Seminar Colour Guide:              
External Faculty Speaker
Wednesday, 10 February 2016, 11:00 Add to calendar Using recombineering to extend the power of CRISPR/Cas9 A. Francis Stewart, Technische Universität, Dresden, Germany Host: Vladimir Benes
ATC - Flex Labs A+B , EMBL Heidelberg
Seminar given by an external postdoc
Thursday, 11 February 2016, 11:00 Add to calendar In vivo mapping of the Mediator complex and implications for its role in transcription regulation Sebastian Gruenberg, Fred Hutchinson Cancer Research Center, USA Host: Lars Velten and Lars Steinmetz
Small Operon, EMBL Heidelberg
Abstract: A key step in regulation of protein encoding genes is the recruitment of coactivator complexes by gene-specific activators. Once recruited, coactivators facilitate transcription initiation by RNA polymerase II (Pol II) through recruitment of general transcription factors and rearrangement of chromatin at gene promoters. The coactivator complex Mediator is required for all cellular Pol II transcription and interfaces with both transcription activators and the basal transcription machinery.
Despite its central role in transcriptional initiation, the in vivo function of Mediator has remained controversial, due in large part to conflicting data about its genome-wide binding generated by ChIP-based methods. In my talk, I will present the development and use of chromatin endogenous cleavage and high-throughput sequencing (ChEC-seq), a method completely orthogonal to ChIP, to probe the in vivo binding of Mediator to the genome.

For ChEC, Mediator subunits Med8, Med17, and Med20 were fused to micrococcal nuclease (MNase) to target calcium-dependent cleavage to specific genomic loci in vivo, followed by high-throughput sequencing of natively cleaved DNA fragments. While Med20-MNase did not cleave DNA, Med8- and Med17-MNase showed appreciable levels of cleavage, allowing for high-resolution, background free, determination of Mediator binding sites genome wide

I will present yet unpublished data showing that Mediator preferentially associates with upstream activating sequences (UASs) rather than core promoters or, as previously proposed, in gene bodies. Our data show striking differences in transcription complex formation at promoters regulated by coactivators SAGA or TFIID. We also find evidence that Mediator binding might have broader implications for genome architecture and suggests a function for Mediator beyond its role as co-activator.
EMBL Distinguished Visitor Lecture
Monday, 15 February 2016, 11:00 Add to calendar Nutritional Regulatory Networks Marian Walhout, University of Massachusetts Medical School, USA Host: Anne-Claude Gavin
Large Operon, EMBL Heidelberg
Abstract: Gene regulation and metabolism lie at the heart of most biological processes. Both are accomplished by complex networks harboring hundreds of nodes and thousands of edges. We study these networks and the interactions between them mainly in the nematode C. elegans, because it is amenable to high-throughput, large-scale genetics and genomics. In addition, we study interspecies network interactions between C. elegans and bacteria, that may help illuminate interactions between mammalian intestinal cells and the gut microbiota.
EMBL Distinguished Visitor Lecture
Tuesday, 16 February 2016, 11:00 Add to calendar Three short stories about sex chromosomes Job Dekker, University of Massachusetts Medical School, USA Host: Yad Ghavi Helm, Aleksandra Pekowska
Large Operon, EMBL Heidelberg
Abstract: The 3D organization of the genome is critical for gene regulation. I will present three examples where sex chromosomes can serve as powerful models to study the folding of chromosomes in general, to identify cis-elements and proteins involved and to determine how chromosome organization and gene regulation are mechanistically linked.
Science and Society
Tuesday, 16 February 2016, 18:00 Add to calendar Meine Darmmikroben und ich: eine innige, aber verwundbare Beziehung Peer Bork, EMBL Heidelberg, Germany Host: Halldór Stefánsson
Print Media Academy
Abstract: Das menschliche Mikrobiom ist die Gesamtheit aller Mikroben, die in oder auf uns leben und somit den Menschen als Ökosystem fungieren lassen, in dem mehr bakterielle als menschliche Zellen zu finden sind. Die unsichtbare Vielfalt der Mikroben war der Forschung lange Zeit nicht zugänglich, kann aber seit kurzem durch massives Sequenzieren des Erbmaterials von Lebewesen (Metagenomik), z.B. in menschlichen Proben wie Hautabstrich oder Stuhl, abgeschätzt und analysiert werden.

