GenScript Double Helix Symposium 2019

Monday, September 30, 2019
W San Francisco

DNA is the only material that can be manipulated and applied in so many industries including biofuels and oils, food and agriculture, space exploration, materials and fabrics, therapeutics and diagnostics, data storage and many more. Through the application of this multifaceted medium, Synthetic Biology and genome editing allow us to not only reimagine many aspects of human life, but also explore a whole new realm of possibilities.

The Double Helix Symposium aims to gather exceptional speakers and scientists from both academia and industry on the subject of DNA manipulation and promote discussion. This initiative is also to provide a learning and networking opportunity for early career scientists.

  • Updates in Genetic Engineering Technology and Method
  • Latest Applications of and Ideas on Synthetic Biology
  • Commercialization Strategy from Academia to Industry

Date and time: 9:00 am - 6:00 pm, Monday, September 30th, 2019

Location: Great Room & Work Room, W San Francisco, 181 3rd St, San Francisco, CA 94103, USA

SynBioBeta Collaboration New!

  • Register Double Helix Symposium to receive a discount code to register SynBioBeta 2019.
  • Posters submitted and accepted by Double Helix Symposium will qualify for a 50% discount on SynBioBeta 2019 Registration.
Speakers & Abstracts

Christopher Bahl

Institute for Protein Innovation, Harvard Institutes of Medicine

George Church

Harvard, MIT

Rhiju Das

Stanford University

Shawn Douglas

UCSF

Michael Fero

TeselaGen Biotechnology

Nathan Hillson

Joint BioEnergy Institute, U.S. Department of Energy (DOE)

Head of Protein Design

Chris received his PhD from the Geisel School of Medicine at Dartmouth where he studied the mechanisms of bacterial virulence. As a postdoctoral fellow with David Baker at the University of Washington, Chris pioneered new methods for computational de novo design of disulfide-rich mini-proteins and peptides. Currently, Chris is the Head of Protein Design at the Institute of Protein Innovation where his group combines de novo protein design and high-throughput laboratory automation to accelerate drug discovery.

Professor

George M. Church, PhD '84, is professor of genetics at Harvard Medical School, a founding member of the Wyss Institute, and director of PersonalGenomes.org, the world's only open-access information on human genomic, environmental, and trait data. Church is known for pioneering the fields of personal genomics and synthetic biology. He developed the first methods for the first genome sequence & dramatic cost reductions since then (down from $3 billion to $600), contributing to nearly all "next generation sequencing" methods and companies. His team invented CRISPR for human stem cell genome editing and other synthetic biology technologies and applications – including new ways to create organs for transplantation, gene therapies for aging reversal, and gene drives to eliminate Lyme Disease and Malaria. Church is director of IARPA & NIH BRAIN Projects and National Institutes of Health Center for Excellence in Genomic Science. He has coauthored 450 papers, 105 patents, and one book, "Regenesis". His honors include Franklin Bower Laureate for Achievement in Science, the Time 100, and election to the National Academies of Sciences and Engineering.

Associate Professor

Dr. Das strives to make the computer modeling of life as agile and engaging as the design of software. His lab at Stanford focuses on medically relevant RNA molecules, developing computational and high-throughput chemical tools for the rapid modeling and design of these molecules. Dr. Das trained in particle physics and cosmology at Harvard and Cambridge before switching to molecular biophysics during his Ph.D. at Stanford and postdoctoral work at the University of Washington. He is an associate professor in the departments of biochemistry and physics at Stanford, and leads the Eterna massive open laboratory, which couples a 250,000-player videogame to the lab's massively parallel experimental tools and deep learning, the first such platform in citizen science.

Assistant Professor

Shawn Douglas earned a B.S. in Computer Science at Yale in 2003, and then a Ph.D. in Biophysics at Harvard in 2009, working in the laboratories of William Shih and George Church. He stayed at Harvard as a Postdoctoral Fellow at the Wyss Institute for Biologically Inspired Engineering, and then started his own lab as an Assistant Professor at UCSF. He was named as one of Popular Science magazine's "Brilliant 10" in 2012 and received a Presidential Early Career Award for Scientists and Engineers (PECASE) award from Barack Obama in 2016.

CEO

Dr. Fero is a California based scientist and entrepreneur who is best known for his work on the fundamental physics of the Electroweak interaction at CERN, MIT and SLAC, systems biology research at Stanford, and synthetic biology at TeselaGen.

