BioMalPar goes virtual!

By guest EMBL Event Reporter Thomas Locke, founder of https://www.fightmalaria.co.uk/

Despite the coronavirus pandemic, EMBL’s BioMalPar conference could still take place online. Nearly 400 participants from around the world attended the virtual meeting to share the latest research into Plasmodium, the malaria-causing parasite.

From onsite to digital

There were both benefits and drawbacks to hosting the conference online. On the plus side, the conference’s barrier to entry was significantly reduced, allowing for a higher-than-usual number of participants to attend, from all over the world and at different stages of career. There was more interaction between speakers and the audience and those who would not normally feel comfortable asking a question in a conference hall could do so more comfortably online. The conference was slightly shorter than usual – just two half days – so there were fewer talks overall and no possibility for workshops; however ‘special interest’ lectures were held instead. Poster sessions could still take place with posters remaining online after the session for more leisurely viewing. On a more specific note, Dr Julian Rayner, a member of the BioMalPar Emeritus Steering Committee, remarked that he missed the asparagus stalls in the streets of Heidelberg, where the conference normally takes place. Asparagus or not, it’s remarkable that, in the face of real challenge and uncertainty, the EMBL BioMalPar conference could still take place, now sixteen years in the running.

BioMalPar virtual conference participation in the comfort of your own home! PHOTO: Thomas Locke

Day 1

The conference began with opening remarks from co-chairs Alfred Cortes of ISGlobal in Spain, Silvia Portugal of the Medical University Heidelberg in Germany and Sam Wassmer of the London School of Hygiene and Tropical Medicine in the UK. They emphasised the novelty of the online conference and outlined some ground rules.

Emerging Challenges and New Tools

The first session of the day was on ‘emerging challenges and new tools’ and was chaired by Andy Waters.

Laurent Dembele of the University of Bamako, Ghana, spoke on the subject of artemisinin resistance. Mutations to a protein called Kelch13 prevent the antimalarial from working, allowing the parasite to become dormant in the blood and to ‘reactivate’ when the drug is no longer in the system. Dembele evaluated two antimalarial drugs (KDU691 and GNF179) in vitro which target P14K, a protein that mediates the aforementioned dormancy. He concluded that KDU691 can selectively kill the dormant Plasmodium rings after treatment with artemisinin, but that GNF179 can kill both dormant and non-dormant rings and was active at multiple stages of the malaria parasite life cycle. A combination of artemisinin and GNF179 could mitigate the risk of artemisinin resistance, it was suggested. This has direct applications to SE Asia, where artemisinin resistance is particularly prevalent.

Simone Reber of the Humboldt University of Berlin spoke about her research into Plasmodium tubulin, a potential target for drug development. Tubulin is a ubiquitous protein that controls cell proliferation and so has direct applications to the treatment of malaria, a disease that depends upon cell replication. Simone characterised tubulin in the malaria parasite and considered drugs that could inhibit it and compared Plasmodium tubulin to a similar shaped human tubulin. A concentration of 2.5 micromoles of inhibitor could kill the Plasmodium tubulin but not the human tubulin, for which 20 micromoles were needed. Tubulin is a promising target for malaria treatment but research into it is limited by the protein’s small size. For 150 micrograms of tubulin – in itself, a rather small sample – 5 litres of blood is needed.

Regina Rabinovich of ISGlobal gave her special interest lecture on COVID-19 and its impact on ‘research and beyond’. She took a step back from the specific biology of malaria to consider global public health in general; ‘from the mitotic spindle to global malaria strategy’, as she called it. She offered a concise history of malaria eradication and addressed recent developments in strategy: a shift away from blanket solutions to region-specific programmes. She also shared the broad public health lessons that we can learn from COVID-19, with particular emphasis on accelerating R&D efforts and cultivating a sense of urgency. She concluded with remarks on the potential impact of the coronavirus in Africa both socially and epidemiologically, with reference to data modelling from the WHO and Imperial College London.

Parasite Biology

Alfred Cortes introduced the second session on ‘parasite biology’.

First to speak was Manoj Duraisingh of the Harvard TH Chan School of Public Health. He spoke on how the P. falciparum egresses from red blood cells. He detailed that the PfPP1 protein is essential for such egress and that it coordinates multiple signals early in egress. He also outlined the role for Hect E3 ligase in egrees and that PfPP1 regulated cGMP levels through PLT-GCalpha.

