Posted by: arrogantscientist | January 29, 2009

The Genetics of Eye Colour

One of the most striking and functionally useful properties of Drosophila is the ease of manipulation of their eye colour.

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Various examples of eye colour. The fly on the far right is wild-type and the one to it's left is w1118/w1118. The others have eye colours produced by the P-elements they contain.

There are two major pathways that give rise to the distinctive, wild-type red colour of Dmel eyes. One gene, known as white is the linchpin of the system and variations of this gene itself, and it’s location, can give any colour from white to red (passing through yellow and orange). (Note that a fully functional white gene leads to red eyes).

The simplest white mutation is one that disables it’s function entirely (w-), such as w1118. Flies homozygous or hemizygous for w1118 have white eyes (picture above, bottom fly), whereas those heterozygous for w1118 and wild-type have the normal red eyes.

The white gene is normally located on the X chromosome, but it doesn’t have to be to produce an eye colour. This means the gene can be used as a ‘marker’ to show the presence of transposeable elements in the genome. Transposeable elements, or P-elements, are able to hop around the genome and land on any chromosome, when a suitable transposease enzyme is present. They occur naturally, but are something extensively exploited for genetic manipulation. It is a relatively simple process to create an artificial P-element and insert it into a genome. But how could you tell if a P-element has become established in a population of flies? Simple, if the P-element contains a white gene to affect the fly’s eye colour, then it’s presence is obvious in a w- background. It is also simple to find out to which chromosome the P-element has inserted itself on by performing crosses and watching where the eye colour goes.

Two factors can affect the eye colour produced by P-element-borne white genes – the allele of white and the position in the genome. The same P-element containing a white gene capable of producing a red colour could produce anything on the white-red spectrum depending on where it lands. This is because the dosage of the white gene product affects the colour – less = lighter eyes. If the P-element lands somewhere where it is poorly transcribed, less protein will be produced, and the fly’s eyes will be lighter. Dosage also allows you to determine if a fly is homozygous for the chromosome carrying the P-element, or heterozygous for another chromosome. Unless the colour is stuck at red or white, flies with two copies should be distinct, with a darker colour, than flies with only one copy.

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P-elements have many uses and in my work I have used them to generate mutants – they can cause deletions when they “hop out”. This involves taking a strain of flies with a single P-element near your gene of interest, introducing a transposease on another chromosome, and the removing the transposease in a later generation. With an eye colour gene on the P-element, you can tell if the transposease has done it’s job. If it has, the fly’s eye colour will change – usually from, say, yellow to white, occasionally getting darker if the P-element is still present, but in a different position. While the transposease is present, the P-elements in every cell of the fly’s body have the potential to move. This is of little consequence in most somatic cells, and only useful in germ-line cells, but if it happens in some of the cells that go on to develop into the eyes, it can have some noticeable effects, such as the two flies above above.

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Eye colour is one of the most versatile genetic markers in Dmel, thanks to the range of colours, non-restrictive localisation of extra white genes and the lack of any negative affects on the fly.

Posted by: arrogantscientist | January 15, 2009

Understanding Evolution – Chance and Randomness

A common misunderstanding, or misrepresentation, of evolution made by anti-evolutionists is that humans could never have resulted from random chance. An equally wrong view would be that there is no random element to the evolutionary process.

To properly comprehend evolution, it is essential to understand how and when randomness and chance have an effect. Here I will discuss the main areas where these play a part. It is important to note however – in evolution, there is no true randomness, rather, what randomness does occur is an unpredictable result of a complicated set of contingencies.

Mutation

The occurrence and character of mutations are essentially random (although, the chance of certain mutations occuring varies depending on conditions). Mutations come in many forms – from Single Nucleotide Polymorphisms to duplications of chromosomes, or even the entire genome. The effects of these mutations vary from nothing, to catastrophic, to beneficial. The improvement of a species or individual is irrelevant at this point – what happens to the propagation of these mutations in the future is, for the most part, non-random (i.e. natural selection).

