Guest post: SmartFlares fail to reflect their target transcripts levels

Czarnek&BeretaThis is a guest post by Maria Czarnek and Joanna Bereta, who have just published the following article in Scientific Reports entitled SmartFlares fail to reflect their target transcripts levels

We got the idea of using SmartFlare probes when working on generating knockout cells. In the era of CRISPR-Cas9 genome editing, the possibility of sorting out knockout cells based on their low target transcript content (mRNAs that contain premature stop codons are removed in a process called nonsense-mediated decay) instead of time-consuming testing of dozens or thousands of clones would be a great step forward. SmartFlare probes seemed to be just the ticket: no transfection, lysis or fixation needed; moreover, the probes were supposed to eventually leave the cells. We were full of hope as the first probes arrived. (more…)


How to Characterize Gold Nanoparticles’ Surface?

Guest post by Elena Colangelo

Our Topical Review on the characterization of gold nanoparticles (GNPs) has just been published in the Bionconjugate Chemistry Special Issue “Interfacing Inorganic Nanoparticles with Biology”.

The literature is abounding in works on GNPs for applications in biology, catalysis and sensing, among others. GNPs’ appeal resides in their optical properties, together with the well-developed methods of synthesis available and the possibility of functionalizing their surface with small molecules of interest, which can readily self-assemble on the GNPs’ surface forming a monolayer.

However, allegedly the structure and organization of self-assembled monolayers (SAMs) at the GNPs’ surface are in fact aspects too often neglected [though surely not on this blog; RL]. Such elucidation is challenging experimentally, but it is crucial not only to ensure reproducibility, but also to design nanosystems with defined (bio)physicochemical and structural properties, which could then be envisioned to assemble in more complex systems from a “bottom-up” approach.

Our Topical Review gives an overview of the current knowledge and methods available to characterize the GNPs’ surface with different molecular details.


Cartoon illustrating the different levels of GNPs’ surface characterization discussed in the Topical Review.

First, the experimental methods commonly used to provide the basic characterization of functionalized GNPs, such as identification and quantification of the ligands within the monolayer, are detailed with the aid of some examples.

Second, the experimental methods providing information on the monolayer thickness and compactness are reviewed.

Third, considering that the SAM’s thickness and compactness do not only depend on the amount of ligands within the monolayer, but also on their conformation, the experimental methods that can provide such insights are recapitulated. However, we also stressed on the limitations intrinsic to these methods and on the challenges associated to the determination of the structure of SAMs on GNPs.

Fourth, we summarized some of the approaches used to give insights into the organization of different ligands within a SAM. Indeed, mixed SAMs on GNPs are useful since they can impart to the nanoparticles different functionalities and offer a way to tune their stability.

Fifth, highlighting again the limited insights into the SAM’s structure and organization that can be gathered with experimental techniques, we detailed some examples where a combination of experimental and computational approaches was able to provide a compelling description of the system and to assess molecular details that could not have been revealed experimentally.

Overall, this Topical Review gives emphasis on the importance of GNPs’ surface characterization and on fact that even though a number of experimental techniques are available, they are intrinsically limited and they cannot provide a fully detailed picture. Hence, it is advantageous to combine experimental and theoretical approaches to design nanoparticles with desired (bio)physicochemical properties [such as, e.g., our paper under review, currently available as a preprint; RL].

Elena at the MRS

I am catching up after an holiday break. I have not spoken yet with Elena who was at the MRS spring conference in San Francisco, but, thanks to blogging, I can tell she seemed to have had a good experience.

Fellow blogger Mary Nora Dickson enjoyed Elena’s first oral presentation at an international conference:

peptide SAMs on gold NPs

Elena Colangelo spoke today in GG about her work on whether the curvature of gold NPs will affect the conformation of adsorbed proteins. This is an important topic, with wide ranging applications from drug delivery to energy. She found that more highly curved NPs inhibit hydrogen bonding, decreasing the amount of beta sheet secondary structures. This work will help to inform future investigations seeking to modify nanoparticles with functional ligands. Thanks!

Thank you Mary for the report and congratulations to Elena 😉

Elena attended some great talks:

Carlo Montemagno’s talk

What an inspiring talk!

On the last slide of his talk, Michelangelo’s quote: The greatest danger for most of us is not that our aim is too high and we miss it, but that it is too low and we reach it

He gave an overview of the cutting-edge projects (in the general areas of environment, health and energy) going on in his lab, IngenuityLab.