Mathieu Brochet of the University of Geneva spoke on his work into the Plasmodium protein, PKG. This protein was previously known to control calcium signals called Ca2+ which, in turn, are critical for Plasmodium life cycle stages in the human and mosquito, namely erythrocytic egress and gametocyte development. How PKG influenced these Ca2+  signals was previously unknown, however, so his research sought to identify a partner protein. He identified ICM1 as this partner protein, finding that when ICM1 was distributed, so was egress, invasion and Ca2+ mobilisation.

Franck Dumetz of the University of Cambridge spoke about his investigations into the presence of ‘G4’ proteins in the P. falciparum genome and whether they play a role in post-transcriptional regulation. He first identified 681 ‘rG4s’ in the transcriptome and used both in vitro and in vivo approaches to find that rG4s can have a regressive impact on translation when they appear on the transcribed strand of a gene. He continued to suggest that there may be novel RNA-binding proteins in Plasmodium that are involved in regulating rG4 motifs.

Venessa Zuzarte-Luis shared her research into why Plasmodium replication in the liver of mammals is particularly high, producing tens of thousands of parasites, compared to replication in reptile and avian species, which only produce dozens of parasites. Vanessa states that this disparity is caused by the parasite’s utilisation of liver-specific methionine adenosyltransferase enzyme (MAT1), and the capacity of that enzyme to generate unlimited amounts of S-adenosylmethionine (SAM). SAM is capable of reverting the impairment of infection, suggesting that the parasites use this abundant resource.

“Omics” Approaches and Evolution

After a poster session on Slack, Julian Rayner began the third session on “omics” approaches and evolution.

Franziska Hentzschel of the University of Glasgow presented her research into the parasite-host interplay in vivo at the single-cell level. She used flow cytometry and single-cell RNAseq to characterise parasite and host cells in circulating blood, bone marrow and the spleen of P. berghei-infected mice. She found that the spleen was preferred as the extravascular site for Plasmodium reservoirs, with the earliest ring stages enriched in putative reticulocytes found there.

Lianne Lansink of the Queensland University of Technology and the University of Melbourne detailed her research into how the malaria parasite adapts in the human host to changes in the environment. She created an environment of lipopolysaccharide, a condition which causes low blood pressure. She reported that this impaired the maturation of the parasites in vivo. The condition also affected parasitic gene expression; ribosome genes were down-regulated and other genes were perturbed in single parasites in a life-stage dependent manner.

Day 2

Epidemiology and Surveillance

The second day of the BioMalPar conference began with a virtual pub quiz. Sam Wassmer then introduced the fourth virtual session of the event: ‘epidemiology and surveillance’.

Chris Drakeley of the London School of Hygiene and Tropical Medicine gave a talk on the use of serology in understanding malaria transmission dynamics. He outlined several use cases of serology in malaria-endemic regions and emphasised the advancements in serological technologies; multiplex bead assays and protein/peptide microarrays allow for the assessment of proteome-wide immune responses which allows for greater granularity of analysis, looking at specific antigens or antigen combinations that cause specific immune responses.

Mario Recker of the University of Exeter spoke about understanding individual-level variations in malaria susceptibility and acquisition of clinical protection. His study sought to identify robust inferences of individual-level protection or susceptibility to malaria by analysing a longitudinal systems-immunological cohort study of Junju, a region of Kenya. He found that one of the most important risk factors to malaria is the number of previously experienced episodes which correlates positively with probability and number of clinical episodes during the upcoming transmission season. He also found that birth year can also have a significant and lasting impact on a child’s susceptibility to clinical malaria, due to the child’s exposure to Plasmodium early on in life.

Manuela Carrasquilla spoke about her research into genome sequencing in Colombia to determine the history of P. falciparum. She analysed 151 clinical samples of the parasite collected in a regional hotspot during a 2016 outbreak linked to mining activities. She determined that the Colombian P. falciparum populations show high levels of genetic structuring and confirmed the presence of five major parasite lineages overlapping in time and space which have been shown to have important functional variation, including drug-resistance genes. Then, combining epidemiological data over a two-year period, she found that almost a third of infections show evidence of shared recent common ancestry, suggesting that increasing mining activities created an opportunity for polyclonal infections and outcrossing.

