Category Archives: FOR PROSPECTIVE STUDENTS

SU course: Structure and dynamics of biological membrane

The second course at Stockholm University is that of Structure and Dynamics of Biological Membrane. The course focuses on the importance of interaction between lipids and the membrane proteins.

This course has a lot of Biochemistry involved. It covers a range of topics and relates them to the biological membranes i.e. lipid bi-layer and the its significance. The course starts with an introduction of types of lipids and their basic structures. Further, their ability to form membranes and various composition of those membranes to hold and facilitate different kind of membrane proteins. The next part was the study of the membrane proteins that populate these membranes and how they fold and insert into the membrane.

Protein translocation lecture – Insertion of membrane protein as depicted in by the interaction of 3D crystal structures, giving an insight into the structural information

After understanding the energetics of membrane protein folding and insertion, we explored various organelles, and the variety of enzyme complex systems that it has to offer, which are (yes, you guessed it correctly) membrane proteins. The most basic systems such as respiration in plants (plant photosystems), mitochondrial respiratory complex are all examples of membrane protein (enzyme) complexes, that play the most crucial role of energy production.  This sounds like revising the basics, however, with great structural and mechanistic insights into each system.

In the course we also did a group activity where we were given a protein and its crystal structure. Based in this we had to determine the function and the mechanism of the protein. The goal was to experience the real life problems faced by a structural biologist and understand the ways adopted to decode the structure based functional mystery. In the demo lab, we test one of these membrane protein to show that they follow Michaelis-Menten kinetics using an artificial system that mimics the actual system very closely.

Further, the instructors of the course are themselves researchers and they are very enthusiastic to tell us about various new advance techniques some of which are developed in their own labs. Most of the lecturers are leading researchers in their own field who have developed some of the first techniques or have come up with the first ever idea revolutionizing the field. To mention one such name is Dr. Gunnar von Heijne. His research on the signal peptide and membrane proteins has been a breakthrough.

Learning from such lecturers reminds me of a famous saying that goes – ‘Hearing from the horse’s mouth’!

Lecture on signal peptide – a breakthrough

Even though the course is very specific, it has enabled us to explores a different aspect of biology that was unknown to many of us to this depth.

Attending such lectures is a different experience in itself, learning about various breakthroughs from experts themselves, gives me an adrenaline rush while encouraging me to be at their place some day!

SU course: Bioinformatics (Part-2)

Today I will be talking about the second half of the Bioinformatics course and the individual project.

2) Structure Prediction

This part of the course also has both the theory and the Lab component. However, this half of the course is lab intensive unlike the previous one which was theory intensive.

This half has its own story. We start by learning about various structures and levels of protein organization. Then we proceed learn about the various types of secondary structures present and the type of interactions that keep them stable in their original conformation. From here we move on to various experimental and computational (main focus) methods of protein structure assignment and prediction.  Structure prediction is of little help unless we use the structure to learn about its functions. To learn about functions, we then align the sequences and structure of this new protein to its homologs. These structures can then be experimentally verified using various techniques. We used the three dimensional structures present in the PDB database to perform various analysis such as modelling new proteins, modelling interactions, morphing, docking new molecules, which have applications in various academic as well as commercial fields.

Secondary structure lecture – Prof. Samuel explaining using models

Just like the first half of the course we had lab sessions that went hand in hand to the theory courses. The lab were much more interesting for most of us, as it was for the first time that we were looking at proteins and predicting their interactions and docking antibodies with antigens. However, as it was the first time handling such programs, most of which are command line based, we needed a lot of help which was provided by four TA’s. David, Sarah, Eloy and Marie, were very helpful in guiding us through the individual steps of the exercise personally. This improved our understanding exponentially.

Project

As I had mentioned earlier that we also have an individual project for the course. Each of us is given a unique sequence of unknown origin. Our task is to find out everything about the sequence using all the tools and software that we have used so far in the lab. Thus, we start by finding the actual sequence by database search and then determine about its evolutionary origin using phylogenetics. Followed by its structure prediction and modelling the protein. To put it in short do everything we learned  and apply on this particular new protein.

Finally, we had another partial exam for the second half of the course.

In general the course is very intensive and demanding. On a typical day, we dedicate at least 8 hours of which 5 hours is at the university and the remaining 3 for the assigned reading for the next day. Personally, I would say that this is the most cumbersome course so far in the MTLS masters, with 2 exams, an individual project, pre-lecture quizzes and the lab exercises all in a span of 5 weeks.  However, we have learned a whole new field associated to biological sciences, and learn about what exactly does bioinformatics comprise apart from the data analysis and its domains that can stand independent to the experimental section.

New beginnings at Stockholm University!

To make an end is to make a beginning.

 

-Edith Lovejoy Pierce

 

After ending one part of our journey at Karolinska Institutet, we move to Stockholm University for the new begining of the second part of this journey .

The new semester at Stockholm University started after almost 1 week of holidays on 21st of January. For most of the students new semester means new courses. However, for the students of MTLS, new semester means new university, new place, meeting new students, making new friends, experiencing new environment and new academic culture, new opportunities, new resources, new social culture, different parties, and many more things…

There is just no end to this list of new and different things. The best description of this feeling of transiting from one institute to another, is the same as visiting the city of Stockholm for the first time and getting the first welcome all over again, except this time with snowy weather!

So today, I am going to tell you something about Stockholm University that I have been able to discover in the past week.

About Stockholm University (SU)

The Stockholm University is known for its research in the basic sciences. The environment of the place is also conducive for the same.

