Donation from ARM

LiB

Being a geek but also a teacher, a few months ago I attended a Train-the-trainer workshop in mbed programming at the ARM headquarters here in Cambridge. I learned about the mbed platform, which, in lay terms, is a little bit like Arduino for industrial purposes: With more horsepower and to be programmed in C or C++. ARM want to enter the educational market and for these purposes designed the Lab-in-a-Box (LiB), a pack of 10 Freescale Freedom FRDM-KL25Z microcontroller boards, the Keil development tool chain, as well as access to state-of-the-art lecturing and course material covering basic embedded electronics and more hardware-specific content. What caught my attention was “If you think this might be useful for your teaching, but you can’t quite afford it, please speak to use…”. Which I did.

Fast-forward a few months, and here I’m sitting in my office holding in hands what probably is the first LiB package in the UK. What for does a molecular biology lab need those, you may ask? The answer is simple: Microcontrollers can replace very complex electric circuits, and with programming skills the development of even complex sensor > processing > output projects becomes possible. The computational and systems biologists of the future are in a prime position to be users of such hardware!

Currently I’m developing a set of about a dozen lectures and practicals for biologists to learn embedded electronics and programming, and I’m hoping to run this as a voluntary course very soon.

Summer student studies

Amgen

Over the past few weeks we have been joined by a handful of summer students: Armin Schöch (MPhil student in Computational Biology), Busra Erarslan (Erasmus student from Turkey) and Juliet Handsaker (Amgen Scholar from University of Warwick).

Summer students are an exciting business. They’re usually in the lab for too short a while to tackle a full blown project, but we tend to only accept them when they’re actually too good to just be shadowing our other group members. So the compromise is to put them on small but risky pilot experiments that are mostly open ended and very much “blue sky”, and often these works are related but not in the very core of our research. One example of a very fruitful summer visit is Alicia Schep’s work that was just published in PLoS ONE (see post below).

This summer, Armin will be working with Radu Zabet on potential origins of transcriptional noise. Busra is part of a collaboration with Kathryn Lilley‘s group and together with her team will be looking into unequally distributed mRNAs in the cell. And last not least, Juliet will be compiling a catalogue of tracheal gene expression from various sources of evidence.

New publication

PLoS_Schep_teaserOur paper A Comparative Analysis of Transcription Factor Expression during Metazoan Embryonic Development by Alicia Schep and myself is finally out in PLoS ONE. This work was our first “experiment” that we put out on arXive before embarking on final publication in a peer-reviewed journal. This will probably also tell you something about the time line of scientific publishing: We submitted on arXive on 8th January and to PLoS ONE on 9th January. With reviewers taking their time and a revision, the final manuscript is online today, almost six months later.

What else is to say? Ah, the science: We looked at gene expression profiles for transcription factors of representatives of vertebrates (Danio rerio, Xenopus tropicalis), a chordate (Ciona intestinalis) and invertebrate phyla such as insects (Drosophila melanogaster, Anopheles gambiae) and nematodes (Caenorhabditis elegans). We clustered TFs for each species based on their quantitative temporal expression profiles. This showed very similar TF expression trends in development in vertebrate and insect species. However, analysis of the expression of orthologous pairs between more closely related species showed that expression of most individual TFs is not conserved, following the general model of duplication and diversification.

Tracheal system goes lung development

copd_teaserA couple of months ago I was asked to join the European Cooperation in Science and Technology (COST) action on “Developmental Origins of Chronic Lung Disease“. While we are in the first instance a transcriptional regulation lab and in the second instance a developmental biology group, we are surely not a disease-oriented group. However, the data integration strategies needed in the understanding of transcriptional regulation and genome-wide studies in general allow us to compare large datasets between fly and human. So I’ve decided to showcase the intersection of Christos Samakovlis‘ very detailed study of RNAi phenotypes in the developing tracheal system of Drosophila with genome-wide association studies in lung disease. I’m going to present these initial results at the COST Conference at Starnberger See this week. We’re quite excited about the results, so let’s see what the lung development and disease communities have to say.