Der prominenteste bakterielle Lebensraum im Menschen ist der Darm, mit durschschnittlich 1,5kg mikrobieller Biomasse, zu der über 1000 verschiedene bakterielle Spezies beitragen, welche wichtige Funkionen für uns übernehmen, aber in seltenen Fällen auch Krankheiten verursachen. Über Infektionen hinaus wurden Mikroben bislang mit mehr als 30 verschiedenen Krankheiten assoziiert und sind somit auch potentielle diagnostische Biomarker, wie ich am Beispiel von Darmkrebs illustrieren werde (Zeller et al. Mol. Sys. Biol., 2014). Während die Hoffnung besteht, dass Abweichungen von der Normalzusammensetzung der Bakterien im Krankheitsfall in aller Welt gleich sind, bleibt die Charakterisierung des Normalen schwierig. Wir fanden vor einigen Jahren heraus, dass in vielen Ländern drei bevorzugte Bakteriengemeinschaften vorherrschen (Enterotypen; Arumugam et al., Nature, 2011), unabhängig von Alter, Geschlecht, BMI oder Herkunft. Diese drei Enterotypen haben möglicherweise Einfluss auf Verdauungseigenschaften oder Medikamentenverträglichkeit. Obwohl die Grobzusammensetzung der Mikrobengemeinschaften in Enterotypen einteilbar ist, sind wir auf der Bakterienstammebene ganz individuell. Die meisten von uns besitzen z.B. das Darmbakterium E.coli, jeder hat jedoch ein paar individuelle Mutationen oder Bakteriengene (Schloissnig et al., Nature, 2013; Zhu et al., Genome Biol. 2015), die unsere Bakteriengemeinschaften individuell auf externe Einflüsse reagieren lassen. Einige Bakteriengene sind z. B. die Träger von Antibiotikaresistenzen und auch diese sind in ihrer Gesamtheit recht individuell und quantifizierbar, wobei es hier große regionale Unterschiede gibt.

Die Individualität unseres Darm-Mikrobioms kann man sich zunutze machen, um z.B. zu verfolgen, was bei erfolgreichen mikrobiellen Therapien wie der Stuhltransplantation eigentlich passiert und wie man dies für die Verbesserung der Behandlung einsetzen kann. Die Sensitivität der Metagenomik ist enorm man kann Bakterienstämme nachweisen, die einem die verspeiste Joghurtsorte verraten oder Pathogene, auch wenn keine Symptome vorhanden sind. Nahrungs- oder Medikamenteneinnahme verändern unsere Mikrobiota, die Forschung ist jedoch in vielen Bereichen erst am Anfang und oft weiß man noch nicht, welche Zusammensetzung gut oder schlecht für den Einzelnen ist und welche Konsequenzen Veränderungen nach sich ziehen. Trozdem ist bereits abzusehen, dass die Mikroben nicht nur für Diagnose und Therapie von Krankheiten nützlich sein werden, sondern dass unsere Symbiose mit den Bakterien durch zielgerichtete Veränderung mittels Diät oder Nahrungszusätze für Gesundheit und Wohlbefinden verbessert werden kann.