Simon Kigozi of the London School of Hygiene and Tropical Medicines presented the results of his analysis of outpatient surveillance data from four health facilities in Uganda. The malaria burden had shifted from younger to older individuals as a result of malaria control methods including long-lasting insecticidal nets (LLINs) and indoor residual spraying of insecticide (IRS).

Pathogenesis and Immunology

Sam Wassmer began the fifth virtual session of the conference on ‘pathogenesis & immunology’. 

Brittany Riggle of the NIH was first to speak on the subject of pathogenesis and her work into CD8+ T cells as a potential avenue for treating cerebral malaria. Using multiplex immunohistochemistry in post-mortem brain samples from children with or without cerebral malaria and with HIV. Diagnosis of cerebral malaria increased the number of CD3+CD8+ T cells engaging the cerebrovasculature. HIV co-infection further increased this engagement. Riggle suggests that CD3+CD8+ T cells could be a promising target for adjunctive therapy for cerebral malaria.

Hannah Fleckenstein of Heidelberg University Hospital spoke about her research into how P. falciparum malaria parasites persist at low parasitemia for months in the human host in the absence of the Anopheles mosquito vector, a poorly understood phenomenon. In the dry season in Mali, the parasites spent longer in circulation before adhering to the endothelium. This adhesion is mediated by knob-like structures on the surface of infected red blood cells which allows for the avoidance of splenic clearance. She found that, in dry season parasites, decreased adhesion resulted in higher levels of splenic clearance which was sufficient to maintain low parasitemia.

Speaking on the subject of monoclonal antibodies, Lawrence Wang of the NIH presented his findings into a sporozoite-neutralising monoclonal antibody called L9. The mAb could immobilise sporozoites in the skin and the liver and cause a phenomenon called ‘dotty death’.  When asked why monoclonal antibodies would be preferred over mass-market drugs, which are cheaper and less laborious to produce, Lawrence responded by saying that some mAbs can offer potentially life-long protection and are a halfway house between a drug and a vaccine.

Emilie Pollenus of KU Leuven spoke about the role of CCR2 in the resolution of MA-ARDS (malaria-associated acute respiratory distress syndrome). This condition is one of the health complications that malaria can cause, contributing to its 400,000 annual death toll. Those with the condition who do not have access to mechanical ventilation have an 80% risk of death, while those with it have a 10-40% risk. Pollenus found that the number of CCR2 monocytes increased during resolution after treatment with antimalarial medicine. In mice where the CCR2 protein was silenced – known as CCR2 KO (knock out) mice – there was a reduction in the number of inflammatory monocytes in the lungs and the spleen, however, this did not affect the resolution of the alveolar edema. Eosinophils – a type of white blood cell – completely disappeared from the lungs upon infection and reappeared with resolution but not in CCR2 KO mice.

Carola Schaefer of the Seattle Children’s Research Institute spoke about creating a laboratory model for P. vivax infection to test interventions against the disease. Using the P.vivax liver humanised mouse model, with the addition of human reticulocytes, parasites were able to invade and replicate Schaefer could also observe gametocytes that were transmitted to mosquitoes in preliminary experiments.. She then tested the in vivo model with P. vivax Duffy Binding Protein (PvDBP) antibodies, an antibody that could potentially inhibit parasite invasion of red blood cells. 95% protection was observed, providing evidence that PvDBP is a promising target for future therapies.

Transmission Biology

Silvia Portugal opened the final virtual session of the conference on transmission biology.

Dennis Klug of Inserm in France presented his research into the function of the protein TEP12 in antiparasitic immunity in Anopheles mosquitoes. When the protein was silenced, there was an increased parasitic load in P. berghei infections in An. gambiae and An. stephensi mosquitoes. However, there was a lower parasitic load with P. falciparum infection, suggesting an unknown adaptation of this parasite species.

Aurelia Balestra of the University of Geneva discussed her identification of CDK-related kinase 5 (CRK5) as a critical regulator of atypical mitosis in the gametogony[KC1]  which is required for mosquito transmission. This kinase interacts with a single Plasmodium-specific cyclin (SOC2), suggesting this cyclin/CDK pair controls DNA replication and M-phase progression.

