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Investigation of the role of water molecules in protein RNA-recognition

Author: System Administrator - Published At: 2017-05-24 11:52 - (5 Reads)
The Allain lab (ETH Zurich)(external link) together with the Sponer group (CEITEC & Masaryk University, Brno, Czech Republic)(external link) has published a paper describing the role of water molecules in the RNA recognition by the RNA recognition motif (RRM) of the Fox-1 protein, which is a regulator of alternative splicing. Its RRM binds to a hexanucleotide RNA target sequence with high affinity and the structure of this complex was determined previously by the Allain lab using Nuclear Magnetic Resonance Spectroscopy (NMR) (Auweter S.D. et. al., (2006) EMBO Journal)(external link). This structure together with a high-resolution X-ray structure of the unbound RRM revealing bound water molecules provided the starting point for molecular dynamics (MD) simulations to further structurally study the role of water in RNA RRM recognition. Based on the results of the MD analyses two selected water binding sites were subsequently studied by NMR, affinity measurements and free-energy calculations. For one of the sites, which is evolutionarily conserved in RRMs, a quantitative agreement between the computational and experimental approaches was found demonstrating the value of MD analyses to analyze hydration patterns involved in RNA-protein recognition.
Read the publications in Nucleic Acids Research (open access)(external link)
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Welcome to Jeffrey Chao and Marc-David Ruepp!

Author: System Administrator - Published At: 2017-05-16 13:41 - (7 Reads)
We would like to welcome Jeffrey Chao (left picture) and Marc-David Ruepp (right picture) who became junior principal investigators of the NCCR RNA & Disease as of May 2017.

Website Chao lab - FMI Basel(external link)

Website Ruepp lab - University of Bern(external link)

Read more about the junior principal investigators of the NCCR RNA & Disease in Vol 5 of the Messenger(external link)

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Press Release / Medienmitteilung Universität Bern

Author: System Administrator - Published At: 2017-05-10 14:07 - (10 Reads)
A possible way to new antibiotics
Two research teams from the University of Bern and the ETH Zurich have developed a new method to shed light onto a mostly unknown process of bacterial protein production. Their results could be used for the design of new antibiotics.
Link to Press Release(external link)

Möglicher Ansatz für neue Antibiotika entdeckt
Zwei Forschungsteams aus Bern und Zürich haben eine neue Methode entwickelt, um einen Einblick in einen bislang kaum erforschten Teil der bakteriellen Proteinherstellung zu erhalten. Die Resultate könnten bei der Entwicklung neuer Antibiotika helfen.
Link zur Medienmitteilung(external link)

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Press Release / Medienmitteilung Universität Bern

Author: System Administrator - Published At: 2017-05-10 12:25 - (11 Reads)
Closing the Gate to Mitochondria
A team of researchers from the Universities of Bern and Freiburg (D) have developed a new method that enables the identification of proteins imported into mitochondria. This leads to a better understanding of disease mechanisms linked to defective cellular functions.
Link to Press Release(external link)
Das Tor zu Mitochondrien schliessen
Ein Forschungsteam der Universitäten Bern und Freiburg (D) hat eine Methode entwickelt, mit der sich importierte mitochondriale Proteine bestimmen lassen. Dies führt zu einem besseren Verständnis von Krankheitsmechanismen, die mit fehlerhaften Zell-Funktionen zusammenhängen.
Link zur Medienmitteilung(external link)
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Portrait Thomas R. Cech im Bund und Tages-Anzeiger

Author: System Administrator - Published At: 2017-05-08 16:57 - (15 Reads)
Ein Portrait von Tom Cech mit dem Titel „Der Dogma-Brecher“ wurde im Bund und Tages-Anzeigerpubliziert. Das von Nik Walter geschriebene Portrait basiert in Teilen auf einem Interview, welches im Rahmen des Besuchs von Tom Chech als NCCR RNA & Disease Seminarredner stattfand.

