Travel report from a research stay at the University of Helsinki
December 2023. Author Ahmed Bargheet
Purpose of the Travel:
My research stay at the University of Helsinki was a strategically planned endeavor, rooted in my role as a Ph.D. candidate deeply engaged in exploring the intricate relationship between various factors and their impact on infants’ gut microbiota, resistome, and mobilome. This journey was a continuation of my comprehensive meta-analysis, which leverages publicly available datasets to understand how antibiotics, gestational age, birth mode, and diet influence the early-life resistome and mobilome. My objective was to delve deeper into the nuances of these relationships, especially focusing on identifying principal bacterial species that carry resistance genes in infant microbiota.
The collaboration with esteemed experts from the University of Helsinki, including Katri Korpela, Alise Ponsero, and Chin Jian, was a crucial element of this stay. Their initial visit to Tromsø laid the groundwork for our bioinformatics methodology. My proposed stay was, therefore, pivotal for the continuation and success of our joint research, especially after their return to Finland. The visit was envisaged as a golden opportunity to expand my skill set in gut microbiology, bioinformatics, and machine learning, and to enhance the analytical rigor of my ongoing study.
Results of the Stay:
The research stay at the University of Helsinki was immensely fruitful and exceeded my expectations. During my time there, I gained substantial experience in bioinformatics and machine learning, which were instrumental in advancing my research skills. Working closely with experts in the field, I was able to delve into complex datasets, enhancing my understanding and proficiency in handling intricate bioinformatics tools and methodologies.
A significant part of my research involved studying the impact of antibiotics, prematurity, birth methods, and milk type on infants’ gut microbiota and resistome. This investigation revealed intriguing patterns and correlations, shedding light on the delicate interplay between these factors and the gut microbiome in early life. The insights gleaned from this analysis are not only academically stimulating but also hold potential implications for public health and pediatric care.
Encouraged by the interesting results, I proposed the incorporation of advanced machine learning approaches to further study the microbiota clusters. This suggestion was well-received and has opened avenues for more nuanced and detailed analysis. The application of machine learning techniques promises to unravel deeper layers of understanding about the gut microbiome, offering a more comprehensive view of its dynamics and influences.
In summary, the research stay at the University of Helsinki was a pivotal phase in my academic journey. It not only provided me with invaluable experience and expertise in the field of bioinformatics and machine learning but also significantly contributed to the progression of my Ph.D. research. The collaborative environment and the exposure to cutting-edge research methodologies have been instrumental in shaping my scientific approach and will undoubtedly be a cornerstone in my evolving academic career.
Travel report from a research stay Roslin Institute, Scotland.
June 2023. Author Gabriela Paz Carril Leiva
I am a PhD candidate at the Norwegian University of Life Sciences, working with the salmon pathogen Piscirickettsia salmonis, the biological agent of SRS (Salmonid Rickettsial syndrome). After completing the main objectives of my project, I have the results I needed for working on the last one, to choose virulence effectors with the potential to be knock-out and impair the pathogenicity of the bacterium. Which was a perfect opportunity to spend three months at The Roslin Institute in Scotland working on this.
I traveled to Edinburgh at the end of January 2023 to start my research stay in the aquaculture group of Dr. Diego Robledo and in the bacteriology group of Dr. Nicola Lynskey. Using molecular biology techniques along with their advice and experience we generated a method to achieve the gene deletion in the bacterial chromosome. Even though, I thought that the time will be enough, in science you cannot count on that, so I could not complete the last part with the resultant mutants. But I was able to send the work done to my lab in Ås and finish the experiments.
The Roslin Institute is part of the Royal (Dick) School of Veterinary at The University of Edinburgh, well known for cloning Dolly the Sheep in 1996, a world-leading institute for animal science research. So, it was a remarkable educational experience improving my laboratory skills and expanding my work experience. Also, this research stay was great for network building and valuable scientific discussions with both research group members who were very supportive and friendly whenever I needed their help.
I had the opportunity of living in Edinburgh, a lovely city that feels like frozen in time with the castle on top and the old town around. And I was lucky enough to get to know some nearby cities, more old castles, and the amazing highlands in Scotland, which made this trip even more valuable.
I am grateful for the travel grant to IBA and the research groups at Roslin for having me, and hopefully, all the collaborative work done will be summarized into a paper soon as planned.
Travel report from a research stay at UiO, Norway
March 2023. Author Srijana Bastakoti
The Report presents the experience and skills gained during my three months of research visit at the University of Oslo (UiO), Institute of Basic Medical Sciences, Oslo, Norway.
