Day 1 :
University Stuttgart, Germany
Keynote: Design of synthetic epigenetic circuits exhibiting positive feedback, memory effects and reversible switching
Time : 10:00-10:45
Albert Jeltsch finished his PhD on Restriction Endonucleases at University Hannover in 1994. Afterwards, he started working on DNA Methyltransferases at Justus-Liebig University Giessen and at the Jacobs University Bremen. Since 2011, he is a Professor of Biochemistry at the University Stuttgart. He is the recipient of the Gerhard-Hess award (DFG) and BioFuture award (BMBF). He has long standing expertise in the biochemical study of DNA and protein methyltransferases, methyl lysine reading domains and in rational and evolutionary protein design. His work has been published in >200 publications in peer reviewed journals and is in the editorial boards of several journals.
We report here the design and experimental validation of synthetic epigenetic memory systems which store information in form of DNA methylation patterns in live bacteria. Key components are a DNA methylation sensitive engineered zinc finger protein controlling a memory operon comprising the CcrM methyltransferase gene and a reporter gene. In the off-state, the memory operon is repressed by the zinc finger protein. It can be triggered by heat, nutrients, UV irradiation or DNA damaging compounds which induce DNA methylation by CcrM. In the induced on-state, methylation marks set in the operator region of the memory operon permanently activate the memory system even after cessation of the trigger signal (positive feedback). Inclusion of a protein degradation tag allowed to establish a reversible switching system. Epigenetic memory switches represent a novel application in synthetic biology with numerous potential applications, for example to set up life biosensors for long term observation of environmental sites for pollution, to ensure cooling chains, as a death switch in containment systems for GMOs, or as cost efficient induction switch in industrial protein production. The large variety of DNA-(adenine-N6)-MTases potentially allows for massive multiplexing of signal storage and potential logical operations depending on more than one input signal.
Institute of Biophysics of CAS, Czech Republic
Time : 10:45-11:30
Martin Falk has completed his PhD from Masaryk University in Brno, CR. He is the Head of the Department of Cell Biology and Radiobiology at the Institute of Biophysics of the Czech Academy of Sciences (Brno, CR). He has authored about 40 papers and book chapters that concern the role of chromatin structure in regulation of cellular processes and biological effects of different types of ionizing radiation. Current research interests include DNA damage and repair, carcinogenesis, tumor cells radio-sensitization, and radiobiology.
Many tumors are resistant to current radiotherapy while ion beam cancer therapy (IBCT) and metal nanoparticles may allow for partial overcoming of this problem. Accelerated ions provide superior therapeutic results over gamma-rays since they are able of inducing complex DNA damages that can be repaired only with difficulty by tumor cells; accelerated ions can also be better focused to the tumor due to energy deposition characteristics (Bragg peak). Selective targeting of radiation effects to tumors can further be improved by metal nanoparticles, such as gadolinium, gold, or platinum nanoparticles studied in our work. These nanoparticles are preferentially internalized by tumor cells and have been recognized to locally amplify the radiation dose upon irradiation. Hence, nanoparticles delivered in tumor cells might increase tumor-specificity and efficiency of radiotherapy at the same time. Importantly, though physical mechanisms related to radiation dose amplification by nanoparticles have been already well described, cellular structures targeted by nanoparticles remain unknown. In this work, we will first discuss biological effects of different kinds of ionizing radiations on normal and tumor cells. Consequently we are going to present quite surprising results on a possible mechanism of nanoparticles-mediated radiosensitization: Under the conditions where 2 nm gadolinium nanoparticles amplify the radiation effects, they remain localized in the cytoplasm and their influence on DSB induction and repair is not significant. This suggests that the radiosensitization mediated by gadolinium and potentially (some) other nanoparticles (of defined parameters) are a cytoplasmic event that is independent of the nuclear DNA breakage, commonly accepted as the main cause of radiation-induced cell killing. Based on recognized intracellular localization of nanoparticles studied, we hypothesize about possible non-DNA targets for (some) nanoparticles.
- Presentation on Takara Bio Europe
Location: Forum 12
Takara Bio Europe, France
Title: Next-gen cloning and purification technologies to rapidly generate synthetic genes and proteins
Time : 11:45-12:15
Malathi Raman has been the European Cloning & Protein Product Manager at Takara Bio Europe since 2011, and manages Takara’s entire Cloning and Protein product range including the innovative In-Fusion® HD Cloning and Capturem™ Protein and Antibody Purification technologies. Prior to joining Takara, she worked as a Post-Doctoral Research Fellow for 3 years, within the group of Professor Terry Rabbitts, at the LIMM in Leeds, United Kingdom, identifying novel protein-protein interactions involved in the pathogenesis of prostate cancer and Ewing’s sarcoma. She obtained her PhD in Cardiac Genetics from Imperial College London, United Kingdom, in 2008.
