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Chu W, Shastry S, Barbieri E, Prodromou R, Greback-Clarke P, Smith W, Moore B, Kilgore R, Cummings C, Pancorbo J, Gilleskie G, Daniele MA, Menegatti S. Peptide ligands for the affinity purification of adeno-associated viruses from HEK 293 cell lysates. Biotechnol Bioeng 2023; 120:2283-2300. [PMID: 37435968 PMCID: PMC10440015 DOI: 10.1002/bit.28495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 06/15/2023] [Accepted: 06/30/2023] [Indexed: 07/13/2023]
Abstract
Adeno-associated viruses (AAVs) are the vector of choice for delivering gene therapies that can cure inherited and acquired diseases. Clinical research on various AAV serotypes significantly increased in recent years alongside regulatory approvals of AAV-based therapies. The current AAV purification platform hinges on the capture step, for which several affinity resins are commercially available. These adsorbents rely on protein ligands-typically camelid antibodies-that provide high binding capacity and selectivity, but suffer from low biochemical stability and high cost, and impose harsh elution conditions (pH < 3) that can harm the transduction activity of recovered AAVs. Addressing these challenges, this study introduces peptide ligands that selectively capture AAVs and release them under mild conditions (pH = 6.0). The peptide sequences were identified by screening a focused library and modeled in silico against AAV serotypes 2 and 9 (AAV2 and AAV9) to select candidate ligands that target homologous sites at the interface of the VP1-VP2 and VP2-VP3 virion proteins with mild binding strength (KD ~ 10-5 -10- 6 M). Selected peptides were conjugated to Toyopearl resin and evaluated via binding studies against AAV2 and AAV9, demonstrating the ability to target both serotypes with values of dynamic binding capacity (DBC10% > 1013 vp/mL of resin) and product yields (~50%-80%) on par with commercial adsorbents. The peptide-based adsorbents were finally utilized to purify AAV2 from a HEK 293 cell lysate, affording high recovery (50%-80%), 80- to 400-fold reduction of host cell proteins (HCPs), and high transduction activity (up to 80%) of the purified viruses.
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Affiliation(s)
- Wenning Chu
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Shriarjun Shastry
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, North Carolina, USA
| | - Eduardo Barbieri
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Raphael Prodromou
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Paul Greback-Clarke
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, North Carolina, USA
| | - Will Smith
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, North Carolina, USA
| | - Brandyn Moore
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Ryan Kilgore
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Christopher Cummings
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, North Carolina, USA
| | - Jennifer Pancorbo
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, North Carolina, USA
| | - Gary Gilleskie
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, North Carolina, USA
| | - Michael A Daniele
- North Carolina Viral Vector Initiative in Research and Learning (NC-VVIRAL), North Carolina State University, Raleigh, North Carolina, USA
- Joint Department of Biomedical Engineering, North Carolina State University and University of North Carolina at Chapel Hill, Raleigh, North Carolina, USA
| | - Stefano Menegatti
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, North Carolina, USA
- North Carolina Viral Vector Initiative in Research and Learning (NC-VVIRAL), North Carolina State University, Raleigh, North Carolina, USA
- LigaTrap Technologies LLC, Raleigh, North Carolina, USA
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Prodromou R, Moore B, Chu W, Deal H, Miguel AS, Brown AC, Daniele MA, Pozdin V, Menegatti S. Molecular engineering of cyclic azobenzene-peptide hybrid ligands for the purification of human blood Factor VIII via photo-affinity chromatography. Adv Funct Mater 2023; 33:2213881. [PMID: 37576949 PMCID: PMC10421628 DOI: 10.1002/adfm.202213881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Indexed: 08/15/2023]
Abstract
The use of benign stimuli to control the binding and release of labile biologics for their isolation from complex feedstocks is a key goal of modern biopharmaceutical technology. This study introduces cyclic azobenzene-peptide (CAP) hybrid ligands for the rapid and discrete photo-responsive capture and release of blood coagulation Factor VIII (FVIII). A predictive method - based on amino acid sequence and molecular architecture of CAPs - was developed to correlate the conformation of cis/trans CAP photo-isomers to FVIII binding and release. The combined in silico and in vitro analysis of FVIII:peptide interactions guided the design of a rational approach to optimize isomerization kinetics and biorecognition of CAPs. A photoaffinity adsorbent, prepared by conjugating selected CAP G-cycloAZOB[Lys-YYKHLYN-Lys]-G on translucent chromatographic beads, featured high binding capacity (> 6 mg of FVIII per mL of resin) and rapid photo-isomerization kinetics (τ < 30s) when exposed to 420-450 nm light at the intensity of 0.1 W·cm-2. The adsorbent purified FVIII from a recombinant harvest using a single mobile phase, affording high product yield (>90%), purity (>95%), and blood clotting activity. The CAPs introduced in this report demonstrate a novel route integrating gentle operational conditions in a rapid and efficient bioprocess for the purification of life-saving biotherapeutics.
