Publications by authors named "Rashid Bashir"

173 Publications

Portable Pathogen Diagnostics Using Microfluidic Cartridges Made from Continuous Liquid Interface Production Additive Manufacturing.

Anal Chem 2021 Jul 12. Epub 2021 Jul 12.

Holonyak Micro and Nano Technology Laboratory, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States.

Biomedical diagnostics based on microfluidic devices have the potential to significantly benefit human health; however, the manufacturing of microfluidic devices is a key limitation to their widespread adoption. Outbreaks of infectious disease continue to demonstrate the need for simple, sensitive, and translatable tests for point-of-care use. Additive manufacturing (AM) is an attractive alternative to conventional approaches for microfluidic device manufacturing based on injection molding; however, there is a need for development and validation of new AM process capabilities and materials that are compatible with microfluidic diagnostics. In this paper, we demonstrate the development and characterization of AM cartridges using continuous liquid interface production (CLIP) and investigate process characteristics and capabilities of the AM microfluidic device manufacturing. We find that CLIP accurately produces microfluidic channels as small as 400 μm and that it is possible to routinely produce fluid channels as small as 100 μm with high repeatability. We also developed a loop-mediated isothermal amplification (LAMP) assay for detection of from whole blood directly on the CLIP-based AM microfluidic cartridges, with a 50 cfu/μL limit of detection, validating the use of CLIP processes and materials for pathogen detection. The portable diagnostic platform presented in this paper could be used to investigate and validate other AM processes for microfluidic diagnostics and could be an important component of scaling up the diagnostics for current and future infectious diseases and pandemics.
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http://dx.doi.org/10.1021/acs.analchem.1c00654DOI Listing
July 2021

Reverse Transcription Loop-Mediated Isothermal Amplification Assay for Ultrasensitive Detection of SARS-CoV-2 in Saliva and Viral Transport Medium Clinical Samples.

Anal Chem 2021 06 25;93(22):7797-7807. Epub 2021 May 25.

Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States.

The COVID-19 pandemic has underscored the shortcomings in the deployment of state-of-the-art diagnostics platforms. Although several polymerase chain reaction (PCR)-based techniques have been rapidly developed to meet the growing testing needs, such techniques often need samples collected through a swab, the use of RNA extraction kits, and expensive thermocyclers in order to successfully perform the test. Isothermal amplification-based approaches have also been recently demonstrated for rapid severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection by minimizing sample preparation while also reducing the instrumentation and reaction complexity. In addition, there are limited reports of saliva as the sample source, and some of these indicate inferior sensitivity when comparing reverse transcription loop-mediated isothermal amplification (RT-LAMP) with PCR-based techniques. In this paper, we demonstrate an improved sensitivity assay from saliva using a two-step RT-LAMP assay, where a short 10 min RT step is performed with only B3 and backward inner primers before the final reaction. We show that while the one-step RT-LAMP demonstrates satisfactory results, the optimized two-step approach allows detection of only few molecules per reaction and performs significantly better than the one-step RT-LAMP and conventional two-step RT-LAMP approaches with all primers included in the RT step. We show control measurements with RT-PCR, and importantly, we demonstrate RNA extraction-free RT-LAMP-based assays for detection of SARS-CoV-2 from viral transport media and saliva clinical samples.
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http://dx.doi.org/10.1021/acs.analchem.0c05170DOI Listing
June 2021

COVID-19 Point-of-Care Diagnostics: Present and Future.

ACS Nano 2021 05 13;15(5):7899-7906. Epub 2021 May 13.

Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 United States.

Point-of-care (POC) detection technologies that enable decentralized, rapid, sensitive, low-cost diagnostics of COVID-19 infection are urgently needed around the world. With many technologies approved for commercialization in the past 10 months, the field of COVID-19 POC diagnostics is rapidly evolving. In this Perspective, we analyze the current state of POC technologies for the diagnosis and monitoring of COVID-19 infection and discuss future challenges in COVID-19 diagnostics. As the COVID-19 pandemic becomes endemic, the advances gained during this past year will likely also be utilized for future prediction of emerging outbreaks and pandemics.
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http://dx.doi.org/10.1021/acsnano.1c02981DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8130524PMC
May 2021

Compliant 3D frameworks instrumented with strain sensors for characterization of millimeter-scale engineered muscle tissues.

Proc Natl Acad Sci U S A 2021 May;118(19)

Querrey Simpson Institute for Bioelectronics, Northwestern University, Evanston, IL 60208;

Tissue-on-chip systems represent promising platforms for monitoring and controlling tissue functions in vitro for various purposes in biomedical research. The two-dimensional (2D) layouts of these constructs constrain the types of interactions that can be studied and limit their relevance to three-dimensional (3D) tissues. The development of 3D electronic scaffolds and microphysiological devices with geometries and functions tailored to realistic 3D tissues has the potential to create important possibilities in advanced sensing and control. This study presents classes of compliant 3D frameworks that incorporate microscale strain sensors for high-sensitivity measurements of contractile forces of engineered optogenetic muscle tissue rings, supported by quantitative simulations. Compared with traditional approaches based on optical microscopy, these 3D mechanical frameworks and sensing systems can measure not only motions but also contractile forces with high accuracy and high temporal resolution. Results of active tension force measurements of engineered muscle rings under different stimulation conditions in long-term monitoring settings for over 5 wk and in response to various chemical and drug doses demonstrate the utility of such platforms in sensing and modulation of muscle and other tissues. Possibilities for applications range from drug screening and disease modeling to biohybrid robotic engineering.
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http://dx.doi.org/10.1073/pnas.2100077118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8126769PMC
May 2021

Diagnostic and prognostic capabilities of a biomarker and EMR-based machine learning algorithm for sepsis.