DIY in the lab

thermistor

I have spent quite a few hours now on temperature monitoring using the Raspberry Pi as cheap server platform and base station for wireless sensors. These things could potentially be interesting for a range of lab applications, where a little investment in time could save you a lot of money. Temperature, light, humidity – all is possible. Please find my detailed instructions here: DIY Remote Temperature Sensor.

Fished out with Haldene’s Sieve

arXivRadu Zabet’s recent submission to arXiv was fished out by research blog Haldene’s Sieve. Although the editors of a journal that we shall briefly call GR didn’t think this work was interesting enough for publication, it’s been really exciting to see the feedback we’ve gotten via alternative routes. If you want to openly discuss our two pre-publications on TF target finding, why don’t you do it via Haldene’s Sieve!?

Two new articles on ArXiv: Facilitated diffusion

teaserArXivWe are happy to announce the submission of two new articles to arXiv prior to publication in peer-reviewed open access journals:

 arXiv:1303.6793: The effects of transcription factor competition on gene regulation

 arXiv:1303.6869: The influence of transcription factor competition on the relationship between occupancy and affinity

If facilitated diffusion, stochastic simulation or transcriptional regulation are your thing, please have a look, send us comments and suggestions, tweet it, write about it on your blog (but let us know so we can engage in a fruitful scientific discussion) etc.

In brief, in arXiv:1303.6793 (Zabet & Adryan) we discuss the influence of TF abundance on the arrival time of TFs on their target sites as well as the time they stay bound to the DNA. There is an “emerging property” in cases where many molecules compete in some sort of molecular traffic jam on the DNA. This noise component may be a contributor to transcriptional noise, which we found pretty interesting.

The second article, arXiv:1303.6869 (Zabet, Foy & Adryan) deals with the discrepancy between “predicted occupancy” of a TF to a binding site on the basis of, say, a PWM, in contrast to a “measured occupancy” when we simulate the system with our GRiP framework. Again, we can show that absolute TF abundances play an important role in gene expression, and also provide a compelling case where selecting “the highest peaks” from a ChIP experiment may not necessarily identify the most affine binding sites.

Cambridge Sequencing Informatics Meeting 5

NGS

It’s the time of the year again. For the 5th time we’re inviting practitioners in the field (those who mangle NGS data) to come and discuss issues they’re encountering in their work. If you’re in the Cambridge area, please come join us in this free meeting on Monday, 15th April 2013 from 9-5.30 in the Centre for Mathematical Sciences (Wilberforce Road, CB3 OWA). Registration is now open.

We’re trying out a new interactive format for this meeting. While there will be a panel-led review of recent advances in the field and short technical talks from manufacturers, as well as a scientific key note (this year by Daniel Gaffney on transcriptional variation in stem cells) at the end of the day, most of the meeting will be relying on your contributions. Everyone is invited (in fact, very strongly encouraged!!!) to formulate 1-2 questions, comments or hints on the analysis of next-generation sequencing data and send them to us on cambridge.sequencing@gmail.com. We’re then trying to group these contributions and work through them during the sessions in this meeting, hopefully yielding interactive discussions where everyone will contribute. Don’t be afraid. Nobody is ‘an expert’, even 5-8 years down the road we’re all still learning. So come, give it a shot!

Royal Society International Scientific Seminar

trachealmeeting

With support of the Royal Society and organised by myself (Boris), I’m very thrilled to welcome PIs from most European tracheal system research labs to the Kavli Centre at Chicheley Hall. They will be joined by a range of researchers interested in lung, vascular and kidney development to discuss the big question: “The Drosophila tracheal system: Still a good model or is it time to move on?”. More information about this unfortunately private meeting can be found here.

Comics and flies

The CSBC’s very own director Steve Oliver is senior author on a poster in comic style. Very accessible, understandable and absolutely not pretentious. I wish more science would be communicated like that. And also, it promotes openness in science. // Our just retired Lord of the Flies, John Roote, together with Andreas Prokop from Manchester, has created some teaching material for Drosophila genetics. It’s been deemed important enough for a University of Cambridge press release.