There is a constant need for faster and more efficient cloning and protein purification methods at all scales within the Synthetic Biology field. Scientists can accelerate the generation of synthetic gene expression constructs using our innovative Next-Gen In-Fusion® HD Cloning Plus technology which is fast (15 mins), highly efficient (>95% cloning efficiency), sequence independent (any insert can be cloned into any vector at any locus), seamless (no extra bp), directional, and HTP ready. After generation of the required expression construct and downstream expression of the target protein, Takara offers Next-Gen Capturem™ technology to allow fast (5-15 mins) and easy resin free purification of high quality and concentrated His-tagged proteins or native untagged antibodies. Our revolutionary Capturem technology, available in miniprep, maxiprep and 96-well plate formats, consists of spin columns or plates containing high-capacity nylon membranes immobilized with either Ni2+ or Protein A, thus allowing His-tagged protein or antibody purification directly from even complex matrices, such as cell supernatants or serum, within minutes. This talk will review several applications of our technologies including HTP antibody cloning, simplified purification of membrane and secreted proteins, fast hybridoma screening, and rapid immunoprecipitation (IP)/co-immunoprecipitation (Co-IP). We will also introduce our new Capturem Trypsin technology that enables 1 min on-column tryptic digests.
- Cellular Systems Biology | Next Generation Sequencing | Plant Synthetic Biology| Synthetic Chemistry| Protein Engineering| Synthetic Genomics| Gene synthesis| Synthetic Gene Networks
Location: Forum 12
Coventry University, UK
Title: Exploring unique compounds from lignin degradation using MnSOD and DyP-type peroxidase enzymes
Time : 12:15-12:45
Sharon Mendel Williams joined Coventry University as a Lecturer in the School of Life Sciences in the year 2014. She has worked as a Post-doctoral Research Fellow in both departments of Chemistry and Biology, Warwick University. He research focuses on biophysics and biochemistry of proteins, and understanding the mechanisms of enzymes. She has a wide range of experience in molecular biology, biochemistry, and chemistry. She is a member of the Royal Society of Chemistry and has been awarded a grant from the RSC research fund to accomplish her research work.
Lignin is an organic polymer found in the cell walls of plants. Lignin can be used to create biofuels, or as an organic hydrocarbon source for a large variety of chemicals and polymers. However, lignin is very robust and current industrial processes for using it are inefficient. Therefore, a useable biological process for degrading lignin would be of great benefit. Understanding the pathway of lignin degradation, and the byproducts, is essential in order to be able to exploit the use of micro-organisms. Furthermore, we can characterize novel bio-products obtained by enzymatic oxidation of lignin, which could have very interesting applications for industrial biotechnology. In the current project DyP-type peroxidases from Gram-negative Pseudomonas fluorescens Pf-5 and recombinant Sphingobacterium MnSOD1 and MnSOD2 cloned into E. coli and were investigated. These are bacterial enzymes that are already known to degrade lignin. Different genetic mutations were introduced, and the resulting enzymes were characterized by using them with different lignin substrates. The reaction compounds were analyzed by reverse phase HPLC/GC-MS. The goal is to improve the effectiveness of the enzymes, increase the production of the enzymes and degrade the lignin into different and more useable compounds. Any of these goals would be of valuable scientific and commercial benefit.
Institute of Biophysics, Czech Republic
Title: Relationship between chromatin structure and chromosomal rearrangements in myelodysplastic syndromes
Time : 12:45-13:15
Dr. Iva Falk, PhD. has completed her Ph.D in the field of Medical Technologies. She is working in the Department of Cell Biology and Radiobiology at the Institute of Biophysics of the Czech Academy of Sciences (Brno, CR). She is participating in research that concerns the role of chromatin structure in regulation of cellular processes. Other research interests include DNA damage and repair, carcinogenesis, tumor cells radio-sensitization, and radiobiology.
MDS is heterogeneous group of clonal hematologic disorders characterized by inefficient hematopoiesis. The incidence of MDS is about 4 cases per 100 000 people. The most typical cytogenetic abnormality arising due to still unknown cause and mediated by still unknown mechanism, is a partial or complete deletion of 5q. To address these questions, we isolated lymphocytes and CD34+ hematopoietic cells from healthy donors and MDS patients. By combining 3D-fluorescence in situ hybridization with BAC probes and high-resolution confocal microscopy, we reconstructed higher-order nuclear organization of the CDR (common deleted region) between bands 5q31 and 5q32. Radial and mutual positions of BAC probes, specific for individual chromosomal bands inside the CDR were determined and suggest that higher-order chromatin structure significantly contributes to formation of 5q deletions associated with MDS. Chromatin in the CDR region forms a giant loop that is, by its base, anchored to the nuclear envelope. Though the initial event and the mechanism of the loop base fragmentation has to be further studied, we suppose that close spatial proximity of loci at the loop base, stabilized by anchoring of these loci to the envelope, could simplify deletions of the whole CDR loop.
KOC University, Turkey
Time : 14:15-14:45
Yaman Arkun research interests are in process dynamics, modeling and control of chemical and biological systems. Research topics include dynamic modeling, model predictive control, large scale complex and hierarchical systems, and optimization. Current application areas are copolymerization reactors, refinery operations, protein folding and systems biology. He completed his BS from Bogazici University, Turkey in 1974 and done his MS in 1976 at University of Minnesota and completed his PhD in 1979 at University of Minnesota. He has held visiting positions at Tennessee Eastman, DuPont and Weyerhauser companies. He has served as the Editor of Journal of Process Control and Associate Editor of Automatica. He has been a trustee and Secretary of Computer Aids in Chemical Engineering (CACHE) Corporation, and a Director of Computers and Systems Technology (CAST), Division of AIChE. He is the recipient of the Donald P Eckman Award given by the American Automatic Control Council. He received TÜBİTAK Science Award in 2004.
