#bacterioraging

[bacteriorage]

The fun thing about going to Oxford is class divides you didn't know even existed. For example I am currently putting my ikea porridge bowl in the sink to soak next to my flatmate's le cruset pans.

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Ok, fun new changes! Firstly, hi! I changed my profile picture and my blog design. Used to be a nice navy blue Dana Scully aesthetic. not anymore! Now I'm here to hurt your eyes.

Secondly, I started up a science account! All my proper science content will be going over there, as well as some studyblr style stuff. It's called @bacteriorage and I'd love if you could check it out :)

[bacteriorage]

Alright besties, new article just dropped and this time it's all about carnivorous plants! It's pretty entry level for now, which is what's gonna allow me to go super in depth later with the forbidden pitcher plant knowledge, but I hope it's fun to read nonetheless :)

Oh, and here's Patricia. She wants you to read the article and follow me on Neocities.

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Ok I have this afternoon and evening to finish the reading for and write an essay. This will be fine. I'm fine.

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gonna try and post more about life at oxford for all you little baby freshers and sixth formers out there. for example. i have spent ages booking tutorials for this term and am now crushed by the realisation that i have to do essay now

[bacteriorage]

Zombie Proteins

So, prion diseases are freaky. Hardly covering new territory here. They are 100% fatal, cause horrifying neurodegenerative symptoms and can be transmitted in any way imaginable. Examples include mad cow disease, chronic wasting disease and scrapie, as well as Creutzfeldt–Jakob disease and fatal familial insomnia in humans.

People usually describe prions as 'misfolded proteins'. But what I didn't know until this morning is that almost all prions are an infectious variant of one specific protein called PrP (the imaginatively-named prion protein). PrP is highly conserved, especially among mammals, and is found all over the body but especially within the nervous system. We don't know its function.

There are a few mutant variants of PrP, some inherited as genetic mutations and others picked up through consumption of or exposure to infected organisms. Those mutant variants, whenever they come into contact with healthy PrP, turns that healthy PrP into more mutant PrP. And so the cycle continues.

Mutant PrP is resistant to all known proteases and has extreme resistance to heat, ionizing radiation and formaldehyde. It can last for years in the soil, in water, in carcasses, in plants, on the ground... you get the gist.

While the function of PrP is unknown, its destruction and accumulation of mutant variants causes spongy holes in nervous tissue. Problems with movement, memory, speech and sight are characteristic, and fingers have even been pointed suggesting it as the cause for Alzheimer's. It feels like this is an area with a lot left to discover, and possibly one that we can turn to our advantage if we can find a way to copy the replicative effects for the purposes of medicine.

What fascinates me most about these proteins is how closely they resemble life. Stick with me here! They self-replicate in a sense, in a similar parasitic way to viruses. However, instead of preying on the genome, they prey on proteins. If prions ever became more complex they could be well on their way to becoming the first solely protein based life form. But can such a life form exist without nucleic acid based life forms to provide it with fully formed proteins to 'turn'?

[bacteriorage]

The Nitrogen Cycle!

Chem revision was making me extremely angry so I decided to chill out and draw plants for a bit. Let me know if you’d like a printable version, it shouldn’t be too hard to make! I hope this helps you as much as it helped me.

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Posters on photosynthesis and respiration :)

[bacteriorage]

The Biochemistry They Don't Teach You In Biology (But Do Teach You In Chemistry)

For those of you doing OCR Biology A who are either also doing AQA Chemistry, or who are just plain interested.

Amino Acids

Amino acids are considered bifunctional, which is pretty self-explanatory; they have two functional groups, the amine and carboxylic acid groups.

The -COOH group is weakly acidic, tending to donate its proton, and the -NH₂ group is weakly basic, tending to accept a proton. This lets the amino acid act as both a weak acid and a weak base.

