June 5th is World Environment Day, and this year there is a clear message – that society should take “urgent action to protect biodiversity”[i]. But what does this mean in practice? If, like me, you feel that we are on the cusp of a sea change when it comes to talking about environmental issues, you may also spend a lot of time thinking about what on earth society can do to respond to the challenges of climate change or mass extinction.
It was, therefore, with interest that I came across the publication of the World Scientists’ Warning of a Climate Emergency[ii] (the ‘Warning’) in the journal of the American Institute of Biological Sciences (“BioScience”), which demands that scientists give their name to a “clear and unequivocal declaration that a climate emergency exists on planet Earth”. Published exactly 40 years after the first World Climate Conference in Geneva, the Warning now has over 13,500 signatories, who commit to the principle that scientists “have a moral obligation to clearly warn humanity of any catastrophic threat”, and to “tell it like it is”.
The Warning not only provides us with statistics, policy suggestions and solutions, but it is a rallying cry for society (and particularly scientists!) to take action. What I find so fascinating about this initiative is that it causes us to stop and think about our role in this debate. What part could, or should we play in issues affecting the future health of planet Earth? How does one reconcile or balance individual action with national or global priorities and policy decisions?
The Science & Society Programme provides a vehicle to explore exactly these kinds of issues through an EMBL lens – we seek to provide a neutral platform for multi-disciplinary dialogue on the ethical, legal and social implications of the life sciences, and in particular, of EMBL’s research.
In fact, the Science & Society 2020 Conference, “Our House is Burning: Scientific & Societal Responses to Mass Extinction”, will specifically address the topic of biodiversity. It will consider the impact of environmental changes on biodiversity, ecosystem services, and human well-being from a societal perspective. Crucially, focus will be placed on potential solutions and types of action: from activism to political strategies, and from local grass-roots conservation groups to global youth movements. It will also evaluate the application of intervention methods, from sustainability solutions to data science and beyond. And, this year, it will take place as a virtual event, with a flat fee of 20 Euros (and free to students under 18). Click here to sign up!
The issues in our upcoming Conference are clearly topical, and the Warning itself also focuses on ‘Nature’ as one of the six key steps for action – to “protect and restore Earth’s ecosystems”. EMBL’s activities and research also directly intersect with five of the six steps for action outlined in the Warning; Energy, Short-lived pollutants, Nature, Food and the Economy. As an organisation, it is, therefore, clear that EMBL has a part to play in this debate. The Green EMBL group was set up last year to lead EMBL’s activities in addressing its environmental impact. The group is bottom-up, and open to all EMBL scientists and staff who have an opinion, idea or desire to act to reduce the environmental impact of EMBL.
I am keen to hear from you. Did you sign the Warning yourself? How do you view your role as a scientist in this issue, and do you consider yourself a ‘Science Activist’? If you are willing to share your view on these questions, or want to know more about the Conference or other Science & Society events, please get in touch.
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.
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.
Alfred Cortes introduced the second session on ‘parasite biology’.
First to speak was ManojDuraisingh 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.
MathieuBrochet 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.
FranckDumetz 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.
LianneLansink 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.
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’.
ChrisDrakeley 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.
MarioRecker 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.
ManuelaCarrasquilla 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.
SimonKigozi 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
SamWassmer began the fifth virtual session of the conference on ‘pathogenesis & immunology’.
BrittanyRiggle 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.
HannahFleckenstein 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, LawrenceWang 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.
EmiliePollenus 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.
CarolaSchaefer 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.
SilviaPortugal opened the final virtual session of the conference on transmission biology.
DennisKlug 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.
AureliaBalestra 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.
InesBento 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. AndyWaters 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 AndyWaters and JulianRayner. 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.
Written by Melissa Burke
Scientific Training Officer, EMBL-EBI
As a Scientific Training Officer I often have to pull together training on topics that are new to me. What’s the first thing I do in this situation? Well, I draw on all of my scientific training and research skills and … Google it. Yep, an internet search is my first step in figuring out what the topic is about and what’s been taught before, and whether there are any materials/images, etc that I can reuse. It’s a great source of inspiration!
But this can also be frustrating and takes quite a lot of time. Material and information tends to be scattered all across the internet. It can be hidden behind paywalls, require a login to access, or lack enough context to be fully understandable. And even then, it is hard to know whether the materials can be reused nor how to credit the original author. I often find myself going round in circles and end up recreating new slides from scratch. Why isn’t there a better way of sharing materials? One that makes them easier to find?
These frustrations are familiar to many trainers across ELIXIR and we’ve been working together to figure out what we can do about it. As bioinformatics trainers we are also scientists or researchers and this problem is something that we’ve experienced with, for example, research data.
The good news is that things are getting better for research data because of the development of the Findable, Accessible,Interoperable and Reusable principles that states materials should be quick to find, easily accessed, will work across a variety of platforms & settings and can be used time and time again. Could the same be possible for training materials?
Wiegers, Luc and van Gelder, Celia W. G. Illustration for the paper “Ten simple rules for making training materials FAIR”. DOI 10.5281/zenodo.3593257
To help answer this question we picked up on work that started at the ELIXIR BioHackathon Europe 2018 to put together 10 Simple Rules for Making Training Materials FAIR
Give a unique identity
Define access rules
Use interoperable format
Make (re)usable for trainers
Make usable for trainees
Keep materials up-to-date
Hopefully these simple rules make it a little bit easier for trainers to start sharing their materials in a way that makes them easier to find, (re)use, and cite. Let’s use this opportunity to spark conversation and collaboration within global training communities that lead to wider and better sharing of materials (and the inspiration that comes with them!).
Want to know more? Read the rules in full in PLoS Computational Biology. Which of the FAIR principles do you think is most important for Training materials? Let us know in the comments.
