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April 8 2021, 2pm GMT, webinar
Abstract Current methods to generate single or combinatorial gene perturbation libraries are labor intense and require multiple ligation and cloning steps. Moreover, increasing sequence diversity negatively affects sequence distribution, resulting in biased libraries and large cell culture demands. I will present our recently developed 3Cs technology for the rapid and cloning-free generation of single and combinatorial gRNA libraries. Due to their low sequence bias, these reagents can be applied with minimal experimental coverages and reduce cell culture demands by at least 10-fold. Despite carefully explaining the 3Cs technology, I will also provide two real-world examples of how my lab applies the 3Cs technology to explore single and combinatorial gene effects. Biography Manuel studied Biotechnology and obtained his PhD from the Max Planck Institute of Biochemistry and the Biozentrum in Basel. For his postdoc, he joined the group of Steven Dowdy at the University of California in San Diego, where he became interested in gene editing technologies. Since December 2015, Manuel is a group leader at the Institute of Biochemistry II at the Medical Faculty of the Goethe University Frankfurt, Germany. His laboratory develops gene editing technologies and applies them to understand the various aspects of cellular transformation and drug resistance. A major achievement of his lab is the development of the 3Cs technology that recently culminated in the foundation of the university spin-off Vivlion for which Manuel is the Chief Scientific Officer.
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Tom Ellis is leading a research team in synthetic genome engineering and synthetic biology in the Department of Bioengineering. His research focuses on developing the foundational tools for accelerating, automating and scaling design-led synthetic genomics and synthetic biology, focusing on research projects in yeast (S. cerevisiae) as well as applied projects in other industrially-relevant and medically-relevant microbes.
Rodrigo Ledesma-Amaro is leading a research group at the interface of synthetic biology and metabolic engineering. His research lab is based in the Department of Bioengineering and the Center for Synthetic Biology and Innovation. His group explores the use of microorganisms for industrial processes as well as for biomedicine.
Dr Nicola Patron, Group Leader for Synthetic Biology at the Earlham Institute in Norwich will give a talk for SynBio.Oxford. Her research focuses on engineering photosynthetic organisms for industrial biotechnology and crops that are healthier to consume and less environmentally damaging to cultivate.
Daniel Nocera is the Patterson Rockwood Professor of Energy at Harvard University. He is widely recognised for his research in the field of renewable energy, in particular artifical photosynthesis. Two of his groundbreaking studies published in Science describe the artifical leaf and its extension to the bionic leaf, which can perform photosynthesis more efficiently than the natural system. These technologies will be of great importance for enabling sustainable food and fuel production independent of large infrastructures. Prof. Nocera's research has been recognised by numerous awards, and Time magazine named him among the 100 Most Influential People in 2009.
Prof. Nocera will present his work on Complete Artificial Photosynthesis: Sustainable and Renewable Carbon, Nitrogen and Phosphorus Cycles.
Paulina Kanigowska is a lab automation engineer. During her PhD at the University of Edinburgh, she worked on Nanoliter DNA assembly and screening at the Edinburgh Genome Foundry and collaborated on the construction of a genome-wide CRISPR gene knockout library. She has worked at Thermo Fisher Scientific and Nuclera and joined Ginkgo Bioworks in Boston about six months ago.
In this presentation, Dr. Kanigowska discusses the role of lab automation across different applications she has worked on, including: high-throughput screening for enzymatic DNA synthesis, DNA assembly miniaturization at an academic biofoundry, and turnaround time modeling at a DNA manufacturing facility.
The engineering of Biology presents infinite opportunities for therapeutic design, diagnosis, and prevention of disease. We use what we know from Nature to engineer systems with predictable behaviors. We also seek to discover new natural strategies to then re-engineer. I will present concepts and experiments that address how we approach these problems in a systematic way. For example, we have engineered components of the gut microbiome to act as both diagnostics and therapeutics for inflammation and infectious disease. In addition, we use living systems to detect and determine the danger of emerging pathogens.
Professor Silver's laboratory works at the interface between systems and synthetic biology to design and build biological systems in both mammalian and prokaryotic cells. She is also a member of the Board of Directors of the International Genetically Engineered Machine (iGEM) competition.
Biology is being transformed by new tools that enable us to interrogate and manipulate biological systems with higher resolution, sensitivity, and throughput than ever before. The Applied Biotechnology Laboratory is being founded at the Crick Institute in January 2021 to develop breakthrough biotechnologies that address major unmet needs in biology and medicine. In this talk, I will discuss two such technologies: the first, called Slide-seq, enables rapid quantification of genome-wide gene expression with single-cell spatial resolution, allowing for the cellular architecture of tissue to be inferred directly from RNA sequencing. The second, ExCOMP, is currently under development and will enable high-throughput mapping of cellular morphology and connectivity in diverse, distributed cell types, such as neurons and immune cells. I will discuss how both of these technologies can be applied to the discovery of new biomarkers or therapeutics. Finally, I will discuss my plans to advance these and other technologies in the Applied Biotechnology Laboratory.
Sam Rodriques is an entrepreneur, technologist, and inventor in the biotechnology space. He has invented a new nanofabrication method, a new approach to sensing neural activity with probes in the bloodstream, and new ways to extract spatial and temporal information from RNA sequencing. Prior to founding the Applied Biotechnology Laboratory, he was an entrepreneur in residence at Petri, a biotech accelerator in Boston, Massachusetts, and co-founded Saturn5, a company developing patient-oriented neurosurgical tools.
Complex non-linear dynamics orchestrate mammalian cell phenotypes in health and disease. In this talk, I will start discussing combined experimental and computational approaches to model multiscale gene expression, proliferation and spatial dynamics in both embryonic stem cell in vitro cultures and intestinal crypts. I will then propose synthetic biology and applications of control theory strategies to directly engineer gene expression dynamics in living mammalian cells, suggesting this as a methodology to both directly couple dynamics to phenotypes, and to design superior stem cell culture protocols and combination therapies in oncology.
Dr Lucia Marucci is a computational biologist, with interdisciplinary experience in Synthetic Biology (control and modelling of synthetic gene regulatory networks) and Systems Biology (modelling and studying the functional role of signalling and cell-cycle dynamics in mammalian cells). After a Bachelor and Master degree in Mathematics and Informatics, she received a Ph.D. degree in Automatic Engineering. After being a PostDoc EMBO fellow in the Centre for Genomic Regulation (CRG), Barcelona, Spain, she joined joined Bristol University as Lecturer in Engineering Mathematics in September 2013. She is currently an EPSRC Early Career Fellow, and Associate Professor in Systems and Synthetic Biology.