Artikel im Bund(external link)

Artikel im Tagesanzeiger(external link)

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NCCR Newsletter No. 5

Author: System Administrator - Published At: 2017-05-03 14:24 - (37 Reads)
The Messenger - The NCCR RNA & Disease Newsletter
The fifth edition of the NCCR RNA & Disease Newsletter -The Messenger has been published:
Editorial
Frédéric Allain
Junior principal investigators of the NCCR RNA & Disease
Fostering the new generation of Swiss RNA researchers
Research highlights
A noncanonical way out of pluripotency / Identifying the drivers amongst the passengers
Unconscious bias
Detecting and mitigating bias
Announcements
People, events, support grants and more

Read The Messenger here
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Helge Grosshans awarded ERC Advanced Grant

Author: System Administrator - Published At: 2017-04-28 22:34 - (19 Reads)
We would like to congratulate Helge Grosshans on being awarded an ERC Advanced Grant. The ERC funded project “Cyclode” will investigate the role of oscillatory gene expression in animal development and aims at deciphering the components of the associated timekeeper.
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Press Release / Medienmitteilung Universität Bern

Author: System Administrator - Published At: 2017-03-14 14:23 - (294 Reads)
Cut the long story short – and stitch it back together
A species of unicellular ciliate has found a special trick to make use of the cellular machinery in seemingly impossible ways. Researchers of the NCCR «RNA & Disease – The Role of RNA Biology in Disease Mechanisms» of the University of Bern have for the first time described a mechanism in detail how so called «junk»-DNA is transcribed before being degraded – and this mechanism is remarkably clever.
Link to Press Release(external link)
Link to the video abstract(external link)
Read the article in Cell (open access).(external link)
Ein DNA-Pantoffelheld
Pantoffeltierchen haben einen ganz besonderen Trick entwickelt, um die Zellmaschinerie auch in scheinbar unmöglichen Situationen noch nutzen zu können. Forschende des Nationalen Forschungsschwerpunkts «RNA & Disease – Die Rolle von RNS in Krankheitsmechanismen» von der Universität Bern haben zum ersten Mal einen Mechanismus beschrieben, wie «Junk»-DNA noch ausgelesen statt gleich abgebaut wird – und dieser ist von erstaunlicher Raffinesse.
Link zur Medienmitteilung(external link)

Press Release / Medienmitteilung Universität Bern

Author: System Administrator - Published At: 2017-03-03 12:54 - (188 Reads)
Genome Editing: Pressing the «Delete» Button on DNA
Until recently, genomics was a «read-only» science. But scientists led by Rory Johnson at the University of Bern and the Centre for Genomic Regulation in Barcelona, have now developed a tool for quick and easy deletion of DNA in living cells. This software will boost efforts to understand the vast regions of non-coding DNA, or «Dark Matter», in our DNA and may lead to discovery of new disease-causing genes and potential new drugs.
Link to Press Release(external link)
Ein «Delete-Knopf» für die DNA
Forschende unter der Leitung des Molekularbiologen Rory Johnson der Universität Bern haben eine Software entwickelt, mit der Teile der menschlichen DNA rasch und einfach aus lebenden Zellen gelöscht werden können. Die Software wird zu einem besseren Verständnis der «Dunklen Materie» unserer DNA führen, der sogenannten nicht-codierenden DNA, und könnte die Suche nach krankheitsverursachenden Genen sowie neuen Therapien erleichtern.
Link zur Medienmitteilung(external link)
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Press Release / Medienmitteilung Universität Basel

Author: System Administrator - Published At: 2017-03-02 11:07 - (196 Reads)
Michael N. Hall awarded Cancer Research Prize
On February 8th, 2017, the American National Foundation for Cancer Research announced that Michael N. Hall, Professor of Biochemistry at the Biozentrum of the University of Basel, has been selected as the winner of the 2017 Szent-Györgyi Prize for Progress in Cancer Research. The award recognizes his groundbreaking discovery of the protein kinase TOR – target of rapamycin – and its role in cell growth control and carcinogenesis.
Link to Press Release(external link)
Michael N. Hall mit Krebsforschungspreis ausgezeichnet
Die amerikanische National Foundation for Cancer Research verleiht Michael N. Hall, Professor für Biochemie am Biozentrum der Universität Basel, den diesjährigen Szent-Györgyi-Preis für Fortschritte in der Krebsforschung. Die Auszeichnung würdigt seine bedeutende Entdeckung der Proteinkinase TOR – Target of Rapamycin – und dessen Rolle bei der Kontrolle des Zellwachstums und der Krebsentstehung.
Link zur Medienmitteilung(external link)