The project that fascinated me the most is the 4D Printer, where the fourth dimension is intended to be the functionality of the complex system built up by single molecules. The general concept is the precise assemble of the functional building blocks found in nature to give new functionalities to the system, where these functionalities are meant to address issues regarding energy, environment and human health.

It may sound too futuristic, but would you ever have imagined having your smartphone, as it looks like today, 10 years ago?

Neelkanth Bardhan’s talk

I had the pleasure to listen to Neelkanth Bardhan’s talk, Gold MRS graduate student awardee, at Symposium GG.

First, I want to say that I found his presentation very clear and easy to follow, nice layout of the slides.

He first went through the motivation of his work: there is the clinical need of safer (compared to X-rays) and less expensive (compared to MRI) detection technologies. He then presented his work aiming to answer this need: developing a biologically-templated nanomolecular probe for high-resolution in vivo sensing and detection. His modular probe is constituted of M13 virus coating single-walled carbon nanotubes (SWNTs). To this construct desired fluorescent dyes and specific targeting ligands can be attached. His results in vivo have shown how this probe is able to target tumours and can be used during real-time surgical intervention.

More details on his work and successful applications of this probe can be found here.

#LearnIT: Blog it! Tweet It! Film It! Wiki It!

That was the name of a staff-student exchange forum which I attended earlier this week. Georgina Turner wrote a blog post on the event at the Digi Learn Blog.

My impression is that there are plenty of exciting opportunities to use social media in teaching but that we have not yet seen the take off. The barriers seem to be more cultural, for both staff and student, than technical. While I am looking forward to the 10 days of Twitter at the University of Liverpool (particularly the last three days as I am already a regular Twitter user), setting up a Twitter account, a YouTube channel or a blog does not require any particular advanced technical skills. It requires a desire to engage and experiment with these tools. There are plenty of open resources to help.

The few things I picked up from the workshop because they resonate with my experience or things I want to do:

  • Students blog/videos etc: open platform or closed? As mentioned by Georgina, we heard from Dr Ian Walkington, and one of his students, Alistair Craig. Ian had asked students to create some videos about climate change (with an engineering angle; I don’t have the exact topic at hand – nor the videos…). They both emphasized that the exercise was an excuse to learn about an academic topic as well as learning how to use efficiently modern communication tools. Ian had made the decision to keep the videos private, i.e. hosted on our University VITAL platform, rather than say YouTube. Alistair seemed to regret that choice and I tend to agree with him that publishing those videos and sharing them more widely would be beneficial for everybody. A great example is the work of @Prof_Dave and his first year Chemistry student video channel. This experiment is further discussed in iTube, YouTube, WeTube: Social Media Videos in Chemistry Education and Outreach, J. Chem. Educ., 2014, 91 (10), pp 1594–1599. We are planning to do something similar for our Biochemistry students from next year as part of a third year module.
  • Georgina mentioned the use of Twitter walls to make lectures to large groups interactive. Sounds like a good idea which I might also experiment next year within another module (quantitative skills to first year biology students where I teach to about ~300 students). I have experimented with Polls Everywhere with some success but Twitter walls offer different possibilities. Georgina mentioned technical difficulties but it looks like our support team has this in hands.

Not discussed in the workshop, but something I have started experimenting with this year and I am very keen to push further in the years to come, is the use of open science notebooks for scientific research projects such as our Honours projects. Gemma Carolan (3rd year student), with the support of Dave Mason, image analyst in our Centre for Cell Imaging (and also new blogger) is currently live publishing her results here. Through this process, students would learn about the benefits of open science, get feedback on their work potentially from scientists around the world, disseminate their research, and also improve their digital literacy skills.

BishopBlog asks: Blogging as post-publication peer review: reasonable or unfair?

An excellent question certainly relevant to Rapha-z-lab. Criticized authors tend to think it is unfair.

Some colleagues/students think that it is fair, but unreasonable (waste of time, etc).

Dorothy Bishop makes a strong case that it is both reasonable and fair; excerpt:

Finally, a comment on whether it is fair to comment on a research article in a blog, rather than going through the usual procedure of submitting an article to a journal and having it peer-reviewed prior to publication. The authors’ reactions to my blogpost are reminiscent of Felicia Wolfe-Simon’s response to blog-based criticisms of a papershe published in Science: “The items you are presenting do not represent the proper way to engage in a scientific discourse”.

Read all of it, here.

On Twitter, Sophie Scott comments:

Indeed. Six papers in Nature journals, one in Science, PNAS, JACS, etc, and nanoparticles can still loose their stripes!