Tag Archives: My Research

Mathematical and Systems Biology

I was in London on Friday for the latest progress meeting of the SysMIC project. It’s a project funded by the BBSRC as a resource for members of its research community: from graduates beginning their career through to established researchers wishing to improve their skills in mathematical and systems biology.

Here’s the course syllabus. There’s also an overview of how SysMIC connects to the BBSRC’s new doctoral training programmes (SysMIC briefing for DTP students – Word file).

At the moment it’s being ‘road-tested’ by some early adopter PhD students (and by me, the only member of the team with what might be classed as ‘rusty’ mathematical skills). At the end of our meeting, we wandered over to the computing lab to chat to these students, who all seemed to be engaging really well. It goes live to registered members of the BBSRC research community in January 2013 – the first cohort of students are PhD students in the new Doctoral Training Partnerships.

I tend to focus more on the mathematical aspects of SysMIC: partly this reflects applications of this kind of training in the biological sciences, and partly because I perceive a rather changeable definition of ‘Systems Biology’. I prefer to think in terms of developing models and using those in a predictive way to design and interpret experiments (my own definition of Systems Biology would be of mathematical modelling that integrates multiple and diverse data sources to model complex systems).

I’m working through the material that’s been prepared so far, and having fun with MatLab, the mathematics platform we chose for SysMIC, and while I have to say I’ve yet to move on to anything mathematically serious, I can see how a more mathematical approach could benefit my own research.

Border Guards vs Drosophila, part 3

The latest in the ongoing saga of our fly shipment from the USA is that our packet of flies finally made it to the lab.  They’ve been in transit for exactly three weeks*, and of course kept in in known conditions.  I’m very grateful to various people at Animal Health, who were able to make an exception to the regulations.

Nonetheless, I think the application of tight control of over the international transport of live insects such as these is a bit over the top – the legislation that I’ve looked through seems principally aimed at commercially important farm stock and other animals important to the human food chain.   I understand there’s a general unhappiness in the UK Drosophila research community, especially since the international postal union recently relaxed its regulations regarding the transport of live Drosophila through regular mail.  I’m not particularly optimistic that we can make a change to the enforcement of the new regulations, but it’s most definitely worth a try.

*After their three week holiday (mostly spent at Stansted Airport), the fly vials are a bit smelly, but at least some of them still have living larvae in. 

See also my previous posts Border Guards vs Drosophila, part 1 and part 2.

Border Guards vs Drosophila, part 1

I have been conducting research using the fruit fly Drosophila melanogaster since I started my PhD in 1982.  In that time I have imported countless consignments of fly strains through the post and by courier (such as Federal Express).  On only  one occasion can I recall having difficulty getting them through customs – a box of female-sterile mutants from France got stuck, and was in a frightful state when they arrived (this was during my PhD).

The general practise is for the sender to affix one of those green customs tags, asserting that the contents are a gift, of no commercial value (typically $1 may be quoted), that they are live insects, but not an agruicultural pest or a vector of disease.  So for over 26 years as a practising Drosophila geneticist, I’ve had but one case where this has presented a problem.

We are referred to Directive 91/496/EEC.  This document brings a wry smile to my face.  As I read it, I notice the very first lines are:

COUNCIL DIRECTIVE of 15 July 1991 laying down the principles governing the organization of veterinary checks on animals entering the Community from third countries and amending Directives 89/662/EEC, 90/425/EEC and 90/675/EEC (91/496/EEC)

So, firstly, someone has suddenly noticed, or reinterpreted, a directive from 18 years ago!, and second, it amends three prior directives.

Article 1 contains the statement  "This Directive shall not apply to veterinary checks on family pets accompanying travellers for non-commercial purposes, other than equidae."  So if was travelling with the flies, and claimed them as pets, it would seem that there wouldn’t be a problem.  And the mention of equidae suggests that the directive might just be intended to apply to larger animals.

