Caleb J. Bashor
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View article: Engineering synthetic phosphorylation signaling networks in human cells
Engineering synthetic phosphorylation signaling networks in human cells Open
Protein phosphorylation signaling networks play a central role in how cells sense and respond to their environment. Here, we describe the engineering of artificial phosphorylation networks in which “push-pull” motifs—reversible enzymatic p…
View article: pYtags enable spatiotemporal measurements of receptor tyrosine kinase signaling in living cells
pYtags enable spatiotemporal measurements of receptor tyrosine kinase signaling in living cells Open
Receptor tyrosine kinases (RTKs) are major signaling hubs in metazoans, playing crucial roles in cell proliferation, migration, and differentiation. However, few tools are available to measure the activity of a specific RTK in individual l…
View article: Ultra-high throughput mapping of genetic design space
Ultra-high throughput mapping of genetic design space Open
Massively parallel genetic screens have been used to map sequence-to-function relationships for a variety of genetic elements. However, because these approaches only interrogate short sequences, it remains challenging to perform high throu…
View article: Author response: pYtags enable spatiotemporal measurements of receptor tyrosine kinase signaling in living cells
Author response: pYtags enable spatiotemporal measurements of receptor tyrosine kinase signaling in living cells Open
Full text Figures and data Side by side Abstract Editor's evaluation Introduction Results Discussion Methods Appendix 1 Data availability References Decision letter Author response Article and author information Metrics Abstract Receptor t…
View article: pYtags enable spatiotemporal measurements of receptor tyrosine kinase signaling in living cells
pYtags enable spatiotemporal measurements of receptor tyrosine kinase signaling in living cells Open
Receptor tyrosine kinases (RTKs) are major signaling hubs in metazoans, playing crucial roles in cell proliferation, migration, and differentiation. However, few tools are available to measure the activity of a specific RTK in individual l…
View article: Cooperative assembly confers regulatory specificity and long-term genetic circuit stability
Cooperative assembly confers regulatory specificity and long-term genetic circuit stability Open
In eukaryotes, links in gene regulatory networks are often maintained through cooperative self-assembly between transcriptional regulators (TRs) and DNA cis-regulatory motifs, a strategy widely thought to enable highly specific regulatory …
View article: Assessing the impact of silicon nanowires on bacterial transformation and viability of <i>Escherichia coli</i>
Assessing the impact of silicon nanowires on bacterial transformation and viability of <i>Escherichia coli</i> Open
In this study nanowires were engineered and we investigated the interface between the biomaterial and bacteria, looking in detail at membrane rupture and cell viability.
View article: Designing Automated, High-throughput, Continuous Cell Growth Experiments Using eVOLVER
Designing Automated, High-throughput, Continuous Cell Growth Experiments Using eVOLVER Open
Continuous culture methods enable cells to be grown under quantitatively controlled environmental conditions, and are thus broadly useful for measuring fitness phenotypes and improving our understanding of how genotypes are shaped by selec…
View article: Complex signal processing in synthetic gene circuits using cooperative regulatory assemblies
Complex signal processing in synthetic gene circuits using cooperative regulatory assemblies Open
Cooperativity in synthetic gene circuits Synthetic biologists would like to be able to make gene regulatory circuits that mimic key properties of eukaryotic gene regulation. Taking a cue from multimeric transcription factor complexes, Bash…
View article: Complex signal processing in synthetic gene circuits using cooperative regulatory assemblies
Complex signal processing in synthetic gene circuits using cooperative regulatory assemblies Open
Eukaryotic genes are regulated by multivalent transcription factor complexes. Through cooperative self-assembly, these complexes perform nonlinear regulatory operations involved in cellular decision-making and signal processing. In this st…
View article: The strength of protein-protein interactions controls the information capacity and dynamical response of signaling networks
The strength of protein-protein interactions controls the information capacity and dynamical response of signaling networks Open
Eukaryotic cells transmit information by signaling through complex networks of interacting proteins. Here we develop a theoretical and computational framework that relates the biophysics of protein-protein interactions (PPIs) within a sign…
View article: The strength of protein-protein interactions controls the information capacity and dynamical response of signaling networks
The strength of protein-protein interactions controls the information capacity and dynamical response of signaling networks Open
Eukaryotic cells transmit information by signaling through complex networks of interacting proteins. Here we develop a theoretical and computational framework that relates the biophysics of protein-protein interactions (PPIs) within a sign…
View article: Understanding Biological Regulation Through Synthetic Biology
Understanding Biological Regulation Through Synthetic Biology Open
Engineering synthetic gene regulatory circuits proceeds through iterative cycles of design, building, and testing. Initial circuit designs must rely on often-incomplete models of regulation established by fields of reductive inquiry—bioche…
View article: A generalizable experimental framework for automated cell growth and laboratory evolution
A generalizable experimental framework for automated cell growth and laboratory evolution Open
In the post-genomics era, exploration of phenotypic adaptation is limited by our ability to experimentally control selection conditions, including multi-variable and dynamic pressure regimes. While automated cell culture systems offer real…
View article: Engineering dynamical control of cell fate switching using synthetic phospho-regulons
Engineering dynamical control of cell fate switching using synthetic phospho-regulons Open
Significance Many long-term cellular decisions in development, synaptic plasticity, and immunity require cells to recognize input dynamics such as pulse duration or frequency. In dynamically controlled cells, incoming stimuli are often pro…
View article: 'Deadman' and 'Passcode' microbial kill switches for bacterial containment
'Deadman' and 'Passcode' microbial kill switches for bacterial containment Open
Biocontainment systems that couple environmental sensing with circuit-based control of cell viability could be used to prevent escape of genetically modified microbes into the environment. Here we present two engineered safeguard systems k…