On Tuesday, July 20th Andreas Horn very successfully defended his PhD thesis. For many years, Andreas was advancing our understanding of how RNA binding proteins control development and cell fate decisions in the model organism Drosophila melanogaster. We are very proud and happy about Andreas’ success and we wish him all the best for his future endeavors.
After being postponed due to the Coronavirus pandemic, the EMBO practical course on measuring translational dynamics by ribosome profiling could finally take place from May 17th to 25th 2021 in a virtual format. 16 participants from research labs across the globe discussed intensively with ten speakers and 12 trainers about how to perform ribosome profiling experiments. Pre-recorded talks provided insight into the different aspects of the technique and used recent examples to illustrate how ribosome profiling can be used to further our understanding of translation and its regulation. Furthermore, Pavel ‘Pasha’ Baranov and his team from the University College Cork provided an excellent online tutorial on the bioinformatic analyses of ribosome data.
I am particular grateful for the insightful talks provided by Nicholas Ingolia (UC Berkeley), Marina Rodnina (MPI Göttingen), Rachel Green (Johns Hopkins), Anne Willis (University of Cambridge), Thomas Preiss (Australia National University), Gerben Menschaert (Ghent University), and Vladimir Benes (EMBL Heidelberg) that made the curse a big success. Also, on behalf of all organizers, I would like to thank Lisa Trinh, Diah Yulianti, Irena Provaznikova (from the EMBL Courses and Conferences Office) and in particular Yvonne Yeboah (form the EMBL teaching lab) for their daily support. Finally, without the expertise of my co-organizers Elisabeth Zielonka (EMBL Heidelberg), Sebastian Leidel (University of Bern), and Pavel ‘Pasha’ Baranov (University College Cork) it would not have been possible to host this course.
Above: Short explanatory movie on ribosome profiling. I would like to thank Daniel Krüger, Julia Schleisiek, Claudiu Grozea, and in particular Yvonne Yeboah and Sebastian Leidel for production of the video. More information on the movie can be found here.
On Friday, October 9th Stefan Reich very successfully defended his PhD thesis. For many years, Stefan was the driving force of the project Systems Biology of the Unfolded Protein Response in Glioma (SUPR-G) and discovered that the UPR can elicit resistance to treatment with folate-based antimetabolites (click here for the publication). We are very proud and happy about Stefan’s success and we wish him all the best for his future endeavors.
It is with heavy heart that we have to inform you that EMBL Heidelberg and the scientific organisers have decided to postpone the EMBO Practical Course: Measuring Translational Dynamics by Ribosome Profiling 2020.
We have taken this difficult decision in order to better play our part in reducing the impact and spread of the novel coronavirus and also in recognition of the fact that many of our speakers and participants are currently finding it difficult to travel.
The new date for this course is still under discussion and will be communicated once it has been agreed.
tRNA modifications – Connecting translation dynamics to cellular quality control
On february 25th, 2020, at 5 p.m., Sebastian Leidel from the University of Bern will give a talk in H53. Sebastian and his lab have pioneered the use of ribosome profiling to understand the importance of tRNA modifications in translation.
tRNAs are key players in mRNA translation linking amino acids to a specific codon sequence. Interestingly, tRNA molecules carry a plethora of chemical modifications of their nucleotides, which are posttranscriptionally introduced by many different enzymatic pathways. Even though huge progress has been made, it is still unclear how most of these tRNA modifications contribute to cellular function. This is of particular importance as GWAS studies have linked different modification pathways to a number of degenerative diseases and cancer. New technologies explored by Sebastian and his lab have provided novel insights into this exciting research field.
We are looking forward to seeing you on Tuesday for an evening of exciting science!
Get motivation letters ready! Registration for the EMBO Practical Course on Measuring Translational Dynamics by Ribosome Profiling is now open. The application deadline is Febraury 9th 2020.
