2019 Archived Content

Cambridge Healthtech Institute’s 11th Annual

Engineering Genes, Vectors, Constructs, and Clones  

Exploring Strategies in Systems Engineering and Synthetic Biology

January 14-15, 2019


The demand for high-quality biotherapeutic proteins has never been greater. Many variables still must be considered during the engineering process, including verification and sequence analysis of the gene or protein of interest, codon optimization, vector construction and clone/host selection – a time-consuming and expensive process. Additionally, protein expression scientists are now exploring new engineering tools including synthetic biology and systems engineering. Ultimately, these tools must be weighed against traditional expression and production strategies to achieve the desired quantity and quality.   

Cambridge Healthtech Institute’s 11th Annual Engineering Genes, Vectors, Constructs, and Clones conference continues the tradition of applying effective engineering strategies for protein expression and production research leading to functional biotherapeutic products. Learn from seasoned, savvy researchers as they share their real-world experiences, applications and results.

Final Agenda


4:00 - 6:00 pm Pre-Conference Registration (Sapphire West Foyer)


7:00 am Registration and Morning Coffee (Sapphire West Foyer)

Systems Biology: Elucidating the Connections
Sapphire 400

9:00 Welcome by Conference Organizer

Mary Ann Brown, Executive Director, Conferences, Cambridge Healthtech Institute

9:05 Chairperson’s Opening Remarks

Simpson Joseph, PhD, Professor, Department of Chemistry & Biochemistry, University of California, San Diego


9:10 COBRAme: A Computational Framework for Genome-Scale Models of Metabolism and Gene Expression

Bernhard Palsson, PhD, Galletti Professor, Bioengineering; Principal Investigator, Systems Biology Research Group, Bioengineering; Professor, Pediatrics, University of California, San Diego

Systems biology has progressed to describe the synthesis and maintenance of microbial proteomes through the formulation of genome-scale network models of metabolism, transcription, translation, protein structures, proteostasis, and stress mitigation. This development offers a mechanistic framework to study a wide range of issues from overall proteome allocation to the expression of a single heterologous protein.

9:50 Using Systems Approaches to Improve Protein Production in Mammalian Cell with Targeted Engineering

Lewis_NathanNathan E. Lewis, PhD, Assistant Professor, Department of Pediatrics, University of California, San Diego

Genomic resources have provided a comprehensive view of all the cell parts in mammalian cells, and systems biology is elucidating how they are all connected. We are now using systems biology modeling and omics data analysis to guide efforts to engineer mammalian cells for protein production.

10:20 Networking Coffee Break (Sapphire & Aqua West Foyer)

Cell-Free Systems
Sapphire 400

10:45 Integrating Cell-Free Protein Expression and Coarse-Grain Molecular Simulation for Rapid Design-Build-Test-Learn Cycles to Discover the Locational Impact of Site-Specific PEGylation

Bundy_BradleyBradley C. Bundy, PhD, Associate Professor, Department of Chemical Engineering, Brigham Young University

A cell-free approach to synthetic biology enables direct control of and access to the biological machinery for rapid Build-Test-Learn engineering cycles. The exponentially growing field is beginning to impact the biotherapeutics, biocatalysis, and biosensing industries. This presentation highlights recent advances combining course-grain molecular simulation with cell-free protein expression screening to rapidly determine the optimal location(s) for site-specific PEGylation.

11:15 Energy Consumption in a Cell-Free Expression System

Joseph_SimpsonSimpson Joseph, PhD, Professor, Department of Chemistry & Biochemistry, University of California, San Diego

Synthetic cells could be used for the production of novel proteins by the incorporation of unnatural amino acids, cytotoxic proteins that are difficult to express in living cells, biofuels, smart materials, and for the development of new medical diagnostics. Although much progress has been achieved in the design and synthesis of artificial cells, presently they are far inferior to living cells in robustness, stability and the production of biomaterials. One of the reasons for the poor performance of synthetic cells is due to inefficient energy regeneration in cell-free protein synthesis (CFPS) systems. I discuss methods to enhance energy regeneration in a cell-free expression system.

11:45 A Cell-Free Protein Synthesis Platform for Robust Epitope Screening and Novel Vaccine Development

Dresios_JohnJohn Dresios, PhD, Senior Biology Director, Chief Scientist and Leidos Technical Fellow, Advanced Solutions Group, Leidos

Expression of antigenic peptides for vaccine screening is challenging due to the poor and/or variable expression of predicted epitopes. In this respect, the value of a screen is minimized if only a small fraction of the epitopes is expressed, or if the expressed peptides are produced at dramatically different levels. Here we describe a cell-free platform for high-yield, balanced peptide expression that enables rapid epitope screening and multi-epitope vaccine development.

