MetaRNA at 10th Young Scientists Symposium 2017

Last year, MetaRNA presented at the 9th Young Scientist Symposium 2016 . This year, Stefano Piccolo – one of the MetaRNA fellow – participates again…but on the other side as part of the organizing committee of the 10th edition of Young Scientist Symposium at IECB in Pessac (Bordeaux – France).

The experience during the last edition of Young Scientist Symposium was so great, that this year Stefano, from the MetaRNA consortium, is part of the organizing committee, and he is looking for the best speakers and sponsors that they can attract.


YYS 2017 organizing committee
From left: Dr. Nina KHRISTENKO, Dr. Josephine ABI-GHANEM, Léonie CUSSOL, Dr. Nassima Meriem GUEDDOUDA, Clémence RABIN, Mégane BORNERIE, Alba HERRERO, Laura BARTOLUCCI,
In font: Stefano PICCOLO (our MetaRNA fellow)

For this 10th edition of the conference, there are two novel features:

  • Round-table career session, with permanent researcher in industry and academia;
  • Three competitive prizes for the best talks and poster by IdEx – Bordeaux University.
    • One of the talk IdEx prize will be attribute by all participants


I hope this year will be even more exciting than before. See you there and do not forget to register!


Young Scientist Symposium 2017



MetaRNA at the 9th Young Scientist Symposium 2016

On the 26th and 27th May 2016, MetaRNA was present at 9th Young Scientist Symposium 2016 in IECB – Pessac (France). Stefano briefs us on the topics that were discussed at this meeting and tells us a little about what he presented there.

Mixing chemistry and biology, the YSS, as the name suggests, is organised for young researchers from both disciplines and from all over the world. With several oral sessions and two poster sessions, PhD students got the opportunity to present their work, discuss the presented research among themselves and with invited researchers from industry and academia.

MetaRNAers Stefano and Sara at the poster session.

All the talks presented an interdisciplinary research approach by combining both chemistry and biology.. This year, we had talks concerning:

  •    Nucleic Acids
  •    Supramolecular Chemistry
  •    Chemistry of 5 senses
  •    Pharmaceutical Chemistry
  •    Genomics
  •    Cancer and Physiology
  •    Career, Industry, Scientific Journalism

I had the opportunity to present some of my results of my PhD project in the first session. My talk was titled Biophysical characterisation of RNA-metabolite complexes by native mass spectrometry.

Stefano giving his talk at YSS.

A few of the MetaRNA members will soon meet again in Bordeaux at the Aptamers in Bordeaux with talks from Beatrix Suess, Jean-Jacques Toulmé, Günter Mayer and posters from Adrien Boussebayle and Stefano Piccolo.

See you soon!

Sara and Stefano


Cell Penetrating Peptides: A System for Delivery

One aspect of design of RNA molecules that serve specific functions is figuring out how to get those molecules inside the cell. In this post, Adrien delves into a system used for drug delivery, known as CPP, or cell-penetrating peptides. Analogues of such technology may be used for delivering RNA molecules developed in vitro into cells.

The ability to have a drug that can be taken up to a very specific location in the body is a long-standing problem. In 1906, the concept of the “magic bullet” was imagined by Paul Ehrlich (a Nobel Laureate for his work in immunology). This concept supposes that we could have what is known as  a magic bullet bring a drug, in a specific way, toward the active site of the drug.

Paul Ehrlich is considered the father of chemotherapy.

The field of drug delivery systems has improved during the last century and there are several types of nano-carriers which are already developed. One of these systems is the Cell Penetrating Peptides (or CPP). CPP are short peptides that are designed to carry molecules (nucleic acids, fluorophore, proteins…) inside the cells by going through the membrane.

Continue reading Cell Penetrating Peptides: A System for Delivery

Meet the Fellow: ISABEL MAICAS

This week, we hear from Isabel who hails from Zaragoza, Spain and is currently working on her PhD in Peter Nielsen’s group in Copenhagen.

