Monthly Archives:   October 2014

Only two days away from the competition
        
28
  28 October, 2014
        


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NTNU_Trondheim iGEM team 2014. From the left: Pål Røynestad, Elias H. Augestad, Eivind B. Drejer, Jacob Lamb, Camilla M. Reehorst, Ronja Hesthammer, Line Aa. Omtvedt.

Written by the NTNU iGEM team together with Rahmi Lale.

The Giant Jamboree competition 2014 is only two days away. Hynes Convention Center in Boston is hosting the event on 30 October – 3 November. Here, 2.500 Synthetic Biology researchers from 245 universities in 32 countries are participating. One of these teams is from NTNU.

An iGEM team from the NT faculty
The 2014 iGEM team from NTNU consists of eight students and three instructors. This year all students are part of the NT faculty, and everyone is either a student of the five-year master or three-year PhD program in biotechnology. Four of us (Camilla M. Reehorst, Line Aa. Omtvedt, HyeWon Lee and Ronja Hesthammer) finished our master program this year, and we have experienced the work with iGEM exciting and educational. Having a master’s degree does not mean you are finished learning, and we think that for most of us the “soup bowl of knowledge” has only just begun to be filled. These four students all undertook the laboratory part of their master’s at the Department of Biotechnology under the biopolymer chemistry branch. Not all of us have attained a job yet, but with the iGEM experience under our wings, the prospects seem a tad brighter. One of us (Eivind B. Drejer) is a fourth year student. He started to swim with the rest of the master student submarines, fully submerged in literature, in August 2014. His master thesis is under the systems biology branch of biotechnology (meaning a lot of computer fiddling), and he has not scheduled laboratory work in his thesis. His iGEM experience is therefore considered to supplement his degree to the point where future employers will tear at each other’s throats for such diverse experience in their workers.

Two of us (Pål Røynestad and Elias H. Augestad) are third year students, and have not yet started work on master’s thesis. Pål is intrigued by the systems biology branch, and will start a computational and modelling-based assignment this autumn. Elias, on the other hand, is interested in molecular biology, and will start a master’s degree at the University of Copenhagen in September 2014. They might be the least experienced (based purely on age and amount of years spent studying biotechnology), but they are very valuable assets to our team. We would be lacking without them. Our last team member (Jacob Lamb) is a PhD student, and out-ranks us all. His field is molecular biology, and he has worked extensively with photosynthetic organisms. Not only does he actually know what he is doing in the lab, he is also a native English speaking type of guy, which means it sounds like he knows what he’s doing (unlike the rest of us that express ourselves with communication stutter steps). We also have three amazing instructors – Eivind Almaas, Rahmi Lale and Martin Hohmann-Mariott. They have participated in this competition before, both as instructors and judges. Their experience and knowledge is sorely appreciated, and to top it off they are very helpful!

Packets containing BioBricks and cool iGEM stickers and pins.

Packets containing BioBricks and cool iGEM stickers and pins.

 

Creating a puzzle from BioBricks
Every year the iGEM foundation sends each participating team packets brimming with what are known as BioBricks. These are biological parts that teams can use in their respective projects. The BioBricks are DNA sequences with specific functions that can be assembled to form a variety of different constructs. The amount of BioBricks in the iGEM registry usually increases from year to year, since each participating team has the opportunity to send in and register new and exciting parts. The BioBricks arrive in small metallic packages that look unmeritedly plain.

Inside, however, is where the magic lies. As illustrated by Elias, opening and examining the ordinary metal plate contents leaves a person smiling and happy.

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Elias handling a BioBrick plate

The DNA sequences in each well are dried before they are shipped, and in order to use them, the DNA must be resuspended in distilled water. Once this is done, the DNA can be transferred into a culture of competent bacteria where the BioBrick parts multiply along with their hosts. Sometimes the BioBricks contain markers, meaning that the transformation success rate can easily be measured. Instead of laborious plating of negative non-transformed bacteria, the researcher can simply look for red cultures (given that the marker was a fluorescent gene that turns the bacteria red) as seen in the picture below.

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Successfully transformed E.Coli DH5α indicated by red colour.

In our project, we wish to use some of these BioBricks to create an inducible expression system in Synechocystis sp. PCC 6803. Doing this is like building a puzzle; every piece belongs to a specific location, and if one piece is missing the whole image is obscured. Adding one BioBrick to another is not necessarily a time consuming process, but because the puzzle consists of many pieces we will need to spend some time getting the final construct together. The process involves enzymatic PCR amplification and ligation (Gibson assembly method), with antibiotic-based selection on agar plates. We recently managed to create our desired construct in E. coli DH5α cells.

