Happy holidays, the preprint is out there!

This is a guest post by Marie Held. Credits are given to Andrew Plested for the title/timing of this post (see here).

It had been a long time coming but the preprint of our manuscript Ex vivo live cell tracking in kidney organoids using light sheet fluorescence microscopy is now available on BioRxiv. Together with the preprint, the associated large body of imaging data has been made publicly available in the online Image Data Resource (IDR) repository. Through the power of OMERO you can have a play with the data or even download it and then re-analyse it.

The imaging has been conducted on the Zeiss Z.1 Lightsheet microscope at the Centre for Cell Imaging at the University of Liverpool, whose ever helpful staff enabled us generating lots and lots of image data and providing an efficient infrastructure for data storage as well as support for image and subsequent data analysis. Of course this is only half the story because the imaging would not have been possible without generating the samples first: A big thank you also goes to the students and academic staff in the Institute of Translational Medicine at the University of Liverpool.

In this study we have generated organoids from dissociated and re-aggregated mouse embryonic kidney tissue and imaged them with a light sheet fluorescence microscope. The microscope optically sections the samples, therefore preserving the three-dimensional context of the sample throughout imaging. We have found organotypic kidney structures in the organoids and evidence for the maturation of cells to the point of forming glomeruli, the basic filtration unit of the kidney. A functional assay showed that the developed tubules display secretory function.

Most importantly though, we have also performed live imaging of organoids made from genetically tagged fluorescing cells. The light sheet microscopy setup combines an illumination that is perpendicular to the detection. Therefore, full frame images can be recorded rapidly and only the section of the sample that is recorded is illuminated, thus vastly reducing photobleaching and phototoxic effects that limit long-term live fluorescence imaging in wide field and in particular confocal scanning fluorescence microscopy. We have then tracked the fluorescing cells with the help of an automated algorithm and subsequently analysed the generated tracking data. We have {started to} analyse the tracking data and can now quantitatively compare between experiments.

Yet, there is so much more that can be done with the images and data and we would love to see which ideas and approaches others might have, so please do not be shy to dig in and have a play. Be sure to let us know though.

Featured image caption: Organoid of mouse embryonic kidney cells formed following dissociation and re-aggregation of embryonic kidney rudiments. Yellow: Pax2+ cells indicating the metanephric mesenchyme, a prerequisite for nephron development, Red: Peanut-agglutinin staining basement membranes of the ureteric tree and developed nephrons.


How to Elucidate the Structure of Peptide Monolayers on Gold Nanoparticles?

I have recently submitted my PhD thesis and we have now pre-printed on bioRxiv the work constituting its major chapter. Together with the pre-print, the data have been made publicly available in an online repository of the University of Liverpool. Well isn’t it perfect timing that this week is open access week? 😉

This work has been conducted nearly entirely during the 2 years of my PhD spent at the A*STAR Institute of Materials Research and Engineering (IMRE) and at the A*STAR Institute of High Performance Computing (IHPC) in Singapore.

In this study, peptide-capped gold nanoparticles are considered, which offer the possibility of combining the optical properties of the gold core and the biochemical properties of the peptides.

In the past, short peptides have been specifically designed to form self-assembled monolayers on gold nanoparticles. Thus, such approach was described as constituting a potential route towards the preparation of protein-like nanosystems. In other words, peptide-capped gold nanoparticles can be depicted as building-blocks which could potentially be assembled to form artificial protein-like objects using a “bottom-up” approach.

However, the structural characterization of the peptide monolayer at the gold nanoparticles’ surface, essential to envision the design of building-blocks with well-defined secondary structure motifs and properties, is poorly investigated and remains challenging to assess experimentally.

In the pre-printed manuscript, we present a molecular dynamics computational model for peptide-capped gold nanoparticles, which was developed using systems characterized by mean of IR spectroscopy as a benchmark. In particular, we investigated the effect of the peptide capping density and the gold nanoparticle size on the structure of self-assembled monolayers constituted of either CALNN or CFGAILSS peptide.

The computational results were found not only to well-reproduce the experimental ones, but also to provide insights at the molecular level into the monolayer’s structure and organization, e.g., the peptides’ arrangement within secondary structure domains on the gold nanoparticle, which could not have been assessed with experimental techniques.

Overall, we believe that the proposed computational model will not only be used to predict the structure of peptide monolayers on gold nanoparticles, thus helping in the design of bio-nanomaterials with well-defined structural properties, but will also be combined to experimental findings, in order to obtain a compelling understanding of the monolayer’s structure and organization.

In this sense, we would like to stress that, in order to improve data reproducibility, enable further analysis and the use of the proposed computational model for peptide-capped gold nanoparticles, we are making the data and the custom-written software to assemble and analyse the systems publicly available.


Snapshots of the final structure of the simulated 5 (left) and 10 (right) nm CFGAILSS-capped gold nanoparticle, illustrating different content and organization of secondary structure motifs.