An integrated microfluidic device for influenza and other genetic analyses

An integrated microfluidic device capable of performing a variety of genetic assays has been developed as a step towards building systems for widespread dissemination. The device integrates fluidic and thermal components such as heaters, temperature sensors, and addressable valves to control two nanoliter reactors in series followed by an electrophoretic separation. This combination of components is suitable for a variety of genetic analyses. As an example, we have successfully identified sequence-specific hemagglutinin A subtype for the A/LA/1/87 strain of influenza virus. The device uses a compact design and mass production technologies, making it an attractive platform for a variety of widely disseminated applications.     

A versatile microfabricated platform for electrophoresis of double- and single-stranded DNA

We demonstrate a versatile microfabricated electrophoresis platform, incorporating arrays of integrated on-chip electrodes, heaters, and temperature sensors. This design allows a range of different sieving gels to be used within the same device to perform separations involving both single- and double-stranded DNA over distances on the order of 1 cm. We use this device to compare linear and cross-linked polyacrylamide, agarose, and thermo-reversible Pluronic-F127 gels on the basis of gel casting ease, reusability, and overall separation performance using a 100 base pair double-stranded DNA ladder as a standard sample. While cross-linked polyacrylamide matrices provide consistently high-quality separations in our system over a wide range of DNA fragment sizes, Pluronic gels also offer compelling advantages in terms of the ability to remove and reload the gel. Agarose gels offer good separation performance, however, additional care must be exercised to ensure consistent gel properties as a consequence of the need for elevated gel loading temperatures. We also demonstrate the use of denaturing cross-linked polyacrylamide gels at concentrations up to 19% to separate single-stranded DNA fragments ranging in size from 18 to 400 bases in length. Primers differing by 4 bases at a read length of 30 bases can be separated with a resolution of 0.9-1.0 in under 20 min. This level of performance is sufficient to conduct a variety of genotyping assays including the rapid detection of single nucleotide polymorphisms (SNPs) in a microfabricated platform. The ability to use a single microelectrophoresis system to satisfy a wide range of separation applications offers molecular biologists an unprecedented level of flexibility in a portable and inexpensive format.     

Random replicators with high-order interactions

We use tools of the equilibrium statistical mechanics of disordered systems to study analytically the statistical properties of an ecosystem composed of N species interacting via random mutual interactions, as well as via deterministic self-interactions of order p>/=2. We show that the main effect of increasing the order of the interactions among the species is to make the system less competitive, in the sense that the fraction of extinct species is greatly reduced. In addition, we find that for p>2 there is a threshold value which gives a lower bound to the concentration of the surviving species, preventing then the existence of rare species and, consequently, increasing the robustness of the ecosystem to external perturbations.     

Separation performance of single-stranded DNA electrophoresis in photopolymerized cross-linked polyacrylamide gels

Considerable effort has been directed toward optimizing performance and maximizing throughput in ssDNA electrophoresis because it is a critical analytical step in a variety of genomic assays. Ultimately, it would be desirable to quantitatively determine the achievable level of separation resolution directly from measurements of fundamental physical properties associated with the gel matrix rather than by the trial and error process often employed. Unfortunately, this predictive capability is currently lacking, due in large part to the need for a more detailed understanding of the fundamental parameters governing separation performance (mobility, diffusion, and dispersion). We seek to address this issue by systematically characterizing electrophoretic mobility, diffusion, and dispersion behavior of ssDNA fragments in the 70-1,000 base range in a photopolymerized cross-linked polyacrylamide matrix using a slab gel DNA sequencer. Data are collected for gel concentrations of 6, 9, and 12%T at electric fields ranging from 15 to 40 V/cm, and resolution predictions are compared with corresponding experimentally measured values. The data exhibit a transition from behavior consistent with the Ogston model for small fragments to behavior in agreement with the biased reptation model at larger fragment sizes. Mobility data are also used to estimate the mean gel pore size and compare the predictions of several models.     

An inexpensive microslab gel DNA electrophoresis system with real-time fluorescence detection

In this paper, we describe the construction of a simple yet powerful gel electrophoresis apparatus that can be used to perform size-selective separations of DNA fragments in virtually any laboratory. This system employs a microslab gel format with a novel gel casting technique that eliminates the need for delicate combs to define sample loading wells. The compact size of the microslab gel format allows rapid separations to be performed at low voltages using submicroliter sample volumes. Real time fluorescence detection of the migrating DNA fragments is accomplished using an inexpensive digital microscope that directly connects to any PC with a USB interface. The microscope is readily adaptable for this application by replacing its white light source with a blue light-emitting diode (LED) and adding an appropriate emission filter. Both polyacrylamide and agarose gels can be used as separation matrices. Separation performance was characterized using standard dsDNA ladders, and correct sizing of a 191 bp PCR product was achieved in 15 min. The low cost and simplicity of this system makes it ideally suited for use in a variety of laboratory and educational settings.     

Enzymatic sculpting of nanoscale and microscale surface topographies

Lithography-free etching of complex surface features is achieved by harnessing the enzyme proteinase K (PK), controlled by bovine serum albumin (BSA), to digest a biodegradable polymer. This bio-sculpting process is used to construct a membraneless filtration device for the size-based isolation and enrichment of cells from whole blood.     

Maturation of auditory temporal integration and inhibition assessed with event-related potentials (ERPs)

Background

We examined development of auditory temporal integration and inhibition by assessing electrophysiological responses to tone pairs separated by interstimulus intervals (ISIs) of 25, 50, 100, 200, 400, and 800 ms in 28 children aged 7 to 9 years, and 15 adults.

Results

In adults a distinct neural response was elicited to tones presented at ISIs of 25 ms or longer, whereas in children this was only seen in response to tones presented at ISIs above 100 ms. In adults, late N1 amplitude was larger for the second tone of the tone pair when separated by ISIs as short as 100 ms, consistent with the perceptual integration of successive stimuli within the temporal window of integration. In contrast, children showed enhanced negativity only when tone pairs were separated by ISIs of 200 ms. In children, the amplitude of the P1 component was attenuated at ISIs below 200 ms, consistent with a refractory process.

Conclusions

These results indicate that adults integrate sequential auditory information into smaller temporal segments than children. These results suggest that there are marked maturational changes from childhood to adulthood in the perceptual processes underpinning the grouping of incoming auditory sensory information, and that electrophysiological measures provide a sensitive, non-invasive method allowing further examination of these changes.     

Fluid mixing in planar spiral microchannels

Mixing of fluids at the microscale poses a variety of challenges, many of which arise from the fact that molecular diffusion is the dominant transport mechanism in the laminar flow regime. While considerable progress has been made toward developing strategies to achieve improved mixing in microfluidic systems, many of these techniques introduce additional complexity to device fabrication and/or operation processes. In this work, we explore the use of compact spiral-shaped flow geometries designed to achieve efficient mixing in a format that can be constructed using a single planar soft lithography step without the need for multilayer alignment. A series of 150 microm-wide by 29 microm-tall channels were constructed, each of which incorporated a series of spiral shaped sections arrayed along the flow path. Five spiral designs with varying channel lengths were investigated, and mixing studies were carried out at flow rates corresponding to Reynolds numbers ranging from 0.02 to 18.6. Under appropriate conditions, transverse Dean flows are induced that augment diffusive transport and promote enhanced mixing in considerably shorter downstream distances as compared with conventional planar straight channel designs. Mixing efficiency can be further enhanced by incorporating expansion vortex effects via abrupt changes in cross-sectional area along the flow path.