Seminar Series CompuGene – ARCHIVE
All guests are very welcome!
April 20, 2018 – Bio Campus B1-01|052 (12:30 p.m.)
Prof. Dr. Barbara Di Ventura (Univ. Freiburg)
“Cells in the spotlight”
May 23, 2018 – B2|03-109 (4 p.m.)
Dr. Dora Tang (MPI Dresden)
Prof. Yolanda Schaerli (Lausanne)
Dr. Dora Tang (MPI Dresden),
Dynamic Protocellular systems
Biology is well equipped in exploiting a large number of out of equilibrium processes to support life. A complete understanding of these mechanisms is still in its infancy due to the complexity and number of the individual components involved in the reactions. However, a bottom up approach allows us to replicate key biological processes using a small number of basic building blocks. This methodology has the added advantage that properties and characteristics of the artificial cell can be readily tuned and adapted. Working between biophysics, materials science and synthetic biology we reimagine and translate the physical phenemona which drive out of equilibrium processes in cells into novel, robust and dynamic systems for synthetic biology applications.
A key property of the cell is its ability to compartmentalize chemical reactions. This allows the cell to control different chemical and physical environments, utilize the membrane as a reaction surface and protect enzymes and proteins from degradation. Membrane delineated compartments based on lipids have been extensively used to fulfill this criteria, however they lack an internal heterogeneity that is characteristic of natural cells. Therefore, membrane free droplets based on coacervation or liquid-liquid phase separation have not only been associated with mechanisms within the natural cell but have offered an alternative model to compartmentalization.
We use a range of techniques to understand the chemical and physical processes which drive molecular organization in lipids, polymers and proteins to rationally control self-assembly for the construction of novel proto-cellular platforms. This methodology is applied to protein-lipid and protein-polymer interactions as well as in-vitro compartmentalized transcription-translation processes which enables us to activate our compartments in a highly controlled manner. In addition, understanding these interactions can give insights to key questions in the origin of life i.e. what were the conditions required to drive molecular organization from disorder? and how did a biological world derive from chemistry?
Methodological and technical expertise:
- Artificial cell synthesis (coacervates, lipid vesicles, hybrid protocells)
- High pressure SAXS and CD for soft matter
- Cell free expression
- Analytical techniques (spectroscopy, DLS, DSC, ITC)
- Lipid Membrane curvature (inverse bicontinuous cubic phases)
Prof. Yolanda Schaerli (Lausanne)
Synthetic gene regulatory networks for pattern formation
During embryonic development, cells acquire different identities, depending on their spatial positions. This developmental process is called pattern formation. The molecular details of pattern formation are complicated, but are thought to be governed by general principles such as the use of morphogen gradients to provide positional information. We build, study and model synthetic gene regulatory networks to improve our understanding of such general principles.
Evolution of gene regulatory networks
What constrains the evolution of gene regulatory networks? What makes a gene regulatory network robust to mutations and/or evolvable? How does the regulatory mechanism of a network influence its evolution? How can gene regulatory networks change extensively, while maintaining overall circuit output? How do mutations in gene regulatory networks interact to produce novel phenotypes? What happens after a gene has been duplicated?
Robustness, cryptic genetic variation and innovation in transcription factor binding
In collaboration with Prof. Payne, ETH Zurich and Prof. Wagner, University of Zurich.
Mutational robustness is a striking and widespread property of biological systems. One consequence of this robustness is that genetic diversity may accumulate in transcription factor binding sites. Such diversity is often referred to as cryptic because it does not manifest as phenotypic diversity unless an environmental or genetic perturbation disrupts the function of the cognate transcription factor. What is the mutational robustness of transcriptional binding sites? How is cryptic genetic diversity accumulated? Does cryptic genetic variation in transcription factor binding sites facilitate evolutionary innovation?
We are using a synthetic gene regulatory circuit in E. coli, molecular evolution experiments and computational modelling to address these questions.
March 7, 2018 – Bio Campus (4 p.m.)
Prof. Eckhard Boles (Frankfurt),
Boles Group (Frankfurt)
The classical human interest into yeasts, lower unicellular eukaryotes, stems from their well-known role in the preparation of wine, beer, and bread. In the last decades attention has focused on some additional functions for yeasts as well as scientific model organisms but also in their use for industrial or medical purposes. Today, yeasts cells are not only indispensable for fundamental research but belong to the most important organisms in industrial biotechnology. The Boles group is using yeasts to study general metabolic and regulatory processes, and is developing technologies to improve the applications of yeasts in biotechnology.
