NTNU – Faculty of Natural Sciences and Technology – Page 5

Coming to Trondheim for my PhD

Hi,
My name is Nikola and I am a new PhD candidate at NTNU. I am from Kikinda, a small town in Serbia and I finished my bachelor and master studies at the University of Novi Sad, also in Serbia. I heard about Trondheim from my friends who have already been here and they shared their experiences with me. I was looking for an interesting PhD position on a project that would be relevant for me, and when I found one, I contacted the Professor who is the head of the project. I was really happy to receive the news that I had been the chosen one. I was also lucky with accommodation, because it can be a problem sometimes. I was able to take over my friend’s apartment.

I arrived in Trondheim on the 11th of August. My first impression was that Trondheim is a really nice city with beautiful nature, fresh air, also with good weather, but it was only the first few days. Now, I can see that it is usually rainy, but I will settle with any weather. Everything else seems nice. People are kind and they always seem to have time for you. Food is good, and I prefer fish. I am really happy because of everything here.

It was a great pleasure to meet my colleagues. I share the office with two more PhD candidates, Susanne and Espen. Including me, several PhD students started at the same time. My supervisor is Mari-Ann Einarsrud and I have great collaboration with her. We start the day around 8 am and finish around 4 pm. Currently, I am reading literature most of the day and preparing myself for a good scientific start.

I have to take an HSE preparation course before I can use the labs. During September I think I can start with my lab experiments and I am looking forward to that.

I will write some more about my PhD and life in Trondheim in my next blog post.

Best regards,

Nikola

Competing in Synthetic biology

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.

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.

“When I grow up, I want to …”

If you ask a child “What do you want to do be when you grow up?”, I’m willing to place a fairly generous sum of money on that “Professor” will not be one of the most common answers you’ll get. After all, it is difficult to compete with cool things like astronauts, princesses, and firemen.

But somewhere along the road perspectives change, and perhaps you are one of those that are currently pondering whether or not you should pursue an academic career after completing your Masters- or PhD- degree. What can you expect when taking this road? And how do you make an academic career, anyway?

A fork in the road
Our journey begins at the crossroad encountered at the end of your Masters degree. What now – do you apply for a PhD position or do you go for an industrial job, whether it is in the context of cellphones, oil, or IT-development? A PhD position normally has a duration of 3-4 years in Norway and thus landing a permanent job in a company like Statoil undeniably is more of a safe bet. Moreover, you’ll likely get paid more money there.

A unique opportunity
Then why choose a PhD degree? I’ll tell you one thing – if I could make the choice again, I still wouldn’t have taken an industrial job even if it paid twice as much as a PhD position. Heck, I wouldn’t have taken it if it paid three times as … weeell, maybe I shouldn’t be too hasty …

The point is that obtaining your PhD degree is a completely unique process and cannot be compared to most of other jobs that may be relevant for you after having obtained your Masters-degree. Think about it – as a PhD candidate, you will get paid to have the freedom and time to utterly absorb yourself in a topic that fascinates you and learn all there is to know about it. The result? You will become an expert on a national, and possibly international (depending on how well you do), level in your field of research. Doing scientific research is like opening the pages of a book that has never been read before – you are discovering new things and, importantly, get the exciting privilege of sharing these news with the rest of the world. Yes – the rest of the world – your scientific publications will be read by hundreds of other researchers, young and old, all across this globe.

It is important to underline that after you have obtained a PhD degree, you’re still highly attractive on the industrial job market – and probably even more so compared to if you “only” had your Masters-degree. Holding a PhD degree certainly doesn’t hurt your chances of landing a permanent position outside of the academic environment.

100% of your time on your research
But what if your thirst for knowledge does not end after your PhD degree – what if the answer to the question “What do you want to be when you grow up?” actually is starting to look alarmingly much like “Professor”? The next step in your pursuit of an academic career would be to enter a so-called postdoctoral (postdoc for short) position. At this point, you will be able to work much more independently as a researcher than you were able to do at the beginning of your PhD studies and it is likely that you will produce some of your finest research work during this stage of your career. You will not have any mandatory courses to attend or lectures to give – you can devote 100% of your focus to research. Trust me, this is something you will miss later on when administrative duties as a lecturer or professor become more time-consuming, leaving less opportunity for sitting down on your own and being creative. Don’t worry, there are up-sides as well later on and I’ll get back to those.

