Acoustic focusing with engineered node locations for high-performance microfluidic particle separation.

Acoustofluidic devices for manipulating microparticles in fluids are appealing for biological sample processing due to their gentle and high-speed capability of sorting cell-scale objects. Such devices are generally limited to moving particles toward locations at integer fractions of the fluid channel width (1/2, 1/4, 1/6, etc.). In this work, we introduce a unique approach to acoustophoretic device design that overcomes this constraint, allowing us to design the particle focusing location anywhere within the microchannel. This is achieved by fabricating a second fluid channel in parallel with the sample channel, separated from it by a thin silicon wall. The fluids in both channels participate to create the ultrasound resonance, while only one channel processes the sample, thus de-coupling the fluidic and acoustic boundaries. The wall placement and the relative widths of the adjacent channels define the particle focusing location. We investigate the operating characteristics of a range of these devices to determine the configurations that enable effective particle focusing and separation. The results show that a sufficiently thin wall negligibly affects focusing efficiency and location compared to a single channel without a wall, validating the success of this design approach without compromising separation performance. Using these principles to design and fabricate an optimized device configuration, we demonstrate high-efficiency focusing of microspheres, as well as separation of cell-free viruses from mammalian cells. These "transparent wall" acoustic devices are capable of over 90% extraction efficiency with 10 µm microspheres at 450 µL min(-1), and of separating cells (98% purity), from viral particles (70% purity) at 100 µL min(-1).

Engineered deletions of HIV replicate conditionally to reduce disease in nonhuman primates.

Antiviral therapies with reduced frequencies of administration and high barriers to resistance remain a major goal. For HIV, theories have proposed that viral-deletion variants, which conditionally replicate with a basic reproductive ratio [R0] > 1 (termed "therapeutic interfering particles" or "TIPs"), could parasitize wild-type virus to constitute single-administration, escape-resistant antiviral therapies. We report the engineering of a TIP that, in rhesus macaques, reduces viremia of a highly pathogenic model of HIV by >3log10 following a single intravenous injection. Animal lifespan was significantly extended, TIPs conditionally replicated and were continually detected for >6 months, and sequencing data showed no evidence of viral escape. A single TIP injection also suppressed virus replication in humanized mice and cells from persons living with HIV. These data provide proof of concept for a potential new class of single-administration antiviral therapies.

Interfacial tension controlled fusion of individual femtolitre droplets and triggering of confined chemical reactions on demand.

This paper describes stepwise on-demand generation and fusion of femtolitre aqueous droplets based on interfacial tension. Sub-millisecond reaction times from droplet fusion were demonstrated, as well as a reversible chemical toggle switch based on alternating fusion of droplets containing acidic or basic solution, monitored with the pH-dependent emission of fluorescein.

On-demand generation of monodisperse femtolitre droplets by shape-induced shear.

We describe a method for creating discrete femtolitre-scale water-in-oil droplets on demand, based solely on a geometrically induced reduction in oil/water interfacial area at microfabricated junction orifices. This on-demand generation method is driven by self-shear of droplets due to interfacial tension induced forces resulting from a localized transition in microchannel height. The magnitudes of shear stresses involved appear to be significantly less than the shearing instabilities used to split off daughter droplets from aqueous mother plugs at microfabricated junctions in continuous water-in-oil segmented flows, which implies that this method may be better suited for studying biochemical reactions and reaction kinetics in droplets of decreased volume without loss of chemical reactivity due to redistribution of surfactant density used to passivate the oil/water interface. Predictable droplet generation rates under constant pressure conditions or the gated formation of one, two or more droplets at a time with fixed pressure pulses have been demonstrated in a similar manner to active on-demand droplet generation strategies, but with a simpler system not needing actuation and sensing equipment beyond a pressure regulator.

Shear-driven redistribution of surfactant affects enzyme activity in well-mixed femtoliter droplets.