Butanol and aromatic compounds
- Short-chain fatty acids, higher alcohols and polyketides
- C5-Technology: Fermentation of pentose sugars with recombinant yeasts
- Sugar uptake and human glucose transporters
- Synthetic organelles and compartmentalization
Prof. Uwe Bornscheuer (Greifswald),
Bornscheuer Group (Greifswald)
Overview of research activities:
Access to biocatalysts
- Identification of new biocatalysts by screening, e.g. from strain collections
- In silico discovery of novel enzymes
- Cloning and functional expression in suitable microbial hosts
- Creation of tailor-made enzymes using directed (molecular) evolution and rational protein design
- Commercial enzymes
- Development of High-Throughput-Systems for directed evolution
- Development & application of bioinformatic tools
- Cloning, expression, purification, characterization of enzymes
- Chemical syntheses
- Chiral analysis (e.g. via gas chromatography or HPLC)
- Process development (e.g. continuous enzymatic synthesis)
- Baeyer-Villiger Monooxygenases
- Synthesis of optically pure compounds, e.g. for pharmaceutical applications
- Modification of fats and oils, e.g. structured triglycerides
- Synthesis of detergents, e.g. sugar esters
Febuary 7, 2017 – B1|01-052 (4 p.m.)
Prof. Sheref Mansy
Protometabolism and artificial cells to probe prebiotic chemistry and synthetic biology
Iron-sulfur clusters are among the most ancient biological cofactors and are involved in a wide variety of functions in living cells. Despite the central role that iron-sulfur clusters play in metabolism, it has remained unclear if the prebiotic chemistry that led to life was shaped by the activity of iron-sulfur catalysts. We find that model prebiotic, redox active iron-sulfur peptides form easily in a manner that is facilitated by UV light and propose a path from small iron-sulfur peptides to ferredoxin-like sequences. The data are most consistent with prebiotic surface exposed, pond or hot spring environments. Our efforts in building artificial cells from component parts will also be presented. Here, artificial cells simply refer to liposomes with encapsulated DNA and transcription-translation machinery that are able to mimic some of the features of cellular life. Since natural living systems live in communities, we built artificial cells that are capable of chemical communication and used these artificial cells to integrate with and control the behavior of bacteria. Similar artificial cells may be used to probe the chemistry that supports cellular life and may serve as a foundation for new life-like technologies.
Prof. Francois Kepes (Paris),
Member of the National Academy of Technologies of France
Analytic and synthetic genomics
The solenoidal framework developed by the speaker since 2003 posits a threefold relation between the relative genomic positioning of co-functional genes, their expression, and the 3-D folding of the chromosome in the cell space. The evidences for, and the consequences of, this framework will be discussed from the fundamental and applied viewpoints.
February 8th, 2018 – Bio Campus (B2|61-201 12:30 p.m.)
Dr. Zascha Weinberg
Computational discovery of novel classes of bacterial non-coding RNAs
The discovery of new classes of non-coding RNAs (ncRNAs) can reveal information about the biological processes that involve these ncRNAs as well as yielding general insights into RNA biochemistry and gene regulation. Riboswitch RNAs directly sense a metabolite and regulate genes accordingly. We devised a strategy to find riboswitches that have evolved specificity to a new metabolite ligand. Such specificity changes are well known in proteins, but only a few examples are known in RNA. I will also describe a more general search strategy for novel structured ncRNAs on a multi-genome/metagenome scale. This search revealed 224 novel ncRNAs of various types. I will also show computational predictions that have been experimentally confirmed.
January 17, 2018 – B1|01 – 052 (“kleiner Hörsaal”) (5 p.m.)