The postdoc stage is quite critical in your career. It’s basically do-or-die: now is the time to show that you have what it takes in terms of being able to come up with new ideas and produce interesting and relevant research, ultimately proving that you are worthy of a permanent position at the university. It is also a stage which seems to scare many graduated PhD candidates – in my experience, very few of the young men and women that obtain their PhD degrees at the Department of Physics where I belong choose to continue down the academic track. There are probably a few reasons for this. One is that postdoc positions are typically short, temporary positions ranging from 1-3 years in duration. That doesn’t offer much stability, which may be an important factor for you if you have or are about to establish a family. Moreover, it is strongly encouraged to do your postdoctoral work somewhere else than you did your PhD work, simply because you get exposed to different research environments and get to acquire new expertise. This can pose a practical obstacle. However, that does not mean that it is impossible to make it if you stay at the same institute as a postdoc due to e.g. family reasons, which I personally did. With that said, given that you have the opportunity to do so, I would encourage you to go abroad – meet new people, see new places, and learn new things that will allow you to develop faster scientifically than if you stayed at your alma mater.

A versatile job
If you work hard in a persistent manner, you will obtain qualifications that allow you to apply for a permanent position at a university: associate professor (førsteamanuensis) or professor. I’m not going to tell you that it is easy to get such a job – but I will tell you that it is worth all the blood and sweat that you need to put into getting it. One thing to note straight away is that it is a really diverse job, in contrast to what many seem to think – you get to teach, do research, supervise younger promising researchers, lead large international projects, and be a spokesperson for your particular field of research and science in general (for instance by writing blog-entries like this). It tests you in many ways, both intellectually and on a personal level – you shouldn’t think of professors as solemn, gray figures sitting in their offices and only peeking out once in a while – it is a truly dynamical profession which requires a lot of interaction with both colleagues and students. To witness your PhD candidate develop from a rookie learning the ropes during his or her first fumbling year into a solid researcher that will turn the tables around and starting teaching you things in the final year is an incredible experience.

Obviously, I cannot hope to encompass all aspects of the academic path in this blog-entry, but perhaps you have a better idea of what to expect if you should choose to pursue this career. It’s not an easy road – but hey, it usually isn’t if something is worthwhile.

Student in Research at The Dept. of Biotechnology

This spring, I had the opportunity to be a “student in research” on a fellow project with Ragnhild I. Vestrum which includes cultivation of cod larvae free from unwanted organisms. Along with Ragnhild, postdoc Torunn Forberg, and several people from the research group “Analysis and control of microbial systems” I have worked about 40 hours on the project.

Student research is work paid by the hour that allows students to participate in research under the guidance of the department the student belongs to. This provides a golden opportunity to specialize in the chosen field of study.

The job description included several relevant tasks for a novice like me. If I were to list everything I have learned during the project this blog post would be very long, but there are many valuable lessons I take with me from here. For example, before the project, I had never heard of autoclaving, although I quickly realized that the autoclave has to be the most widely used machine at the department (device used to sterilize equipment). I did learn how to make various culture media containing the algae agar which I later learned to pour into Petri dishes. This is perhaps the ABC in the biotech world, but I think it was incredibly helpful to learn both sterile technique and how to make your own petri dishes, when the only previous knowledge we have of petri dishes is that they are readily available in the lab.

There were also some practical preparations with equipment setup such as culture bottles etc. One thing was to learn about the optimal living conditions for cod larvae, another was to see problem solving in action – working from your own ideas without a recipe, and all the practical problems one encounters along the way. Only now have I realized how important it is to make creative and adaptable solutions, and I witnessed several ingenious McGyver solutions as challenges arose.

Here appeared the good cooperation between the employees of the department, how many came with improvements in procedures done earlier. Everyone plays an important role with their own expertise. It is clear that the good team spirit and relaxed atmosphere contributes to a creative and spacious environment to work in. The department has an incredibly warm, tolerant and welcoming environment.

In addition, I got the answer to everything I asked about and more, with a particularly educational guidance. I have probably asked the same question 3-4 times and received a patient and thorough answer every time. The supervisor has been eager to show and explain the experiments and procedures even on things I could not work with (because it is a sterile experiment), and given me insight into the research world. I also got to attend another research project down on SeaLab where we collected samples to analyze of R-and K-selected communities, so the experience I am left with is both broad and specific.

Although it has been incredibly fun and useful to learn specific tasks, I think perhaps that the totality of the experience is most important. I have seen how it is to do research in the big picture; preparation, teamwork and how many things cannot be planned exactly and need to be dealt with spontaneously since you are working with living material. How one is dependent on suppliers, sharing equipment, replication, HSE procedures and applications to experiments with animals, that planning and preparation are very important but also being creative in terms of both equipment and procedure – there is no common formula when doing research that has not been done earlier.

Okay, but what is the catch here, you might ask? Before I was a bit worried that it would interfere with my exam period when the project was planned for April and May, but it turned out to be zero problems when it was made clear that no studying would be sacrificed for the project and that I had to say no if it did not work out. It has been very flexible and the working hours were planned for when it was convenient for me. It has by no means affected my school plan negatively, and I think that if this is made clear in the job description, more people will want to apply for a “student in research” position. That is the main reason why my fellow students did not apply for the position.

