International Trip 2015-2016: Copenhagen

Copenhagen Trip 2015

Science Honours Academy

Written reportage by: Hugo Damstra (Molecular Life Sciences), Dido van der Gon (Physics), Joyce Kromwijk (Chemistry), Sten Tonkens (Biology), Livia Wilod Versprille (College of Pharmaceutical Sciences)

On Monday evening we arrived in Copenhagen at our beautiful hostel. After quickly dropping our bags in the room, we went to the ‘Steaks and Veggies’ restaurant for our vegetarian buffet. The evening was free for everyone. The next morning, we visited the Technical University of Denmark (DTU), where we had a few lectures about wind turbines and a tour of the campus to see how they improve and test the turbines. We also had the opportunity to go into a real working turbine. After a lunch provided by the committee, we drove to the Nanoscience Centre. Where we had some interesting lectures about Evolutionary Chemical Biology and NanoGeoScience. After the lectures we had a tour of the labs, where we saw many state of the art techniques to study all kinds of materials and compounds. This was the end of the program and we walked straight to the restaurant. However the day was not ended yet, and many students visited some bars or saw some of the city by night.

The next day, we visited the Centre of Biopharmaceuticals and the Faculty of Computer Science. The group was split in two and we took turns. A the Centre of Biopharmaceuticals we had some interesting lectures about the research they are conducting on proteins, peptides and other biopharmaceutical compounds. We also had a lecture about how they set up a spinoff company. Besides the lectures we also had a lab tour of their three labs. At the Faculty of Computer Science, we had a lot of different lectures on different topics. We started with two lectures by the Niels Bohr institute, Faculty of Physics. The first lecture was about how the climate in Greenland has developed over the years. Then we had a lecture about how to make (new) faster computers, which can be used for quantum calculations. After this we had some small lectures about bioinformatics, and what they do. The final two lectures were about Alzheimer’s disease and the other one about protein folding. For the last time we had dinner at “Steaks and Veggies”. This evening you could choose between a free evening, going swimming or going bowling.

The last day was not the busiest day, because we only had to go to the botanical gardens. In the botanical gardens we first had a lecture about the research they conduct, specifically about the quinine as a medicine for malaria. Then we had an extensive tour of the greenhouses. After that we had an afternoon off. Everyone visited different places and had a great dinner.

In short we had a fun and interesting week with topics for everyone. We had a chance to see and experience something of Copenhagen. The trip was well organised by the international trip committee.

A complete overview of every day in Copenhagen can be found below. A photo report of the trip can be downloaded at the bottom of this report.

Tuesday 10/11

Technical University of Denmark (DTU)

The first excursion of the Copenhagen trip was to the Technical University of Denmark (DTU) Risø campus. Upon arrival we received some introductory lectures on the purpose of the visit. We had tours of three departments within the Risø campus: the wind turbine test facility, the drivetrain facility and a tour through the section Materials Science and Advances Characterisation (MAC). The lectures were very useful for the accompanying tour. The first one was about the general process of generating energy using wind turbines by senior scientist C. Bak, then a lecture about mapping the average wind speeds across the world. This is fundamental information when placing a wind turbine since small changes in location can have drastic effects on the efficiency and output of a wind turbine. The third lecture was about the wind turbine test facilities in Høvsøre and Østerild. With wind turbines increasing in size, new and bigger test facilities are needed to determine turbine outputs. This started with the Høvsøre facility in 2002. The Høvsøre wind conditions allow an almost uninterrupted wind speed coming from the North Sea and can cope with turbines of 165 metres in length, when the blades are pointing upwards. The Østerild facility is also located on the coast, with wind coming from the North Sea and made testing of the world’s largest turbines possible, such as the Vestas V164, with a blade diameter of a staggering 160 metres (equivalent to the wingspan of an Airbus A380 per blade) and a total height of 220 metres. The test facility in Risø was not built to cope with turbines that big and is now being used for more fundamental research such as the turbulence generated behind the spinning blades. In front of the wind turbines at the same height as the shaft connecting the blades to the generator, a device was placed to record wind speeds so that the turbine output could be calculated. The airflow at the rear of the turbine was measured using lasers for the research on turbine turbulence.

