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Cambridge Healthtech Institute’s 7th Annual
Engineering Genes, Vectors, Constructs and Clones
Upstream Decisions Lead to Downstream Success
January 19-20, 2015

Protein expression is never a simple task and the demand for high-quality biotherapeutic proteins continues to grow. Bottlenecks arise frequently because functional recombinant proteins are difficult to produce, thus protein expression engineers are often forced to return to the drawing board. This usually requires designing new cloning schemes, including lengthy verification and sequence analysis of the gene or protein of interest, moving a gene from one vector to another, transfecting the vector in an alternative host, re-characterizing the expressed protein or any of the above—an inefficient, time-consuming and expensive process.

Cambridge Healthtech Institute’s Seventh 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.


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Final Agenda 


SUNDAY, JANUARY 18


4:00-5:00 pm Short Course Registration

5:00-8:00 Pre-Conference Dinner Short Courses (More Details >>)


4:00-8:00 Main Conference Registration


MONDAY, JANUARY 19

7:30 am Conference Registration and Morning Coffee


Synthetic Biology

9:00 Chairperson’s Opening Remarks

Mark Welch, Ph.D., Director, Gene Design, DNA2.0, Inc.


Keynote Presentation

9:10 Design, Build, Test and Learn Strategies for Genome Engineering

Ryan T. GillRyan T. Gill, Ph.D., Associate Professor, Chemical and Biological Engineering, University of Colorado and Associate Director and Fellow, Renewable and Sustainable Energy Institute

Advances in DNA synthesis and sequencing are enabling new approaches for engineering biological systems. Such approaches build off of decades of broader efforts in the engineering and computational sciences to direct the design of proteins, pathways and organisms to perform desired functions. This presentation describes such approaches and how they are being applied to improved production of various target molecules.


9:50 The Engineering of Artificial Cellular Nanosystems Using Synthetic Biology Approaches

TanCheemengCheemeng Tan, Ph.D., Assistant Professor, Biomedical Engineering, University of California, Davis

Artificial biological systems represent effective platforms to test synthetic components beyond cells, to produce target molecules in vitro and enable new therapeutic approaches. I discuss two popular ones. Cell-free systems are isolated circuits assembled with biological components to perform defined tasks in vitro. But artificial cells are biomimetic and compartmentalized compositions of transcription-translation machinery combined with biological information. These systems are widely relevant for producing bio-commodities and biomedical applications.

10:20 Coffee Break

10:45 An Integrative Genome-Scale E. coli Model for Targeted Experimentation in Systems and Synthetic Biology

IliasTagkopoulosIlias Tagkopoulos, Ph.D., Assistant Professor, Computer Science and Genome Center, University of California, Davis

We present an integrative Escherichia coli model that bridges the transcriptional, signal transduction and metabolic layers through a constraint-based framework. Training of this modeling over the most extensive normalized genome-scale compendium resulted in a performance highly predictive of growth and expression under various environments. We discuss how such models can be used in synthetic biology in conjunction with automated design platforms and new extensions for integration of proteomics and condition-specific predictions.

11:15 Mammalian Systems and Synthetic Biotechnology for Recombinant Protein Production

DongYupLeeDong-Yup Lee, Ph.D., Assistant Professor, Chemical and Biomolecular Engineering, National University of Singapore; Senior Research Scientist, Bioprocessing Technology Institute, A*STAR

The increasing demand for recombinant therapeutic proteins highlights the need to constantly improve the efficiency, yield and quality of these products from mammalian cells. We have recently established a “mammalian systems and synthetic biotechnology” framework where omics-data-driven and hypothetical model-driven approaches are integrated to study their growth characteristics, enhance cellular performance and design novel biological products or functions. This talk presents several applications of the framework.

11:45 Expansion of the Genetic Alphabet

Floyd RomesbergFloyd Romesberg, Ph.D., Associate Professor, Chemistry, The Scripps Research Institute

We have generated an expanded genetic alphabet consisting of the two natural base pairs, A–T and G–C, and a third unnatural base pair of our own design. Recently, we have demonstrated that Escherichia coli may be engineered to import the requisite unnatural triphosphates, and that the resulting six-letter DNA is efficiently replicated and transcribed within the cell. This represents the first semi-synthetic organism that can store and retrieve increased information in its genome.

