[show abstract][hide abstract] ABSTRACT: Recent experimental work has described an elegant pattern of branching in the development of the lung. Multiple forms of branching have been identified, including side branching and tip bifurcation. A particularly interesting feature is the phenomenon of 'orthogonal rotation of the branching plane'. The lung must fill 3D space with the essentially 2D phenomenon of branching. It accomplishes this by rotating the branching plane by 90 degrees with each generation. The mechanisms underlying this rotation are not understood. In general, the programs that underlie branching have been hypothetically attributed to genetic 'subroutines' under the control of a 'global master routine' to invoke particular subroutines at the proper time and location, but the mechanisms of these routines are not known. Here, we demonstrate that fundamental mechanisms, the reaction and diffusion of biochemical morphogens, can create these patterns. We used a Partial Differential Equation model that postulates 3 morphogens, which we identify with specific molecules in lung development. We found that cascades of branching events, including side branching, tip splitting and orthogonal rotation of the branching plane, all emerge immediately from the model, without further assumptions. In addition, we found that one branching mode can be easily switched to another, by increasing or decreasing the values of key parameters. This shows how a 'global master routine' could work by the alteration of a single parameter. Being able to simulate cascades of branching events is necessary to understand the critical features of branching, such as orthogonal rotation of the branching plane between successive generations, and branching mode switch during lung development. Thus, our model provides a paradigm for how genes could possibly act to produce spatial structures. Our low-dimensional model gives a qualitative understanding of how generic physiological mechanisms can produce branching phenomena, and how the system can switch from one branching pattern to another using low-dimensional 'control knobs'. The model provides a number of testable predictions, some of which have already been observed (though not explained) in experimental work.
The Journal of Physiology 11/2013; · 4.38 Impact Factor
[show abstract][hide abstract] ABSTRACT: The detection of bacterial pathogens plays an important role in many biomedical applications, including clinical diagnostics, food and water safety, and biosecurity. Most current bacterial detection technologies, however, are unsuitable for use in resource-limited settings where the highest disease burdens often exist. Thus, there is an urgent need to develop portable, user-friendly biosensors capable of rapid detection of multiple pathogens in situ. We report a microfluidic chip for multiplexed detection of bacterial cells that uses antimicrobial peptides (AMPs) with species-specific targeting and binding capabilities. The AMPs are immobilized onto an electrical impedance microsensor array and serve as biorecognition elements for bacterial cell detection. Characterization of peptide immobilization on the sensors revealed robust surface binding via cysteine-gold interactions and vertical alignment relative to the sensor surface. Samples containing Streptococcus mutans and Pseudomonas aeruginosa were loaded in the chip, and both microorganisms were detected at minimum concentrations of 10(5) cfu/mL within 25 min. Measurements performed in a variety of solutions revealed that high-conductivity solutions produced the largest impedance values. By integrating a highly specific bacterial cell capture scheme with rapid electrical detection, this device demonstrates great potential as a next-generation, point-of-care diagnostic platform for the detection of disease-causing pathogenic agents.
Journal of the Association for Laboratory Automation 07/2013; · 1.46 Impact Factor
[show abstract][hide abstract] ABSTRACT: We present a compact mobile phone platform for rapid, quantitative biomolecular detection. This system consists of an embedded circuit for signal processing and data analysis, and disposable microfluidic chips for fluidic handling and biosensing. Capillary flow is employed for sample loading, processing, and pumping to enhance operational portability and simplicity. Graphical step-by-step instructions displayed on the phone assists the operator through the detection process. After the completion of each measurement, the results are displayed on the screen for immediate assessment and the data is automatically saved to the phone's memory for future analysis and transmission. Validation of this device was carried out by detecting Plasmodium falciparum histidine-rich protein 2 (PfHRP2), an important biomarker for malaria, with a lower limit of detection of 16 ng mL(-1) in human serum. The simple detection process can be carried out with two loading steps and takes 15 min to complete each measurement. Due to its compact size and high performance, this device offers immense potential as a widely accessible, point-of-care diagnostic platform, especially in remote and rural areas. In addition to its impact on global healthcare, this technology is relevant to other important applications including food safety, environmental monitoring and biosecurity.