“If you can’t explain it simply, you don’t understand it well enough” is very well said by Albert Einstein. I had the same feeling, when I realized that I needed to uncover the hidden knowledge of my PhD research topic, which would enable me to express my understanding about it with more clearly and loudly to other scientific communities. To achieve this, I chose to visit UiO research group and work under someone adept at exploring Next Generation Sequencing (NGS) data analysis needed for my PhD research. I am glad that IBA has supported me for making this happen.
I am Srijana Bastakoti, a third-year PhD student from The Arctic University of Norway (UiT), Tromsø. I aim to expand my skills and experience in scientific research work related to omics science and medical health, and to form a self-owned organization that will work towards creating scientific reforms. This research visit has enabled me to gain an understanding of the transcriptomics analysis, making my research ideas/results easy to convey to the scientific community, including the public more simply and clearly.
To begin with, I would like to share glimpses where I was occupied with all those heavy RNA seq raw files versus me after being educated on the topic.
It was very overwhelming for me until I was in expertise hand at UiO because I had to perform pre-processing of raw files by myself. Thereafter, Maiju Pesonen, a statistician at the faculty of
medicine, guided me for the analysis of differentially expressed genes (DEGs). The main aim in the study was to identify the DEGs present in Staphylococcus aureus cocultured with Streptococcus anginosus and human tonsillar cells. The survival factors expressed by S. aureus during coculture was identified. Some of the up-regulated genes might be targets for intervention to prevent either colonization or infection in the throat region in the future.
During this period, I have increased my competence in NGS data analysis and implemented the technique in my PhD project. I also got connected with a potential collaborative research group at UiO – Institute of Basic Medical Sciences, which is dealing with omics analysis and expression analysis. As I intended to explore transcriptomics data generated from the host-pathogen interaction model, this institute became the perfect platform for training, which is directly applicable to my ongoing and future scientific projects. Ultimately, after the complete exploration of data analysis, I felt like all the hidden knowledge behind the analysis was exposed to me. I believe to expand this knowledge further to my research group. I develop an understanding of handling heavy sets of RNA-seq data, and transcripts analysis, including gene expression analysis. Moreover, I also had an opportunity to present my work in the research group followed by fruitful discussions with the researchers both before and after my stay. I was very grateful to meet potential collaborators and meet people with several other interests. I am immensely thankful to Maiju and other group members for welcoming me and providing a friendly atmosphere whenever possible.
Apart from this scientific achievement, I saw the change in beautiful nature in those months. I was glad to escape the dark period in Tromsø and to see some bright side in Oslo.
To sum up, this research stay has been very beneficial for the successful completion of my research. It has enhanced my knowledge regarding RNA/DNA-seq data analysis. I encountered recently updated techniques in the field of NGS bioinformatics, which I can apply in my further research data analysis. I was able to fill all the knowledge gap that I had before going to this research stay.
Now I am more confident to discuss and work on both the biological and bioinformatic perspective of my study – more clearly and loudly to other scientific communities. My hearty thankfulness goes to Jukka Corander, a professor, at the Department of Biostatistics, UiO for inviting me to his research group, and to IBA for funding this research visit for making this happen. Thank you very much 😊
Travel report from a research stay at Bangladesh
January 2023. Author Muhammad Asaduzzaman
I am a PhD Research Fellow at University of Oslo (UiO) and my research focus is antimicrobial resistance (AMR) in One Health (OH) approach. My current project includes an exploratory observational study in Bangladesh to quantify the clinically significant drug resistant bacteria in air with spatial diversity. In December 2022, I visited the ‘Laboratory of Food Safety and One Health’ at International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Bangladesh in connection with this OH-AMR project.
The food safety and OH laboratory at icddr,b is a well-equipped collaborative site with the Government of Bangladesh through directorate general of health services (DGHS) and foreign institutions. Particularly, this lab is highly resourced for OH sampling and analysis from food value chain. In our project, the air samples were collected from both urban and rural settings in four distinct environments in Bangladesh– i) Urban food markets ii) Urban residential area iii) Rural poultry farms and iv) Rural households. In this lab, I had the opportunity to learn the bacterial identification, antibiotic susceptibility testing and sample storage for further analysis. We (I and the lab team) also sorted out the process and sample selection for further metagenomic analysis required for my study.
My research stay was short but impactful. In this trip, I met with several scientists at icddr,b who are interested for future research collaboration. I also needed the approval from several disciplines at icddr,b to publish manuscript using the lab data from this project. I recapitulated and improved my laboratory skills. The laboratory head introduced me with all staffs and their ongoing projects on OH-AMR. We have discussed about several research outcomes and future endeavors based on the current study and beyond.
I am so grateful for the travel grant from The National Graduate School in Infection Biology and Antimicrobials (IBA) without which my current research stay would not be possible.
Travel report from a research stay at the University Medical Center Utrecht (UMCU), The Netherlands.