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FMI News Article

Author: System Administrator - Published At: 2017-01-20 12:39 - (317 Reads)
Cell fate regulation by LIN41: activity determined by binding location

Helge Großhans and his group at the Friedrich Miescher Institute for Biomedical Research (FMI) have elucidated the mode of action of the RNA-binding protein and stem cell factor LIN41. In an animal model, they showed that LIN41 silences four specific mRNAs, by two distinct mechanisms. They found that the choice of mechanism is determined by where on the mRNA LIN41 binds. As the proteins whose production LIN41 inhibits are responsible for cell maturation, these new findings could be relevant for future stem cell therapies.

Link to FMI News Article(external link)
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Press Release / Medienmitteilung Universität Basel

Author: System Administrator - Published At: 2017-01-13 12:45 - (387 Reads)
Treating cancer with drugs for diabetes and hypertension
A combination of a diabetes medication and an antihypertensive drug can effectively combat cancer cells. The team of researchers led by Prof. Michael Hall at the Biozentrum of the University of Basel has also reported that specific cancer cells respond to this combination of drugs. The results of the study have now been published in “Science Advances”.
Link to Press Release(external link)
Krebsbekämpfung mit Diabetes- und Bluthochdruckmedikamenten
Mit einer Kombination aus einem Diabetesmedikament und einem Blutdrucksenker können Krebszellen effektiv bekämpft werden. Wie das Forscherteam unter der Leitung von Prof. Michael Hall vom Biozentrum der Universität Basel im Fachjournal «Science Advances» zudem berichtet, sprechen spezifisch Krebszellen auf diese Wirkstoffkombination an.
Link zur Medienmitteilung(external link)
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Press Release / Medienmitteilung Universität Bern

Author: System Administrator - Published At: 2017-01-13 12:34 - (339 Reads)
How complex cells originated
Mitochondria are the “power plants” of complex cells. In order to provide the cell with energy they need protein building blocks, which are imported from the outside. Over billions of years the “protein import machines” necessary for this process have developed differently than previously assumed, as biochemists in Bern have discovered. This also casts a new light on the evolution of complex cells.
Link to Press Release(external link)

Wie komplexe Zellen entstanden sind
Mitochondrien sind die «Kraftwerke» komplexer Zellen und versorgen diese mit Energie. Dazu brauchen sie Protein-Bausteine, die von aussen importiert werden. Die dafür notwendigen «Protein-Import-Maschinen» haben sich über die Jahrmilliarden anders entwickelt als bisher angenommen, wie Berner Biochemiker herausgefunden haben. Dies wirft auch ein neues Licht auf die Evolution komplexer Zellen.
Link zur Medienmitteilung(external link)
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FMI News Article

Author: System Administrator - Published At: 2017-01-11 12:00 - (343 Reads)
Small RNAs interact with newly synthesized transcripts to silence chromatin

Yukiko Shimada, Fabio Mohn, and Marc Bühler at the FMI elucidated an important mechanistic detail of small RNA mediated chromatin silencing. They showed in fission yeast that the small RNA in the RNA induced silencing complex (RISC) interacts with nascent transcripts and not with complementary DNA to induce heterochromatin formation. In addition, both the transcription rate and transcript processing have an impact on the silencing process.

Link to FMI News Article(external link)
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ETH Zurich News Article / Artikel

Author: System Administrator - Published At: 2017-01-06 14:11 - (358 Reads)
A highly paid award in the field of medicine
ETH structural biologist Nenad Ban is to be awarded one of Europe’s most highly paid prizes in the field of medicine: he is set to receive the Ernst Jung Prize for Medicine 2017 for his description of the atomic structure of cellular protein production machinery.
ETH News - English(external link)

Hochdotierte Medizin-Auszeichnung
Der ETH-Strukturbiologe Nenad Ban wird mit einem der höchstdotierten Medizinpreisen Europas ausgezeichnet: Für die Beschreibung der atomaren Struktur der zellulären Proteinherstellungsmaschinerie wird ihm der Ernst Jung-Preis für Medizin 2017 verliehen.
ETH News - Deutsch(external link)
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NCCR Newsletter No. 4

Author: System Administrator - Published At: 2016-12-15 13:55 - (453 Reads)
The Messenger - The NCCR RNA & Disease Newsletter

The fourth edition of the NCCR RNA & Disease Newsletter -The Messenger has been published.