What is your background in science? What is a brief description of the project you work on?
I did my Bachelor in Chemistry. During that period I did some internships in different laboratories with different backgrounds, from inorganic to analytical chemistry. But, I have always felt certain curiosity about biology and that is why I end up doing a Master in molecular and cellular biology.

I did my Master’s project at the INA (Nanoscience Institute of Aragón) in Zaragoza, Spain (where I am also from) and my project focused on the synthesis and characterization of different nanoparticles, together with the study of their cytotoxicity profile and the subsequent cellular response. This was a grateful experience where I found a perfect field of study as I was able to combine Chemistry and Biology.

And this brought me to where I am now, doing my PhD at Peter E. Nielsen`s group at the department of cellular and molecular Medicine at Copenhagen`s University, Denmark! My project aims to discover novel dendrimer vehicles for in vivo delivery of aptamer probes and oligonucleotide drugs, optimizing cell delivery and minimizing toxicity.    

isabelWhat led you to decide to do a PhD? What do you hope to accomplish during your PhD?
From the very beginning of my degree I knew I wanted to do a PhD, I guess it is because I really enjoy working in a lab. It can be frustrating sometimes but there is also a feeling of curiosity involved and the happiness when there are good results, this is the best!!  

During my PhD I would like to have nice results for my project, learn from the everyday work and continue enjoying what I am doing. I also have as a personal challenge learning Danish and discover more about this beautiful little country.

Continue reading Meet the Fellow: ISABEL MAICAS

Meet the Fellow: STEFANO PICCOLO

This week, we hear from Stefano, who is an Italian chemist doing his PhD in Bordeaux, France. Along with a liking for good wine, a project around mass spec was what pulled Stefano towards his PhD in Valerie Gabelica’s lab.

What is your background in science (and otherwise)?
Since high school, I felt close to chemistry and technology so I spent my university studies (5 years) in chemistry, the last two years of them on the fence between bio-inorganic and pure organic synthesis. In the end, I found a good compromise by completing my Master’s degree in chemistry on organic synthesis methodology and characterizations of peptide-inspired supramolecules, inside the Bio-Organic Chemistry Lab in University of Padova (Italy).

Then, I got a permanent position as laboratory technician in Pharmaceutical Dep of the same university, in charge for Mass Spectrometry facility and Organic chemistry teaching lab.

What does your lab do? What is a brief description of the project you work on?
My host lab, Valérie Gabelica’s BiophyMS Team, works on biophysical characterization of nucleic acids structures, both DNA and RNA, and non-covalent complexes in general with mass spectrometry.

My PhD project aims to develop a method to characterize the biophysical properties of RNA-metabolite complexes, using mass spectrometry and some advances in this flexible technique.


Continue reading Meet the Fellow: STEFANO PICCOLO

The Warburg Effect

You have been reading a lot on the RNA world: from riboswitches to aptamer biosensors designed by methods such as SELEX. Today, we talk about the metabolism portion of our consortium, and specifically a metabolic phenomenon that cancer cells undergo, known as the Warburg Effect.

One of the defining differences between unicellular organisms, such as bacteria, and multi-cellular organisms, such as human beings, is that unicellular organisms are evolutionarily driven to divide and reproduce as quickly as possible under conditions of excess nutrition. When nutrients are scarce, they stop the production of biomass and change their metabolic activity to cope with conditions of starvation.

You could think of unicellular organisms as an anarchy, where every man is for himself. In contrast, a multi-cellular organism is an intricate bureaucratic network, where each cell is given a singular task that it must accomplish and several control systems are in place to dissuade aberrant individual cell proliferation, even when nutrient availability exceeds the levels at which cell division is supported. Cancer occurs when cells overcome the control of the systems in place; that is, they no longer respond, properly, to the expression of growth factors due to acquisition of genetic mutations that alter the signalling pathways that cells use to communicate with each other and their environment.

The expression of these genes, known as oncogenes, also lead to an altered metabolism in cancer cells as compared to normal cells. Indeed, one of the best-known metabolic abnormality in cancer cells is the Warburg Effect, first introduced by the German physiologist, Otto Warburg, who received the Nobel Prize in Physiology for this discovery in 1931.