The EMBL Events team has been working harder than ever during the coronavirus pandemic, figuring out new ways to bring our scientific programme online and trying out new technologies to make our virtual events a valuable experience for all.
Tim Nürnberger was the first event organiser to lead the EMBL transition into the digital world, organising the EMBO | EMBL Symposium: The Four-Dimensional Genome. Tim did an outstanding job (as always!) in a very short amount of time, gained a great deal of experience and is now helping the rest of team with the upcoming virtual events. So, in this Meet the EMBL Events Team edition, we are more than happy to introduce you to him.
At EMBL since: 2010 Number of organised conferences/courses: 73 (!)
First thing you do before a conference/course starts and first thing you do after it finishes:
Before: Take a deep breath, have a cup of coffee and expect the unexpected!
After: Just relax!
If you weren’t a conference officer, what would you be doing?
Travelling around the world.
What is the strangest/funniest thing that has ever happened in a course/conference?
A coach with a large group of registered conference participants drove up just outside the ATC main entrance, all of them taking pictures in front of and inside the ATC like being on a sightseeing trip, and left just a few minutes later without taking part or being interested in the conference at all.
If you were a superhero what power would you like to have?
Time travel would be kind of cool to witness some historic moments, or to travel to the future!
The current pandemic has forced many event organisers to freeze all ongoing projects with no end date in sight. The impact on the events industry has been dramatic, but it has also provided the opportunity to rethink how we do events and explore other avenues such as virtual conferencing.
The EMBL Course and Conference Office has just successfully completed its first virtual conference, which we managed to put together within a couple of weeks with the tireless work of the scientific organisers, the EMBL IT and AV teams. It has been an interesting experience, not without hiccups of course, but we have learned a lot and are looking forward to applying those learnings to our next online event in May.
We are happy to share with you some of the steps we followed to quickly turn an onsite conference into a virtual format and how we dealt with the challenges we were faced with.
Commit all your speakers
Once it was clear we were going to try to go virtual with this event, we had to make sure we had all the invited speakers on board to be able to pull together a high-quality programme. Of course, not all of them could join, but if you manage to get the majority of the originally planned speakers, you are good to go!
Explore the technical limitations
One critical thing of course is the technical setup that needs to be tested and working properly during the conference. If you have a dedicated IT and AV team, you are in a good position, as they will be the supporting pillars of your virtual conference. Involve them early on, as they can best advise on and set up the streaming platform. Also, should there be any unexpected technical problems, they will be able to fix those quickly or come up with a working alternative.
For instance, in our recent virtual conference, the server crashed due to an automatically scheduled password change on the EMBL media site (talk about bad timing!), and it was only thanks to our great AV team that we managed to migrate the conference to a new platform (Zoom) within the hour. The programme was adjusted accordingly to accommodate the break and things ran smoothly from then on.
Define the programme
Now that you have the speakers and the software established, it is time to consider the programme. Originally, you would have had 2 or 3 days full of talks with the occasional coffee break and meals in between. However, in a virtual event, it is just not possible to do that. When you define your programme, ask yourself “How long would you sit and listen to online talks?”. Probably not longer than 3-4 hours, so consider this when assigning the speaker slots.
Make it widely accessible
Ideally, your choice of timing of the programme would cover at least 2 time zones so that more participants can join in (e.g. start in the afternoon for CET, which would be morning for ET). For participants in other time zones, you could consider recording and streaming the talks on-demand.
Cover all presentation formats
Live streaming of all talks (invited, short talks and poster presentations) may be what you would expect in an ideal world, but for the reasons we described in the previous two points, it is just not possible. Therefore, in our case, we decided to live stream only the invited talks, while giving the participants the chance to access the pre-recorded short talks and digital posters in a dedicated time slot in the main programme as well as on-demand. Q & A were then taken to the main discussion platform.
Provide a discussion platform
One of the great benefits of in-person conferences are the peer discussions and networking opportunities which can result in great collaborations and career advancement.
In a virtual event, these are of course a bit limited, but a dedicated discussion platform outside of the main streaming software can help foster collaborations and knowledge exchange. We chose Slack as the main discussion platform for Q & A which worked very well, but there are many other applications out there that can offer a similar experience.
Involve your sponsors
If you have committed sponsors to support your event, you would want to provide them with opportunities to reach out to the community. Depending on what package they have booked, you can replace the onsite services with online benefits, such as a pre-recorded short talk, a discussion channel, online banners, logo placements or adverts.
Test, test, test!
Most importantly, before you launch the online conference, make sure to test everything. Schedule test sessions with each of your speakers and chairs to make sure that all works well on their end as well before going live.
But remember that even if you follow all the steps and make sure that every tiny detail is thought of, you may still end up having some unexpected problems during the live stream, just as you may encounter difficulties at an onsite event. The truth is that for all of us (both event organisers and participants) this is a new experience from which we can only …
…Learn and improve
For our first virtual conference we are extremely grateful to have received so much constructive feedback that we are currently working on implementing in the future. Our participants have been amazingly understanding and willing to help us improve. At the end of the day, despite some technical difficulties during this test run, looking at the feedback we realise that we have managed to achieve our goal to connect the community and get the science across.
“Congratulations for organising this very first virtual meeting. It was really great despite some technical issues. It was really good and thus too short.”
“Science and technology help people in good and bad times. This conference was for me a fresh breeze of exciting science and a taste of life normality during forced social distancing. Thanks!”
“The Four-Dimensional Genome EMBL Symposium was great! Many inspiring talks on chromatin & nuclear organization with partially unpublished data. I couldn’t have participated hadn’t it been VIRTUAL: thanks to @EMBLEvents team & all organizers for making it possible!”