How does the environment play a role in biodiversity?

Biodiversity – in all its forms and interactions – is the variety of life on Earth. Climate change is exacerbating biodiversity loss, and vice versa. Ahead of the EMBO | EMBL Symposium ‘The Organism and its Environment’ (1–4 March 2020), we talk to Scientific Organiser and EMBL Director General Edith Heard about the impact the environment has on biodiversity and the role of research in solving global challenges.

Does the environment play a large role in the creation of biological diversity?

Biodiversity is the variety of life on Earth. This life, in all its shapes and sizes, occurs in the context of ecosystems: it relies on and interacts with other organisms and the physical environment. Biodiversity represents the collective ‘knowledge learned’ by evolving species over millions of years, about how to survive the vastly varying environmental conditions Earth has and is experiencing. These varying environmental conditions cause natural variations in biodiversity, as well as genetic and epigenetic changes, within and between species over time. Today, scientists are trying to understand the basis of these natural variations, as they will allow us to understand how life evolves.

Fish populations have declined at an alarming rate, and half the world’s shallow water coral reefs have been lost in just 30 years.

But biodiversity is also a measure of the health of any ecosystem. Recent trends in biodiversity loss show very clearly that humans are destroying ecosystems on a massive scale. According to the Director General of the World Wildlife Fund (WWF), increased pollution, deforestation, climate change and other manmade factors have created a “mind-blowing” crisis. The WWF Living Planet Report 2018 (WWF LPR, 2018) also states that freshwater fish populations have declined by more than 80% on average since 1970 and half of the world’s shallow water coral reefs have been lost in the last 30 years (WWF LPR, 2018). Alongside this, deforestation of tropical rainforests means we are currently losing more than 100 species of plants and animals a day (Holley, 2017). In short, human’s influence on the environment greatly impacts biodiversity and we are currently burning the library of life.

How can you determine the effect of the environment on an organism?

The environment can affect an organism in a multitude of ways. The impact can be transient or longer term; within an individual or across generations. The environment can also lead to molecular, cellular, physiological or behavioural changes. For example, the expression of genes in an organism can be influenced by the external environment, such as where the organism develops or factors associated with where it is located. Gene expression could also be influenced by an organism’s internal environment, including hormones or metabolism. Finally, the genome itself – genetic factors that vary between individuals in natural populations – could also influence gene expression.

Research groups at EMBL look at how variety in organisms comes about

Untangling the impact of genetic and environmental variation can be very challenging and for a long time, scientists have tended to focus on minimising variations in the environment in order to understand how changes in genotype affect phenotype. This, alongside the deeply embedded “one genotype = one phenotype” metaphor, has meant that environmentally induced phenotypic variation has been ignored in favour of ‘‘more useful and precise’’ study of genetic polymorphisms. This is despite the fact that from as far back as the early 1900s, scientists have known that the phenotype of an individual depends on the interaction between its genotype and environmental cues! Today, we finally have the power to consider the impact of the environment on phenotype. We can make precise measurements at the molecular, cellular and organism scales in controlled environments that can be varied and we can sequence genomes at the same time.

We can also take human data paired with environmental data – for example in the context of some of EMBL’s research interests such as infectious disease and microbiomes – to understand the quantitative effects of the environment and its influence on human biology. Pioneering projects such as Tara Oceans have also allowed us to research the interactions between organisms and the environment by generating reference data, discovering emergent ecological principles and developing predictions about how ecosystems will be affected by a changing environment. Understanding how organisms exist together and in changing environments is of fundamental importance for our understanding of biological principles and our knowledge of life.

What challenges are currently being faced in this field?

Studying organisms in their environment will become increasingly important.

Understanding the behaviour of individual molecules, cells or whole organisms is already challenging. Understanding how the environment influences an organism – or populations of organisms – represents a whole new scale in complexity. This is an area that I think EMBL could uniquely contribute to in the future. It will be necessary to shift from researching organisms mainly in the laboratory to studying them in their environment. We will also need to ensure the rapid development of technologies and tools to meet these scientific needs. Alongside this, we need new approaches to integrate large, complex data sets and make sense of them. To rise up to this challenge, we need theory. We are now in a unique position to address the dynamics and complexity of living matter across multiple scales and in the context of changing environment. But we need theory to address societal and planetary issues too. We must aim for a rate of scientific discovery that outpaces the rate of calamity such as biodiversity loss, ecosystem degradation, epidemics and climate change.

What can be done to prepare for the future with regard to biological diversity, the organism and its environment?

