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April 15, 2014

Videos and photos from the Pallen Inaugural

Follow-up to Nothing in Microbiology makes Sense except in the Light of Evolution from The Microbial Underground

Live streamed version:




Slidecast version (better sound quality and no need to look at my ugly mug!)


Photos from the day here:

https://www.dropbox.com/sh/ao2xx91qrjl8rtu/2FijtEacI9


Nothing in Microbiology makes Sense except in the Light of Evolution

Writing about web page https://storify.com/mjpallen/palleninaugural

Here is online companion to my Inaugural Lecture.



April 03, 2013

Warwick Medical School establishes a new £4–million Division of Microbiology and Infection


Welcome to our new blog, the Microbial Underground, a subversive, provocative, informative blog from Warwick's Division of Microbiology and Infection, blending enthusiasm with scepticism for all that is new in the microbial sciences, with a focus on fast-moving, high-throughput technologies!

Warwick Medical school has this week established a new Division of Microbiology and Infection, with over £4 million of investment launching a vibrant new research community of around twenty staff and students, headed up by me, Mark Pallen.

I would like to think the rationale for such an initiative is self-evident: after all, there are more microbes on our planet than there are stars in all the galaxies in the observable universe! And microorganisms have played a pivotal role in the history of science, for example in establishing that DNA carries genetic information. Millions of diabetics now rely on biotechnological exploitation of a bacterium, E. coli, to make insulin.

But of course, microbes are not just friends but also foes, as evidenced by the havoc wrought in Germany in 2011 by a Shiga-toxin-producing strain of E. coli .

I am joining the Division as Professor of Microbial Genomics. My own interests are fairly wide-ranging and span the divide between basic and applied research in bacteriology, with a particular focus on using genome sequences to understand how bacterial pathogens evolve, spread and cause disease. Recently, I have been worked closely with industrial and international collaborators to exploit new DNA sequencing approaches to identify and characterize the strain of E. coli that caused such a devastating outbreak of infection in Germany, with papers in NEJM and Nature Biotech. I am also author of a popular book, The Rough Guide to Evolution and was chief instigator behind Baba Brinkman's Rap Guide to Evolution, a provocative celebration of Darwin’s legacy through the medium of Hip Hop: I star in the video for I'm a African!

But enough of me: this initiative brings a wealth of new academic talent to the University of Warwick!

AchtmanLet's start with Professor Mark Achtman, who is about to joins us from Cork in Ireland. Mark brings a world-class reputation in the field of bacterial evolution and epidemiology, as evidenced by high-impact papers in the most prestigious scientific journals, including Science magazine (check him out on Google Scholar).

I have heard Paul Keim describe Mark as a "force of nature"! Mark has used his formidable research talents to attack some of the big questions about human existence—for example, using DNA sequences from a bacterium that lives in our stomachs to work out how humans spread out of Africa to people the world, or exploring the origins, evolution and spread of the bacterium that causes the plague, including the Black Death pandemic which killed around a third of the inhabitants of Europe in the fourteenth century. Professor Achtman harnesses robots and computers to laboratory research to create an exhilarating high-throughput approach to microbiology (check out this video from his former life in Cork)!

Associate Professor Nick Waterfield(@nick_waterfield) will soon be joining us from the University of Bath. Dr Waterfield brings a broad research vision to investigations of how bacteria interact with the organisms they infect, using high-throughput screens in insects and other invertebrates to shed light on important human infections. Check out Nick's old web page at Bath here.

Several authorities, including the Academy of Medical Sciences, the Wellcome Trust and the Medical Research Council, have stressed the urgent need for capacity building in academic clinical microbiology. The need for new investment in this area has been reinforced by the recent headline-grabbing report from the UK’s Chief Medical Officer Dame Sally Davies, ramming home the need for a better understanding of the evolution and spread of multi-drug resistant pathogens and how we can best avoid and treat the infections they cause. With all that in mind, Warwick Medical School is delighted to recruit a world-class clinical academic, Dr Esther Robinson to a Clinical Associate Professorship. Dr Robinson comes not only with a DPhil from the University Oxford, but also with accreditation to work as a consultant medical microbiologist in the NHS. With clinical sessions at the Heart of England NHS Trust, she will act as an important bridge between the new Division and translational research into clinical microbiological problems.

Several early-career academics are also joining the new Division:

  • Dr Emma Denham(@gingermicrobe) is joining us at Assistant Professor Level, bringing with her basic and translational research expertise in Gram-positive bacteria (as evidenced by two Science papers!). We anticipate making one additional appointment at this level.
  • Dr Chrystala Constantinidou and Dr Andy Millard are taking up Principal Research Fellowships, with an emphasis on high-throughput DNA sequencing and analysis.

The new Division will also benefit from state-of-the-art laboratory facilities, including a MiSeq high-throughput sequencing instrument.

Our aim is for the new Division to have a global reach. With that in mind, we have already initiated links with Dr Martin Antonio at the MRC Centre in Gambia, who now has a visiting academic position within the new Division and will co-supervising two PhD students here. We are also keen to see the new Division act as a starting point for a new campus-wide Research Centre that will integrate laboratory-based research with a much wider range of research activities, from epidemiology to the history of medicine, from medicinal chemistry to clinical infectious diseases, while also catalyzing links with other key regional, national and global stake-holders, including the health services, industry, government and NGOs.

To catch up on our news and track our progress, please follow this blog and follow us on Twitter (@WarwickMicrobio), plus follow all of us individually on Twitter too!

Oh, and we do have a web site too, which you can watch being built (but aren't web sites all rather 20th century these days?).

The game's afoot! The excitement begins!


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  • I have just seen this paper on the ~7–thousand–year auroochs genome: http://www.genomebiology.com/20… by Mark Pallen on this entry
  • Hi Chris, You are right that there is nothing implicit in being Open Access that guarantees a right … by Mark Pallen on this entry
  • Good to see it on biorxiv. I didn't fully follow the second point about elife, your criticism seems … by Chris Keene on this entry
  • Congratulations to Professor Achtman. by on this entry
  • Hi Shilp, glad that you found it useful . I used seqtk sample. So if I had 100 reads for 90% seqtk s… by Andrew Millard on this entry
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