Reducing Uncertainty Through Mutual Information in Structural and Systems Biology.

Systems biology models are useful models of complex biological systems that may require a large amount of experimental data to fit each model's parameters or to approximate a likelihood function. These models range from a few to thousands of parameters depending on the complexity of the biological system modeled, potentially making the task of fitting parameters to the model difficult - especially when new experimental data cannot be gathered. We demonstrate a method that uses structural biology predictions to augment systems biology models to improve systems biology models' predictions without having to gather more experimental data.

Visualizing PIEZO1 Localization and Activity in hiPSC-Derived Single Cells and Organoids with HaloTag Technology.

PIEZO1 is critical to numerous physiological processes, transducing diverse mechanical stimuli into electrical and chemical signals. Recent studies underscore the importance of visualizing endogenous PIEZO1 activity and localization to understand its functional roles. To enable physiologically and clinically relevant studies on human PIEZO1, we genetically engineered human induced pluripotent stem cells (hiPSCs) to express a HaloTag fused to endogenous PIEZO1.

Stochastic Gradient Bayesian Optimal Experimental Designs for Simulation-based Inference.

Simulation-based inference (SBI) methods tackle complex scientific models with challenging inverse problems. However, SBI models often face a significant hurdle due to their non-differentiable nature, which hampers the use of gradient-based optimization techniques. Bayesian Optimal Experimental Design (BOED) is a powerful approach that aims to make the most efficient use of experimental resources for improved inferences.

Pneumatic computers for embedded control of microfluidics.

Alternative computing approaches that interface readily with physical systems are well suited for embedded control of those systems. We demonstrate finite state machines implemented as pneumatic circuits of microfluidic valves and use these controllers to direct microfluidic liquid handling procedures on the same chip. These monolithic integrated systems require only power to be supplied externally, in the form of a vacuum source.

Phase-Optimized Peristaltic Pumping by Integrated Microfluidic Logic.

Microfluidic droplet generation typically entails an initial stabilization period on the order of minutes, exhibiting higher variation in droplet volume until the system reaches monodisperse production. The material lost during this period can be problematic when preparing droplets from limited samples such as patient biopsies. Active droplet generation strategies such as antiphase peristaltic pumping effectively reduce stabilization time but have required off-chip control hardware that reduces system accessibility.

Fabrication of Multilayer Molds by Dry Film Photoresist.

Dry film photoresists are widely employed to fabricate high-aspect-ratio microstructures, such as molds for microfluidic devices. Unlike liquid resists, such as SU-8, dry films do not require a cleanroom facility, and it is straightforward to prepare uniform and reproducible films as thick as 500 µm. Multilayer patterning, however, can be problematic with dry film resists even though it is critical for a number of microfluidic devices.

High-resolution integrated piezoresistive sensors for microfluidic monitoring.

Microfluidic devices are traditionally monitored by bulky and expensive off-chip sensors. We have developed a soft piezoresistive sensor capable of measuring micron-level strains that can be easily integrated into devices via soft lithography. We apply this sensor to achieve fast and localized monitoring of pressure, flow, and valve actuation.

Cell patterning by surface tension pinning in microfluidic channels.

We present a simple method to pattern multiple cell populations inside a microfluidic channel. The microchannel is partially filled with a cell suspension, and the position of the liquid boundary remains pinned by surface tension. Cells then adhere only in the filled portion of the channel, producing a very sharp boundary.

Microfluidic filter device with nylon mesh membranes efficiently dissociates cell aggregates and digested tissue into single cells.

Tissues are increasingly being analyzed at the single cell level in order to characterize cellular diversity and identify rare cell types. Single cell analysis efforts are greatly limited, however, by the need to first break down tissues into single cell suspensions. Current dissociation methods are inefficient, leaving a significant portion of the tissue as aggregates that are filtered away or left to confound results.

Microfluidic device for rapid digestion of tissues into cellular suspensions.

The ability to harvest single cells from tissues is currently a bottleneck for cell-based diagnostic technologies, and remains crucial in the fields of tissue engineering and regenerative medicine. Tissues are typically broken down using proteolytic digestion and various mechanical treatments, but success has been limited due to long processing times, low yield, and high manual labor burden. Here, we present a novel microfluidic device that utilizes precision fluid flows to improve the speed and efficiency of tissue digestion.

Compartmentalized Culture of Perivascular Stroma and Endothelial Cells in a Microfluidic Model of the Human Endometrium.

The endometrium is the inner lining of the uterus. Following specific cyclic hormonal stimulation, endometrial stromal fibroblasts (stroma) and vascular endothelial cells exhibit morphological and biochemical changes to support embryo implantation and regulate vascular function, respectively. Herein, we integrated a resin-based porous membrane in a dual chamber microfluidic device in polydimethylsiloxane that allows long term in vitro co-culture of human endometrial stromal and endothelial cells.

Patterning of sharp cellular interfaces with a reconfigurable elastic substrate.

Micropatterned cocultures are a useful experimental tool for the study of cell-cell interactions. Patterning methods often rely on sequential seeding of different cell types or removal of a barrier separating two populations, but it is difficult to pattern sharp interfaces between pure populations with low cross-contamination when using these approaches. Patterning by the use of reconfigurable substrates can overcome these limitations, but such methods can be costly and challenging to employ in a typical biology laboratory.

Vacuum pressure generation via microfabricated converging-diverging nozzles for operation of automated pneumatic logic.

