Improved reproducibility by assuring confidence in measurements in biomedical research.

'Irreproducibility' is symptomatic of a broader challenge in measurement in biomedical research. From the US National Institute of Standards and Technology (NIST) perspective of rigorous metrology, reproducibility is only one aspect of establishing confidence in measurements. Appropriate controls, reference materials, statistics and informatics are required for a robust measurement process. Research is required to establish these tools for biological measurements, which will lead to greater confidence in research results.

DNA molecules descending a nanofluidic staircase by entropophoresis.

A complex entropy gradient for confined DNA molecules was engineered for the first time. Following the second law of thermodynamics, this enabled the directed self-transport and self-concentration of DNA molecules. This new nanofluidic method is termed entropophoresis. As implemented in experiments, long DNA molecules were dyed with cyanine dimers, dispersed in a high ionic strength buffer, and confined by a nanofluidic channel with a depth profile approximated by a staircase function. The staircase step depths spanned the transition from strong to moderate confinement. The diffusion of DNA molecules across slitlike steps was ratcheted by entropic forces applied at step edges, so that DNA molecules descended and collected at the bottom of the staircase, as observed by fluorescence microscopy. Different DNA morphologies, lengths, and stoichiometric base pair to dye molecule ratios were tested and determined to influence the rate of transport by entropophoresis. A model of ratcheted diffusion was used to interpret a shifting balance of forces applied to linear DNA molecules of standard length in a complex free energy landscape. Related metrics for the overall and optimum performance of entropophoresis were developed. The device and method reported here transcend current limitations in nanofluidics and present new possibilities in polymer physics, biophysics, separation science, and lab-on-a-chip technology.

A robust diffusion-based gradient generator for dynamic cell assays.

This manuscript describes a new method to generate purely diffusive chemical gradients that can be modified in time. The device is simple in its design and easy to use, which makes it amenable to study biological processes that involve static or dynamic chemical gradients such as chemotaxis. We describe the theory underlying the convection-free gradient generator, illustrate the design to implement the theory, and present a protocol to align multiple layers of double sided tape and laminates to fabricate the device. Using this device, a population of mammalian cells was exposed to different concentrations of a toxin within a concentration gradient in a 48 h experiment. Cells were probed dynamically by cycling the gradient on and off, and cell response was monitored using time-lapse fluorescence microscopy. The experiment and results illustrate the type of applications involving dynamic cell behavior that can be targeted with this type of gradient generator.

On-chip CO2 control for microfluidic cell culture.

Carbon dioxide partial pressure (P(CO(2))) was controlled on-chip by flowing pre-equilibrated aqueous solutions through control channels across the device. Elevated P(CO(2)) (e.g. 0.05 atm) was modulated in neighboring stagnant channels via equilibration through the highly gas permeable substrate, poly(dimethylsiloxane) (PDMS). Stable gradients in P(CO(2)) were demonstrated with a pair of control lines in a source-sink configuration. P(CO(2)) equilibration was found to be sufficiently rapid (minutes) and stable (days) to enable long-term microfluidic culture of mammalian cells. The aqueous solutions flowing through the device also mitigated pervaporative losses at sustained elevated temperatures (e.g. 37 C), as compared to flowing humidified gas through the control lines to control P(CO(2)). Since pervaporation (and the associated increase in osmolality) was minimized, stopped-flow cell culture became possible, wherein cell secretions can accumulate within the confined environment of the microfluidic culture system. This strategy was utilized to demonstrate long-term (> 7 days) microfluidic culture of mouse fibroblasts under stopped-flow conditions without requiring the microfluidic system to be placed inside a cell culture incubator.

Stable nanoparticle aggregates/agglomerates of different sizes and the effect of their size on hemolytic cytotoxicity.