Clin Transl Sci 2021 Jul 2;14(4):1578-1589. Epub 2021 May 2.

Department of Bioengineering, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA.

Sepsis is a major cause of mortality among hospitalized patients worldwide. Shorter time to administration of broad-spectrum antibiotics is associated with improved outcomes, but early recognition of sepsis remains a major challenge. In a two-center cohort study with prospective sample collection from 1400 adult patients in emergency departments suspected of sepsis, we sought to determine the diagnostic and prognostic capabilities of a machine-learning algorithm based on clinical data and a set of uncommonly measured biomarkers. Specifically, we demonstrate that a machine-learning model developed using this dataset outputs a score with not only diagnostic capability but also prognostic power with respect to hospital length of stay (LOS), 30-day mortality, and 3-day inpatient re-admission both in our entire testing cohort and various subpopulations. The area under the receiver operating curve (AUROC) for diagnosis of sepsis was 0.83. Predicted risk scores for patients with septic shock were higher compared with patients with sepsis but without shock (p < 0.0001). Scores for patients with infection and organ dysfunction were higher compared with those without either condition (p < 0.0001). Stratification based on predicted scores of the patients into low, medium, and high-risk groups showed significant differences in LOS (p < 0.0001), 30-day mortality (p < 0.0001), and 30-day inpatient readmission (p < 0.0001). In conclusion, a machine-learning algorithm based on electronic medical record (EMR) data and three nonroutinely measured biomarkers demonstrated good diagnostic and prognostic capability at the time of initial blood culture.
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http://dx.doi.org/10.1111/cts.13030DOI Listing
July 2021

Neuromuscular Junction Model Optimized for Electrical Platforms.

Tissue Eng Part C Methods 2021 04 30;27(4):242-252. Epub 2021 Mar 30.

Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA.

Neuromuscular junctions (NMJs), specialized synapses between motor neurons and muscle fibers, are essential for muscle activity. A simple and reproducible cell-based NMJ platform is needed to test the impact of chemicals on the neuron-muscle communication. Our platform utilizes genetically modified neurons and muscle cells, optimized culture conditions, and commercially available multielectrode array system for recording action potentials. Neuronal cells (NSC34) were optogenetically modified with channelrhodopsin chimera to allow for simultaneous, light-mediated, millisecond-precise activation of neuronal population. This signal is propagated through functional synapses to the muscle fibers. Muscle cells (C2C12) were modified by incorporating gap junction protein (Connexin-43) to improve intracellular communication without affecting muscle differentiation. This communication between muscle fibers resulted in better signal propagation and signal strength. Optimized culture medium facilitated the growth and differentiation of both cell types together. Our system was validated using vecuronium, a muscle relaxant, which abolished the muscle response. This model provides a unique tool for establishing a NMJ platform that is easy to record and analyze. Potential applications include nondestructive long-term screening of drugs affecting the NMJ.
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http://dx.doi.org/10.1089/ten.TEC.2020.0292DOI Listing
April 2021

Tip-Based Cleaning and Smoothing Improves Performance in Monolayer MoS Devices.

ACS Omega 2021 Feb 1;6(5):4013-4021. Epub 2021 Feb 1.

Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.

Two-dimensional (2D) materials and heterostructures are promising candidates for nanoelectronics. However, the quality of material interfaces often limits the performance of electronic devices made from atomically thick 2D materials and heterostructures. Atomic force microscopy (AFM) tip-based cleaning is a reliable technique to remove interface contaminants and flatten heterostructures. Here, we demonstrate AFM tip-based cleaning applied to hBN-encapsulated monolayer MoS transistors, which results in electrical performance improvements of the devices. To investigate the impact of cleaning on device performance, we compared the characteristics of as-transferred heterostructures and transistors before and after tip-based cleaning using photoluminescence (PL) and electronic measurements. The PL linewidth of monolayer MoS decreased from 84 meV before cleaning to 71 meV after cleaning. The extrinsic mobility of monolayer MoS field-effect transistors increased from 21 cm/Vs before cleaning to 38 cm/Vs after cleaning. Using the results from AFM topography, photoluminescence, and back-gated field-effect measurements, we infer that tip-based cleaning enhances the mobility of hBN-encapsulated monolayer MoS by reducing interface disorder. Finally, we fabricate a MoS field-effect transistor (FET) from a tip-cleaned heterostructure and achieved a device mobility of 73 cm/Vs. The results of this work could be used to improve the electrical performance of heterostructure devices and other types of mechanically assembled van der Waals heterostructures.
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http://dx.doi.org/10.1021/acsomega.0c05934DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7876835PMC
February 2021

Emergency ventilator for COVID-19.