Finally, I would like to thank Ingrid Bakke for the opportunity to participate in this project. I have learned a lot and got a taste of biotechnology in practice. Thanks to Ragnhild for super guidance and cooperation, patience and work hours filled with laughter. Such a project provides a broader perspective and decreases the distance to the research world, and is really something I highly recommend that the department continues with in the future.

Taking care of knowledge

Blog post with Astrid Lægreid (not on the photo) from The Department of Cancer Research and Molecular Medicine:

It is often overlooked that after you publish your research results you have not necessarily provided your new knowledge to your colleagues in the best possible way. Today’s biomedical science is very much dependent on the use of computers, to analyse and integrate the various types of data and facts that you and your fellow scientists have produced. And whereas a computer can do many things, it has difficulty in understanding what is so easily understood by us when we read a scientific publication.

Although much research is done to improve the way computers can analyse text (the field of text mining), we excel in hiding facts and new knowledge in our publications. We use for instance words that can have multiple meanings, names that seem funny (sonic hedgehog) but do not mean anything to a computer, or we mention some facts in a context that greatly changes the meaning of a sentence (for instance by using the simple word ‘not’). We therefore need to reach out to computers and help them a bit with understanding the real knowledge that we have hidden so well in text. This is even more interesting if one wants to pursue the main goal we have set for our research at NTNU: using a systems biology approach for making new biological discoveries.

Systems biology is based on a computer dealing with knowledge about biological systems or processes (like cell division; or regulation of the activity levels of genes). It is widely believed that a systems biology-based understanding of the human will allow great discoveries for improved health care. Systems biology has been made possible by the tremendous advancements in laboratory technologies that are now available to get massive amounts of data about the processes, cells and organs of our bodies. Once these data have been interpreted and published, system scale biomedical knowledge can be integrated into computer models in order to enable improved disease management and higher precision medicine. However, in order to succeed, we need to take proper care of this knowledge.

In our daily work we have developed various computer models of cell lines which we use in laboratory experiments, and each time we had to get the information for these models by reading many papers because only a very small amount of the information was available through databases. This made us think that it would be great of at least one part of the information for these models would be readily available for computers: information from the area of gene regulation. One small, but very important part of this is the knowledge about the system that connects the information in a particular class of proteins (transcription factors, TFs) with the particular DNA sequences in the genome in the vicinity of genes (recognition sequences, or transcription factor binding sites): This system essentially links the protein world with the DNA world and dictates which genes are active and which genes remain silent. We have recently launched a large effort in building a resource for this that covers three of the most important biological systems: human, mouse and rat (1, 2).

Of course we know that the DNA binding TFs are only a very small part of the very complex system of gene regulation, and it will take a very big group of scientists to take care of all the diverse forms of knowledge in the literature. And there we are lucky that we are not alone in realizing the importance of this. We have identified many researchers world-wide and found them willing to join us in a global consortium within the field of taking care of, or ‘curating’ gene regulation knowledge, and we are now discussing with them how we can best structure existing efforts and launch new efforts to jointly build a series of resources covering the complete domain of gene regulation in all organisms.

Existing databases and knowledge sources within our consortium include amongst others the Gene Ontology databases, PAZAR, TFCat, TFactS and RegulonDB, as well as DBD- and IntAct at the European Institute of Bioinformatics (EBI). Existing and new resources are designed in such a way that the information can be easily integrated into computer models. The consortium is named ‘Gene Regulation Consortium’ (short: GRECO), and is led by us.

Our basic objective is to extend on what we now only do for the DNA binding transcription factors from mouse, human and rat, and do it for the full field of gene regulation with many particular types of regulatory proteins, many types of regulatory RNAs, and many different structural and functional elements encoded in the DNA which allows the gene regulation system to fine-tune the activity of genes appropriate for a specific cellular function, and do it for all organisms.

The aims of GRECO are to:

Foster communication across the field of gene regulation

Assess the state of the art in annotating components and relationships important to describe gene regulation events

Identify common initiatives, avoid redundancy, fill knowledge gaps

Extend and align ontologies and controlled vocabularies

Promote common data exchange formats

Promote common curation quality guidelines

Attract funding to support communication and initiate new curation initiatives

We were fortunate to receive some financial support from NTNU to organize the first GRECO workshop on April 5, at the Toronto University campus, as a satellite meeting of The Seventh Conference of the International Society for Biocuration, ISB2014. We met with partners from the UK, Switzerland, Germany, the USA, Mexico, Brazil and Saudi Arabia, presented our ideas for this initiative and laid out the foundation for a joint strategy for acquiring additional project support from international funding organisations like the National Health Institutes in the USA, the Horizon 2020 programme from the European Union, or National funding agencies like NFR.