Ines Bento of the University of Texas Southwestern Medical Centre presented her findings into mosquito-human sporozoite transmission. She found that sporozoites in the salivary glands of the mosquito are in synchrony with the vector’s behaviour, leading to lower parasitic load in the day compared to the night, when the mosquito is more prone to bite.

Bento’s talk concluded the session and was the last talk of the conference. Andy Waters then gave a memorial presentation on Shahid Khan, a malariologist who passed away in late 2019. He began his career with a degree in Parasitology from the University of Glasgow and then worked as a technician at the University of Oxford. He completed a PhD at Cambridge and a Postdoc at NIMR in London. Tributes were made to Shahid by his colleagues; he was described as the ‘sunshine’ of the laboratory and recently wrote a children’s bedtime story entitled ‘There’s a mosquito in my room’, which is available to download here.

The conference was formally closed with remarks from Andy Waters and Julian Rayner. They called the virtual meeting a successful and ‘wonderful experiment’.

About the author

I’m Thomas Locke, the Editor of Fight Malaria, a website that aims to distil the science of malaria and make it more accessible to the public. Every week, we summarise some of the malaria research highlights in a sixty-second podcast called ‘Malaria Minute’ and also interview various stakeholders in the fight against malaria. You can learn more about the initiative here. I was fortunate to work as an ‘Event Reporter’ for this year’s BioMalPar and offer a summary below. I’d like to offer thanks to EMBL for covering the cost of my ticket.

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Generating meaningful images – a report from Seeing is Believing 2019

By event reporters Liz Haynes @actin_crazy and Stephan Daetwyler @Daetwyler_St

Seeing is Believing event reporters Liz Haynes & Stephan Daetwyler, PHOTO: Liz Haynes/Stephan Daetwyler

The field of biology owes some of its most compelling discoveries to careful visual observation. From Van Leeuwenhoek’s use of new microscopes to describe microscopic “animalcules” in the late 1600s, to Ramon y Cajal’s pioneering 19th century work illustrating beautiful and complex neuronal architecture. Images inspire us, help us generate new hypotheses, and shed light into the tiny worlds yet unexplored. Indeed, these observations uniquely help us understand the structures and dynamics of life, something that would not be achievable with approaches like biochemistry alone.

The images are only as valuable as the amount of information that we can deduce from it.

Generating meaningful images, however, is not an easy task. There have always been limits to what we can observe, due to the properties of the sample or the techniques that we can apply to it. These are the boundaries that microscopists seek to push. A successful imaging experiment requires an amenable sample, a contrast agent to reveal the structures of interest, and a microscope that is capable of capturing an image at a relevant scale. Moreover, the images are only as valuable as the amount of information that we can deduce from it. Therefore, image storage, accessibility and analysis are crucial. Each one of these steps offers opportunities for optimisation and new technologies.

Co-organiser Jan Ellenberg opens the Seeing is Believing symposium, PHOTO: Liz Haynes & Stephan Daetwyler

The EMBO | EMBL Symposium “Seeing is Believing: Imaging the Molecular Processes of Life” (9-12 October 2019) presented us with exciting new developments in all of these fields, coupled with a drive to make new progress available as quickly as possible to the community through preprints, open-source initiatives, and resource sharing.

Advances in sample preparation

At the heart of every imaging approach is the sample. Even the best microscope is ineffective with dim or improperly prepared samples. At Seeing is Believing, we saw an emphasis on using expansion of samples to help overcome the resolution limits of microscopy and solve some traditionally difficult problems. In particular, we were impressed with expansion-based approaches to study centriole structure (Paul Guichard, Ultrastructural Expansion Microscopy) and resolve microtubules tightly packed within axons (Lukas C. Kapitein). By far, the biggest emphasis in sample improvement was on the development of new fluorescent probes and biosensors. Kai Johnsson presented design strategies for the improvement of live cell dyes, and introduced new MaP dyes that are SNAP and HALO compatible, and importantly require no wash to clear unbound probe. Periklis Pantazis presented a mechanosensor based on the Piezo1 stretch activated ion channel, allowing users to visualise mechanical stress within a live cell. Atsushi Miyawaki wowed the audience by meeting the challenge to “be better than a firefly” with a new variant of luciferase named AkaBLI, which his lab generated through targeted evolution. This improved luciferase allowed them to visualise neuronal activity within freely behaving mice and marmosets.