Research, research and more research! Environmental problems such as the hole in the ozone layer or acid rain were solved by sound scientific approaches. We need to learn from these past scientific and societal successes. Today the ever-increasing numbers of new technologies are allowing us to collect, measure and store data at unprecedented scales. We also need to bring ecologists, zoologists, population geneticists and environmental experts together to address these research questions. Together we can apply cutting-edge technology with rigour, attract new scientific talent and disseminate knowledge to global communities.

What inspired you to organise this symposium?

As a geneticist and epigeneticist, I have explored the intersection between genotype and the environment and how that produces a phenotype. From observing many areas of research – ranging from social insects such as bees and ants, to plant vernalisation and variations between identical twins – I felt that the time is ripe to bring together scientists from many different areas. I also wanted this to be a symposium that would attract scientists from different areas to EMBL.

At EMBL, we want to understand the molecular basis of life. Until now, EMBL has been known for exploring genomic, molecular, structural and cell biology at the level of individual organisms. Looking ahead, we want to study organisms in the context of their physical and biological environments not just in isolation. In order to truly understand life on Earth, we need to study organisms in nature, not just in the lab. One way to understand life at the molecular level will be to try to bring relevant ecosystems back to the lab, to measure and perturb them under controlled conditions. The speakers we’ve invited are experts from many different areas of biology or ecology, and will bring exciting new perspectives to our research.

The EMBO|EMBL Symposium: The Organism and its Environment will take place at EMBL Heidelberg, Germany, from 1-4 March 2020

What is the greatest benefit of this symposium for the scientific community?

The symposium is an opportunity to address how organisms are influenced by a changing environment. It will bring together different research disciplines and go beyond pure genetic or ecological perspectives of phenotypic variation. Geneticists, molecular biologists, evolutionary biologists and ecologists do not necessarily meet under ordinary circumstances. This meeting will enable such interactions and cross-fertilisation.

What will be the main highlight of the symposium?

Today we are in a unique position to address the complexity and dynamics of life at multiple scales, from molecules to ecosystems. We also need to consider the idea that change including in the environment is not necessarily a bad thing. After all, without change, evolution could not occur and none of the amazing biodiversity of life on our planet would exist! I hope that a highlight of this symposium will be some wonderful new insights into evolutionary processes.

 

References

Holley D., (2017). General Biology II, Organisms and Ecology. Indianapolis: Dog Ear Publishing, 898.

World Wildlife Fund, (2018). Living Planet Report: Aiming higher [PDF] https://wwf.panda.org/knowledge_hub/all_publications/living_planet_report_2018/ [Accessed 25 July 2019].

https://wwf.panda.org/knowledge_hub/all_publications/living_planet_report_2018/

However the WWF DG is quoted by several articles as describing the crisis as mind-blowing, for example: “https://www.voanews.com/science-health/report-earth-has-lost-60-percent-its-wildlife-1970

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We’ve proved it, biologists can also program

“Like punning, programming is a play on words.” Alan J. Perlis.

You don’t have to be a programmer to have programming skills. Writing code is an essential part of being a programmer (duh!), but is also a vital component of being a scientific developer, software developer or computer scientist. You can utilise computer programs to automate tedious and repetitive tasks, extract results from experimental data, apply models to solve your research questions or purely have fun with your own projects.

Today is Programmers’ Day (yay!🥳) and we want to recognise all those who submerge themselves in the deepest mysteries of code (especially their own) and aim to automate the future.

If you’re looking to start venturing into the programming world or embark on your next project, get some inspiration from some scientists who are helping out at our EMBL Events’ courses.

Florian Huber PHOTO: Marietta Schupp/EMBL

“What do I love about programming? It allows me to go from zero to one: gaining new biological insights from data.” Florian Huber (Postdoctoral Fellow, at the Typas Group in EMBL Heidelberg and the Beltrao Group at EMBL–EBI in Hinxton).

 

 

 

 

Ullrich Köthe PHOTO: Ullrich Köthe

“Automated image analysis has always been an interesting and fun field of research, but thanks to the deep learning revolution and the wide availability of wonderful neural network libraries, we can now actually solve hard practical problems.” Ullrich Köthe (Group Leader in the Visual Learning Lab Heidelberg).

 

 

Valentyna Zinchenko PHOTO: Carolina Cuadras/EMBL

“Programming skills allow you to automate the routineparts of your job and focus more on the exciting ones. At some moment you just have so much data, that you would not want to process it manually. You would not wash your clothes by hand if you have a washing machine, would you? Then why analyzing your data manually, when you can have it done by a machine as well?” Valentyna Zinchenko (Predoctoral Fellow in the Kreshuk Group).