The second group we visited was the drivetrain facility. The drivetrain is located in the nacelle of the wind turbine and includes the generator, transmission, gears, etc. The test setup was a Vestas V47 nacelle connected to a large motor. The nacelle was connected to the power grid to test the output of the nacelle. The theoretical maximum efficiency is around 60%, which corresponds to a maximum efficiency of 45-50% in the field. The facility also enables researchers to strain the shaft, bearings and gearbox with increasing loads such as fluctuations in speed, torque or emergency shutdowns. The V47 nacelle stands on a support bed that is attached to 8 metal supporting rods, which were cross-linked with metal bars that could either be tightened or loosened to mimic wind turbine tower flexibility.

Lastly, we visited the microscopy department of the MAC section. They are focussing on processing, structure, properties and performance of metals and alloys. They used transmission electron microscope (TEM) and scanning electron microscope (SEM) for the examination of cracks in metal. These are electron microscope techniques where they image the inside of a sample with TEM and the surface of a sample with SEM, using electrons to create an image instead of conventional light waves. The use of electrons results in much bigger magnifications. Another technique they used was computed tomography EM to visualize how cracks propagate within the sample. After everyone completed each of the three tours we gathered in the DTU auditorium for a nice lunch prepared by the International Trip Committee.

Nanoscience

One of the, in my opinion, most exciting facilities we visited during our stay in Copenhagen was the Nano Science Centre. Being a cross faculty between the Faculty of Natural Sciences and the Faculty of Health, it consists of a vast array of different research groups, each with its own speciality ranging from Membrane Properties to Condensed Matter Physics. The centre also introduced the first full Bachelor- and Master’s education in nanoscience in Denmark. To give us a good impression of the research this faculty does, Mortem Medal from the research group Evolutionary Chemical Biology and Tue Hassenkam from the research group NanoGeoScience gave us a short lecture about the work their do after which we had to see the lab facilities.

The group of Evolutionary Chemical Biology, led by Mortem Medal studies several phenomena in biology and complex structures which play a role in molecular and biochemical processing. The group uses polymers for synthesis and biomolecular screening. The polymers are used for biochemical assays and studying the structures of macromolecules and their function. This knowledge obtained from this research can come in handy when treating specific diseases such as Alzheimer’s disease.

The focus of NanoGeoScience’s research is to apply nanotechnology in order to reveal the secrets of nature. This fundamental aspect is mixed with requests from the industry to ensure a more sustainable way of living. A few examples of cases they work on are: ensuring cleaner drinking water, storing waste more safely and producing more oil from existing reservoirs. These processes can be controlled on nana-scale. The NanoGeoScience group is the most interdisciplinary research group at the University of Copenhagen. The scientists working for this group have amongst other things a background in biology, chemistry, physics, geology and engineering.

After the lectures, scientists working for the two research groups showed us around the laboratories. Sanne Schoffelen from Nijmegen who is currently doing her post-doc at the group of Mortem Medal showed the brand-new labs their group is using currently. The lab hall had to be built from scratch and since 2014 they are able to perform their syntheses in the very modern and fresh looking laboratory. In the basement of the building they work in, some high resolution mass spectrometers were located in order to analyse their compounds.

The group of NanoGeoScience uses many state of the art techniques and devices to study all kinds of materials. In order to get a little bit more acquainted with the techniques they use, every staff member who is specialized in one of the techniques gave a short presentation about the device they use and what kind of information they obtain from studying materials with that specific device. In the basement, the group has an electron microscope which is able to observe all kinds of materials at high magnification. This way they can get wind of the sample’s morphology and on top of that, the technique can provide a quantitative element analysis. Another technique the group uses to determine the exact composition of a sample is X-ray photo-electron spectroscopy. This method provides more information on the chemical composition at 1-10 nm from the sample’s surface. The last technique object was Atomic Force Measurement which uses a tip which can measure the forces between itself and the sample. These forces are used to reveal more information about the surface of the object which is analysed.

Before visiting the Nanoscience centre I expected to hear more about research involving catalysts, quantum dots and colloids since this is what comes to mind when I think about nanoscience. It came to me as a surprise that nanoscience can also be used in protein research and in geosciences. The diversity of the Nanoscience centre showed that nanoscience is a fundamental part of a lot of research that is currently done and that these very small particles can make a huge difference in our lives.

Wednesday 11/11

Centre of biopharmaceuticals

In the morning or afternoon of Wednesday, depending on the group you were in, we visited the Centre for Biopharmaceuticals. Professor Kristian Strømgaard gave an introduction of the department. The department has bonds with several departments; these are the School of Pharmacy, the Faculty of Pharmaceutical Sciences, the faculty of health and Medical Science, and the Medical Centre.