The visible marker is a red fluorescent protein, and as can be seen in the picture below, the colonies casts a red hue. When the inducible expression system is functional, we wish to use this to up-regulate genes that might cause the bacteria to fixate more carbon, with the overall aim of the project is to decrease carbon dioxide emissions from factory exhaust.

We are planning on up-regulating glucose oxidase in Synechocystis in order to achieve this. Glucose oxidase is an enzyme that exhausts the oxygen level in our bacteria. The idea is that the bacteria will start metabolising more carbon dioxide once the oxygen is depleted; however, the growth rate of the bacteria will most likely suffer with our intervention, and we therefore hope that the carbon dioxide uptake is greater than the loss in growth rate compared to a wild-type Synechocystis culture. We are excited to see how well our construct will develop, and will rejoice the day our instrument is implemented in factory chimneys.

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Desired construct in E. coli DH5αcells with red fluorescent protein marker.

Hoping for a gold medal
The realistic hope is that we receive a gold medal at the iGEM world final in Boston, Massachusetts in October-November 2014. Gold medals are given to any team that satisfy a set of criteria and quality standards determined by the iGEM administration. These criteria can be tricky, but we are confident in our abilities to achieve our goals. In addition to bronze, silver and gold medals, teams compete for special awards for a variety of contributions. These awards are only given to one team each year, and are therefore a symbol of greatness. The NTNU_Trondheim iGEM team 2014 has high ambitions and we aspire for greatness, but being humble we do not expect any special prizes. That being said, we would all like to proudly return home with a solid glass trophy in our greedy little hands.

 

Forsker Grand Prix – Targeting Drugs Through the Post
        
9
  9 October, 2014
        


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Nanometer sized particles show remarkable properties


Using the analogy of a postman delivering a letter to the correct address, I tried to explain how modern science and technology can help guide a drug to the diseased site, where it is expected to deliver its desired function.

The idea I had in mind was to use simple words during the presentation to reach out to a larger audience. The reason for this was two-fold: the general language used in the event was Norwegian (including all presentations except two) which meant that the majority audience comprised local people or Norwegians doing research in Science and secondly, English as a foreign language may not be able to stand out when used alongside sarcasm or pun. On the contrary, I stuck to using expressive pictures that would enable the audience to spin a tale in their minds. This technique works when it is important to convey complicated research to a range of people who stem from various backgrounds, not necessarily doing Science. The most important thing that worked for my presentation was the comparison I drew between my nano particles (NPs) that are designed to reach the target site and deliver the drug and a postman delivering a letter to the right address.

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The core is made of iron (egg yolk) and the shell is made of gold (egg white)

The egg analogy
The idea of this analogy came up while I was brain storming myself to come up with an easy to understand system that can help others understand how the core-shell Fe@Au NPs comprising an Fe core (egg yolk, rendering magnetic properties) and Au shell (egg white, rendering optical properties) can provide both targeting and tracking capabilities to our NPs, making them smart systems for targeting drugs.

The judges felt that the social implications of this research was easily understandable as one of the major problems of medicines, if taken inappropriately, at wrong times or in combinations that do not go together is that they cause a lot of side effects. As the drug reaches both healthy and unhealthy cells, higher drug dosage is required which further enhances side effects and thus, a vicious cycle. This effect can be minimized by using smart targeting systems that seek for the diseased site and deliver its payload when it reaches the site of action, just like our NPs.

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A drug can be squeezed out of the nano particles just like squeezing out water from a sponge

The wet sponge and postman analogies
Further, our NPs also have a stimuli sensitive polymeric layer which can change shape and structure when there is a change in temperature or/and acidity of the medium. This enables squeezing out of the drug similar to squeezing out of water from a water-laden sponge.

The outermost layer of our NPs contains a special molecule (PEG) that hides the NPs from the body’s defense mechanisms allowing them to be in the circulation long enough to reach the target site.

In a similar way that an effective postal system delivers a letter to your friend’s address without allowing others to know what message it contains, our NPs are capable of delivering the cargo to the diseased site without being detected by the body’s immune system.