January 2023. Author: Jeanette Slettnes Grunnvåg
My name is Jeanette Slettnes Grunnvåg. I am a PhD student at the Host-microbe interactions group at UiT – The Arctic University of Norway, where I work with identification of novel enzyme targets for clinical control of vancomycin resistant Enterococcus faecium using Activity-based protein profiling (ABPP). This is a method where we use chemical probes that bind with enzymes to pull-down the targets of these probes. I am now more than 1 year into my PhD and have identified sets of proteins belonging to the serine hydrolase, glycosidase, and kinase/ two component system enzyme families, which I am interested in studying further.
To know whether these enzyme targets are of clinical relevance I travelled to the lab of our project partner Professor Rob Willems at the University Medical Center Utrecht (UMCU) in the Netherlands to isolate transposon mutants from a transposon mutant library they have located in their lab. The library consists of mutants of the bacteria where a transposon has been inserted into a gene to disrupt the function of that gene. By studying mutants where the enzymatic function of our identified enzyme targets has been knocked out, we can get some insight into the importance of that enzyme for the bacteria.
Unfortunately, the isolation process turned out to be more difficult than first expected, as science often can be, so I did not manage to isolate as many mutants as I was hoping for. I was fortunate to work under the guidance of Dr. Janetta Top who taught me the whole procedure of the transposon mutant isolation procedure and who was there to discuss when the process was yielding some unexpected results. Now I have the resources and knowledge to pass along and continue the work at our own lab in Tromsø.
The Netherlands is quite different from Norway in terms of landscape, but culturally quite similarly, so it felt both foreign and familiar at the same time. Utrecht is a buzzing student town with lots of wonderful restaurants and a beautiful centrum. The housing I was living at was situated in a quiet street next to a park which I had a lovely view over.
I also went to the De Hoge Veluwe National Park for a day of biking and hiking in beautiful surroundings, and just as I was leaving, I got to see some red deers. Of course, I also travelled to Amsterdam which a 25 min train journey away from Utrecht. All in all, I had an eventful and challenging stay in the Netherlands. Thank you to IBA for the financial support for this trip.
Travel report from a research stay at Umeå University – Sweden
December 2022. Author: Unni Lise Jonsmoen.
I am a PhD candidate at the Norwegian University of Life Sciences (NMBU) working with characterizing appendages found on bacterial endospores of Bacillus cereus strains. From September to December 2022 I visited the Biophysics and Biophotonics group at Umeå University, located in the north of Sweden.
The Biophysics and Biophotonics group is a part of Physics department and led by Magnus Andersson. They have their expertise in characterizing physical properties of pili structures on various bacterial species, in addition to experience working with endospores. Magnus Anderssons group are specialized in developing and applying advanced optical techniques to study biological systems, and I got to use their Laser Tweezer setup to conduct single cell manipulation and study spore aggregation and the physical characteristics of the endospore appendages. The neat system they had enabled me to pull on and measure the force response of individual fibers, pick up single spores and drag them around in a suspension. This allowed me to interact with the samples and see in real-time how spores and cells interact.
Working interdisciplinary between biology and physics provided valuable insights to experimental design consideration and a practical way of thinking outside of the standard biology. Magnus included me in several of the ongoing projects in their lab and connected me with people that could help me along in my PhD project.
The physics building at Umeå University.
The stay was eventful, and people in the group and other colleagues were great at taking initiative and including me in their afterwork activities. After a few weeks I joined IKSU (Idrottsklubben Studenterna i Umeå) which is the largest sports facility in Scandinavia. They offered a large variety of different classes and training facilities, such as climbing hall, swimming pool, and indoor beach volleyball courts. Because of the large variety of activities, it was a great place to meet people and do activities outside the lab and was quickly integrated into my new routine. A small group of PhDs and PostDocs also went outdoor swimming once a week in a lake close to campus. For the last week of my stay the lake had frozen over and we needed to make a hole in the ice to take a dip.
I would like to thank Umeå University, and especially the Biophysics and Biophotonics group, for the hospitality and IBA for the financial support for this visit.
There were a lot of nice walking and cyling paths all over the city, also along the beautiful Umeälven
Travel report from a research stay at Université Laval in Quebec, Canada.
July 2022. Author: Olaug Elisabeth Torheim Bergum.
I am studying for a PhD at NTNU in Trondheim. The project I am part of involves a longitudinal multi-omics approach. Specifically, we treated E. coli with a novel in-house produced antibiotic named betatide. During growth, we sampled for transcriptomics, proteomics and metabolomics at 8 different timepoints. Our goal is to integrate the individual omics to in detail examine the SOS response in E. coli, and how E. coli responds to the different treatments over a time course.
