Multiomics to Mechanisms Best Poster Awards

The EMBO|EMBL Symposium: Multiomics to Mechanisms: Challenges in Data Integration took place virtually 15 – 17 September 2021. With over 400 participants, this was the biggest multi-omics conference since it began in 2017. We had 96 posters presented virtually, and are excited to share the research from the three best poster prize winners. 

Identification of transcription factor signaling molecules by coupling gene expression and metabolomics

A portrait picture of Daniela Ledezma‑Tejeida
Daniela Ledezma‑Tejeida, ETH Zurich, Switzerland (Photo credit: Stefania Laddage)

Abstract

Bacteria need to adapt to changes in their environment in order to survive. Transcription factors (TFs) bind metabolites that signal such changes and in turn alter gene expression. Escherichia coli has the best characterized transcriptional regulatory network involving 300 predicted TFs, of which ~75% have a metabolite‑binding domain. However, the binding partners of only 95 TFs have been identified due to low-throughput of common in vitro identification methods. Here, we combined metabolomics and gene expression data obtained in vivo across several growth conditions to identify TF‑metabolite interactions of four TFs without a known binding partner: CdaR, CsgD, FlhDC and GadX. We have validated our method by accurately predicting the known binding partners of ArgR, TyrR and CysB, three highly studied TFs. The in vivo nature of our approach can not only identify new TF‑metabolite interactions but also provide insight into the most functionally relevant.

View Daniela’s poster

Towards topology‑based multi‑omics pathway enrichment and its application in toxicology

A portrait picture of Sebastian Canzler, Helmholtz‑Centre for Environmental Research
Sebastian Canzler, Helmholtz‑Centre for Environmental Research ‑ UFZ, Germany

Abstract

The call for an application of (multi‑)omics data in toxicology became highly prominent in recent years, since omics experiments are intended to generate comprehensive information on molecular changes in cells and tissues more quickly, more accurately, and with fewer resources than ever before. The associated hopes explicitly include the reduction of live animal testing and an increased number of analyzed substances that can be tested. Therein, multi‑omics data are essential to comprehensively infer mechanistic knowledge on molecular response pathways to subsequently guide and aid chemical risk assessment. However, currently available multi‑omics pathway enrichment methods struggle to cope with different aspects hampering their application in computational toxicology, e.g., the utilization of insufficient enrichment methods, missing support for time‑ and concentration resolved data, and restrictions on the pathway sources. Most approaches utilize a sequential data integration and thereby completely ignore the connections between different omics layers. With ToPaFC, we present the first step towards a consistent and simultaneous multi-omics-based pathway enrichment that accounts for those obstacles and explicitly takes the underlying pathway topology into account. Right now, we can deal with up to eight different pathway databases and two omics layers (trans/meta or prot/meta). The pathway topology is reflected in two different ways: i) the importance of a node (omics feature) is measured based on its connections and its relative localization within the pathway and ii) the influence of each node on the network is specified by the weight of its outgoing edges, whether they are inhibiting, neutral, or activating. With this integration of edge information along the pathway, our method inherently accounts for consistent molecular changes of the features. The derived node‑centered pathway representation is combined with measured multi‑omics features to calculate a topology‑based pathway fold change that accounts for consistent changes within the molecular response.

View Sebastian’s Poster

Computational approaches to scrutinize results from spatial proteomics of operable pancreatic cancer and neighboring tissue

A portrait picture of Ábel Szkalisity, University of Helsinki, Finland
Ábel Szkalisity, University of Helsinki, Finland