So when it's in an acidic solution, it will act as a base, accept the proton and become a cation. In alkaline situation, it will act as an acid and donate its proton, becoming an anion. In an intermediate (not necessarily neutral) pH, it will become a zwitterion - simultaneously an anion and cation. The Schrödinger's cat of ions, perhaps? It flips back and forth between its usual uncharged form and the zwitterion form.

The pH where the amino acid exists as a zwitterion is called its isoelectric pH, by the way.

But wait! There's actually something more that biology isn't telling you. You've been told there are 20 naturally occurring amino acids, right? Wrong. There are 20 naturally occurring α-amino acids, also known as 2-amino acids. They are called 2-amino acids because their amine group is on carbon 2, as counted from the carboxylic acid group which is standard. There are actually many more amino acids with different lengths of carbon chain, for example the neurotransmitter GABA, pictured below. It is a 4-amino acid.

On the topic of α-amino acids, they are all actually optical isomers (enantiomers) because the 2nd carbon is bonded to 4 different groups. Only the L isomer naturally occurs.

DNA

Aside from knowing the details of how everything in DNA bonds together, there is only one bit of detail chemistry goes further into with DNA, and that is the anti-cancer drug cisplatin. It looks like this.

The way it works is essentially acting as guanine-specific glue. It sticks to one guanine base by replacing its chlorine with one of the nitrogens on guanine, and then the process repeats with another guanine base. This process distorts the shape of DNA, stops it replicating and causes all those delightful chemotherapy side effects we know and hate.

And that's pretty much it! I hope this was helpful and interesting to at least some of you. Have a good day now :)

[bacteriorage]

An Exhaustive (And Exhausted) List of the Pros and Cons of Taking Four A-Levels

It’s been a hot second since I wrote a school advice post, mostly because I have been the one in need of school advice as of late. However, today I have been thinking back on my own life choices because I have 6 A-level exams this week and I’m not entirely sure I’m going to survive it’s nearing the end of my school career.

For context, I take chemistry, biology, maths and further maths, got all 9s at GCSE and have an offer from Oxford to study biology. Baller credentials if you ask me. So without further ado, here we go:

Pros:

You get to study more stuff you enjoy, which if you are indecisive or a nerd is a huge bonus. If you took further maths GCSE, for example, you’ll be super bored in year 1 maths A level, so having something more interesting to do in further maths was a great help.

You can afford to do badly in a subject. This is great because if you love a subject but can’t get good grades, you can still take it and not need to worry about how this affects your university entry. Bear in mind, however, that the extra time spent on a fourth subject will impact your other grades.

Having a broad range of knowledge is always helpful.

It’s worth trying out 4 A-levels, if only to check out which subjects you like or to see if you can handle the workload.

Cons:

I have so many exams. As mentioned earlier, I have six exams this week. Which might not seem a lot now, but trust me, it sucks. I’m pretty sure I just failed chem, but I have to get up and do maths paper 3 tomorrow.

Don’t expect to have much of a social life on top of the homework. Remember that A-levels are designed to be taken 3 at a time, so regardless of how easy you find it the workload and time you spend on it will pile up quickly. As a guide, I would generally have 1-2 hours a day to myself during weekdays, and I’d spend a few hours on the weekend catching up. If that doesn’t sound sustainable, this is not the path for you.

You will burn out. This is a fact of life. Doing this much work is actually really bad for your mental health! If you’re not in a good place right now, don’t bother. It literally isn’t worth it.

Speaking of it not being worth it, universities literally do not care if you’re doing 4 A-levels. Not even Oxbridge, not even secretly. Because it isn’t realistic to be able to do all that! Don’t put yourself through this just because you want a better chance at getting into uni. It won’t work.

So yeah, that’s my advice! In terms of me, I don’t regret doing 4. Well, I do, but I also wouldn’t choose any differently because I love further maths too much and chemistry gives me too much valuable background knowledge to drop either one. I really, really dislike chemistry though. Don’t do chemistry unless you absolutely have to.

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All About Rabies!