PLoS One 2020 30;15(12):e0244963. Epub 2020 Dec 30.

College of Agricultural, Consumer, and Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, United States of America.

The COVID-19 pandemic disrupted the world in 2020 by spreading at unprecedented rates and causing tens of thousands of fatalities within a few months. The number of deaths dramatically increased in regions where the number of patients in need of hospital care exceeded the availability of care. Many COVID-19 patients experience Acute Respiratory Distress Syndrome (ARDS), a condition that can be treated with mechanical ventilation. In response to the need for mechanical ventilators, designed and tested an emergency ventilator (EV) that can control a patient's peak inspiratory pressure (PIP) and breathing rate, while keeping a positive end expiratory pressure (PEEP). This article describes the rapid design, prototyping, and testing of the EV. The development process was enabled by rapid design iterations using additive manufacturing (AM). In the initial design phase, iterations between design, AM, and testing enabled a working prototype within one week. The designs of the 16 different components of the ventilator were locked by additively manufacturing and testing a total of 283 parts having parametrically varied dimensions. In the second stage, AM was used to produce 75 functional prototypes to support engineering evaluation and animal testing. The devices were tested over more than two million cycles. We also developed an electronic monitoring system and with automatic alarm to provide for safe operation, along with training materials and user guides. The final designs are available online under a free license. The designs have been transferred to more than 70 organizations in 15 countries. This project demonstrates the potential for ultra-fast product design, engineering, and testing of medical devices needed for COVID-19 emergency response.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0244963PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7773325PMC
January 2021

Rapid isothermal amplification and portable detection system for SARS-CoV-2.

Proc Natl Acad Sci U S A 2020 09 31;117(37):22727-22735. Epub 2020 Aug 31.

Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801;

The COVID-19 pandemic provides an urgent example where a gap exists between availability of state-of-the-art diagnostics and current needs. As assay protocols and primer sequences become widely known, many laboratories perform diagnostic tests using methods such as RT-PCR or reverse transcription loop mediated isothermal amplification (RT-LAMP). Here, we report an RT-LAMP isothermal assay for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus and demonstrate the assay on clinical samples using a simple and accessible point-of-care (POC) instrument. We characterized the assay by dipping swabs into synthetic nasal fluid spiked with the virus, moving the swab to viral transport medium (VTM), and sampling a volume of the VTM to perform the RT-LAMP assay without an RNA extraction kit. The assay has a limit of detection (LOD) of 50 RNA copies per μL in the VTM solution within 30 min. We further demonstrate our assay by detecting SARS-CoV-2 viruses from 20 clinical samples. Finally, we demonstrate a portable and real-time POC device to detect SARS-CoV-2 from VTM samples using an additively manufactured three-dimensional cartridge and a smartphone-based reader. The POC system was tested using 10 clinical samples, and was able to detect SARS-CoV-2 from these clinical samples by distinguishing positive samples from negative samples after 30 min. The POC tests are in complete agreement with RT-PCR controls. This work demonstrates an alternative pathway for SARS-CoV-2 diagnostics that does not require conventional laboratory infrastructure, in settings where diagnosis is required at the point of sample collection.
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http://dx.doi.org/10.1073/pnas.2014739117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7502724PMC
September 2020

Variable Membrane Dielectric Polarization Characteristic in Individual Live Cells.

J Phys Chem Lett 2020 Sep 19;11(17):7197-7203. Epub 2020 Aug 19.

Department of Biomedical Engineering, Yonsei University, Wonju 26493, Korea.

Investigation of the dielectric properties of cell membranes plays an important role in understanding the biological activities that sustain cellular life and realize cellular functionalities. Herein, the variable dielectric polarization characteristics of cell membranes are reported. In controlling the dielectric polarization of a cell using dielectrophoresis force spectroscopy, different cellular crossover frequencies were observed by modulating both the direction and sweep rate of the frequency. The crossover frequencies were used for the extraction of the variable capacitance, which is involved in the dielectric polarization across the cell membranes. In addition, this variable phenomenon was investigated by examining cells whose membranes were cholesterol-depleted with methyl-β-cyclodextrin, which verified a strong correlation between the variable dielectric polarization characteristics and membrane composition changes. This study presented the dielectric polarization properties in live cells' membranes that can be modified by the regulation of external stimuli and provided a powerful platform to explore cellular membrane dielectric polarization.
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http://dx.doi.org/10.1021/acs.jpclett.0c01427DOI Listing
September 2020

Preoperative vascular surgery model using a single polymer tough hydrogel with controllable elastic moduli.

Soft Matter 2020 Sep 13;16(34):8057-8068. Epub 2020 Aug 13.

Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.

