Avian flu: taking flight?

On 16th November a duck breeding farm in Yorkshire tested positive for avian flu, so as you can imagine DEFRA was on the scene immediately, introducing a 10km restriction zone and culling all 6,000 birds on the farm to prevent further spread of the disease. But why? Is avian flu so contagious, that such an extreme response was warranted? Is it that dangerous? Let's find out shall we. Avian flu is caused by the influenza A strain of the influenza virus (although A does not stand for avian). All subtypes of influenza A are adapted to be able to use birds as a host, but are not always zoonotic (can pass from animals to humans). Influenza A is what is known as an  single stranded antisense RNA virus, meaning its single strand of RNA (3'-5') runs complementary to viral mRNA (5'-3')  that it encodes. This means it must carry RNA polymerase within the virion particle, as the viral RNA cannot be directly translated into protein, it  must be transcribed first, rather like DNA. Influenza A can be categorised into 2 subtypes based on the protein used to construct its membrane: Hemagglutinin (H) or Neuraminidase (N) . The H protein causes agglutination of red blood cells in the host, and mediates the binding of a virion particle to the host cell and entry of the viral genome into the host cell genome.  Whereas N is an enzyme that breaks the glycosidic bonds in the monosaccharide, neuraminic acid, commonly found in animal cells as glycoprotein and it also controls the release of new virion particles from host cells. Different strains of influenza virus encode for different types of N and H which all play a specific role in the viral lifecycle, for example H5N1 virus  contains type 5 Hemagglutinin and type 1 Neuraminidase (oh how I love arbitrary numbers used to name pathogens). Interestingly, these 2 proteins form the antigens that allow antibodies produced by B cells to bind to the microbe, so macrophages can phagocytose it. Ok,  I think I've indulged you enough in the virus' structure and nomenclature, so let's talk about the birds. The outbreak in Yorkshire recently was H5N8 strain, which is of very little threat to people. In fact no one has died from it. Ever. The avian flu strains that you really have to worry about are H7N9 continually reported in poultry in China, and H5N1, which has a 60% case mortality rate across 15 countries (since 2003). Migratory fowl can act as asymptomatic carriers for the virus, which is probably how it reached the UK in the first place, and strains like H5N1 are not limited to birds and people; in New England 400 harbour seals were killed by the pathogen in a 1978 epidemic. Ok, so we know that certain strains of influenza A are deadly to people, but if the H5N8 strain poses no threat to us, why were all the ducks killed? Well, because of the high mutation rate of the virus, and its ability to hybridise with strains from other species, it could quickly become a human epidemic. So before we start arguing over the 'poor ducks' that were 'murdered', we must consider the potential threat of any strain of influenza to humans.

