Professional Education

  • Bachelor of Science, Columbia University (2005)
  • Doctor of Philosophy, University of California Berkeley (2012)

Stanford Advisors

Current Research and Scholarly Interests

I am interested in applying Synthetic Biology towards improving genetically encoded probes for studying the Human Gut Microbiota.

Journal Articles

  • Avoidance of Truncated Proteins from Unintended Ribosome Binding Sites within Heterologous Protein Coding Sequences. ACS synthetic biology Whitaker, W. R., Lee, H., Arkin, A. P., Dueber, J. E. 2014


    Genetic sequences ported into non-native hosts for synthetic biology applications can gain unexpected properties. In this study, we explored sequences functioning as ribosome binding sites (RBSs) within protein coding DNA sequences (CDSs) that cause internal translation, resulting in truncated proteins. Genome-wide prediction of bacterial RBSs, based on biophysical calculations employed by the RBS calculator,1 suggests a selection against internal RBSs within CDSs in Escherichia coli, but not those in Saccharomyces cerevisiae. Based on these calculations, silent mutations aimed at removing internal RBSs can effectively reduce truncation products from internal translation. However, a solution for complete elimination of internal translation initiation is not always feasible due to constraints of available coding sequences. Fluorescence assays and Western blot analysis showed that in genes with internal RBSs, increasing the strength of the intended upstream RBS had little influence on the internal translation strength. Another strategy to minimize truncated products from an internal RBS is to increase the relative strength of the upstream RBS with a concomitant reduction in promoter strength to achieve the same protein expression level. Unfortunately, lower transcription levels result in increased noise at the single cell level due to stochasticity in gene expression. At the low expression regimes desired for many synthetic biology applications, this problem becomes particularly pronounced. We found that balancing promoter strengths and upstream RBS strengths to intermediate levels can achieve the target protein concentration while avoiding both excessive noise and truncated protein.

    View details for DOI 10.1021/sb500003x

    View details for PubMedID 24931615

  • Design and Implementation of a Biomolecular Concentration Tracker. ACS synthetic biology Hsiao, V., de Los Santos, E. L., Whitaker, W. R., Dueber, J. E., Murray, R. M. 2014


    As a field, synthetic biology strives to engineer increasingly complex artificial systems in living cells. Active feedback in closed loop systems offers a dynamic and adaptive way to ensure constant relative activity independent of intrinsic and extrinsic noise. In this work, we use synthetic protein scaffolds as a modular and tunable mechanism for concentration tracking through negative feedback. Input to the circuit initiates scaffold production, leading to colocalization of a two-component system and resulting in the production of an inhibitory antiscaffold protein. Using a combination of modeling and experimental work, we show that the biomolecular concentration tracker circuit achieves dynamic protein concentration tracking in Escherichia coli and that steady state outputs can be tuned.

    View details for DOI 10.1021/sb500024b

    View details for PubMedID 24847683

  • Engineering robust control of two-component system phosphotransfer using modular scaffolds PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Whitaker, W. R., Davis, S. A., Arkin, A. P., Dueber, J. E. 2012; 109 (44): 18090-18095


    Synthetic biology applies engineering principles to facilitate the predictable design of biological systems. Biological systems composed of modular parts with clearly defined interactions are generally easier to manipulate than complex systems exhibiting a large number of subtle interactions. However, recreating the function of a naturally complex system with simple modular parts can increase fragility. Here, inspired by scaffold-directed signaling in higher organisms, we modularize prokaryotic signal transduction to allow programmable redirection of phosphate flux from a histidine kinase to response regulators based on targeting by eukaryotic protein-protein interaction domains. Although scaffold-directed colocalization alone was sufficient to direct signaling between components, this minimal system suffered from high sensitivity to changing expression levels of each component. To address this fragility, we demonstrate how to engineer autoinhibition into the kinase so that phosphotransfer is possible only upon binding to the scaffold. This system, in which scaffold performs the dual functions of activating this autoinhibited kinase and directing flux to the cotargeted response regulator, was significantly more robust to varying component concentrations. Thus, we demonstrate that design principles inspired by the complex signal-transduction pathways of eukaryotes may be generalized, abstracted, and applied to prokaryotes using well-characterized parts.

    View details for DOI 10.1073/pnas.1209230109

    View details for Web of Science ID 000311149900082

    View details for PubMedID 23071327



    Spatial control over enzyme organization presents a promising posttranslational strategy for improving metabolic flux. Directly tethering enzyme polypeptides has had inconsistent success. Use of a separate scaffold molecule, built from modular protein-protein interaction domains, provides designable control over enzyme assembly parameters, including stoichiometry, as well as providing scalability for multiple enzymes. Thus, metabolic flux can be optimized by expression of these scaffolds in vivo. It is important to note that exploration of the use of synthetic scaffolds for improving metabolic flux is in its early stages. Accordingly, in this chapter, we describe efforts to date, hypotheses for scaffold function, and parameters to consider for application to new pathways.

    View details for DOI 10.1016/B978-0-12-385075-1.00019-6

    View details for Web of Science ID 000291321200019

    View details for PubMedID 21601098

  • Toward scalable parts families for predictable design of biological circuits CURRENT OPINION IN MICROBIOLOGY Lucks, J. B., Qi, L., Whitaker, W. R., Arkin, A. P. 2008; 11 (6): 567-573


    Our current ability to engineer biological circuits is hindered by design cycles that are costly in terms of time and money, with constructs failing to operate as desired, or evolving away from the desired function once deployed. Synthetic biologists seek to understand biological design principles and use them to create technologies that increase the efficiency of the genetic engineering design cycle. Central to the approach is the creation of biological parts--encapsulated functions that can be composited together to create new pathways with predictable behaviors. We define five desirable characteristics of biological parts--independence, reliability, tunability, orthogonality and composability, and review studies of small natural and synthetic biological circuits that provide insights into each of these characteristics. We propose that the creation of appropriate sets of families of parts with these properties is a prerequisite for efficient, predictable engineering of new function in cells and will enable a large increase in the sophistication of genetic engineering applications.

    View details for DOI 10.1016/j.mib.2008.10.002

    View details for Web of Science ID 000261866200015

    View details for PubMedID 18983935