Archive for May, 2012

I went down to Birmingham with Chris Hill, one of the MSc students joining the lab for the summer to meet Barry Leadbetter, who has made seminal contributions to our understanding of choanoflagellates. Now that we are armed with genome sequences, these unicellular eukaryotes look very much to be the the descendants of the unicellular ancestor of metazoa. They have a tyrosine kinome, which is a hallmark of metazoa, since virtually all cell-cell communication in animals involves tyosine phosphorylatioin at some point, even though tyrosine phosphate only accounts for ~2% of protein phosphorylation in a mammalian cell. Even more exciting from our perspective, was the analysis done by Alessandro Ori, which identified genes in choanoflagellates that might encode enzymes for heparan sulfate and chondroitin sulfate biosynthesis.

Barry provided us with detailed instructions and, most importantly, the benefit of his years of experience of growing these animals. We brought cultures of M Brevicolis and of S Rosetta back to the lab and we now embark on the adventure of growing these creatures, with the aim of seeing if we can find biochemical evidence for heparan sulfate.

More information on these organisms here and here.


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A superb FGF Gordon Research Conference closes. One frequent question was the identity of the first paper on FGFs . Thankfully it is a paper published by a learned society, so it is available from the Company of Biologists as a PDF.

Studies on the growth of tissues in vitro VI. The effects of some tissue extracts on the growth of periosteal fibroblasts

Trowell, OA and Willmer, EN

JOURNAL OF EXPERIMENTAL BIOLOGY Volume: 16 Issue: 1 Pages: 60-70 Published: JAN 1939

Well worth a read in my opinion. When I first got a copy from the library, I caught a bad cold from the dust on the volume. Now the PDF is available, this should no longer be a problem!

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Gareth Holder’s paper, just published in Soft Matter, is the latest from a long-standing collaboration with Peter Weightman in Physics and Ed Yates in Integrative Biology. The paper highlights some surprising features of heparin. Unlike an uncharged model polysaccharide heparin chains clearly have the potential to produce long-range order. Our next challenge is to see if this holds up in mixtures and in the presence of proteins. Nonetheless, this work raises intriguing possibilities for extracellular matrices to possess long-range order of nanoscale structural units

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A rather interesting video, courtesy of William Birch at IMRE, which suggests that zebrafish can detect CS released by injured fish and that this causes a fear response. Makes sense, in that injury to skin would release CS and uninjured fish would want to move away from whatever has bitten the injured fish.

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Arrived at les Diablerets late afternoon for the FGF Gordon Research Conference. A fantastic conference venue and it is great to have a week to look forward to discussions with colleagues on our favourite proteins.

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Richard Pickersgill from Queen Mary University of London will deliver a seminar on Monday 14th May at 13:00 in LT3 entitled “Structural insights into the bacterial type II secretion system “.

Richard’s work is an example of the contribution that structural biology can make to infection biology, food security and biotechnology. In particular, he will describe his latest results on the bacterial type II secretion system. Richard is an entertaining and lively speaker and his talks are always enjoyable.

The first part of the seminar is concerned with synthetic biology underpinning industrial biotechnology, the second with studies of a bacterial secretion system important in human disease and food security. Firstly, some highlights will be presented from recent work on carbohydrate active enzymes and enzymes of cobalamin biosynthesis. Remarkably, several of the cobalamin biosynthetic enzymes trap (and do not readily release) their products. Another way of trapping reactive and labile pathway intermediates is to enclose them and the enzymes of the pathway in a microcompartment (bioreactor) and I shall briefly describe work on bacterial microcompartment shell proteins. The second part of the seminar will look at the molecular basis of the interaction between the outer-membrane secretin and the lipoprotein pilotin essential for its correct assembly in the outer-membrane of several bacteria. These and other essential interactions will be discussed along with opportunities for halting the secretion system and preventing disease.

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Vito Volterra’s birthday was May 3. Volterra was a noted Italian mathematician, who is perhaps best known for developing differential and integral equations and his contributions to mathematical biology, a key area of endeavour nowadays. He lost his job at the University of Rome for refusing to attend Benito Mussolini’s party to drink with them.

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