Advent Science Day Twenty-Four

So. What's all this about human eye colour, then? Remember how you were taught in high school that brown is dominant, and blue is recessive? And how the one awkward kid with green eyes always left disappointed?

Well... you'll be unsurprised to hear that it is, in fact, more complicated than that.

We'll start with the bit that isn't a lie. Brown eyes are dominant. Even having one copy of "the brown eyed gene" will mean you probably have brown eyes. There are, however, several "brown eyed genes" governing the production and deposition of melanin in the iris, all of which need to work to give you those brown eyes.

So, from what we've learned so far, we can deduce that blue, the "recessive" colour, is the absence of brown, and the colour of an unpigmented iris? Sadly not. A completely unpigmented iris is a pinkish-grey colour deriving from the visibility of its blood supply, and can be found in albinos, ie people with no melanin *anywhere*. Blue eyes come from a genetic mutation that massively downregulates melanin production in the stroma of the iris, ie the layers closest to the surface. The lower layers still contain melanin, which can be demonstrated by dissection and microscopy.

So how does that make eyes blue? The answer is physics, more specifically, Rayleigh scattering, which I am not even going to pretend to understand myself, save that light with longer wavelengths (ie red and yellow) is preferentially absorbed by the melanin in the lower layers of the iris, leaving the shorter blue and purple wavelengths to be reflected and then scattered in the stroma. This is similar to the effect that causes the sky to be blue on a sunny day, and also means that yes, blue eyes *can* change colour according to lighting conditions.

The next colour to look at is grey. It is thought that grey irises reflect and scatter light in a similar way to blue, but in a much less frequency-dependent way (Mie scattering). The best theories we have so far for why this happens is that grey eyes have more collagen deposits than blue eyes, or that they simply have slightly more melanin than blue eyes.

Next, we'll look at the little-known (in humans) eye colour amber. Amber eyes are low on melanin, like blue eyes, but have deposits of pigments called lipochromes in the iris, which is, well, an amber colour. The genetics of amber eyes are poorly understood, probably because it is rare to carry genes that produce amber eyes without also carrying at least one brown-eye gene, which would mask it.

Green eyes are usually a combination of a strong blue colour with either some amber pigment or a little melanin in the stroma of the iris, effectively putting a yellow filter over the blue structural colour to produce green.

Hazel is a catch-all term for greenish-browns, often with concentric rings of different colours caused by different amounts of melanin deposition different distances from the pupil.

And how about violet eyes, the mainstay of terrible Mary Sue fanfic? In the real world, they are a result of incomplete albinism- melanin producing genes that just about work, a little bit, but can't really produce enough pigment to convey proper protection against the sun. Tiny amounts of structural blue colour as described above combine with the red colour of the iris' blood supply to make eyes that appear violet. So if you ever see a Mary Sue with violet eyes but hair that is any colour other than white-blonde, you can now get as annoyed as I do about it :D

It's also worth taking away from this article that blue and green eyed people *still have melanin in their irises*. So while it's rare for two light-eyed people to have a brown-eyed child, it's far from impossible, and should not be taken as more than circumstantial evidence to doubt paternity.

To end on a final, awesome note: I didn't actually know about the amber eye gene(s) until I researched this article. My dad has bright green eyes and my mum dark brown, so I'd always been a bit confused about how I got these strange golden brown eyes that weren't explained in any of the textbooks. But now it seems abundantly clear that my mum is heterozygous for the dark brown gene, and my dad's green eyes are presumably the result of one amber gene over blue. Allowing me to inherit my dad's visible amber gene and (presumably) my mum's invisible one. - eyes like mine!

Happy Christmas.

P.S. Any questions from the floor? I will try to answer them between now and new year.

Advent Science Day Twenty-Three

Temperature Sensitivity

So, remember how I blithely mentioned about the agouti gene, which restricts black pigmentation in horses to the points, ie nose, ears, feet and tail? Today I'm going to tell you how it works.