Medical Sciences Division, Radcliffe Department of Medicine, Oxford
Abstract: Inflammation is driven by the chemokine network, which is a validated therapeutic target. Traditional anti-chemokine therapies that target single chemokines or receptors fail in treating inflammation, as diseased tissue typically expresses multiple chemokines that interact polyvalently with their receptors, making the chemokine network highly robust to attack. Evolution and natural selection for over 250 million years has resulted in the creation of a diverse arsenal of anti-inflammatory salivary peptides in tick saliva. One class of small peptides in tick saliva suppress chemokine-driven inflammation by acting as “ligand traps” – binding and neutralizing multiple chemokines, and are called evasins. These peptides combat inflammation at the site of tick bite and enable them to suck blood for days to weeks. We have developed a biotechnology platform – Bug-to-Drug – that uses yeast surface display of tick peptides. This has allowed us to efficiently mine tick salivary transcriptomes for evasin-like peptide molecules that bind chemokines. We have identified 12 novel CC and 30 novel CXC-binding evasins that are potent inhibitors of chemokine signaling, and are working to develop them as therapeutics for inflammatory disease.
Further information on: Prof. Dr. Shoumo Bhattacharya:
Shoumo Bhattacharya is Professor of Cardiovascular Medicine in the RDM Division of Cardiovascular Medicine at the University of Oxford and is based at the Wellcome Trust Centre for Human Genetics. He read medicine at the All India Institute of Medical Sciences in New Delhi, and trained in cardiology at Northwick Park and Hammersmith Hospitals in London, where he was also a MRC Training Fellow with James Scott working on RNA editing. He followed this with BHF and NIH Fellowships at the Dana-Farber Cancer Institute with David Livingston working on transcription factor protein interactions. He was a Wellcome Trust Senior Fellow at Oxford from 1998 to 2008, working on the transcriptional control of heart development, and their role in left-right patterning. He was elected Fellow of the Royal College of Physicians in 2003, awarded the Graham Bull Prize from the Royal College of Physicians in 2005, elected Fellow of the Academy of Medical Sciences in 2006. He was awarded a BHF Chair in 2009, and elected to a statutory Professorship at the University of Oxford in 2010. His primary role as BHF Chair has been the development of novel therapeutics and targets. The major focus of his lab is now the development of anti-inflammatory peptide therapeutics isolated from tick saliva that may have applications to myocarditis, post-myocardial infarction injury and myocardial fibrosis.
December 6, 2017 – B1|01 – 052 (4 p.m.)
Prof. Dr. Andreas Möglich,
Faculty of Biology, Chemistry & Earth Sciences,
“Controlling Nucleic Acids by Light”
Sensory photoreceptors mediate sensation of incident light and enable diverse organisms to derive spatial and temporal environmental cues for vital adaptations of physiology, behavior and lifestyle. Sensory photoreceptors excel in the reversibility, noninvasiveness and spatiotemporal precision of the responses they elicit. For precisely these reasons, sensory photoreceptors have found frequent use as genetically encoded, light-gated actuators in optogenetics, that is, the control by light of cellular events. Within an analytic, top-down branch, the Möglich lab focuses on elucidating the structural, mechanistic and functional bases that underpin the action of sensory photoreceptors. In a synthetic, bottom-up branch, they seek to engineer novel photoreceptors with custom-tailored light-regulated function: on the one hand, engineered photoreceptors broaden the scope of optogenetics, and on the other hand, they provide a crucial touchstone for the mechanistic understanding of signal transduction processes.
Research Projects include: Light-regulated Histidine Kinases – Engineering, Light-regulated Histidine Kinases – Structure & Mechanism, Regulating Transcription and DNA Cleavage by Light, Mechanism of Light-Oxygen-Voltage Receptors, Optogenetic Control of Cyclic-Nucleotide Signaling
December 6, 2017 – B1|01 – 052 (5 p.m.)
PD Dr. phil. Joachim Boldt,
Institut für Ethik und Geschichte der Medizin,
“Ethik und Philosophie in der Synthetischen Biologie “
CV: from 1991 to 1997, Dr. Joachim Boldt read philosophy and German language and literature in Heidelberg, Sheffield and Berlin. He obtained his PhD on Kierkegaard in 2005 at the Humboldt-Univ. In Berlin. Since the end of 2005 he works at the Institut für Ethik and Geschichte der Medizin in Freiburg
His research interests are: Ethics in synthetic biology, ethics questions in the field of technological improvements of human abilities, advice on ethics and clinical ethics, vulnerability as key term in medical and philosophical ethics.
November 8, 2017 – B2|03 – 109 (4 p.m.)