To study the toxicity of nanoparticles under relevant conditions, it is critical to disperse nanoparticles reproducibly in different agglomeration states in aqueous solutions compatible with cell-based assays. Here, we disperse gold, silver, cerium oxide, and positively-charged polystyrene nanoparticles in cell culture media, using the timing between mixing steps to control agglomerate size in otherwise identical media. These protein-stabilized dispersions are generally stable for at least two days, with mean agglomerate sizes of ∼23 nm silver nanoparticles ranging from 43-1400 nm and average relative standard deviations of less than 10%. Mixing rate, timing between mixing steps and nanoparticle concentration are shown to be critical for achieving reproducible dispersions. We characterize the size distributions of agglomerated nanoparticles by further developing dynamic light scattering theory and diffusion limited colloidal aggregation theory. These theories frequently affect the estimated size by a factor of two or more. Finally, we demonstrate the importance of controlling agglomeration by showing that large agglomerates of silver nanoparticles cause significantly less hemolytic toxicity than small agglomerates.

Microfluidic directed self-assembly of liposome-hydrogel hybrid nanoparticles.

We present a microfluidic method to direct the self-assembly of temperature-sensitive liposome-hydrogel hybrid nanoparticles. Our approach yields nanoparticles with structural properties and highly monodisperse size distributions precisely controlled across a broad range relevant to the targeted delivery and controlled release of encapsulated therapeutic agents. We used microfluidic hydrodynamic focusing to control the convective-diffusive mixing of two miscible nanoparticle precursor solutions (a DPPC:cholesterol:DCP phospholipid formulation in isopropanol and a photopolymerizable N-isopropylacrylamide mixture in aqueous buffer) to form nanoscale lipid vesicles with encapsulated hydrogel precursors. These precursor nanoparticles were collected off-chip and were irradiated with ultraviolet (UV) light in bulk to polymerize the nanoparticle interiors into hydrogel cores. Multiangle laser light scattering in conjunction with asymmetric flow field-flow fractionation was used to characterize nanoparticle size distributions, which spanned the approximately 150 to approximately 300 nm diameter range as controlled by microfluidic mixing conditions, with a polydispersity of approximately 3% to approximately 5% (relative standard deviation). Transmission electron microscopy was then used to confirm the spherical shape and core-shell composition of the hybrid nanoparticles. This method may be extended to the directed self-assembly of other similar cross-linked hybrid nanoparticle systems with engineered size/structure-function relationships for practical use in healthcare and life science applications.

Controlled self-assembly of monodisperse niosomes by microfluidic hydrodynamic focusing.

Niosomes are synthetic membrane vesicles formed by self-assembly of nonionic surfactant, often in a mixture with cholesterol and dicetyl phosphate. Because of their inner aqueous core and bilayer membrane shell, niosomes are commonly used as carriers of treatment agents for pharmaceutical and cosmetic applications or contrast agents for clinical imaging applications. In those applications, niosomes are considered as a more economical and stable alternative to their biological counterpart (i.e., liposomes). However, conventional bulk method of niosome preparation requires bulk mixing of two liquid phases, which is time-consuming and not well-controlled. Such mixing conditions often lead to large niosomes with high polydispersity in size and thus affect the consistency of niosome dosage or imaging quality. In this study, we present a new method of niosome self-assembly by microfluidic hydrodynamic focusing to improve on the size and size distributions of niosomes. By taking advantage of the rapid and controlled mixing of two miscible fluids (i.e., alcohol and water) in microchannels, we were able to obtain in seconds nanoscaled niosomes with approximately 40% narrower size distributions compared to the bulk method. We further investigated different parameters that might affect on-chip assembly of niosomes, such as (1) conditions for the microfluidic mixing, (2) chemical structures of the surfactant used (i.e., sorbitan esters Span 20, Span 60, and Span 80), and (3) device materials for the microchannel fabrication. This work suggests that microfluidics may facilitate the development and optimization of biomimetic colloidal systems for nanomedicine applications.

Magnetic connectors for microfluidic applications.

We present a new type of microfluidic connector that employs a ring magnet on one side of the microfluidic chip and a disc magnet on the other side to produce a sealed connection between external tubing and inlets or outlets of microfluidic devices. The connectors are low-cost, simple to use and assemble, and reusable. We used numerical (finite element) simulations in order to optimize their geometry. Configurations that achieve interfacial forces in the range of 2 N to 15 N are discussed. Several types of gasket materials were explored. Finally, we demonstrate an application of these connectors in a microfluidic device used to generate liposomes.

Quantum dot FRET-based probes in thin films grown in microfluidic channels.