We covered ways in which proteins can fail to fold properly due to gene mutations on Day Fourteen. However, there are proteins which can fold properly at, say, 30 degrees celsius, but the increased molecular motion will make them fall apart at the 37-40 degrees that is normal mammalian body temperature.

So, if you have one of those mutations in a melanin-producing protein, you can see why the extremities of the body, where surface temperature is likely to be colder, are darker, because more of the melanin-producing protein is present in its working form.

The same effect can be seen in many mammals- Siamese cats are very well known, as are Himalayan rabbits and guinea pigs, all of which in their most common form are white with dark noses, ears, feet and tails.

And it explains why Siamese kittens are born pure white. Awww.

Temperature sensitive mutant plants and even moulds are a very useful biological model- it's one of the few ways to study the effects of a gene being turned on or off in the same individual organism as opposed to across a population.

Advent Science: Day Twenty-Two

A case study: horse coat colour. For no reason other than that it's one of the most complex visible genetic systems that is fully understood and predictable. Also, it's cool.

There are two basic genes on which the rest of horse colour and patterning is built: the Black/Red gene and the agouti gene. Black is dominant over Red, so only a homozygous Red horse will display the red colour. A plain Red horse is "chestnut", and a plain black horse is (possibly slightly surprisingly) "black". The agouti gene is a modifier on the black pigment, restricting it to the "points", ie nose, tail, ears and feet, of the horse. Agouti is dominant, explaining the relative rarity of true black horses (they need to be homozygous for two recessive genes), and gives rise to the familiar "bay" colouration, a chestnut body with a varying amount of black hair concentrated at the extremities of the horse.

Chestnut and Bay:

The next category of genes is "dilution" genes, which predictably reduce the amount of pigmentation produced in the horse's skin. There are three well known ones, dun, cream and champagne. Dun is a dominant gene that lightens Red to a yellowish colour and Black to a mousy brown, often with darker legs and a strip along the back. Bay Dun is the stereotypical colour of Przewalski's horses, the only true wild horses, and thought to be (based on cave paintings) the colour of horses pre-domestication. Another dilution gene, Cream, is interesting genetically because while it is technically dominant, it is highly dosage-dependent, ie a horse with only one Cream allele will be much darker than one with two. Thus, Red is diluted to a similar yellowish colour to Dun but without the darker markings, giving rise to the Palomino and Buckskin colours (single-allele dilution of chestnut and bay respectively) and Cremello (double dilution of chestnut). Cream can also act on black hair, but not so strongly, resulting in black horses that are slightly dark brown, and prone to sun-bleaching. Other similar dilution genes exist, and possession of two or three of them is one way of getting a "white" horse that actually turns out to be a pale cream colour when genetically tested.

Bay Dun:

Next, we look at genes that cause multicolour patterning. These are all of the form "colour-and-white" - although many of them look like a white horse with small coloured patches, genetically they take one of the above mentioned base colours and add white bits to it. These can cause a huge variety of patterns, and are another way of getting a "white" horse- these horses are actually a coloured with all-over white markings. British English uses "piebald" for a white-on-black horse and "skewbald" for a white-on-another-colour horse. The white patterning genes all add in a dominant fashion to the previously explained colour schemes, though it is possible for a horse with one of these genes to actually not display any visible white marks.

Some "white" genes are lethal when homozygous dominant- foals are born healthy and completely white but do not have a functional large intestine- this is known as Lethal White Syndrome. For this reason, genetic testing has become very useful when breeding horses with white patterning, as you can then avoid crossing two horses with one copy of the lethal white gene. Such a cross would result in, as with Mendel's pea plants, 1/4 chance of a solid coloured foal (two recessive alleles), a 1/2 chance of a white-patterned foal (one dominant, one recessive) and a 1/4 chance of a foal suffering from Lethal White syndrome. Given that the same 1/2 chance of a patterned foal is present when crossing a white-patterned and a solid horse, with no risk of Lethal White, arranging the former mating would seem negligent at best.