Read The Messenger here
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Medienmitteilung / Press Release Universität Basel

Author: System Administrator - Published At: 2016-12-08 15:24 - (467 Reads)
Forscher finden «Krebssignatur» in Proteinen
Das Team von Prof. Mihaela Zavolan vom Biozentrum der Universität Basel hat die Herstellung ribosomaler Proteine in unterschiedlichsten Geweben untersucht und entdeckt, dass verschiedene Krebsarten eine spezifische «Signatur» aufweisen. Wie die Forscher in «Genome Biology» berichten, eignet sich diese «Krebssignatur» auch zur Prognose des Krankheitsverlaufs.
Medienmitteilung Deutsch(external link)
Researchers uncover protein-based “cancer signature“
The team led by Prof. Mihaela Zavolan at the Biozentrum, University of Basel, has investigated the expression of ribosomal proteins in a wide range of human tissues including tumors, and discovered a cancer type specific “signature“. As the researchers report in “Genome Biology“, this “cancer signature” could potentially be used to predict the progression of the disease.
Press Release - English(external link)

Link to the Original Research Article (open access)(external link)
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The NCCR RNA & Disease awards 4 PhD fellowships to its associate members

Author: System Administrator - Published At: 2016-12-07 09:00 - (530 Reads)

Following a call for associate members to submit proposals for PhD projects that will be conducted in collaboration with NCCR member labs, the NCCR RNA & disease has selected the following 4 projects for funding:
  • Role of miRNAs in the regulation of human T cell activation and functions in multiple sclerosis in the lab of Silvia Monticelli (IRB Bellinzona) in collaboration with Jonathan Hall (ETHZ)
  • Structural basis for ribosome-mediated Alopecia-neurological defects-endocrinopathy in the lab of Vikram Panse (UZH) in collaboration with Frédéric Allain and Nenad Ban(both ETHZ)
  • Analysis of epigenetic and non-coding RNA pathways in prostate cancer in the lab of Raffaella Santoro (UZH) in collaboration with Constance Ciaudo (ETHZ)
  • Investigating the role of stress granules as an innate cellular antiviral defence mechanism in the lab of Volker Thiel (UniBE) in collaboration with Oliver Mühlemann (UniBE)
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News Article Contagion Website

Author: System Administrator - Published At: 2016-12-02 17:00 - (466 Reads)
Zika Virus in Breast Milk Inactivated by Pasteurization and Prolonged Storage

A recently published paper reporting how the Zika virus can be inactivated in breast milk has been featured in the news section of the Contagion website. In this news article Volker Thiel (last author of the study) comments on their recent findings.

Link to the News Article on the Contagion Website(external link)

Link to the Original Research Article in the Virus Research Journal (open access)(external link)
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New Insights into NMD

Author: System Administrator - Published At: 2016-11-29 15:25 - (509 Reads)


The Mühlemann lab of the University of Bern published a high-confidence set of endogenous transcripts that are targeted by nonsense-mediated mRNA decay (NMD) in HeLa cells. These NMD targets were identified by conducting a meta-analysis of transcript level changes under knockdown and rescue conditions of three NMD factors (UPF1, SMG6 and SMG7) followed by high throughput transcriptome sequencing at the NGS technology platform in Bern. This study revealed that the SMG6 and SMG7 degradation pathways are highly redundant regarding the RNAs they target. Moreover, it identified a substantial fraction of transcripts annotated as “non-coding” in the database as NMD substrates, indicating that in fact they are translated. The authors also confirmed that introns located more than 50 nucleotides downstream of the stop codon, upstream ORFs and long 3’ UTRs are features enriched among NMD targets.
Click here to read the article published in the RNA Journal (open access)(external link)
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The National Centers of Competence in Research (NCCR) are a research instrument of the Swiss National Science Foundation

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