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Gold nano particles of different sizes and shape vary in optical properties

Demanding but enjoyable experience
On the overall, the whole experience to do popular science was an exciting one, more so, because it stood out with its inherent characteristics. A few months of continuous understanding of one’s own research benefits to the society so as to convince the audience was a well-accepted challenge. The bigger challenge was in presenting a really complicated field of targeted drug delivery to common minds, without using too much technical vocabulary, yet making a clear point as to why I am doing this research. One important experiment that I tried in the process was to present before researchers from other fields (my brother, a few close friends), besides sitting down with the other contestants during coaching sessions and otherwise to run through the text and confirm that it should not be difficult to understand the scenarios. My supervisor and the group also helped in giving a patient ear to things that they know way better from experience in the same field. What amazed them was how important it is to tell a story about your research, while simultaneously engaging the audience! Presenting one’s research cannot be that demanding, but presenting it with dramatic content, eager eyes while simultaneously playing to the gallery, was something I enjoyed a lot.

Forsker Grand Prix should be popularized further and if possible, various versions (different language for instance) should be hosted. At the end of the day, it is the good vibe that the whole team and the overall project gave, which will always be remembered, besides the loads of things that I learned from the process of communicating to the general audience, a topic that I have now worked on for more than 7 years!

 

From shooting stars to weather at the edge of space
        
3
  3 October, 2014
        


rosmarie-de-wit-blog-shooting-starsRosmarie de Wit is doing her PhD in the Atmosphere and Environmental Physics group at NTNU. She collaborates with MORTEN the meteor radar, and together they measure small shooting stars in order to study weather at the edge of space. Rosmarie introduced MORTEN to the world during Forsker Grand Prix 2014. If you missed it but would like to meet him as well: this is your chance.

What would you wish for if you would see 10 000 shooting stars every day? Chocolate cake, new skis or a holiday to Hawaii? Well, after living in Trondheim for 3 years, I would definitely wish for improved weather forecasts. And guess what? Shooting stars can help us with that!

The weather at the edge of space
Meteorologists need very precise models to know what the weather will do next. It turns out it gets a lot easier to make a good forecast if all the air, from the surface and all the way up to 100 km (which I’ll call the edge of space, since it is so far away), is included in the weather models. But before these high air layers can be included in the models, we need to know what is going on up there. In other words: we need to measure weather at the edge of space.

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Rosmarie de Wit during her presentation at “Forsker Grand Prix”

And this is where shooting stars come in. Every day, 50 000 kg of space dust comes towards the Earth. That is a lot of dust, but luckily the atmosphere protects us and most of the dust burns up before it reaches the ground. The largest of these burning dust specs we can see: these are shooting stars. But there are many more much smaller dust specs burning up. These small shooting stars are called meteors. We cannot see them with the naked eye, but we can measure them.

A meteor trail reveals the weather
When a meteor enter the atmosphere, all the air molecules start to bump into it. The meteor gets very hot, and at about 100 km it burns up. When this happens, the meteor leaves a trail of charged particles behind. And it is this meteor trail that can tell us a lot about the weather at the edge of space.

MORTEN, the meteor radar
Luckily, we can measure this trail with an instrument called a ‘meteor radar’. NTNU has such a meteor radar, and his name is MORTEN. MORTEN can measure these small shooting stars by sending out a radio wave, or ‘pings’. These ‘pings’ travel all the way through the air until they reach the meteor trail. When they reach the trail of charged particles, they are reflected and bounce back to Earth. Now MORTEN listens, and when he hears the ‘pings’ again he knows he has detected a meteor.

MORTEN sees about 10 000 mini-shooting stars every day. But how can we use those to measure weather at the edge of space? Well, did you ever realize how the trail of clouds left behind by an airplane moves in the air? The trail moves because it is blown with the wind. The same happens to those meteor trails 10 times higher up in the sky. So by checking how fast a meteor trail moves MORTEN the meteor radar can measure the winds 100 km above the ground.

But that is not all. If you have ever seen a shooting star, you know they disappear very fast. A meteor trail only lasts for about 2 seconds, but it depends on the temperature how long it lasts exactly. The warmer it is, the faster the trail disappears. By timing how long it takes before the trail has disappeared, MORTEN the meteor radar can therefore also tell us the temperatures at the edge of space.

MORTEN can make my wish come true
So by measuring small shooting stars, we can study weather at the edge of space. And by studying weather at the edge of space, we can help improve those weather forecasts, and make my wish come true!

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Atmospheric physicists say hello to MORTEN