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Affiliation(s)
- Raphael Prodromou
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC 27695, USA
| | - Brandyn Moore
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC 27695, USA
| | - Wenning Chu
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC 27695, USA
| | - Halston Deal
- Joint Department of Biomedical Engineering, North Carolina State University and University of North Carolina at Chapel Hill, 911 Oval Drive, Raleigh, NC 27695, USA
| | - Adriana San Miguel
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC 27695, USA
| | - Ashley C. Brown
- Joint Department of Biomedical Engineering, North Carolina State University and University of North Carolina at Chapel Hill, 911 Oval Drive, Raleigh, NC 27695, USA
| | - Michael A. Daniele
- Joint Department of Biomedical Engineering, North Carolina State University and University of North Carolina at Chapel Hill, 911 Oval Drive, Raleigh, NC 27695, USA
- Department of Electrical and Computer Engineering, North Carolina State University, 890 Oval Drive, Raleigh, NC 27695, USA
| | - Vladimir Pozdin
- Department of Electrical and Computer Engineering, Florida International University, 10555 West Flagler St., Miami, FL 33174, USA
- Department of Mechanical and Materials Engineering, Florida International University, 10555 West Flagler St., Miami, FL 33174, USA
| | - Stefano Menegatti
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC 27695, USA
- Biomanufacturing Training and Education Center (BTEC), 850 Oval Drive, Raleigh, NC 27606, USA
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Chu W, Prodromou R, Moore B, Elhanafi D, Kilgore R, Shastry S, Menegatti S. Development of Peptide Ligands for the Purification of α-1 Antitrypsin from Cell Culture Fluids. J Chromatogr A 2022; 1679:463363. [DOI: 10.1016/j.chroma.2022.463363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 11/16/2022]
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Day K, Schneible JD, Young AT, Pozdin VA, Van Den Driessche G, Gaffney LA, Prodromou R, Freytes DO, Fourches D, Daniele M, Menegatti S. Photoinduced reconfiguration to control the protein-binding affinity of azobenzene-cyclized peptides. J Mater Chem B 2021; 8:7413-7427. [PMID: 32661544 DOI: 10.1039/d0tb01189d] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The impact of next-generation biorecognition elements (ligands) will be determined by the ability to remotely control their binding activity for a target biomolecule in complex environments. Compared to conventional mechanisms for regulating binding affinity (pH, ionic strength, or chaotropic agents), light provides higher accuracy and rapidity, and is particularly suited for labile targets. In this study, we demonstrate a general method to develop azobenzene-cyclized peptide ligands with light-controlled affinity for target proteins. Light triggers a cis/trans isomerization of the azobenzene, which results in a major structural rearrangement of the cyclic peptide from a non-binding to a binding configuration. Critical to this goal are the ability to achieve efficient photo-isomerization under low light dosage and the temporal stability of both cis and trans isomers. We demonstrated our method by designing photo-switchable peptides targeting vascular cell adhesion marker 1 (VCAM1), a cell marker implicated in stem cell function. Starting from a known VCAM1-binding linear peptide, an ensemble of azobenzene-cyclized variants with selective light-controlled binding were identified by combining in silico design with experimental characterization via spectroscopy and surface plasmon resonance. Variant cycloAZOB[G-VHAKQHRN-K] featured rapid, light-controlled binding of VCAM1 (KD,trans/KD,cis ∼ 130). Biotin-cycloAZOB[G-VHAKQHRN-K] was utilized to label brain microvascular endothelial cells (BMECs), showing co-localization with anti-VCAM1 antibodies in cis configuration and negligible binding in trans configuration.
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Affiliation(s)
- Kevin Day
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, North Carolina, USA.
