Rahmi Lale

Rahmi Lale is working as a researcher at the Department of Biotechnology, NTNU. He, together with Martin Hohmann-Marriott, are working on Synthetic Biology and Photosyntesis

After obtaining his Master's degree at Ankara University, Turkey, he moved to Norway and he has been working at NTNU since 2003. Rahmi writes blog posts about NTNU iGEM (International Genetically Engineered Machines) together with the team.

Employee profile with contact information

We won the gold medal at the iGEM competiton
        
15
  15 December, 2014
        


iGEM teams from above.

iGEM teams from above.

Written by the NTNU iGEM team together with Rahmi Lale.

The Giant Jamboree is over. It feels like a chapter in our lives has ended. The Jamboree was massive, just check out this picture, and there are an overwhelming amount of impressions left…and YES, we achieved our goal and won the gold medal. What is left now is a small void, and we are all yearning to get back into the iGEM competition next year.

The conference was held at Hynes Convention Centre in Boston, MA between 29th of October and 3rd of November. This is the first time the Jamboree has been held outside of MiT, and it was purely because of the sheer volume of people: there were 245 multidisciplinary teams from all over the world with over 2 300 participants. First day was only for registration, which did not entail much excitement. We got a t-shirt each, but since we had organised our own t-shirts with sponsor logos on we did not use the distributed ones. However, they will make good memories in time. That night we dined at the top of the Prudential centre with Rahmi Lale, our sole attending instructor. That was an amazing experience – delicious food, great wine, a fantastic view and of course the best of company. Needless to say the team had a great time. Our iGEM adventure in Boston was off to a good start.

The team giving the oral presentation.

The team giving the oral presentation.

 

Walking out with our heads held high
Our presentation was scheduled as the second presentation on the first day after registration. At the time we found ourselves unlucky since we would get less time to practice compared to the other teams, but in retrospect it worked out better this way. Once the presentation was over, we could all lower our shoulders and enjoy the other presentations to the fullest. Our oral presentation went quite well. We made no mistakes and got good feedback from the judges and the audience on the idea behind the project and the project itself. There were no questions we could not answer, and we walked out of the auditorium with our heads held high. From this point onward, our time was spent listening to other teams presenting their work, participating in workshops and attending poster sessions. Because of the amount of attending people, there were 10 different presentations happening at the same time and we had to pick a favorite based on written abstracts. We mostly went to presentations together, but sometimes our interests did not coincide and we split up. However, we always met up for lunch and dinner.

The team having lunch together at what came to be our usual spot.

The team having lunch together at what came to be our usual spot.

 

Great exchange from other presentations
Some of the presentations were impressive. The shear amount of work some teams put down, and the results they had achieved were mind-blowing. One team, that later won the undergraduate first place, had designed a system for making proteins more heat resistant by circularising them using linkers calculated by a system they had designed themselves. In addition, they proved their theory and design by increasing the heat stability of a protein crucial for replicating the methylation patterns of parent DNA strands so that it could be used in PCR. Another team, that later won the postgraduate first place, had designed and built a low cost hand-held device for detecting rancidity in olive oil. Oil rancidity is a problem in commercial olive oil, and their system could correctly identify 8 out of 9 samples for rancidity for under US $100. We won’t go into the details about every team, but the bottom line is that there were great projects and great scientists present at the conference. During poster sessions we got to mingle, explaining interesting parts about our project and listening to other participants enthusiastically talk about their projects. We even got to talk to professors and judges which was rewarding given the knowledge they possess.

The team at the poster session.

The team at the poster session.