Seminar given by an external postdoc
Thursday, 3 March 2016, 14:15 Add to calendar To be announced Michaela Müller-McNicoll, Goethe University Frankfurt, Germany Host: Janosch Hennig
Small Operon, EMBL Heidelberg
Tags: Biocomputing, Structural Biology
EMBL Distinguished Visitor Lecture
Monday, 7 March 2016, 11:00 Add to calendar To be announced C. David Allis, Tri-Institutional Professor, Joy and Jack Fishman Professor, Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, USA Host: Predocs: Niccolo Arecco and Kyung-Min Noh
Large Operon, EMBL Heidelberg
External Faculty Speaker
Thursday, 10 March 2016, 11:00 Add to calendar Effects of histone core mutations on nucleosomal dynamics - studies by molecular dynamics modeling and single molecule fluorescence. Joerg Langowski, German Cancer Research Center (DKFZ), Biophysics of Macromolecules, Germany Host: Karin Sasaki/Stephanie Alexander
Small Operon, EMBL Heidelberg
Tags: Biophysics
Science and Society
Friday, 18 March 2016, 15:00 Add to calendar The infinite foetus: connecting person and placenta through time and space Julienne Rutherford, University of Illinois, Chicago, USA Host: Halldór Stefánsson
Large Operon, EMBL Heidelberg
Abstract: The foetus as a biological entity has labile boundaries. 1) It is an individual with its own genome, but that genome is the collaborative output of two other individuals, which in turn exponentialises into past generations. 2) The watery world in which it develops also has a temporal signature that reaches into the past and extends beyond gestation, through phenomena that conceptually coalesce within the Developmental Origins Paradigm. 3) The foetus as an entity does not exist without its placenta. While the placenta is an extrasomatic foetal organ it must be conceptually incorporated with the foetus as the biological bridge between generations. A biological view of the foetal experience that is restricted to the time and space of the foetus s body alone is inadequate to fully situate individuals, communities, and species within the intergenerational ecologies they create and inhabit. Framing the foetus as the fruit of previous generations and the seed from which future generations grow gives rise to a biology of life history that is Moëbian rather than linear. Data and impressions from Dr. Rutherford s work with marmoset monkeys, vervet monkeys, and humans will illuminate the themes discussed above.
External Faculty Speaker
Tuesday, 22 March 2016, 11:00 Add to calendar Modeling biological signaling with spatial and stochastic detail. Steve Andrews, Fred Hutchinson Cancer Research Centre, USA Host: Karin Sasaki
Small Operon, EMBL Heidelberg
Abstract: All biological cells sense their environment using cell signaling, in which chemicals bind to receptors, the receptors initiate a chain of events, and these events initiate cellular responses. Experimental biologists have mapped out many of these signaling pathways by now. However, the reason for the pathway designs, and how well they actually function, are largely open questions. I am pursuing these topics using computational modeling. In particular, I developed software for simulating the reaction and diffusion dynamics of tens of thousands of individual biomolecules (the Smoldyn program, which is widely used, and which I will also present a course on). I also quantified information transfer in yeast cell signaling using experimental data. I found that yeast signaling, and likely others, is much more precise than previously believed. Tags: Cell Biology
External Faculty Speaker
Thursday, 24 March 2016, 11:00 Add to calendar Proteostasis network analysis and its capacity in amyloid remodeling Janine Kirstein, Leibniz Institute for Molecular Pharmacology, Berlin, Germany Host: Nassos Typas
Small Operon, EMBL Heidelberg
EMBL Distinguished Visitor Lecture
Thursday, 14 April 2016, 11:00 Add to calendar To be announced Erika L. Pearce, Max Planck Institute of Immunobiology and Epigenetics, Germany Host: Matthias Hentze
Large Operon, EMBL Heidelberg
External Faculty Speaker
Monday, 2 May 2016, 11:00 Add to calendar To be announced Claire Wyart, Institut du Cerveau et de la Moelle Épinière, , France Host: Yannick Schwab
Small Operon, EMBL Heidelberg
Tags: Cell Biology
Science and Society
Wednesday, 4 May 2016, 15:00 Add to calendar Experiments in democracy: why should we care about public engagement in science? James Wilsdon, Sheffield University, United Kingdom Host: Halldór Stefánsson
Large Operon, EMBL Heidelberg
EMBL Distinguished Visitor Lecture
Thursday, 2 June 2016, 11:00 Add to calendar To be announced Timothy J. Mitchison, Harvard University, USA Host: François Nédélec
Large Operon, EMBL Heidelberg
External Faculty Speaker
Thursday, 22 September 2016, 11:00 Add to calendar To be announced Dolf Weijers, Wageningen University, Netherlands Host: Marcus Heisler
Small Operon, EMBL Heidelberg
External Faculty Speaker
Tuesday, 18 October 2016, 11:00 Add to calendar To be announced Cayetano Gonzalez, Barcelona Institute for Science and Technology, Spain Host: Anne Ephrussi
Small Operon, EMBL Heidelberg