Abstract

The advance of laser‑microdissection technologies coupled with proteomics enables unprecedented insights into tissue proteomes. However, the limited availability of patient materials coupled with the high dimensional output of proteomics necessitates data integration across studies to safeguard the reliability of the results. We microdissected morphologically benign and neoplastic pancreas and surrounding stromal areas from 14 patients with early pancreatic ductal adenocarcinoma and analyzed their protein compositions with nLC‑MS/MS. The results indicated downregulated digestive functions in the malignant exocrine tissue and lower metabolic activity in the stroma vs. exocrine pancreas. Intriguingly, the majority of the most significant proteins for survival originated from the morphologically benign exocrine regions, suggesting that these areas may harbor early, predisposing changes. To scrutinize this idea, we compared their proteomes to proteomics data of 12 healthy control pancreatic samples obtained from publications. The protein identification and quantification pipeline from the raw mass spectrometer files were standardized to minimize variation introduced by search engines or protein sequence databases. Altogether, we identified 7,099 proteins in 67 samples involving 5 tissue types from 2 experiments and 5 batches. We investigated two independent strategies for rendering the values comparable. First, batch effects within experiments were corrected for with ComBat and the abundances across experiments were aligned with housekeeping protein normalization. However, this approach required full observations, removing over 90% of the identified proteins from the analysis. Hence, our second approach involved applying Group Factor Analysis to directly extract factors that reveal relationships between the tissue types in our study without compromising the protein coverage. These approaches not only showed that our main results are independent of the data analysis pipeline but also implicated changes in the mRNA splicing machinery as important players in pancreatic cancer. By surveying 165 patients from The Cancer Genome Atlas we revealed that increased transcriptional complexity indeed associates with poor survival in this disease.

View Ábel’s Poster

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Record attendance at New Approaches and Concepts in Microbiology

Written by event reporter Magdalena Wutkowska.

This year’s EMBO|EMBL Symposium: New Approaches and Concepts in Microbiology took place 7-9 July 2021. For the first time in its history, the meeting was held virtually, with a record of over 650 attendees from all over the world. The three day programme featured six sessions, 36 talks, discussion panels and countless posters showcasing the newest scientific advances in the field.

This was my second time reporting during a virtual conference organised by EMBL, the first one being the EMBO Workshop: Molecular Mechanisms in Evolution and Ecology. It is interesting to note, even though the two meetings started with quite different scopes and aims, over time they began to resemble one another. Both meetings welcomed topics in microbiology that use cutting-edge techniques to disentangle and unravel microorganisms’ intricate worlds. The two meetings followed a similar format, which included a fairly intuitive online platform with links to presentations, posters, chats and a variety of other information prepared by the organisers.

A table with a laptop, a thermos with coffee or tea and a notebook on a desk.
My setup for the symposium

Pre-symposium sessions

As part of New Approaches and Concepts in Microbiology, three special pre-symposium sessions explored transitioning to starting a lab, the nooks and crannies of publishing presented from the editor’s perspective and the future of scientific meetings in a post-pandemic world. The panelists shared many insightful ideas distilled from decades of experience in their work, and usually this type of knowledge is not so readily available, especially to early-career scientists.

From my personal perspective, the pre-symposium session on the future of scientific meetings was one of the most interesting, and is also a topic that will affect everyone in the scientific community. Gerlind Wallon representing EMBO shared results of a recent survey in which scientists were asked what they expected from meetings in the future and how did they perceive the online meetings that became a sudden reality for the scientific community, since the onset of the pandemic.

Scientific sessions

The scientific programme of the conference was fully packed with impressive and wide-ranging talks tackling most of the ‘big’ areas and pressing topics in microbiology. The first day was dedicated to systems biology, followed by the environment and antibiotics. The presentations on the second day dealt with regulation, signalling, protein machines and cell biology. The final day’s sessions covered novel approaches to study pathogenesis, infection, and microbiomes.

A common and reoccurring theme in many talks was the role of viruses in microbial systems and processes. The importance of that topic was strongly emphasised during the 1st day’s panel discussion on phage-microbe interactions, which  highlighted some new and exciting perspectives on viruses.

The highlights from the conference have been instantly reported on Twitter using #EESMicrobiology. If the data presented during a talk has already been published, there is usually a link to the associated paper(s) in the tweet.

Onsite to virtual to hybrid?