The difference in metabolism in normal (left) vs. cancer (right) cells due to the Warburg effect.

The Warburg Effect shows that one of the prime differences in normal versus cancer cells is that when there is oxygen availability, normal cells go through what is known as aerobic respiration. That is, most of their cellular energy, or adenosine triphosphate (ATP), comes from oxidative phosphorylation. In this process, pyruvate, a product of glycolysis, enters the mitochondria, also known as the powerhouse of the cell, and goes through the tricarboxylic acid (TCA) cycle to help run the electron transport system. The Warburg Effect states that cancer cells go through aerobic glycolysis, meaning that they consume much more glucose to produce most of their cellular energy, or ATP, through glycolysis and instead of using the pyruvate in the TCA cycle, they convert it to lactic acid.   

Since the discovery of the Warburg effect, we have learned that tumor-related metabolic alterations are not limited to the balance between glycolytic fermentation and oxidative phosphorylation. There are key tumor genes, such as p53 and Myc that regulate metabolism in cancer cells in a much more complex manner.  

The Warburg Effect is an important example of the value in understanding the links between cellular metabolism and growth control for better treatments to human cancer.

Further reading:
Otto Warburg. On the Origin of Cancer Cells. Science (1956).

Meet the Fellow: ESTHER VOLZ

This week, we hear from Esther Volz as she shares her experiences leading to her PhD and bit about her interests outside of science. She is doing her PhD in the R&D division of DSM, a Dutch-based multinational life and material science company.

What does your lab do? What is a brief description of the project you work on?
I started my PhD at the DSM Biotechnology Center in Delft (Netherlands) which is the R&D core facility for a broad range of life science products. My main objective within the MetaRNA network is to bridge the gap between ongoing research and industrial applications by developing molecular biosensors that can be directly applied to enhance industrial process performances. Since the development of such biosensors is pretty new to me I decided to start a first collaboration with the lab of Günter Mayer in Bonn where I am currently working on my first biosensor target, improving my table soccer skills and learning how to select an aptamer.


What is your background in science (and otherwise)? What led you to decide to do a PhD?
I studied bioengineering. That basically means that you learn how to convince all kind of microorganisms to do what you want them to do, e.g. to produce antibiotics, biopolymers, vaccines, yoghurt or (probably the most joyful example) alcohol. If you keep studying a bit longer you can learn even more fancy things, such as how to build nano-scale devices out of DNA, how to purify antibodies that potentially cure cancer and how to mimic human tissue so accurate so that even stem cells do not realize that they are outside the body.

It was due to those multiple opportunities that bioengineering offers that I decided to stay in research a bit longer and not to start working directly at a company. In my opinion a PhD should enable you to work independently on diverse challenging projects and should open many doors for future personal and scientific development.

Continue reading Meet the Fellow: ESTHER VOLZ

Meet the Fellow: VAKIL TAKHAVEEV

This week, we hear about Vakil’s scientific motivations and aspirations. He is doing his PhD in Matthias Heinemann’s lab in Groningen.

What is your background in science (and otherwise)?

My earliest research experience was walking in forests surrounding my Siberian village and collecting and describing various species of moss and lichen growing on the ground among grass, on tree trunks, in bogs and at the edges of brooks. That was when I was seven. That time I wanted to become a botanist, geneticist, mathematician, physicist, programmer and writer at the same time. For the next ten years I hadn’t solved the dilemma which path in the above-mentioned list to choose loving them all so I moved to Moscow to study bioengineering and bioinformatics which I thought would include everything I liked. And indeed during the years at university I dived in calculus and probability theory, researched microevolution of one tiny bristle worm living in a northern sea, took part in setting up a web-server for examining protein structures, became acquainted with the powerful tool of analytical science called mass-spectrometer, wrote several poems including one in German. For my graduation project I moved to Leiden, a spectacular Dutch town with myriads of canals and brick bridges over them, to find out how human ageing affects splicing – a sophisticated process of rearranging RNA sequence. There I fulfilled my passion of uniting different fields: biology, programming and math (here, in the form of statistics) in one project.