Advances in microscopy

New imaging methods on show at Seeing is Believing, PHOTO: EMBL Events

The features of our microscopes directly determine which questions we can address. Seeing is Believing highlighted exciting new development in building cutting-edge microscopy tools. Reto Fiolka presented a novel single-objective light-sheet microscope enabling imaging of live cells in microfluidics devices or 3D environments with 200 nm lateral resolution. Kevin Dean complemented novel light-sheet development by presenting an axially swept light-sheet microscope ideally suited for all clearing techniques that provides an unprecedented field of view enabling whole tissue imaging with sub-micron resolution. With her imaging approach, Alexandra Pacureanu surprised the audience with how X-ray holographic nano-tomography is capable of resolving the fine, dense and complex neuronal circuitry in large tissues or even organism providing a new route to understand how the nervous system processes information.

Nobel Prize winner Stefan Hell spoke on how to attain 1 nm resolution with super-resolution microscopy, PHOTO: Liz Haynes & Stephan Daetwyler

Further impressive advances were presented in fast volumetric imaging (Lars Hufnagel, light field imaging) and high-resolution imaging, e.g. MINFLUX by Stefan Hell, correlative EM imaging by Harald Hess and Lucy Collinson, GI-SIM/LLS-SIM by Dong Li, and 3D-STED deep in a tissue by Joerg Bewersdorf.

Advances in data analysis

All acquired data is meaningless if we cannot extract information from it. At Seeing is Believing, it became obvious how artificial neuronal networks have become important for image analysis. Applications range from segmentation to denoising an image (BGnet, W.E. Moerner and Noise2Void, A. Krull/Florian Jug). Particularly, the convolutional network architecture U-Net has become an important tool. To provide a user-friendly environment to apply those state-of-the art image analysis tools, Anna Kreshuk presented the iLastik platform as an easy to use tool. A new fundamental approach to handle, visualise and process the large amount of data coming from the microscopes was presented by Ivo Sbalzarini. Instead of using pixels to save an image, adaptive particles approximate the image content. Furthermore, Gaudenz Danuser gave a thought-provoking talk on how current perturbation-based approaches in cell biology can mislead us in our analysis. Danuser emphasised that the observed phenotype from a perturbation of a system (e.g. loss of a protein’s function) is not equal to the real function of the gene. For example, cutting a wire from the battery to the electronic board of radio would lead to the “phenotype” loss of sound. However, the function of the wire was simply to provide power to the radio, not to produce sound! As a better perturbation-free alternative, Danuser introduced a concept used in econometrics known as Granger causality.

Advances in biology

All of these new developments culminated in impressive new insights into biological processes. There were many talks on mitochondria and endoplasmic reticulum dynamics revealed by novel live-cell super-resolution techniques. Suliana Manley gave one of the most intriguing of those talks, on modes of asymmetric and symmetric mitochondrial division.

Co-organiser Jennifer Lippincott-Schwartz presents how RNA moves around the cell and is translated at different locations, PHOTO: Liz Haynes & Stephan Daetwyler

Jennifer Lippincott-Schwartz also gave a stunning presentation on how RNA granules can hitch a ride through an ANXA-11 mediated connection to lysosomes, and how ALS associated mutations in ANXA-11 break this connection. Furthermore, an intriguing new mRNA reading frame sensor (Moon and Sun tags) was presented by Sanne Boersma of the Tanenbaum lab to understand stochasticity of mRNA translation.

To conclude, the field of microscopy has grown so much that some may feel we have solved all the theoretical problems, and only engineering challenges are left – hardware improvements, new materials, new engineering solutions. At the closing dinner of the conference, however, Atsushi Miyawaki from RIKEN beautifully summarised how he felt about the future of microscopy, and of Seeing is Believing. Standing in the banquet hall of the Heidelberg Castle, he told us that castles in Japan remain unfinished. This state of incompletion is not due to any fault of the architects, but a feature of beauty, as it was believed that things that were incomplete had room to grow, and that growth is valuable. No matter how high our achievements are in the field of microscopy and image analysis, there will always be unforeseen avenues of growth. Attending Seeing is Believing has hopefully prepared us to follow those avenues, and to share what we find so we may all grow together.

