All posts by Tina Svingerud

From the writing course “Better together” in Bergen, Norway

Author: Muhammad Asaduzzaman

Muhammad Asaduzzaman, PhD Research Fellow at the University of Oslo and IBA member, received funding from us to attend a course in Bergen. This is what he has written as a report from his course:

Since my arrival in Norway early this year, this is my first trip to any Norwegian city other than Oslo. When Tina informed the last minute offer to join a course on popular science writing in Bergen from 14-18 October, it seemed to be a great opportunity for me as a first year PhD student.  This course was organized by DEEP (Norwegian Research School for Dynamics and Evolution of Earth and Planets) and the students came from three research schools – IBA (The National Graduate School in Infection Biology and Antimicrobials), NORBIS (National research school in bioinformatics, biostatistics and systems biology) and DEEP.

Group photo of participants (photo credit: Dr Muhammad Asaduzzaman)

As mentioned in the course website, this is definitely a successful initiative to develop basic writing skill in clear and concise way. This course has redefined my way of thinking in writing both scientific and general context. We learn many things but forget again without practice. This 5 day course is a complete package of sharing idea, writing in own way, polishing with others’ feedback and development of a final draft. The basic, simple but important steps I have learnt here is the use of active voice, continued flow, cutting needless and repetitive words, use of strong voice and avoid the long noun/adjective strings. In addition, we have realized the beauty of peer review how it improves the write-up skill for self and others. 

The most important instruments in a training course are the proactive mentor/instructor and attentive participants. Mathew Stiller-Reeve, senior Meteorological researcher, school teacher, science communication expert and founder of SciSnack writing community is such a wonderful person to conduct this type of courses. Maybe we were the great attendee as well ( ). Because Mathew evaluated us as “You all impressed me by your hard work and development throughout the course. I really enjoyed watching your articles develop throughout the week”

The instructor, Mathew Stiller-Reeve with Dr. Asad (photo credit: Dr. Muhammad Asaduzzaman)

Disregarding the flow we learnt, I can’t resist myself to tell about the city of Bergen. Bergen is a nice green city with an amazing amalgamation of sea and hills. I booked my hotel (unintentionally) near the most of the tourist attractions like Mount Floyen and the Funicular (Floibanen), Bryggen, Fish Market, theatre hall, several museums in university of Bergen, Bergenhus fortress etc. I was fortunate to visit the Natural History Museum when it was reopened after 3 years’ restoration process on October 14. I really enjoyed my stay in this city of scenic beauty with little boring rain.

Nice buildings in Bryggen area (photo credit: Dr Muhammad Asaduzzaman)

Finally, my impression about this basic writing course is that all PhD students in their first year should attend this interdisciplinary training. The organizers can also think of an advanced course on scientific article writing for those who have attended this course and some sort of grant writing training for final year PhD students and postdocs.

I express my gratitude to IBA for the travel support as well as for the opportunity to attend this excellent course.

Balint Csoboz is back from a workshop on “Epigenetics of infectious and non-communicable diseases” in Cape Town South Africa.

Balint Csoboz, post doc at the University of Tromsø and IBA member, received funding from us to attend a course in South Africa. This is what he has to report from the stay:

Between the 16th and the 19th of September, I was attending the workshop “Epigenetics of infectious and non-communicable diseases” in Cape Town South Africa. The meeting was organized by the South African component of the ICGEB (International Center for Genetic Engineering and Biotechnology). I have received partial funding from the meeting organizers for the attendance and the reason I applied for the support of IBA was to complement this funding in order to be able to manage the travel costs for the course.

Participants at the workshop (photo private).

ICGEB is an intergovernmental organization funded by the United Nations, which runs 46 state-of-the-art laboratories and forms an interactive network with over 65 Member States. ICGEB also offers a set of courses (https://www.icgeb.org/activities/meeting-and-courses/) and opportunities for short and long-term PhD/postdoc fellowships (https://www.icgeb.org/activities/fellowship/) to which I would highly encourage anyone to check out and apply for.


