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Search Publications by: David J. Ross (Fed)

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Displaying 1 - 25 of 58

Ligify: Automated genome mining for ligand-inducible transcription factors

February 21, 2024
Author(s)
Simon d'Oelsnitz, Andrew Ellington, David J. Ross
Prokaryotic transcription factors can be repurposed into biosensors for the ligand-inducible control of gene expression, but the landscape of chemical ligands for which biosensors exist is extremely limited. To expand this landscape, we developed Ligify, a

Effects of DNA Template Preparation on Variability in Cell-Free Protein Production

August 13, 2022
Author(s)
Eugenia Romantseva, Nina Alperovich, David Ross, Steven Lund, Elizabeth Strychalski
DNA templates for protein expression remain an unexplored source of variability in the performance of cell-free expression (CFE) systems for protein production. To characterize this variability, we investigated the effects of two common DNA extraction

Method for reproducible automated bacterial cell culture and measurement

August 8, 2022
Author(s)
David Ross, Peter Tonner, Olga Vasilyeva
Microbial cell culture is one of the most commonly performed protocols for synthetic biology, and laboratories are increasingly using 96-well plates and laboratory automation systems for cell culture. Here we describe a method for reproducible microbial

The allosteric landscape of the lac repressor

April 13, 2022
Author(s)
Drew S. Tack, Peter Tonner, Abe Pressman, Nathanael David Olson, Eugenia Romantseva, Nina Alperovich, Olga Vasilyeva, David J. Ross, Sasha F. Levy
Allostery is a fundamental biophysical mechanism where the activity of a biomolecule is regulated by the binding of a ligand. Despite playing a central role in many biological processes, a quantitative understanding of allostery is lacking. To

A Roadmap for LIMS at NIST Material Measurement Laboratory

April 11, 2022
Author(s)
Gretchen Greene, Jared Ragland, Zachary Trautt, June W. Lau, Raymond Plante, Joshua Taillon, Adam Abel Creuziger, Chandler A. Becker, Joe Bennett, Niksa Blonder, Lisa Borsuk, Carelyn E. Campbell, Adam Friss, Lucas Hale, Michael Halter, Robert Hanisch, Gary R. Hardin, Lyle E. Levine, Samantha Maragh, Sierra Miller, Chris Muzny, Marcus William Newrock, John Perkins, Anne L. Plant, Bruce D. Ravel, David J. Ross, John Henry J. Scott, Christopher Szakal, Alessandro Tona, Peter Vallone
Instrumentation generates data faster and in higher quantity than ever before, and interlaboratory research is in historic demand domestically and internationally to stimulate economic innovation. Strategic mission needs of the NIST Material Measurement

Single-cell measurement of plasmid copy number and promoter activity

March 5, 2021
Author(s)
Bin Shao, Jayan Rammohan, Daniel Anderson, Nina Alperovich, David J. Ross, Christopher Voigt
We have developed a method to simultaneously count plasmid DNA, RNA transcripts, and protein expression in single living bacteria. From these data, the activity of a promoter in units of RNAP/s can be inferred. This work facilitates the reporting of

Genetic circuit design automation

April 1, 2016
Author(s)
Alec Nielsen, Bryan Der, Jonghyeon Shin, Prashant Vaidyanathan, Douglas Densmore, Vanya M. Paralanov, Elizabeth Strychalski, David J. Ross, Christopher Voigt
Computation can be performed in living cells using DNA-encoded circuits that process sensory information and control biological functions. Their construction is time-intensive, requiring manual part assembly and balancing of regulator expression. We

Thermodynamics of the Hydrolysis Reactions of +--D-galactose 1-phosphate, sn-glycerol 3-phosphate, 4 nitrophenyl phosphate, phosphocreatine, and 3-phospho-D-glycerate

May 1, 2009
Author(s)
Robert N. Goldberg, Brian E. Lang, Catherine T. Lo, David J. Ross, Yadu D. Tewari
Microcalorimetry, high-performance liquid chromatography, and an enzymatic assay have been used to conduct a thermodynamic investigation of five phosphate hydrolysis reactions: α-D-galactose 1 phosphate(aq) + H2O(l) = D-galactose(aq) + orthophosphate(aq)

Multiplexed "Detectorless" Electrophoresis

December 14, 2008
Author(s)
David Ross, Jason Kralj
A new microfluidic electrophoresis device and technique is described that is designed specifically for multiplexed, high throughput separations. The device consists of an array of short (3 mm) capillaries connecting individual sample reservoirs to a common

Electrokinetic Sample Dilution and Concentration in Microfluidics

October 16, 2008
Author(s)
David J. Ross, K G. Olsen, Laurie E. Locascio
A new method is demonstrated which can be used to produce streams of variable, controlled analyte concentration. The method works by electrokinetically manipulating the analyte velocity so that it is different in different parts of a channel. Because of