Framed! Reproducing and Revisiting 150-Year-Old Charts

The Statistical Atlases published by the Census Bureau in the late 1800s utilized a number of novel methods for displaying data. In this paper, we examine the use of framed spine and mosaic plots used in two plates of the Statistical Atlas of 1870. We use forensic statistics to recreate the data using available census information, and then use that data to create framed charts using modern plotting methods. We then examine the effectiveness of the framed charts compared to other alternatives with a user study. The data and code for this study are available online.     

Microfluidic patterning of nanodisc lipid bilayers and multiplexed analysis of protein interaction

We report a microfluidic method for precisely patterning lipid bilayers and a multiplexed assay to examine the interaction between the lipids and protein analytes. The lipids were packaged into nanoscale lipid bilayer particles known as Nanodiscs and delivered to surfaces using microfluidic channels. Two types of lipids were used in this study: biontinylated lipids and phosphoserine lipids. The deposition of biotinylated lipids on a glass surface was confirmed by attaching streptavidin coated quantum dots to the lipids, followed by fluorescent imaging. Using this multiplexed grid assay, we examined binding of annexin to phosphoserine lipids, and compared these results to similar analysis performed by surface plasmon resonance.     

Redox cycling in nanofluidic channels using interdigitated electrodes

Amperometric detection is ideally suited for integration into micro- and nanofluidic systems as it directly yields an electrical signal and does not necessitate optical components. However, the range of systems to which it can be applied is constrained by the limited sensitivity and specificity of the method. These limitations can be partially alleviated through the use of redox cycling, in which multiple electrodes are employed to repeatedly reduce and oxidize analyte molecules and thereby amplify the detected signal. We have developed an interdigitated electrode device that is encased in a nanofluidic channel to provide a hundred-fold amplification of the amperometric signal from paracetamol. Due to the nanochannel design, the sensor is resistant to interference from molecules undergoing irreversible redox reactions. We demonstrate this selectivity by detecting paracetamol in the presence of excess ascorbic acid. Figure  

Micro magnetic stir-bar mixer integrated with parylene microfluidic channels

Previously, we reported a micro magnetic stir-bar mixer driven by an external rotating magnetic field and its rapid mixing performance in polydimethyl-siloxane (PDMS) channels. The PDMS piece with embedded fluid channels were manually aligned to a glass substrate and assembled. In this paper, we report the fabrication and testing results of a micro magnetic stir-bar monolithically integrated in parylene surface-micromachined channels with improved design features, including small tolerance of the stir-bar to channel wall (10 microm). Using of parylene based microchannels with improved design not only provides improved mixing, but also eliminates certain problems associated with PDMS-based channels. For example, porosity of PDMS causes evaporation and absorption of chemicals and thus channels made of PDMS are prone to cross-contamination. We have also demonstrated that the magnetic stir-bar can be used to pump liquid in micro channels.     

Electrophoresis on a polyester thread coupled with an end-channel pencil electrode detector

We present the design and characterization of a low cost, thread-based electrophoretic device with integrated electrochemical detection. The device has an end-channel pencil graphite electrode placement system for performing electrochemical detection on the thread electrophoresis platform with direct sample pipetting onto the thread. We also established the use of methylene blue and neutral red as a pair of reference migration markers for separation techniques coupled with electrochemical detection, as they have different colors for visual analysis and are both electroactive. Importantly, neutral red was also found to migrate at a similar rate to the EOF, indicating that it can be used as a visual identifier of EOF. The utility of our system was demonstrated by electrophoretic separation and electrochemical detection of physiologically relevant concentrations of pyocyanin in a solution containing multiple electroactive compounds. Pyocyanin is a biomarker for the detection of pathogenic Pseudomonas aeruginosa and has a redox potential that is similar to that of methylene blue. The system was able to effectively resolve methylene blue, neutral red, and pyocyanin in less than 7 min of electrophoretic separation. The theoretical limit of detection for pyocyanin was determined to be 559 nM. The electrophoretic mobilities of methylene blue (0.0236 ± 0.0007 mm²/V·s), neutral red (0.0149 ± 0.0007 mm²/V·s), and pyocyanin (0.0107 ± 0.0003 mm²/V·s) were also determined.     

Substrate-dependent kinetics in tyrosinase-based biosensing: amperometry vs. spectrophotometry

Despite the broad use of enzymes in electroanalytical biosensors, the influence of enzyme kinetics on the function of prototype sensors is often overlooked or neglected. In the present study, we employ amperometry as an alternative or complementary method to study the kinetics of tyrosinase, whose catalytic activity results in o-quinone products. We further compare our results for four monophenolic substrates with those obtained from ultraviolet-visible spectrophotometry and show that the results from both assays are in good agreement. We also observe large variations in the enzyme kinetics for different monophenolic substrates depending on the R-group at the para position. To further study this effect, we investigate the stability of quinone products in the enzymatic assay. This information can in principle be utilized to discriminate between different phenolic species by monitoring the reaction rate.     

SINGLET OXYGEN INDUCES FRANK STRAND BREAKS AS WELL AS ALKALI- AND PIPERIDINE-LABILE SITES IN SUPERCOILED PLASMID DNA

A covalently closed, circular, supercoiled plasmid was exposed to singlet oxygen by a separated-surface sensitizer. For each exposure, the quantity of single oxygen entering the DNA target solution was estimated by its oxidation of histidine. After singlet oxygen exposure, some DNA samples were treated to disclose occult lesions. Agarose gel electrophoresis was then used to resolve the unrelaxed supercoils from the relaxed circular and linear species, and all bands were quantitated fluorometrically. Exposure of supercoiled plasmid DNA to singlet oxygen induced frank DNA strand breaks, alkali-labile sites (pH 12.5, 90 degrees C, 30 min), and piperidine-labile sites (0.4 M, 60 degrees C, 30 min), all in a dose-dependent manner. Yields of alkali-labile and piperidine-labile sites ranged from one to four times the frank strand break yield. Replacement of buffered H2O by buffered D2O as the DNA solvent for singlet oxygen exposures increased DNA lesion yields by a factor of 2.6 (averaged over lesion classes). Our data for the detection of frank strand breaks is at variance with published results from studies in which singlet oxygen was derived from a thermolabile endoperoxide dissolved in the DNA solution.     

A bio-barcode assay for on-chip attomolar-sensitivity protein detection

Functionalized nanoparticles hold great promise in realizing highly sensitive and selective biodetection. We report a single disposable chip which is capable of carrying out a multi-step process that employs nanoparticles--a bio-barcode assay (BCA) for single protein marker detection. To illustrate the capability of the system, we tested for the presence of prostate specific antigen (PSA) in buffer solution and goat serum. Detection was accomplished at PSA concentrations as low as 500 aM. This corresponds to only 300 copies of protein analytes using 1 microL total sample volume. We established that the on-chip BCA for PSA detection offers four orders of magnitude higher sensitivity compared to commercially available ELISA-based PSA tests.