In the Centre of Biopharmaceuticals they research everything related to proteins and peptides. They also try to discover drugs, because the drugs are proteins or peptides, the drugs are big and are administered intravenously. This drug research is primarily focussed on protein-protein interactions, membrane proteins, and organic chemistry peptides. Thus this is interdisciplinary research, primarily focussed on biology and chemistry. The centre also has a spinout company, focussed on a particular drug.

This short introductory lecture was followed by three small lectures; “Case Studies in Protein Medical Chemistry” by Professor Kristian Strømgaard, “Chemical Synthesis to Probe Enzyme Function” by Assistant Professor Andreas S. Madsen, and “Molecular Function and Pharmacology of Membrane Proteins” by Postdoc Tim Lynagh.

The first lecture, “Case Studies in Protein Medical Chemistry”, had two examples of researches in that research group. The first research had its focus on protein-protein interactions. The proteins were targeting interactions in the brain, specifically the glutamate receptors, when over stimulated they can cause a stroke. They engineered a compound that could act as a novel treatment for stroke and could pass the blood-brain barrier. Before they tried a protein, they tried a small molecule; however none of the compounds worked. This protein was turned into a drug and a spin-off company was formed.

The second research had its focus on introducing unnatural amino acids into transporter proteins. They genetically modified the genes to see the molecular details of inhibitor binding. The introducing of unnatural mutagenesis of neurotransmitter transporters shows them where the transporters are, and how they function. This eventually can help them develop better drugs for neurotransmitter transporters.

The second lecture, “Chemical Synthesis to Probe Enzyme Function”, was focussed on mimicking nature’s structure and function. They were focussing on HDAC inhibitors and lysine deacetylation. They do this to see how deacetylation of lysine can affect gene transcription. They are also interested in epigenetics, because the genes provide the identity of our proteins. Epigenetic mechanisms are also interesting, because they affect temporal, cell and tissue specific expression levels. This research group also does a lot of chemical synthesis, docking studies and organic synthesis of substrates. Their aim is to develop more selective drugs and drugs with fewer side effects.

The third lecture, “Molecular Function and Pharmacology of Membrane Proteins”, had its aim more at drug receptor interactions and membrane drug interactions. This group was especially focussed on ion channels and used regular mutagenesis to expand the genetic code to get shorter proteins. Do shorter proteins work or not? They do these experiments to see where the drugs and proteins bind to the target, in order to create more selective drugs.

After the three lectures we had a lab tour in the three laps; The Pless Lab, The Olsen Lab, and the Strømgaard Lab: Semi-Synthesis of Proteins.  The labs all had a different lab. They were roughly divided into three categories, the chemical synthesis lab; the Pless lab, the biology lab; the Olsen lab, and the semi-chemical synthesis/semi-biology lab; the Strømgaard lab. In all labs we saw some instruments and examples were given of their experiments.

After the lab tours Assistant Professor Anders Bach, Consultant at Avilex Pharma, gave a lecture about creating a spin-off company. In a spin-off company the academics and industry comes together in order to get a drug on the market. Trying to get a drug on the market is a long and hard road.

The day consisted of a lot of interesting lectures about the experiments they conduct. The lab tour also gave a good overview of how the experiments are performed. In short, it was a very interesting and informative morning.

Computer Sciences

On Wednesday afternoon we (group A) went to the Faculty of Computer Sciences. Where we had a couple of very interesting presentations. We started with two presentations by the Niels Bohr Institute, the Faculty of Physics. Niels Bohr is a very famous Danish theoretical physicist who received the Nobel Prize in 1922. The first presentation by a teacher of the centre of Ice and Climate was about Ice core analysis and interpretation of ice-core derived data. In order to study the climate change we’re now going through. He told about why they do this kind of research: to find out more about what the climate was like in the past. The differences with nowadays and to predict what it will look like in the (near) future. He also told a lot about what it was like to be in the field, collecting the ice cores, working on Greenland. I have to say that it looked beautiful, the great white planes!

The second presentation was about a new kind of computer because the ones we are using right now are getting too slow. They are at the moment trying to make a quantum computer, something really very difficult. The principle is that you use photons to store data and to run processes. The big advantage of this kind of computer is that it can process more at the same time. Instead of calculating ten sums, sum by sum. It calculates the ten sums at the same time.