Dr. Rodrigo Lesdema Amaro
Imperial College London, UK
„Multilevel strain engineering in Yarrowia lipolytica for the production of fuels and chemicals”
o Synthetic Biology: The group is interested in using and developing new synthetic biology tools that allow us to precisely manipulate microbial cells in a reliable, predictable and standardized way. In particular, we are interested in those cutting edge techniques that permit a fine tuning of metabolic pathways.
o Metabolic Engineering: The manipulation and optimization of microbial metabolic pathways are the keys for biotechnology and a bio-based economy. The research group is highly interested in hacking metabolism using synthetic biology tools to create new properties and enhanced behaviors in microbial cells. The engineering strategies are not only designed to produce new high-value products or higher amount of pre-existing products but also to facilitate the downstream and upstream parts of the bioprocesses.
o Microbial biotechnology and Microbial communities: Microorganisms are important for both industrial bioprocesses and biomedicine (i.e. gut or skin microbiota). The lab is interesting in a wide array of organisms, from yeast (S. cerevisiea and Y. lipolytica), fungus (A. gossypii) and bacteria (E.coli and Acetobacter) to complex microbial consortia (human and industrial microbiota).
o Applications in Industrial biotechnology and biomedicine: As a summary the lab is interested in applying the engineered microorganisms using synthetic biology to the production of 1) high-value chemicals and fuels (biodiesel, lipid-derived compounds, food additives, etc) 2) biomaterials for biomedicine and environmental applications (bacterial cellulose) and 3) understanding microbiome and dysbiosis leading to diseases (skin microbiome, wound healing).
November 8, 2017 – B2|03 – 109 (5 p.m.)
Dr. Geoff Baldwin
Imperial College London, UK
“An integrated workflow for synthetic biology: from parts to systems and the evolution of new function”.
Research work in the Baldwin lab focuses on the development of synthetic biology approaches to facilitate the engineering of new biological systems for real-world applications. To this end we have developed foundational tools, like our BASIC DNA assembly method, that transform our ability to rapidly prototype new biological designs. We are also developing enhanced methods for accurate metrology to better understand and model the relationship between input design and phenotypic response. These fundamental developments are being applied across a broad range of projects that address gene circuit design; RNA feedback control; in vivo directed evolution for the generation of new protein specificity and functionality; engineering protein nanocages as vectors for targeted drug delivery.”
October 26, 2017 – B2|61 – 102 (5 p.m.)
Prof. Robert Murphy
Carnegie Mellon University, USA
„Learning the Assembly Instructions of a Cell”
Prof. Dr. Robert Murphy studied biochemistry at Columbia Univ, New York, and received his PhD in 1980 from the California Institute of Technology. He is now the Ray and Stephanie Lane Professor of Computational Biology and Professor of Biologica Sciences Biomedical Engineering and Machine Learning at the Carnegie Mellon Univ., Pennsylvania. He is also honorary professor of biology in Freiburg as well as a external senior fellow at the Freiburg Institute of Advanced Studies. He is on the editorial board of several journals and served on a number of advisory panels, to name just few of his scientific activities during his career.
Prof. Murphy’s research interests include
- Interpretation of Protein Location Patterns from Fluorescence Microscope Images
- Endosomal pH Regulation in Erythroid and Non-Erythroid Cells
- Interpretation of Protein Location Patterns from Fluorescence Microscopy
- Endosomal pH Regulation in Erythroid and Non-Erythroid Cells
- Genes required for Receptor Recycling after Endocytosis
October 25, 2017 – B1|01 – 52 (5 p.m.)
Prof. Ivo Große
Institut für Informatik,
Prof. Dr. Ivo Große (*1969, Berlin) studied physics and biophysics at the Humboldt-Univ. in Berlin („Diplom“ 1995) and did his PhD at Boston Univ. (1999). He worked as a postdoc in the field of gene recognition and promotor recognition at the Institute for Molecular Biology and Biochemistry at the Freie Univ. Berlin (1999–2000) and at the Cold Spring Harbour Laboratory (2001–2002) as well as a group leader in the area of data integration and the analysis of marker, sequence, expression, chromatin-IP and metabolomdata at the IPK Gatersleben (2003-2007). He has been teaching bioinformatics at the Institute of Computer Sciences at the Martin-Luther-Univ. Halle-Wittenberg since 2003. Sicne 2007 he is professor for bioinformatics at the Institute of Computer Sciences in Halle.