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Chu W, Prodromou R, Day KN, Schneible JD, Bacon KB, Bowen JD, Kilgore RE, Catella CM, Moore BD, Mabe MD, Alashoor K, Xu Y, Xiao Y, Menegatti S. Peptides and pseudopeptide ligands: a powerful toolbox for the affinity purification of current and next-generation biotherapeutics. J Chromatogr A 2020; 1635:461632. [PMID: 33333349 DOI: 10.1016/j.chroma.2020.461632] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/14/2020] [Accepted: 10/15/2020] [Indexed: 02/08/2023]
Abstract
Following the consolidation of therapeutic proteins in the fight against cancer, autoimmune, and neurodegenerative diseases, recent advancements in biochemistry and biotechnology have introduced a host of next-generation biotherapeutics, such as CRISPR-Cas nucleases, stem and car-T cells, and viral vectors for gene therapy. With these drugs entering the clinical pipeline, a new challenge lies ahead: how to manufacture large quantities of high-purity biotherapeutics that meet the growing demand by clinics and biotech companies worldwide. The protein ligands employed by the industry are inadequate to confront this challenge: while featuring high binding affinity and selectivity, these ligands require laborious engineering and expensive manufacturing, are prone to biochemical degradation, and pose safety concerns related to their bacterial origin. Peptides and pseudopeptides make excellent candidates to form a new cohort of ligands for the purification of next-generation biotherapeutics. Peptide-based ligands feature excellent target biorecognition, low or no toxicity and immunogenicity, and can be manufactured affordably at large scale. This work presents a comprehensive and systematic review of the literature on peptide-based ligands and their use in the affinity purification of established and upcoming biological drugs. A comparative analysis is first presented on peptide engineering principles, the development of ligands targeting different biomolecular targets, and the promises and challenges connected to the industrial implementation of peptide ligands. The reviewed literature is organized in (i) conventional (α-)peptides targeting antibodies and other therapeutic proteins, gene therapy products, and therapeutic cells; (ii) cyclic peptides and pseudo-peptides for protein purification and capture of viral and bacterial pathogens; and (iii) the forefront of peptide mimetics, such as β-/γ-peptides, peptoids, foldamers, and stimuli-responsive peptides for advanced processing of biologics.
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Affiliation(s)
- Wenning Chu
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Raphael Prodromou
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Kevin N Day
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - John D Schneible
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Kaitlyn B Bacon
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - John D Bowen
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Ryan E Kilgore
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Carly M Catella
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Brandyn D Moore
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Matthew D Mabe
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Kawthar Alashoor
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY 14642
| | - Yiman Xu
- College of Material Science and Engineering, Donghua University, 201620 Shanghai, People's Republic of China
| | - Yuanxin Xiao
- College of Textile, Donghua University, Songjiang District, Shanghai, 201620, People's Republic of China
| | - Stefano Menegatti
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606.
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Abstract
While antibodies remain established therapeutic and diagnostic tools, other protein scaffolds are emerging as effective and safer alternatives. Affibodies in particular are a new class of small proteins marketed as bio-analytic reagents. They feature tailorable binding affinity, low immunogenicity, high tissue permeation, and high expression titer in bacterial hosts. This work presents the development of affibody-binding peptides to be utilized as ligands for their purification from bacterial lysates. Affibody-binding candidates were identified by screening a peptide library simultaneously against two model affibodies (anti-immunoglobulin G (IgG) and anti-albumin) with the aim of selecting peptides targeting the conserved domain of affibodies. An ensemble of homologous sequences identified from screening was synthesized on Toyopearl® resin and evaluated via binding studies to select sequences that afford high product binding and recovery. The affibody-peptide interaction was also evaluated by in silico docking, which corroborated the targeting of the conserved domain. Ligand IGKQRI was validated through purification of an anti-ErbB2 affibody from an Escherichia coli lysate. The values of binding capacity (~5 mg affibody per mL of resin), affinity (KD ~1 μM), recovery and purity (64-71% and 86-91%), and resin lifetime (100 cycles) demonstrate that IGKQRI can be employed as ligand in affibody purification processes.
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Affiliation(s)
- Annalisa Barozzi
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA; (A.B.); (R.A.L.); (K.N.D.); (R.P.)
| | - R. Ashton Lavoie
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA; (A.B.); (R.A.L.); (K.N.D.); (R.P.)
| | - Kevin N. Day
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA; (A.B.); (R.A.L.); (K.N.D.); (R.P.)
| | - Raphael Prodromou
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA; (A.B.); (R.A.L.); (K.N.D.); (R.P.)
| | - Stefano Menegatti
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA; (A.B.); (R.A.L.); (K.N.D.); (R.P.)