After the presentations by the Niels Bohr Institute followed some presentations about the department of bioinformatics, which were, if I may say so, very interesting. We started with three presentations by a postdoc, a master student and a PhD-student. They all talked about what bioinformatics is and their research. In bioinformatics you work mostly with DNA, RNA and Protein folding. You treat the big data, the immense amount of data you gather when sequencing DNA or RNA. How do you programme your computer so that it can do these calculation in less than 15 years?  How can you order these data so that you know what the DNA sequence means? What proteins has the cell made? These are the kind of questions bioinformatics is about. The kind of research you do is off course also in this direction. For example you can look at the differences between cells on different locations in your body. Do they produce other proteins? How does this come? You can see what proteins they produce by sequencing the RNA, why they only produce these proteins? Up to now nobody knows. Another example of what you can do with bioinformatics is comparing the DNA of people with a certain disease to that of healthy people. To see if there is a difference and if possible help to find a cure by for example genetic manipulation.

Then followed a small talk with ten reasons for studying bioinformatics in Copenhagen. I won’t give all ten reasons but one of them was that Copenhagen University is the sixth university in Europe and another that bioinformatics is a very new field of study and because of this there is a lot of research to do.

And last but not least followed two more presentations about research concerning bioinformatics. One was about Alzheimer’s disease, the other one about protein folding. Both were very interesting. They are investigating Alzheimer’s by comparing the MRI scans of healthy brains to brains suffering from Alzheimer’s disease. And also by comparing the DNA of these patients. For analysing the large amounts of data you gather from both the MRI scans and the DNA sequencing you need bioinformatics. The last presentation was about protein folding. It told about how to simulate the folding and structure of proteins. For small proteins you can just apply all the basic physics rules. But when you’re treating larger proteins this takes too long to calculate. Here again you need to use bioinformatics to programme a computer to calculate this quickly. It still is a very new field of research and still a lot of research has to be done!

Thursday 12/11

Botanical Gardens

The last day in Copenhagen we went to the Botanical Gardens. Before we actually visited the Botanical Gardens themselves, we had a lecture from Nina Rønsted in the Geological Museum of Copenhagen. Nina Rønsted is Professor of Higher Plants at the Natural History Museum of Denmark, University of Copenhagen. She is known for her work on taxonomy and phylogeny of species with medical purposes (primarily monocotyledons). Our lecture however, was about the Cinchona. This is the genus of a medicinal plant which contains quinine in the bark. Quinine is an important drug that is used as a treatment for malaria. This tree was originally discovered in Peru, Bolivia, Ecuador, Columbia and Brazil. So, Nina went on an expedition to this part of the world to find different kinds of Cinchona species in order to classify them. She also measured the quinine concentrations in the bark for each species. With this information you can easily identify the medical properties of the plant via the phylogeny of it.

The next stop was the greenhouse in the botanical gardens. The great greenhouse in the botanical garden was constructed in 1874. It was funded by J.C. Jacobsen, the founder of Carlsberg (everybody should be familiar with him after this trip). He opened the gardens for the public and to this day, it is still open for everyone. The greenhouse itself is 16 meters tall in the centre and completely filled with foliage. There were spiral stairs reaching all the way up so you could walk around the canopy. Once up there, everywhere you looked there were different kinds of leaves/plants. Once back on the ground there were some extraordinary species we had to see. The Amorphophallus titanium for example. This plant only flowers ever 7-10 years, but once he does. It produces an enormous flower that can reach up to 3 meters. Sadly, but very likely, we did not see it bloom. There were however many other kinds of interesting plants in the greenhouse. Especially culinary plants. We had to see a cinnamon tree, sniff a citrus leave and eat a bunch of cocoa beans (cocoa beans sound tastier than they actually are).

Plants were not the only living creatures in the botanical gardens. During our visit we had to enjoy a high pitched chirp here and there. You wouldn’t think so but the sound actually came from tiny poisonous frogs. Don’t worry, the frogs in the botanical gardens were not poisonous because they did not get the proper food. In the wild they would eat certain insects that contained poisonous substances. These insects had in turn their toxins from eating poisonous plants. But since these plants do not exist in Denmark, visitors of the botanical gardens do not have to fear for their lives.

Aside from the greenhouse, there was a big park with a nice lake in the middle. After our tour through the greenhouse, we had some time to enjoy the gardens themselves. Although many trees had already lost their leaves (we went in November) the gardens were still very nice. We walked beneath the grapevine around the lake and spotted some birds (mostly crows). After that we headed into the city to visit some more places in Copenhagen. The botanical gardens is a really special place considering it is built in the middle of the city (the whole complex is 10 hectares!). It is truly one of the most beautiful botanical gardens I have ever seen.

Copenhagen-Photo_Reportage