Small coloured spots on a white background (or more properly a white overlay with small spots of the base colour) are caused by a gene called Leopard, and cause effects stereotypical of Appaloosa horses, as shown below. There is a small "halo" around each spot where the skin is still dark but the hair growing from it it white.

Tobiano patterning:
Sabino patterning:
Appaloosa "leopard" pattern:

The final major gene we will look at is the Grey gene. A Grey horse, regardless of what other colour genes it carries, will start off showing the colour dictated by those other genes, and then slowly fade to white hair as it gets older. A grey horse can start off any other colour combination as above, and the Grey gene is dominant. A grey horse is distinguishable from a white one by its dark skin, which will remain pigmented even when the hair growing from it has faded to pure white.

Young grey horse:
Older grey horse, now almost completely white-haired:

So how *do* you get an actually white horse? There is another dominant gene which, if present, will produce a completely white coat. A true-white horse can be distinguished from cream or grey by its pink skin and hooves- compare and contrast the picture of the older grey horse above with the white below.

White horse:

There are of course other genes that can add on to this basic set, the most obvious being Roan (white hairs intermingled with whatever other coat colour the horse has), Sooty (similar, but with dark hairs), and Pangare, which lightens the belly and the insides of the legs.

So, putting this all together, to determine how a horse got its colour, you ask in order:
1. Is the base colour red or black?
2. If red, is the agouti gene present to cause black points?
3. Are there any dilution genes present?
4. Are there any white patterning genes present?
5. Does the horse carry the Grey gene?

As all the genes described in 2-5 are dominant, you can then work out what colour foals can (and can't) be born to horses with particular coat colours. And probably pay obscene amounts of money to studs as a result ;-)

And finally, I apologise for any misuses of terminology related to horses. I am a geneticist, not a horse person...

Advent Science Day Twenty-One

So, yesterday I casually mentioned tissue matching in organ transplantation. What's going on there, I hear you ask. That it is genetic should be pretty obvious, given that close relatives are far more likely to be able to provide transplantable tissue, and that unrelated transplant donors are generally of the same race as the recipient.

The answer lies in a set of cell surface proteins called antigens, which are expressed from a group of genes called the Major Histocompatibility Complex (MHC). There are quite a lot of these genes; in humans, there are 140 known genes in the MHC, spanning 3.6 million base pairs (that's about 0.1% of your entire genome).

These genes are known for being highly polymorphic, ie there are hundreds of different alleles of them known in the population- so many that other than identical twins the odds of two individuals having the same set are far, far higher than the number of people on the earth. They also recombine (swap bits around between the maternal and paternal chromosomes) far more often than other cells, when making gametes (sex cells).

So, every human has a unique pattern of these things, and the closer yours are to your transplant donor, the less strong the immunosuppressant drugs you need to stop you rejecting it. Huzzah!

So why doesn't a pregnant mother reject her foetus? Well, the placenta doesn't express the most prevalent antigens at all, thus avoiding detection by the mother's immune system (placental tissue is made by the baby, not the mother) and only expresses just enough of some others to avoid being tagged as a foreign object by the mother for having no MHC proteins at all. And then it forms a syncitium, a thick barrier made of layers of maternal and foetal cells which blocks any migratory immune cells from crossing between mother and baby.

It's not perfect; you may have heard of rhesus disease, which is caused when a rhesus-negative mother (see day 11) gives birth to a rhesus-positive baby. It is highly likely that during the birth, the mother and baby's blood will meet, which causes the mother's body to raise antibodies against the rhesus protein in the baby's blood. This is usually fine for the *first* baby, which is no longer inside the mother by the time the antibodies are there in sufficient concentration to do any damage, but subsequent pregnancies with a Rh+ baby can end up with anaemia in the baby due to small numbers of anti-rhesus antibodies managing to cross the placenta. Happily, modern medicine can deal with this, with Rh- women in developed countries routinely being given an injection of anti-rhesus antibodies towards the end of pregnancy so that these antibodies will destroy the foetal red blood cells before the mother's immune system has time to discover them and react.

