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).
Balancing work with family life can be difficult, and often the opportunities for parents to advance their careers are limited as a result. EMBL and EMBO are both working to make attending scientific events easier, with EMBL providing onsite childcare at their conferences and symposia in EMBL Heidelberg, and EMBO offering childcare grants to cover the costs of having a child looked after while one or both parents attend an EMBO funded course or conference.
To avoid any confusion between the two options, here is an overview of what you might be eligible for to help you get the most out of your career and your family.
At a glance
EMBL onsite childcare
EMBO childcare grant
EMBL Conferences, EMBO Workshops or EMBO| EMBL Symposia taking place at the EMBL Advanced Training Centre Heidelberg, Germany.
EMBO Courses, Workshops or EMBO| EMBL Symposia. The EMBL Course and Conference Office deals only with those events taking place at the EMBL Advanced Training Centre Heidelberg, Germany. Grants for other EMBO events should be applied for directly to the individual event organisers.
Who and where?
Children are looked after on campus by our highly qualified kindergarten teachers in the EMBL Kinderhaus, Heidelberg, Germany.
Childcare grants are available to offset child care costs incurred by participants or speakers of EMBO events. Eligible costs include fees for a baby-sitter or child-care facility, travel costs for a care giver, or travel costs for bringing the child to the city/town where the meeting is being held, etc.
The two main languages of the teachers are German and English.
8:30am – 5:50pm for the duration of the conference
Grant applicable for costs incurred in relation to child care costs during the meeting.
A subsidised fee of €100 per child is payable by the conference participant
A total of €1000 is available per meeting, with a general cap of €500 per person. This can be allocated based on need at the discretion of the organisers.
All necessary equipment such as meals, beds, toys and diapers are provided.
Eligible costs include fees for a baby-sitter or child-care facility, travel costs for a care giver, or travel costs for bringing the child to the city/town where the meeting is being held, etc.
Who is eligible?
One or both parents must be registered participants, organisers or speakers at the corresponding conference. The child must be between 3 months and 3 years of age.
Childcare grants are available to anyone attending the event (speakers, organisers, trainers, participants etc.)
How to apply
Registration for childcare must be made online 6 weeks before the start of the event by using the “register for childcare link” on the individual conference website.
Applicants must indicate during the abstract or motivation letter submission process how much funding they would like to apply for, and what it will be used for. They should also indicate at what stage of their career they are.
As childcare spaces are limited, registration will be on a first-come first-served basis. Your place can only be confirmed after payment of the registration fee. The selection is handled by the EMBL Course and Conference Office.
The amount of money awarded for the childcare grant is dependent upon the number of applicants per event. The selection is handled by the organisers of the respective meetings.
email@example.com or Tel.: +49 (0)6221 387 8797.
Please contact the organisers of the individual event for more information.
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.
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.
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.
10 years after it all started, VIZBI came back to its original stomping grounds, the ATC at EMBL in Heidelberg. As its name suggests, VIZBI “Visualizing Biological Data” is a blend of several worlds. Of biology, with its long history in visualizations that goes back to Ancient Greek text books, and of art and scientific illustration.
VIZBI is also inseparable from computer science and its tools to transform big data into human readable entities. And finally, VIZBI incorporates concepts of design and visual perception to make visualizations engaging and enlightening.
Highlighting spectacular biological images
At VIZBI 2010, microscopic images were omnipresent. Back then, I was embarking on my postdoc project, a large-scale microscopy screen of RNAs in cells. My memories tell me that this was the main focus of the conference. Indeed, a quick check of the 2010 program confirms that almost the entire community of light sheet microscopy and image processing were in attendance at the first ever event.
VIZBI 2019 continued to highlight spectacular biological images. A phenomenal augmented reality installation showed them in 3D, EM-tomography simulations by Peijun Zhang animated the 64-million atoms assembling into HIV particles, and Lucy Collinson shared the high numbers of high-resolution EM data collected at the Francis Crick Institute. This large amount of data is annotated with the help of amateurs, for example in their citizen science project at the Zooniverse “Etch a cell”.