Cell signaling is the process by which extracellular information is transmitted into the cell to perform biological functions. RAS-MAPK signaling pathway controls several cellular processes such as cell growth, proliferation, and gene expression. Activation of EGFR (Epidermal growth factor receptor) by binding of its specific ligands starts ERK signaling pathway. Phosphorylated EGFR exhibits great increase in the enzymatic activity of its cytoplasmic tyrosine kinase domain. Adaptor protein Grb2 binds to the phosphorylated RTK followed by recruitment of SOS, forming Grb2-SOS complex. Ras, which is a small GTP binding protein, interacts and transforms to its active conformation by exchanging GDP for GTP. Active Ras acts as an important switch which starts phosphorylation of MAPK pathway that consists of the Raf/MEK/ERK signaling cascade. However, in this paper we present a dynamic model that describes the molecular mechanisms involved in RAS-MAPK signaling. The model is derived from mass-action kinetics and conservation laws. Models exist in the literature for RAS and MAPK pathways separately. Our model combines the two systems and studies their interactions under feedback. Well-known mechanism of deactivation of the Grb2-SOS complex by ERK is included as an inhibitory feedback action in the model. Bistability (i.e., ability to switch between two stable steady-states separated by an unstable steady-state) is a desired trait that most biological processes exhibit. We establish conditions under which bistability and oscillations exist for this important pathway. In particular, we show how the negative and positive feedback loops affect the dynamic characteristics that determine the cellular outcome.
University of Houston, USA
Title: Advanced work flow for efficient multiplexing synthesis of genes in high fidelity – Next generation of gene synthesis
Time : 14:45-15:15
Xiaolian Gao is professor of Biology and Biochemistry at University of Houston. Her major research interests are related to large scale biology. Her lab uses chemical and biophysical methods in combination to address questions of biomolecules concerning how their structures, molecular dynamics, intermolecular interactions, and molecular recognition play roles in biological processes. In synthetic biology, she has led projects of miniaturized parallel production using digital photochemistry for programmable oligonucleotide synthesis on microchips, which was now advanced to become a revolutionary technology for massive production of oligonucleotides that fulfill the needs of rapid progress of today’s DNA technologies, including gene/genome synthesis, sequencing of the various nucleic acid molecules. In a recent report, collaborators and students of Dr. Gao has established robust laboratory work flow for accurate multiplex gene synthesis [reported in Science Reports “High-fidelity de novo synthesis of pathways using microchip-synthesized oligonucleotides and general molecular biology equipment” (2017) in print.. Dr.Gao is also a proficient structural biologist for using NMR methods to elucidate structures of ligand-DNA complexes.
This presentation will describe our synthetic biology project aiming a streamlining process of multiplex high fidelity gene synthesis using microchip oligo building blocks. This process features miniaturization, computation bioinformatics design, optimized work flow, low material consumption, long and high sequence accuracy, low error DNA constructs through efficient production process. Specifically, our work established a simple and easy to use flow column method (immobilized cellulose-binding-mutS column) to remove error-containing sequences from the final oligo gene-building blocks which are designed as such that they can be processed by ligation and PCR to give defined long (kb) DNA constructs. The reported workflow required about an hour of bench time for oligo processing, and attained less than 1 error per kb DNA, which is translated to ~80% success rate of full length EGFP (720 bp) gene cloning. The workflow hands more than ten genes in parallel. Has the potential for application in pathway gene cluster synthesis.
- Special Session
Location: Forum 12
John B Carrigan has completed his PhD in 2005 from the University College Dublin and carried out postdoctoral both in Dublin and in Copenhagen. He has been involved with several startups, most recently biobased advanced materials company, Cellulac Ltd. He is the CSO in SOSV responsible for scientific due diligence, recruitment, product development analysis in addition to other work. He has published several papers in the area of protein engineering, enzymology, metabolomics and cellulosic biofuels
SOSV’s Cork-based global bioaccelerator initiative, which is dedicated to funding and building startups for the purpose of aiding humanity. Having founded the worlds first life sciences accelerator in Cork in 2014. SOSV now operates two accelerator programs, IndieBio based in San Francisco and RebelBio again based in Cork. These accelerators are responsible or establishing many synthetic biology startups around the world including Perfect Day Foods, Memphis Meats, Microsynbiotix and the German based Saphium Biotech. We provide the mechanism by which young scientists, entrepreneurs and tinkerers can shape their own destiny and make something that matters. RebelBio provides seed funding and mentorship to drive the transition of science to a business in only four months, before launching its graduate companies into the world of biotechnology to make their fortune, buffered by the company’s many alumni, partners and partner investors.
- Presentation on Explora Biotech Srl