Chromosomes and Sex

In total, humans have 46 chromosomes in every cell (excluding gametes). These 46 are made up of 2 copies of 23 individual chromosomes. Any one chromosome however, is not exactly the same as it’s sister – each is replete with large or small, but typically recessive, differences.
This is important when considering where the chromosomes go during sex. During meiosis and the creation of gametes (sperm and eggs), the compliment of the resulting daughter cells is halved to one copy of each chromosome (23 total). In the daughter cell where, 1a ends up in has no bearing on where 2a ends up, and so on for each of the 23 chromosomes. This shuffling process is random with all possible combinations having an equal chance of occurring.

Another process, known as Chromosomal Crossover (or “Crossing over”) ensures no two chromosomes of the same number are the identical copies of each other. For example, in a population of sperm, no two will contain a 1a with exactly the same compliment of genes as any other 1a. This is achieved by “swapping” homologous sections of chromosome while they are lined up close to each other (1a may swap material with 1b, 2a with 2b etc.).  This process is again not genuinely random, but it is almost entirely unpredictable.

These two processes conspire to ensure every sperm is sacred unique. Each egg is also unique. Now to make a new organism only one sperm and one egg are required. Assuming each sperm has an equal chance of getting to, and successfully fertilising an egg, the possibility one will reach it with its unique set of genes is minuscule. Especially when you consider the actual occurrence of sex is presumed.

Essentially, the pseudo-randomness here is what produces variation between individuals. The variation created is not guided in any way (e.g. by the needs of the organism). Natural selection can act on these variations – individuals carrying beneficial variations are more likely to be able to breed and pass on these traits to their offspring.

Genetic Drift

The other major actor at the same level as natural selection is genetic drift – a process by which traits spread across a population. Unlike the non-random “guiding force” of natural selection, there is an element of randomness to genetic drift. It is especially important for the spread of mutations that are not acted on by natural selection – ones that produce no beneficial or negative effect for the individual carrying them. The easiest way to understand genetic drift is by major disruption to a population, for example, the “bottleneck effect”. Consider a population of 100 creatures of the same species (use you imagination – penguins, fundamentalist Christians, murlocs – they all work fine). 25% carry allele A only (AA), 25% carry allele B only (BB) and 50% carry both A and B (AB). If you pick a breeding pair at random and build the population back up to 100, then there is a chance either allele A or B will not be present in this new population (i.e. if both of your pair were AA then only allele A would be present in the new population). The higher the frequency of an allele in the initial population increases the probability it will be present in the new population, but no allele is entirely safe – unless it’s present in 100% of individuals – it’s down to chance.

Genetic drift is sufficient to cause variations in separate populations of the same organism, even without natural selection.

In conclusion, Evolution is not a random process and anyone that claims it is does not understand it. It’s outcomes and processes are predictable to some extent. Unpredictability is caused by randomness and chance that act mainly at two levels – during the creation of variation, and during the spread of variation.

Posted by: arrogantscientist | January 12, 2009

Balancer Chromosomes –

As a running commentary to some pictures, I thought I would give some information on why Dmel is such an amazing genetic tool.

In this post I will introduce Balancer Chromosomes, and why they are so important in genetics. To maintain picture-mediated interest, here’s a picture:

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Heterozygous FM7i females (FM7i/X, above) have heart shaped, red eyes. FM7i/FM7i females and FM7i/Y males have bar shaped red eyes.

If you look at the wild-type fly a couple of posts down, you’ll notice the fly above has different shaped eyes. This change in eye shape is a dominant mutation in the gene Bar, and is the most prominent marker of first chromosome balancer, FM7, in adult flies.

Dmel have four chromosomes, one (X/Y), two and three being important, four being rather small. There are two copies of each per normal cell. Females have two X chromosomes (X/X), males have one X, one Y (X/Y). A fly with a wild-type genome would be expressed as +/Y ; +/+ ; +/+ ; +/+ on paper (if the fly was male). + just indicates a wild-type chromosome, in the order, 1, 2 ,3, 4.

During meiosis, i.e during the production of eggs and sperm (gametes), two processes ensure no two gametes are the same.
The first is how the chromosomes line up and segregate – one of each chromosome goes to each gamete, but whether X or Y ends up with 2a or 2b, 3a or 3b and 4a or 4b is random, but predictable.
The second process, chromosome crossover, is more subtle and unpredictable. While the chromatids are lined up together, it is possible for sections to swap places with each other. This is particularly an issue if your gene of interest were to move to the other chromatid, when all your predictions assume it doesn’t.