For a more comprehensive summary of all talks presented at Seeing is Believing, and to get links to preprints, publications, and resources, visit our blog at https://seeingbelievingweb.wordpress.com/

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Happy birthday VIZBI!

By guest blogger, Helena Jambor, PhD, TU Dresden, @helenajambor

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.

Venn diagram of VIZBI disciplines: microscopy and EM data, transcriptomics and computer science. (Note: a 5-circle Venn cannot show all possible overlaps, which is fully intended here)

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).

Data visualization

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.

Making absence visible, a project by Keynote speaker Moritz Stefaner. Photo: H.Jambor

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.)

Feedback wanted!

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!

Technical Challenges

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).

Flash talks

“Data dancing” © Alex Diaz

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!

 

P.S. Many more highlights I was unable to cover here. Check https://vizbi.org/2019/ for all posters and slides of the flash talks, check #VIZBI on twitter and my public collection of participants twitter handles (https://twitter.com/helenajambor/lists/vizbi2019).

The VIZBI organising team – James Procter, George Luca Ruse, Seán O’Donoghue, Christian Stolte, photo: H.Jambor

 

 

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Highlights from the 2019 Visualizing Biological Data (VIZBI) Workshop

Meeting report by EMBL event reporter Dagmara Kaczynska

In March I had the amazing opportunity to take part at the 10th Visualizing Biological Data (VIZBI) workshop as an EMBL event reporter. This year VIZBI lasted for 3 days and included various sessions: DNA, RNA, Proteins, Cellular Systems, Tissues & Organisms as well as Populations & Ecosystems. As it was my first VIZBI conference I had wondered how it is possible that one workshop contains such a diversity of topics. Who is the audience? Who are the speakers? Even if you missed the VIZBI workshop this year, let’s relive it together.

What is VIZBI?

To start uncovering VIZBI let’s first visit the website. It shows that VIZBI focuses mostly on how data is represented, not only what it presents. What’s more, we learn that the audience consists of a variety of crafts such as scientists, medical illustrators, graphic designers, artists and computer scientists. This multidisciplinarity is also visible in the program of the conference. Although most of the speakers are researchers, we can also expect talks from statisticians, computer scientists, animators and data visualization experts. This collaborative approach of VIZBI makes it possible to find common patterns and guidelines to make a good visualization of biological data. Most importantly, participants of the VIZBI conference believe that good visualization is the key to scientific communication.

While thinking about a visualization, think about data first

To begin with, let’s slice and dice the ‘biological data visualization’ concept by asking – what is visualization? As the first keynote speaker, Hadley Wickham, pointed out most of us has a very different perception on what it actually means.

As the workshop touched upon topics varying from DNA to ecosystems there are also many ways to visualize them. Regardless of the field of study, Hadley Wickham recommended to ‘firstly, think about the data’. The main goal is to decide on a message and a story behind the findings. After answering these fundamental questions one can start looking for the best means to visualize them.

Biological data is complex

Following his recommendation, let’s take a look at data presented during the conference. It was not surprising to learn that biological data is, quite simply, complex – regardless of whether one studies genomes, proteins or tissues. Philippe Collas discussed the complexity of a genome, composed of various elements, that forms different structures.  He made a point by saying that ‘three dimensions (3D) matters’ and an image is just a representation of a real case scenario.

Life happens in 3D so images cause danger of misinterpretation

Almost all the speakers mentioned that life happens in 3D, which causes many struggles in the visualization and interpretation of data. When Lucy Collinson introduced electron microscopy data she emphasized that 2D views (such as images) of 3D scenes (such as proteins) can be misinterpreted.

However, this problem concerns all biological fields. For example, Philippe Collas and Andy Yates discussed the complexity of a genome. Susan Clark presented how the 3D organization of epigenome is disrupted in cancer.

Moreover, Marc Baaden tackled the difficulties of recapitulating dynamics in a static image. In contrast, Loïc Royer showed 4D videos of morphogenesis and challenges with microscopes such as focus or stabilization of images as well as the importance of digital image processing.

Data and visualizations need to be cleaned and structured

In order to form the main message of a discovery, one needs to understand the complexity of data. Many speakers advised to clean and structure data as a first step of analysis. Here, Moritz Stefaner showed the image from Ursus Wehrli ‘The Art of Clean Up’ to represent the art of tidying up.