Materials used in organ mimics for medial simulation and education require tissue-like softness, toughness, and hydration to give clinicians and students accurate tactile feedback. However, there is a lack of materials that satisfy these requirements. Herein, we demonstrate that a stretchable and tough polyacrylamide hydrogel is useful to build organ mimics that match softness, crack growth resistance, and interstitial water of real organs. Varying the acrylamide concentration between 29 or 62% w/w with a molar ratio between cross-linker and acrylamide of 1 : 10 800 resulted in a fracture energy around ∼2000 J m. More interestingly, this tough gel permitted variation of the elastic modulus from 8 to 62 kPa, which matches the softness of brain to vascular and muscle tissue. According to the rheological frequency sweep, the tough polyacrylamide hydrogels had a greatly decreased number of flow units, indicating that when deformed, stress was dispersed over a greater area. We propose that such molecular dissipation results from the increased number of entangled polymers between distant covalent cross-links. The gel was able to undergo various manipulations including stretching, puncture, delivery through a syringe tip, and suturing, thus enabling the use of the gel as a blood vessel model for microsurgery simulation.
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http://dx.doi.org/10.1039/d0sm00981dDOI Listing
September 2020

Simultaneous time-varying viscosity, elasticity, and mass measurements of single adherent cancer cells across cell cycle.

Sci Rep 2020 07 30;10(1):12803. Epub 2020 Jul 30.

Department of Mechanical Science and Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.

Biophysical studies on single cells have linked cell mechanics to physiology, functionality and disease. Evaluation of mass and viscoelasticity versus cell cycle can provide further insights into cell cycle progression and the uncontrolled proliferation of cancer. Using our pedestal microelectromechanical systems resonant sensors, we have developed a non-contact interferometric measurement technique that simultaneously tracks the dynamic changes in the viscoelastic moduli and mass of adherent colon (HT-29) and breast cancer (MCF-7) cells from the interphase through mitosis and then to the cytokinesis stages of their growth cycle. We show that by combining three optomechanical parameters in an optical path length equation and a two-degree-of-freedom model, we can simultaneously extract the viscoelasticity and mass as a function of the nano-scaled membrane fluctuation of each adherent cell. Our measurements are able to discern between soft and stiff cells across the cell cycle and demonstrated sharp viscoelastic changes due to cortical stiffening around mitosis. Cell rounding before division can be detected by measurement of mechanical coupling between the cells and the sensors. Our measurement device and method can provide for new insights into the mechanics of single adherent cells versus time.
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http://dx.doi.org/10.1038/s41598-020-69638-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7393350PMC
July 2020

Modulating electrophysiology of motor neural networks via optogenetic stimulation during neurogenesis and synaptogenesis.

Sci Rep 2020 07 27;10(1):12460. Epub 2020 Jul 27.

Department of Bioengineering, University of Illinois, Urbana-Champaign, Engineering Hall, 1308 W Green St, Urbana, IL, 61801, USA.

Control of electrical activity in neural circuits through network training is a grand challenge for biomedicine and engineering applications. Past efforts have not considered evoking long-term changes in firing patterns of in-vitro networks by introducing training regimens with respect to stages of neural development. Here, we used Channelrhodopsin-2 (ChR2) transfected mouse embryonic stem cell (mESC) derived motor neurons to explore short and long-term programming of neural networks by using optical stimulation implemented during neurogenesis and synaptogenesis. Not only did we see a subsequent increase of neurite extensions and synaptophysin clustering, but by using electrophysiological recording with micro electrode arrays (MEA) we also observed changes in signal frequency spectra, increase of network synchrony, coordinated firing of actions potentials, and enhanced evoked response to stimulation during network formation. Our results demonstrate that optogenetic stimulation during neural differentiation can result in permanent changes that extended to the genetic expression of neurons as demonstrated by RNA Sequencing. To our knowledge, this is the first time that a correlation between training regimens during neurogenesis and synaptogenesis and the resulting plastic responses has been shown in-vitro and traced back to changes in gene expression. This work demonstrates new approaches for training of neural circuits whose electrical activity can be modulated and enhanced, which could lead to improvements in neurodegenerative disease research and engineering of in-vitro multi-cellular living systems.
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http://dx.doi.org/10.1038/s41598-020-68988-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7385114PMC
July 2020

Rapid, multiplexed detection of biomolecules using electrically distinct hydrogel beads.

Lab Chip 2020 06;20(13):2274-2283

Department of Chemistry, University of Illinois at Urbana-Champaign, 505 South Mathews Ave., Urbana, Illinois 61801, USA.

Rapid, low-cost, and multiplexed biomolecule detection is an important goal in the development of effective molecular diagnostics. Our recent work has demonstrated a microfluidic biochip device that can electrically quantitate a protein target with high sensitivity. This platform detects and quantifies a target analyte by counting and capturing micron-sized beads in response to an immunoassay on the bead surface. Existing microparticles limit the technique to the detection of a single protein target and lack the magnetic properties required for separation of the microparticles for direct measurements from whole blood. Here, we report new precisely engineered microparticles that achieve electrical multiplexing and adapt this platform for low-cost and label-free multiplexed electrical detection of biomolecules. Droplet microfluidic synthesis yielded highly-monodisperse populations of magnetic hydrogel beads (MHBs) with the necessary properties for multiplexing the electrical Coulter counting on chip. Each bead population was designed to contain a different amount of the hydrogel material, resulting in a unique electrical impedance signature during Coulter counting, thereby enabling unique identification of each bead. These monodisperse bead populations span a narrow range of sizes ensuring that all can be captured sensitively and selectively under simultaneously flow. Incorporating these newly synthesized beads, we demonstrate versatile and multiplexed biomolecule detection of proteins or DNA targets. This development of multiplexed beads for the electrical detection of biomolecules, provides a critical advancement towards multiplexing the Coulter counting approach and the development of a low cost point-of-care diagnostic sensor.
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http://dx.doi.org/10.1039/d0lc00243gDOI Listing
June 2020

Simultaneous electrical detection of IL-6 and PCT using a microfluidic biochip platform.

