Meet the Fellow: EDUARDO GOICOECHEA SERRANO

 

It’s Saturday – time for another Meet the Fellow post! Today, we talk to Eduardo Goicoechea Serrano.
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Hi there! My name is Eduardo. I am currently working at the University of Warwick, doing my PhD on synthetic biology. I thought I might tell you a bit more about myself

What is your background in science (and otherwise)?

Aka “How did I end up here?” Basically I always liked Biology. I had quite the mixed aspirations when I was a kid (the usual secret agent or astronaut, yes, but you’re dealing with someone who at one point fancied the idea of becoming a GEMOLOGIST), but eventually took the road towards science, and became the centre of the “Huh?” looks and the “So what is it that you’re working in?” at family gatherings.

I started my undergrad in Biology, but since Spanish education system is an complex, ever-changing nightmare, after year 3 I changed to Biochemistry (a second cycle degree, meaning you could only get by finishing a first cycle in bio, chem, medicine…). After that, I went back to Biology, and exchanged some of the subjects I had already taken at Biochem for their equivalents in Biology, and finished in one year. The next school year I did my Biotechnology masters at Kingston University, in London. Not bad for my first contact with the UK educational system.

Continue reading Meet the Fellow: EDUARDO GOICOECHEA SERRANO

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What are aptamers Pt. II: Spinach

This week, we hear from Adrien again on a particular RNA based aptamer, known as the Spinach aptamer. Adrien explains how this aptamer works, what makes it unique and the types of applications it can serve.

The most famous example of an aptamer-based biosensor is the Spinach aptamer. This aptamer mimics the Green Fluorescent Protein (GFP), one of the most-used tools in molecular biology because it is possible to target GFP to different parts of the cell, and, using a blue light, obtain visual information.

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The target of the Spinach aptamer is DMHBI, a derivative (i.e. a compound made from) of the hydroxybenzlidene imidazolinone (HBI). HBI also happens to be the fluorophore of the Green Fluorescent Protein (GFP). DMHBI is non fluorescent under UV light. When the DMHBI molecule is bound by RNA, its is held very tightly. Normally, the atoms of a molecule shift or rotate along their bond. However, but in the RNA-bound state, DMBHI must release its excess shifting energy as fluorescence. Specifically, the compound emits a light at a wavelength of 529 nm (which is the wavelength corresponding to the color green).
The Spinach aptamer can be coupled to a second aptamer chosen to bind a target molecule of interest. This coupling is what makes the Spinach so uniquely useful: fluorescence is visible only if the second aptamer is bound to the target molecule. Another way to think about this concept is that the Spinach will be bright green only if the binding molecule is in the cell or test tube.

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(a). Both DFHBI (green ball) and Spinach are non-fluorescent until binding occurs and activates the fluorescence of the Spinach-DFHBI complex. Stem loop 3 of Spinach can tolerate insertion of additional sequences, and it is the region that is modified to generate sensors. (b) In Spinach-based sensors, Spinach is modified to include a transducer region (magenta) and a recognition module (cyan). (c) In the absence of DFHBI and ligand (orange hexagon), the Spinach-based sensor displays minimal fluorescence. However, upon target binding, the recognition module of the sensor folds and induces folding of the Spinach portion of the sensor. The Spinach-based sensor is then able to bind DFHBI and activate fluorescence. From Strack et al. (2014).

In the last two weeks, we have covered the basic concepts of aptamer binding, SELEX, and the Spinach aptamer. To conclude, aptamers are developed for a lot of purposes, such as making riboswitches, detection of cell metabolites, live tracking of RNA molecules, simultaneous detection of mRNA and protein, etc. The diversity of function which originates from RNA structure is at the heart of aptamer development. It is a field of research both fascinating and full of opportunity to develop a plethora of novel “nano-tools”.

Meet the Fellow: RUBEN VAZQUEZ-URIBE

In this installment of Meet the Fellows, we hear from Ruben Vazquez-Uribe.