Computational Staff Scientist

Dr. Nathan Hillson received his Doctorate in Biophysics from Harvard Medical School. He was a postdoctoral researcher at Stanford University School of Medicine. Nathan is currently the Head of the BioDesign Department at the Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory. He is also a Principal Investigator at the U.S. Department of Energy's Agile BioFoundry together with being the Co-Founder and Chief Scientific Officer at TeslaGen Biotechnologies Inc. Dr. Hillson has developed experimental wetware, software, and automated laboratory devices. He had recently created PIACE, a highly efficient chromosomal integration method to engineer metabolic pathways in bacteria. Nathan also worked to develop the patented j5 DNA Assembly Software to create scar-less plasmids by combining designed DNA oligos and cloning strategies such as SLIC and Gibson. Dr. Hillson aims to create these automated platforms to standardize microbial engineering, DNA construction, and sequence validation.

Possu Huang

Stanford University

Lynn J. Rothschild

NASA Ames Research Center

Sri Kosuri

Octant Bio, UCLA

Jin Billy Li

Stanford University

Eric Wang

GenScript

Cedric Wu

GenScript

Assistant Professor

Dr. Possu Huang received his PhD from Caltech with the first demonstration of a computationally designed novel protein-protein interface. He subsequently conducted postdoctoral research at the University of Washington before starting his group at Stanford. His research focuses on advancing the understanding of proteins for the engineering of novel therapeutics and other protein-based nanotechnology. He has contributed to a large number of de novo designed proteins, most notably to the unlocking of the design principles behind the TIM barrel fold. His group uses computational modeling, structural biology and experimental library optimization to continue the expansion of protein-based molecular platforms, as well as creating new design tools with modern neural network architectures.

Sr Research Scientist

Lynn Rothschild is passionate about the origin and evolution of life on Earth r elsewhere, while at the same time pioneering the use of synthetic biology to enable space exploration. She wears several hats as a senior scientist NASA's Ames Research Center and Bio and Bio-Inspired Technologies, Research and Technology Lead for NASA Headquarters Space Technology Mission Directorate, as well as Adjunct Professor at Brown University (full cv available https://vivo.brown.edu/display/lr3). Her research has focused on how life, particularly microbes, has evolved in the context of the physical environment, both here and potentially elsewhere. Rothschild has brought her imagination and creativity to the burgeoning field of synthetic biology, articulating a vision for the future of synthetic biology as an enabling technology for NASA's missions, including human space exploration and astrobiology. Since 2011 she has served as the faculty advisor of the award-winning Stanford-Brown iGEM (international Genetically Engineered Machine Competition) team, which has pioneered the use of synthetic biology to accomplish NASA's missions, particularly focusing on the human settlement of Mars, astrobiology and such innovative technologies as BioWires and making a biodegradable UAS (drone) and a bioballoon. Her lab is testing these plans in space on in the PowerCell synthetic biology secondary payload on a DLR satellite, EuCROPIS, launched in December 2018.

CEO

Sri is cofounder and CEO of Octant, a synthetic biology drug discovery startup that is building comprehensive maps of the interactions between chemicals and hundreds to thousands of human drug targets. He is on leave from UCLA, where he is an Associate Professor at UCLA in the Chemistry and Biochemistry Department, where his lab has worked on gene synthesis and multiplexed assays to explore questions in protein biochemistry, human genetic variation, gene regulation, chemical biology, synthetic biology, and functional genomics. Sri previously worked at the Wyss Institute and Harvard with George Church, where he built numerous technologies in gene synthesis, DNA information storage, gene editing, and large-scale multiplexed assays. He helped build Gen9, a gene synthesis company, as a member of the SAB and was the first employee of Joule Unlimited, an engineered algal biofuel company. He is a Searle Scholar (2015), NIH New Innovator (2014), and received his ScD in Biological Engineering at MIT working with Drew Endy (2007) and BS in Bioengineering at UC Berkeley working with Adam Arkin (2001).

Associate Professor

Jin Billy Li, Ph.D., is Associate Professor with tenure at Stanford University Department of Genetics. He received his bachelor' degree at Tsinghua University in Beijing China and PhD degree in Genetics from Washington University in St. Louis. After his postdoctoral training with Professor George Church at Harvard Medical School, he started his laboratory at Stanford in 2010. In his own lab, he has focused on studying RNA editing mediated by ADAR enzymes. His laboratory has made major contributions to the identification and mapping of RNA editing as well the regulation of functions. His current work focuses on two fascinating aspects of ADAR. One is the major biological function that is to evade dsRNA sensing to suppress autoimmunity. The other is to harness the endogenous ADAR enzyme for transcriptome engineering that holds great potential for RNA-based therapeutics.