Biomed Microdevices 2020 05 18;22(2):36. Epub 2020 May 18.

Department of Bioengineering, University of Illinois at Urbana-Champaign, 1102 Everitt Lab, MC 278, 1406 W. Green St, Urbana, IL, 61801, USA.

Sepsis, a life-threatening organ dysfunction caused by a dysregulated host response, leads the U.S in both mortality rate and cost of treatment. Sepsis treatment protocols currently rely on broad and non-specific parameters like heart and respiration rate, and temperature; however, studies show that biomarkers Interlukin-6 (IL-6) and Procalcitonin (PCT) correlate to sepsis progression and response to treatment. Prior work also suggests that using multi-parameter predictive analytics with biomarkers and clinical information can inform treatment to improve outcome. A point-of-care (POC) platform that provides information for multiple biomarkers can aid in the diagnosis and prognosis of potentially septic patients. Using impedance cytometry, microbead immunoassays, and biotin-streptavidin binding, we report a microfluidic POC system that correlates microbead capture to IL-6 and PCT concentrations. A multiplexed microbead immunoassay is developed and validated for simultaneous detection of both IL-6 and PCT from human plasma samples. Using the POC platform, we quantified plasma samples containing healthy, medium (~10pg/ml) and high (~10pg/ml) IL-6 and PCT concentrations with various levels of significance (P < 0.05-P < 0.00001) and validated the concept of this device as a POC platform for sepsis biomarkers.
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http://dx.doi.org/10.1007/s10544-020-00492-6DOI Listing
May 2020

Smartphone-based multiplex 30-minute nucleic acid test of live virus from nasal swab extract.

Lab Chip 2020 05;20(9):1621-1627

Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Illinois, USA. and Department of Bioengineering, University of Illinois at Urbana-Champaign, Illinois, USA.

Rapid, sensitive and specific detection and reporting of infectious pathogens is important for patient management and epidemic surveillance. We demonstrated a point-of-care system integrated with a smartphone for detecting live virus from nasal swab media, using a panel of equine respiratory infectious diseases as a model system for corresponding human diseases such as COVID-19. Specific nucleic acid sequences of five pathogens were amplified by loop-mediated isothermal amplification on a microfluidic chip and detected at the end of reactions by the smartphone. Pathogen-spiked horse nasal swab samples were correctly diagnosed using our system, with a limit of detection comparable to that of the traditional lab-based test, polymerase chain reaction, with results achieved in ∼30 minutes.
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http://dx.doi.org/10.1039/d0lc00304bDOI Listing
May 2020

Ultrasensitive detection of nucleic acids using deformed graphene channel field effect biosensors.

Nat Commun 2020 03 24;11(1):1543. Epub 2020 Mar 24.

Holonyak Micro and Nanotechnology Laboratory, University of Illinois, Urbana, IL, USA.

Field-effect transistor (FET)-based biosensors allow label-free detection of biomolecules by measuring their intrinsic charges. The detection limit of these sensors is determined by the Debye screening of the charges from counter ions in solutions. Here, we use FETs with a deformed monolayer graphene channel for the detection of nucleic acids. These devices with even millimeter scale channels show an ultra-high sensitivity detection in buffer and human serum sample down to 600 zM and 20 aM, respectively, which are ∼18 and ∼600 nucleic acid molecules. Computational simulations reveal that the nanoscale deformations can form 'electrical hot spots' in the sensing channel which reduce the charge screening at the concave regions. Moreover, the deformed graphene could exhibit a band-gap, allowing an exponential change in the source-drain current from small numbers of charges. Collectively, these phenomena allow for ultrasensitive electronic biomolecular detection in millimeter scale structures.
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http://dx.doi.org/10.1038/s41467-020-15330-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7093535PMC
March 2020

Development of 3D neuromuscular bioactuators.

APL Bioeng 2020 Mar 10;4(1):016107. Epub 2020 Mar 10.

Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.

