The ISBGroup Blog

Hello!

My name is Tilda and I have been in the isb
group before, but this November I started my phd here. I am financed by an EU
project called precise4Q. The project aims at personalising treatment of stroke
by developing model-based decision support systems. I will be working with combining
mechanistic multi-level models and machine learning models.

We have gotten money – and lot’s of it!

While on a 6h train ride between Malmö and Stockholm, I at last have time to share some of the good news that have come to us, one after the other, but that I haven’t had the time to share with you here until now. The good news is that we have had a series of successful grant applications, which mean that we now have reached a whole new level, in terms of money flows, and that our group will significantly grow in the next 2-3 months.

This new money
flow actually started about a year ago, when I got money for a new 2
year postdoc position from AstraZeneca, i.e. approx 3 MSEK (300 000
USD). In this postdoc, we will create models for a new type of
animal-free experiments, called organ-on-a-chip. In this technique, you
build a system of realistic 3D organs made up of human cells, which are
interconnected by an artificial blood flow. This is a supercool
possibility, which is ideal for both modelling, for replacing animal
experiments, and for understanding diseases.

This grant was then
followed by a new EU project, called PRECISE4Q, which was approved in
January this year. In this project, we will make use of our multi-level
mathematical models for diabetes and cardiovascular disease, to create a
new clinically useful tool. The basis of this tool will be quite
general, and applicable to a wide range of diseases, but the focus will
be on helping patients who have or who are at risk of suffering a
stroke. The total budget of this project is 60 MSEK (approx 6 million
USD), and of that approx 4 MSEK goes to my group (400 000 USD).

After that, during the spring, I used these already approved projects to
write applications about other projects, which could build upon my
already approved projects. And this too has now started to bear fruit.

First off was an application to SSF, the Swedish Foundation for
Strategic Research. They have awarded me and a researcher from
Karolinska Institutet in Stockholm (Roland Nilsson) a grant of 7.5 MSEK
in total, out of which I will receive 3.5 MSEK (~350 000 USD). The topic
of this project is to use my modelling to extract quantitative fluxes
for all of the metabolic reactions in a cell; this is possible because
of Roland’s unique experimental skills, where he tags metabolites
outside of the cell with C13 carbon molecules, and then uses mass
spectrometry to measure where these tagged carbon molecules ends up in
all in metabolites inside the cell. We will use these money to both
transform this tool from a big potential to something that is useful in
practice, and then also to apply the technique to understanding both
metabolic diseases and cancer on a new level – useful for both research,
drug development, and diagnosis.

The last major grant we got,
and just a few days ago, this Thursday, was from VR, the Swedish
Research Council. This high-prestige grant builds upon my previous
collaboration with AstraZeneca, and will allow us to spend 4.2 MSEK (420
000 USD) to further strengthen our collaboration with AstraZeneca. More
specifically, we will make use of the new and more complete models
developed within the PRECISE4Q EU network (mentioned above) to
understand how a brand new diabetes drug, dapagliflozin, works, and if,
how, and when it can be used to also treat cardiovascular diseases like
stroke, heart attack, and heart failure. This project will also allow us
to understand more about which patients that should have which
treatments, and more about the different mechanisms at play in the newly
sub-divided grouping of diabetes into 5 sub-types.

One very good
aspect of this new situation is that we are really well-prepared for it.
This is due, in part, to some very useful grants we have gotten from the Swedish Foundation
for Research without Animal Experiments. Using this money, we have been
able to train talented undergraduate students in real research projects,
which they have done in parallel to their M.Sc. studies, by awarding
them scholarships (several of the recent blog posts have been devoted to presenting new such students). These new, and previous old, such quite unique students are now ready and eager
to start as Ph.D. students, and they are much more well-trained than
normal applicants would be, which we could find in normal open
announcements. For this reason, we already now know that we will be able to
fill all of the new positions with really great people, and are therefore
looking much forward to working with for, at least, the next 4-5 years. However, all of the new positions will be announced in open competition, so if you are a great candidate, who wants to join our group, don’t hesitate to apply, or to contact me for discussions on joint collaborations or positions.

All in all, it is also a very great feeling to suddenly have such
much money now at our disposal. And also quite humbling. Now we need to
really demonstrate to our funders that we can convert these great money into the equally great
research we have described in our visionary applications. Into research
that will be useful for both other researchers and for those who want to
develop and use new and improved treatments – both treatments such as drugs, and
treatments such as yoga and meditation. It will be great fun to enter this
next step in our group’s development!