Balancer chromosomes typically contain multiple inverted sections and one or more marker genes. The inverted regions entirely prevent crossover, and if it were to occur, the markers splitting apart would highlight there’s a problem. The markers also make it very clear where the the balancer is, which also tells you the location of the other chromosome, even if it is phenotypeless and visually indistinguishable from wild-type.

All this conspires to make genetic crosses with balancers totally predictable and verifiable.

But that’s not all balancer chromosomes are good for. Mutations are often detrimental, and if left in a stock of flies with a wild-type counterpart, after a number of generations they will be lost. Some can be kept on their own, if they are viable enough, but some mutations are poorly viable, or totally lethal. In this case, in order for the stock of flies to persist, a wild-type copy of the gene must be present to rescue the lethality. If present on a wild-type chromosome, the mutation will be lost from the stock as the wild-type chromosome takes over. However, if the wild-type copy is present on a balancer, the balancer cannot take over as they are homozygous lethal. In the case of a recessive lethal mutation, this creates a situation where they need each other – only files containing the lethal chromosome and the balancer can survive.

There are numerous different balancers (with many variations) for each chromosome , named for the chromosome they stabilise. For example, in FM7i the F stands for first and the indicates it is multiply-inverted. Each carrying dominant mutations to make them obvious. Here are a couple of examples of markers, one for each chromosome.

FM7i:

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Bar-eyed FM7i male, full genotype FM7i/Y ; +/+ ; +/+ ; +/+.

The coolest thing about this variant of FM7 (i) is these flies actually glow green under UV light, thanks to the virtues of GFP.This allows you to tell larvae apart.

CyO:

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Curly winged female, full genotype: w1118/w1118 ; +/CyO ; +/+ ; +/+. (w1118 is not a balancer, it indicates there is a mutation on each X chromosome, which gives the fly white eyes).

Curly is often found on SM balancers.

Stubble:

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Stubble male (look at the hairs), full genotype: X/Y ; +/+ ; +/TM3, Sb ; +/+.

Read More…

Posted by: arrogantscientist | January 7, 2009

This Blog, Me and My Aims

I am currently in my second year of studying for a PhD. I work mainly with Drosophila melanogaster, messing around with their DNA and RNA.

I started this blog mostly for my own benefit – an important part of being a scientist is being able to explain what you do to the lay public, and this is my way of practicing. I also agree with the idea that you only know if you really know something when you try and explain it to someone else. Doing this forces me to do background reading I may have tactically relegated to desk-levelling material.

My other motivation is I feel science has a hell of a lot to offer to everyone – what the word “science” covers is  absolutely vast , and a lot of it is really interesting. The majority,  however, is hidden from the majority. Behind lab doors in the hands of scientists that don’t just consider that an esoteric journal isn’t the only place to show their work. Depressingly often, what the public do get to see is the media-filtered, watered down version of science with emphasis on perceived or over-hyped controversies. They never get to see what a scientist does day to day, how they think, or why they think their bizarre area or freaky organism is so amazing.

What can I do about this? Obviously it’s limited – I only graduated just over a year ago. But in that time, I have amassed a library of images of my work, which in their own right are visually and scientifically interesting. Only a subset of this make it into reports or presentations I produce, and the audiences for this are exceptionally limited (no further than other academics). It seems to me that it is a huge waste to horde these pictures on a hard drive where no-one will ever see them.

My aim here is to show the images I have already, and any I produce in the future, related to my work and not, hopefully to impart upon others the sense of wonder I get looking at the world under a microscope.

Don’t let my name fool you into thinking I’m not a nice person, it is essentially (in my view) a parody. Some scientists may sound arrogant, but the world of science-arguments is very different to “pop-arguments”. Scientists tend to be objective – they don’t tend to make personal arguments, and even relish the chance to have their ideas contested by others. Generally, they don’t wade into arguments when they don’t know what they’re talking about, preferring ones where they can speak with confidence.

I do have some strong personal views on what are non-controversial issues in science, but are politically charged in real life. For example, religion, evolution, the paranormal and the thing I hate the most – faith. As a scientist I never have “faith” in anything – I have the best view I can based on the available evidence, but never faith that something is correct or present without evidence. And then I will test that view, no matter who’s opinions it goes against, even my own. Essentially, I believe (with the weight of the whole of science behind me) that a scientific philosophy is the only really fulfilling way to live, and understand, your life.

