Our review on fibroblast growth factors (FGFs) as tissue repair and regeneration factors, which we made available as a preprint from the time of submission is now published at PeerJ. (more…)
Posts Tagged ‘extracellular matrix’
FGFs in tissue repair
Posted in Biochemistry, Development, Fibroblast growth factor, Glycobiology, Peer review, Science process, Science publishing, tagged extracellular matrix, FGF, Fibroblast growth factor, glycosaminoglycan, heparan sulfate, regenerative medicine, tissue repair on January 12, 2016|
Of nanoparticles, cells and polyanions
Posted in Biochemistry, Chemistry, Fibroblast growth factor, Glycobiology, Nanotechnology, Scientific progress, tagged antithrombin III, chondroitin sulfate, extracellular matrix, FGF, Fibroblast growth factor, glycosaminoglycans, heparan sulfate, heparin, imaging, Nanoparticle, Nanoparticles, Nanotechnology, polysaccharide, Science progress on June 12, 2015|
Of nanoparticles, cells and polyanions
It is the end of semester 2 so it’s marking season. Since we double mark (a good thing), the final year research projects are marked by both supervisor and an assessor, a member of staff who is not involved in the project. One of the projects I marked was Gemma Carolan’s on “How do SmartFlares RNA detection probes reach the cytosol? Available are the PDF of report, and posts here and here.
I had a sense of déjà vu while reading the project – the clear endosomal location of the SmartFlares, regardless of the DNA sequences brought me back to the days when antisense was the technology of the future for medicine.
While evaluating new technology it is useful to go back and look at other high flying technology. The reality is that it takes decades before we know whether the promise (and hype) were justified; this is true for any hot topic from stem cells to nanoparticles and graphene.
Antisense effects can be mediated by RNAse H, an enzyme that specifically cleaves RNA-DNA duplexes and which protects our cells from RNA viruses. There are other mechanisms, e.g., interference with splicing or translation, but the RNAse-H mediated transcript degradation should be central to many antisense effects. There were many papers reporting specific effects (evidenced by differences between sense, antisense and scrambled oligonucleotides sequences). These certainly contributed to success of individuals and of institutions, e.g., in UK Research Assessment Exercise and grant awards.
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Responding to questions raised on PubPeer
Posted in Biochemistry, Glycobiology, Imaging, Peer review, Post publication peer review, Research integrity, tagged extracellular matrix, glycosaminoglycans, heparan sulfate, heparin, imaging, Research integrity, Science progress, VEGF on May 28, 2015|
I am a fan of PubPeer, as it provides a forum for discussion between authors and the wider community, something I have discussed in a number of posts (two examples being here and here). Two days ago, My colleague Mike Cross came by my office, having just delivered a pile of exam scripts for second marking (it’s exam and marking season), asking if I had seen a comment on our paper on PubPeer. I had not – too many e-mails and too busy to look at incoming!
So I looked at the question, which relates to panels in two figures being identical in our paper on neuropilin-1 and vascular endothelial growth factor A (VEGFA) – indeed they are labelled as being identical.
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Quentin Nunes, PhD
Posted in Biochemistry, Glycobiology, tagged extracellular matrix, glycosaminoglycans, heparan sulfate, heparin, PhD, polysaccharide on February 19, 2015|
Congratulations to Quentin Nunes, who today successfully defended his PhD today. His first paper from his thesis work was published in late 2013 in Pancreatology. This was an analysis, using public datasets of mRNA expression data, of the putative heparin-binding protein network in the healthy pancreas and in pancreatic digestive diseases. The latter part of his thesis work will be submitted for publication soon (watch this space!) and is a proteomics analysis of heparin-binding proteins in mouse pancreas and in a mouse model of acute pancreatitis.