[show abstract][hide abstract] ABSTRACT: Stem cell-based disease modeling presents unique opportunities for mechanistic elucidation and therapeutic targeting. The stable induction of fate-specific differentiation is an essential prerequisite for stem cell-based strategy. Bone morphogenetic protein 2 (BMP-2) initiates receptor-regulated Smad phosphorylation, leading to the osteogenic differentiation of mesenchymal stromal/stem cells (MSC) in vitro; however, it requires supra-physiological concentrations, presenting a bottleneck problem for large-scale drug screening. Here, we report the use of a double-objective feedback system control (FSC) with a differential evolution (DE) algorithm to identify osteogenic cocktails of extrinsic factors. Cocktails containing significantly reduced doses of BMP-2 in combination with physiologically relevant doses of dexamethasone, ascorbic acid, beta-glycerophosphate, heparin, retinoic acid and vitamin D achieved accelerated in vitro mineralization of mouse and human MSC. These results provide insight into constructive approaches of FSC to determine the applicable functional and physiological environment for MSC in disease modeling, drug screening and tissue engineering.
[show abstract][hide abstract] ABSTRACT: Identifying potent drug combination from a herbal mixture is usually quite challenging, due to a large number of possible trials. Using an engineering approach of the feedback system control (FSC) scheme, we identified the potential best combinations of four flavonoids, including formononetin, ononin, calycosin, and calycosin-7-O- β -D-glucoside deriving from Astragali Radix (AR; Huangqi), which provided the best biological action at minimal doses. Out of more than one thousand possible combinations, only tens of trials were required to optimize the flavonoid combinations that stimulated a maximal transcriptional activity of hypoxia response element (HRE), a critical regulator for erythropoietin (EPO) transcription, in cultured human embryonic kidney fibroblast (HEK293T). By using FSC scheme, 90% of the work and time can be saved, and the optimized flavonoid combinations increased the HRE mediated transcriptional activity by ~3-fold as compared with individual flavonoid, while the amount of flavonoids was reduced by ~10-fold. Our study suggests that the optimized combination of flavonoids may have strong effect in activating the regulatory element of erythropoietin at very low dosage, which may be used as new source of natural hematopoietic agent. The present work also indicates that the FSC scheme is able to serve as an efficient and model-free approach to optimize the drug combination of different ingredients within a herbal decoction.
Evidence-based Complementary and Alternative Medicine 01/2013; 2013:541436. · 1.72 Impact Factor
[show abstract][hide abstract] ABSTRACT: Rebuilding injured tissue for regenerative medicine requires technologies to reproduce tissue/biomaterials mimicking the natural morphology. To reconstitute the tissue pattern, current approaches include using scaffolds with specific structure to plate cells, guiding cell spreading, or directly moving cells to desired locations. However, the structural complexity is limited. Also, the artificially-defined patterns are usually disorganized by cellular self-organization in the subsequent tissue development, such as cell migration and cell-cell communication. Here, by working in concert with cellular self-organization rather than against it, we experimentally and mathematically demonstrate a method which directs self-organizing vascular mesenchymal cells (VMCs) to assemble into desired multicellular patterns. Incorporating the inherent chirality of VMCs revealed by interfacing with microengineered substrates and VMCs' spontaneous aggregation, differences in distribution of initial cell plating can be amplified into the formation of striking radial structures or concentric rings, mimicking the cross-sectional structure of liver lobules or osteons, respectively. Furthermore, when co-cultured with VMCs, non-pattern-forming endothelial cells (ECs) tracked along the VMCs and formed a coherent radial or ring pattern in a coordinated manner, indicating that this method is applicable to heterotypical cell organization.
[show abstract][hide abstract] ABSTRACT: Kidney transplant recipients who have abnormally high creatinine levels in their blood often have allograft dysfunction secondary to rejection. Creatinine has become the preferred marker for renal dysfunction and is readily available in hospital clinical settings. We developed a rapid and accurate polymer-based electrochemical point-of-care (POC) assay for creatinine detection from whole blood to identify allograft dysfunction. The creatinine concentrations of 19 blood samples from transplant recipients were measured directly from clinical serum samples by the conducting polymer-based electrochemical (EC) sensor arrays. These measurements were compared to the traditional clinical laboratory assay. The time required for detection was <5 min from sample loading. Sensitivity of the detection was found to be 0.46 mg/dL of creatinine with only 40 μL sample in the creatinine concentration range of 0 mg/dL to 11.33 mg/dL. Signal levels that were detected electrochemically correlated closely with the creatinine blood concentration detected by the UCLA Ronald Reagan Medical Center traditional clinical laboratory assay (correlation coefficient = 0.94). This work is encouraging for the development of a rapid and accurate POC device for measuring creatinine levels in whole blood.
