Differentiating Live Versus Dead Gram-Positive and Gram-Negative Bacteria With and Without Oxidative Stress Using Buoyant Mass Measurements.

Expeditious and accurate determination of pathogenic bacteria cell viability is of great importance to public health for numerous areas including medical diagnostics, food safety, and environmental monitoring. In this work a cell buoyant mass classifier approach is presented to assess bacteria cell viability in real time. Buoyant mass measurements for live and dead Gram-positive and Gram-negative bacteria populations were acquired with a commercial suspended microchannel resonator, Archimedes, to generate receiver operating characteristic (ROC) curves.

Integrated Methods to Manufacture Hydrogel Microparticles with High Protein Conjugation Capacity and Binding Kinetics via Viral Nanotemplate Display.

Genetically modified tobacco mosaic virus (TMV) can serve as a potent nanotemplate for high capacity protein conjugation through covalent coupling to its coat proteins with precise nanoscale spacing. TMV's own genomic RNA can also be exploited for orientationally controlled assembly onto various platforms with sequence and spatial selectivity via nucleic acid hybridization. Here we describe detailed methods for fabrication of hydrogel microparticles with capture DNA sequences, chemical activation and programming of TMV templates, TMV assembly with the microparticles and protein conjugation via bio-orthogonal click reactions.

Mass and density measurements of live and dead Gram-negative and Gram-positive bacterial populations.

Monitoring cell growth and measuring physical features of food-borne pathogenic bacteria are important for better understanding the conditions under which these organisms survive and proliferate. To address this challenge, buoyant masses of live and dead Escherichia coli O157:H7 and Listeria innocua were measured using Archimedes, a commercially available suspended microchannel resonator (SMR). Cell growth was monitored with Archimedes by observing increased cell concentration and buoyant mass values of live growing bacteria.

Microfluidic fabrication of hydrogel microparticles containing functionalized viral nanotemplates.

We demonstrate rapid microfluidic fabrication of hybrid microparticles composed of functionalized viral nanotemplates directly embedded in polymeric hydrogels. Specifically, genetically modified tobacco mosaic virus (TMV) templates were covalently labeled with fluorescent markers or metalized with palladium (Pd) nanoparticles (Pd-TMV) and then suspended in a poly(ethylene glycol)-based solution. Upon formation in a flow-focusing device, droplets were photopolymerized with UV light to form microparticles.

Fabrication of uniform DNA-conjugated hydrogel microparticles via replica molding for facile nucleic acid hybridization assays.

We identify and investigate several critical parameters in the fabrication of single-stranded DNA conjugated poly(ethylene glycol) (PEG) microparticles based on replica molding (RM) for highly uniform and robust nucleic acid hybridization assays. The effects of PEG-diacrylate, probe DNA, and photoinitiator concentrations on the overall fluorescence and target DNA penetration depth upon hybridization are examined. Fluorescence and confocal microscopy results illustrate high conjugation capacity of the probe and target DNA, femtomole sensitivity, and sequence specificity.

Hierarchical assembly of viral nanotemplates with encoded microparticles via nucleic acid hybridization.

We demonstrate hierarchical assembly of tobacco mosaic virus (TMV)-based nanotemplates with hydrogel-based encoded microparticles via nucleic acid hybridization. TMV nanotemplates possess a highly defined structure and a genetically engineered high density thiol functionality. The encoded microparticles are produced in a high throughput microfluidic device via stop-flow lithography (SFL) and consist of spatially discrete regions containing encoded identity information, an internal control, and capture DNAs.

Epi-allelic Erk1 and Erk2 knockdown series for quantitative analysis of T cell Erk regulation and IL-2 production.

Erk activation is often used as a downstream pathway indicator of TCR signaling, generally in terms of both Erk1 and Erk2 isoforms measured together. In order to investigate potential distinctions between Erk1 and Erk2 regulation and effects downstream of TCR ligation, we generated a series of stable and independent Erk1 and Erk2 shRNA knockdown lines in the 1B6 T cell hybridoma. We observed no compensatory effect by opposite isoform upregulation, and found similar fractions of total phosphorylated Erk1/2 across this epi-allelic series in response to both anti-CD3 and peptide-MHC stimulation of TCR.

Quantitative network signal combinations downstream of TCR activation can predict IL-2 production response.

Proximal signaling events activated by TCR-peptide/MHC (TCR-pMHC) binding have been the focus of intense ongoing study, but understanding how the consequent downstream signaling networks integrate to govern ultimate avidity-appropriate TCR-pMHC T cell responses remains a crucial next challenge. We hypothesized that a quantitative combination of key downstream network signals across multiple pathways must encode the information generated by TCR activation, providing the basis for a quantitative model capable of interpreting and predicting T cell functional responses. To this end, we measured 11 protein nodes across six downstream pathways, along five time points from 10 min to 4 h, in a 1B6 T cell hybridoma stimulated by a set of three myelin proteolipid protein 139-151 altered peptide ligands.