Neuronal control of skeletal muscle bioactuators represents a critical milestone toward the realization of future biohybrid machines that may generate complex motor patterns and autonomously navigate through their environment. Animals achieve these feats using neural networks that generate robust firing patterns and coordinate muscle activity through neuromuscular units. Here, we designed a versatile 3D neuron-muscle co-culture platform to serve as a test-bed for neuromuscular bioactuators. We used our platform in conjunction with microelectrode array electrophysiology to study the roles of synergistic interactions in the co-development of neural networks and muscle tissues. Our platform design enables co-culture of a neuronal cluster with up to four target muscle actuators, as well as quantification of muscle contraction forces. Using engineered muscle tissue targets, we first demonstrated the formation of functional neuromuscular bioactuators. We then investigated possible roles of long-range interactions in neuronal outgrowth patterns and observed preferential outgrowth toward muscles compared to the acellular matrix or fibroblasts, indicating muscle-specific chemotactic cues acting on motor neurons. Next, we showed that co-cultured muscle strips exhibited significantly higher spontaneous contractility as well as improved sarcomere assembly compared to muscles cultured alone. Finally, we performed microelectrode array measurements on neuronal cultures, which revealed that muscle-conditioned medium enhances overall neural firing rates and the emergence of synchronous bursting patterns. Overall, our study illustrates the significance of neuron-muscle cross talk for the development of neuromuscular bioactuators.
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http://dx.doi.org/10.1063/1.5134477DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7064368PMC
March 2020

Interaction variability shapes succession of synthetic microbial ecosystems.

Nat Commun 2020 01 16;11(1):309. Epub 2020 Jan 16.

Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.

Cellular interactions are a major driver for the assembly and functioning of microbial communities. Their strengths are shown to be highly variable in nature; however, it is unclear how such variations regulate community behaviors. Here we construct synthetic Lactococcus lactis consortia and mathematical models to elucidate the role of interaction variability in ecosystem succession and to further determine if casting variability into modeling empowers bottom-up predictions. For a consortium of bacteriocin-mediated cooperation and competition, we find increasing the variations of cooperation, from either altered labor partition or random sampling, drives the community into distinct structures. When the cooperation and competition are additionally modulated by pH, ecosystem succession becomes jointly controlled by the variations of both interactions and yields more diversified dynamics. Mathematical models incorporating variability successfully capture all of these experimental observations. Our study demonstrates interaction variability as a key regulator of community dynamics, providing insights into bottom-up predictions of microbial ecosystems.
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http://dx.doi.org/10.1038/s41467-019-13986-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6965111PMC
January 2020

Integration of Graphene Electrodes with 3D Skeletal Muscle Tissue Models.

Adv Healthc Mater 2020 02 16;9(4):e1901137. Epub 2020 Jan 16.

Department of Bioengineering, Nick J. Holonyak Micro and Nanotechnology Laboratory and Carle Illinois College of Medicine, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.

Integration of conductive electrodes with 3D tissue models can have great potential for applications in bioelectronics, drug screening, and implantable devices. As conventional electrodes cannot be easily integrated on 3D, polymeric, and biocompatible substrates, alternatives are highly desirable. Graphene offers significant advantages over conventional electrodes due to its mechanical flexibility and robustness, biocompatibility, and electrical properties. However, the transfer of chemical vapor deposition graphene onto millimeter scale 3D structures is challenging using conventional wet graphene transfer methods with a rigid poly (methyl methacrylate) (PMMA) supportive layer. Here, a biocompatible 3D graphene transfer method onto 3D printed structure using a soft poly ethylene glycol diacrylate (PEGDA) supportive layer to integrate the graphene layer with a 3D engineered ring of skeletal muscle tissue is reported. The use of softer PEGDA supportive layer, with a 10 times lower Young's modulus compared to PMMA, results in conformal integration of the graphene with 3D printed pillars and allows electrical stimulation and actuation of the muscle ring with various applied voltages and frequencies. The graphene integration method can be applied to many 3D tissue models and be used as a platform for electrical interfaces to 3D biological tissue system.
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http://dx.doi.org/10.1002/adhm.201901137DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8029654PMC
February 2020

Localized Dielectric Loss Heating in Dielectrophoresis Devices.

Sci Rep 2019 12 12;9(1):18977. Epub 2019 Dec 12.

Department of Electrical and Computer Engineering, Marquette University, Milwaukee, Wisconsin, 53233, USA.

Temperature increases during dielectrophoresis (DEP) can affect the response of biological entities, and ignoring the effect can result in misleading analysis. The heating mechanism of a DEP device is typically considered to be the result of Joule heating and is overlooked without an appropriate analysis. Our experiment and analysis indicate that the heating mechanism is due to the dielectric loss (Debye relaxation). A temperature increase between interdigitated electrodes (IDEs) has been measured with an integrated micro temperature sensor between IDEs to be as high as 70 °C at 1.5 MHz with a 30 V applied voltage to our ultra-low thermal mass DEP device. Analytical and numerical analysis of the power dissipation due to the dielectric loss are in good agreement with the experiment data.
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http://dx.doi.org/10.1038/s41598-019-55031-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6908616PMC
December 2019

Engineering geometrical 3-dimensional untethered in vitro neural tissue mimic.

Proc Natl Acad Sci U S A 2019 12 3;116(51):25932-25940. Epub 2019 Dec 3.