We are thrilled to have a great line-up of speakers and tutors including Nicholas Ingolia (University of California, Berkeley, USA), Rachel Green (Johns Hopkins University School of Medicine, Baltimore, USA), Thomas Preiss (The Australian National University, Canberra, AU), Anne Willis (University of Cambridge, UK), Marina Rodnina (Max Planck Institute for Biophysical Chemistry, Göttingen, DE), Gerben Menschaert (BIOBIX, University of Ghent, BE), and Vladimir Benes (EMBL Heidelberg). During the course, we aim to provide both insight into the theoretical background of ribosome profiling as well as practical sessions with hands-on experimentation and computational training on how to perform ribosome profiling experiments and to analyze the resulting data. We are very much looking forward to your application and to meeting you at the Advanced Training Centre at EMBL Heidelberg in May!
An EMBO practical course on Measuring Translation Dynamics by Ribosome Profiling is coming up in May 2020. Fantastic speakers are supporting the course including Nicholas Ingolia (University of California, Berkeley, USA), Rachel Green (Johns Hopkins University School of Medicine, Baltimore, USA), Thomas Preiss (The Australian National University, Canberra, AU), Anne Willis (University of Cambridge, UK), Marina Rodnina (Max Planck Institute for Biophysical Chemistry, Göttingen, DE), and Gerben Menschaert (BIOBIX, University of Ghent, BE). The Couse is organized by Sebastian Leidel, Pavel Baranov and Jan Medenbach and will include numerous lectures as well as hands-on training on how to perform ribosome profiling experiments and how to analyze the data. More information will be available soon on the EMBL courses website.
From October 8th to 10th 2018, a hands-on methods course took place at the University of Regensburg, aimed at training PhD students in the latest methods of ribonucleoprotein (RNP) analysis. Topics included the quantification of protein-RNA interactions, single molecule analyses of RNPs by fluorescence resonance energy transfer (FRET) or fluorescence in situ hybridization (FISH), RNA structure probing, and comprehensive capture of RNA-binding proteins by interactome profiling from cultured cells. The course attracted PhD students from labs around the globe, some travelling from as far as Canberra, Australia, to get insight in and training on a variety of biophysical and biochemical methods. The design of the course was also aimed at fostering interactions between the participants, allowing them to build networks with peers working on related topics. Besides the lectures and the practical hands-on training, it was particularly the vivid and intense discussions among the participants that made this course a big success.
We are extremely grateful for the support of many expert speakers and trainers that delivered lectures on the latest methodological developments and that supervised the experimental work. In particular we want to thank the invited speakers from industry and academia that travelled to Regensburg to provide expert guidance: Rastislav Horos (European Molecular Biology Laboratory, EMBL, Heidelberg), Agatha Korytowski (Malvern Panalytical), Stefanie Nunes Rosa (Swedish University of Agricultural Sciences, Uppsala), Joel Perez-Perri (EMBL Heidelberg), Bruno Sargueil (CNRS/Paris Descartes University), and Ralf Seidel (Peter Debye Institute for Soft Matter Physics, Universität Leipzig).
The course was organized by the Graduate Research Academy RNA Biology of the Collaborative Research Centre 960 (SFB960, Ribosome formation: principles of RNP biogenesis and control of their function) that also provided financial support.
A particular highlight is coming up next week: Prof Thomas Cech will be awarded a honorary doctorate by the University of Regensburg. Tom Cech, now Professor at the University of Colorado at Boulder and director of the BioFrontiers Institute, was awarded the Nobel Prize in chemistry in 1989 jointly with Sidney Altman for the discovery of the catalytic activity of RNA. His revolutionary discovery of self-splicing in Tetrahymena thermophila radically changed the way we were thinking about RNA – what was previously considered a mere carrier of genetic information turned out to play the key function in fundamental biological processes. Exemplarily, protein synthesis is catalyzed by the RNA moiety of the large ribosomal subunit which promotes the peptidyl transfer reaction by which peptide bonds are formed between amino acids. His discovery also had a huge impact on my own scientific career and convinced me that RNA is the most interesting biomolecule to study. I am very much looking forward to the Symposium on Monday, October 22nd (starting 3:30p.m. in lecture hall H51) and to finally get the opportunity to meet Tom Cech in person!
