Meet the Trainer – Katharina Danielski

Meet Katharina Danielski, Field Application Scientist at 10x Genomics, who is an organiser and trainer at the EMBL Course: Immune Profiling of Single Cells (10 – 13 February 2020).

 

 

 

What is the greatest benefit of the course for the scientific community?

It provides researchers with an overview of what is currently possible when studying the immune system at the single-cell level. There are so many new technologies and methods available these days that scientists are overwhelmed with keeping track of everything new. The 10x Genomics Single-Cell Immune Profiling solution allows you to study a broad range of aspects all derived from the same single cell: sequence information of paired full-length T cell or B cell receptor transcripts; gene expression profile; cell surface protein markers; antigen specificity. Linking all these pieces of information back to the same cell is opening a lot of new ways to study the adaptive immune response that were just not possible before.

Are the methods used in this course unusual or new?

The ability to study single cells to the extent as it is currently possible with various assays on the market is still very recent. We are only beginning to scratch the surface of the biological information that will be uncovered in the coming years thanks to the methods discussed in this course, among others.

In comparison to other training environments, what do you enjoy most about teaching at EMBL?

I enjoy teaching at EMBL because of the high level of organisation that the EMBL team displays. The EMBL Heidelberg Campus is also a particularly beautiful location situated on top of a hill surrounded by forests. But most importantly: the food in the canteen is legen- wait for it -dary.

What is your number one tip related to the course?

Don’t be shy. The trainers are more than happy to answer your questions and discuss your projects and  experiments…but skip breakfast so you can fill up on lunch at the EMBL Canteen. You will thank me later.

What, in your opinion, is the most crucial scientific discovery of the past 100 years?

I don’t think any single discovery on its own could be labeled as “the most crucial”. Science in the past 100 years has made so many giant leaps for mankind.

Where is science heading in your opinion?

Studying gene expression of (single) cells spatially resolved within their morphological context of an intact tissue section.

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Meet the Trainer – Dr. Anders Ståhlberg

Meet Dr. Anders Ståhlberg, Associate Professor at the University of Gothenburg and  Sahlgrenska University Hospital in Sweden, and organiser of the EMBO Practical Course: Single-Cell Omics (12 – 18 May 2019) and EMBL Course: “Liquid Biopsies” (23 – 28 September 2019).

Anders’ research focuses on basic tumour biology and cancer diagnostics.

What is the greatest benefit of the Liquid Biopsies course for the scientific community?

Liquid biopsy analysis is an emerging tool in biological/medical research as well as in clinical diagnostics. However, most analyses require ultrasensitive methods. In this course we cover both theoretical aspects and practical consideration that need to be addressed to utilise the potential of liquid biopsy analysis, and use both state-of-art techniques and novel approaches.

What could the techniques in this course be used for in the bigger picture?

The applied techniques include ultrasensitive analysis of DNA, proteins and single-cells. These techniques can be applied to a wide range of applications in any type of liquid biopsy. In addition, these techniques can be used on any type of challenging sample types. Application areas include cancer, immunology, prenatal testing, forensics, evolution studies, drug screening, pathogen detection and beyond.

In comparison to other training environments, what do you enjoy most about teaching at EMBL?

The superb facilities, including everything from course arrangement to the research lab. However, the best part of EMBL courses is the dynamic interactions between teachers, tutors, staff and all students. It is a perfect environment to network and discuss science.

What is the strangest or funniest thing that has ever happened in a course?

The course dinners are very enjoyable and may end in unexpected but fun ways.

What challenges is your research field facing?

Translating basic research into clinical use.

Where is science heading in your opinion?

The amount of generated data will increase dramatically with all available high-throughput methods. One major challenge is to translate this data into useful information.

What was your first ever job?

I got my first job when I was 15 years old in basic industry, making valves.

If you weren’t a scientist, what would you be?

A teacher or farmer.

What is the greatest risk you’ve ever taken?

In science, saying no to academically rewarding positions and instead following my research interest with an unsure future.

What is your favourite book?

I cannot resist a good fantasy book.

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Meet the Trainer – Estefanía Lozano-Andrés

Meet Estefanía Lozano-Andrés, a Marie Sklodowska-Curie PhD Candidate at the University of Utrecht in the Netherlands. We first met Estefanía in 2016 when she was a participant at the EMBL Course “Extracellular Vesicles: from Biology to Biomedical Applications” and she is back as a trainer at this year’s course.

What is your research focus, and what challenges is the field facing?