We hope to present some of our work at the Virtual Physiological Human (VPH) Conference 2014 in Trondheim in September 2014. The VPH mission is to contribute to developing a real predictive, preventive and participatory medicine by enabling the building of stronger transdisciplinary ties between the life sciences, the mathematical sciences and engineering throughout the whole spectrum of basic, translational and applied research.

References

1) Tripathi S, Christie KR, Balakrishnan R, Huntley R, Hill DP, Thommesen L, Blake JA, Kuiper M, Lægreid A. Gene Ontology Annotation of Sequence specific DNA-binding Transcription Factors: Setting the Stage for a Large Scale Curation Effort. Database Aug 27; bat062 2013.

2) Chawla K; Tripathi S; Thommesen L; Lægreid A; Kuiper M. TFcheckpoint: a curated compendium of specific DNA-binding RNA polymerase II transcription factors. Bioinformatics 2013 ;Volume 29.(19) p. 2519-2520.

Super strong and deformable Aluminium

PhD Candidate Min Zha. Photo: Per Henning/NTNU

In my PhD project, I have applied a new technology for future production of nanostructured metals. I have studied two different types of aluminium (aluminium containing magnesium and aluminium containing bismuth) with this technology.

My goal was to find a suitable process for light metals having superior high strength combined with good deformability. Such materials can be produced by having a good combination of the inner structure components such as foreign atoms and small size grains (crystals). In fact, the grains (crystals) had a size ranging from the nano-level to a few micro-meters.

My project was very successful:
1) I was able to design a process where aluminium containing magnesium had strength typical of high strength steels. Since both aluminium and magnesium are very light, I believe such a high strength can open up for innovative products in many sectors, such as advanced components in cars, mobile phones, computers, aircrafts, subsea constructions and sport equipment.

2) For the aluminium containing bismuth, one demonstrated high strength and an optimum distribution of the bismuth particles in the aluminium. Also here, the right combination of the inner structure at small scale was the successful factor. I believe this material is a candidate for new and better products such as bearing components in cars. Since bismuth is soft, this material has self-lubrication properties and this is important for a wide range of components in everyday life.

Popular technology world-wide
The applied technology is called ‘Equal Channel Angular Pressing’ (ECAP). Over the last decade, it has attracted the interest of many research institutions world-wide. The ECAP technology allows very high deformation of the material, without affecting the shape. This makes this process available for further processing to advanced, or complex shaped products.

What is a theoretical physicist?

Thanks to the unstoppable Sheldon Cooper and the rest of the crew in the popular sitcom “The Big Bang Theory”, the world has been granted a peek at what life is like for young physicists – both on and off campus. Solving complicated equations day and night, with several whiteboards always at hand in their apartment, spending their sparetime watching Firefly with extra commentaries, and pulling all-nighters battling orcs in World of Warcraft – yes, the Big Bang Theory physicists fully embrace the nerd within. But how accurate is the presented picture when comparing to everyday life for a physicist at, say, NTNU?

Not far from the truth
I suppose the answer will depend on who you ask, but surprisingly much is true! Now, not all theoretical physicists have a special shelf-spot for a limited edition Batman belt-buckle, but I think it is fair to say that the majority of us do embrace the nerd within when it comes to our passion for physics. A theoretical physicist is a curious being – he or she is driven by a desire to explore, understand and explain the unknown. Imagine that you are able to discover an equation which describes a physical phenomenon and that you are the first one to ever write down this equation. This is what theoretical physicists do! They unlock the secrets of nature and expose them both in terms of a mathematical language and in terms of how to interpret the equations physically.

Social skills needed
Some people may think that physicists are asocial, awkward beings incapable of interacting socially with much success. This is very far from the truth. Being a physicist often entails very much interactions with other researchers, especially from other parts of the world. This task comes with responsibility: it is important to grasp at least the basic elements of the culture of the researcher you are communicating with in order to treat them with respect and understanding. I have collaborators both in the United States and in Japan, and I can assure you that these cultures are very different. In turn, this influences the way that I communicate and express myself with my collaborators. Being a theoretical physicist allows you to get to know completely different parts of the world and learn about what these cultures value and cherish – interestingly, you also get to know yourself better in this process.

Curious about how the world works
The life of a theoretical physicist is very exciting. You find yourself day after day at the frontier of what we know about nature and how it works, and you are a part of pushing that frontier further ahead with your contribution. If you are a curious human being who enjoys math and wants to understand how the world works, I can warmly recommend exploring the path of theoretical physics – whether you own the complete set of Star Trek DVD’s or not.

More information about Theoretical Physics at NTNU