Pandemics brought many tragic events, but on the other hand, it gave us a chance to rethink many issues and come up with alternatives for our actions. Virtual meetings are perhaps one of the broadly acquired tools, which in my opinion should further be used to make science more available for people and lower our impact on the environment. Will the next “New Approaches and Concepts in Microbiology” be held in a hybrid format?

Unexpected perks of attending online meetings from a favourite place!

This blogpost was written by Magdalena Wutkowka, Postdoc in Anne Daebeler’s Group, Soil and Water Research Infrastructure, Biology Centre CAS, České Budějovice (CZ).

Learn more on how to become an event reporter for EMBL Events.

 

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Meet the Trainer – Jonathan Manning

PHOTO: Jonathan Manning

The Introduction to RNA-seq and Functional Interpretation course (21 – 25 February 2022) is now open for applications and we thought we would introduce you to one of the course trainers, Jonathan Manning.

Jonathan is a Bioinformatician in the Gene Expression group. His role is to expand capacity for single-cell RNA-seq analysis, the Expression Atlas resource, in dialogue with the Human Cell Atlas project. Jon gives us his tips for when looking for scientific training and some inside information on what he would be if he wasn’t a Bioinformatician.

What is your research focus and why did you choose to become a scientist?

My answer here is going to be awkward, in that I don’t have a research focus! Much of my career has been as a ‘service’ Bioinformatician working in various bioscience institutes performing custom analysis for a variety of different experiment types in different biological fields. In my current role at EMBL-EBI I build and maintain RNA-seq pipelines we run the same way over a large number of experiments. In both cases, I use the outputs of other people’s research (tools as well as data) to produce the best results I can for the questions at hand.

I actually started out in Biochemistry due to a fascination with the molecular machinery of life. But I discovered early on that the lab was not for me, and I’ve been on the ‘dry’ side of things ever since.

Where do you see this field heading in the future?

In common with many other fields, machine learning and artificial intelligence will play progressively bigger roles in this field in the coming years, with ‘Big Tech’ companies such as Google having ever greater involvement. I’m sure this will be a double-edged sword, and people such as myself will have to run to keep up, but there’s no denying the potential of these techniques and I foresee some exciting results.

How has training influenced your career? 

I’d say my early Bioinformatics training (a Masters by Research and PhD after that) was pretty pivotal for me, setting me on a whole new path. After that my training was more incremental, for example, some introductory RNA-seq analysis similar to that offered at EMBL-EBI, followed up with a lot of self-teaching.

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

Be focused, choose courses that are related to your immediate objectives, and have clear goals about what you want to get out of the training. If you don’t have ways to immediately apply and expand what you’ve learned then the training quickly fades. I often find it more useful to do training only once I’ve tried to do something myself, so that I know which bits are tricky for me and what questions I need to get answers for.

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

I’d really love to study historical linguistics, an interest I’ve picked a bit late in the day. I also learned to dance a bit over the last several years, maybe I’m a professional dancer in another universe where I started earlier!


Interested in this course? Apply by 12 November 2021

For more upcoming events on cancer research take a look at our event listing.

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EMBL is looking for scientists with artistic talent!

Are you a scientist who is interested in structural biology and bioinformatics and passionate about arts?

This is your chance to showcase your talent!

EMBL is looking for scientists with an artistic vein who can transform scientific theories into art.

What do you need to do?

Create an original piece of art representing scientific and/or societal concepts relating to a structure in the Protein Data Bank.

Need some inspiration? Look here: http://www.wwpdb.org/

If your artwork is selected, it will be hosted on www.artsteps.com, an innovative, web-based application targeted at the PDB research community.

“This art exhibition is part of the EMBL Conference: Bringing Molecular Structure to Life: 50 Years of the PDB run by our team, the Protein Data Bank in Europe. Through this project we aim to provide new interpretations of molecular structures through artwork. And this allows the introduction of complex scientific themes in a more accessible form to the general public,” explained David Armstrong, Scientific Database Curator from EMBL-EBI.