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, NC 27695-7905, USA
- Correspondence: ; Tel.: +1-919-753-3276
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Day K, Prodromou R, Saberi Bosari S, Lavoie A, Omary M, Market C, San Miguel A, Menegatti S. Discovery and Evaluation of Peptide Ligands for Selective Adsorption and Release of Cas9 Nuclease on Solid Substrates. Bioconjug Chem 2019; 30:3057-3068. [DOI: 10.1021/acs.bioconjchem.9b00703] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Kevin Day
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Engineering Building 1, 911 Partners Way, Raleigh 27695-7905, United States
| | - Raphael Prodromou
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Engineering Building 1, 911 Partners Way, Raleigh 27695-7905, United States
| | - Sahand Saberi Bosari
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Engineering Building 1, 911 Partners Way, Raleigh 27695-7905, United States
| | - Ashton Lavoie
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Engineering Building 1, 911 Partners Way, Raleigh 27695-7905, United States
| | - Mohammad Omary
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Engineering Building 1, 911 Partners Way, Raleigh 27695-7905, United States
| | - Connor Market
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Engineering Building 1, 911 Partners Way, Raleigh 27695-7905, United States
| | - Adriana San Miguel
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Engineering Building 1, 911 Partners Way, Raleigh 27695-7905, United States
| | - Stefano Menegatti
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Engineering Building 1, 911 Partners Way, Raleigh 27695-7905, United States
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, 850 Oval Drive, Raleigh, North Carolina 27606, United States
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Saberi-Bosari S, Omary M, Lavoie A, Prodromou R, Day K, Menegatti S, San-Miguel A. Affordable Microfluidic Bead-Sorting Platform for Automated Selection of Porous Particles Functionalized with Bioactive Compounds. Sci Rep 2019; 9:7210. [PMID: 31076584 PMCID: PMC6510793 DOI: 10.1038/s41598-019-42869-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 04/01/2019] [Indexed: 11/09/2022] Open
Abstract
The ability to rapidly and accurately evaluate bioactive compounds immobilized on porous particles is crucial in the discovery of drugs, diagnostic reagents, ligands, and catalysts. Existing options for solid phase screening of bioactive compounds, while highly effective and well established, can be cost-prohibitive for proof-of-concept and early stage work, limiting its applicability and flexibility in new research areas. Here, we present a low-cost microfluidics-based platform enabling automated screening of small porous beads from solid-phase peptide libraries with high sensitivity and specificity, to identify leads with high binding affinity for a biological target. The integration of unbiased computer assisted image processing and analysis tools, provided the platform with the flexibility of sorting through beads with distinct fluorescence patterns. The customized design of the microfluidic device helped with handling beads with different diameters (~100-300 µm). As a microfluidic device, this portable novel platform can be integrated with a variety of analytical instruments to perform screening. In this study, the system utilizes fluorescence microscopy and unsupervised image analysis, and can operate at a sorting speed of up to 125 beads/hr (~3.5 times faster than a trained operator) providing >90% yield and >90% bead sorting accuracy. Notably, the device has proven successful in screening a model solid-phase peptide library by showing the ability to select beads carrying peptides binding a target protein (human IgG).
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Affiliation(s)
- Sahand Saberi-Bosari
- Department of Chemical and Biomolecular Engineering, NC State University, Raleigh, NC, 27695, USA
| | - Mohammad Omary
- Department of Chemical and Biomolecular Engineering, NC State University, Raleigh, NC, 27695, USA
| | - Ashton Lavoie
- Department of Chemical and Biomolecular Engineering, NC State University, Raleigh, NC, 27695, USA
| | - Raphael Prodromou
- Department of Chemical and Biomolecular Engineering, NC State University, Raleigh, NC, 27695, USA
| | - Kevin Day
- Department of Chemical and Biomolecular Engineering, NC State University, Raleigh, NC, 27695, USA
| | - Stefano Menegatti
- Department of Chemical and Biomolecular Engineering, NC State University, Raleigh, NC, 27695, USA. .,Biomanufacturing Training and Education Center (BTEC), NC State University, Raleigh, NC, 27695, USA.
| | - Adriana San-Miguel
- Department of Chemical and Biomolecular Engineering, NC State University, Raleigh, NC, 27695, USA.
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