The workshop was focusing on many interesting aspects of epigenetics associated with infectious diseases as the epigenetics of host-pathogen interactions, the manipulation of epigenetics as host-directed drug therapy for infectious and non-communicable diseases, the analysis of micro- and long non-coding micro RNA in different pathologies or the role of epigenetics in modulation of host immune responses in diseases. This workshop provided insights of methods and models to identify epigenetic targets such as DNA methylation, covalent modification of histones, and the expression of non-coding RNA. During the poster sessions, I was introduced to methods that will certainly benefit my research on virally induced cancer. Like the technique of performing dual RNA sequencing of the host and infectious agent during infection and the usage and design of artificial epigenetic (gene) silencing by the means of gene editing.

Poster session during the workshop (photo private)

I also felt very lucky because I had the chance to get familiar with the history and the culture of the host country and visit the surroundings of Cape Town during the meeting. Especially, hiking the Table Mountain was a great experience, which is elected to be one of the Natural wonders of the world.

I feel that my attendance of the workshop was fruitful and rewarding. I managed to familiarize myself with the field of epigenetics and non-coding RNA research, which would be very useful for my postdoctoral project.


I am grateful for the support of IBA, which allowed me to participate in this course and have this fantastic experience.

The view of Table Mountain from the bay of Cape Town (photo private)

Reminder: IBA travel grants for research stays in Norway and abroad is open with the deadline October 15th.

A new round of applications for the IBA travel grants for research stays in Norway and abroad is open with the deadline October 15th.

Illustrasjonsfoto: Colourbox.no

The grants are for research stays at a lab/research group and does not include conference- and course-related expenses.

Send in your application here!

We need:

–  an outline of the planned work at the host institute

–  a tentative budget explaining how you will use the funds you are asking for

– a signed invitation letter from the host/hosting institution

– a signed recommendation letter from your main supervisor

The grants are open for PhD students and medical research (“forskerlinje”) members

For more information about applying and maximum funding levels see here.

Last year we funded students to go to Belgium, USA and Spain, this year it might be your turn.

Read more about previous research stays in our archives, and please get in touch with Tina if you have any additional questions!

PhD student Diana Karina Diaz Canova is back from a course on Viral Bioinformatics and Genomics

Diana Karina Diaz Canova, PhD student at the University of Tromsø, recently received funding from IBA to attend a course on Viral Bioinformatics and Genomics in Scottland.

She just came back, and you can read under what she says about her research and the bioinformatic training course!

Photo: private. Group photo of participants on the Viral Bioinformatics and Genomics

My PhD research project is focused on improving MVA-vectored vaccine safety by determining potential recombination between MVA-vectored vaccine and naturally occurring Fennoscandian cowpox viruses (CPXVs) during coinfection/superinfection of mammalian cells. The risk of recombination is considered low because MVA multiplies poorly in most mammalian cells. However, we have demonstrated recombination occurred between MVA vaccine vector and CPXV. As part of my PhD project, I will analyse the genomes of hybrid progeny viruses from recombination between MVA – vectored vaccine and Cowpox virus. These genomes were sequenced by Next Generation Sequencing technology. However, successful analysis of these genomes sequences requires a good knowledge of bioinformatics analyses.

Therefore, I was motivated to attend the 5th Annual Training Course on Viral Bioinformatics and Genomics (19-23rd Aug 2019) organised by the Medical Research Council (MRC) – University of Glasgow Centre for Virus Research (CVR). I believed that attending the course will equip me with the right bioinformatic tools and also the impetus to analyse my sequence data.

The course was focused in analysing high-throughput sequence (HTS) datasets using bioinformatics tools, UNIX command-line and bash scripts. During the five-day course, different topics such as HTS sequencing technologies, reference assembly, variant calling, de novo assembly, metagenomics analyses, phylogenetic analysis etc. were covered through lectures and practical sessions.

The course was well structured and organized in such a way making it easy to comprehend for participants, like me with basic experience of UNIX command lines. The course coordinators dedicated the first day to introduce the UNIX command lines. In addition, after every lecture we had a practical session where we could put what we have learnt into practice. During the practical sessions, we analysed viral genome sequences using different bioinformatics tools.

Photo: private. Learning by building lego

The instructors used fun and creative ways such as Lego building for teaching reference assembly. The courses instructors were not only bioinformaticians but have extensive knowledge and real hands on experience in viral genome sequence analysis. This was quite helpful because we could discuss the current challenges we are facing in our individual project with them. I have got some feedback which I intend incorporating into my subsequent analysis.

