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FGFs in tissue repair


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.

The inspiration for the review came from a lecture I gave at Wenzhou Medical University entitled “FGFs, morphogens, growth factors or hormones?”, which examined the evidence for FGFs performing these functions. One key part of the lecture related to the work of Ula Polanska, when she undertook her PhD in Liverpool with Tarja Kinnunen, on the functions of FGFs in C. elegans (published here and here). Ula discovered that the same FGF ligand and receptor performed both endocrine functions and morphogen/growth factor functions. During the planning of the lecture and after, I had a series of discussions with Chao Jiang, my friend and colleague who hosts me on my visits to Wenzhou. Chao and I bounce off each other in terms of generating ideas and new syntheses, and the result was the seed for the review. I wrote an outline on the flight back to Europe and then discussed the concept with my co-authors. As we gathered information and mined the literature, including the very substantial Chinese literature, I realised that there were two reviews. So we wrote this one, focussed on the non-cancer translational potential of FGFs. The other one will doubtless see the light of day in a few years!

One lesson from writing the review is that the Chinese scientific literature is very substantial, but the rest of the world doesn’t have a great deal of access to it. Even with help, we had trouble finding many articles – we only used about a fifth of the Chinese references we had identified. In many cases we were unable to secure the original papers, while in a few instances the papers were clinical reports of such brevity that they were not useful. The latter issue is being dealt with, as China upgrades its research enterprise. The former issue remains an obstacle. However, the increasing internationalisation of science, whereby labs and Departments have people who can read papers in all the major languages of science, coupled to the move to open access and better internet cataloguing of the literature is eroding this obstacle.

Another lesson is the pleasure of open review.  This is so constructive. Two of the reviewers chose the open route and they really put their backs into the task. The result is a much improved text. The review history is available too.

 

SimpleDSFviewer


Today we published a preprint at PeerJ that describes a program Changye Sun wrote to analyse and view differential scanning fluorimetry data. This is a brilliant technique for studying interactions of small and no so small molecules with proteins.  We focus on protein-polysacchairde interactions, but it works equally well in numerous other settings, including screening for enzyme inhibitors.

The code and compiled versions of the program are on GitHub – there is a link in the preprint.  The preprint also provides exemplar raw data, which are used in worked examples and a user manual.

It’s free, its open, so enjoy!

 


Congratulations Dr Li and Dr Sun

Yong Li successfully defended his PhD thesis on Monday November 16 and Changye Sun on Tuesday November 17. For that instant they were both “Docs”, now they are Postdocs!

It has been a big adventure for both, a lot of hard work, interspersed with play of course. Now its onto the next stage of career and life.

Groundhog day


Much has been written about the peer review process and its flaws. Richard Smith, a former editor of the British Medical Journal has stated that since peer-review doesn’t work, we shouldn’t do it

I have recently come across another example of the flaws in peer review. I reviewed a manuscript last year and identified what I believed to be technical problems and suggested at least major revision. The other two reviewers agreed; the three of us had homed in independently on the same technical issues.

Move forward a year and the paper is published in another (equally “prestigious”) journal, no changes.

So I will now amend my New Year resolution (still holding firm) from 2014 and 2015.

In addition to only reviewing for open access journals, I will from now on only review for journals where the review is open and published or where I am free to publish the review. That, at least, will avoid the ethical tension between participating in anonymous peer-review and then wanting to publish the critique when nothing has changed in the paper.

Why Groundhog day? This is not the first time I have had this experience.

A new habit


I went to a most useful talk this morning by Stephen Carlton (@LivUniOA) on the Univeristy repository. I had whinged about this as being nearly unusable, but then I jumped in on an early version.

The repository is now useable, though it is quirky. A few lessons from my efforts to update my entries.
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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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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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