To learn multi-omics integration, I arranged a three-month research stay (April-July 2022) at Professor Arnaud Droit’s group at Université Laval in Quebec, Canada. The group develops bioinformatic tools for analysis of omics data, including the R packages timeOmics and netOmics for integrating longitudinal omics data and network exploration of multi-omics, respectively. The team members assisted me in tailoring the R packages to my data sets, allowing me to gain the maximum of biological information from the experiments. The result section of my articles can now be filled with some beautiful multi-omics figures! My group at NTNU is mainly working in a wet lab, so working in a bioinformatic lab was a new experience for me and accelerated my learning process as I easily could ask the team members for help if my R code experienced some hurdles. On top of all, I did not only boost my R skills, but also my French as I was the only non-French speaking person in a group of almost 30 people.
The stay in Quebec has been a great experience. In terms of learning outcomes, I have improved from zero skills in multi-omics integration to being able to integrate big data sets. It is also noteworthy that Quebec is a very beautiful city! As I lived in old town, I was always amazed by the surroundings when I stepped out of my flat. However, don’t let yourself trick from the weather of the pictures. Some might say that Trondheim has an unstable weather, but after my Quebec experience I was introduced to a next level wobbly transition between hot and cold and sun and rain. I am very grateful for the support from IBA, it has been three educational and exciting months!
Travel report from a research stay at Robert Koch Institute in Berlin, Germany.
Report from December 2021 (travel in 2019). Author: Diana Diaz Cánova, PhD student at the Artic University of Norway- UiT.
My name is Diana Diaz Cánova, I am a PhD student at the Molecular Inflammation research group (MIRG) at the Artic University of Norway- UiT. As part of my PhD project, I performed sequencing of recombinant viruses and the parental viruses as well as Fennoscandian cowpox viruses. To get further insight into these viruses, the viral sequence data needed to be analysed using the appropriate bioinformatics tools. However, I did not have any experience in bioinformatics analysis. In addition, bioinformatic analysis of Poxvirus genomes is usually very challenging because of the terminal repeats. To overcome these challenges, I needed the expertise of bioinformaticians with experience in Poxvirus genome analyses and specialized sequencing techniques.
Robert Koch Institute (RKI) at Berlin, Germany is a well renowned public health institute. RKI has a Consultant Laboratory Poxviruses, in the division Highly Pathogenic Viruses. This institute works with classical virological methods as well as modern molecular methods such as next generation sequencing (NGS), Nanopore sequencing (third generation sequencing) and Sanger sequencing (first generation sequencing). Based on these attributes, I chose Robert Koch Institute (RKI) at Berlin, Germany for my research stay. I was highly convinced that the experience from my research stay would be productive and helpful towards the actualization of my PhD goals. In 2019, I travelled to and started my short research stay at RKI, Berlin. Prior to the research stay, I had never worked with bioinformatic tool and analysis. I always knew that at some point of my PhD I would need to fill this knowledge gap. This was the moment!
I was fortunate to work full time with a seasoned bioinformatician, Annika Brinkmann, for two weeks. It was wonderful getting a thorough guidance from her into the world of bioinformatics. The two weeks research stay were quite intense and productive. We started with the basic bioinformatics and installing of programs. Thereafter, we did the quality control of my data and genome assembly of my viruses. During this research stay, I acquired bioinformatics skills that I made me to be able to analyse my sequence data on my own in Tromsø. At RKI, I also had the opportunity to visit the poxviruses laboratories at the institute. At the end of my research stay, the Head of the Division asked me to present my project to the research group and share the results that we obtained after two weeks of work. I was a pleasure for me to present and have a nice discussion with professionals that work in the same field. After this first short research stay, the plan was to go back at RKI for a longer time, but the Covid-19 pandemic interrupted the plan. Though I could not go for second research stay, my first short research stay at RKI was so helpful. Overall, the research stay has been very insightful for me and also enhanced productive for my PhD project.
I am so grateful for the support from The National Graduate School in Infection Biology and Antimicrobials (IBA). I would not have had this enriching experience without the travel grant.
Travel report from a research stay at the Norwegian University of Life Sciences (NMBU), Norway.
October 2021. Author: Runa Wolden – PhD student – UiT.
My name is Runa Wolden, a PhD student in the Paediatric Infection group at UiT The Arctic University of Norway. Early this semester I went to the Norwegian University of Life Sciences (NMBU). During my stay, I was able to purify a possible new bacteriocin.
What a privilege it was after a minimum of travel during the pandemic to be able to head south for a research stay. For one month, I was going to live in Oslo and work at NMBU in Ås. By train, it is only a half hour journey between the two cities.
Working on experiments in Tromsø, I had found a possible new bacteriocin from a skin commensal. Bacteriocins are peptides produced by bacteria to inhibit growth of closely related bacterial species. As bacteriocins can be candidates for novel antimicrobial agents, I wanted to purify the compound.