Attending the course was a good and rewarding experience. Although the five days course was intensive, it was at the same time very productive because I could learn the main bioinformatics tools that are relevant to achieve the goals of my PhD research project.

I would like to thank to the National Graduate School in Infection Biology and Antimicrobials (IBA) for grating me the travel grant assistance to attend this course.

PhD student Christopher Frölich is back from a course on Structural Bioinformatics

PhD student from the University of Tromsø, Christopher Frölich, received funding from IBA to attend a course on Structural Bioinformatics in the UK. He just came back, and you can read his report under.

Photo: Christopher Frölich. Cambridge next to Newton´s apple tree.

From the 16th to the 20th of September 2019 I visited the Wellcome Genome Campus in Cambridge to attend a course on Structural Bioinformatics. The course was organised by the European Molecular Biology Laboratory (EMBL), was internally oriented, and explored the various usages of bioinformatic data for structure determination. The talks were given by several different speakers and were always broken up into two parts; the first being an in-depth lecture and the second being a series of hands-on exercises to apply what we had just learned. During the practical parts, we got the opportunity to explore situations such as how mutations may change or interfere with pre-existing enzymatic functions, as well as molecular docking.

Photo: Christopher Frölich. Session on protein protein docking

My personal highlight was one of the molecular docking experiments where we modelled protein-protein interactions. In addition, each participant had the opportunity to present their own work in form of a poster, leading to fruitful discussions and networking sessions amongst us attendants.

I am quite happy that I was able to attend this course since it provided insights into how to use bioinformatic data to predict structures. In addition, the speakers provided helpful open access tools to solve different scientific questions.

The Wellcome Genome Campus is modern, offers everything you need for a short term stay, and is roughly 30 minutes from the city centre of beautiful Cambridge.

Photo: Christopher Frölich. Hixton hall, hotel on the campus.

I really would like to thank IBA for providing the travel grant and making this fantastic experience possible.

PhD student Syeda Mariam Riaz is back from an EMBL course on “Finding evidence in research publications”

PhD student from the University of Bergen, Syeda Mariam Riaz , received funding from IBA to attend an EMBL-EBI course on “Finding Evidence in Research publications” at the Wellcome Genome Campus in Cambridge,  UK. This is what she has to report on the stay.

Foto: privat. Group photo taken at the workshop.

My PhD study aims to understand the immune pathogenesis of primary and post-primary tuberculosis using human material from the pre-antibiotic era. Primary and post-primary tuberculosis are two different disease entities caused by Mycobacterium tuberculosis. Experimental studies using various animal models have given useful insight into immune pathogenesis of primary TB, characterized by the granulomatous immune response which is very effective in controlling infection. However, there is a paucity of information on the immune pathogenesis of post-primary TB. Untreated human tissue was no more readily available after the introduction of antibiotics in the 1950s. This forced investigators to develop and use animal models for study. Use of animal models and lack of availability of human tissue for confirmation resulted in a new paradigm for TB pathogenesis dating back to the late 20th century. This has guided the research on TB since then and unfortunately diverted the focus from the true pathogenesis of post-primary TB. 

My PhD thesis requires a lot of literature review of difficult to access articles of the early 19th Century. To increase my understanding of the literature review I went to Hinxton, UK to attend a two-day workshop on Finding Evidence in Research Publications arranged by EMBL. It was a very informative workshop where I was introduced to Europe PMC, an EMBL data resource site. In the workshop, they also taught us how the researcher shares and cite data. We were introduced to different tools to search for data cited in the literature along with methods of text mining and annotation and searching for datasets on a specific research topic. It was for the first time that EMBL was organizing such workshop and this provided us with great opportunity to learn. I also got the chance to meet researchers from diverse background, to discuss new ideas with them and learn from their experiences. I am very grateful to IBA for sponsoring this course as it helped me build a network and gain international experience and exposure. 

Deadline Nov. 10th : Conference – Turning the Tide on Antimicrobial Resistance 4

Turning the Tide of Antimicrobial resistance (TTA) and IBA invite all IBA members to  the 4th Turning the Tide of Antimicrobial Resistance Conference.

The conference is a High impact meeting on Tuberculosis & Machine learning for Antimicrobial Resistance. Detailed information can be found of the conference homepage.

Have a look at the program, and sign up here no later than November 10th.