My main research interest is the study of Extracellular Vesicles (EVs), which are nano-sized membrane-enclosed particles released by cells. EVs contain selected proteins, lipids and nucleic acids that reflect the status and origin of cells, making them very attractive for biomarker profiling. However, their small size hampers robust detection of single EVs, so more sensitive technology needs to be developed to truly exploit the potential of EVs. Particularly, I am interested in the use of flow cytometry to analyse EVs in a high-throughput and multiparametric manner, but there are quite some challenges to overcome like the optimisation of EV-labelling strategies, the development of reference materials and the standardisation of measurements.

You attended the EMBL Course on Extracellular Vesicles 3 years ago and now you are one of the trainers in this year’s course. How has the course influenced your career?

The course had a great impact on my scientific career. When I was selected to attend the course, I was at an early stage of my PhD and it helped me to develop as a scientist and to have a more critical eye. Thanks to the course I met many leading researchers in the field and it’s probably one of the reasons why I am currently a Marie Skłodowska-Curie Early Stage Researcher within the TRAIN-EV Consortium, which brings together leading European scientists working on EVs (grant agreement No 722148). I was thrilled to know that this year I could attend the course as a trainer to help all the participants during the practical sessions and to shed some light on the use of flow cytometry for EV analysis.

What is your number one tip for people looking for scientific training?

Don’t be afraid to engage with people, it can really help you to find out about great training opportunities that could further improve your career. And always try to make the most out of any given moment.

If you weren’t a scientist, what would you be?

A multifaceted artist, I love creating things. Painting, writing and photography make me very happy. Fun fact: when I was a child I wanted to be a professional gift wrapper.

If you were a superhero what power would you have?

Teleportation, I would really enjoy to travel across space (and time).

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BioMalPar’s most loyal friends

Meet Prof. Peter Preiser and Dr. Stefan Rahlfs, two of BioMalPar’s most loyal participants, who have not missed a conference since 2009 and 2010 respectively. They recount their experience from previous events of the series and share with us their expectations of the upcoming conference.

How has the conference developed over the years in your opinion and what makes you come back every year?

PP: The BioMalPar conference is unique in that it is one if not the only annual conference that focuses on the molecular and cellular aspects of the malaria parasite. It therefore has always represented an ideal meeting to catch up with the latest developments in the field. Due to its focus on giving PhD students a chance to present their work the meeting always had a “new” feel to it which I particularly appreciated.

SR: The conference has always drawn participants from all over the world, and presented interesting talks by both experienced and young researchers. However, getting to the conference venue used to be much more difficult and the early events took place in office rooms and a tent (it was pretty hot in there!). But things have changed significantly since then. Now there is a new parking garage, a new conference centre, which I like very much – light, modern, scientific.  The best part is the “helix” where you have to find your way walking on a base pair bridge .

PP: Clearly the conference has changed over time – this was partly due to the end of the EU funded BioMalPar programme and therefore the discontinuation of the PhD programme, but still it retained its focus on giving young researchers an opportunity to present their work. Today the meeting is a nice balance between young and more established researchers, which means there are the hot-off-the-press type presentations representing the work of a single researcher along with the more comprehensive research achieved through a multi-team effort.

SR: The quality of the talks remains impressive with a good mixture of topics. There is always a keynote lecture followed by short talks. Workshops and flash talks are now included and I have learned a lot about different people especially the ones receiving the Lifetime achievement award.

PP: The establishment of the Lifetime achievement award was something that I felt was particularly important as it provided many of the young researchers attending the meeting a perspective of the immense contributions the previous, slightly older generation had made to the field.

What’s the best memory you have of a BioMalPar conference?

PP: For me it has always been the relaxed attitude of the meeting and the opportunity to discuss science over a beer at the posters or outside (weather permitting) on a mild spring evening. Many fantastic ideas were generated through these discussions.

SR: The things that always stay in my mind are the fantastic venue, attractive program, nice age-mixture of people and the friendly atmosphere. I always go home with respect for others’ work but also with new ideas for my own research. At one of the BMP conferences I personally met Prof. Hagai Ginsburgh, and once he combined his stay in Germany with a trip to our Giessen-University for some days. This was very impressive and constructive at the same time.

In your opinion, what challenges is malaria research facing and how does coming to BioMalPar address these problems?

PP: I think the effort to control and eliminate malaria has made significant progress and we are now getting to a critical phase in the global effort. It is now important to ensure that efforts to control the disease are not slackened and that funders continue to support this important health initiative. From a research perspective we still have key challenges in terms of drug resistance and the lack of an efficient vaccine, not to mention the issue of P. vivax. It is particularly in these areas where BioMalPar can stimulate the right discussions and interactions that will eventually lead to significant benefits in controlling the disease.

