Metagenomics and Ribosome Profiling Smartly Explained

The science behind molecular biology is advancing fast and scientists are eager to create and share new content. But the more content is being created, the harder it is to reach the desired audience. Therefore, the scientific community has had to come up with new attractive formats to help spread valuable scientific content.

One format that is currently popular is explainer videos, which combine both, audio and visual elements to untangle a topic. It has been proved that when one sense is activated we keep part of the information, but with the activation of multiple senses we can process and store far more.

We have therefore created explainer videos as part of our e-learning series.

“It was a great experience working on this project for our virtual courses. We are very fortunate to have Daniel Krüger, a former PhD student creating the graphics for these videos. This immensely improved the communication between the scientific advisers and the graphic designer because they speak the same language,” said EMBL Training Lab Manager Yvonne Yeboah, who came up with the idea of creating the explainer videos and led their production.

The first explainer video we are introducing deals with metagenomics, the genomic analysis of microbes by direct extraction and cloning of DNA, that allows studying communities of organisms directly in their natural environment.

“Our metagenomics course encompasses many different in silico and experimental approaches to understand and gain insights into microbial communities. Therefore, we thought that the visualisation of a video would provide students with an attractive overview that helps to connect and integrate all the aspects covered in the course,” explained José Eduardo González-Pastor, who organised the EMBO Practical Course: Microbial Metagenomics: A 360° Approach and acted as scientific advisor for the videos.

The second explainer video deals with the topic of ribosome profiling, a method that allows researchers to quantitatively analyse translation genome-wide and with high resolution. The video gives a comprehensive overview on how this technique works, what ribosome protected fragments (RPFs) are and what information we can obtain from them.

“Ribosome profiling is still an emerging technology. Therefore, it is great to have a concise summary that explains the method to students. I will certainly use the video for lectures and on my website,” said Sebastian Leidel and Jan Medenbach, both organisers of the EMBO Practical Course: Measuring Translational Dynamics by Ribosome Profiling and scientific advisors for the video.

Visit EMBL’s YouTube channel to find more exciting scientific content.

 

 

 

Follow us:

Meet the Trainer – José Eduardo González-Pastor

meet the trainer - eduardo gonzalezJosé Eduardo González-Pastor – one of the main organisers at the upcoming EMBO Practical Course: Microbial Metagenomics: A 3600 Approach (12 – 19 June 2019) – conducts his research on the mechanisms of adaptation of microorganisms to extreme conditions using metagenomic and metatranscriptomic approaches at the Center of Astrobiology (CSIC-INTA) in Madrid, Spain.

What is the greatest benefit of the course for the scientific community?

One of the greatest difficulties in the study of microbial communities is that a large percentage of the environmental microorganisms can not be cultivated. Numerous tools, called “omics” have been developed, such as metagenomics, metatranscriptomics and metaproteomics, which allow access and study of all microorganisms in these communities. In this course, we explain most of these methodologies from theory and practice, and how to use them to properly design experiments to answer certain scientific questions related to microbial communities.

What could the techniques in this course be used for in the bigger picture?

The “omics” techniques allow us to better understand the functioning of microbial communities in their natural environment and not exclusively in laboratory conditions. In addition, one of the techniques, namely functional metagenomics, is very useful for recovering enzymes of interest in biotechnology from the microorganisms of the environment.

Are the methods used in this course unusual or new?

In the course we will explain some recent methods in functional metagenomics, such as the screening of metagenomic libraries using microfluidics techniques.

In comparison to other training environments, what do you enjoy most about teaching at EMBL?

The support from the EMBL Course and Conference team in the organisation of the course is impressive. All the logistics and other matters such as the preparation of the laboratory are handled very professionally by them. We, as trainers and organisers, only need to dedicate ourselves to coordinating the scientific part, and that leaves us time to interact with the students.

What challenges is your research field facing?

The methods of massive sequencing of DNA are generating a lot of information, but we still do not understand the function of a very high percentage of genes, which encode hypothetical or unknown proteins. Even for Escherichia coli, the best studied of all organisms, half of all the proteins encoded in its genome, around 2,000, have never been experimentally characterised. Thus, we need the combination of new and classic methods to be able to understand the molecular functioning of the organisms.

What, in your opinion, is the most crucial scientific discovery of the past 100 years?

The discovery of the structure of DNA.

What is the most interesting paper you’ve read in the past year?

GABA-modulating bacteria of the human gut microbiota. Nat Microbiol. 2019 Mar;4(3):396-403. doi: 10.1038/s41564-018-0307-3. Strandwitz P, Kim KH, Terekhova D, Liu JK, Sharma A, Levering J, McDonald D, Dietrich D, Ramadhar TR, Lekbua A, Mroue N, Liston C, Stewart EJ, Dubin MJ, Zengler K, Knight R, Gilbert JA, Clardy J, Lewis K.

Human microbiota and depression!! Microorganisms are much more relevant than we thought.

Where is science heading in your opinion?

Applied research is being favoured more than basic research, and it is a serious mistake, since much of the advances in applied science have their origin in basic research. The scientific community faces very complicated challenges in applied science without having solved many basic questions about the functioning of organisms. How can we undertake the search for new tools to fight pathogenic microorganisms if we still do not know the function of a large majority of their proteins?

What was your first ever job?

Postdoctoral position at Harvard University, Department of Molecular and Cellular Biology. Cambridge, MA, USA.

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

Architect, musician or chef, in this order.

What is the strangest or funniest thing that has ever happened in a course?

It was not so funny but strange. In the first course that I collaborated as a trainer and speaker (not as an organiser), “Metagenomics: From Bench to Data Analysis”, the two EMBO organisers had to leave in the middle of the course for personal and urgent reasons, and suddenly one of the course assistants gave me the keys of the rooms and I had to take responsibility for organising the course until the end. Possibly I did not do it badly, since the EMBO organisers decided to invite me to be also an organiser of the following editions of this course, which is now “Metagenomics: a 360º Approach”.

If you were a superhero what power would you have?

To be able to access the minds of others.

What is your bucket list for the next 12 months?

Decrease administrative tasks and complete the writing of several pending articles.

What holiday tip can you give people – e.g. a place / restaurant / attraction you have visited in the world that people should definitely make the effort to see?

To visit the Antarctic.

What is the greatest risk you’ve ever taken?

Crossing the Drake Passage (Sea of Hoces) by ship to go from Punta Arenas (Chile) to the Antarctic.

What is your favourite book?

The Little Chronicle of Anna Magdalena Bach, by Esther Meynell

What is your favourite recipe? Please provide details!

Black rice with seafood (paella negra de marisco, in Spanish). Rice is cooked in a sauce with tomato, red and green peppers and onions, then it is added a broth made with fish, seafood remains and squid ink. During cooking, shrimps, clams, squids and green beans are added.

Follow us: