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Krausz AD, Korley FK, Burns MA. The Current State of Traumatic Brain Injury Biomarker Measurement Methods. BIOSENSORS 2021; 11:319. [PMID: 34562909 PMCID: PMC8469272 DOI: 10.3390/bios11090319] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 12/16/2022]
Abstract
Traumatic brain injury (TBI) is associated with high rates of morbidity and mortality partially due to the limited tools available for diagnosis and classification. Measuring panels of protein biomarkers released into the bloodstream after injury has been proposed to diagnose TBI, inform treatment decisions, and monitor the progression of the injury. Being able to measure these protein biomarkers at the point-of-care would enable assessment of TBIs from the point-of-injury to the patient's hospital bedside. In this review, we provide a detailed discussion of devices reported in the academic literature and available on the market that have been designed to measure TBI protein biomarkers in various biofluids and contexts. We also assess the challenges associated with TBI biomarker measurement devices and suggest future research directions to encourage translation of these devices to clinical use.
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Affiliation(s)
- Alyse D. Krausz
- Biomedical Engineering Department, University of Michigan, Ann Arbor, MI 48109, USA
| | - Frederick K. Korley
- Emergency Medicine, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Mark A. Burns
- Biomedical Engineering Department, University of Michigan, Ann Arbor, MI 48109, USA
- Chemical Engineering Department, University of Michigan, Ann Arbor, MI 48109, USA
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2
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Enzyme‐Based Logic Gates and Networks with Output Signals Analyzed by Various Methods. Chemphyschem 2017; 18:1688-1713. [DOI: 10.1002/cphc.201601402] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Indexed: 01/16/2023]
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3
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Enzyme Logic Systems: Biomedical and Forensic Biosensor Applications. SPRINGER SERIES ON CHEMICAL SENSORS AND BIOSENSORS 2017. [DOI: 10.1007/5346_2017_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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4
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Verma A, Fratto BE, Privman V, Katz E. Design of Flow Systems for Improved Networking and Reduced Noise in Biomolecular Signal Processing in Biocomputing and Biosensing Applications. SENSORS 2016; 16:s16071042. [PMID: 27399702 PMCID: PMC4969838 DOI: 10.3390/s16071042] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 06/21/2016] [Accepted: 06/24/2016] [Indexed: 02/07/2023]
Abstract
We consider flow systems that have been utilized for small-scale biomolecular computing and digital signal processing in binary-operating biosensors. Signal measurement is optimized by designing a flow-reversal cuvette and analyzing the experimental data to theoretically extract the pulse shape, as well as reveal the level of noise it possesses. Noise reduction is then carried out numerically. We conclude that this can be accomplished physically via the addition of properly designed well-mixing flow-reversal cell(s) as an integral part of the flow system. This approach should enable improved networking capabilities and potentially not only digital but analog signal-processing in such systems. Possible applications in complex biocomputing networks and various sense-and-act systems are discussed.
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Affiliation(s)
- Arjun Verma
- Department of Physics, Clarkson University, Potsdam, NY 13699, USA.
| | - Brian E Fratto
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699, USA.
| | - Vladimir Privman
- Department of Physics, Clarkson University, Potsdam, NY 13699, USA.
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699, USA.
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Razavi S, Su S, Inoue T. Cellular signaling circuits interfaced with synthetic, post-translational, negating Boolean logic devices. ACS Synth Biol 2014; 3:676-85. [PMID: 25000210 PMCID: PMC4169742 DOI: 10.1021/sb500222z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Indexed: 12/11/2022]
Abstract
A negating functionality is fundamental to information processing of logic circuits within cells and computers. Aiming to adapt unutilized electronic concepts to the interrogation of signaling circuits in cells, we first took a bottom-up strategy whereby we created protein-based devices that perform negating Boolean logic operations such as NOT, NOR, NAND, and N-IMPLY. These devices function in living cells within a minute by precisely commanding the localization of an activator molecule among three subcellular spaces. We networked these synthetic gates to an endogenous signaling circuit and devised a physiological output. In search of logic functions in signal transduction, we next took a top-down approach and computationally screened 108 signaling pathways to identify commonalities and differences between these biological pathways and electronic circuits. This combination of synthetic and systems approaches will guide us in developing foundations for deconstruction of intricate cell signaling, as well as construction of biomolecular computers.
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Affiliation(s)
- Shiva Razavi
- Department of Biomedical Engineering, Department of Cell Biology, and Center for Cell
Dynamics, Johns Hopkins University School
of Medicine, Baltimore, Maryland 21205, United
States
| | - Steven Su
- Department of Biomedical Engineering, Department of Cell Biology, and Center for Cell
Dynamics, Johns Hopkins University School
of Medicine, Baltimore, Maryland 21205, United
States
| | - Takanari Inoue
- Department of Biomedical Engineering, Department of Cell Biology, and Center for Cell
Dynamics, Johns Hopkins University School
of Medicine, Baltimore, Maryland 21205, United
States
- Japan
Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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6
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Biosensors with built-in biomolecular logic gates for practical applications. BIOSENSORS-BASEL 2014; 4:273-300. [PMID: 25587423 PMCID: PMC4264359 DOI: 10.3390/bios4030273] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 08/15/2014] [Accepted: 08/22/2014] [Indexed: 01/20/2023]
Abstract
Molecular logic gates, designs constructed with biological and chemical molecules, have emerged as an alternative computing approach to silicon-based logic operations. These molecular computers are capable of receiving and integrating multiple stimuli of biochemical significance to generate a definitive output, opening a new research avenue to advanced diagnostics and therapeutics which demand handling of complex factors and precise control. In molecularly gated devices, Boolean logic computations can be activated by specific inputs and accurately processed via bio-recognition, bio-catalysis, and selective chemical reactions. In this review, we survey recent advances of the molecular logic approaches to practical applications of biosensors, including designs constructed with proteins, enzymes, nucleic acids, nanomaterials, and organic compounds, as well as the research avenues for future development of digitally operating “sense and act” schemes that logically process biochemical signals through networked circuits to implement intelligent control systems.
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7
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Mailloux S, Guz N, Zakharchenko A, Minko S, Katz E. Majority and minority gates realized in enzyme-biocatalyzed systems integrated with logic networks and interfaced with bioelectronic systems. J Phys Chem B 2014; 118:6775-84. [PMID: 24873717 DOI: 10.1021/jp504057u] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Biocatalytic reactions operating in parallel and resulting in reduction of NAD(+) or oxidation of NADH were used to mimic 3-input majority and minority logic gates, respectively. The substrates corresponding to the enzyme reactions were used as the input signals. When the input signals were applied at their high concentrations, defined as logic 1 input values, the corresponding biocatalytic reactions were activated, resulting in changes of the NADH concentration defined as the output signal. The NADH concentration changes were dependent on the number of parallel reactions activated by the input signals. The absence of the substrates, meaning their logic 0 input values, kept the reactions mute with no changes in the NADH concentration. In the system mimicking the majority function, the enzyme-biocatalyzed reactions resulted in a higher production of NADH when more than one input signal was applied at the logic 1 value. Another system mimicking the minority function consumed more NADH, thus leaving a smaller residual output signal, when more than one input signal was applied at the logic 1 value. The performance of the majority gate was improved by processing the output signal through a filter system in which another biocatalytic reaction consumed a fraction of the output signal, thus reducing its physical value to zero when the logic 0 value was obtained. The majority gate was integrated with a preceding AND logic gate to illustrate the possibility of complex networks. The output signal, NADH, was also used to activate a process mimicking drug release, thus illustrating the use of the majority gate in decision-making biomedical systems. The 3-input majority gate was also used as a switchable AND/OR gate when one of the input signals was reserved as a command signal, switching the logic operation for processing of the other two inputs. Overall, the designed majority and minority logic gates demonstrate novel functions of biomolecular information processing systems.
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Affiliation(s)
- Shay Mailloux
- Department of Chemistry and Biomolecular Science, Clarkson University , Potsdam, New York 13699-5810, United States
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Bakshi S, Zavalov O, Halámek J, Privman V, Katz E. Modularity of Biochemical Filtering for Inducing Sigmoid Response in Both Inputs in an Enzymatic AND Gate. J Phys Chem B 2013; 117:9857-65. [DOI: 10.1021/jp4058675] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Saira Bakshi
- Department
of Chemistry and Biomolecular Science and ‡Department of Physics, Clarkson University, Potsdam, New York
13676, United States
| | - Oleksandr Zavalov
- Department
of Chemistry and Biomolecular Science and ‡Department of Physics, Clarkson University, Potsdam, New York
13676, United States
| | - Jan Halámek
- Department
of Chemistry and Biomolecular Science and ‡Department of Physics, Clarkson University, Potsdam, New York
13676, United States
| | - Vladimir Privman
- Department
of Chemistry and Biomolecular Science and ‡Department of Physics, Clarkson University, Potsdam, New York
13676, United States
| | - Evgeny Katz
- Department
of Chemistry and Biomolecular Science and ‡Department of Physics, Clarkson University, Potsdam, New York
13676, United States
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Privman V, Fratto BE, Zavalov O, Halámek J, Katz E. Enzymatic AND logic gate with sigmoid response induced by photochemically controlled oxidation of the output. J Phys Chem B 2013; 117:7559-68. [PMID: 23731012 DOI: 10.1021/jp404054f] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We report a study of a system which involves an enzymatic cascade realizing an AND logic gate, with an added photochemical processing of the output, allowing the gate's response to be made sigmoid in both inputs. New functional forms are developed for quantifying the kinetics of such systems, specifically designed to model their response in terms of signal and information processing. These theoretical expressions are tested for the studied system, which also allows us to consider aspects of biochemical information processing such as noise transmission properties and control of timing of the chemical and physical steps.
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Affiliation(s)
- Vladimir Privman
- Department of Physics, Clarkson University, Potsdam, New York 13676, USA
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10
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Electrode interfaces switchable by physical and chemical signals for biosensing, biofuel, and biocomputing applications. Anal Bioanal Chem 2012; 405:3659-72. [DOI: 10.1007/s00216-012-6525-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 10/23/2012] [Accepted: 10/24/2012] [Indexed: 01/26/2023]
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Halámková L, Mailloux S, Halámek J, Cooper AJ, Katz E. Enzymatic analysis of α-ketoglutaramate--a biomarker for hyperammonemia. Talanta 2012; 100:7-11. [PMID: 23141304 PMCID: PMC3496271 DOI: 10.1016/j.talanta.2012.08.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 08/13/2012] [Accepted: 08/14/2012] [Indexed: 12/31/2022]
Abstract
Two enzymatic assays were developed for the analysis of α-ketoglutaramate (KGM)-an important biomarker of hepatic encephalopathy and other hyperammonemic diseases. In both procedures, KGM is first converted to α-ketoglutarate (KTG) via a reaction catalyzed by ω-amidase (AMD). In the first procedure, KTG generated in the AMD reaction initiates a biocatalytic cascade in which the concerted action of alanine transaminase and lactate dehydrogenase results in the oxidation of NADH. In the second procedure, KTG generated from KGM is reductively aminated, with the concomitant oxidation of NADH, in a reaction catalyzed by L-glutamic dehydrogenase. In both assays, the decrease in optical absorbance (λ=340 nm) corresponding to NADH oxidation is used to quantify concentrations of KGM. The two analytical procedures were applied to 50% (v/v) human serum diluted with aqueous solutions containing the assay components and spiked with concentrations of KGM estimated to be present in normal human plasma and in plasma from hyperammonemic patients. Since KTG is the product of AMD-catalyzed hydrolysis of KGM, in a separate study, this compound was used as a surrogate for KGM. Statistical analyses of samples mimicking the concentration of KGM assumed to be present in normal and pathological concentration ranges were performed. Both enzymatic assays for KGM were confirmed to discriminate between the predicted normal and pathophysiological concentrations of the analyte. The present study is the first step toward the development of a clinically useful probe for KGM analysis in biological fluids.
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Affiliation(s)
- Lenka Halámková
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699, USA
| | - Shay Mailloux
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699, USA
| | - Jan Halámek
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699, USA
| | - Arthur J.L. Cooper
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699, USA
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Katz E, Wang J, Privman M, Halámek J. Multianalyte digital enzyme biosensors with built-in Boolean logic. Anal Chem 2012; 84:5463-9. [PMID: 22656194 DOI: 10.1021/ac3007076] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Novel biosensors based on the biocomputing concept digitally process multiple biochemical signals through Boolean logic networks of coupled biomolecular reactions and produce output in the form of a YES/NO response. Compared to traditional single-analyte sensing devices, biocomputing approach enables a high-fidelity multianalyte biosensing, particularly beneficial for biomedical applications.
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Affiliation(s)
- Evgeny Katz
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York 13699, United States.
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13
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Bocharova V, Zavalov O, MacVittie K, Arugula MA, Guz NV, Dokukin ME, Halámek J, Sokolov I, Privman V, Katz E. A biochemical logic approach to biomarker-activated drug release. ACTA ACUST UNITED AC 2012. [DOI: 10.1039/c2jm32966b] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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