After an interaction on Twitter with a colleague who is associated with #LongCovid and #TeamClots, he asked me for some references. I thought what to send, and then realised that references plus something a bit more than a Tweet might be useful, so here goes.
(more…)Posts Tagged ‘heparan sulfate’
Some thoughts on SARS-CoV-2 and heparan sulfate
Posted in Biochemistry, Covid-19, Fibroblast growth factor, Glycobiology, Nervous system, Viruses, tagged glycosaminoglycans, heparan sulfate on March 20, 2022| 2 Comments »
Heparin inhibits SARS-cov-2 cell infectivity
Posted in Biochemistry, Covid-19, Glycobiology, Scientific progress, Viruses, tagged Coronaviruses, heparan sulfate, heparin, SARS-CoV-2, science on April 29, 2020|
With new data in hand, our first preprint on SARS-cov-2 receptor binding domain (RBD) interacting with heparin now has a sibling, which demonstrates that heparin inhibits the infection of Vero cells by SARS-cov-2
Some of the key points of the team’s new work are:
- Inhibition of viral infectivity in a Vero cell model by heparin, which is a better inhibitor for SARS-cov-2 than SARS-cov.
- Analysis of the interactions of a more extended library of model heparins with the SARS-cov-2 receptor binding domain. As with many other heparin-binding proteins, these data show that while sulfation is critical for RBD binding, the amount of sulfate is not, but instead it is the spatial arrangement of sulfate groups that is most important.
Together the data point to heparin being a potentially useful therapeutic to reduce infectivity. (more…)
Congratulations Dr Alghrair
Posted in Biochemistry, Nanotechnology, tagged heparan sulfate, influenza virus, Nanoparticles, Nanotechnology, PhD on May 24, 2018|
Today was the culmination of Zaid’s PhD journey, when he successfully defended his thesis on the use of gold nanoparticles to probe the mechanism of action of a peptide that inhibits ‘flu virus infectivity. Though he approached his viva with trepidation, his beaming face afterwards told a different story. The usual smattering of corrections, a paper already up on Bioarxiv ready to submit for peer review and another to put up on Bioarxiv, and in a few weeks he will be truly done, with a CV to match.
Congratulations Dr Baradji
Posted in Biochemistry, Fibroblast growth factor, Glycobiology, Imaging, tagged Biophysics, chondroitin sulfate, heparan sulfate, PhD, research, science on December 6, 2017|
Congratulations to Aiseta!
On Monday 4 December Aiseta Baradji successfully defended her thesis. A long journey and a hard one as ever with its ups and downs, surprises and a certain amount of head scratching over data that push us in new directions. In the end a great thesis that will be consulted in the labs of her supervisors for a long time. Now onto the next phase.
Positions open
Posted in Biochemistry, Chemistry, Glycobiology, tagged Alzheimer's disease, EU, heparan sulfate, neuroscience, postdoctoral position, research, science on March 23, 2017|
Two postdoc positions are available in my lab.
Both are part of the larger, European Commission-funded FET-Open programme, ArrestAD, which has recently been funded.
Position 1 aims to characterise heparin-binding proteins in Alzhiemer’s disease.
Position 2 aims to develop inhibitors to Golgi sulfotransferases. (more…)
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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