Department of Bioengineering, University of Illinois, Urbana-Champaign, Urbana, IL 61801;

Formation of tissue models in 3 dimensions is more effective in recapitulating structure and function compared to their 2-dimensional (2D) counterparts. Formation of 3D engineered tissue to control shape and size can have important implications in biomedical research and in engineering applications such as biological soft robotics. While neural spheroids routinely are created during differentiation processes, further geometric control of in vitro neural models has not been demonstrated. Here, we present an approach to form functional in vitro neural tissue mimic (NTM) of different shapes using stem cells, a fibrin matrix, and 3D printed molds. We used murine-derived embryonic stem cells for optimizing cell-seeding protocols, characterization of the resulting internal structure of the construct, and remodeling of the extracellular matrix, as well as validation of electrophysiological activity. Then, we used these findings to biofabricate these constructs using neurons derived from human embryonic stem cells. This method can provide a large degree of design flexibility for development of in vitro functional neural tissue models of varying forms for therapeutic biomedical research, drug discovery, and disease modeling, and engineering applications.
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http://dx.doi.org/10.1073/pnas.1916138116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6926042PMC
December 2019

Publisher Correction: Combining Biomarkers with EMR Data to Identify Patients in Different Phases of Sepsis.

Sci Rep 2019 Nov 19;9(1):17419. Epub 2019 Nov 19.

Department of Statistics, University of Illinois at Urbana Champaign, Illini Hall, 725S Wright St #101, 61820, Champaign, IL, USA.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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http://dx.doi.org/10.1038/s41598-019-53691-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6864078PMC
November 2019

Neuromuscular actuation of biohybrid motile bots.

Proc Natl Acad Sci U S A 2019 10 16;116(40):19841-19847. Epub 2019 Sep 16.

Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801;

The integration of muscle cells with soft robotics in recent years has led to the development of biohybrid machines capable of untethered locomotion. A major frontier that currently remains unexplored is neuronal actuation and control of such muscle-powered biohybrid machines. As a step toward this goal, we present here a biohybrid swimmer driven by on-board neuromuscular units. The body of the swimmer consists of a free-standing soft scaffold, skeletal muscle tissue, and optogenetic stem cell-derived neural cluster containing motor neurons. Myoblasts embedded in extracellular matrix self-organize into a muscle tissue guided by the geometry of the scaffold, and the resulting muscle tissue is cocultured in situ with a neural cluster. Motor neurons then extend neurites selectively toward the muscle and innervate it, developing functional neuromuscular units. Based on this initial construct, we computationally designed, optimized, and implemented light-sensitive flagellar swimmers actuated by these neuromuscular units. Cyclic muscle contractions, induced by neural stimulation, drive time-irreversible flagellar dynamics, thereby providing thrust for untethered forward locomotion of the swimmer. Overall, this work demonstrates an example of a biohybrid robot implementing neuromuscular actuation and illustrates a path toward the forward design and control of neuron-enabled biohybrid machines.
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http://dx.doi.org/10.1073/pnas.1907051116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6778261PMC
October 2019

Multi-cellular engineered living systems: building a community around responsible research on emergence.

Biofabrication 2019 07 10;11(4):043001. Epub 2019 Jul 10.

Pragmatic Health Ethics Research Unit, Institut de recherches cliniques de Montreal and Department of Neurology and Neurosurgery, McGill University, Canada.

Ranging from miniaturized biological robots to organoids, multi-cellular engineered living systems (M-CELS) pose complex ethical and societal challenges. Some of these challenges, such as how to best distribute risks and benefits, are likely to arise in the development of any new technology. Other challenges arise specifically because of the particular characteristics of M-CELS. For example, as an engineered living system becomes increasingly complex, it may provoke societal debate about its moral considerability, perhaps necessitating protection from harm or recognition of positive moral and legal rights, particularly if derived from cells of human origin. The use of emergence-based principles in M-CELS development may also create unique challenges, making the technology difficult to fully control or predict in the laboratory as well as in applied medical or environmental settings. In response to these challenges, we argue that the M-CELS community has an obligation to systematically address the ethical and societal aspects of research and to seek input from and accountability to a broad range of stakeholders and publics. As a newly developing field, M-CELS has a significant opportunity to integrate ethically responsible norms and standards into its research and development practices from the start. With the aim of seizing this opportunity, we identify two general kinds of salient ethical issues arising from M-CELS research, and then present a set of commitments to and strategies for addressing these issues. If adopted, these commitments and strategies would help define M-CELS as not only an innovative field, but also as a model for responsible research and engineering.
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http://dx.doi.org/10.1088/1758-5090/ab268cDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7551891PMC
July 2019

Smartphone-imaged microfluidic biochip for measuring CD64 expression from whole blood.

Analyst 2019 Jul 16;144(13):3925-3935. Epub 2019 May 16.

Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.