What’s more, structuring your visualization will help an audience understand the concept better. Hadley Wickham believes that orthogonal components make it easier to compare and remember (in this case using purr library in R).

Data analysis needs to be well documented (preferably in a form of code)

It is obvious that the analysis of biological data is not trivial.  What’s more, one set of data may lead to many different observations. Most of the speakers drew attention to the importance of documenting data and pipelines of analysis. Many advised to use codes. ‘A code is readable, reproducible text’ as Hadley Wickham presented. Most scientists, especially those from RNA and DNA fields such Charlotte Soneson, Irmtraud Meyer and Wolfgang Huber, shared the same opinion.

Data needs story for visualization

Now, when data is cleaned and tackled it is time to decide on the message and a story. Then, one can investigate possible ways of visualizing the findings. How can one find the best way to visualize data? Probably the most common advice was by trial and error, learning what others do, using design concepts, consulting with others. However, if you really have a clear purpose it will be much easier. Moritz Stefaner also believes that scientists have too much trust in the defaults. For example, he showed that rainbow gradient is not necessarily the best one!

Data analysis and visualization need iterations

According to Moritz Stefaner, Loïc Royer and Hadley Wickham, iterations are the key for a good data analysis and visualization. Prototyping and modifying should be a habit of all scientists. Only by iterating can we create something of great value and importance. One needs to ‘create a bunch of bad visualizations that need to be iterated as long as you find the best solution’ Hadley Wickham summarized.

Illustrations and animations capture the complexity of data

As mentioned above, the VIZBI society cares and makes an effort to prepare good visualizations. They believe that visualization is the key to every communication – illustrations and animations make a concept easier to understand. A recipient is able to grasp a research idea much faster. Janet Iwasa also showed that animation enables showing the complexity of biological data as they are in 3D. It can make a hypothesis more accurate and discoveries much clearer. She compared a model figure with a snapshot of her animation to illustrate the difference in perception.  What’s more, to make an animation one needs to fully understand a concept to illustrate it, which makes a finding more precise.

Conclusions

To conclude, although at first sight it seems that all VIZBI session are very diverse, in fact they have a lot in common. All present ways to visualize biological findings based on data. Having said that, the data and visualization techniques are very versatile, but there is a common pipeline. To make data clear to everyone the clue is to find the best way to visualize it by iterating and modifying different solutions. In order to find the best means we need to focus on a main message and story. To create a story we need to fully understand the data by cleaning, structuring and analyzing. Keeping a good documentation in the form of codes, storyboards and notes make findings transparent and reproducible to others. Communication is key in the progress of science, and scientists can improve their visualization methods and skills. VIZBI participants believe that it is worth putting in a lot of effort to make data more understandable and memorable.

Remember to have fun and use your creativity! I definitely had a lot of fun as an event reporter at the 2019 VIZBI workshop, and will incorporate all these lessons in my daily research.

If you have any questions or would like to discuss biological data visualization, please write me a message.

All the images were taken during the conference using private phone. All the images are set to presenter’s names. There are no images of slides that presenters asked not to tweet about.

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Organoids: Modelling Organ Development and Disease in 3D Culture

EMBO | EMBL Symposium – Heidelberg, 10-13 September 2018
Meeting report by Veronica Foletto

Following the huge success of the 2016 symposium ‘Organoids: Modelling Organ Development and Disease in 3D Culture’, Hans Clevers, Jürgen Knoblich, Melissa Little, and Esther Schnapp joined forces to organise a second such symposium this year. On the afternoon of 10 September, 460 scientists from all over the world gathered in the auditorium of the EMBL Advanced Training Centre (ATC) in Heidelberg.

Hans Clevers, a leading expert on organoids, welcomed everyone and led the opening session. The first keynote lecture was given by Jürgen Knoblich, who reported on progress in his lab using cerebral organoids to model the complexity of the human brain and, in particular, to study microcephaly. The subsequent talks showed how organoids derived from different tissues provide useful models for the recapitulation of certain diseases such as Helicobacter pylori infection and secretion of the VacA toxin in the stomach, as discussed by Xuebiao Yao or models of early development, with Nicolas Rivron introducing the blastoid: a type of organoid similar to an early embryo, which can be used to study developmental processes in 3D.