We developed a microfluidic platform for splitting well-mixed, femtoliter-volume droplets from larger water-in-oil plugs, where the sizes of the daughter droplets were not limited by channel width. These droplets were separated from mother plugs at a microfabricated T-junction, which enabled the study of how increased confinement affected enzyme kinetics in droplets 4-10 microm in diameter. Initial rates for enzyme catalysis in the mother plugs and the largest daughter drops were close to the average bulk rate, while the rates in smaller droplets decreased linearly with increasing surface to volume ratio. Rates in the smallest droplets decreased by a factor of 4 compared to the bulk rate. Traditional methods for detecting nonspecific adsorption at the water-oil interface were unable to detect evidence of enzyme adsorption, including pendant drop tensiometry, laser scanning confocal microscopy of drops containing labeled proteins in microemulsions, and epifluorescence microscopy of plugs and drops generated on-chip. We propose the slowing of enzyme reaction kinetics in the smaller droplets was the result of increased adsorption and inactivation of enzymes at the water-oil interface arising from transient interfacial shear stresses imparted on the daughter droplets as they split from the mother plugs and passed through the constricted opening of the T-junction. Such stresses are known to modulate the interfacial area and density of surfactant molecules that can passivate the interface. Bright field images of the splitting processes at the junction indicate that these stresses scaled with increasing surface to volume ratios of the droplets but were relatively insensitive to the average flow rate of plugs upstream of the junction.

Differential effect of concurrent chemotherapy regimen on clinical outcomes of preoperative chemoradiotherapy for locally advanced rectal cancer.

PURPOSE: The purpose of this study was to evaluate the differential effect of chemotherapy regimen in preoperative chemoradiotherapy (CRT) for locally advanced rectal cancer. METHODS: The medical records of 279 patients who underwent preoperative CRT followed by surgery for cT3/4 rectal cancer from 2003 to 2010 were retrospectively reviewed. Thirty-four patients were treated with one cycle of i.v. bolus 5-fluorouracil (5-FU) during 1st week (group A), 214 patients with two cycles of i.v. bolus 5-FU during 1st and 5th week (group B), and 31 patients with oral capecitabine on the days with radiotherapy (group C). Propensity score matching was performed between three groups. RESULTS: Median follow-up was 60.1 months. Five-year locoregional recurrence-free survival (LRFS), distant metastasis-free survival (DMFS), disease-free survival (DFS) and overall survival (OS) rates were 91.2, 83.3, 75.0, and 84.5%, respectively. Thirty-one patients per group were allocated to three groups via propensity score matching. On univariate analysis, concurrent chemotherapy regimen was not a significant prognostic factor for survival outcomes in the matched group analysis (OS, p=0.175; DFS, p=0.481; DMFS, p=0.515; LRFS, p=0.456). In addition, there was no significant difference in the sphincter preserving surgery rate, circumferential resection margin status, and pathologic response between three groups (p=0.441, 1.000, 0.818, respectively). As regards to treatment-related toxicity, 9 patients showed grade 3 neutropenia in group B, while there was no grade 3 or higher toxicity in groups A and C. CONCLUSION: The concurrent chemotherapy regimen (5-FU #1 vs 5-FU #2 vs capecitabine) did not have a significant effect on treatment outcomes in locally advanced rectal cancer patients receiving neoadjuvant CRT.

A Bioreactor Method to Generate High-titer, Genetically Stable, Clinical-isolate Human Cytomegalovirus.

Human cytomegalovirus (HCMV) infection is a major cause of morbidity and mortality in transplant patients and a leading cause of congenital birth defects (Saint Louis, 2016). Vaccination and therapeutic studies often require scalable cell culture production of wild type virus, represented by clinical isolates. Obtaining sufficient stocks of wild-type clinical HCMV is often labor intensive and inefficient due to low yield and genetic loss, presenting a barrier to studies of clinical isolates. Here we report a bioreactor method based on continuous infection, where retinal pigment epithelial (ARPE-19) cells adhered to microcarrier beads are infected in a bioreactor and used to produce high-titers of clinical isolate HCMV that maintain genetic integrity of key viral tropism factors and the viral genome. In this bioreactor, an end-stage infection can be maintained by regular addition of uninfected ARPE-19 cells, providing convenient preparation of 107-108 pfu/ml of concentrated TB40/E IE2-EYFP stocks without daily cell passaging or trypsinization. Overall, this represents a 100-fold increase in gain of virus production of 100-times compared to conventional static-culture plates, while requiring 90% less handling time. Moreover, this continuous infection environment has the potential to monitor infection dynamics with applications for real-time tracking of viral evolution.