[show abstract][hide abstract] ABSTRACT: The reaction and diffusion of morphogens is a mechanism widely used to explain many spatial patterns in physics, chemistry and developmental biology. However, because experimental control is limited in most biological systems, it is often unclear what mechanisms account for the biological patterns that arise. Here, we study a biological model of cultured vascular mesenchymal cells (VMCs), which normally self-organize into aggregates that form into labyrinthine configurations. We use an experimental control and a mathematical model that includes reacting and diffusing morphogens and a third variable reflecting local cell density. With direct measurements showing that cell motility was increased ninefold and threefold by inhibiting either Rho kinase or non-muscle myosin-II, respectively, our experimental results and mathematical modelling demonstrate that increased motility alters the multicellular pattern of the VMC cultures, from labyrinthine to a pattern of periodic holes. These results suggest implications for the tissue engineering of functional replacements for trabecular or spongy tissue such as endocardium and bone.
Interface focus: a theme supplement of Journal of the Royal Society interface 08/2012; 2(4):457-64. · 2.21 Impact Factor
[show abstract][hide abstract] ABSTRACT: Left-right (LR) asymmetry is ubiquitous in animal development. Cytoskeletal chirality was recently reported to specify LR asymmetry in embryogenesis, suggesting that LR asymmetry in tissue morphogenesis is coordinated by single- or multi-cell organizers. Thus, to organize LR asymmetry at multiscale levels of morphogenesis, cells with chirality must also be present in adequate numbers. However, observation of LR asymmetry is rarely reported in cultured cells.
Using cultured vascular mesenchymal cells, we tested whether LR asymmetry occurs at the single cell level and in self-organized multicellular structures.
Using micropatterning, immunofluorescence revealed that adult vascular cells polarized rightward and accumulated stress fibers at an unbiased mechanical interface between adhesive and nonadhesive substrates. Green fluorescent protein transfection revealed that the cells each turned rightward at the interface, aligning into a coherent orientation at 20° relative to the interface axis at confluence. During the subsequent aggregation stage, time-lapse videomicroscopy showed that cells migrated along the same 20° angle into neighboring aggregates, resulting in a macroscale structure with LR asymmetry as parallel, diagonal stripes evenly spaced throughout the culture. Removal of substrate interface by shadow mask-plating, or inhibition of Rho kinase or nonmuscle myosin attenuated stress fiber accumulation and abrogated LR asymmetry of both single-cell polarity and multicellular coherence, suggesting that the interface triggers asymmetry via cytoskeletal mechanics. Examination of other cell types suggests that LR asymmetry is cell-type specific.
Our results show that adult stem cells retain inherent LR asymmetry that elicits de novo macroscale tissue morphogenesis, indicating that mechanical induction is required for cellular LR specification.
Circulation Research 02/2012; 110(4):551-9. · 11.86 Impact Factor
[show abstract][hide abstract] ABSTRACT: Infectious diseases cause many molecular assemblies and pathways within cellular signaling networks to function aberrantly. The most effective way to treat complex, diseased cellular networks is to apply multiple drugs that attack the problem from many fronts. However, determining the optimal combination of several drugs at specific dosages to reach an endpoint objective is a daunting task.
In this study, we applied an experimental feedback system control (FSC) method and rapidly identified optimal drug combinations that inhibit herpes simplex virus-1 infection, by only testing less than 0.1% of the total possible drug combinations.
Using antiviral efficacy as the criterion, FSC quickly identified a highly efficacious drug cocktail. This cocktail contained high dose ribavirin. Ribavirin, while being an effective antiviral drug, often induces toxic side effects that are not desirable in a therapeutic drug combination. To screen for less toxic drug combinations, we applied a second FSC search in cascade and used both high antiviral efficacy and low toxicity as criteria. Surprisingly, the new drug combination eliminated the need for ribavirin, but still blocked viral infection in nearly 100% of cases.
