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Posts Tagged ‘imaging’


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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Inspiration for this post comes from various sources, including Arjun Raj’s posts on the STAP papers (here and here) and that by The Spectroscope (here)
and my previous posts on the question of whether science does self-right.

I take issue with the trivialisation of data fabrication. (more…)

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Update June 5
Standards, who needs them? I am just back from the E-MRS spring meeting in Strasbourg, which was most enjoyable, though someone seems to have forgotten about the “Spring” bit. Meanwhile, out in the world of science we continue to witness ridiculous decisions regarding manipulated and falsified data by journals and a quite stunning self-justification by a materials scientist who looks to be the next serial fraudster. (more…)

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The assiduous reader will recall that on March 22 I formally contacted MIT regarding the re-use of images in multiple papers by Francesco Stellacci. This includes one instance of an image being re-used to describe a different experiment, which so far has resulted in a correction.
MIT have got back to me stating that they don’t have a report for me yet (I guess Friday was a deadline for delivery of an interim decision), but will get back to me at the end of May. Like many of us, MIT will have their hands full dealing with financial fallout. Nonetheless, I hope that this does not distract them too much from the necessity to ensure academic integrity. I look forward to hearing from them in due course, though depending on their interim decision, I may be bound by confidentiality.

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http://www.intelliagence.fr/Page/Offer/ShowOffer.aspx?popup=1&OfferId=47887&rwndrnd=0.9729958744719625.

either go through the ABG website, the University of Liverpool website or contact Dave Fernig directly.

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A number of events are worthy of a post, but the most urgent to bring to my readers’ attention is a development at Nature Materials. They have issued a correction to the 2008 paper by Francesco Stellacci, Nature Materials 7, 588 – 595 (2008). Thanks to Pep (despite stating he would no longer comment on this blog) for pointing this out in a comment on my blog entitled “Responses-to-evidence-of-self-plagiarism“. I have raised the issue of data re-use multiple times (no pun intended!) including these posts:
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