12:15 pm Sponsored Presentation (Opportunity Available)

12:45 Session Break

1:00 Luncheon Presentation: Systematic Engineering of Biological Systems

MarkWelchMark Welch, Ph.D., Director, Gene Design, DNA2.0, Inc.

Current gene synthesis technologies allow unprecedented capability to tailor biological systems for a wide range of purposes. We describe how gene synthesis in concert with machine learning methods can be used to identify and engineer gene, pathway, genome or protein sequence variables critical for performance. Examples of application for protein expression, pathway optimization and protein engineering are discussed.


Analyzing Constructs, Optimizing Codons,
and Enabling Vectors

2:00 Chairperson’s Remarks

Joseph D. Kittle, Jr., Ph.D., Assistant Professor, Chemistry and Biochemistry, Ohio University; Founder and CSO, MTL, LLC

2:05 A Condition-Specific Codon Optimization Approach for Improved Heterologous Gene Expression

HalAlperHal Alper, Ph.D., Associate Professor, Chemical Engineering, University of Texas at Austin

Traditional codon optimization neglects many factors known to influence synonymous codon distributions. This talk describes an alternative approach for codon optimization that utilizes systems-level information and codon context for the condition under which heterologous genes are being expressed. Additionally, a probabilistic algorithm is used to generate multiple variants of a given gene. Translational efficiency improvements of nearly 2.9-fold over commercial gene optimization algorithms were seen in yeast.

 

2:35 A Scoring System for Predicting Solubility of Protein Constructs

BrianChiswellBrian Chiswell, Ph.D., Assistant Professor, Touro College; Owner and Founder, Dimensions BioSciences

The amino acids chosen to be included in a protein expression construct can greatly affect the usability of a protein in the laboratory. Dimensions BioSciences has developed a scoring system that systemically analyzes the primary and secondary structure of a construct and determines the amino acid sequence most likely to remain soluble throughout purification and downstream experiments. Current applications and calibrations for our scoring system will be presented.

3:05 A Dual Host Vector for Fab Phage Display and Expression of Multiple Antibody Formats in Mammalian Cells

IsidroHotzelIsidro Hötzel, Ph.D., Senior Scientist, Antibody Engineering, Genentech, Inc.

Phage display is widely used in discovery of therapeutic antibodies. A bottleneck in the screening of clones from phage display libraries is the subcloning of variable regions to mammalian vectors for expression of IgG. We developed a vector for Fab phage display that expresses multiple antibody formats in mammalian cells without reformatting, expediting the screening of clones derived by phage display.

3:35 Presentation to be Announced


3:50 Refreshment Break

4:15 Quantification of Cytosolic Plasmid DNA Degradation Using High-Throughput Sequencing: Implications for Gene Delivery

MarkBanaszakMark M. Banaszak Holl, Ph.D., Professor, Chemistry and Biomedical Engineering, University of Michigan

Cytosolic DNA degradation plays an important role in decreasing transgene expression; however, the cleavage locations remain largely unexplored. High-throughput sequence mapping of cytosolic nuclease cleavage sites for Luciferase plasmid in HeLa cells revealed the following most common cut sites: the poly(A) region between the β-lactamase gene and the cytomegalovirus promoter, the 5’ end of the β-lactamase gene, the OriC region, the SV40/poly(A) region, the luciferase gene and the CMV promoter.

4:45 Recombinant Protein Expression and Engineering: Generation of Expression Vectors and Protein Binders

AgustinCorreaAgustín Correa, Ph.D., Research Scientist, Recombinant Protein Unit, Institut Pasteur de Montevideo

Recombinant protein expression is a valuable tool in many industrial applications; however, expression problems often arise. We have generated a vector suite for easy cloning and evaluation of different expression parameters affecting recombinant protein production yields. An attractive application for some recombinant proteins is their use as binding reagents. We evaluated a new library design derived from Sac7d variants (Affitins) to generate binding proteins that can work as potent protein inhibitors.

5:15 Thinking beyond the Plasmid: Rapid Engineering of Stable Protein Expression and Improved Bacterial Strains Using Chromosomal Engineering

JosephKittleJoseph D. Kittle, Jr., Ph.D., Assistant Professor, Chemistry and Biochemistry, Ohio University; Founder and CSO, MTL, LLC

Major bacterial protein production systems use plasmids as vectors. We present new data demonstrating high levels of proteins expression without plasmids. We show how this leads to faster development times, and can substantially lower cost of production.

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



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