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


7:00 am Registration and Morning Coffee

Systems Biology: Elucidating the Connections

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


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

Nathan 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

Cell-Free Systems

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

Bradley 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

Simpson 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

John 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 Productivity through Diversity - a Protein Production Toolbox to UNLOCK PICHIA

Iskandar Dib, PhD, Principal Scientist, Process Development & Analytics, VTU Technology GmbH

12:45 Session Break

12:55 Luncheon Presentation to be Announced

1:25 Luncheon Presentation II (Sponsorship Opportunity Available)

Tools for Enhancing Expression: Codons, Constructs, and Clones

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

Patricia 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

Christopher 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

Join your peers and colleagues for interactive roundtable discussions.


4:30 High-Throughput Antibody Construct Generation and Expression

Chao-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

Tuck 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.

5:30 Sponsored Presentation (Opportunity Available)

6:00 - 7:15 Welcome Reception in the Exhibit Hall with Poster Viewing

7:15 Close of Day


8:00 am Registration and Morning Coffee

Novel Tools Are Enhancing Production

8:30 Chairperson’s Remarks

Mark Welch, PhD, Vice President, Research and Development, ATUM

8:35 Titer Estimation for Quality Control (TEQC) Method: A Practical Approach for Optimal Production of Protein Complexes Using the Baculovirus Expression Vector System

Yuichiro 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.

9:05 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.

9:35 Sponsored Presentation (Opportunity Available)

9:50 Coffee Break in the Exhibit Hall with Poster Viewing

11:00 Genetic Engineering Process Optimization in CHO Cells

Stephanie L. Sandefur, MS, Consultant Biologist, Bioproduct Research & Development, Eli Lilly and Company

11:30 A Multi-Landing Pad DNA Integration Platform for Mammalian Cell Engineering

Liliana Wroblewska, PhD, Principal Scientist, Biomedicine Design, Pfizer

Reliable, large-scale engineering of CHO cells through precise insertion of large amounts of heterologous DNA into well-characterized genomic loci would have broad applications for mammalian synthetic biology, recombinant protein production, and biomanufacturing. Using multi-gene payload vectors, cell lines with multiple landing pads, and recombinase technology, we demonstrated controlled integration of up to nine copies of a monoclonal antibody (about 100 kb of heterologous DNA), and a corresponding linear increase in antibody expression.

12:00 pm Talk Title to be Announced

Pierre-Alain Girod, PhD, CSO, Selexis SA

12:30 Session Break

12:40 Luncheon Presentation (Sponsorship Opportunity Available) or Enjoy Lunch on Your Own

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

Click here for more details.

*Separate registration required

* The program is subject to change without notice, due to unforeseen reason.

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