Immunology: your life depends on it

The mechanisms employed by the human body to destroy and to resist pathogen infection are simply breathtaking. The field of immunology is vast, and often taken for granted by the less inquisitive of our race, so my aim for this post is to dispel any doubt about how vital our immune system is, and perhaps put the fear of the fictional god in your heart. Let's start with the basics: most mammalian immune systems are split into 2 tiers: the innate and adaptive immune systems. The innate response is usually triggered by pathogens being detected by pattern recognition receptors, which respond to generic microorganism components or the cries for help from body cells. The innate immune system is therefore non-specific, so it does not produce antibodies, but it can act on a wide range of microbes, making it the first and main line of defence against disease in the human body. There are multiple components to this immune system; surface barriers like our skin and mucus,  mechanical barriers like coughing up mucus filled with pathogens to protect the lungs and respiratory tract and biological barriers, like the gut flora in our intestines which competes against parasitic pathogens. Inflammation in response to injury is also part of the innate system; compromised cells release signalling molecules (like cytokines) to dilate blood vessels and attract white bloods cells (leukocytes), specifically phagocytes, which digest the invading pathogens. The mammalian complement system is is another vital part of this response. Essentially, complement proteins bind to carbohydrate receptors on the surface of microbes, triggering a cascade of protease-like molecules which break down the surface of a microbe, rendering it inactive. It's a bit like the body's version of a gatling gun. The final elements of the innate system are the natural killer cells, which detect cells with low levels of a surface marker called MHC, meaning the cells are infected or cancerous, and they are destroyed. NK cells aren't concerned about trivial things like collateral damage... 
Let's now move on to the adaptive immune system, which is definitely my favourite, if you can have a favourite layer of the immune system. It is more potent, and is capable of remembering microbes because of their signature antigens, to speed up immune response. Therefore the adaptive immune system is antigen specific, so can recognise specific antigens in antigen presentation of cells. This system employs more variants of leukocytes, known as lymphocyte B cells and T cells. The B cells produce antibodies to target specific antigens on microbes, causing them to bind together, making it easier for phagocytosis to occur. The T kills can split into 2 kinds: T helper cells and T killer cells. T killer cells kill cells infected with pathogens (viruses in particular), and each one recognises a specific antigen (like everything in this system). When activated T killer cells release cytotoxins into compromised cells, inducing apoptosis. How neat. T helper cells regulate the immune response, by directing other cells to perform immunological tasks like digesting pathogens or producing antibodies. The most impressive thing about B and T cells is that their daughter cells can become long-lived memory cells, which remember specific antigens encountered in the past, and so can produce a particularly powerful immune response if that antigen is detected in the body again. Just from this brief overview of the immune system (trust me, this is heavily summarised), I hope you can see how vital every mechanism is to our health. Your heart may keep blood flowing around your body, your lungs may be the centre of gas exchange, but they would be meaningless without the protection the immune system affords your body. Next post I'll be describing what happens when the immune system fails. Trust me, it will be terrifying. 

Retrotransposons: bringing disco back?

Sorry about the cliffhanger in the last post. I lied, I'm moving on to a new topic today: the humble retrotransposon, although its hardly humble considering 48% of our genome is made up of transposons or their remnants. A retrotransposon is a piece of DNA that doesn't code for a protein (no DNA codes directly for proteins, but you know what I mean), but it codes for an abnormal piece of RNA. It can roam the genome freely, unlike most other RNA molecules. They can replicate infinitely using this RNA intermediate, and thus increase the frequency of certain elements of the genome. But how exactly do they do this as RNA? Well, it does this by breaking the rules. The biological dogma states that DNA codes for RNA, which codes for proteins, and they code for nothing. However the retrotransposon can use an enzyme known as reverse transcriptase, which it codes for, to become deoxyribonucleic acid again. Retroviruses can also do this with their genetic material (hence the 'retro' in their names). Retrotransposons can induce mutations, and cause malfunction in gene regulating mechanisms by inserting themselves between, or even directly into genes, which makes them useful for studying epigenetic mechanisms like DNA methylation. In mice for example the variation in expression of a retrotransposon due to methylation affects expression of the agouti coat colour gene, as usually RNA from retrotransposons messes up control of downstream agouti gene keeping it switched on continuously, leading to coat colour variability between genetically identical individuals, purely due to molecular modifications to the DNA. Furthermore, the mutations introduced by retrotransposons are very stable, because the base sequence at the insertion site stays constant as they transpose via semi-conservative DNA replication. As retrotransposons age they often accumulate mutations, and so are unable to retrostranspose. Transposition and survival of retrotransposons within the host genome are regulated both by retrotransposon- and host-encoded factors, to avoid deletion of elements of the retrotransposon and the host genome, in a symbiotic relationship that has existed for millions of years between retrotransposons and their hosts. The study of how retrotransposons and their host genomes have co-evolved mechanisms to regulate; transposition, specific insertion sites, and mutational outcomes to optimise each other's survival is still a developing field, which I find quite amazing, considering that the retrotransposons represent about 50% of our genome. We don't even know if most of them do anything, they're almost like outsiders in our own bodies...

Can RNA even be kawaii?

