News in 2014
STUDENT UPDATE: BIMSB researchers in New York
BIMSB researchers travelled to New York in December 2014 for their annual exchange workshop with NYU faculty and to contribute to and attend the Departmental Developmental Genetics Meeting on December 4 - 5, 2014.
The bilateral workshop inspired new faculty members and exchange students to follow and intensify their joint projects.
ERC funding for Baris Tursun to elucidate direct reprogramming of cells - cell fate research without stem cells!
Research on cell fate determination in C. elegans is not at all a basic science question, it is relevant for development, diseases and molecular pathologies as well as regenerative therapies.
Baris Tursun receives his ERC grant to closely look at the molecular basis of direct reprogramming of cells, which has the potential to serve the needs of regenerative medicine. In his proposal ‘REPROWORM’, his group aims to understand how cells and tissues may turn from one differentiated state to another directly, which would allow to circumvent risks of pluripotent stem cells. This so-called transdifferentiation or direct cell fate conversion is by nature restricted and underlies inhibitory mechanisms, which need to be elucidated. The roundworm C. elegans is one of the most suited genetic model organism since all of its 959 cells has a determined fate, the organism’s genome was the first to be entirely sequenced and it is amenable for genetic engineering, imaging of the fully transparent organism as well as single cell analyses. The results of this project will lead to translational potential for innovative regenerative approaches.
Baris Tursun received his PhD degree at the Center for Molecular Neurobiology of the University of Hamburg and then worked as Postdoc and Research Scientists at Columbia University in Oliver Hobert’s lab. Baris Tursun joined the BIMSB at the MDC in February 2012 as Independent Junior Group leader, working on gene regulatory mechanisms of direct conversion of cell types. To demonstrate the potential of the European C. elegans scientific community, Baris co-organized the first Berlin C. elegans Meeting in spring 2014.
Further information can be found in the MDC's press release.
STUDENT UPDATE: Sebastian Mackowiak successfully defends his doctoral thesis
Sebastian Dominik Mackowiak, N Rajewsky group, has successfully defended his doctoral thesis "Computational analysis of post-transcriptional regulation and computational identification of micropeptides" with the grade magna cum laude at the "Lebenswissenschaftliche Fakultät der Humboldt-Universität zu Berlin" on November 17, 2014.
Thesis reviewers: N. Rajewsky, M. Selbach and E. Klipp.
Doctoral commission: N. Rajewsky, M. Selbach, E. Klipp, U. Heinemann, H. Herzel
This research was funded by the MSBN and MDC.
PUBLICATION: New substrates and novel functions for an old Enzyme
Dicer plays a central role in RNA interference (RNAi) and the biogenesis of small RNAs/microRNAs. Dicer is known to "dice" RNA hairpins into small RNAs. Rybak-Wolf et al mapped and analyzed Dicer-binding sites in human cells and C. elegans. This study uncovered many novel targets which are "diced" by Dicer, but also provides evidence that Dicer stably binds to hundreds of mRNAs without dicing them. This new "passive" mode of Dicer binding has functionally important consequences.
The illustration shows how the new BIMSB
building will look after completion in 2018.
(Fig.: Staab architects for the MDC)
BIMSB construction site handed over
What seems to be only a small step in a construction project marks a giant leap for the Berlin Institute for Medical Systems Biology (BIMSB).
The piece of land for the new 7-story building for the BIMSB on the central historical campus of the Humboldt University was handed over to the MDC officially on Monday, November 17, and construction works, such as ground testing and preparations for the excavations started immediately. The completion of the building is scheduled for 2018.
LECTURE SERIES: Scientific colleagues come together in Winter Semester 2014/15 to present lectures on the topic of Computational biology: from basic research to applications in human health. Please note that this series will be held on Campus Buch. All are welcome to attend.
