PepTalk 2017
PepTalk 2017
Archived Content

Pipeline 4 Header 

Fourth Annual
Engineering Genes, Vectors, Constructs, and Clones
Upstream Decisions Lead to Downstream Success
January 21-22, 2013 


Day 1 | Day 2Download Pipeline 4 Brochure 

To meet the goal of producing functional biotherapeutic proteins at even higher levels requires engineering (science) and insight (art). This meeting applies effective engineering strategies for protein discovery research that leads to functional biotherapeutic products. Learn from seasoned savvy researchers as they share their real-world experiences, applications, and results.


4:00-5:00 pm Registration for Short Courses

5:00 – 8:00 Recommended Dinner Short Courses (SC1-SC4)*

*Separate Registration Required


4:00-8:00 pm Conference Registration


7:30 am Conference Registration and Morning Coffee


Synthetic Biology 

8:55 Chairperson’s Opening Remarks
Mark Welch, Ph.D., Director, Gene Design, DNA2.0, Inc. 


9:10 Methods and Applications for Assembling Large DNA Constructs

Dan GibsonDaniel Gibson, Ph.D., Associate Professor, Synthetic Biology, J. Craig Venter Institute

We recently showed that it is possible to reverse this process and synthesize bacterial cells starting from digitized information.  To make this happen, our group needed to learn how to sequence, synthesize, and transplant entire chromosomes.  This work and new powerful methods for constructing small and large DNA molecules starting from chemically-synthesized oligonucleotides will be discussed.

9:50 Next-Generation Gene Synthesis

Joseph Jacobson, Ph.D., CTO, Gen9; Associate Professor, Massachusetts Institute of Technology

Next-generation gene synthesis has the prospect of vastly increasing the number of synthetic genes which can be synthesized globally per period.   The advent of this new technology should be enabling to the field of Synthetic Biology with wide ranging applications from protein therapeutics to enzymes to synthetic clones.

10:20 Coffee Break

10:45 Self-Regulatory Recombinant Protein Production through an Integrative Synthetic Biology Approach

Ilias Tagkopoulos, Ph.D., Assistant Professor, Department of Computer Science & U.C. Davis Genome Center, University of California, Davis

We will present our efforts towards an integrative approach to engineer synthetic circuits through modeling, simulation and characterized library construction. We use all-atoms models to predict promoter strength in order to engineer and characterize libraries of promoter variants. We then use mathematical optimization and graph-theoretic techniques to find the optimal circuit configuration. We will discuss how these advances were used towards the engineering of a self-regulatory circuit for recombinant protein production.

11:15 Automated Design of Synthetic DNA to Rationally Control and Balance Protein Expression

Howard Salis, Ph.D., Assistant Professor, Biological & Chemical Engineering, Pennsylvania State University

We’ve developed a biophysical model and optimization method, called the RBS Calculator, that predicts the translation rate from bacterial mRNA sequences and designs synthetic sequences to rationally control protein expression over a 100,000-fold dynamic range. Additionally,the RBS Library Calculator, allows researchers to identify the optimal protein expression levels with minimal experimentation. These methods reduce cloning efforts while systematically maximizing protein titers.

11:45 The MoClo System: A Modular Cloning System for Standardized Assembly of Multigene Constructs

Sylvestre Marillonnet, Ph.D., Director, Research, Icon Genetics, GmbH

We have developed a modular cloning system for standardized assembly of multigene constructs. Basic genetic elements such as promoters, gene coding sequences and terminators are cloned as level 0 entry modules. Multigene constructs are then assembled from basic modules using a series of Golden Gate cloning reactions that allow assembly of multiple DNA fragments at each cloning step.

12:15 pm Close of Session


12:30 Design, Assembly, Editing and Interspecies DNA Transfer of Large Genetic Constructs

Federico Katzen, Ph.D., Senior Staff Scientist, Life Technologies

We developed a set of reagents and software tools that facilitate the design, and enable efficient assembly of genetic constructs. Solutions based on the double strand break-repair mechanism allow simultaneous joining of DNA fragments ranging from a few base pairs to tens of kilobases. Microediting can be performed using a multisite directed mutagenesis approach based on homologous recombination. A conjugal transfer method allows interspecies mobilization of the constructs avoiding ex vivo DNA manipulation.