Microfluidic devices with integrated pneumatic logic enable automated fluid handling without requiring external control instruments. These chips offer the additional advantage that they may be powered by vacuum and do not require an electricity source. This work describes a microfluidic converging-diverging (CD) nozzle optimized to generate vacuum at low input pressures, making it suitable for microfluidic applications including powering integrated pneumatic logic.

Scaling of pneumatic digital logic circuits.

The scaling of integrated circuits to smaller dimensions is critical for achieving increased system complexity and speed. Digital logic circuits composed of pneumatic microfluidic components have to this point been limited to a circuit density of 2-4 gates cm(-2), constraining the complexity of the digital systems that can be achieved. We explored the use of precision machining techniques to reduce the size of pneumatic valves and resistors, and to achieve more accurate and efficient placement of ports and vias.

Pain reduction and financial incentives to improve glucose monitoring adherence in a community health center.

Self-monitoring of blood glucose is a critical component of diabetes management. However, patients often do not maintain the testing schedule recommended by their healthcare provider. Many barriers to testing have been cited, including cost and pain.

A Macro-to-Micro Interface for the Control of Cellular Organization.

The spatial organization of cellular communities plays a fundamental role in determining intercellular communication and emergent behavior. However, few tools exist to modulate tissue organization at the scale of individual cells, particularly in the case of dynamic manipulation. Micromechanical reconfigurable culture achieves dynamic control of tissue organization by culturing adherent cells on microfabricated plates that can be shifted to reorganize the arrangement of the cells.

Microfabrication of High-Resolution Porous Membranes for Cell Culture.

Microporous membranes are widely utilized in cell biology to study cell-cell signaling and cell migration. However, the thickness and low porosity of commercial track-etched membranes limit the quality of cell imaging and the degree of cell-cell contact that can be achieved on such devices. We employ photolithography-based microfabrication to achieve porous membranes with pore diameter as small as 0.

Microfluidic serial dilution ladder.

Serial dilution is a fundamental procedure that is common to a large number of laboratory protocols. Automation of serial dilution is thus a valuable component for lab-on-a-chip systems. While a handful of different microfluidic strategies for serial dilution have been reported, approaches based on continuous flow mixing inherently consume larger amounts of sample volume and chip real estate.

Pneumatic oscillator circuits for timing and control of integrated microfluidics.

Frequency references are fundamental to most digital systems, providing the basis for process synchronization, timing of outputs, and waveform synthesis. Recently, there has been growing interest in digital logic systems that are constructed out of microfluidics rather than electronics, as a possible means toward fully integrated laboratory-on-a-chip systems that do not require any external control apparatus. However, the full realization of this goal has not been possible due to the lack of on-chip frequency references, thus requiring timing signals to be provided from off-chip.

A co-culture device with a tunable stiffness to understand combinatorial cell-cell and cell-matrix interactions.

Cell behavior on 2-D in vitro cultures is continually being improved to better mimic in vivo physiological conditions by combining niche cues including multiple cell types and substrate stiffness, which are well known to impact cell phenotype. However, no system exists in which a user can systematically examine cell behavior on a substrate with a specific stiffness (elastic modulus) in culture with a different cell type, while maintaining distinct cell populations. We demonstrate the modification of a silicon reconfigurable co-culture system with a covalently linked hydrogel of user-defined stiffness.

Live imaging reveals active infiltration of mitotic zone by its stem cell niche.

Stem cells niches are increasingly recognized as dynamic environments that play a key role in transducing signals that allow an organism to exert control on its stem cells. Live imaging of stem cell niches in their in vivo setting is thus of high interest to dissect stem cell controls. Here we report a new microfluidic design that is highly amenable to dissemination in biology laboratories that have no microfluidics expertise.

Optical stimulation and imaging of functional brain circuitry in a segmented laminar flow chamber.

Microfluidic technology is emerging as a useful tool for the study of brain slices, offering precise delivery of chemical factors along with robust oxygen and nutrient transport. However, continued reliance upon electrode-based physiological recording poses inherent limitations in terms of physical access, as well as the number of sites that can be sampled simultaneously. In the present study, we combine a microfluidic laminar flow chamber with fast voltage-sensitive dye imaging and laser photostimulation via caged glutamate to map neural network activity across large cortical regions in living brain slices.

Fibroblasts influence muscle progenitor differentiation and alignment in contact independent and dependent manners in organized co-culture devices.

Myoblasts are precursor muscle cells that lie nascent to mature skeletal muscle. Once muscle is damaged, these cells migrate, fuse, and regenerate the muscle tissue. It is known that skeletal muscle can partially regenerate in vivo after muscle tissue damage.

Semi-autonomous liquid handling via on-chip pneumatic digital logic.

This report presents a liquid-handling chip capable of executing metering, mixing, incubation, and wash procedures largely under the control of on-board pneumatic circuitry. The only required inputs are four static selection lines to choose between the four machine states, and one additional line for power. State selection is simple: constant application of vacuum to an input causes the device to execute one of its four liquid handling operations.

Microenvironmental regulation of the sinusoidal endothelial cell phenotype in vitro.

Unlabelled: Liver sinusoidal endothelial cells (LSECs) differ, both structurally and functionally, from endothelial cells (ECs) lining blood vessels of other tissues. For example, in contrast to other ECs, LSECs possess fenestrations, have low detectable levels of platelet endothelial cell adhesion molecule 1 expression, and in rat tissue, they distinctively express a cell surface marker recognized by the SE-1 antibody. These unique phenotypic characteristics seen in hepatic tissue are lost over time upon culture in vitro; therefore, this study sought to systematically examine the effects of microenvironmental stimuli--namely, extracellular matrix and neighboring cells, on the LSEC phenotype in vitro.