12:15 pm An Automated and High-Throughput, One-Step Transient to Stable Cell Line Generation Process Utilizing the PiggyBac Transposon Element

Marissa Piper, Senior Biologist, Eli Lilly and Company

12:30 Targeting SNPs in DNA Repair Genes to Generate Genomically Stable CHO Cell Lines

Philipp Spahn, PhD, Postdoctoral Scholar, Department of Pediatrics, University of California San Diego

12:45 Session Break

12:55 Luncheon Presentation I: Build Better Biologics with Machine Learning and Synbio

Gustafsson_ClaesClaes Gustafsson, Co-Founder and CCO, ATUM (formerly DNA2.0)

This presentation will showcase how ATUM combines recent developments in genome engineering, automation, big data and product analytics to increase efficiency of engineering and developability of biologics and cell lines. Cell lines generated using the LeapIn® transposase combined with optimized vector constructs, proprietary codon optimization and QSAR-based protein engineering allow for an information rich and efficient optimization of mAbs, bispecifics, CAR-T molecules, and the increasingly complex biologics approaching the market place.

1:25 Luncheon Presentation II (Sponsorship Opportunity Available)

Tools for Enhancing Expression: Codons, Constructs, and Clones
Sapphire 400

2:00 Chairperson’s Remarks

Chao-Guang Chen, PhD, Senior Scientist, Research Department, CSL Limited

2:05 Synonymous Codon Selection to Improve Protein Folding Yield

Clark_PatriciaPatricia L. Clark, PhD, O’Hara Professor of Chemistry & Biochemistry; Concurrent Professor of Chemical & Biomolecular Engineering, University of Notre Dame

We have developed a sensitive system to detect effects of synonymous codon substitutions on the co-translational folding of proteins expressed in E. coli, coupling the success of folding to E. coli fitness. We find that position-specific synonymous codon changes can have dramatic effects on folding yield, particularly at those positions that correspond to sub-domain “motif” structures.

2:35 Translational Attenuation Strategies to Improve Soluble Yields in Bacterial Expression Systems

Gray_ChristopherChristopher H. Gray, PhD, Staff Scientist & Team Leader (Structural Biology), Drug Discovery Program, CRUK Beatson Institute

High levels of protein expression in Eschericha coli frequently produce inclusion bodies. Alleviating strategies, modulating transcription or folding, are often modestly successful. We have enhanced soluble expression by manipulating translation, slowing the processing of target transcripts by regulating ribosome binding or by incorporating rare codons at strategic positions within the cDNA. This specific attenuation of translation results in greater soluble yields and offers a novel strategy to enhance production.

3:05 Find Your Table and Meet Your BuzZ Session Moderator

3:15 BuzZ Sessions with Refreshments (Sapphire & Aqua Foyer)

Join your peers and colleagues for interactive roundtable discussions.

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4:30 High-Throughput Antibody Construct Generation and Expression

Chen_Chao-GuangChao-Guang Chen, PhD, Senior Scientist, Research Department, CSL Limited

Antibody construct generation, also referred to as IgG reformatting, is a key step in antibody-display phage library screening. Following library screening, positive Fab expression constructs must be converted into IgG format before they can be expressed as soluble antibodies for further testing and characterization. An efficient strategy for high-throughput antibody construct generation and expression that solves many of the technical challenges associated with IgG reformatting will be presented.

5:00 Rapid Construction of Recombinant Plasmids by QuickStep-Cloning

Wong_Tuck_SengTuck Seng Wong, PhD, Senior Lecturer, Chemical and Biological Engineering, University of Sheffield

Molecular cloning is an essential step in biological engineering. Megaprimer-based PCR of a whole plasmid is a widely used method. However, linear amplification, use of self-annealing megaprimers and difficulty of performing point insertion of DNA are some of its limitations. QuickStep-Cloning overcomes these problems yet retains the simplicity of whole-plasmid amplification. It utilizes asymmetric PCRs to create a megaprimer pair with 3’-overhangs, and hence, facilitates the subsequent exponential whole-plasmid amplification.