DNA Constructs and Clones 

2:00 Chairperson’s Remarks

Dominic Esposito, Ph.D., Director, Protein Expression Laboratory, Advanced Technology Program, SAIC-Frederick, Inc.

2:05 Recombi-Mutagenesis: A Rapid and Efficient Method to Generate Site-Directed Mutagenesis via Recombineering

JrGang Cheng, Ph.D., Associate Professor, Center for Neuroscience, University of North Carolina Chapel Hill

Recombineering has been used to generate vectors for transfecting mammalian cell lines and expressing proteins. Due to the strand invasion during homologous recombination, mutation on the donor DNA can be introduced into acceptor DNA construct via targeting. Utilizing the specificity of recombineering and the convenience of “transitory” positive selection, one can easily insert mutation into DNA constructs to alter the protein and its function.

2:35 Combinatorial Cloning Libraries for Simplified Expression Clone Construction

Dominic Esposito, Ph.D., Director, Protein Expression Laboratory, Advanced Technology Program, SAIC-Frederick, Inc.

Using a modified Multisite Gateway cloning strategy, we have developed a platform allowing simplified construction of expression clones from sequence validated libraries of elements. This platform is compatible with the thousands of extant Gateway entry clones commercially available, and utilizes a small set of well tested backbone vectors for expression in multiple host organisms.  The details on the libraries and platform technology will be discussed along with case studies of its use for microscale protein production and screening studies.

3:05 Molecular Tools for Facilitating Protein Expression and DNA Manipulation

Yoav Peleg, Ph.D., Research Scientist, Biological Chemistry, The Israel Structural Proteomics Center (ISPC), Weizmann Institute of Science

Despite the large body of knowledge accumulated on expression of recombinant proteins in E. coli system, protein production, primarily of eukaryotic origin, remains a challenge. This talk will focus on strategies to overcome some of the bottlenecks in protein expression emphasizing methods for increasing yield and solubility. Novel strategies for DNA manipulation, including cloning and mutagenesis, that should facilitate the entire process from gene to protein, will be presented.

Lucigen3:35 New Tools for Producing Endotoxin-Free Proteins, Biotinlyated Proteins and Biosynthetic Pathways or Very Large Proteins

David Mead, Ph.D., CEO & Founder, Lucigen Corp.

Lucigen will present several novel products for cloning and protein expression including: competent E. coli cells lacking lipopolysaccharide (LPS) for endotoxin-free protein and DNA production, the Expresso® Biotin system for unbelievably fast expression and isolation of pure protein and a new technology for cloning and expression of complete biosynthetic pathways.

3:50 Refreshment Break

4:15 Novel Viral and Non-Viral Gene Transfer Technologies

Mark Kay, Ph.D., Professor, Pediatrics and Genetics, Stanford University

I will discuss new minicircle DNA vectors and why they provide 10 to 1000 times more robust long term transgene expression. I will also discuss new methods for developing designer AAV vectors with novel properties.

4:45 Vector Design for High-Throughput Protein Production

D. Mitchell Magee, Ph.D., Assistant Professor, Research, Center for Personalized Diagnostics,The Biodesign Institute, Arizona State University

This talk will review our experience with vector design and recombinatorial cloning strategies.  There will first be an overview of the pipeline and key vector design considerations.  Thereafter, we will report on results of using the pipeline in applications for high-throughput production and purification of recombinant proteins for affinity reagent generation.  In addition, data will be presented to show the pipeline in protein microarray applications for identifying antibodies against Mycobacterium tuberculosis.

5:15 Panel Discussion with Afternoon Speakers

5:45 – 7:00 Welcome Reception in the Exhibit Hall with Poster Viewing

7:00 Close of Day

Day 1 | Day 2Download Pipeline 4 Brochure