So basically it's a balancing act that usually works.

Advent Science Day Twenty


Once upon a time there was a woman named Karen Keegan who needed a kidney transplant. So they tested her three sons to determine if any of them had sufficiently matching tissue to make a transplant viable.

And the results of the tests came back, and showed that she was not the mother of her children. Now, one might assume some horrible mix-up at a maternity hospital at this point, but it was also clear from the tests that all three brothers had the same father. Further testing of extended family members showed that Keegan's sons were definitely related to her, just not to the extent that she could be their mother.

At first, the doctors were really rather confused. And then they realised that Karen Keegan was a chimera- she somehow had some organs with one set of DNA, and others with another. Her blood sample, which had been used to carry out the genetic test, had the other genes to her ovaries and thus the ones she had passed to her children.

Chimerism is caused by the fusion of fraternal twin zygotes, usually only a few days after fertilisation. The end result is a perfectly "normal" person, and the vast majority of chimeras go undetected. It's now thought that people with two eyes of different colours are likely to be chimeric, and the very rare cases of true hermaphroditism, ie a person with both male and female sex organs, are probably likewise found in chimeric humans.

It is thought that identical twin embryos can fuse as well, but of course this is pretty much undectable if the fusion completes. There is a suggestion that conjoined twins can sometimes be the result of incomplete fusion as well as incomplete splitting of embryos.

Advent Science Day Nineteen

Today, I am going to tell you about tortoiseshell cats.

First, here is a gratuitous excuse for a picture of a tortoiseshell cat, showing the characteristic ginger and brown mottled patterning:

You may be aware that the vast, vast majority of tortoiseshell cats are female, and the few male ones are pretty likely to be infertile. It should be obvious, then, that the sex chromosomes are involved somewhere down the line, and this is indeed the case.

At the stage of embryonic development where the zygote consists of a few hundred cells, all but one X chromosome shuts down and is never heard from again. This chromosome becomes a small structure at the edge of the nucleus called a Barr body, which is the usual diagnostic tool for detecting chromosomal abnormalities- for example a male with Klinefelter Syndrome (XXY sex chromosomes) will have one Barr body per cell, whereas a chromosomally normal male would have none. As a side note, it is demonstrable from this that the developmental differences in women with Turner Syndrome (has only one sex chromosome, an X) are all laid down in the very early embryo, as after that stage *all* women have only one active X chromosome per cell.

So, how does this make a tortoiseshell cat? There is a gene on the X chromosome that has two alleles, which for the sake of simplicity we will call Orange and Black. So in a heterozygotic female cat, ie one with one copy of Orange and one copy of Black, the few tens of cells which will later become the skin of the cat will all randomly have one of these genes inactivated and thus solely express the other one. And each one of these cells will divide during later development to become a patch of skin cells all with ginger or black fur, thus leading to the random mottled effect.

This effect is known as mosaicism, and for obvious reasons the vast majority of human females (and a few males) are in fact a chromosomal mosaic. However, genes which make this obvious from visual inspection don't really exist in humans.

Male cats, of course, have only one X chromosome, expressing either the Orange or the Black gene. Which, of course, also explains why the majority of pure-ginger cats are male; the Orange allele is recessive, and inherited in the same way as colour-deficieny in humans (explained yesterday). The very rare male tortoiseshell cat has the equivalent of Klinefelter Syndrome in humans, and is XXY.

Advent Science Day Eighteen

Sex Linkage

Everything I've explained so far has dealt with genes on chromosomes 1-22, ie all the chromosomes that aren't the sex chromosomes. So, what happens if a gene is on one of the sex chromosomes?

You probably know that females have two X chromosomes and males have one X and one Y chromosome*. Now, the Y chromosome is actually rather smaller than the X chromosome, and contains very few genes other than those required to cause a person to be male. (yes, female is in some ways a default.) However, the X chromosome does actually contain quite a lot of genes whose absence causes a disease.