VP of Marketing

VP of R&D

Dr. Cedric Wu obtained a PhD degree in Cellular and Molecular Biology from University of Wisconsin - Madison where he also received post-doc training in nucleic acid, surface and analytical chemistry. Dr. Wu possesses more than twenty years of combined experience working in academia, government and industry. He invented and published more than 20 articles and patents, as well as numerous trade secrets. Dr. Wu, currently, is leading the R&D team in GenScript focusing on on protein, antibody engineering, nucleic acid chemistry, genome editing, bioinformatics, data storage, semiconductor chip development and gene synthesis.

Agenda

9:00 - 9:40

Registration and Poster/Exhibit Setup

9:40 - 9:45

Welcome Remarks

9:45 - 10:15

De novo design of G protein mimetics: generalizable tools for allosteric control of G protein-coupled receptors.
Christopher Bahl, Ph.D., Head of Protein Design, Institute for Protein Innovation, Harvard Institutes of Medicine
Read More »
Generalizable tools to stabilize the active conformational state of GPCRs will facilitate protein purification and structure determination, as well as accelerate the engineering of molecules which act as agonists or antagonists. Using de novo protein design, we have developed novel Galpha mimetic proteins that are thermostable, selectively bind to the active state of GPCRs, and can bind to a wide range of different GPCRs.

10:15 - 10:45

The de novo design of a self-assembling superantigen for targeted immunotherapy
Possu Huang, Ph.D., Assistant Professor, Stanford University
Read More »
Highly specific and orthogonal oligomers have broad applications in synthetic biology. In stark contrast to DNA origami, a protein-based molecular toolkit that enables LEGO-style molecular assembly remains elusive. Helical fragments that twist into coiled-coils have been the workhorse for decades. Nonetheless, the monomeric components based on coiled-coils often have practical limitations, which greatly limit their application. As an alternative, we investigate the utility of repeat protein structures for heterodimer assembly. By designing stable self-assembling toroid structures de novo, we are able to create novel oligomers, which can be used to assemble molecular logic gates. We hope to apply this principle to develop a novel cancer immunotherapy that can potentially address the shortcomings of current approaches.

10:45- 11:15

Octant: Mapping the Functional Relationships between Chemicals and Human Biology
Sri Kosuri, Ph.D., cofounder and CEO, Octant Bio; Assistant Professor, UCLA
Read More »
Octant is a new drug discovery company that uses synthetic biology, genome engineering, next-generation sequencing, and computational tools to simultaneously measure the activity of thousands of engineered reporters at once in human cells in a single well. We use this experimental platform to map thousands of chemicals against engineered cell line libraries designed to report on the activity of hundreds to thousands of drug targets. To begin, we focused the Octant platform on mapping chemical interactions with the G-protein coupled receptors (GPCRs). The ~800 human GPCRs are the most important class of drug receptors and are the ultimate targets of a third of FDA-approved drugs, more than half of all prescriptions, and as well as many natural products, nutraceuticals, recreational drugs, fragrances, and flavors. We've built, optimized, and scaled a platform that systematically maps large libraries of chemicals and GPCRs at orders-of-magnitude less cost and labor than conventional assay technology. In this talk, I will discuss the technologies and experiments that led to Octant's founding, as well as how we are beginning to point the platform.

11:15 - 11:45

U.S. DOE Agile BioFoundry: Overview and Recent Highlights
Nathan Hillson, Ph.D., Director of Synthetic Biology Informatics, Joint BioEnergy Institute, U.S. Department of Energy (DOE)
Read More »
The overarching goal of the DOE Agile BioFoundry (ABF) is to enable biorefineries to achieve 50% reductions in time to bioprocess scale-up (as compared to the current average of around 10 years) by establishing a distributed BioFoundry that productionizes synthetic biology. Toward achieving this goal, the ABF has brought together domain expertise and infrastructure that is distributed across 8 U.S. National Labs (LBNL, SNL, PNNL, NREL, ANL, ORNL, LANL, and INL). This talk will introduce the ABF, and provide some research and development highlights (including work with industry) from the first 3 years of its operations.