Mark your calendars! From October 8th to 12th the Graduate Research Academy RNA Biology of the Collaborative Research Center 960 (SFB960 – Ribosome formation: principles of RNP biogenesis and control of their function) is hosting a practical course on modern methods for the analysis of ribonucleoproteins (RNPs). Diverse topics will be covered ranging from biophysical analyses (such as isothermal calorimetry and thermophoresis), single-molecule RNP studies (single-molecule FRET and FISH), RNA structure probing and the latest RNA interactome capture methodology. In the morning, renowned experts will deliver lectures to introduce the individual topics, followed by hands-on experimentation in the afternoon. All lectures are open to the public, so even if you didn’t register, you certainly don’t want to miss out on the exciting talks by Rastislav Horos (EMBL Heidelberg), Agatha Korytowski (Malvern Panalytical GmbH), Stefanie Nunes Rosa (Swedish University of Agricultural Sciences, Uppsala), Joel Perez-Perri (EMBL Heidelberg), Bruno Sargueil (CNRS/ Paris Descartes University), and Ralf Seidel (Universität Leipzig)!
On Wednesday, November 29th, Jan successfully finished the final phase of his Habilitation by delivering a lecture in front of the entire faculty.
`I want to thank everybody who supported me along the way, in particular my lab and the colleagues in the Biochemistry I department of the University of Regensburg, especially Gunter Meister. Also without the help of our colleagues in the Collaborative Research Center 960 (Sonderforschungsbereich SFB960), our excellent collaborators, and the funding (provided by BioSysNet, DFG and BMBF) we would not have succeeded with our scientific work that was an essential part of the Habilitation.´
It is a german tradition to prepare a handcrafted hat as a present for candidates that have just obtained their doctoral degree. Jan also got a super-cool Drosophila hat for his Habilitation – thank you to everybody who helped crafting it!
Good news! We are happy to announce that our review on the function of the Drosophila RNA-binding protein Sex-lethal (Sxl) was recently accepted. Sxl is particularly interesting: it is a rather small RNA-binding protein with a simple architecture, nonetheless it engages in the regulation of multiple aspects of gene expression to direct female development. The review is open access and can be downloaded here. Let us know what you think about it!
‘A very well organized and extremely helpful course on RNA-Seq analysis featuring top-notch speakers and experts in the field’
– that is how one of the participants summarized the recent bioinformatics course on ‘Analysis of NextGen RNA-Seq data for expression profiling and protein-binding RNAs’ that took place from October 10th to 14th at the University of Regensburg. The Graduate Research Academy RNA Biology hosted several renowned experts in the field that delivered fascinating, public lectures addressing state-of-the-art methods for gene expression profiling and RNP analysis. Afterwards 18 selected participants had the opportunity for some hands-on training on actual datasets. We are happy that so many interested students from seven different universities joined us. And apparently, according to the feedback we got, for the participants the course really did make a difference:
‘with the combination of excellent speakers and target-oriented hands-on training, this one-week course increased my knowledge on current NGS tools and enabled me to analyze my own datasets’
During five intense days, a broad variety of topics was covered. These ranged from practical considerations for setting up sequencing experiments (Stefan Kirsch, Fraunhofer ITEM), Sequence alignment and quality assessment (Steve Hoffmann, Universität Leipzig and Nicholas Strieder, Universität Regensburg), pecularities of high-throughput data analysis (Rainer Spang, Universität Regensburg), differential gene expression and alternative transcript level analyses (Simon Anders, FIMM Helsinki, Charlotte Soneson, University of Zurich and Grischa Tödt, EMBL Heidelberg) to probing of RNPs (CLIP, Markus Hafner, NIH Bethesda) and translation (Ribosomal Profiling, Jan Medenbach, Universität Regensburg).
We are extremely grateful to the instructors and tutors and would like to thank all of them for their generous support! Their help, commitment, dedication, and willingness to share knowledge made a real difference and the course a big success!