Validogen 5:30 Productivity through Diversity - a Protein Production Toolbox to UNLOCK PICHIA

Dib_IskandarIskandar Dib, Head, Process Development & Analytics, VALIDOGEN GmbH (formerly VTU Technology GmbH)

Novel product classes and current trends in biopharma production ask for versatile and yet robust expression systems. VALIDOGEN’s answer is a yield-enhancing protein production toolbox known as UNLOCK PICHIA enabling fine-tuning of protein expression by its diversity of molecular tools and expression strategies for Pichia. Continuous expansion & improvement of its technology platform facilitates the targeted debottlenecking of protein expression all the way from transcription and translation to translocation, protein folding and secretion.

6:00 - 7:15 Welcome Reception in the Exhibit Hall with Poster Viewing (Sapphire Ballroom)

7:15 Close of Day


8:00 am Registration and Morning Coffee (Sapphire West Foyer)

Novel Tools Are Enhancing Production
Sapphire 400

8:45 NEW: Chairperson’s Remarks

Claes Gustafsson, Co-Founder and CCO, ATUM (formerly DNA2.0)

8:50 Titer Estimation for Quality Control (TEQC) Method: A Practical Approach for Optimal Production of Protein Complexes Using the Baculovirus Expression Vector System

Takagi_YuichiroYuichiro Takagi, PhD, Associate Professor, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine

The baculovirus expression vector system (BEVS) is becoming the method of choice for expression of many eukaryotic proteins and protein complexes. However, what influences the overall production of proteins or protein complexes remains largely unclear. We developed the Titer Estimation for Quality Control (TEQC) method, which enables researchers to quantitatively optimize protein expressions utilizing BEVS in a highly reproducible fashion.

9:20 Engineering Non-living Mimics of Eukaryotic Cells that Communicate and Quorum Sense

Niederholtmeyer_HenrikeHenrike Niederholtmeyer, PhD, Postdoctoral Fellow, Devaraj Lab, Department of Chemistry and Biochemistry, University of California, San Diego

Artificial cell-mimics may have applications in sensing and production of biomaterials, tasks that will benefit from communication between cell-mimics. We developed a porous artificial cell-mimic containing a nucleus-like DNA-hydrogel compartment that can express and display proteins and communicate with neighboring cell-mimics through diffusive protein signals. We found that communication between cell-mimics allows distribution of tasks and collective responses.

9:50 Coffee Break in the Exhibit Hall with Poster Viewing (Sapphire Ballroom)

11:00 Genetic Engineering Process Optimization in CHO Cells

Stephanie L. Sandefur, MSc, Consultant Biologist, Bioprocess Research & Development, Eli Lilly and Company

Over the past decade, considerable progress has been made in improving the effectiveness and efficiency of generating highly productive recombinant CHO cell lines. While these efforts have been primarily centered on driving cell culture productivity, more recently, focus has turned to approaches to impact product quality. This presentation describes potential approaches to maximizing the effectiveness of host cell engineering and reducing the time to successfully impact biotherapeutic product quality profiles.

11:30 De novo DNA Synthesis Using Enzymes

Sebastian Palluk, MSc, CTO, Ansa Biotechnologies

DNA synthesis, the ability to "write" DNA, is a foundational technology in life sciences research and engineering. Currently, all synthetic DNA is made using organic chemistry via a method that has remained unchanged for 35 years and has approached a plateau. This talk describes current efforts in the field of enzymatic DNA synthesis and presents a novel DNA synthesis technology that is based on polymerase-nucleotide conjugates.

12:00 pm Research Cell Bank Generation in under 14 Weeks by Integrating Single Cell Analysis into the SUREtechnology Platform

Girod_Pierre-AlainPierre-Alain Girod, PhD, CSO, Selexis SA


Currently, Selexis’ SUREtechnology Platform™ generates research cell banks in as little as 14 weeks, with optimal clone selection requiring 6-8 of those weeks. Single-cell analysis platforms, capable of parallel analyses, have the capacity to reduce those timelines, but must be optimized to each cell system.  Selexis has integrated the BEACON® optofluidic platform into the SUREtechnology Technology workflow plus developed a clone prediction tool that collectively shave weeks off the current development timelines. Case studies discussed.  

12:30 Session Break

Pall_Biotech 12:40 Luncheon Presentation I A SMART Platform for Scalable Biotherapeutic Development: DNA to 200L Single-use Stirred-tank Bioreactor – a Case Study and Workflow

Goel_DivyaDivya Goel, Celltheon

12:55 Luncheon Presentation II (Sponsorship Opportunity Available)

1:10 Close of Engineering Genes, Vectors, Constructs, and Clones Conference

5:45 - 8:45 Recommended Dinner Short Courses*

SC5: Transient Protein Production in Mammalian Cells - Detailed Agenda

Click here for more details.

*Separate registration required


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