What led you to decide to do a PhD?

I always wanted to do a PhD as I was interested in science since my childhood. PhD is about becoming an independent researcher, a person leading projects, formulating and solving tasks; and I would like to turn to a professional like that.

Continue reading Meet the Fellow: VAKIL TAKHAVEEV

Meet the Fellow: ADAM MOL

Today we hear from Adam Mol, who is working in Beatrix Suess’ lab at TU Darmstadt, Germany!

What is your background in science (and otherwise)? What led you to decide to do a PhD?
I completed my studies in the field of Biotechnology at the University of Silesia, Katowice, Poland. My master project was carried out in the Department of Genetics where I was working in plant genetics. This research was related to drought resistance in cereal crops. My work there allows me expand my knowledge about molecular biology and piqued my interest of Science. This experience gave me a great opportunity to enter into real scientific life for what I would like to thank my advisors Prof. Mirosław Małuszynski and Dr. Agata Daszkowska-Golec.

Next as a graduate student I have been continuing my scientific carrier as a member of Vilardell’s lab at the Molecular Biology Institute of Barcelona (IBMB), Barcelona, Spain. I have been investigating research related to alternative splicing in human cells. My work at IBMB was very important step in my scientific carrier which gives me opportunity to improve both my theoretical and experimental knowledge about biomedicine.

And now I am convinced that I would like to continue my scientific interests as a PhD student.


What does your lab do? What is a brief description of the project you work on?
Currently I do my doctoral studies at Synthetic RNA Biology group headed by Prof. Beatrix Suess at Technical University of Darmstadt, Darmstadt, Germany. A main focus of our research is the development of active aptamers. The group has very good background in in vitro selection of aptamers as well good establish in vivo screening system. Also we try to find application of aptamers as synthetic riboswitches. Second focus in our group is related to disease. We work with natural regulatory RNA: siRNA in bacteria, microRNA in inflammations as well with alternative splicing in hypoxia.

Continue reading Meet the Fellow: ADAM MOL

Antibiotic Resistance and Metabolism

This week, we hear from Leonie about the relationship between a very important global health problem – antibiotic resistance – and research on metabolism.

According to the Centre for Disease Control and Prevention at least 23,000 people die each year in the United States due to infections from antibiotic resistant bacteria. But the problem is not limited to the US and occurs in all parts of the world. The World Health Organization calls antibiotic resistance a major global health threat. Therefore, limiting or reversing antibiotic resistance evolution as well as the development of new antibiotics is crucial to guarantee treatment of bacterial infections also in future.

But hey – why are we talking about antibiotic resistant on our metaRNA blog?

One strategy to deal with the emerging health threat is to understand the resistance mechanisms in greater detail.  87% of the metabolites in a bacterial cell change their abundance when exposed to antibiotics. Some changes seem to be dependent on the antibiotic class whereas others appear to be general metabolic changes caused by antibiotics.

Screen Shot 2016-02-22 at 23.00.50
Taken from “How to Fight Back Against Antibiotic Resistance” by Gautam Dantas and Morten Sommer in  American Scientist.

So far metabolomics hasn’t played a big role in the antibiotic resistance research field, even though there is evidence that not only metabolic profiles change during antibiotic treatment but also resistance-conferring mutations directly affect the bacterial metabolism. For example the amino acid metabolism or lipopolysaccharide synthesis can be affected by the development of antibiotic resistance. Other mutations were shown to affect the choice or ability to process different carbon or nitrogen sources.

The analysis of resistant mutations in regard of metabolic fluxes offers consequently a great potential to understand resistance mechanisms and what exactly happens in resistant cells. A detailed understanding of these processes might help to open up avenues of potential new treatment strategies or the development of new drugs. Another link between resistance and metabolism are reversible phenotypic adaptations of bacteria to antibiotics that are not manifested in the genome. These adaptations can result in temporarily highly resistant bacteria, called persisters. This phenotypic adaptation is also an important piece to understand the puzzle of antibiotic resistance and is consequently an interesting target of research.