Network based meta-analysis prediction of microenvironmental relays involved in stemness of human embryonic stem cells
Posted in Biochemistry, Development, Fibroblast growth factor, Glycobiology, tagged extracellular matrix, FGF, Fibroblast growth factor, glycosaminoglycans, heparan sulfate, heparin, polysaccharide, research, science on October 24, 2014| 3 Comments »
Virginie’s first paper on her thesis work, “Network based meta-analysis prediction of microenvironmental relays involved in stemness of human embryonic stem cells” was published yesterday at PeerJ. She first put it up as a preprint (v1 here
revised v2 here and then submitted it – my first experience of this and something I will certainly do again.
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A prize worth winning: How many extracellular proteins bind to heparan sulfate?
Posted in Biochemistry, Chemistry, Development, Fibroblast growth factor, Glycobiology, Scientific progress, tagged antithrombin III, chondroitin sulfate, extracellular matrix, FGF, Fibroblast growth factor, glycosaminoglycans, heparan sulfate, heparin, polysaccharide, Science progress on October 10, 2014| 5 Comments »
There are many prizes for cultural activities, of which science is one. This week has seen the announcement of the Nobel prizes, a little earlier the IgNobels were awarded. There are, of course many other prizes. I have decided to set up my own.
A question that bugs me and which loomed large while I read the excellent review by Ding Xu and Jeff Esko from UCSD on “Demystifying Heparan Sulfate–Protein Interactions” is how many extracellular proteins are there? (more…)
How neuropilin-1 binds heparin/heparan sulfate and publishing in the PeerJ
Posted in Glycobiology, Peer review, Science publishing, tagged extracellular matrix, glycosaminoglycans, heparan sulfate, heparin, Neuropilin, polysaccharide, protein chemistry on June 26, 2014| 1 Comment »
Kat’s paper on the interactions of neuropilin-1 with a heparan sulfate mimetic library of modified heparins is now published in The PeerJ
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We are 5!
Posted in Development, Fibroblast growth factor, Glycobiology, Muscle, Nanotechnology, Nervous system, Zebrafish, tagged extracellular matrix, FGF, Fibroblast growth factor, glycosaminoglycans, heparan sulfate, neuroscience, research, Research integrity, Science progress on September 11, 2013|
The Fibroblast Growth Factor Gordon Research conference is biennial, so it almost follows a Martian calendar and next year it will be five years old. The fifth Gordon Research conference on Fibroblast Growth Factors will be held in Ventura, California, March 1-7 2014. This is THE meeting for all things FGF and assembles an eclectic mix of leaders in the field, young PIs, industry scientists and scientists in training. A Gordon Research Seminar will precede the full meeting. This was introduced at the last GRC (May 2012) and was very successful. (more…)
PhD position available on “Short- and long-range structure of the extracellular matrix
Posted in Fibroblast growth factor, Glycobiology, Imaging, Nanotechnology, tagged extracellular matrix, Fibroblast growth factor, glycosaminoglycans, heparan sulfate, imaging, Nanoparticle on March 12, 2013|
either go through the ABG website, the University of Liverpool website or contact Dave Fernig directly.
Ruoyan’s paper on the diversification of the structural determinants of fibroblast growth factor-heparin interactions published
Posted in Development, Fibroblast growth factor, Glycobiology, tagged extracellular matrix, FGF, Fibroblast growth factor, glycosaminoglycans, Graduate students, heparan sulfate, polysaccharide on September 28, 2012| 1 Comment »
Ruoyan’s paper on “Diversification of the structural determinants of fibroblast growth factor-heparin interactions; implications for binding specificity” has been accepted for publication at the Journal of Biological Chemistry. The heart of her PhD thesis, this paper takes a hard look at the specificity of the interactions of six FGFs spanning five subfamilies with heparin and allied polysaccharides. She dissects the sites in the FGFs that are responsible for binding the sugars using the “Protect and Label” approach and the sites in the sugar that the FGFs binds using a combination of DSF, SRCD, biosensors and sugar libraries. As ever in biology, in important regulatory interactions there isn’t one binding site, instead these FGFs recognise what are best described as families of consensus sites in the sugar. Specificity in these consensus binding sites is elegantly illustrated by PCA and specificity maps to the evolutionary relationships of the FGFs.
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