This is why there are so many more boys than girls with colour vision deficiencies**- at least one of the genes required for normal colour vision in humans is situated on the X chromosome, which means boys have only one chance to get a working copy, but girls have two. This also means that a woman with a colour deficiency is guaranteed to pass it on to her sons, but cannot have a daughter with it unless her father also has it. The daughters of a colour-deficient father are, of course, guaranteed to be at least carriers of that allele, while his sons cannot.

THe other famous sex-linked condition is haemophilia, a disease in which sufferers' blood does not clot properly due to a mutation in one of the genes that codes for a protein which signals the blood clot formation process. At this point, you may remember that haemophilia is a condition which *only* affects boys. Actually the truth is rather less pleasant: girl foetuses with haemophilia are non-viable.

On that lovely note, I will stop for today, and tomorrow look at some of the weirder effects that can be caused by sex linkage.

*I am aware that this is a very simplistic view. This is a series about genetics rather than gender.

**The popular term for red/green deficiency and indeed several other less common forms is "colour-blindness", which is actually a rather misleading term; actual complete lack of colour vision is extremely rare, whereas the inability to see one colour while able to discern others perfectly well is rather more common.

Advent Science Day Seventeen

Yes, I know it's after midnight. I actually wrote it this morning and forgot to post it...

So, what's a carrier of a genetic disease, then? Well, in the case of a recessive single-gene disease, it's someone who is heterozygotic for that gene, ie they have one dominant, healthy allele, and one recessive, disease-causing allele. As with Mendel and his pea plants, if two "carriers" have children, one in four of them will have two recessive alleles and hence the disease.

Simple, right? Actually, no. You'll be able to work out from what I've already told you that a carrier of a disease will be expressing the diseased protein as well as the healthy one, in roughly equal amounts. These individuals do not have the disease because, in most cases, either half the amount of healthy protein is enough, or the body will detect that it doesn't have enough and upregulate production of that protein. Which will, of course, also upregulate production of the diseased version, which will hang around the cell doing nothing until it is tagged by the recycling machinery and broken up to have its parts reused.

So, you'll be unsurprised to here that there are instances in which there *are* effects from having one healthy and one diseased copy of a particular gene, the textbook example here being sickle-cell anaemia. Patients with this condition have a mutation in haemoglobin, the protein that carries oxygen in the blood, which causes the haemoglobin molecules to clump together and bend the red blood cell into a curved shape which not only is less efficient at carrying oxygen, but has more trouble fitting down the narrowest capillaries to provide that oxygen to the tissues that need it.

People with two faulty copies of this gene have the predictable symptoms of being unable to oxygenate their body properly, and a higher potential for organ problems caused by the capillaries supplying blood being blocked. One copy "just" leaves you needing to be careful if you take a lot of exercise or go somewhere with a low oxygen level like up a mountain, or if you have other blood-related conditions as well, which is only to be expected as half your haemoglobin is faulty.

So, why is sickle cell anaemia so prevalent? There are areas of Africa in which 25% of the population have either one or two copies of the faulty gene, despite the selection pressure against having sickle cell anaemia. The answer lies in the prevalence of malaria in the same areas- heterozygotes for sickle cell disease have blood cells that are harder for the Plasmodium parasite that causes malaria to infect. SO these people are less likely to die young of malaria, and thus more likely to pass on their malaria-resistance gene that "just happens" to have horrible disadvantages attached...

Advent Science Day Sixteen

Two case studies today, because examples really are the best way to teach this sort of thing.

The first is cystic fibrosis, which is the most common single-gene serious (ie, life-shortening) condition among people of European descent. CF is caused by a fault in a gene that codes for a protein that transports chloride ions across cell membranes, and is particularly interesting for this series because one missing amino acid (in the most common form of CF) can have such wide-ranging effects across the whole body. The most well-known symptom is that the natural mucus in the lungs forms too thick and sticky, making it hard to cough up and also a breeding ground for bacteria of various types. However, pretty much anywhere there is epithelium (surface cells) there are chloride ion channels, and this results in problems with things getting stuck in the digestive tract, low fertility (due to blocking of narrow tubes) and liver disease due to bile duct obstruction.