This cascade search provides a versatile platform for rapid discovery of new drug combinations that satisfy multiple criteria.
International Journal of Nanomedicine 01/2012; 7:2281-92. · 3.46 Impact Factor
[show abstract][hide abstract] ABSTRACT: A new bacteria microarray patterning technique is developed by patterning thick polycationic polymers on glass surface, which generates high-coverage and high-precision E. coli cell patterns. Cell immobilization efficiency is greatly improved, compared to conventional monolayer surface patterning approach. Cell viability tests show very low cytotoxicity of polyethyleneimine (PEI). This advancement should further accelerate biomedical and bacteriological researches in the micro scale.
[show abstract][hide abstract] ABSTRACT: The sensitivity and detection time of an aptamer based biosensor for detecting botulinum neurotoxin (BoNT) depend upon the formation of proper tertiary architecture of aptamer, which closely correlates with the combinatorial effects of multiple types of ions and their concentrations presented in the buffer. Finding the optimal conditions for four different ions at 12 different concentrations, 20,736 possible combinations, by brute force is an extremely laborious and time-consuming task. Here, we introduce a feedback system control (FSC) scheme that can rapidly identify the best combination of components to form the optimal aptamer structure binding to a target molecule. In this study, rapid identification of optimized ionic combinations for electrochemical aptasensor of BoNT type A (BoNT/A) detection has been achieved. Only about 10 iterations with about 50 tests in each iteration are needed to identify the optimal ionic concentration out of the 20,736 possibilities. The most exciting finding was that a very short detection time and high sensitivity could be achieved with the optimized combinational ion buffer. Only a 5-min detection time, compared with hours or even days, was needed for aptamer-based BoNT/A detection with a limit of detection of 40 pg/ml. The methodologies described here can be applied to other multi-parameter chemical systems, which should significantly improve the rate of parameter optimization.
[show abstract][hide abstract] ABSTRACT: Human pluripotent stem cells hold promising potential in many therapeutics applications including regenerative medicine and drug discovery. Over the past three decades, embryonic stem cell research has illustrated that embryonic stem cells possess two important and distinct properties: the ability to continuously self-renew and the ability to differentiate into all specialized cell types. In this article, we will discuss the continuing evolution of human pluripotent stem cell culture by examining requirements needed for the maintenance of self-renewal in vitro. We will also elaborate on the future direction of the field toward generating a robust and completely defined culture system, which has brought forth collaborations amongst biologists and engineers. As human pluripotent stem cell research progresses towards identifying solutions for debilitating diseases, it will be critical to establish a defined, reproducible and scalable culture system to meet the requirements of these clinical applications.
Regenerative Medicine 09/2011; 6(5):623-34. · 3.87 Impact Factor
[show abstract][hide abstract] ABSTRACT: Cells constantly sense many internal and environmental signals and respond through their complex signaling network, leading to particular biological outcomes. However, a systematic characterization and optimization of multi-signal responses remains a pressing challenge to traditional experimental approaches due to the arising complexity associated with the increasing number of signals and their intensities.
We established and validated a data-driven mathematical approach to systematically characterize signal-response relationships. Our results demonstrate how mathematical learning algorithms can enable systematic characterization of multi-signal induced biological activities. The proposed approach enables identification of input combinations that can result in desired biological responses. In retrospect, the results show that, unlike a single drug, a properly chosen combination of drugs can lead to a significant difference in the responses of different cell types, increasing the differential targeting of certain combinations. The successful validation of identified combinations demonstrates the power of this approach. Moreover, the approach enables examining the efficacy of all lower order mixtures of the tested signals. The approach also enables identification of system-level signaling interactions between the applied signals. Many of the signaling interactions identified were consistent with the literature, and other unknown interactions emerged.
This approach can facilitate development of systems biology and optimal drug combination therapies for cancer and other diseases and for understanding key interactions within the cellular network upon treatment with multiple signals.