SU has two campuses.

1. Frescati campus or the main camous

2. Albanova campus

The Frescati campus (evening shot)

The Frescati campus is very near to the Universitet metro station. It is easily accessible by bus or metro. Albanova campus is just 2 bus stops away from the Frescati campus. Frescati campus has a lot of open lawns and is very close to the nature and environment. It has a lot of trees around the campus. ON the other hand the Albanova campus is right next to a lake surrounded by trees. Thus, the environment on campus is very pleasant.

Registering at SU

Now, to get started, ne of the first things required is to register and to activate student account. This can be done at the Infodesk in the Studenthuset (Student house). The account activation provides us with the login credentials for the course registration. Using these credentials, courses can be registered on Ladok, the central system for course registration in Sweden. The student account activation also enables us to apply for the library card, which is used to borrow books and take printouts.

Info desk at Student huset
Source: SU website

Further, the Stockholm University student union (SUS) registration can be done in the same building i.e. Studenthuset’s ground floor. The student union enables you to access various activities like fencing, belle dancing, gym, etc. The registration at the student union is also important for the housing queue to apply for an accommodation through SSSB.

Our courses at SU

We have 5 courses in the SU semester:

1.  Bioinformatics

2. Applied Programming in Life Sciences 2

3. Structure and dynamics of Biological Membranes

4. Methods in Molecular Life Sciences

5. Comparative Genomics

I will be writing about these courses as we progress through the semester, so stay tuned for more updates!

Fourth course: Frontiers in Translational Medicine (Part-2)

Project

The second aspect of this course was the group project. The aim of this project was to get hands on experience in various techniques that we learned during the course and to experience life of a researcher. The project was performed in groups of 6 students. Each group was assigned a technique based on which the experiment had to be designed and each member of the group was assigned a specific role. The technique assigned to the group and individual role was mostly based on a poll conducted earlier. The techniques covered were, CRISPR, FACS, Immunofluorescence based microscopy, and qPCR.

For example, my group was assigned the FACS technique and we had a communicator, a coordinator, technical experts, scientific responsible and a data analyst.
As a group we had to design a simple research question that could be answered using FACS. Once we had the question, we made a list of materials required. We were given a strict budget of 10000kr. The challenge was to stick to the budget and still be able to have a realistic research question that can be answered. Fortunately, to guide us we were assigned mentors who are experts in that particular technique.
The first pitch of our research proposal was just before the Christmas holidays to our faculty. After approval of the proposal, list of required materials was ordered so that it would arrive by the time university reopens after the holidays.
We had four days to perform our experiments and a day to analyze data and prepare for the final presentation.
On the first day, after making a detailed plan of the experimental timeline and collecting our order we started with our experiments.

Here is our group member (Diana) preparing to transfect cells PC: Luca

Finally on the day of presentation, each group presented their research project and various difficulties that they had faced. As this was the first independent venture into designing a project for most of us, everything did not turned out as we speculated.

However, this experience taught us about various practical difficulties and limitations that can be learned only by experience. For example, estimating experimental efficiency in the lower range, etc. Further, we learned to handle situations, work in teams, come up with last minute alternative plans or design fall back plans. And last but not the least to troubleshoot our experiment.

Final presentation by CRISPR group.

At the end of all the presentations we had a final feedback session with faculties from every subject at Karolinska Institute. We discussed and gave suggestion on how the courses can be improved and what part of the course were specifically helpful. As this is relatively new course, the administration and the faculties are very enthusiastic and take feedback on improving the course structure and content based on the student feedback very seriously, so that the new batch of students can get the best with relative ease.

Batch photo with the course coordinators (Louisa Cheung, Anton Larsson,Fulya Taylan and Lars Arne)
Credit: Gunter

Fourth course: Fromtiers in Translational Medicine (Part-1)

The final course at Karolinska is Frontiers in Translational Medicine or FTM. This course is of 16.5 credits and thus the longest course.

The course has two main aspects:

1) The theory lectures and facility visits

2) Project

Today I will be talking about the theory lectures and facility visits.

The course is designed to give an introduction to various fields of research in complex diseases and the application of next generation high throughput techniques to develop improved therapeutic approaches that can be eventually used in clinics.

Initially, we were introduced to various types of animal models such as  Mice and Zebra fish. We also visited the zebra fish facility at KI and learned about the breeding techniques, and its potential applications in research.

Zebra fish facility at KI
Source: Presentation slides (Zebra fish facility)

In the following weeks we lectures on various advanced molecular techniques such as FACS, CRISPR Cas-9 system and a special lecture on Organ-on-Chip. In the same week we also had our first lab of the programme. The objective of this lab was to get hands on experience in genotyping techniques. We performed genotyping in groups of 5 per team, using two techniques: Pyrosequencing and Taqman based sequencing. The samples we used were from a patient, donated for research study. Post lab, we did some troubleshooting and tried to hypothesize the possible cause of deviation from the expected results, carried out from previous studies.

One of the most interesting part of the course was the Proteomics Day. We  had lectures in the morning from various researchers from the proteomics core facility at Scilife Labs. They talked about techniques used for proteomics studies. One of the lecture was on the development of the Human Protein Atlas. Post lunch we visited the proteomics facilities and explored the labs and various equipment such as FACS, CyTOF (Mass cytometer), Confocal Microscopes and its variations, specialized instruments to perform ELISA analysis, and last but not the least Mass Spectrometer.

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