This paper describes the development of new fluorescence resonance energy transfer (FRET)-based quantum dot probes for proteolytic activity. The CdSe/ZnS quantum dots are incorporated into a thin polymeric film, which is prepared by layer-by-layer deposition of alternately charged polyelectrolytes. The quantum dots, which serve as fluorescent donors, are separated from rhodamine acceptor molecules, which are covalently attached to the film surface by a varying number of polyelectrolyte layers. When excited with visible light, the emission color of the polyelectrolyte multilayer film appears orange due to FRET between the quantum dots and molecular acceptors. The emission color changes to green when the rhodamine molecules are removed from the surface by enzymatic cleavage. The new probe design enables the use of quantum dots in bioassays, in this study for real-time monitoring of trypsin activity, while alleviating concerns about their potential toxicity. Application of these quantum dot FRET-based probes in microfluidic channels enables bioanalysis of volume-limited samples and single-cell studies in an in vivo-like environment.

The microfluidic palette: a diffusive gradient generator with spatio-temporal control.

This paper describes a new microfluidic device called the "microfluidic palette", capable of generating multiple spatial chemical gradients simultaneously inside a microfluidic chamber. The unique aspect of this work is that chemical gradients are generated by diffusion, without convection, and can either be held constant over long periods, or modified dynamically. We characterized a representative device with a 1.5 mm circular chamber where diffusion takes place, and three access-ports for the delivery and removal of solutes. The gradient stabilizes in approximately 15 min for small molecules and can be maintained constant indefinitely. We demonstrate overlapping gradients with different spatial location and a controlled rotation of a diffusive gradient around its centre. Finally, we demonstrate the applicability of this tool to study the chemotactic response of the bacteria P. aeruginosa to glucose.

T7-based linear amplification of low concentration mRNA samples using beads and microfluidics for global gene expression measurements.

We have demonstrated in vitro transcription (IVT) of cDNA sequences from purified Jurkat T-cell mRNA immobilized on microfluidic packed beds down to single-cell quantities. The microfluidically amplified antisense-RNA (aRNA) was nearly identical in length and quantity compared with benchtop reactions using the same starting sample quantities. Microarrays were used to characterize the number and population of genes in each sample, allowing comparison of the microfluidic and benchtop processes. For both benchtop and microfluidic assays, we measured the expression of approximately 4000 to 9000 genes for sample amounts ranging from 20 pg to 10 ng (2 to 1000 cell equivalents), corresponding to 41 to 93% of the absolute number of genes detected from a 100 ng total RNA control sample. Concordance of genes detected between methods (benchtop vs. microfluidic) and repeats (microfluidic vs. microfluidic) typically exceeded 90%. Validation of microarray by Real-time PCR of a panel of five genes suggests transcription of genes present is approximately six times more efficient with the microfluidic IVT compared with benchtop processing. Microfluidic IVT introduces no bias to the gene expression profile of the sample and provides more efficient transcription of mRNA sequences present at the single-cell level.

Development of aptamer-based affinity assays using temperature gradient focusing: minimization of the limit of detection.

A method is described for an aptamer-based affinity assay using a combination of two nonconventional techniques, temperature gradient focusing (TGF) and field-amplified continuous sample injection TGF (FACSI-TGF), with fluorescence detection. Human immunodeficiency virus reverse transcriptase (HIVRT) is used as the protein target for the assay. The TGF and FACSI-TGF assays are compared to similar results obtained with conventional CE. A range of starting aptamer concentrations are used to determine the optimal LOD for human immunodeficiency virus reverse transcriptase (HIVRT) using each approach. The results indicate that the LODs for HIVRT obtained with TGF and FACSI-TGF are comparable to or even lower than the LODs obtained with conventional CE in spite of the inferior detector used for the TGF and FACSI-TGF assays (arc lamp and low-cost CCD for TGF versus LIF with PMT for CE). It is hypothesized that this is due to the greater reproducibility of the TGF and FACSI-TGF techniques since they do not employ a defined sample injection. The lowest LOD achieved with the new aptamer assay approach is more than an order of magnitude lower than that reported for a similar CE-based aptamer assay for the same target.

Liposome-templated supramolecular assembly of responsive alginate nanogels.