 

The gold medal we wanted
After the award ceremony on Monday, we left the hall feeling absolutely good about ourselves. We had won the gold medal!!! YEAAHHH!!! We could now proudly return to Norway, NTNU and the rest of our sponsors. We made it. Even though we achieved a gold medal, all of our team members still wish we had done more. Our project had such a potential, and even though we gave proof of the concept for our idea, we did not actually get any empirical results concerning increased carbon capture using our proposed genetic circuit. The parts are there, and they are fully functioning, so maybe, just maybe, someone will pick up where we left off, and take our project into the next level. With that I would like to thank all my team mates – I think we have grown close over the past year, and I hope we remain friends. We would also like to thank our instructors (Rahmi Lale, Martin Hohmann-Marriott, and Eivind Almaas from the Department of Biotechnology), and our sponsors (Department of Biotechnology, Programme for Bioinformatics at NTNU, Rectorate at NTNU, Skretting, Sparebank 1 SMN, Enova, GenScript, Geneious and Sat Sapienti).

And last but not least, our readers – Thank you.

The attending team members at the giant Jamboree in Boston, MA.

The attending team members at the giant Jamboree in Boston, MA.

 

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


igem-team

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.

elias-biobrick

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.

transformed-ecoli

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.

construct-ecoli

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.

 

Competing in Synthetic biology
        
26
  26 August, 2014
        


ntnu-igem

Figure 1. The iGEM official logo decorated with the NTNU colours and logo.

Written by the NTNU iGEM team together with Rahmi Lale.

Synthetic biology is an interdisciplinary field with the aim of modifying and/or engineering organisms to perform specific functions (e.g. synthesis of desired compounds). The fulfilment of these aims is based on altering the genetic structure of the organism, which governs its internal processes. A computer-based example of synthetic biology would be to fuse the iGEM official logo with the NTNU colours and logo (figure 1).

International competitions for scientists
The iGEM (international genetically engineered machine) foundation is a non-profit organization that promotes the advancement of research and development of synthetic biology. This is achieved by hosting international competitions for scientific teams on both graduate and undergraduate levels. The competition is within the field of synthetic biology, with the aim of cultivating scientific innovation and creativity through collaboration. The iGEM competition began in 2003 at MIT in Boston (USA), and started out as a course given during an Independent Activities period. In the years following, it expanded to become an international competition, with participating teams from more than 35 countries from all continents.

NTNU has participated in iGEM for four consecutive years and has previously been the sole participating team from Norway. To our great joy, this year the University of Oslo has also registered for the competition, reflecting the increasing awareness of and interest in iGEM in Norway. The iGEM competition is rapidly evolving, and high school teams may participate in a High School iGEM. In a hope that Norwegian high school teams will appear in the near future, we have participated in activities and conversation at events such as “Open day” (picture 2) and “Researcher’s night”.

Picture 2. Right picture: “Open day”-stand of the NTNU iGEM team with activities such as pipetting loading dye onto an agarose gel. From the left: Eivind Bøe Drejer and Silje Maurset. Left picture: We had prepared agar plated with various creative images of red, white and blue bacteria at the stand.

Picture 2. Right picture: “Open day”-stand of the NTNU iGEM team with activities such as pipetting loading dye onto an agarose gel. From the left: Eivind Bøe Drejer and Silje Maurset. Left picture: We had prepared agar plated with various creative images of red, white and blue bacteria at the stand.

 

iGEM directly to the world final
Normally, teams are selectively filtered through regional competitions, and only the elite teams meet for the world final in Boston; however, this year iGEM celebrates its 10th anniversary, and the regional competitions are abolished. Instead, every registered team proceeds directly to a giant jamboree (world final) in Boston (USA) in October-November. This year 246 teams will participate. Every team must present their project through a poster and an oral presentation, and due to the amount of participating teams the giant jamboree lasts for five consecutive days. Even though the competition is months away, we can feel a strong spark of excitement whenever thinking about the reward of meeting likeminded scientists with a wide variety of views and ideas. The Jamboree is also open to non-participating individuals for a fee.

NTNU iGEM in social media
We hope that people reading this would like to follow us at Twitter “@NTNUiGEM” and Facebook “NTNU iGEM”, and make sure to check out our wiki web site. Note that this site is under construction, but since we have computationally competent people working on it, it should start looking decent pretty soon. Please don’t hesitate to contact us if you have any questions. We will be happy to answer almost anything on our Facebook page or through our Twitter account. Hope to hear from you!

In our next blog post, we will provide more information about our team and research.