With me, your host Lucy, someone who is entirely too excited about viruses in general <3

Please bear in mind I wrote this all as several Discord messages and I'm on mobile so I'm trying my best here.

Let's start with a little bit of Diagnosis Detectives! This case is taken from Virusphere by Frank Ryan, an excellent book that I highly recommend. A healthy 73 year old Canadian man presented to hospital with a headache and fever. This swiftly progressed to muscle spasms, excessive salivation, aggression, anxiety and a host of other neurological symptoms. He slowly lost all his mental faculties. After questioning, his family said he'd been bitten by a bat a few months ago but they hadn't treated the bite as it didn't seem serious. By this point doctors had a vague idea of what must be going on, but no treatment worked. The man fell into a coma and, when medical intervention was removed after two months, he died. As you may have guessed by now, the man had rabies.

[Image ID: A rendering of two rabies viruses. They have bullet-shaped capsids and are covered in proteins. End ID]

Rabies is caused by some members of the genus Lyssavirus such as the Australian bat lyssavirus and the imaginatively named rabies virus. These viruses are fairly average-sized and have a bullet-shaped capsid. They also have an RNA genome which is pretty cool.

The natural host of the lyssavirus is bats. Bats are often asymptomatic carriers of rabies. They are actually asymptomatic carriers of a lot of things - bats host the highest number of viruses of any living thing.

[Image ID: A bat that is grinning like it just told a really bad joke. End ID]

That's not necessarily a bad thing. Even humans have natural viruses that live in us constantly, just like we have a bacterial microbiome. Our virome, as it is called, has been shown to have an effect on both the health of us, the host, and also the microbiome (thanks bacteriophages!). But I'm not here to fangirl about bacteriophages. That can wait for another time. My point is, lyssaviruses usually live decent, non-rabies-causing 'lives' inside bats. That is, until they cross the species barrier in a process called zoonosis. Yes, that's how covid came about too. And, in fact, all the recently emerged viral diseases, such as the original SARS and HIV.

Lyssaviruses' host cells of choice are nerve cells, and they are also found in the saliva which aids in transmission.

Almost all rabies cases are transmitted by a bite from an infected animal, such as a bat, dog or fox. No human-to-human bite cases have ever been recorded. All human-to-human transmissions are the result of organ transplants. Which, uh, kinda sucks.

The lyssaviruses' mode of operation, once they're inside a non-host organism (which can include any warm-blooded animal, and some strains can even infect reptiles) is to go straight for the brain. They enter the nervous system and slowly work their way up the brain stem into the cerebral cortex and meninges. This process usually takes between 1 and 3 months, though it can take as little as 4 days and as much as 6 years, depending on where the bite is and how much virus was transmitted.

Once the virus reaches the brain, it causes inflammation which cause the initial symptoms of fever and headaches. From there brain damage sets in, causing all those lovely neurological symptoms that can range from paralysis to hallucinations to changes in behaviour.

Interestingly, this is an example of a pathogen changing a host's behaviour to facilitate transmission. The virus makes the host more aggressive and impulsive by damaging its cerebral cortex, so it's more likely to bite something or someone and pass on the virus. Smart! Or, well, evolutionarily beneficial.

You may also have heard of rabies causing hydrophobia. This happens in about 80% of cases and can be so awful that even the mention of drinking can cause horrible throat spasms. If you want to upset yourself, there's a lovely video on the Wikipedia article for rabies of an infected man trying to drink water. It's fascinating, and heartbreaking. Anyway, this makes the victim less likely to want to swallow, meaning their mouth is always full of virus-filled saliva for when they actually do bite someone.

After symptoms have set in, death is rapid - 2 to 10 days after the first fever, though as seen with the example at the start, this can last longer with the right interventions. Nevertheless, the victim will die. Only 14 people have survived rabies after symptoms set in.

