Aptamers 2016 – Oxford, UK

Adam Mol  was in Oxford at the beginning of the month for the Aptamers Conference. To find out more about this conference, check out @LPMHealthcare,  @AptamerSociety or #AptaOx16 on twitter.

Gladly, I would like to announce that on 04-05 April, I participated in Aptamers 2016: 3rd Oxford symposium on Aptamers. The meeting took place at St Hilda’s College, Oxford, UK. This year the symposium chair was Professor Beatrix Suess from Technical University of Darmstadt, Germany.

aptamer conf 1

Aptamers 2016 was an excellent symposium! It brought together academic and industrial aptamer researchers. During the meeting, therapeutic, diagnostic, analytical as well as basic research applications of aptamers were addressed. The symposium was divided into five sessions:

  1. SELEX – New technological developments
  2. Small molecule binding aptamers – Characterization and their application for gene control
  3. Aptamers as diagnostic tools
  4. Therapeutic aptamers
  5. Further Technologies

aptamer conf 2

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Meet the Fellow: JOSI BUERGER

Our Meet the Fellow series is almost coming to a close, as we have now met 14 out of 15 Fellows. Today we hear from Josi Buerger based at Biosyntia. Find her on twitter at @josi_bee.

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?josi 1

To be perfectly honest, the only reason I enrolled for Molecular Biosciences at my university was because I had good marks in Biology at school… In hindsight, this wasn’t due to any inherent talent on my side, but because I had a fantastic teacher.

This was problematic once I started my undergraduate studies. I had trouble engaging with topics outside of their practical context. In fact, in my second year, I switched to a joint Philosophy and Biology degree and was convinced that research was not for me. Not until honours classes did I re-discover my interest in science, as teaching at that level was centered on critical thinking that encouraged discussion.

I focused on taking courses on applied biotechnology, as I realised I enjoyed engineering and problem solving. I also learnt that I appreciate lab work, despite all its frustrations. I focused my Masters on metabolic engineering and feel incredibly lucky to have my PhD based in a dynamic start-up that builds biosustainable solutions.

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The EUSynBio Symposium 2016

Josi Buerger attended the EUSynBio Symposium in London last weekend. Here is a personal account of the conference and why you should go next year…

The first Symposium of the European Association of Students and Post-docs in Synthetic Biology (EUSynBioS) advertised itself as an “open, funky, and slightly unconventional synbio event”.  I’ve been involved with parts of the EUSynBioS community before so I decided to attend the 1.5 day conference.

The symposium was held at Imperial College last Saturday, the 9th of April and included a visit to the London Hackspace the next day. The morning session was kicked off with an inspiring talk by Dr Tom Knight on the future of synthetic biology and the importaeusynbio symponce of in silico approaches. This was followed by students and early-stage researchers presenting their research. SynBio is of course about building tools for any application, so the presentation topics ranged from rhodopsin engineering in E. coli  to changing the lifestyle of Pseudomonas. Overall the atmosphere was very pleasant – never one to hold back in the question section myself, some great discussions took place.

Coffee breaks allowed for networking with other attendees. For example, I learned about the Cambridge Hackathon happening early this summer and even talked with industrial designers who were interested in this new field of engineering.

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Meet the Fellow: AAKRITI JAIN

Editor of two (!) synthetic biology blogs and not afraid to move cross-country AND cross-discipline: Aakriti Jain.

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?

My background is in chemical engineering but I got interested in synthetic biology during my undergraduate, while working in Jay Keasling’s lab at UC Berkeley. I’m thankful for this experience as it introduced me to the world of biological research(which, in my opinion, is vastly different from high school classroom biology). It was through this introduction into biology (from an engineer’s perspective) that motivated me to explore more cellular metabolism, since I found out quickly that this was an important, and sometimes limiting, aspect of synthetic biology.

Hopefully during my PhD I will not only learn some pretty cool techniques and develop amazing science, but also gain more confidence in my scientific knowledge.


What led you to decide to do a PhD?

As an engineer, I always thought I would go straight into industry, but thankfully I decided to do a Master’s before entering the corporate workforce and quickly realized that academia is where my passions lie (at least for now!)


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?

Ask every scientist in your life to help you find the perfect PhD for you. Luckily (or not) science is a really collaborative endeavour, and scientists always know of other scientists and other opportunities. Ask them advice on institutes as well as professional colleagues. Apart from this, and more importantly, take some time to think deeply about what you want to spend the next 3-4 years working on. This will be your project and it should be something that motivates you every day!

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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.

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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.


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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

Engineering Life for Long Term Space Missions

Stories can inspire people to imagine and create the future. In fact, a lot of our predictions about the technology of the future come from science fiction stories. Take for example the mission to the moon in the novel “From the Earth to the Moon” published in 1865. Jules Verne tells the story of how the US sends 3 men to the moon, in a spaceship named Columbiad, launched in a rocket that weighs 9,000 kg at the cost of 12.1 bn dollars. 104 years later, in 1969 the US in fact sent 3 men to the moon in a spaceship named Columbia, weighing 11,000 kg, at the cost of 14.4 bn dollars. The list of science fiction inspiring today’s technology is long and although not all come true (sorry, still no lightsabers…), many of them are really accurate.

Stories can inspire people to imagine and create the future

One of the most popular subjects for science fiction novels are missions to and colonization of Mars. As a human species we have been setting our eyes on Mars for a long time. Many projects are currently under development. For example, Mars Direct is a project with the goal of starting a human colony on Mars within the next decade (1). In the same manner, NASA aims to have technologies to land humans on Mars by 2030 (2). In the private sector, Elon Musk, the CEO of Space Exploration Technologies Corporation (SpaceX) has targeted 2026 for a Mars landing with plans to establish permanent colonies(3). Maybe  one day the first generation of humans will contemplate a blue sunset on Mars, but before that could happen we have a long way to go. Because, the farther you go into space, the less you can depend on Earth.

Continue reading Engineering Life for Long Term Space Missions