This
is a picture of our group during a recent group meeting. Not all were
there, but most of them were. Some of the people in the picture are
excellent M.Sc. students in the end of their studies, who we now can
offer 2 Ph.D. positions. Apart from that, we will
hire two new people, one new Ph.D. student, and one postdoc, but also those will probably be recruits building on previous collaborations and projects. To help as manage all of these new people, we are also very fortunate that Gunnar’s second-in-command in the group, Associate Professor Elin Nyman, now is due to come back after an almost 2.5 year long leave in Harvard,
Portland, and an almost 1 year maternity leave. For all of these
reasons, made possible thanks to the new money described in the post
above, our group will now take a step up to functioning on a new level –
one with more senior people, more people financed fully by the group itself, and with
long-term funding secured. Now we will be able to fully focus on all of
the great research projects we are working on, without worrying if the money will ebb out in the middle of the project!

Hi!

My name is Kajsa and I just finished my bachelor at the engineering biology
program. This autumn, and maybe the spring, I’m joining the research preparatory
course. I´m also teaching in a beginners programming course at campus Valla, so
I will spend some time there as well. In my spare time I like to stay active,
which includes everything from movie nights to climbing Sweden’s highest
mountain Kebnekaise.

Here in the
ISB group I will get the chance to continue with the project I was involved in during
the bachelor. In the bachelor project we created a new liver model describing
fatty acid conversion. Now, I will continue the work of the previous students
Valentin Kindesjö, Thirza Poot and Johanna Fridberger to put together a model
that describes fatty acid and glucose fluxes during the day and how it’s
affected by different factors such as insulin and cortisol. My main focus will
be at the fatty acid part and I will continue to work on my liver model as well
as Valentin’s adipose- and cortisol module, which all will be parts of the
bigger model.

I will also
look at newly published data on body fat distribution in connection to diseases
such as type 2 diabetes and coronary heart disease. A future goal is to connect
the data to our models and being able to describe how the fatty acid
homeostasis is affected by stress factors such as disturbed cortisol levels and
why this in some cases cause diseases. By doing this, we are getting closer to
simulating clinical studies and predicting diseases.

Hello,

My name is Jonna and I am a Dutch student doing my
internship at the ISB group. I will be staying in Sweden to work on this
project for 3 months. Back home I am a master student in the Medical
Engineering program of Eindhoven Universtity of Technology. This externship is
the final part of my master studies.

Previously I have done most of my projects on
bioinformatics/data analysis so I am very excited to learn more about the
systems biology modeling techniques. This project is a great opportunity to
gain more modeling experience. During my
time here I will be working on modeling the liver.

In my free time I like to swim and explore the city/area a
bit since I am new in town. I’ve spent many of my holidays in Scandinavia (mostly
Sweden) so I am very happy to be living here for a few months. I have had a
part-time job in a swimming pool where I received my first aid certificate,
which I used my first morning in Linköping during helping a patient in the
street after a traffic accident in the city center. So my time in Sweden
started out quit hectic, hopefully that is not a precursor to how the coming
months will be.

I am looking forward to meeting all group members and working
on the project within the ISB group.

Hello!

My name is Anton Tornerefelt, I’ve just finished my third
year studying engineering biology.

Having recently finished my Bachelor’s project, which
sparked my interest in systems biology and modeling, I was eager to continue
working on this topic. Thankfully, I was granted the opportunity to work with
the ISB group for almost a year. My work will be focused on the different effects of
T-cell differentiation.

When I am not working, I enjoy wasting my time on watching movies and occasionally jogging.

I am looking forward to work and to bond with all colleagues here at the ISB-group!

Hi, my name
is Henrik, I’ve been accepted to the research preparation course (the
internship).

The subject of the internship is not completely decided yet, but it will involve the connection
between a brain function and the blood circulation.

Up until
now I’ve finished my bachelor project and with that my 3rd year at
the Engineering Biology program.

I am an
active person and like to train, previously I’ve been doing sports (mainly
swimming), and I spend a lot of my time at the gym.

I am looking forward to my time with the ISB group and am hoping for a fun and a instructive period.

Elin was recently awarded the prestigious AstraZeneca Science Award 2017 in the category Post-Doc. All the short-listed candidates was invited to the ceremoni with dinner at the Guildhall in the centre of the historic city of Cambridge. The top-right picture shows Elin being interviewed directly after the prize ceremony answering the typical question “how does it feel”.

In october, I went to Barcelona to attend the annual meeting of the European Society for Magnetic Resonance in Medicine and Biology (ESMRMB). Gunnar also came for one day. I presented a poster about my work modelling liver function. I also presented a poster and gave a short “lightning talk” on behalf of Mikael Forsgren, who could not attend.

/Markus