SR: It is still a disease occurring in poor countries and resistance is always a problem. Although bed nets help a lot and a vaccine is available (which is not very effective, but the best mankind has been able to provide so far), research must go on. And in rural areas infrastructure for distribution of newly developed drugs or vaccines needs to be installed. For research there is a gap between industry (monetary research) and universities (basic research), which is due to their different settings.

Looking at the programme of this year’s conference, what do you think will be the highlight and what would you like to see in the next edition in 2020?

PP: This is hard to say as based on the titles there appear to be many new and exciting topics on the programme. I am quite intrigued about the work going on with the mosquito vector and possible ways a better understanding in this area may provide us with better tools for intervention. I am also excited about the use of stem cells to study malaria parasites, as this technology would significantly help me to address some of the questions I am interested in.

I think one of the key things that I would like to see develop more in the future is a better link between the basic research presented at the BioMalPar conference and how this could be utilised in a more clinically relevant context. For example, how does our understanding of malaria immunology help in developing a better vaccine or how do we use the vast amounts of genomic data more effectively for the discovery of new drugs, new vaccine targets or even better diagnostic markers. Some of this is already happening but a lot more can be done.

Prof. Preiser, you will present a short talk titled “Comparative mapping of Plasmodium proteomes provides new insights into erythrocyte remodelling”.  What can participants expect to learn from your talk?

I have always wondered about how the malaria parasites changes its host cell. In particular, I was intrigued about the apparent differences that different malaria parasite species have developed in modifying the same type of host cell. However, most of our knowledge on this is based on the study of a single parasite species P. falciparum. My lab has therefore tried to develop new approaches to study the differences the different plasmodium species have developed by using human, simian and rodent malaria parasite species and identify all the different proteins that the parasite exports into the host cell. This approach has given us some very surprising results that I will talk about during the meeting.

Dr. Rahlfs, you will present a poster titled “Glucose 6-phosphate dehydrogenase 6-phosphogluconolactonase: characterization of the Plasmodium vivax enzyme and inhibitor studies”.  Can you give us a short preview of your poster?

As a member of the “Becker-lab” in Giessen we are focusing on redox metabolism as drug target and on redox regulations in general and under stress. A number of gene knockouts of our group but also others mostly do not have big impact (due to redundancy), but the importance of the Glucose 6-phosphate dehydrogenase 6-phosphogluconolactonase (GluPho) in P. falciparum has been demonstrated by a lethal phenotype. Now we would like to expand this knowledge also on P. vivax. We cloned P. vivax glucose 6-phosphate dehydrogenase (PvG6PD), the C-terminal and NADPH-producing part of PvGluPho, recombinantly produced it in Escherichia coli, purified and characterised the enzyme. IC50 values of several compounds were determined on P. vivax G6PD, inhibitors that had been previously characterised on PfGluPho.

 

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Meet the Trainer – Andrew Filby

Meet Dr. Andrew Filby, Director of the Flow Cytometry Core Facility at Newcastle University, which supports cutting-edge research through the provision of a comprehensive cytomics resource to both internal and external research groups, operating at the forefront of cytometric applications and method-focused research. Andrew Filby is one of the organisers of the EMBO Practical Course: The Fundamentals of High-End Cell Sorting (11 – 15 November 2019).

What is the greatest benefit of the course for the scientific community?

The ability to physically separate (sort) cells of a particular type or subtype is fundamental in so many biological questions. Teaching and empowering researchers how to do this well is very important.

What could the techniques in this course be used for in the bigger picture?

Cell sorting can be used for so many different reasons, ranging from basic discovery research right through to clinical trials and cell therapies.

Are the methods used in this course unusual or new?

Cell sorting has been around since the 1960s and the principles remain quite stable. However, in this course we teach students the practical as well as the theoretical aspects. The course is run by experts in the field and in a “real world” environment where attendees will be trained in two functioning flow cytometry/cell sorting core facilities.

In comparison to other training environments, what do you enjoy most about teaching at EMBL?

Everything about EMBL is set up for delivering excellent training in biological sciences and in particular the practical, hands-on elements. The training labs are amazing spaces and looked after very well. The canteen is also a highlight!

What is your number one tip related to the course?

Roll your sleeves up and get involved. Ask questions and interact with your trainers as much as possible.

What is your research focus, in 15 words or less?

I want to measure everything about every cell in the body!

What challenges is your research field facing?

The data we generate now is very complex. We have thousands of measurements on millions of cells, sometimes with image and spatial information too. The informatics skills and solutions needed can be immense.

What, in your opinion, is the most crucial scientific discovery of the past 100 years?

The invention of the cell sorter!

If you were a superhero what power would you have?

I would like to shrink myself so that I could travel around the human body and see the cells and processes for myself.

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