September 6, 2017 – B1|01 – 52 (5 p.m.)
Dr. Thomas E. Gorochowski,
BrisSynBio Synthetic Biology Research Centre,
University of Bristol, UK
„Using sequencing to scale-up the design of synthetic genetic circuits”
Synthetic genetic circuits are composed of many interconnected parts that must function together in concert to implement desired biological computations. Unfortunately, genetic parts often display unexpected changes in their performance due to contextual effects within a design or unintended interactions with the host cell. In this talk, I will demonstrate how we have been using sequencing technologies and mathematical modelling to tackle this problem. I will show how RNA-sequencing can be used to reveal the inner workings of large genetic circuits to understand why some designs fail, and show how DNA-sequencing can support the rapid exploration of billions of different genetic circuits to better understand critical design features. Such capabilities provide a more complete view of inner workings of genetic circuits as they function and will help improve our understanding of the rules governing the effective construction of larger and more complex biological systems.
July 26, 2017 – B1|01 – 52 (4 p.m.)
iGEM-Team TU Darmstadt
“iGEM 2017: engineering of E.coli for synthesis of ´designed´chitosan oligomers useful in medical applications”
July 26, 2017 – B1|01 – 52 (5 p.m.)
Prof. Bruno Moerschbacher,
Institut für Biologie und Biotechnologie der Pflanzen
Universität Münster, Germany
“Biotechnological production of third generation chitosans”
June 29, 2017 – B1|01 – 52 at 12:30
Priv.-Doz. FH-Prof. Dr. Michael Sauer
University of Natural Resources and Life Sciences
“Synthetic and diverse – microbiology on duty in industry”
In our societies quest to mitigate greenhouse gas emissions and petroleum use, industrial microbiology plays a key-role for the provision of processes for fuel and chemical production from renewable resources. Clearly, the microorganism is in the center of the process and care should be taken for its choice. Industrial production conditions are generally very harsh for the microorganism. Nevertheless, the host cells should be very efficient, which opens a vast area of conflict for the industrial microbiologist. Synthetic biology and metabolic engineering provide optimal tools for the rational design of biocatalysts. However, biodiversity is a major resource which should be tapped first. Nature solved many problems, which we face in industrial context – be it natural stress resistance or efficiency of metabolic pathways. However, all too often the rich source of natural diversity is neglected in favor of “pet” or model organisms. I propose that the fastest and most reliable path to efficient and economically viable microbial production processes uses both – natural diversity and synthetic biology. This concept shall be exemplified with bacterial and yeast host systems for the production of 1,3-propanediol, or sugar alcohols, respectively.
June 7, 2017 – B1|01 – 102 (4 p.m.)
Dr. Kathrin Messerschmidt, Universität Potsdam
Orthogonal, light-inducible protein expression platform in yeast Sacchararomyces cerevisiae
The project Cell2Fab (from cells to fabrication) aims at the generation of a novel cellular regulation system on the basis of circular yeast chromosomes (xYAC) thereby facilitating highly regulated production of small to large cohorts of proteins and peptides in the yeast Saccharomyces cerevisiae. Successfully generated xYACs will enable us to access new areas of synthetic biosystems as for example: production of complex protein machines consisting of several subunits like naturally occurring multi-protein complexes of technical interest, production of entirely novel complexes with technical application areas and metabolic engineering.
Our protein expression system consists of different parts. First part is the AssemblX cloning system that allows easy and fast cloning of multiple protein expression cassettes, artificial operons, and regulatory systems. Second part is a regulation system composed of artificial transcription factors and their corresponding promoters. Furthermore, we establish regulation systems that allow the light-inducible protein expression.Overall, our system is designed as an open and flexible platform that allows customer-oriented adjustments to ensure fast and adequate adaptation to the needs of future users.
June 7, 2017 – B1|01 – 102 (5 p.m.)
Dr. Vahid Shahrezaei, Imperial College London
Cell size and growth rate regulation of stochastic gene expression
Cells adopt their physiology globally in response to different growth conditions. This includes changes in cell division rate, cell size, and also in gene expression. These global physiological changes are expected to affect noise in gene expression in addition to average expression. Gene expression is inherently stochastic and the amount of noise in proteins depend on parameters of gene expression and cell division cycle. Here we use models of stochastic gene expression inside growing and dividing cells to study the effect of cell division rate and cell size on noise in gene expression. In the first part of my talk, I will talk about modelling work inspired by E Coli data on global regulation with division rate. In the second part of the talk, I discuss how the single moleucle RNA Fish data can be used to infer specific form of global regulation of gene expression by cell size in fission yeast.