STUDENT UPDATE: Yasuhiro Murakawa successfully defends his doctoral thesis
Yasuhiro Murakawa, Landthaler group, has successfully defended his doctoral thesis "Functional Characterization of the Human RNA-binding Protein RC3H1 and Endoribonuclease DICER1" with the grade magna cum laude at the Department of Biology, Chemistry and Pharmacy of Freie Universität Berlin on October 14, 2014.
Thesis reviewers: U. Heinemann and M. Landthaler
Doctoral commission: U. Heinemann, M. Landthaler, O. Daumke, E. Knapp, V., G. Weber
This research was funded by the DAAD and the MDC.
STUDENT UPDATE: Mathias Munschauer successfully defends his doctoral thesis
Mathias Munschauer, Landthaler group, has successfully defended his doctoral thesis "High-resolution profiling of protein-RNA interactions" with the grade summa cum laude at the Department of Biology, Chemistry and Pharmacy of Freie Universität Berlin on August 22, 2014.
Thesis reviewers: U. Heinemann and M. Landthaler
Doctoral commission: U. Heinemann, M. Wahl, C. Scharff, M. Landthaler, B. Loll
This research was funded by the MDC-NYU PhD Exchange Program and was jointly conducted with the laboratory of Christine Vogel at NYU.
PUBLICATION: The very early influence of parents !!!
Two studies on the very early role of mom and dad were just recently published by the N Rajewsky lab.
In the first study Stoeckius et al (20114b) could demonstrate, that the early embryo does not only follow signals of maternal gene products and post-transcriptional regulation thereof. By metaboloic labeling and crosses of divergent C. elegans strains, they could identify and analyze paternal RNA’s (mRNA; siRNA piRNA) which co-lead the earliest events in the zygote and embryo.
The second study was performed in a long-standing collaboration with research teams at the MDC and at NYU. It offers a deep insight into the oocyte-to-embryo transition in Caenorhabditis elegans (Stoeckius et al 2014a). The researchers elucidate the very early events in the oocyte, soon after fertilization, including first waves of RNA degradation, relevant signals and protein-RNA interactions. Both of these innovative approaches were already commented on Neff et al (2014).
Stoeckius M., Gruen D., Kirchner M., Ayoub S., Torti F., Piano F., Herzog M., Selbach M., Rajewsky N. Global characterization of the oocyte-to-embryo transition in Caenorhabditis elegans uncovers a novel mRNA clearance mechanism. EMBO Journal 33: 1751-1766 (2014)
STUDENT UPDATE: Henning Kuich successfully defends his doctoral thesis
Henning Kuich, Kempa group, has successfully defended his doctoral thesis "Towards understanding organ-derived metabolic signatures in blood" with the grade summa cum laude at the Department of Biology, Chemistry and Pharmacy of Freie Universität Berlin on July 28, 2014.
Thesis reviewers: S. Spuler and S. Kempa
Doctoral commission: S. Spuler, S. Kempa, P. Knaus, O. Daumke, B. Loll
This research was funded by a MDC PhD scholarship.
SEMINAR SERIES: Hans R. Schoeler - Distinguished Speaker in the BIMSB Seminar Series
On July 1 and 2, the Berlin Institute for Medical Systems Biology had the pleasure to host Hans Schoeler from the MPI for Molecular Biomedicine in Muenster.
Hans is a pioneer in the field of stem cell research and his name is closely linked to one of the main factors that enables these cells to form every possible cell type of the body: the gene regulating protein Oct4. Hans was one of the first to discover its role in mouse embryonic stem (ES) cells and later used it to show that ES cells are totipotent and able to form even oocytes. As a distinguished speaker in the Systems Biology Seminar Series, he presented his recent work on deciphering the molecular mechanisms underlying Oct4’s function in stem cells and the mammalian germ line. In a second lecture, which was part of the Systems Biology Lecture Series “Stem Cells” that aims to provide in-depth education of PhD students interested in this topic, he explained how factors like Oct4 can be used to reprogram normal body cells into multi- or pluripotent stem cells. The hope is to exploit such a process for regenerative medicine.