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A note on my pictures and articles – please do not reproduce these anywhere else without my explicit permission, which I will likely give if asked. Please respect the fact I have put time and effort into producing them. All the pictures are my work, unless otherwise stated.

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Posted by: arrogantscientist | January 7, 2009

Another Type of Non-fly

I’ve been planning to put up a post containing some nice Drosophila pictures, and explaining about balancer chromosomes – one of the reasons they’re such a great genetic system to work with, but haven’t been able to yet. The microscope I use to take pictures in the lab is currently not working well enough to take good quality pictures. We’re playing with a couple of different lighting systems, and the one that’s currently hooked up results in too much light being reflected off the white CO2 pad to get a clear picture of anything on it. I did overcome this slightly using a glass observation dish, which produces a mostly non-reflective background in a variety of colours, but as CO2 does not pass through glass (last time I checked, anyway) it can’t be used with anything that needs anaesthetising.

So I thought I’d stick up some more spider pictures for now. I don’t know what this spider is, but it’s roughly 3x the size of the zebra spiders below and is frankly too big to photograph (can’t zoom out far enough). But here are some pictures of it’s eyes.

Actually looks like these are two different spiders, possibly of the same species. I thought I’d only taken pictures of one of these, but apparently not, as the hairs on the head are different in the first two pictures (eye colour is a trick of the light):

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Another shot of the top one after the break…

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Posted by: arrogantscientist | January 3, 2009

Zebra Spiders

Well it didn’t take much research to find out what these lab-dwelling spiders are. Looks like they are Salticus scenicus, or Zebra Spiders.

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According to Wikipedia, these spiders are usually 5-7mm long and the males are slightly smaller than the females. They are jumping spiders and of their eight eyes they make use of the large pair at the front for binocular vision. They eat prey about their own size (Drosophila are the perfect size for them – see below) but do not live in webs. I presume the web-like structures I found them with were egg sacs, which the mothers protect.

The males are slightly smaller, and of two I found together, I think the one above is female, and the one below is male. The one in the previous spider-related post looks female too.

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Drosophila are roughly half the size of these spiders, as you can see from the next image.

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You’ll notice the fly in this picture has different eyes from the wild-type fly in the post below. These yellow, heart-shaped eyes, as opposed to the wild-type red, round eyes, show that one copy of the balancer chromosome FM7c is present in this fly. Balancer chromosomes are one of the genetic tools that make Drosophila such a powerful model organism, but I wont go off on a tangent here, as this post is about spiders.

And if you’re wondering – these flies/spiders are not dead. Flies, and apparently spiders, can be safely anaesthetised using CO2. That’s why they don’t fly or run away when you stick them in silly poses. Read More…

Posted by: arrogantscientist | January 2, 2009

The Greatest Model Organism

Drosophila melanogaster, or fruit flies*, are by far the most commonly used and understood model organisms in genetics. Despite not looking very similar, we have probably learned more about humans by studying Drosophila than we have studying Homo sapiens.

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This is a wild-type (Oregon R) adult female. Read More…

Posted by: arrogantscientist | December 31, 2008

Biological Control

I have no idea what this spider is, but it is resident in a web behind one of the microscopes in the lab. It’s actual size is roughly 5mm long, and I think this illustrates exactly why microscopes are so cool – they let you see intricate, complex things you could never appreciate with the naked eye.

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Read More…

Posted by: arrogantscientist | December 30, 2008

This Blog

I’m not a big blogging person, but thought I’d give it a go anyway.

As far as I can see, it’s not worth starting a blog if all you have to offer is opinions. People generally aren’t interested in each other’s, so I’ll do my best to limit most of my posts to “original” content.

There are two sources of original content I can offer. Hardcore Drosophila genetics and light-microscope imagery.  I guess the latter is probably of more interest to a general/general scientific audience, but some of the former may be of interest to anyone getting started in the field. Genetics is a complicated and esoteric language to learn, and I am familiar with some of the obstacles, so whenever I put anything up about it, it will be aimed at beginners.

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