The Laboratory of Microbial Gene Technology at NMBU had the knowledge I needed to make progress with my experiments. It was a great pleasure to collaborate with so welcoming and highly skilled colleagues. The leader of the research group, Professor Dzung B. Diep, facilitated my stay and gave me a lot of advice. Researcher Kirill Ovchinnikov has shown me everything in the lab and taught me many new techniques. Because of my stay at NMBU, I came back to Tromsø with a purified bacteriocin that I can do further experiments with. The results are promising and hopefully they will lead to a paper quite soon that summarizes the work so far.
The situation with the corona pandemic made it difficult to plan for an exchange abroad. This domestic exchange was a very good alternative. Thanks to IBA for their travel support!
Travel report from a research stay at Washington University in St. Louis and Icahn School of Medicine at Mount Sinai Hospital
June 2021. Author: Lena Hansen – PhD student – UiB
I am a PhD candidate at the University of Bergen and the topic of my thesis is antibody responses to influenza after infection and vaccination. From January to December 2020, I visited two labs in the US.
The first part of the trip was spent in Ali Ellebedy’s lab at Washington University in St. Louis. St. Louis is located in Missouri and is the second largest city in the state with a population of around 300 000. The Ellebedy lab specialises in B cell responses and monoclonal antibody production (mAb). I am really interested B cells and I have always wanted to learn how to make mAbs, so this was a perfect fit for me. mAb cloning is a pretty complex process that involves single cell sorting, cloning, sequencing and protein expression, so there were a lot of different methods to learn. During my time here, I made human mAbs from blood samples that were collected during the swine flu pandemic in 2009 and managed to make several mAbs that we could use for characterisation.
The second half of the trip was spent in Florian Krammer’s lab at Icahn School of Medicine at Mount Sinai in New York City. The Krammer lab works with characterisation of antibodies and studies the mechanisms that enable them to protect the host from infection. I worked on characterising the mAbs that I had made in St. Louis and tried to determine which influenza viruses and proteins they bound to and if/how they protected mice from influenza infection. Characterising these mAbs was a really fun process and felt like solving a puzzle at times.
Although the lab work went more or less according to plan, the trip ended up being more eventful than I had expected. The COVID-19 pandemic, BLM protests and a relatively chaotic presidential election made an already special year even more memorable. This was actually my first time visiting the US and I am a little disappointed that I was not able to experience these two great cities under normal non-pandemic circumstances, but I had an amazing time, nonetheless. I am very thankful for the funding I got from IBA to support this visit.
Travel report from a research stay at Pennsylvania State University – USA
February 2021. Author: Christina Bleis – PhD student – UiT
From March 11th to December 1st 2020, I had the pleasure to work on my PhD at the Center for Disease Dynamics (CIDD) at the Pennsylvania State University in US. Penn State is a top 25 research university with over 100,000 students. Penn State campus called the University Park was a gorgeous sight to meet every morning I came into work. One of the famous tourist sites on campus is the statue of the Nittany Lion which is the official athletic symbol of Penn State and naturally depicted on university clothing.
Penn State is located in a small town called State College with the charming nickname Happy Valley. Unfortunately, due to covid many attractions were closed and there were restrictions on social gatherings. Despite this, my research stay was a very exciting experience and highly productive in terms of PhD project progress.
The focus of my PhD is investigating how the enteric bacterium Vibrio cholerae survives the passage through the stomach, and subsequently causes the disease cholera. While working at Penn State I examined this by performing a transposon-insertion sequencing screen – or in other words a global genetic screen. This screen allowed me to identify 25 genes in V. cholerae important for surviving acidic conditions. Now that I am back in Norway, I will be looking into these genes further, so the research stay has resulted in material for one of my publications.
I have also received grant support from the Norwegian PhD School of Pharmacy (NFIF).
I would like to thank IBA for making this research stay possible.
Travel report from a research stay at GlucoSet in Norway – Eric Juskewitz
January 2021. Author: Eric Juskewitz – PhD student – UiT
I am Eric, a PhD fellow in Microbiology at the UiT. With entering the last year of my PhD journey thoughts of the big “what’s next?” started to bubble up and are keeping me awake at night. Most of them revolve around possibilities the industry might have to offer.
Researching opportunities, I became aware of a partly funded industry internship offered by Digital Life Norway. Though my schedule was extremely packed, I signed up without hesitation. With the blessing of my PI, I put that schedule on hold for three months and embarked on my voyage to discover the unknown land of industry.
The journey took me to Trondheim, where I joined the team of GlucoSet – a medtech start-up that is in the development phase of its product. So, what did a microbiologist learn in a company that is building a glucose sensor for ICU patients, made of glass fibre and polymers?