Both lectures were very well received by scientists from the MDC campus and all over Berlin. Thank you, Hans, for this stimulating visit!
STUDENT UPDATE: Kerstin Baethge successfully defends her doctoral thesis
Kerstin Baethge, Landthaler group, has successfully defended her doctoral thesis "Functional characterization of the FET family of RNA-binding proteins" with the grade magna cum laude at the Department of Biology at Humboldt-Universität zu Berlin on June 26, 2014.
Thesis reviewers: M. Landthaler, C. Schmitz-Linneweber and O. Daumke
Doctoral commission: M. Landthaler, C. Schmitz-Linneweber, O. Daumke, H. Saumweber and U. Ohler
This research was funded by the BMBF.
CONFERENCE: Berlin Summer Meeting 2014 - From Systems Biology to Systems Medicine
Systems biology is now a major focus in basic life science and are moving into the focus of medical sciences. Exciting high-throughput technologies and computational approaches hold the promise of better understanding life in health and disease and of opening new roads towards individualized therapy.
We thank the speakers and participants for joining this inspiring scientific meeting and our sponsors and funding agencies for financial support.
Nikolaus Rajewsky (MDC) with the certificate of the honorary PhD together with Eugenio Gaudio (Dean of the Faculty for Pharmacology and Medicine of Sapienza University), Luigi Frati (President of Sapienza University), and Giuseppe Macino (Director of the Department for Cellular Biotechnology and Hematology of Sapienza University) (from left). (Photo/Copyright: Gabriele Martin)
Finally a PhD in Biology!
Nikolaus Rajewsky, physicist, mathematician and bioinformatician is a world renowned expert in RNA biology, specializing in the role and function of non-coding RNA in biological processes and gene regulation. Trained in the exact sciences, he applies mathematical and computational methods to analyze biological data. His experimental lab uses model organisms such as flat or round worms to produce data to tackle developmental, stem cell and disease related questions. He works with his interdisciplinary team of young scientists in integrating sophisticated experimental and computational procedures.
For these innovative approaches and groundbreaking findings from the previous years – the role, function and interaction of micro RNAs and RNA binding proteins – he now received an honorary PhD from La Sapienza University of Rome. The ceremony took place on Wednesday, June 11, 2014 in Rome. In gratitude for this scientific honor, Nikolaus Rajewsky did not only give a scientific speech but also performed a piano concert. He played, together with Anna-Carina Jungkamp, the two Suites Op. 5 and 17 by S. Rachmanainov for two pianos.
Further information can be found in the MDC's press release.
SEMINAR SERIES: Xiaoliang Xie - Distinguished Speaker in the BIMSB Seminar Series
Sunney Xie from Harvard University gave a very well received talk as a distinguished speaker in the Systems Biology (BIMSB) Seminar Series.
During the talk, Sunney presented his recent work in the emerging field of single cell genomics, demonstrating how the new technology will not only help to advance our understanding in basic science, but also lead to novel clinical applications.
CONFERENCE: Berlin C. elegans Meeting 2014, May 15 - 17
Large and lively conference on C. elegans research is held at the MDC.
Organized by Baris Tursun, Nikolaus Rajewsky and Janine Kirstein-Miles (FMP), this is one of the largest meetings of the European worm community since years. Prior to his presentation, Nikolaus started with a personal note: "When I came to the MDC, seven years ago, I was the only researcher using C. elegans as a model. In my wildest dreams I would not have believed that once more than 300 worm researcher would convene on the MDC's campus!"
The conference hosts several leaders in the field for keynote and invited presentations. Additional presentations were selected from more than 200 abstracts, and poster sessions allow further presentation and intense discussions.
For more information, please check the conference homepage.
Further information in German can be found in the article "Wo C. elegans drauf steht, ist Systembiologie drin!" and in the German radio feature.
