A farewell to NanoBubbles: from Nathanne Rost

This was my last week in the NanoBubbles project, in which I worked as a post-doctoral researcher in the Post-Publication Peer Review (PPPR) initiative for almost three years. My main tasks consisted of critically analysing articles and posting comments on PubPeer (an online journal club).

For such purposes, we selected articles in the nanobiosciences field, especially claiming the intracellular use of nanoparticles. In this kind of publication, it comes the main question: which was the uptake mechanism of the nanoparticles in the cells, and did the particles reach the cytosol? Nanoparticles usually internalise in cells by endocytosis, and are therefore entrapped in endosomes, which they need to escape in order to reach cytosolic targets or compartments. In many articles, this is not discussed even though the efficiency of the nanomaterials for intracellular purposes is concluded. This scientific question is the origin of the NanoBubbles project, and in the PPPR initiative we commented on this issue by evaluating the consistency among the rationale of the work, claims and data provided. Other points were also highlighted in our comments, and the most common issues we found are discussed here.

In this process, I contributed with my expertise in nanoparticles synthesis and characterization for analysing the articles and write the comments. This involved many meetings to combine our research backgrounds (mainly in physics, chemistry, biology and philosophy) and I learnt a lot from my co-workers. It was a subproject that thrives on synergy and I have the feeling that all of us were learning a lot from each other. We standardised our comments on PubPeer aiming to have more transparency (by adding an authorship list of people who wrote the comments, as well as a contribution statement), and better clarification of our thoughts. The PPPR team was composed by me, Federico Boem, Maha Said, Mustafa Gharib, YJ Erden, Frédérique Bordignon and Raphaël Lévy. Our initiative was presented in Better nanoscience through open, collaborative, and critical discussions (Rost et. al., 2024).

At the beginning of the project, I also worked with some of the computer scientists in the group, for creating the corpus or articles for PPPR, and later to some extent to investigate miscitations.  Moreover, despite of annotating the articles, I was also organising the PPPR team workflow by suggesting meetings and deadlines, implementing tools, keeping track of the comments under preparation, creating a list of articles to be annotated, and checking the outcomes of our reviews (author’s replies, other people commenting on the same articles after us, correction of the articles, and some private messages we received regarding our reviews).

Preventing errors in the scientific literature starts by talking about the problems in science. As a community, we have the responsibility of doing so by sharing our knowledge. This is why I enjoyed taking part of courses given to early career researchers to discuss about research integrity (CARA course, GSChem school, European School On Nanosciences & Nanotechnologies), how to detect problems in articles and what to do to mitigate the effects. In such occasions we prepared activities with examples of PPPR, or how a poorly detailed protocol increases the replication crisis, and those spaces were opportunities to share experience and listen to the students.

I also had the pleasure of representing NanoBubbles in conferences, workshops, and symposia (CRS local chapters meeting, SFNano and SFNanoJr seminar, Raman Nanotheranostics mini-conference, GDR RNA meeting, Beilstein Nanotechnology Symposium) by presenting posters or sharing our findings in oral presentations. This was important to make more scientists aware of how needed science correction is. Of course, I also benefited from an expanded network.

In investigating how, when and why science fails to correct itself, I learnt what the word ‘synergy’ means. Before this experience, I never realised that I could directly work with researchers coming from such different backgrounds. Moreover, we made progress in our project, we constantly interacted with each other to discuss ideas – there was always something going on. This also makes me think that correcting science is an endless process and research integrity – something I have gained a lot of knowledge through in this project – also constitutes an everlasting challenge. What I learnt from this post-doctoral experience will always be applied to my research practices.

If I wanted to write the names of NanoBubbles members who somehow contributed to my work, this would mean the entire team. Therefore, a big thank you to every team member (current and past) for this amazing journey together. To the permanent members, thank you for gathering all of us together.

This is my farewell to the NanoBubbles project, but only the beginning of my contributions to the correction of science.

Nathanne Rost (a very proud Nanobubbles member).