 Article 2 has a series of clarifications

1. For the purposes of this Directive, the definitions contained in Article 2 of Directive 90/425/EEC shall apply as necessary.

2. In addition:

(a) ‘documentary check’ shall mean verification of the veterinary certificates or documents accompanying an animal;

(b) ‘identity check’ shall mean verification, by visual inspection only, for consistency between the documents or certificates and the animals and for the presence and conformity of the marks which must appear on the animals;

(c) ‘physical check’ shall mean a check of the animal itself, possibly including sampling and laboratory testing and, where appropriate, additional checks during quarantine;

(d) ‘importer’ shall mean any natural or legal person whopresents animals for importation into the Community;

(e) ‘consignment’ shall mean a quantity of animals of the same species, covered by the same veterinary certificate or document, conveyed by the same means of transport and coming from the same third country or same part of such country;

(f) ‘border inspection post’ shall mean any inspection post located in the immediate vicinity of the external border of one of the territories referred to in Annex I to Council Directive 90/675/EEC of 10 December 1990 laying down the principles governing the organization of veterinary checks on products entering the Community from third countries (5) and designated and approved in accordance with Article 6.

 Further on, Article 4 says:

2. Without prejudice to the exemptions pursuant to Article 8, the official veterinarian must carry out a physical check on animals presented at the border inspection post. That check must include, in particular:

(a) a clinical examination of the animals in order to ensure that they conform to the information provided in the accompanying certificate or document and that they are clinically healthy.

That’s a real cracker.  I look forward to a witnessing a vet conducting a physical (and clinical!) check on the insects, and ensuring the flies are indeed healthy.  Do we really think this is intended to apply to a laboratory fly?  I can’t see a definition of ‘animal’ in the document.

We are also referred to this piece of UK legislation: Statutory Instrument 2006 No. 1471 – The Animals and Animal Products (Import and Export) (England) Regulations 2006

I’ve yet to plough through that text, but birds seem to feature.  Perhaps flies=birds because they have wings?   Anyway, this one will run and run…

 

 

Border Guards vs Drosophila, part 2

It’s all got rather Kafka-esque as I try to resolve the ongoing Drosophila importation crisis!  It transpires that the people who have decided that importation of Drosophila should be covered by legislation aimed quite properly at preventing the import of diseased farm animals are a subsidiary of Defra (the Department for Environment, Food and Rural Affairs) called Animal Health.

Now clearly these people have a vitally important job, particularly in light of recent outbreaks of bluetongue, foot and mouth and the potential threat of avian influenza (to which we can add the problems currently afflicting honey bees).  But nowhere on their website do I see indication of why they feel they need to hold up my harmless flies, which are not an agricultural pest, transmit no disease, are not harmful, and in any case would be unable to survive outdoors anyway.  To add to that list of characteristics, these are weak strains carrying recessive lethal mutations.  This is how they describe themselves and their responsibilities:

Animal Health is the government’s executive agency primarily responsible for ensuring that farmed animals in England, Scotland and Wales are healthy, disease-free and well looked after.

We also have responsibility for managing outbreaks of notifiable animal diseases, and in this way we support the farming industry, helping it compete successfully worldwide, protect the welfare of farmed animals and safeguard public health from animal bourn disease.

The agency become Animal Health on 1st April 2007 following the merger of the State Veterinary Service (SVS), Dairy Hygiene Inspectorate and Egg Marketing Inspectorate and the Wildlife Licensing and Registration Service.

We are sponsored by, and work on behalf of, the Department for the Environment, Food and Rural Affairs (Defra), the Scottish Executive and Welsh Assembly Government across Great Britain implementing the animal health and welfare policies primarily on farms, at livestock markets and during transport.

We also work for the Food Standards Agency to protect public health by ensuring that dairy hygiene and egg production standards are met.

We also regulate the trade in endangered species.

None of this seems to put the importation of research invertebrates under their control.