Week 1-4: While entangled by medical infusion sets and massaging a saline bag to simulate a heartbeat, I mimicked the basics of a bloodstream system. With that, we tested if the product would influence measurements of an ICU patient monitor. The first lesson learned: How to develop test setups and adhere to industrial standards.
Week 5-8: Working in the R&D department I learned the production steps and could finally bring my lab training into play. Here I learned much about quality management: Especially for medical products, everything needs to be documented flawlessly.
Week 9-12: I faced the biggest challenge of the internship: Getting rid of dust to ensure that the final device is dust-free. It sounds trivial, but having enormous dust yields around, problem-causing lab equipment and the pressure of real production soon to start, it got exciting! After taking stocks, staying level-headed and resolving one problem at the time we got the situation under control. This was when I got my key insight:
Being a good scientist will land you a job anywhere. Even if the topic is out of your comfort zone, analytical thinking, statistics and engaging with literature are always needed. And with my training, I have those skills in tow already. Add some project management knowledge and a “done is better than perfect” attitude and you are set.
Being back in Tromsø, my approach to work has changed. My PhD is getting DONE and it´s okay that it will perhaps not be nominated for best publication ever. Thanks to this experience, I also freed up headspace. Without constantly thinking about my PhD, I got to explore other interest, strengthened my LaTeX skills, learned about project management and attended various webinars. I probably wouldn’t have had the mental capacity to do them if it wasn’t for the change of scenery.
I am thankful for the extra funding offered by IBA. It helped to prove my worth as a scientist, gave me a small and welcomed break from my PhD and let me now sleep easier when I am thinking about my future.
Travel report from a research stay at the University College London – Magnus Nygård Osnes
August 2020. Author: Magnus Nygård Osnes. PhD student – Norwegian Institute of Public Health.
I was in London for a research stay that was supposed to have lasted from Feb 8. to May 8. Unfortunately, I was forced to leave early on March 12. due to the COVID pandemic. Despite the interruption, I benefited greatly from the experience and had a good collaboration with our partners there.
In London, I was warmly welcomed at the Darwin Building at University College London (UCL) by my hosts Lucy van Dorp and Francois Balloux. I was given a seat with the main group that is working the closest with Francois and Lucy and granted access to a working station and the vital coffee machine. The group included several PhD-students and postdocs working on phylodynamics on topics such as tuberculosis, human genetics, and even parasites on tropical frogs. With the group, I attended lectures at UCL on bacterial population dynamics, systems of phages and mobile genetic elements, and lectures on machine learning. It was a great experience to see the breadth of topics covered by the phylogenetic community at UCL.
UCL on the left and the character cards of the people in the Genetics department on the right
In my PhD-project, I am working on the pathogen Neisseria gonorrhoeae (Ngon). The purpose of the trip to London was to collaborate with Francois and Lucy on our project on a multi-locus sequence type (MLST) of Ngon that has been responsible for a high percentage of the treatment failure cases globally. While I was there, I performed phylogeographic analyses to describe the dispersal patterns of the MLST over time and mapped important evolutionary events such as the acquisition of antimicrobial resistance determinants on time dated phylogenies. Lastly, we used these results to study how the dispersal of the pathogen lineages correlated with known drug treatment regimes. The result is a paper showing how the success of different lineages of the MLST has correlated with the acquisition of important AMR determinants, and that establishment of the lineage in America facilitated its further global dissemination. The paper is submitted to a good journal with a fitting scope and is currently under review.
Another reason to go to London was to visit my co-supervisor Xavier Didelot at Warwick University, starting with the Royal Society meeting in London on March 25. This was too interrupted, due to the bans on social gatherings that took place around this time and recommendations to limit unnecessary travel.
All in all, despite the interruption by the pandemic, this was a great experience.
I had a lot of progress on my projects while I was there and I would like to thank the National Graduate School in Infection Biology and Antimicrobials for the financial support that made this research stay possible!
Travel report from a research stay at Pennsylvania State University – Antal Martinecz
July 2020. Author: Antal Martinecz. Researcher, UiT.
I have spent the period between August 2019 and July 2020 at Pennsylvania State University (Penn State) in the US. This has been partially funded using travel grants from the IBA and NFIF PhD schools.
Penn State is located in a tiny university town called State College which is a remote place a couple hundred kilometers from the nearest big city. Even with my previous experience of living in a university town (Tromsø), many aspects of living there were unexpected and were often a pleasant surprise. Here, basically all services are aimed at people affiliated with the university. The extent of this is illustrated by the fact that even at local supermarkets such as Walmart, there is usually a large section where one can buy clothes and other things with the university’s or the university football team’s logo on it.