The work I will talk about is not published by this recent review gives a good overview of the topic: http://www.sciencedirect.com/science/article/pii/S1369527415000636
May 3, 2017 – B1|01 – 102 (5 p.m.)
Dr. Patrick Cai, University of Edinburgh, UK
March 29, 2017 – B2/03, 109 (5 p.m.)
Prof. Gábor Balázsi, Stony Brook University, NY (USA)
„Gene expression control for biology and medicine”
March 8, 2017 – B2/03, 109
Philosophy Winter School
4:00 p.m. Andrea Loettgers
5:00 p.m. Andreas Kaminski / Colin Glass
6:30 p.m. Dinner
March 1, 2017 – B1/01, 52 (5 p.m.)
Dr. Stefan Kubick, Fraunhofer-Institut für Zelltherapie und Immunologie IZI, Potsdam
„Cell-free Bioproduction: Engineering Proteins for Therapy, Diagnostics and Biotechnological Applications”
February 1, 2017 – B2/03, 109 (5 p.m.)
Prof. Peter Swain, University of Edinburgh
“Multiple input pathways improve perception in a MAP kinase signalling network”
December 7th, 2016 – B1/01, 52
Prof. Anke Becker, LOEWE-Zentrum für Synthetische Mikrobiologie, Marburg
Cancelled – a new date will be announced soon
November 2nd, 2016 – B1/01, 52 (5 p.m.)
Dr. Gabriele Gramelsberger, TU Darmstadt/FU Berlin
„Temporale Regime der Synthetischen Biologie”
October 12th, 2016 – B1/01, 52
Prof. Victor Sourjik, Max Planck Institute for Terrestrial Microbiology & LOEWE Center for Synthetic Microbiology (SYNMIKRO) (4 p.m.)
“Understanding and engineering signaling specificity of bacterial chemoreceptors.”
Prof. Thorsten Mascher, TU Dresden (5 p.m.)
“Bacillus subtilis as a SynBio host: from whole cell bio-sensors to orthogonal genetic switches“
July 6th, 2016- B1/01, 52 “kleiner Hörsaal”
Dr. Guy-Bart Stan, Imperial College London (4 p.m.)
„Designing smarter synthetic biology systems: de novo biomolecular feedback and shared resources considerations for engineered bacterial cells”
Dr. Chris Barnes, University College London (5 p.m.)
“Designing robust gene circuits using sequential Monte Carlo”
June 16th, 2016 – B2/16, 102 (5 p.m.)
Prof. Kobi Benenson, ETH Zürich, Switzerland
“Biological computing – from concepts to applications”
June 1st, 2016- B1/01, 52
Dr. Diego Oyarzún, Biomathematical Sciences, Dept of Mathematics, Imperial College London, UK (4 p.m.)
“Gene circuits for self-tuning metabolic pathways”
Prof. Paul Freemont, Imperial College London , UK (5 p.m.)
„Using cell free systems for prototyping synthetic biology designs”
May 11th, 2016- B1/01, 52
Prof. Dr. Sebastian Maerkl, École polytechnique fédéral de Lausanne (4 p.m.)
“Cell-Free Synthetic Biology”
Prof. Friedrich Simmel, Technische Universität München, Germany (5 p.m.)
„Communication and computation in engineered cell-free and bacterial systems”
April 6th, 2016 – B1/01, 52
Dr. Christoph Zechner, ETH Zurich (4 p.m.)
Molecular circuits for dynamic noise filtering
Prof. Wilfried Weber, Albert-Ludwigs-Universität Freiburg (5 p.m.)
Designing interactive Cells and Materials
March 16th, 2016- B1/01, 52
Dr. Mark Isalan, Imperial College London (4 p.m.)
„Gene circuits for engineering synthetic developmental patterns: how many ways can you make a stripe?”
Dr. Tom Ellis, Imperial College London (5 p.m.)
“Balancing biology with engineering to produce molecules and materials”