The second day began early with an interesting ‘Meet the Editors’ session, in which scientists had the chance to talk directly to editors working for many scientific publishers (Springer, Nature, The Company of Biologists, Wiley, Cell Press and EMBO press) and to understand their vision.

Afterwards, Meritxell Huch chaired the session ‘Stem Cells and Development’, in which scientists presented advancements in the use of cerebral (Wieland Huttner) and pancreatic (Anne Grapin-Botton) organoids for deciphering cellular mechanisms during human development, and of gastruloids for studying the patterning of the antero-posterior axis (Denis Duboule). Near the end of the session, Bon-Kyoung Koo described how to efficiently use CRISPR technology to perform genetic studies in intestinal organoids. The session ended with a series of 2-minute flash talks, after which networking and interactions were encouraged during lunch, where there was an opportunity to meet the day’s speakers.

The beautiful helices of the ATC then provided the venue for the first poster session, where around 90 presenters had the chance to discuss their research with fellow scientists, editors, and a scientific evaluating committee. It was absolutely inspiring to see how many people work on organoid research!

The afternoon session, ‘Organoids from tissue stem cells’, included talks on organoids derived from taste stem cells (Peihua Jiang), cochlear cells (Albert Edge), and intestinal cells (Hans Clevers). Madeline Lancaster explored the possibility of studying differentiated human cerebral organoids which self-assemble in the stereotypic organisation of the early human embryonic brain and have functional motor-neuronal circuits.

Among this ‘zoo of organoids’ as humorously defined by Jürgen Knoblich there was room for organoids derived from snake venom glands (Yorick Post): the organoid toolbox seems to be extendable to non-mammalian cultures as well!

On Wednesday morning, James Wells introduced the session ‘Recreating organs from pluripotent stem cells’. This addressed cell fate decisions in the developing mouse thyroid gland or lung (Sabine Costagliola), the human lung (Jason Spence and Hans-Willem Snoeck), the human salivary gland (Cecilia Rocchi), and the human forebrain (Flora Vaccarino), studied primarily through single-cell transcriptome and enhancer analyses. Finally, it was the turn of Mathew Garnett, who started by showing that the worldwide number of new cases of cancer each year is around twice the population of Switzerland.

Interested in using precision organoid models to study cancer and patients’ responses to treatment, Garnett is now contributing to the development of the Human Cancer Models Initiative. Its goal is to create a new generation of molecularly annotated cancer models, which will be widely beneficial to the scientific community.

After the second poster session, there were talks on ‘Organoids and disease modelling’, introduced by Anne Grapin-Botton. Among the topics covered were the use of 3D organoids to model liver regeneration and disease (Meritxell Huch), and to study cancers of the bladder (Michael Shen), pancreas (David Tuveson), breast (Martin Jechlinger), and colon (Henner Farin).

The day ended beautifully with the conference dinner in the EMBL canteen and the delightful live music that brought together the diverse group of researchers once again.

The final day of the conference was dedicated to ‘Cells and materials in regenerative medicine’. Matthias Lutolf discussed some of the ongoing efforts in his research group to develop next-generation organoids through tissue engineering. Meritxell Cutrona reported advances in nanoparticle tracking in 3D structures, which is particularly useful for drug delivery. Lakmali Atapattu described 3D bioprinting of tumoroids. Henrik Renner presented a high throughput-compatible workflow for the generation, culture, and optical analysis of neural human organoids. Rob Coppes and Melissa Little reported on promising progress in improving cancer treatment, using glandular and kidney organoids, respectively. James Wells gave a talk on the applications of gastrointestinal organoids, concluding with some food for thought for the audience: “It is better to collaborate, than to compete.”

The Symposium ended with the poster prizes, sponsored by EMBO Reports, EMBO Molecular Medicine, and Sartorius. Personally, I found these four days extremely stimulating, full of opportunities for interaction and discussion. I believe most of my fellow researchers got the same feeling: 3D organoid systems are revolutionising molecular biology and driving the development of better clinical therapies, and we are all contributing to this revolution.

What will we be able to achieve with organoids in two years’ time?

Stay tuned, the meeting will be back in 2020!

@LunardiLabCIBIO

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