The only way to treat rabies is to get vaccinated within 10 days of a possible infected bite. You can also get vaccinated beforehand but due to the cost of the vaccine only people with high chances of catching it are given it. The high cost of the vaccine also means it is hard to find in developing countries. This is especially awful because those countries usually have high populations of bats, stray dogs or both, which can cause huge risks to the human population. Rabies is classed as a neglected tropical disease.

And on that lovely note, thanks for reading my massive infodump on one of the best-known viruses! I think its one of those viruses that really does deserve its terrifying reputation. Best of luck to anyone who does end up exposed. Luckily, the vaccine is 100% effective if given in good time!

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At this point I'm p much convinced that RuBisCO is the source of all of my problems

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Alright besties, life update time! So, exams are creeping ever-closer and I’m not enjoying that! But there’s plenty to keep me busy in the meantime, obviously. I’m still frantically studying but in the meantime I’m trying to frantically prepare myself for university. I’ve got my driving test on the 4th (wish me luck!) and I’m spending a lot of time applying for student loans and stuff.

I visited Oxford a while back and absolutely adored it. I could spend a solid week in the natural history museum, the centre of town is gorgeous and there’s plenty to do! I’m especially looking forward to living in a city since my current commute to anything is at least an hour. I’m also lucky enough to be going to an open day at my college soon so I’ll be hopping on the train in the half term. All I can say is, thank god the uni is covering travel costs.

Other than that, my life is trying and failing to study at the moment! Which sounds pessimistic, but hey, at least my reasons are shifting from ‘I’m too tired’ to ‘it’s too nice a day to waste’. So that’s something! I hope the rest of you are enjoying the sunshine.

Oh, and before I go. Are any of you guys attending/offer holders for Wadham? I really want to meet some of the people I’ll be living with.

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The relationships between different organic chemicals as demonstrated by my lovely assistant, butane :)

This is everything you need to know for AS level chemistry, click to zoom in and see detail!

[bacteriorage]

All About Guillain-Barré Syndrome

Here’s some info I gathered up for a school project! This is a really fascinating neurological disease so I hope you all enjoy reading about it.

Guillain-Barré syndrome (GBS) is a neurological autoimmune disease of the peripheral nervous system. It is usually triggered by anything that can elicit an immune response, including bacterial or viral infection or vaccination. Triggers are generally respiratory or gastrointestinal infections. An antibody-mediated attack to the Schwann cells causes destruction of the myelin sheath, which reduces the speed of neural impulses and can lead to damage to the axon itself.

Initial symptoms include numbness, tingling, muscle weakness, pain and coordination difficulties. In the hours, days or even weeks after the onset of these, further symptoms can include paralysis of various body parts, problems speaking, chewing or breathing, visual distortion and issues with defecation and urination alongside moderate to severe pain. Symptoms will then stabilise for weeks or months before gradually improving. 

(image from Wikipedia)

Diagnosing the syndrome requires testing for loss of deep tendon reflexes, and also a nerve conduction velocity test as the speed with which signals are transmitted is usually reduced. The muscle weakness is also symmetrical which can aid in ruling out other disorders, as can checking the speed of onset.

Intravenous immunoglobulin is the most common treatment for GBS, in order to regulate the immune system. Plasmapheresis (plasma exchange) is also sometimes used. Depending on the patient and variation, various other treatments including ventilation may be necessary. Recovery can take a year, and one in five patients is left with long term difficulty. Death rate is 7.5%.

There is a lot of worry amongst vaccine hesitant and anti-vaccine people that vaccinations, including covid-19 vaccines, cause an increased incidence of GBS. In terms of the influenza vaccine, there has been a recorded increase in the number of cases of GBS by 1 or 2 cases per million after the seasonal flu vaccine program. However, this is lower than the number of GBS cases caused by catching the flu under normal circumstances. Though there has been little research into it, evidence suggests that the same is true for covid-19.

Sources:

The UK government

The NHS

The USA National Institute of Neurological Disorders and Stroke

The World Health Organisation

Mayo Clinic