I spent an hour or so on the phone to them this morning, but I’ve been unable to make them budge.  I’m not quite sure what to do.  Perhaps we need to make a trip to the USA so we can bring them back as pets (and therefore exempt under the European Directive I was quoted).

I am beginning to feel like a character in a Franz Kafka novel, so I’ve tagged this blog article "humour".  If I didn’t laugh, I would cry.

My Research: DmWRNexo is a 3'-5' exonuclease

ResearchBlogging.org

The latest publication from our project investigating a Drosophila homologue of WRN exonuclease is now online.  

Ivan Boubriak, Penelope A. Mason, David J. Clancy, Joel Dockray, Robert D. C. Saunders, Lynne S. Cox (2008). DmWRNexo is a 3′–5′ exonuclease: phenotypic and biochemical characterization of mutants of the Drosophila orthologue of human WRN exonuclease Biogerontology DOI: 10.1007/s10522-008-9181-3

Abstract The premature human ageing Werner’s syndrome is caused by loss or mutation of the WRN helicase/exonuclease. We have recently identified the orthologue of the WRN exonuclease in flies, DmWRNexo, encoded by the CG7670 locus, and showed very high levels of mitotic recombination in a hypomorphic PiggyBac insertional mutant. Here, we report a novel allele of CG7670, with a point mutation resulting in the change of the conserved aspartate (229) to valine. Flies bearing this mutation show levels of mitotic recombination 20-fold higher than wild type. Molecular modelling suggests that D229 lies towards the outside of the molecule distant from the nuclease active site. We have produced recombinant protein of the D229V mutant, assayed its nuclease activity in vitro, and compared activity with that of wild type DmWRNexo and a D162A E164A double active site mutant we have created. We show for the first time that DmWRNexo has 3′-5′ exonuclease activity and that mutation within the presumptive active site disrupts exonuclease activity. Furthermore, we show that the D229V mutant has very limited exonuclease activity in vitro. Using Drosophila, we can therefore analyse WRN exonuclease from enzyme activity in vitro through to fly phenotype, and show that loss of exonuclease activity contributes to genome instability.  

What are the Header images?

The header images are all related to Drosophila:

polytene chromosomes

Above: These are the giant polytene chromosomes found in a variety of tissues in Drosophila – these are from the salivary gland cells of the third instar larva.  Calvin Bridges (see picture of the fly lab below) devised maps based on the banding patterns of these chromosomes – maps still in use today.

wing blade clones

Above:   A close-up image of a small area of a Drosophila wing blade. Each cell on the wing blade bears a single hair.  This wing is from a fly that is heterozygous for a recessive mutation, multiple wing hairs (mwh), that causes each cell to bear a tuft of bristles.  You can see some of the cells show this phenotype: these have resulted from an event that has made these cells homozygous for mwh – we have used this to assess the function of a Drosophila homologue of the human locus WRN, mutation of which causes a progeroid condition. See our recent publication

fly lab

 Above: This a part of a photo showing members of the Morgan fly lab in the early 20th century. Those pictured are (from left to right) Edgar Anderson, Alexander Weinstein, S.C. Dellinger, Calvin Bridges, an "hooured guest", H. J. Muller and T. H. Morgan.  The occasion pictured is to celebrate Alfred Sturtevant‘s demobilisation in 1918 (he can be seen in the whole image).

fruit fly

 Above: The beast itself – this is a photograph of a male Drosophila melanogaster.

ommatidia

Above: The Drosophila eye is typical of insects: a compound eye composed of numerous facets – this is a scanning electron micrograph showing some ommatidia and bristles in the Drosophila eye.

FlyTree – Academic heritage of Drosophila research

Here’s an cool page showing academic pedigrees of Drosophila workers: FlyTree.

 It’s interesting to see how few steps it takes to get back as far as T. H. Morgan!  For example, here’s where I fit in the grand scheme: Robert in FlyTree.

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