Nanosized gel particles (nanogels) are of interest for a variety of applications, including drug delivery and single-molecule encapsulation. Here, we employ the cores of nanoscale liposomes as reaction vessels to template the assembly of calcium alginate nanogels. For our experiments, a liposome formulation with a high bilayer melting temperature (Tm) is selected, and sodium alginate is encapsulated in the liposomal core. The liposomes are then placed in an aqueous buffer containing calcium chloride, and the temperature is raised up to Tm. This allows permeation of Ca2+ ions through the bilayer and into the core, whereupon these ions gel the encapsulated alginate. Subsequently, the lipid bilayer covering the gelled core is removed by the addition of a detergent. The resulting alginate nanogels have a size distribution consistent with that of the template liposomes (ca. 120-200 nm), as confirmed by transmission electron microscopy and light scattering. Nanogels of different average sizes can be synthesized by varying the template dimensions, and the gel size can be further tuned after synthesis by the addition of monovalent salt to the solution.

Counterflow rejection of adsorbing proteins for characterization of biomolecular interactions by temperature gradient focusing.

A new technique is described for the analysis of small molecules in samples containing serum proteins and for the measurement of the binding of small molecules to serum proteins. The new technique is based on temperature gradient focusing (TGF) and takes advantage of the counterflow used with TGF to exclude serum proteins from the analysis channel while small molecules are focused for detection. The technique is demonstrated for the measurement of the binding constant between a small molecule and serum albumin using both a direct measurement of the free fraction of the small molecule as well as using a competitive binding assay.

Using pattern homogenization of binary grayscale masks to fabricate microfluidic structures with 3D topography.

Because fluids at the microscale form three dimensional interfaces and are subject to three dimensional forces, the ability to create microstructures with modulated topography over large areas could greatly improve control over microfluidic phenomena (e.g., capillarity and mass transport) and enable exciting novel microfluidic applications. Here, we report a method for the fabrication of three-dimensional relief microstructures, based on the emergence of smooth features when a photopolymer is exposed to UV light through a transparency mask with binary motifs. We show that homogeneous features emerge under certain critical conditions that are also common to other, apparently unrelated, phenomena such as the emergence of macroscopic continuum properties of composite materials and the rates of ligand binding to cell membrane receptors. This fabrication method is simple and inexpensive, and yet it allows for the fabrication of microstructures over large areas (centimetres) with topographic modulation of features with characteristic dimensions smaller than 100 micrometres.

Microfluidic directed formation of liposomes of controlled size.

A new method to tailor liposome size and size distribution in a microfluidic format is presented. Liposomes are spherical structures formed from lipid bilayers that are from tens of nanometers to several micrometers in diameter. Liposome size and size distribution are tailored for a particular application and are inherently important for in vivo applications such as drug delivery and transfection across nuclear membranes in gene therapy. Traditional laboratory methods for liposome preparation require postprocessing steps, such as sonication or membrane extrusion, to yield formulations of appropriate size. Here we describe a method to engineer liposomes of a particular size and size distribution by changing the flow conditions in a microfluidic channel, obviating the need for postprocessing. A stream of lipids dissolved in alcohol is hydrodynamically focused between two sheathed aqueous streams in a microfluidic channel. The laminar flow in the microchannel enables controlled diffusive mixing at the two liquid interfaces where the lipids self-assemble into vesicles. The liposomes formed by this self-assembly process are characterized using asymmetric flow field-flow fractionation combined with quasi-elastic light scattering and multiangle laser-light scattering. We observe that the vesicle size and size distribution are tunable over a mean diameter from 50 to 150 nm by adjusting the ratio of the alcohol-to-aqueous volumetric flow rate. We also observe that liposome formation depends more strongly on the focused alcohol stream width and its diffusive mixing with the aqueous stream than on the sheer forces at the solvent-buffer interface.

Standard Practice for Bulk Sample Collection and Swab Sample Collection of Visible Powders Suspected of Being Biological Agents from Nonporous Surfaces: collaborative study.