BMC Systems Biology 05/2011; 5:88. · 2.98 Impact Factor
[show abstract][hide abstract] ABSTRACT: The coffee ring phenomenon has long been known for its ability to concentrate particles at the rim of a dried liquid droplet, yet little is known about its particle separation capability. Here, we elucidate the physics of particle separation during coffee ring formation, which is based on a particle-size selection mechanism near the contact line of an evaporating droplet. On the basis of this mechanism, we demonstrate nanochromatography of three relevant biological entities (proteins, micro-organisms, and mammalian cells) in a liquid droplet, with a separation resolution on the order of ∼100 nm and a dynamic range from ∼10 nm to a few tens of micrometers. These findings have direct implications for developing low-cost technologies for disease diagnostics in resource-poor environments.
[show abstract][hide abstract] ABSTRACT: We present a microfluidic platform, which provides a simple and efficient means for handling and processing Pseudo-nitzschia, a neurotoxin-producing marine algae. Currently, analyzing the production of such toxins is complicated by multiple environmental factors and high variability among individual Pseudo-nitzschia species. To address this issue, we developed a device that can precisely trap single and multiple cells for subsequent lysis to extract relevant intracellular molecules. Our results show a cell trapping efficiency of up to 96%, which is achieved by hydrodynamic flow focusing. Additionally, complete cell lysis via ultrasonication can be accomplished within a few seconds. This platform can be applied to other algae and non-algae cell types with minimal modification, thus providing a valuable tool for studying biological intracellular mechanisms at the single and multi-cell level.
[show abstract][hide abstract] ABSTRACT: The ability to control cellular functions can bring about many developments in basic biological research and its applications. The presence of multiple signals, internal as well as externally imposed, introduces several challenges for controlling cellular functions. Additionally the lack of clear understanding of the cellular signaling network limits our ability to infer the responses to a number of signals. This work investigates the control of Kaposi's sarcoma-associated herpesvirus reactivation upon treatment with a combination of multiple signals. We utilize mathematical model-based as well as experiment-based approaches to achieve the desired goals of maximizing virus reactivation. The results show that appropriately selected control signals can induce virus lytic gene expression about ten folds higher than a single drug; these results were validated by comparing the results of the two approaches, and experimentally using multiple assays. Additionally, we have quantitatively analyzed potential interactions between the used combinations of drugs. Some of these interactions were consistent with existing literature, and new interactions emerged and warrant further studies. The work presents a general method that can be used to quantitatively and systematically study multi-signal induced responses. It enables optimization of combinations to achieve desired responses. It also allows identifying critical nodes mediating the multi-signal induced responses. The concept and the approach used in this work will be directly applicable to other diseases such as AIDS and cancer.
PLoS ONE 01/2011; 6(6):e20998. · 3.73 Impact Factor
[show abstract][hide abstract] ABSTRACT: This work reports on optoelectronic-based heaters that can transduce low-power optical images into high-power heating to melt frozen liquids and form desired microfluidic circuitry. The mechanism of optoelectronic heating (OEH) was studied and characterized. OEH relies on photocurrent heating in the illuminated parts of actuating images. Resolution was affected by dark current heating. Photocurrents and dark currents were measured and related to the operating parameters. Successful melting of a frozen media within seconds with 2 mW light patterns and a 4 V operating voltage was demonstrated with feature sizes down to 200 μm × 200 μm. Strategies to increase resolution were addressed. It was shown that the size and location of heating areas can be reliably and rapidly reconfigured by changing the actuating image.
[show abstract][hide abstract] ABSTRACT: A major challenge in stem cell-mediated regenerative medicine is the development of defined culture systems for the maintenance of clinical-grade human embryonic stem (hES) cells. Here, we identify, using a feedback system control scheme, a unique combination of three small molecule inhibitors that enables the maintenance of hES cells on a fibronectin-coated surface through single cell passaging. After 20 passages, the undifferentiated state of the hES cells was confirmed by OCT4, SSEA4 and NANOG expressions, whereas their pluripotent potential and genetic integrity were demonstrated by teratoma formation and normal karyotype, respectively. Our study attests to the power of the feedback system control scheme to quickly pinpoint optimal conditions for desired biological activities, and provides a chemically defined, scalable and single cell passaging culture system for hES cells.