Development and applications of a beta-catenin oligonucleotide microarray: beta-catenin mutations are dominantly found in the proximal colon cancers with microsatellite instability.

beta-catenin mutations have been identified in a variety of human malignancies; most of these are missense mutations restricted at hot-spot areas in exon 3. beta-catenin mutations are known to be highly associated with colorectal cancers with microsatellite instability (MSI). More than 70 beta-catenin mutations have been reported in colorectal cancers, and approximately 90% of beta-catenin mutations have been found in 11 codons (codons 29, 31, 32, 33, 34, 35, 37, 38, 41, 45, and 48) as missense mutations or in-frame deletions. We have developed an oligonucleotide microarray for detecting beta-catenin mutations at these 11 codons. The developed oligonucleotide microarray can detect a total of 110 types of beta-catenin mutations, including the 60 mutations reported previously. Nine beta-catenin mutations were identified in this study by five different methods, i.e., PCR- single-strand conformational polymorphism, denaturing high performance liquid chromatography, direct sequencing, cloning-sequencing, and with an oligonucleotide microarray. All nine of the mutations were identified by denaturing high performance liquid chromatography, cloning-sequencing, and by the oligonucleotide microarray. However, PCR-single-strand conformational polymorphism missed 1 beta-catenin mutation and direct sequencing missed 2. Five beta-catenin mutations from 74 colorectal carcinomas (34 proximal colon cancers and 40 distal colorectal cancers) and 4 beta-catenin mutations from 31 colorectal cancer cell lines (7 from the proximal colon, 6 from the distal colorectum, and 18 unknown) were identified. In colorectal carcinomas, all 5 of the beta-catenin mutations were found in proximal colon tumors. In colorectal cancer cell lines, 2 of 4 cell lines with beta-catenin mutations originated from the proximal colon, and the remaining 2 cell lines were simply described as having originated from the colon. Considering the relationships among beta-catenin mutations, MSI, and tumor location, the frequency of beta-catenin mutations was found to be meaningfully higher in colorectal carcinomas with MSI than in those with microsatellite stability (P < 0.001); moreover, MSI was found to be more frequent in proximal colon tumors (P < 0.01). In addition, beta-catenin mutations were also found to be associated with proximal colon cancer (P = 0.017).

Insulinoma cell line (MIN6) adhesion and spreading mediated by Arg-Gly-Asp (RGD) sequence conjugated in thermo-reversible gel.

We have functionalized gels with a putative cell-binding (-Arg-Gly-Asp-) (RGD) domain in an effort to regulate mammalian cell behavior in cells entrapped with gel. Adhesion molecules composed of Gly-Arg-Gly-Asp-Ser (GRGDS) peptides and cell recognition ligands were inculcated into thermo-reversible hydrogel composed of N-isopropylacrylamide, with a small amount of succinyl poly(ethylene glycol) (PEG) acrylate (MW 2000) used as a biomimetic extracellular matrix (ECM). The GRGDS-containing p(NiPAAm-co-PEG) copolymer gel was studied in vitro for its ability to promote cell spreading and to increase the viability of cells by introducing PEG spacers. Hydrogel lacking the adhesion molecules proved to be a poor ECM for adhesion, permitting only a 20% spread of the seeded cells after 10 d. When PEG spacer arms, immobilized by a peptide linkage, had been integrated into the hydrogel, conjugation of RGD promoted cell spread by 300% in a 28-d trial. In addition, in a serum-free medium, only GRGDS peptides conjugated with the spacer arm were able to promote cell spread.

Spatial tuning of acoustofluidic pressure nodes by altering net sonic velocity enables high-throughput, efficient cell sorting.