The draft ASTM Standard, "Standard Practice for Bulk Sample Collection and Swab Sample Collection of Visible Powders Suspected of Being Biological Agents from Nonporous Surfaces," was validated in a collaborative study consisting of 6 teams comprised of Civil Support personnel and First Responders, 2 levels of Bacillus anthracis Sterne and Bacillus thuringiensis Kurstaki spores, and 7 nonporous surfaces. The sample collection standard includes collection of the bulk sample (Method A) using a dry swab to push the sample onto a collection card and collection of residual sample (Method B) using an onsite test kit followed by a wet swab intended for additional onsite testing. Method A is to be performed prior to Method B in order to preserve unadulterated sample as potential criminal evidence. While statistical differences were observed between surfaces, between teams, and the interaction of surfaces and teams for the various sample types collected, these differences are due to the very low variability of the data and a much more narrow distribution than an ideal normal distribution, rather than to any practical differences. The data demonstrate that from both the 1.0 and 0.01 g powder samples, high levels of spores (mean >10(6) CFU) are recovered from the 7 surfaces by both the dry swab used in bulk sample collection (Method A) and the wet swab (Method B) sampling of the residual powder after bulk sample collection. Thus, after bulk sample collection, there is a high level of residual spores remaining for onsite biological testing and both Methods A and B should be performed in the field.

Cleavage of peptides and proteins using light-generated radicals from titanium dioxide.

Protein identification and characterization often requires cleavage into distinct fragments. Current methods require proteolytic enzymes or chemical agents and typically a second reagent to discontinue cleavage. We have developed a selective cleavage process for peptides and proteins using light-generated radicals from titanium dioxide. The hydroxyl radicals, produced at the TiO(2) surface using UV light, are present for only hundreds of microseconds and are confined to a defined reagent zone. Peptides and proteins can be moved past the "reagent zone", and cleavage is tunable through residence time, illumination time, and intensity. Using this method, products are observed consistent with cleavage at proline residues. These initial experiments indicate the method is rapid, specific, and reproducible. In certain configurations, cleavage products are produced in less than 10 s. Reproducible product patterns consistent with cleavage of the peptide bond at proline for angiotensin I, Lys-bradykinin, and myoglobin are demonstrated using capillary electrophoresis. Mass characterization of fragments produced in the cleavage of angiotensin I was obtained using liquid chromatography-mass spectrometry. In addition to the evidence supporting cleavage at proline, enkephalin and peptide A-779, two peptides that do not contain proline, showed no evidence of cleavage under the same conditions.

Simultaneous concentration and separation of coumarins using a molecular micelle in micellar affinity gradient focusing.

We report the use of a molecular micelle for the simultaneous separation and concentration of neutral and hydrophobic analytes using micellar affinity gradient focusing (MAGF). The technique, MAGF, combines the favorable features of micellar electrokinetic chromatography and temperature gradient focusing. The focusing of neutral coumarin analytes was accomplished by the use the molecular micelle, poly(sodium undecenyl sulfate) (poly-SUS). Concentration enhancements of 10-25-fold/min were achieved for focusing of the coumarin dyes. The effect of varying the temperature gradient on the resolution of two of the coumarin dyes was also investigated, demonstrating that improved resolution could be achieved by reducing the steepness of the temperature gradient. In addition, with scanning-mode MAGF (in which the peaks are sequentially scanned past a fixed detection point by varying the buffer counterflow velocity), the use of poly-SUS was shown to produce repeatable and quantitative analyte peaks, making quantitative separations possible with the MAGF technique. Finally, it was shown that peak areas could be increased in scanning MAGF by reducing the scan rate so that the sensitivity of the method can be adjusted as needed.

Cellular immobilization within microfluidic microenvironments: dielectrophoresis with polyelectrolyte multilayers.

The development of biomimetic microenvironments will improve cell culture techniques by enabling in vitro cell cultures that mimic in vivo behavior; however, experimental control over attachment, cellular position, or intercellular distances within such microenvironments remains challenging. We report here the rapid and controllable immobilization of suspended mammalian cells within microfabricated environments using a combination of electronic (dielectrophoresis, DEP) and chemical (polyelectrolyte multilayers, PEMS) forces. While cellular position within the microsystem is rapidly patterned via intermittent DEP trapping, persistent adhesion after removal of electronic forces is enabled by surface treatment with PEMS that are amenable to cellular attachment. In contrast to DEP trapping alone, persistent adhesion enables the soluble microenvironment to be systematically varied, facilitating the use of soluble probes of cell state and enabling cellular characterization in response to various soluble stimuli.