My PhD is on the mathematical modeling of antibiotic treatments. Specifically, I am interested in approaches that allow us to learn more from clinical trials and therefore better guide the design of subsequent clinical trials. As a result, my work requires me to be familiar with and connect multiple fields of research (medicine, microbiology, mathematics, epidemiology). Therefore being part of the Centre of Infectious Disease Dynamics (CIDD) Penn State was hugely beneficial for my work. CIDD houses groups from different departments and faculties in order to facilitate better collaboration between us. The mixing of groups were further encouraged by intentionally seating people from different groups into the same offices. This has been a great experience, as it exposed me to ideas and researches to other related fields that helped me to gain some perspectives on my own research. Among other benefits, having these interactions taught me how to explain my research in a way that can be understood by other researchers that are not close to my field. Being able to do so made writing my PhD thesis and manuscripts so much easier. Finally, at CIDD we had regular department-wide meetings and presentations 2-3 times a week on various research-related topics either by invited speakers or PIs within the department. This allowed me to learn more about works within my field, as well as the types of problems there are and how they are solved in fields loosely related to mine.
In addition to having one of the best infectious disease departments in the US (among other great departments), the university has the informal reputation of being one of the best party universities. This does not mean that there are constant wild parties, it simply means that the campus life is vibrant. There are many social events and other activities throughout the year catering to students and staff allowing everyone to have a satisfying social life in addition to their studies and work.
Having a great community at the department also meant that I could make many new friends and form new connections. The department encouraged this further by organizing weekly coffee mornings and other regular informal events where we could chat and get to know our colleagues outside the context of work.
This travel report would not be complete without mentioning COVID-19. The department and the university went into a lockdown from early March and as a result, I have spent my last four months within my apartment. It has been quite manageable as the university is surrounded by nature so I could always go for a run or a walk. Furthermore, online services such as food delivery, shopping and grocery delivery options are abundant. Therefore I could slowly assemble a home office and get back to work slowly and quickly regain a sense of normalcy in my life.
Finally, in the US, therapy is also very common and readily available currently in the form of online sessions due to the pandemic. As a result, I have been able to weather the pandemic and lockdown without anxieties or adverse effects on my mental health. This even included being able to easily prepare for and defend my PhD remotely in the beginning of June.
Travel report from a three-week research internship in June of 2019 at IGTP Badelona, Spain
April 2020. Author: Niruja Sivakumar. Medical research student at NTNU.
Last summer I was lucky enough to spend three weeks at Germans Trias i Pujol Research Institute (IGTP) in Badelona, Spain where my co-supervisor Marte Dragset was completing her post-doc. We’ve been working on identifying and studying the mechanism of novel virulence genes in pathogenic mycobacteria to both get a better understanding of host-pathogen interactions and to discover possible future treatment targets. We had already identified and verified a handful of novel virulence genes in a clinical strain of Mycobacterium avium through mouse experiments based off a transposon mutant library created by Marte. One of them, a probable MFS transporter, was of special interest and we wanted to study it further in other mycobacterial strains.
Mycobacteria are notoriously hard to genetically manipulate but with Marte’s expertise in bacterial virulence and the facilities provided at IGTP, a research institute accredited as a Centre of Excellence by the Spanish Government, we succeeded in creating a homologue mutant in Mycobacterium marinum through a specialized transduction method. During my stay there we were also able to perform in vivo infection experiments in common fruit fly since the Drosohpila melanogaster- and M. marinum infection model to study mycobacterial virulence was developed and implemented at IGTP.
I am grateful for the support I received from IBA and for the opportunity which was valuable in several ways. It was exciting to collaborate with my co-supervisor and successfully get an end product to bring back home for future experiments. I got to learn about the different projects and methods used in her lab group and the experience provided valuable insight into how different approaches shapes a lab environment and how cultural, social and structural barriers plays into that. As side from the scientific value I was lucky to explore beautiful Barcelona and I am filled with gratitude for the people I met and the hospitality I received.
Sindre Ullmann is back from a one-week research visit to Cambridge, UK
December 2019. Author: Sindre Ullmann
PhD student from NTNU and IBA member Sindre Ullmann recently went to Cambridge for a research visit.
In the section under, you can read what Sindre has to say about the stay.
As a result of conversations with Felix Randow about our two laboratories research projects it was discovered that the Randow group had developed a fluorescent probe which might have the potential to be very interesting applied in my project. They were so generous that they offered to share this probe with us and invited me to come and visit. This offer was to good to refuse as travelling to visit the UK Medical Research Council Laboratory (MRC) of Molecular Biology and getting hands on with the probe would be a rewarding and valuable experience moving forward in my project.