Sepsis, a life-threatening syndrome that contributes to millions of deaths annually worldwide, represents a moral and economic burden to the healthcare system. Although no single, or even a combination of biomarkers has been validated for the diagnosis of sepsis, multiple studies have shown the high specificity of CD64 expression on neutrophils (nCD64) to sepsis. The analysis of elevated nCD64 in the first 2-6 hours after infection during the pro-inflammatory stage could significantly contribute to early sepsis diagnosis. Therefore, a rapid and automated device to periodically measure nCD64 expression at the point-of-care (POC) could lead to timely medical intervention and reduced mortality rates. Current accepted technologies for measuring nCD64 expression, such as flow cytometry, require manual sample preparation and long incubation times. For POC applications, however, the technology should be able to measure nCD64 expression with little to no sample preparation. In this paper, we demonstrate a smartphone-imaged microfluidic biochip for detecting nCD64 expression in under 50 min. In our assay, first unprocessed whole blood is injected into a capture chamber to immunologically capture nCD64 along a staggered array of pillars, which were previously functionalized with an antibody against CD64. Then, an image of the capture channel is taken using a smartphone-based microscope. This image is used to measure the cumulative fraction of captured cells (γ) as a function of length in the channel. During the image analysis, a statistical model is fitted to γ in order to extract the probability of capture of neutrophils per collision with a pillar (ε). The fitting shows a strong correlation with nCD64 expression measured using flow cytometry (R = 0.82). Finally, the applicability of the device to sepsis was demonstrated by analyzing nCD64 from 8 patients (37 blood samples analyzed) along the time they were admitted to the hospital. Results from this analysis, obtained using the smartphone-imaged microfluidic biochip were compared with flow cytometry. Again, a correlation coefficient R = 0.82 (slope = 0.99) was obtained demonstrating a good linear correlation between the two techniques. Deployment of this technology in ICU could significantly enhance patient care worldwide.
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http://dx.doi.org/10.1039/c9an00532cDOI Listing
July 2019

Perspective: The promise of multi-cellular engineered living systems.

APL Bioeng 2018 Dec 11;2(4):040901. Epub 2018 Oct 11.

Boston University, Boston, Massachusetts 02215, USA.

Recent technological breakthroughs in our ability to derive and differentiate induced pluripotent stem cells, organoid biology, organ-on-chip assays, and 3-D bioprinting have all contributed to a heightened interest in the design, assembly, and manufacture of living systems with a broad range of potential uses. This white paper summarizes the state of the emerging field of "multi-cellular engineered living systems," which are composed of interacting cell populations. Recent accomplishments are described, focusing on current and potential applications, as well as barriers to future advances, and the outlook for longer term benefits and potential ethical issues that need to be considered.
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http://dx.doi.org/10.1063/1.5038337DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6481725PMC
December 2018

Matrix Topography Regulates Synaptic Transmission at the Neuromuscular Junction.

Adv Sci (Weinh) 2019 Mar 17;6(6):1801521. Epub 2019 Jan 17.

Department of Bioengineering University of Illinois at Urbana-Champaign Urbana IL 61801 USA.

Recreation of a muscle that can be controlled by the nervous system would provide a major breakthrough for treatments of injury and diseases. However, the underlying basis of how neuron-muscle interfaces are formed is still not understood sufficiently. Here, it is hypothesized that substrate topography regulates neural innervation and synaptic transmission by mediating the cross-talk between neurons and muscles. This hypothesis is examined by differentiating neural stem cells on the myotubes, formed on the substrate with controlled groove width. The substrate with the groove width of 1600 nm, a similar size to the myofibril diameter, serves to produce larger and aligned myotubes than the flat substrate. The myotubes formed on the grooved substrate display increases in the acetylcholine receptor expression. Reciprocally, motor neuron progenitor cells differentiated from neural stem cells innervate the larger and aligned myotubes more actively than randomly oriented myotubes. As a consequence, mature and aligned myotubes respond to glutamate (i.e., an excitatory neurotransmitter) and curare (i.e., a neuromuscular antagonist) more rapidly and homogeneously than randomly oriented myotubes. The results of this study will be broadly useful for improving the quality of engineered muscle used in a series of applications including drug screening, regeneration therapies, and biological machinery assembly.
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http://dx.doi.org/10.1002/advs.201801521DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6425454PMC
March 2019

Detecting sepsis by observing neutrophil motility.

Nat Biomed Eng 2018 04;2(4):197-198

Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.

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http://dx.doi.org/10.1038/s41551-018-0223-0DOI Listing
April 2018

Monolayer MoS Nanoribbon Transistors Fabricated by Scanning Probe Lithography.

Nano Lett 2019 03 4;19(3):2092-2098. Epub 2019 Mar 4.

Department of Mechanical Science and Engineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States.

Monolayer MoS is a promising material for nanoelectronics; however, the lack of nanofabrication tools and processes has made it very challenging to realize nanometer-scale electronic devices from monolayer MoS. Here, we demonstrate the fabrication of monolayer MoS nanoribbon field-effect transistors as narrow as 30 nm using scanning probe lithography (SPL). The SPL process uses a heated nanometer-scale tip to deposit narrow nanoribbon polymer structures onto monolayer MoS. The polymer serves as an etch mask during a XeF vapor etch, which defines the channel of a field-effect transistor (FET). We fabricated seven devices with a channel width ranging from 30 to 370 nm, and the fabrication process was carefully studied by electronic measurements made at each process step. The nanoribbon devices have a current on/off ratio > 10 and an extrinsic field-effect mobility up to 8.53 cm/(V s). By comparing a 30 nm wide device with a 60 nm wide device that was fabricated on the same MoS flake, we found the narrower device had a smaller mobility, a lower on/off ratio, and a larger subthreshold swing. To our knowledge, this is the first published work that describes a working transistor device from monolayer MoS with a channel width smaller than 100 nm.
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http://dx.doi.org/10.1021/acs.nanolett.9b00271DOI Listing
March 2019
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