Colourful confocal images or images of tissues also provided the inspiration to many works of illustrators on display that combined science and art, for example the double win of best poster and best art to a depiction of tubulin in a mitotic spindle by Beata Mierzwa @beatascienceart, a hugely talented artist and scientist (who also sells cool cytoskeleton-printed leggings and mini-brain organoid dresses).
At VIZBI 2019, visualizations of data – as opposed to images – gained a much more prominent spot. All keynote speakers were from the technology side. Hadley Wickham presented the history of ggplot2. Ggplot2 (and yes, there once was a ggplot1!) is the R universe for visualizing pretty much everything that comes in numbers and is now merged into the tidyverse. Being a visualization talk, all slides were themselves beautiful, I love the tidyverse playfully represented as stars of our universe! The second keynote was by Janet Iwasa who presented her animation work that heavily relies on 3D and computer graphics software used for animation films. Instead of earning her money in the film industry, she decided to put it to good use for biology. Janet first used her skills in her PhD project to visualize motor proteins “walking” along the cytoskeleton, and these days produces Oscar®-worthy movies showing biology, such as the origin of life or the life cycle of HIV. And everyone take note: all her films start as a storyboard on paper, which is what I teach as good practice for all visualization designs.
Making the invisible visible
The third keynote was by Moritz Stefaner, a data designer who is enticed by biological data but appalled by the time-scales in biological projects (too long!). Luckily, he hasn’t given up on us just yet, and keeps producing phenomenal visualizations. For example, showing absence and loss is notoriously hard, but Moritz found a beautiful way to make the invisible visible in his designs for “Where the wild bees are” with Ferris Jabr for Scientific American.
Moritz left us hungry for more when also showing his data-cuisine project, that visualizes data about food and turns food into data: the number of berries picked in Finland become a layered dessert, and common causes of death are encoded as praline fillings – you never know which one you’ll get! (Luckily this was with Belgium pralines, so all deaths are sweet.)
Visualizations of data were in the spotlight of many other projects too. This is of course owed to the many possibilities of large-scale methods that swamped biology with data in recent years: RNAseq, inexpensive genome sequencing, mass-spec at fantastic scales, robotics driven biochemistry and medicine, image processing that turns images into insights by quantifying signals and so on. RNA sequencing, for example, fuelled Susan Clark’s project tracing methylations in cancer, Phillippe Collas’ ambitious endeavour to understand 3D genome architecture, and is empowered by Charlotte Soneson’s “iSEE” software to interactively analyse data from high throughput experiments and the project of Kirsten Bos tracing human pathogens back thousands of years by sequencing tiny dental samples. And of course, of the biggest data projects in biology is the ENSEMBL genome browser, which was officially released as pre-alpha version VIZBI (check it out: 2020.ensembl.org), the very approachable Andy Yates and his team are looking for feedback!
Visualizations of high-dimensional datasets are not without problems. The technical challenges were addressed by David Sehnal who showed computational infrastructure to visualize protein structures (MolStar). The mathematical problems of dimensionality reductions were a topic of Wolfgang Huber’s talk, and a tool to visualize, and thereby find(!), batch effects, “proBatch”, was presented in the flash talk by Jelena Čuklina (they welcome beta-testing by users!). Teaching science visualizations, I often see a great need to discuss ethical and practical aspects. Critically assessing limitations and challenges of scientific visualizations might be a topic to be expanded in future, when VIZBI enters its second decade. This should be coupled with visual perception research, after all, we are no longer limited by computational power, but rather by what our eyes and brains can comprehend (see Miller 1956).
Speaking of flash talks: the conference organisers did such a great job in highlighting every single one (!) of the posters by one-minute talks. I tremendously enjoyed them, admittedly in part because I have a short attention span. Among the talks and art was also “Data dancing” by Alex Diaz. He showed that art and beauty can also be found in statistics and numbers blossoming like flowers across the page. On that note: see you next year in San Francisco!