You can create your artwork using any technique or media.

And why should scientists submit their artwork?

“The exhibition will allow scientists to present their area of work or interest in a new context through the medium of art. This will also help them to think about how to communicate their work, particularly to people from a non-scientific background,” said David Armstrong.

Please bear in mind that we will need a high-resolution image of the artwork to be able to present it in the virtual exhibition.

Together with the artwork, the following data provided by you will be displayed:

  • Name of the submitter
  • Affiliation of the submitter
  • Research stage
  • Which protein the artwork is linked to
  • What technique/tools were used to create the final piece
  • Short description about the artwork.

The opening of the exhibition will take place on 13 October 2021, during the launch of the virtual conference platform for the EMBL Conference: Bringing Molecular Structure to Life: 50 Years of the PDB and will stay open for one year.

We are looking forward to getting to know the artist in you!

More information and submission details can be found on the conference website.

 

 

 

 

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Why virtual sponsorship is valuable

Since the start of the COVID-19 pandemic, most events have been hosted entirely virtually. Companies looking to achieve their marketing objectives by means of events sponsorship have now been faced with the question of whether or not to invest in virtual events.

Virtual Booth Image

The major challenge that we have observed is that many companies expect the same outcome from their virtual event sponsorship as from an in-person meeting. We often hear that while in-person conferences offer possibilities for networking and casual talks, the virtual format is difficult and less efficient in this respect. At our in-person meetings, for example, exhibition booths with big banners are placed in the hall, right next to the catering area. Participants have enough time to walk around and strike a spontaneous conversation with sponsors during the breaks. The virtual format, however, is different. Participants usually attend virtual conferences from their home, often juggling work and family duties. They are more selective about the kind of content they access and prefer to schedule their interactions.

At first glance, this focused approach to attending virtual conferences may not seem as beneficial for sponsors. At the same time, however, there are several ways in which virtual meetings can lend themselves well to providing opportunities for sponsors.

🌎 Wider reach

The number of participants at virtual conferences is normally much higher than at in-person meetings due to them being more affordable and more accessible. The sponsors’ brands could therefore reach wider and more diverse audiences.

💸 Lower cost

Similar to the registration fees, the cost of virtual sponsorship is lower. In addition, companies save on the usual costs associated with sponsoring or exhibiting at a conference such as travel and accommodation for staff, booth design and set-up and shipping. With all this budget left unused, companies have the opportunity to invest in producing content that is relevant and engaging for participants.

📣 More diverse advertising formats

Sponsoring a virtual conference also means making use of all digital content formats available in the virtual venue – banners, videos, flyers, white papers, polls and webinars can all be used to further engage with participants. Digital booths give participants the opportunity to access at the time that is suitable for them, browse material, chat with booth staff, or have a video call to quickly get the answer of a pressing question about the company’s products they are using.

🗓 Extended exposure of branded material

Participants are generally given access to our virtual venues for an average of 4 weeks. In this way, sponsors get extended exposure for their brands and products and have the option to follow up with participants after the end of the meeting is over.

📈 Campaign insights

Contrary to physical conferences, measuring the success of your marketing efforts and the ROI of your sponsorship is much easier at virtual meetings. The built-in tools of the virtual conference software we use provide valuable insights on the performance of your individual marketing campaigns and help you assess your approach in the future.

Virtual sponsorship is a relatively new concept and one that many companies are still hesitant about. With all of EMBL’s events staying virtual until the end of 2021 and the possibility of hosting hybrid events once we go back on-site, it is now clear that virtual sponsorship is here to stay. It is therefore important to understand that it not only offers opportunities for companies to reach their target audiences in times where face-to-face interaction is limited but it also helps them stay connected with the scientific community.

Interested in supporting an EMBL conference as a virtual sponsor? Get in touch with us at sponsorship@embl.de!

Subscribe to our biannual Events Sponsorship E-Newsletter.

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