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

To remove mites, simply rapidly turn over stocks. The mite life cycle is longer than that of the flies, and they also normally hang on to the vials/bottles more effectively. If you turn young flies over into vials with mite proof seals (compacted cotton wool, or flugs) around five times in seven days, the final vial should contain only flies. After two weeks, the vial can be checked for mites. If none are present, then the problem is solved. If mites are still present, rinse and repeat, however, I have never experienced an instance where this method did not work first time.

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.

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.

How can I protect my portable data?

TrueCrypt is an open source encryption programme that works on Mac, Linux and Windows. If used properly, even the FBI can’t decrypt your files.
It works by storing your data in “containers” that can only be read by entering your password. When opened, they appear as Drives connected to your computer (just like when you plug a USB stick in), giving you instant access to your files.

It can encrypt entire computer systems (perfect for laptops), entire discs (internal or external HDDs, USB sticks), or just stand-alone containers that can be moved around like any other file. External drives can be set to auto-mount when plugged in.

When it has been set up, the only extra output of effort for you is entering a password when you plug the disc into a new computer.

Understanding TrueCrypt takes a short while, as does setting up encryption and getting used to it, but there are excellent guides included. It’s a small effort I suspect most people won’t make, due to laziness or naivety. The chance data loss will come back and bite you is small. But if it happens, you will sorely regret not looking after your stuff properly. And I will say I told you so.

Just like looking after your physical possessions, the security of your data and personal information is ultimately your responsibility.

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.

The four sections highlighted below provide basic information about the gene forked:

General Information

This section contains the identity of the gene. The Name of the gene is given along with its Symbol (f), which can be used as an abbreviation. The unique CG (Computed Gene) number and FB ID are also given, but are often not stated in publications for named genes. Genes without a name are referred to by their CG number. The Gene Model Status tells you whether the gene is known to or thought to exist (current). Genes found not to exist can still be looked up for reference.

Genomic Location

This section tells you exactly where the gene is in the genome. The important bits are the Chromosome (and arm if the gene is on an autosome), the Sequence Location and the orientation of the gene (shown by a [+] or [–]). The Genomic Maps section gives a visual representation of the area surrounding the gene, showing other nearby genes and their orientations. The buttons Get genome region and Get FastA allow you to download the entire gene sequence, or just the parts you’re interested in (e.g. exons only). The four most useful are: Gene region – the whole sequence as it is in the genome, Transcripts – the mature mRNA sequence(s) produced from the gene, the CDS (coding sequence) – the sections of the mRNA transcript(s) that are actually translated into protein, and the Translations – the protein(s) produced from the gene.

Summary Information

This is the section to look at if you want a quick overview of what a gene does. The molecular function, biological processes and phenotypes annotations tell you what is known, or predicted, about the gene’s function. For a more detailed description of phenotypes, the Phenotypic Descriptions of Classical Alleles button will take you to a page containing information about different alleles, with links to the publications in which they were originally described.

Stocks and Reagents

Every available stock relevant to the gene you’re interested in is listed here, with links to where they can be ordered.

1. S. Tweedie, M. Ashburner, K. Falls, P. Leyland, P. McQuilton, S. Marygold, G. Millburn, D. Osumi-Sutherland,
A. Schroeder, R. Seal, H. Zhang, and The FlyBase Consortium.
FlyBase: enhancing Drosophila Gene Ontology annotations.
Nucleic Acids Research (2009) 37: D555-D559; doi:10.1093/nar/gkn788.

Student debt is supposed to be interest free, so in theory is better than any other loan you can get. The interest you do pay on the loan is set every September, matching the inflation rate from the previous March. Well, it DID, until for the first time, the rate next September will be 0%, and your debt will not increase.

However, inflation is currently negative, at -0.4%. While the government is more than happy to apply the highest rating of inflation to loans to maximise the money they get back, the policy of following inflation is suddenly, and quietly, dropped to prevent loans deflating like the rest of the economy. Decreasing the amount owed does not mean the a loss of money for the government or taxpayer – they are effectively taking money from you – to the tune of £40 per year on a debt of £10,000 – the vast majority of students owe considerably more than this.

This comes at a time when MPs are being called out for literally stealing thousands of pounds of taxpayer’s money as “expenses”. They are, simply put, a bunch of wankers.

Follow this link for a petition regarding the issue on the No. 10 website. I wont be holding my breath for fair treatment, though.

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.

Science has always viewed Intelligent Design, and particularly Irreducible Complexity, as a “God of the Gaps” argument – what can’t currently be explained is God’s business, until science sufficiently explains it.

Now however, it is ironic that the scientific evidence for Irreducible Complexity should come from the scientist’s plaything – Drosophila.

The two phenotypes shown below, headless and bodyless, were initially thought to be the product of mutations in two different genes, but it turns out to be from just one, now called sliced.

The headless phenotype.

The bodyless phenotype.

There are two points about this gene that together show it is irreducibly complex:

1. Any mutation to this gene, even silent, causes one of the above phenotypes.

2. This gene is not present in any other organism.

Essentially this means evolution cannot act on this gene, or explain its existence. As any mutation to the gene is lethal, there are no variations that can be passed on from generation to generation, as required by evolution. The same gene is not present in any organism, which refutes the evidence for common ancestry required for evolution to work – evolution does not allow for genes to be created from nothing.

The two phenotypes of sliced.

Evolution cannot explain these phenotypes – the only explanation is the hand of God.

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 (aka, The Esoteric Git’s Method)

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…

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

Here’s a closeup to finish:

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.