11:45 - 12:00

Lightning Talk: Organism Making and Modding - How modern AI driven enterprise software is revolutionizing biotechnology
Michael J. Fero, Ph.D., CEO, TeselaGen Biotech
Read More »
Until recently identifying and modifying microbes to improve production of chemicals and enzymes via fermentation has been a slow and somewhat artisanal process. With advances in recombinant methods and DNA synthesis, systems can now be put in places that vastly accelerate product development of everything from fragrances to future fuels. In this talk we will review the progress made and show how AI driven systems can be implemented that completely automate organism modification R&D.

12:00 - 13:00

Lunch Networking and Poster Viewing

13:00- 13:30

Rapid assembly of gene variant libraries and multi-gene pathways with semiconductor technologies
Cedric Wu, Ph.D., VP of R&D, GenScript Biotech
Read More »
Engineering synthetic biological systems requires the design, build and testing of multi-gene networks. To optimize a synthetic system with the best combination of DNA parts, synthetic biologists need to test all possible variations of individual components and be able to screen in a combinatorial design space. But such combinatorial engineering approaches are hindered by the difficulty of simultaneously assembling numerous large, multi-gene constructs from a collection of DNA parts. Here, we introduce our newly developed variant library synthesis platforms, which creates well-designed mutant libraries containing all desired variants with unbiased distribution. Additionally, our combinatorial library synthesis platform enables in-parallel construction of thousands of multiplexed gene variants in an efficient and economical way. Both platforms utilize our patented semiconductor-based oligonucleotide microarray fabrication technology allowing complete control over codon usage and amino acid distribution. Libraries generated using this method are highly customizable and capable of generating over 1x108 variants. As a result, our platform enables faster, easier, and more cost-effective engineering of metabolic pathways and microbial strains in comparison to alternative approaches.

13:30- 14:00

Synbio and NASA's missions
Lynn Rothschild, Ph.D., Sr Research Scientist, Bio and Bio-Inspired Technologies, Research and Technology Lead for NASA HQ STMD
Read More »
The time has come to for NASA to exploit synthetic biology in pursuit of its missions, including aeronautics, earth science, astrobiology and most notably, human exploration. Conversely, NASA advances the fundamental technology of synthetic biology as no one else can because of its unique expertise in the origin of life and life in extreme environments, including the potential for alternate life forms. This enables unique, creative "game changing" advances. NASA's drivers will greatly increase the utility of synthetic biology solutions for military, health in remote areas and commercial purposes.

14:00 - 14:45

Keynote: Scripting genomes & epigenomes
George Church, Ph.D., Professor at Harvard & MIT
We have improved the cost & quality of reading, writing, editing genomes 10 million fold. Synthetic libraries enable read design+evolution strategies for gene therapies, organs, viral resistance via recoding, and radically engineered proteins.

14:45- 15:15

Folding DNA into tiny tools for cryo-electron microscopy
Shawn Douglas, Ph.D., Assistant Professor, UCSF
Read More »
The idea of using designer molecular scaffolds to overcome technical challenges in structural biology is not new. Indeed, it was frustration with the difficulties of protein crystallization that inspired Ned Seeman to establish an entirely new field nearly 40 years ago: DNA nanotechnology. Since then, extraordinary advances have been made in solving high-resolution structures by cryo-electron microscopy. However, cryo-EM comes with its own set of technical challenges for which Seeman's vision of programmable nanoscale control remains relevant. In this talk, I will describe our efforts to create a suite of DNA origami nanostructures to aid in structure determination of certain small (<100 kDa) macromolecules by cryo-EM. We have found that our tools can help overcome issues related to poor particle contrast, preferential orientation, and pseudo-symmetry. We think our approach shows great promise for solving unknown structures that thus far have remained beyond the reach of cryo-EM.

15:15 - 15:50

Coffee Break and Poster Viewing

15:50 - 16:20

RNA technologies developed through an internet-scale videogame
Rhiju Das, Ph.D., Associate Professor, Stanford University
Read More »
This talk will present an unconventional approach to empirical scientific problems. Self-assembling RNA molecules present compelling substrates for the rational interrogation and control of living systems, but imperfect computational models hinder the design of new RNAs that function properly when synthesized. The Eterna project engages an internet-scale community of >200,000 videogame players to solve currently intractable RNA design problems. Uniquely, Eterna participants not only manipulate simulated molecules but also control remote experimental pipelines for high-throughput RNA synthesis, structure mapping, and functional characterization. Recent achievements include the design of ligand-sensing riboswitches that operate at their thermodynamic limit, instantiation of all binary logic gates responding to oligonucleotide inputs, and calculators of analog arithmetic expressions involving input molecule concentrations, which may be useful for point-of-care diagnosis of active tuberculosis, sepsis, and other global health threats.

