönsson, Liana Fasching, Jenny Nelander Wahlestedt, Mansoureh Shahsavani, Ronny Falk, Anna Falk, Patric Jern, Malin Parmar, and Johan Jakobsson in Cell Reports. Published online January 3 2017 doi:10.1016/j.celrep.2016.12.010

Many of the retroviruses that have been built into the human DNA do not exist in species other than humans and our closest relatives – gorillas and chimpanzees.   NeuroscienceNews.com image is for illustrative purposes only.

[garudabluffs]

But more than anything, these findings illustrate that the genome is not just an instruction manual but an entire ecosystem. “There are interactions between prey and predators,” says Feschotte. “All of these really complicated biological interactions, they’re all happening in the genome.”

An Ancient Battle Is Playing Out in the DNA of Every Embryo

Millions of years ago, retroviruses invaded the human genome. Today some of these viral remnants threaten the developing embryo while others fight to defend it.

READ MORE https://www.wired.com/story/an-ancient-battle-is-playing-out-in-the-dna-of-every-embryo/?bxid=5cc9dfde3f92a477a0e6fdbd&cndid=55263628&esrc=OIDC_SELECT_ACCOUNT_PAGE&mbid=mbid%3DCRMWIR012019%0A%0A&source=Email_0_EDT_WIR_NEWSLETTER_0_DAILY_ZZ&utm_brand=wired&utm_mailing=WIR_Daily_071723

[canadianabroadvery]

Evolution Runs Faster on Short Timescales

Evolution progresses much more quickly over years or centuries than it does over geologic time. Now the oldest viruses on the planet are enabling scientists to calibrate this evolutionary clock.

fascinating reading

[agreenroad]

The Well-Known Hazards of Coronavirus Vaccines - Dr Mercola

The Well-Known Hazards of Coronavirus Vaccines – Dr Mercola

Dangerous coronavirus experiments led by Dr. Anthony Fauci went on in the U.S. until 2014 when President Obama ordered the work to stop due to safety violations at three biolabs. Fauci then moved the operations to the Wuhan lab in China and continued coronavirus experiments right up until the time that the COVID-19 pandemic occurred

The COVID-19 pandemic may have been generated to ensure that…

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[slimlastforskolins]

Silencing retroviruses to awaken cell potential -- ScienceDaily

Silencing retroviruses to awaken cell potential — ScienceDaily

Embryonic stem cells have the potential to differentiate into any type of cell in the human body. Once differentiated though, the newly minted somatic cells live out the rest of their days as that specific cell type and never again have the capacity to differentiate. Or so the theory goes.

In a study published last week in Cell Reports, a team led by researchers from the University of Tsukuba…

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