Particle sorting using acoustofluidics has enormous potential but widespread adoption has been limited by complex device designs and low throughput. Here, we report high-throughput separation of particles and T lymphocytes (600 µL min(-1)) by altering the net sonic velocity to reposition acoustic pressure nodes in a simple two-channel device. The approach is generalizable to other microfluidic platforms for rapid, high-throughput analysis.

Probing cell-free gene expression noise in femtoliter volumes.

Cell-free systems offer a simplified and flexible context that enables important biological reactions while removing complicating factors such as fitness, division, and mutation that are associated with living cells. However, cell-free expression in unconfined spaces is missing important elements of expression in living cells. In particular, the small volume of living cells can give rise to significant stochastic effects, which are negligible in bulk cell-free reactions. Here, we confine cell-free gene expression reactions to cell-relevant 20 fL volumes (between the volumes of Escherichia coli and Saccharomyces cerevisiae ), in polydimethylsiloxane (PDMS) containers. We demonstrate that expression efficiency varies widely among different containers, likely due to non-Poisson distribution of expression machinery at the observed scale. Previously, this phenomenon has been observed only in liposomes. In addition, we analyze gene expression noise. This analysis is facilitated by our use of cell-free systems, which allow the mapping of the measured noise properties to intrinsic noise models. In contrast, previous live cell noise analysis efforts have been complicated by multiple noise sources. Noise analysis reveals signatures of translational bursting, while noise dynamics suggest that overall cell-free expression is limited by a diminishing translation rate. In addition to offering a unique approach to understanding noise in gene circuits, our work contributes to a deeper understanding of the biophysical properties of cell-free expression systems, thus aiding efforts to harness cell-free systems for synthetic biology applications.

Fast mixing and reaction initiation control of single-enzyme kinetics in confined volumes.

A device with femtoliter-scale chambers and controlled reaction initiation was developed for single-molecule enzymology. Initially separated substrate and enzyme streams were rapidly mixed in a microfluidic device and encapsulated in an array of individual microreactors, allowing for enzyme kinetics to be monitored with millisecond dead times and single-molecule sensitivity. Because the arrays of chambers were fabricated by micromolding in PDMS, the chambers were monodisperse in size, and the chamber volume could be systematically controlled. Microreactors could be purged and replenished with fresh reactants for consecutive rounds of observation. Repeated experiments with statistically identical initial conditions could be performed rapidly, with zero cross-talk between chambers in the array.

Pelvic actinomycosis with hydronephrosis and colon stricture simulating an advanced ovarian cancer.

Pelvic actinomycosis is an uncommon disease in humans. It has nonspecific and variable clinical features, and thus it is difficult to diagnose. Moreover, appropriate management is delayed or overlooked because it can sometimes simulate advanced ovarian cancer. We report a case of pelvic actinomycosis which manifested with hydronephrosis and bowel stricture, lymph node enlargement and increased level of tumor marker caused by a large pelvic mass. Since this case showed clinical findings mimicking an advanced ovarian carcinoma, it was surgically diagnosed as actinomycosis after neoadjuvant chemotherapy.

Patterning enzymes inside microfluidic channels via photoattachment chemistry.

We have developed a general method for photopatterning well-defined patches of enzymes inside a microfluidic device at any location. First, a passivating protein layer was adsorbed to the walls and floor of a poly(dimethylsiloxane)/glass microchannel. The channel was then filled with an aqueous biotin-linked dye solution. Using an Ar+/Kr+ laser, the fluorophore moieties were bleached to create highly reactive species. These activated molecules subsequently attached themselves to the adsorbed proteins on the microchannel walls and floor via a singlet oxygen-dependent mechanism. Enzymes linked to streptavidin or avidin could then be immobilized via (strept)avidin/biotin binding. Using this process, we were able to pattern multiple patches of streptavidin-linked alkaline phosphatase inside a straight microfluidic channel without the use of valves under exclusively aqueous conditions. The density of alkaline phosphatase in the patches was calculated to be approximately 5% of the maximum possible density by comparison with known standards. Turnover was observed via fluorogenic substrate conversion and fluorescence microscopy. A more complex two-step enzyme reaction was also designed. In this case, avidin-linked glucose oxidase and streptavidin-linked horseradish peroxidase were sequentially patterned in separate patches inside straight microfluidic channels. Product formed at the glucose oxidase patch became the substrate for horseradish peroxidase, patterned downstream, where fluorogenic substrate turnover was recorded.