 

Adrian Wolny PHOTO: Carolina Cuadras/EMBL

“Whenever I build something, be it a new machine learning model or my pet project, I always try to make it easy to understand and generic enough so that other people could use it in their work. I try to open source my projects whenever I can and contribute back to the community. There is nothing more rewarding than seeing your little piece of software used by others to find answers to their own research questions.” Adrian Wolny (Visiting Researcher at EMBL and PhD candidate at Heidelberg University).

 

Pavel Baranov PHOTO: Pavel Baranov

“The relationship between computer science and modern biology is akin to that between mathematics and physics.” Pavel Baranov (Professor of Biomolecular Informatics, University College Cork, Ireland)

 

 

 

 

It’s no secret that managing biological data efficiently can be overwhelming and feel impossible. If you’re a biologist who’s interested in learning how to process, analyse, organise and interpret your almost innumerable data sets – preferably with the most suitable and state-of-the-art techniques and tools out there – EMBL Events has got you covered.

EMBL Course: Deep Learning for Image Analysis, Apply by 20 September 2019

EMBL Course: Exploratory Analysis of Biological Data: Data Carpentry, Apply by 5 November 2019

EMBL Course: Analysis and Integration of Transcriptome and Proteome Data, Apply by 10 November 2019

EMBL Course: Immune Profiling of Single Cells, Apply by 10 November 2019

EMBO Practical Course: Microbial Metagenomics: A 360º Approach, Apply by 27 January 2020

EMBO Practical Course: Measuring Translational Dynamics by Ribosome Profiling, Apply by 9 February 2020

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Fostering friendly collaborations across organisations

Guest blog post by Jürgen Deka, Head of External Scientific Training, EMBL

The International Day of Friendship (annually on 30th July) got me thinking about our friends in the scientific training field, and our collaborations with them which enable us all to deliver our high-level scientific conferences and courses.

It’s important to have a goal to work towards, and at EMBL Events we generally benchmark ourselves against Cold Spring Harbor Laboratory and Keystone Symposia in the US, and the Wellcome Genome Campus in the UK. A bit of healthy competition is good for the soul, and I think we all thrive on challenges! It allows all four of us to provide top-class training to benefit as many scientists as possible throughout the world, and in this sense we all have the same aim.

“Competition has been shown to be useful up to a certain point and no further, but cooperation, which is the thing we must strive for today, begins where competition leaves off.”    

Franklin D. Roosevelt

If you are looking to establish and foster friendly collaborations in scientific training, here are 6 tips that can help you achieve your goal:

  1. Keep in regular contact
  2. Align your goals with each other
  3. Be aware of what the other organisations are doing and talk to them openly so you can adapt your plans accordingly
  4. Don’t arrange meetings with the same audiences too close together. If people are going to attend both meetings – either as speakers, participants or sponsors – there needs to be some space in between
  5. Find ways to work together in order to highlight and complement your strengths
  6. Learn from each other, but don’t try to be like the others – work on developing your own strengths

Here’s how we work with our counterparts to allow us all to offer the best science possible worldwide:

  • Cold Spring Harbor Laboratory: With the Cold Spring Harbor Laboratory we have very close ties. We alternate one of our most popular conferences with our friends at CSHL, the EMBO Workshop ‘Protein Synthesis and Translational Control’. We align our programme plans in order to provide added value for our scientific community. Discussion and exchange between the programme heads and other members of staff takes place on a regular basis.
  • Keystone Symposia: As with the other research institutes, EMBL’s collaboration with Keystone Symposia is a long-standing one. We exchange our thoughts and ideas and align our conference programmes once per year. Our friends at Keystone Symposia have been particularly open and collaborative with regards to the alignment of their symposia taking place in Europe.
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Balancing training with family

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
Eligibility 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.
Languages The two main languages of the teachers are German and English. N/A
Childcare times 8:30am – 5:50pm for the duration of the conference Grant applicable for costs incurred in relation to child care costs during the meeting.
Financial details 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.
What’s provided? 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.
Allocation process 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.
Contact details childcare@embl.de or Tel.: +49 (0)6221 387 8797. Please contact the organisers of the individual event for more information.
Website EMBL Onsite Childcare

EMBL childcare testimonials

EMBO Childcare Grants

Press release – EMBO childcare grants now available

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BioMalPar’s most loyal friends

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

 

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