What is a brief description of the project you work on?
In my research topic I design and study the dynamics of synthetic gene circuits. Our goal is to develop tools and devices to program cells in the way we program robots nowadays. With these genetic circuits we aim to integrate the molecular signals of multiple metabolic and environmental sensors in order to connect it with specific complex cellular programs.

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What is your background in science (and otherwise)?
I did my bachelor in environmental engineering, and during my first research projects I worked with biological water treatment processes. Our objective was to evaluate different parameters and the performance of the processes, however I got more interested in processes happening in the molecular level of the microorganism I was using. Furthermore, I felt the need to learn and develop tools to improve these molecular processes. Therefore as a next step in my career I decided to do my master in molecular biology. During my master I decided to focus on projects in the areas of synthetic and systems biology. On my projects I mainly learnt and applied technics for metabolic engineering, synthetic biology and mathematical modeling.

Why are you motivated to work on this topic?
There is significant interest in designing robust and reliable organisms that can assist on long-duration space exploration missions. In this matter, advances in synthetic biology have shown that it is possible to program cells to sense, integrate, record and process molecular signals while connecting them with specific cellular processes. Therefore programming cells in a computer-like manner to solve different challenges in space exploration is a really appealing topic for me, and it holds plenty of interesting engineering challenges and opportunities to be solved.

What led you to decide to do a PhD?
I like science and doing research.

An ITN is about international collaboration – what has your experience been so far in living in a country that is, perhaps, quite different from your own? What are some tips you would give to new PhD students (or students in general) who are moving to a different country?
Effective communication is not only about the language, the cultural factor also posses a communication barrier. In some countries there is a hierarchal organization between PhD student and supervisor, while I have found that in other countries like the Netherlands or Denmark communication with your supervisor is more effective if you see them as colleague and have a more open and direct communication with them.

It hasn’t been that long since we were interviewing for PhDs; what are some pointers you would give to students looking for a PhD to do during their undergraduate or Master’s?
Three things:

  • Become as independent as possible.
  • Trust your decisions.
  • Don’t expect to be good and feel completely comfortable with your future new lab, at least in the beginning. You might have got the hang of it in your previous lab, but you need to consider that you will be a new student in a completely different lab. Don’t get frustrated in the beginning, just accept that you will be new, and focus on adapting to the new lab and trusting what you know and enjoy.

What do you like to do for fun?
I like science fiction and videogames.

What is your favorite food?
Thick crust pizza and deep dish pizza.

What are aptamers?

Today, Adrien Boussebayle explains the focus of his PhD to us: aptamers. And admits some lab secrets…

 

What a strange word… Aptamer comes from the Latin “aptāre “ (to put into position, fit together, join), and from the Greek “meros” (part). By definition, an aptamer is a single-strand DNA or RNA which can bind a specific target with high specificity (uniqueness of binding) and high affinity (strength of binding). These targets can be small, like a Zn2+ ion or as big as protein and even entire cells.

Aptamer are selected by a process called SELEX (Systematic Evolution of Ligand by Exponential Enrichment) by combining your desired binding target in contact with a large number of potential aptamers. The researcher constructs a large RNA or DNA aptamer pool, also known as a SELEX library, composed of several tens (usually 30 to 80) of random nucleotides. Overall, this selection library will contain 1013 to 1016 unique pieces of RNA or DNA.

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This pool of potential aptamers is incubated with the binding target, which is bound to a solid matrix. The matrix is used to filter out low-affinity or non-specific binders. The remaining sequences will have some binding properties. The selected aptamers are amplified (i.e. multiple copies are made) and used in the next SELEX round. Each round will produce a smaller aptamer pool with improves binding properties.

Continue reading What are aptamers?

Meet the Fellows: ADRIEN BOUSSEBAYLE

Welcome to the second instalment of our weekly Meet the Fellows series. Here we get to meet Adrien Boussebayle!

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What does your lab do? What is a brief description of the project you work on? What is your background in science (and otherwise)? Why are you motivated to work on this topic? What do you hope to accomplish during your PhD?