Micro RNA (miRNA) is the cutest form of RNA in the human body (by an official vote). It is a member of the Non-coding RNA family, and targets mRNAs instead of the DNA, unlike most molecules involved in  epigenetic mechanisms, like methyl or acetyl groups. It is only around 21 bases long, but there are at least 1,000 different kinds in our cells. The majority act as post-transcriptional regulators of gene expression, but they don't just stop production of RNA at its source, no no, that would be too simplistic, they actually bind to it and control its actions in the cell. Typically they achieve this by binding to the 3' untranslated region (3' UTR) at the end of an mRNA molecule. The 3' UTR plays a vital role, despite the fact it does not code for any amino acids. At this point you might be thinking; if it doesn't code for amino acids, then wouldn't it be spliced out of the pre-mRNA by splicosome enzymes with the other introns? The answer is no, the 3' UTR is retained because it acts as a regulatory sequence, which allows miRNA to bind to specific base sequences which it recognises on the mRNA. The vital region involved in this interaction is the bases in positions 2-8 on the miRNA molecule, but the base sequence match does not have to be perfect for the molecules to bind. Once attached the miRNA prevents the translation of  mRNA into protein, but if there is a 100% 8 base match between the miRNA and mRNA, the mRNA is completely destroyed by hydrolytic enzymes attached to miRNA (tiny but mighty). A single miRNA can simultaneously influence the translation of many differently spliced forms of a particular mRNA molecule, but it can also influence entirely different kinds of proteins, coded by different genes, which have the same 3' UTR sequence - it seems as though that sequence at the end of the mRNA is all that matters to miRNA. Therefore it is a tricky molecule to study, as it can affect such a wide variety of proteins. There is another level of beauty to this already remarkable molecule, to do with evolution and even cancer drugs. Tune in next post to find out more! (so enticing...)

The pathogen that isn't: Mad Cow disease

Microbiology is a field that never fails to surprise me, but there was one particular disease I read about this week, and it really takes the microbiological cake in my opinion. Bovine spongiform encephalopathy (BSE) ravaged European cattle herds from 1987 to around 1999, and many would argue the beef industry is still reeling from its effects - especially in the UK, where beef exports were banned until 2006. Europe was worst hit because of its climate of all things. The main protein substitute used in the diets of cattle worldwide is soy bean, but in Europe the colder climate means they cannot be grown. So instead the ground up, heat treated remains of animals that died of disease or that were unable to enter the human food chain for some other reason, were used to give protein to commercial cattle. But the carcasses were heat treated weren't they? That would kill most pathogens capable of spreading disease to cattle, but BSE wasn't most pathogens. BSE appears to be caused primarily by mis-folded proteins known as prions (a combination of the words protein and infection). That stands in stark contrast to everything we know about how diseases spread; through viruses, bacteria or other living pathogens, all of which contain nucleic acids in genetic material of some sort: DNA or RNA. Prions are just non-living proteins, which act as a template, causing all proteins in their vicinity to become mis-folded also, and a chain reaction begins. This new, misshapen protein structure makes them more stable, so they accumulate in infected tissue, causing tissue damage and apoptosis. The majority of proteins affected by prions are in the brain, so symptoms of a prion linked disease include neuronal loss and therefore brain damage (hence BSE's more common name: mad cow disease). At this point, it seems that the spongiform encephalopathies caused by prions are unstoppable, as conventional antibiotics or other vaccinations are ineffective on a non-living disease vector. In the UK the epidemic of BSE was dealt with by culling all animals suspected to be infected, and the carcasses had to be placed in an alkaline hydrolysis digester. This literally lifesaving technology consists of an insulated steam-jacketed stainless steel vessel which operates at up to 70 psi and 149 C into which sodium hydroxide and water is added, heated and continuously circulated. This process degrades proteins into salts of free amino acids and the temperature and alkali concentrations deactivate prions by destroying their peptide bonds. If they reach the human food chain, prions can cause the neurodegenerative disorder Creutzfeldt-Jakob Disease (CJD), which has a 100% 1 year case mortality rate. A whole population could be wiped out if the contaminated meat was widespread enough. Terrifying right? And this wasn't even my Halloween post...