The *other* interesting thing about cystic fibrosis is that it varies greatly in severity. It's actually entirely possible for a mild version to remain undiagnosed until the patient is in their thirties and forties, and their body is no longer able to compensate as it did, or at least until fertility problems present themselves in adulthood.

And after the past couple of weeks, you should be able to understand how you can have a mild version of a single gene disease. While the most common cause of CF is a mutation in which one amino acid is deleted from the protein, rendering it completely non-functional, there are other known mutations in the same gene. Some of these produce protein that, as mentioned yesterday, works just about well enough that the patient can live a life relatively free of medical treatment, though may still struggle when exercising due to impaired lung function.

The other disease we'll take a brief look at is Huntington's Disease, because it's unusual in that it's actually a *dominant* gene that causes it. Huntington's is a neurodegenerative disease, and the reason that it is still so prevalent despite being a dominant gene is that, unlike most genetic disorders, the symptoms do not usually become noticeable until the patient is around forty years old, and therefore is quite likely to have already bred and passed on the gene.

So. How on earth do you get a dominant genetic disorder when we've already covered in detail how a recessive gene is a *lack* of normal protein? The reason lies in a loop region of the protein in question, which is called Huntingtin. This loop consists of a long chain of the amino acid glutamine, coded for by the sequence CAGCAGCAGCAGCAG etc etc. In people who do not suffer from Huntington's, this loop region is around 10-30 glutamines long. However, the longer this region is in the DNA, the more unstable is the replication machinery's bond to the DNA, and this can result in mutations that increase the number of CAG repeats present.

And when that number reaches a threshold of about 35 repeats, a misfolded version of huntingtin is produced, and it is that which causes the degeneration of the central nervous tissue over time. And it doesn't matter if you also have a copy of the gene that produces the functional protein- if you have any of the mutant form, you will eventually get the disease. Interestingly, though, the longer your glutamine repeat section is, the earlier in your life symptoms are likely to appear.

Tomorrow: You have probably heard about "carriers" of genetic diseases. We'll look at what that actually means, and (surprise surprise!) why it is not actually as simple as all that! Again!

Advent Science Day Fifteen

So, yesterday I explained how even a small genetic mutation can make a non-functional protein, and then I said it's not as simple as all that. The reason for this is that proteins are not just "functional" or "not functional"- many small mutations actually make proteins that just about work, ish.

A good example of this is actually human eye colour, although I am going to be simplistic here. You probably know that brown eyes are dominant over blue eyes, and can probably guess by now that the "recessive" gene that causes blue eyes is actually a lack of brown-producing gene. The fun bit is that blue eyes are not actually a *complete* lack of pigment. People with blue eyes still produce a small amount of the brown pigment melanin, which over the unpigmented pinkish colour of the iris, produces a bluish colour. It's worth noting here that albinism is the "no pigment at all" version of this mutation This is, again, a simplistic view, as there are actually several proteins which are necessary for melanin production, but we can ignore that for the moment.

So, how does that work? We'll take a hypothetical pigment producing protein here, which picks up a mutation that converts a positively charged amino acid to an uncharged one of about the same size. The protein isn't entirely happy; it's not holding together as well as the unmutated (wild type, to use the technical term) version. However, it just about clings on, and manages to catalyse the reaction to make melanin at maybe 20% of the rate the wild type would. It's just not enough to make brown eyes, but it is enough to make a difference to the colour of the iris.

And yes, there are mutations that don't really have an effect on protein function at all- sometimes you can insert, delete or change an amino acid and be entirely unaware of it. It's also possible to have one mutation cancel out another- this is termed a "rescue" mutation in genetics. To drag out our example of the positive-to-negative-charge mutation again, if our hypothetical protein with a positive instead of a negative charge at the crucial place on the binding site meets its binding partner that has a negative instead of a positive, the interaction may well work, when if only one of the two mutations were present, it would not.