The truth is, when I finished high school, I didn’t think I would go so far in my studies. I first did a technical university diploma for two years in biological engineering. Seeing that biology is complex and very interesting at the same time, I decided to continue studying in a BSc in Microbiology, Cellular and Molecular Biology. Then I accomplished a Master degree in biochemistry and chemical biology. What I really liked during my studies, is that I could have a good overview of all the different field related to biology, either on the chemical/physical interface during my Master, or on the molecular biology and in vivo part during my Bachelor’s.

Currently I am at the TU Darmstadt in a lab working on synthetic RNA biology, and I am working on the development of new aptamers and riboswitches.

Continue reading Meet the Fellows: ADRIEN BOUSSEBAYLE

What is RNA?

By the editors.

As you might have gathered, the main focus of this blog is RNA in all its variations. Let’s take a look at what makes RNA special and why we should study it!

I asked my flatmate what he remembered about RNA. Here is what he said:

“RNA? Well, I know it’s not DNA! I could tell you about DNA.
Hmm, I do know it has an R in it. So…. rhino nucleic acid?”

Close enough, I suppose. The letters RNA are an abbreviation for ribonucleic acid, which is a single-stranded molecule of nucleic acids closely related to those found in DNA. Though the basic building blocks of RNA and DNA are more similar than different, RNA is emerging as a fascinating molecule in its own right.
Continue reading What is RNA?

Meet the Fellows: SARA MASACHIS

Welcome to the first post in our weekly series, Meet the Fellows. Each blog post will feature a short interview with one of the fellows of the metaRNA network. Today we have the pleasure to meet Sara Masachis!

 

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What is your background in science (and otherwise)? Why are you motivated to work on your research topic? What do you hope to accomplish during your PhD?

My background is in Molecular Biology, I’ve been trying to unravel the genetic and molecular mechanisms that enable a pathogen to effectively interact with its host and survive while working in Antonio Di Pietro’s Lab at UCO Spain. I’m deeply grateful for this experience that allowed me to discover my inner motivation for science. I was working with a plant pathogenic fungus called Fusarium that I realized the lack of genetic regulator tools for Molecular Biology, not only for this fungus but for the vast majority of “non-model” organisms; therefore I became interested in the potential of the extremely powerful field of synthetic biology.

During my PhD I hope to develop myself both personally and scientifically at the same time I’ll try to contribute to the global scientific knowledge.

Continue reading Meet the Fellows: SARA MASACHIS

What is an ITN?

ITNs have been described as the “golden PHDs”, but what does that mean?

In this post you can discover a bit more about this funding scheme and the opportunities it offers, both professional and personal.

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For each of the Fellows that are part of the metaRNA network, an ITN is a fantastic research opportunity: we get paid to do what we love. At the same time, our network is contributing to a bigger picture of innovation for the future.

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The root of ITNs lie in the Marie Skłodowska-Curie actions, an EU funding initiative to support scientific endeavours with an endowment of €6.16 billion. This grant is allocated to a number of projects under the Horizon 2020 remit, which is coordinated by the European Framework Programme for Research and Innovation. Innovative Training Networks (ITN) are an aspect of this funding scheme dedicated to educating promising young researchers at doctoral level. They will finance over 25 000 PhD students… and 15 of them will be the topic of this blog!

This funding scheme enables each of us to immerse ourselves in research and education for three years, but they also create an invaluable network of knowledge around a common topic: RNA and metabolism. The Fellows have a wide range of scientific backgrounds and this allows for the kind of interdisciplinary approach that generates innovative solutions. 

In addition to interdisciplinarity, ITNs also foster personal and professional mobility. Every Fellow has moved to a new EU country for their project. Faced with a new language and a new culture, we have quickly needed to learn transferable skills and collaboration.

Ultimately, learning is the integral aspect of an ITN. Each one of us has been provided with unique ideas frominside and outside our field and the opportunity to travel and collaborate. But on a daily basis, we are also challenged by research that we know nothing about and ways of thinking that are completely new. 

 

The individual network members are a truly diverse group of people. This blog will introduce them one by one in the new weekly “Meet the Fellows” post series. Get ready to meet Sara Masachis this Friday!