During my visit I got experience with using and imaging the probe. All the while I also got to see how a different research group approaches investigating host-pathogen interactions between the human immune system and pathogenic bacteria. Visiting the MRC also provided me with many new acquaintances as the people in the Randow group was very welcoming and including, something which led to both evening football playing, Christmas party and numerous communal lunch and coffee breaks.
Travelling back, I carry with me new insights, knowledge and hands on expertise with the fluorescent probe.
The support from The National Graduate School in Infection Biology and Antimicrobials allowed me to make time and budget-room in a busy PhD project to undertake this journey.
JANINE LIEDTKE IS BACK FROM A THREE WEEK RESEARCH VISIT AT THE VRIJE UNIVERSITEIT IN BRUSSEL, BELGIUM
August 2019. Author: Janine Liedtke
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!
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.
MY SIX MONTHS AT UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL, USA
July 2019. Author: Hera Kim
IBA student and recipient of the IBA travel grant for research stays abroad, Hera Kim, has spent six months in the US working on her PhD (she is currently enrolled at NTNU in Trondheim). This is what she had to say about it!
In the period of January to June 2019, I conducted research at University of Massachusetts Medical School, USA as a visiting student researcher in Dr. Kate Fitzgerald’s lab. The purpose of this research visit was to continue the functional studies of my gene of interest and get trained in advanced in vitro and in vivo infection models that can be applied to my Ph.D. studies.
Immunometabolism, or interplay between immunity and metabolism, is a rapidly growing field in immunology. As many studies have clearly highlighted how crucial metabolism is and its remodeling during infection and inflammation, our research group, led by Prof. Richard K. Kandasamy is particularly interested in changes in metabolism and associated changes in metabolite levels regulating the immune response. We have identified novel differentially regulated metabolites in Toll-like receptors signaling pathway from our initial metabolomics screen and aim to identify the role of these novel metabolites in innate immune signaling. Just then, I got a great opportunity to go abroad to continue my functional studies.
The most important and interesting part of my stay was to get trained in in vivo infection models. Hands-on-training with in vivo model definitely improved my understanding of physiologic concepts and increased the confidence in handling the model and a number of related techniques. I was also highly encouraged to meet researchers from other labs and share research ideas with colleagues, which helped me to build the key networks and increased opportunities for collaboration and publication. Moreover, attending several departmental presentations and related activities allowed meto gain in-depth knowledge in molecular mechanisms controlling the inflammatory responses. Now I believe that these skills and experiences will allow me to complete a larger-scale project in Trondheim and I hope to share this knowledge with my colleagues.
Overall, the stay has been productive on both a professional and personal front and I can highly recommend going for a research stay aboard to others. It is great for gaining research experience in a different environment, building your network, and broaden your perspective.
Lastly, I would like to thank the IBA school for the financial support. This funding has allowed me to truly grow as a researcher in my profession.
My six months at Washington University, St. Louis and at Icahn School of Medicine, New York, USA
January 2019. Author: Anders Madsen.
IBA student and the recipient of the IBA travel grant for research stays abroad, Anders Madsen, has spent six months in the US working on his PhD (he is currently enrolled at The University of Bergen). This is what he had to say about it!
From July to December 2018 I conducted research in Dr. Ali Ellebedy’s lab at Washington University in St. Louis and in Professor Florian Krammer’s lab at Icahn School of Medicine at Mount Sinai in New York. As a medical research student at University of Bergen, my project aims at better understanding the antibody response to influenza. The purpose of this research visit was to address fundamental questions about the immune response to influenza by generating monoclonal antibodies from human B-cells.
Although influenza is a harmless disease for most people, it accounts for around 300 000 to 600 000 deaths every year. A major goal in the field of influenza is to develop an efficient prophylactic vaccine that provides long-lasting protection against a broad range of influenza viruses. The current seasonal influenza vaccines do not have these traits. My research project in USA involved generating monoclonal antibodies against neuraminidase (NA), which is a protein located on the surface of the influenza virus. We found that the antibodies targeting NA could bind to a broad range of influenza viruses, and were able to protect mice from lethal influenza infection. Our findings will bring valuable insight into the NA-specific antibody response to influenza. We plan to publish our results in a high-ranking international journal, and hope that it will contribute to generate better vaccination strategies for influenza in the future.
What I bring back to Norway is an increased knowledge of immunology and influenza, and a broader view of research in general. I have learned many new laboratory techniques and experiments, which we plan to establish here at the Influenza Centre, University of Bergen. The research visit has strengthened the collaboration with the research groups in USA, and I have made lifelong friends. To be given the opportunity to learn from world leading influenza researchers has been an invaluable experience for me as a young scientist. I will always remember my six months in USA – not because of the country itself, or because it is the longest I’ve ever been away from home, or even because it was the most hardworking months of my life, but because of the inspiring people I worked with.
I am very thankful for the IBA travel grant, which made this research visit possible.