The conference fee is covered for all IBA members.

Please note that in accordance with our guidelines we do not cover travel and accommodation expenses for conferences.

Deadline October 15th – IBA TRAVEL GRANT APPLICATIONS

A new round of applications for the IBA travel grants for research stays in Norway and abroad is open with the deadline October 15th.

Illustrasjonsfoto: Colourbox.no

The grants are for research stays at a lab/research group and does not include conference- and course-related expenses.

Send in your application here!

We need:

–  an outline of the planned work at the host institute

–  a tentative budget explaining how you will use the funds you are asking for

– a signed invitation letter from the host/hosting institution

– a signed recommendation letter from your main supervisor

The grants are open for PhD students and medical research (“forskerlinje”) members

For more information about applying and maximum funding levels see here.

Last year we funded students to go to Belgium, USA and Spain, this year it might be your turn.

Read more about previous research stays in our archives, and please get in touch with Tina if you have any additional questions!

Extended Deadline October 1st – IBA COURSE : ONE HEALTH APPROACH TO BACTERIAL ZOONOSES OF PUBLIC HEALTH INTEREST

Illustrasjonsfoto: Colourbox.no

IBA is offering a course in “One health approach to bacterial zoonoses of public health interest” on 21-23 October 2019, at the Faculty of Veterinary Medicine, NMBU – Campus Adamstuen in Oslo. The course will feature lectures on the most common bacterial zoonoses in Norway and state-of-the-art methods used in surveillance and research. There will also be opportunity to present your research in poster format as well as networking through dinners and activities in the evening

Registration closed.

IBA will cover the course expenses as well as travel and accommodation for members that are PhD students, medical “forskerlinje” students and postdocs (please review our funding guidelines here). For other members we cover the course fee only.

For more details including the program see the course page.

JANINE LIEDTKE IS BACK FROM A THREE WEEK RESEARCH VISIT AT THE VRIJE UNIVERSITEIT IN BRUSSEL, BELGIUM

IBA member (from The Norwegian University of Life Sciences in Oslo) and recipient of the IBA travel grant for research stays abroad, Janine Liedtke, has spent three weeks in Belgium working on her PhD. This is what she had to say about it!

Vrije Universiteit, Brussels.

The aim of my PhD project is to investigate bacterial spore surface structures, known as “appendages”. The presence of appendages among many spore forming Bacillus and Clostridium species suggest that they have an important biological function. Despite the fact that several studies already have been on spore appendages, their genetic identity and role remain elusive because of their extreme resistance towards chemical as well as enzymatic treatments. We want to overcome these issues by using state-of-the-art techniques like the latest electron microscopy and mass spectrometric techniques. For these purpose, we work closely together with our national and international partners, since they can provide us with the latest techniques as well as with their expertise.

I have succeeded to develop a method that allows extraction of a high amount and nearly pure appendages. This has already lead to high quality TEM images of the structure of the fibres, which has not been reported yet. However, due to the high resistance and hydrophobic behaviour of the appendages, we faced several difficulties to degrade and solubilize the appendage structure for further mass spectroscopic analyses.

At the same time, our collaboration partner Prof. Ute Krengel (UiO), who became a part of my supervisor team, introduced us to Prof. Han Remaute from the VUB in Belgium. Prof. Remaute has extensive expertise on working with bacterial surface-associated amyloid fibres and he gave me the great opportunity to use state of the art electron microscopy techniques in his lab to study the structure of the appendages in further detail. We decided to have a first “short” visit to test if those techniques are suitable for determining the structure of the appendages. Luckily, it turned out that their technique can provide us with a high-resolution model of our structure. Additionally with the support of the group members Dr. Mike Sleutel and Dr. Jolyon K. Claridge, I was also able to conduct further chemical treatments of appendages to test their solubility and stability.

During my first visit, we made good progress in improving the resolution of the appendage structure and gained more information of the chemical properties of the appendages. At the same time, I got the chance to join a highly motivated group with who I discussed many new ideas and from who I learned another way to approach my project.

My research visit would not had been possible without the grant from the National Graduate School in Infection Biology and Antimicrobials (IBA) and I am very grateful for the support. I have been invited to a longer research visit in Prof. Han Remautes lab and a plan to go there to continue and finalize the work on the structure on the spore appendages.