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“Gynandromorph: Noun: An abnormal individual, esp. an insect, having some male and some female characteristics.”

While setting up several hundred crosses over the past few days, I saw thousands of flies. One of them in particular caught my eye:

A gynandromorph.

Left

Right

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Often, the quality of a Drosophila lab can be judged by the quality of the stocks kept within. If you are using Drosophila as a scientific tool, it is never acceptable to have mites present in your cultures.

Mite infestations can spread impressively quickly, but are actually easy to get rid of.

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We don’t know how many blueprints for life there are.

The diversity of life on Earth is staggering. There are bacteria that can live in oil, vampire bats, cockroaches that can survive nuclear war, whales more than 33 metres long, mammals that can think, learn and understand their world.

Yet no matter how different any two organisms, all life shares the same basic set up. Reproducible instructions are read translated into all the life we see around us, with the sole purpose of passing those instructions onto the next generation.

Nucleic acids, particularly DNA, are the only molecules known that can carry the information required for life. Are there others? If we one day find extraterrestrial life, will it contain DNA? With only one data point, we can’t even know if life on earth is even diverse. There may be types of life out there that we can’t even imagine. It would be nice to find out.

Support the Science is Vital campaign. Join more that 20,000 scientists that have signed the petition calling for the protection of science research funding in the UK.

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I have only worked in one lab at one university and am aware I’m extrapolating from a single data point here, but data security at the institutional level is poor and pretty much non-existent at the personal level.

Most of the people I work with are older than me. They have enough knowledge of computers to use Word and to produce crap PowerPoint graphs. They use and lose portable hard drives and USB sticks as if they are immediately replaceable. Which of course they are. Nobody thinks twice about data security.

Perhaps the IT department should take some responsibility and provide users with a secure system they can use? Educate users so they can protect their own data? In my experience, they don’t. They provide a (reasonably secure) network at work*, but nothing else.
*I can access other people’s data, if I wish. Pro security.

The thing that really irks me about all this is uncrackable data security is simple to implement, for free. TrueCrypt.

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FlyBase[1] is the database used daily by anyone that works on Drosophila. It contains all the information there is to know about the Drosophila melanogaster genome (and others), including gene annotations, expression data, phenotypic data and any stocks publicly available.

The wealth of information available is the main obstacle to be overcome by anyone new to large databases such as FlyBase. There are many in-depth guides on how to use FlyBase, but often only a small snippet of information is what you’re after when you look up a gene.

The best way to understand FlyBase is to use it. The purpose of this guide is to help anyone new to it get into it for the first time and basic information about a gene.

This section will highlight a few of the most immediately useful pieces of information displayed on a typical gene page, using forked as an example.

The phenotype of forked.

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puzzledponderer posted today on songs about science, which has inspired me to post my favourites. I agree that watching scientists sing is usually a pretty bloody painful experience, but there are songs out there performed by musicians and comedians that do a much better job of promoting science. Here are my four favourites, in reverse order:

4. The Large Hadron Collider Rap

Admittedly full of scientists embarrassing themselves, but still excellent.

3. Hard ‘n Phirm – Trace Elements

The perfect mix of science, comedy and country music.

2. Tim Minchin – Storm

Technically a “beat poem” and strictly more about rational thought destroying the stereotypical strawman, but the guy’s a genius.

1. The Portal Song

I suspect this song will be more well known by younger geeks, as it’s from a computer game. When you first hear this song in context at the end of Portal it’s an absolute delight that will put a grin across your face that will last until long after the song has ended. If you think you’re ever likely to play the game, don’t listen to it now if you haven’t heard it before, it’s not a spoiler, just an exceptionally rare experience that should be savoured.

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An updated version of this post can now be found here: http://arrogantscientist.wordpress.com/sexing-drosophila/

Being able to tell male Drosophila apart from female Drosophila is about the most basic requirement for Drosophila genetics. There’s nothing dumber than trying to mate two females together, or more frustrating than putting a male in with a vial full of virgins (for you that is, I’m sure the male would disagree).

So, here are three ways to tell them apart.

The Bad Way

Male (left) and Female (right) wild-type Drosophila (OregonR).

The above picture shows a clear difference in size between the male and female flies, but the place to look here is the lower abdomen – the tergites here are black on the male and not in the female. This is simple, but in practice it is not a good way to tell them apart. The different body shapes and colours between stocks and individuals can vary significantly, and the distinction is rarely as clear as above. Often, inexperienced people use this as the way to tell them apart, but if you do, you will at some point get stuck, and are very likely to make a mistake.

The Right Way 

Sex combs on a male fly.

Male Drosophila have a patch of bristles (the black bits above) on their forelegs, used during courtship, that females do not. If it has sex combs, it’s a male. This method is probably the most accurate, but rarely used to sex drosophila in practice. It would take far too long to look at the forelegs of every fly you need, when it is possible to sex the fly from a distance (especially since you have to know what you’re looking for to even be able to notice the sex combs).

The Best Way

Ideally, you need to be able to sex flies accurately, but quickly. The best method is to simply look at their genitals.

Drosophila genitals, front view. (Male left, female, right).

These rarely differ in appearance between individuals, and can be seen from a distance and from various angles.

Drosophila genitals, side view. (Male left, female, right).

In practice, someone experienced in sexing flies will use a combination of these three methods. With a little practice, it is easy to become proficient at separating males from females, no matter what phenotypes the flies may have.

Things to remember

Depending on the genotype, age, conditions and other factors, individuals can vary significantly. If in doubt, try verifying using the sex combs, but if you can’t, just don’t use the fly.

If it has has an egg sticking out of it… it’s a female.

Males are not always smaller than females (especially if you are dealing with tubby mutants – often found on TM balancers).

Hermaphrodites can occur, but they’re very rare. I might have a picture of one I found somwhere…

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These pictures are of some fungi I found residing on a [refrigerated] grape juice agar plate (usually used to collect Drosophila eggs).

It’s interesting to see that two colonies don’t grow into each other:

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

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.

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.

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.