Creating fluid and air-stable solid supported lipid bilayers.

Solid supported lipid bilayers are rapidly delaminated when drawn through the air/water interface. We have discovered that a close packed monolayer of specifically bound protein prevents this process. The protection mechanism worked in two ways. First, when protein-protected bilayers were drawn through the air/water interface, a thin bulk water layer was visible over the entire bilayer region, thereby preventing air from contacting the surface. Second, a stream of nitrogen was used to remove all bulk water from a protected bilayer, which remained fully intact as determined by fluorescence microscopy. The condition of this dried bilayer was further probed by fluorescence recovery after photobleaching. It was found that lipids were not two-dimensionally mobile in dry air. However, when the bilayer was placed in a humid environment, 91% of the bleached fluorescence signal was recovered, indicating long-range two-dimensional mobility. The diffusion coefficient of lipids under humid conditions was an order of magnitude slower than the same bilayer under water. Protected bilayers could be rehydrated after drying, and their characteristic diffusion coefficient was reestablished. Insights into the mechanism of bilayer preservation were suggested.

The Vroman effect: a molecular level description of fibrinogen displacement.

The molecular level details of the displacement of surface adsorbed fibrinogen from silica substrates were studied by atomic force microscopy, immunochemical assays, fluorescence microscopy, and vibrational sum frequency spectroscopy. The results showed that human plasma fibrinogen (HPF) can be readily displaced from the interface by other plasma proteins near neutral pH because the positively charged alpha C domains on HPF sit between the rest of the macromolecule and the underlying surface. The alpha C domains make weak electrostatic contact with the substrate, which is manifest by a high degree of alignment of Lys and Arg residues. Upon cycling through acidic pH, however, the alpha C domains are irreversibly removed from this position and the rest of the macromolecule is free to engage in stronger hydrogen bonding, van der Waals, and hydrophobic interactions with the surface. This results in a 170-fold decrease in the rate at which HPF can be displaced from the interface by other proteins in human plasma.

Production of interleukin-8 by human neutrophils stimulated with Trichomonas vaginalis.

Neutrophils are the predominant inflammatory cells found in the vaginal discharges of patients infected with Trichomonas vaginalis. Although chemoattractants, such as leukotriene B(4) and interleukin-8 (IL-8), are found in the vaginal discharges of symptomatic trichomoniasis patients, little is known about the mechanism of how neutrophils accumulate or mediate initial inflammatory response after acute T. vaginalis infection. We examined IL-8 production in neutrophils activated by T. vaginalis and evaluated the factors involved in T. vaginalis adherence that might affect IL-8 production. When human neutrophils were stimulated with live trophozoites, T. vaginalis lysate, or T. vaginalis excretory-secretory products, the live trichomonads induced higher levels of IL-8 production than the lysate or products did. When live trichomonads were pretreated with various inhibitors of proteinase, microtubule, microfilament, or adhesin (which are all known to participate in the adherence of T. vaginalis to vaginal epithelial cells), IL-8 production significantly decreased compared with the untreated controls. Furthermore, an NF-kappaB inhibitor (pyrrolidine dithiocarbamate), a mitogen-activated protein (MAP) kinase (MEK) inhibitor (PD98059), and a p38 MAP kinase inhibitor (SB203580) significantly suppressed IL-8 synthesis in neutrophils. These results suggest that live T. vaginalis, particularly adherent trophozoites, can induce IL-8 production in neutrophils and that this action may be mediated through the NF-kappaB and MAP kinase signaling pathways. In other words, T. vaginalis-induced neutrophil recruitment may be mediated via the IL-8 expressed by neutrophils in response to activation by live T. vaginalis.