STUDENT UPDATE: Alexander Baltz successfully defends his doctoral thesis
Alexander Georg Baltz, Landthaler group, has successfully defended his doctoral thesis "The mRNA-bound Proteome of a human cell-line and in early Drosophila embryogenesis" with the grade summa cum laude at the Department of Biology, Chemistry and Pharmacy of Freie Universität Berlin on May 5, 2014.
Thesis reviewers: M. Wahl and M. Selbach
Doctoral commission: M. Wahl, M. Selbach, S. Sigrist, V. Erdmann, D. Horbelt
This research was funded by the MDC-NYU PhD Exchange Program and was jointly conducted with the laboratory of Stephen Small at NYU.
Successful HFSP research grant!
A tri-national team was recently selected for funding by the Human Frontier Science Program.
Nikolaus Rajewsky is a member of the team on 'Deciphering non-coding RNA regulatory networks and their role in cancer cell biology' in cooperation with Brian Brown from Mount Sinai School of Medicine, New York. The team aims to identify the factors that govern ncRNA-mediated competing endogenous RNA activity. This will lead to a large scale annotation of of nc-RNA regulatory networks and to their role in cancer relevant cell functions. The participants in the project-leading experts in RNA biology, computation, biochemistry and oncology - decided to join forces to reach the next level of insight into the complex function of ncRNAs for health and disease.
The selection process was highly competitive, 34 winning teams out of 844 submitted proposals, and emphasizes scientific excellence and relevance of designated projects.
LECTURE SERIES: Scientific colleagues from Campus Buch, Berlin, TU Dresden and MPI Molecular Biomedicine in Muenster come together in Summer Semester 2014 to present lectures on the topic of Stem Cells. Please note that this series will be held on Campus Buch. All are welcome to attend.
PUBLICATION: MDC scientists unravel the RNA helicase activity of the protein MOV10 and connect it to a mRNA degradation pathway
A tight control of mRNA processing, translation, and turnover is essential for proper regulation of gene expression. These processes are facilitated and regulated by mRNA-binding proteins through dynamic association with their target mRNAs. RNA helicases constitute a group of ATP-dependent enzymes that remodel both RNA-RNA structures (RNA unwinding activity) and RNA-protein complexes (RNPase activity). These molecular functions are key elements for the regulation of mRNA-life cycle.
An important aspect of uncovering the functional properties of RNA helicases is to identify their RNA targets and investigate their mode of action on these transcripts.
Lea Gregersen, a PhD student in Markus Landthaler’s laboratory, and colleagues at the BIMSB were able to comprehensively characterize the RNA-binding pattern and activity of the putative helicase MOV10, using photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) in combination with next-generation sequencing.
The scientists demonstrated and analysed major MOV10 functions: it binds to thousands of mRNA transcripts, with its binding sites located mainly in 3’ UTRs, and strikingly, it performs 5’ to 3’ directional helicase activity in vitro and in vivo. Moreover, MOV10 interacts with UPF1, a crucial component of the nonsense-mediated mRNA decay pathway. The knockdown of MOV10 results in increased mRNA half-lives of UPF1-regulated transcripts, suggesting that MOV10 functions in UPF1-mediated mRNA degradation as an RNA clearance factor to resolve structures and displace proteins.
The article MOV10 Is a 5′ to 3′ RNA Helicase Contributing to UPF1 mRNA Target Degradation by Translocation along 3′ UTRs can be found on the Molecular Cell website.
STUDENT UPDATE: Lea Gregersen successfully defends her doctoral thesis
Lea Haarup Gregersen, Landthaler group, has successfully defended her doctoral thesis "Functional Characterization of the RNA Helicase MOV10" with the grade summa cum laude at the Department of Biology, Chemistry and Pharmacy of Freie Universität Berlin on January 14, 2014.
Thesis reviewers: M. Wahl and M. Landthaler
Doctoral commission: M. Wahl, U. Heinemann, S. Rickert-Sperling, D. Horbelt and M. Landthaler
This research was funded by the MDC Helmholtz Graduate School Molecular Cell Biology.