16:20 - 16:50

ADAR1 RNA editing evades MDA5-Mediated dsRNA sensing in innate immunity
Jin Billy Li, Ph.D., Associate Professor, Stanford University
Read More »
Adenosine-to-Inosine (A-to-I) RNA editing, catalyzed by ADAR enzymes, is an important post-transcriptional mechanism critical for life. ADAR1, one of the ADAR family members, is primarily responsible for the editing of the majority of RNA editing sites that are located in long double-stranded RNAs (dsRNAs) formed by inverted repeats. Mice deficient with ADAR1 editing are embryonic lethal, failing to form liver due to the induction of the type-I interferon response. This lethality phenotype can be fully rescued by concurrent loss of MDA5, a cytosolic dsRNA sensor of long dsRNAs. The "self" long dsRNAs that fail to undergo RNA editing by ADAR1 are recognized as "non-self" RNA by MDA5. Loss-of-function mutations in ADAR1 and gain-of-functions mutations in MDA5 are observed in a number of autoimmune diseases. Our recent work reveals that some, but not all, dsRNAs need to be edited to evade innate immune response.

16:50 - 17:20

Easier working with DNA for the future of science & MolecularCloud Award Ceremony
Eric Wang, VP of Marketing, GenScript Biotech

17:20 - 17:55

Poster Flash Session

17:55 - 18:00

Closing Remarks
Posters
P1 RipTide Ultra High-Throughput Rapid DNA Library Preparation for Next Generation Sequencing
Azeem Siddique,1,3 Gaia Suckow,1,3 Nils Homer,2 Jorge Bahena,1,3 Phillip Ordoukhanian,1,3 Steve Head,1,3 Keith Brown3
1The Scripps Research Institute, La Jolla, CA; 2Fulcrum Genomics, Somerville, MA; 3iGenomX, Carlsbad, CA
P2 Elucidation of Enigma in Adaptationally Evolved Saccharomyces cerevisiae for Ethanol Production from Brown Macroalgae
Yusuke Sasaki1,2, Yasuo Yoshikuni1,2,3
1US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
2Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
P3 BLiSS: The Black List Sequence Screening pipeline
Lisa Simirenko1, Jan-Fang Cheng, Samuel Deutsch, and Nathan J. Hillson 
1U.S. Department of Energy Joint Genome Institute, Walnut Creek, California
P4 A screening method to identify efficient sgRNAs in Arabidopsis, used in conjunction with cell‑specific lignin reduction
Yan Liang1,2*, Aymerick Eudes1,2, Sasha Yogiswara1,2, Beibei Jing1,2, Veronica T. Benites1,3, Reo Yamanaka1,4, Clarabelle Cheng-Yue1,2, Edward E. Baidoo1,3, Jenny C. Mortimer1,2, Henrik V. Scheller1,2,5* and Dominique Loqué1,2,5
1Joint BioEnergy Institute, Emeryville, CA 94608, USA; 2Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; 3Biological Systems Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; 4School of Public Health, University of California, Berkeley, CA 94720, USA; 5Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
P5 Accelerating the Design-to-Build transition using the Build-Optimization Software Tools (BOOST)
Ernst Oberortner, Nathan J. Hillson, Jan-Fang Cheng, Samuel Deutsch
DOE Joint Genome Institute (JGI)
P6 Self generated protein drug from auto translation of mRNA by the help of Ribosome and t-RNA in our body (mRNA capsule)
Aritra Kumar Dan1, Tamoghni Mitra
1School Of Biotechnology, KIIT
P7 Engineering Bacteria to Form Multicellular Cohesive Patterns for the Assembly of Hybrid Living Materials
Maria T. Orozco Hidalgo1, Marimikel Charrier1, Dong Li1, Nicholas Tjahojno1, Behzad Rad1, Paul D. Ashby1, Kathleen Ryan2, Caroline Ajo-Franklin1,3 
1Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA; 2Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA; 3Department of Biosciences, Rice University, Houston, TX.
P8 The Utility of Genetically Edited Turkey Muscle for Cell-based Meat Production
Marie Gibbons (Harvard Medical School, North Carolina State University), Cory Smith (Harvard Medical School), Bobby Dhadwar (Harvard Medical School), Jorge Piedrahita (North Carolina College of Veterinary Medicine), George Church (Harvard Medical School)
Registration

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  • Symposium Souvenir
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