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Selvam K, Najib MA, Khalid MF, Yunus MH, Wahab HA, Harun A, Zainulabid UA, Fadzli Mustaffa KM, Aziah I. Isolation and characterization of ssDNA aptamers against BipD antigen of Burkholderia pseudomallei. Anal Biochem 2024; 695:115655. [PMID: 39214325 DOI: 10.1016/j.ab.2024.115655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 08/19/2024] [Accepted: 08/27/2024] [Indexed: 09/04/2024]
Abstract
BACKGROUND Melioidosis is difficult to diagnose due to its wide range of clinical symptoms. The culture method is time-consuming and less sensitive, emphasizing the importance of rapid and accurate diagnostic tests for melioidosis. Burkholderia invasion protein D (BipD) of Burkholderia pseudomallei is a potential diagnostic biomarker. This study aimed to isolate and characterize single-stranded DNA aptamers that specifically target BipD. METHODS The recombinant BipD protein was produced, followed by isolation of BipD-specific aptamers using Systematic Evolution of Ligands by EXponential enrichment. The binding affinity and specificity of the selected aptamers were evaluated using Enzyme-Linked Oligonucleotide Assay. RESULTS The fifth SELEX cycle showed a notable enrichment of recombinant BipD protein-specific aptamers. Sequencing analysis identified two clusters with a total of seventeen distinct aptamers. AptBipD1, AptBipD13, and AptBipD50 were chosen based on their frequency. Among them, AptBipD1 exhibited the highest binding affinity with a Kd value of 1.0 μM for the recombinant BipD protein. Furthermore, AptBipD1 showed significant specificity for B. pseudomallei compared to other tested bacteria. CONCLUSION AptBipD1 is a promising candidate for further development of reliable, affordable, and efficient point-of-care diagnostic tests for melioidosis.
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Affiliation(s)
- Kasturi Selvam
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Kubang Kerian, 16150, Kelantan, Malaysia
| | - Mohamad Ahmad Najib
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Kubang Kerian, 16150, Kelantan, Malaysia
| | - Muhammad Fazli Khalid
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Kubang Kerian, 16150, Kelantan, Malaysia
| | - Muhammad Hafiznur Yunus
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Kubang Kerian, 16150, Kelantan, Malaysia
| | - Habibah A Wahab
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800, Pulau, Pinang, Malaysia
| | - Azian Harun
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, 16150, Kelantan, Malaysia; Hospital Universiti Sains Malaysia, Kubang Kerian, 16150, Kelantan, Malaysia
| | - Ummu Afeera Zainulabid
- Department of Internal Medicine, Kulliyyah of Medicine, International Islamic University Malaysia, Kuantan, 25200, Pahang, Malaysia
| | - Khairul Mohd Fadzli Mustaffa
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Kubang Kerian, 16150, Kelantan, Malaysia
| | - Ismail Aziah
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Kubang Kerian, 16150, Kelantan, Malaysia.
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Fang Z, Feng X, Tang F, Jiang H, Han S, Tao R, Lu C. Aptamer Screening: Current Methods and Future Trend towards Non-SELEX Approach. BIOSENSORS 2024; 14:350. [PMID: 39056626 PMCID: PMC11274700 DOI: 10.3390/bios14070350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 07/15/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024]
Abstract
Aptamers are nucleic acid sequences that specifically bind with target molecules and are vital to applications such as biosensing, drug development, disease diagnostics, etc. The traditional selection procedure of aptamers is based on the Systematic Evolution of Ligands by an Exponential Enrichment (SELEX) process, which relies on repeating cycles of screening and amplification. With the rapid development of aptamer applications, RNA and XNA aptamers draw more attention than before. But their selection is troublesome due to the necessary reverse transcription and transcription process (RNA) or low efficiency and accuracy of enzymes for amplification (XNA). In light of this, we review the recent advances in aptamer selection methods and give an outlook on future development in a non-SELEX approach, which simplifies the procedure and reduces the experimental costs. We first provide an overview of the traditional SELEX methods mostly designed for screening DNA aptamers to introduce the common tools and methods. Then a section on the current screening methods for RNA and XNA is prepared to demonstrate the efforts put into screening these aptamers and the current difficulties. We further predict that the future trend of aptamer selection lies in non-SELEX methods that do not require nucleic acid amplification. We divide non-SELEX methods into an immobilized format and non-immobilized format and discuss how high-resolution partitioning methods could facilitate the further improvement of selection efficiency and accuracy.
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Affiliation(s)
- Zhihui Fang
- Key Laboratory of Specialty Agri-Products Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China; (Z.F.); (X.F.); (F.T.); (H.J.); (S.H.)
| | - Xiaorui Feng
- Key Laboratory of Specialty Agri-Products Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China; (Z.F.); (X.F.); (F.T.); (H.J.); (S.H.)
| | - Fan Tang
- Key Laboratory of Specialty Agri-Products Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China; (Z.F.); (X.F.); (F.T.); (H.J.); (S.H.)
| | - Han Jiang
- Key Laboratory of Specialty Agri-Products Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China; (Z.F.); (X.F.); (F.T.); (H.J.); (S.H.)
| | - Shuyuan Han
- Key Laboratory of Specialty Agri-Products Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China; (Z.F.); (X.F.); (F.T.); (H.J.); (S.H.)
| | - Ran Tao
- Shenzhen Key Laboratory of Advanced Thin Films and Applications, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Chenze Lu
- Key Laboratory of Specialty Agri-Products Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China; (Z.F.); (X.F.); (F.T.); (H.J.); (S.H.)
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Chen C, Song X, Yu Y, Wang X, Xu H, Ji W, Ma J, Zhao C, Feng S, Wang Y, Su XD, Wang W. Aptamer-based nanointerferometer enables amplification-free ultrasensitive detection and differentiation of SARS-CoV-2 variants. Anal Chim Acta 2023; 1260:341207. [PMID: 37121656 PMCID: PMC10085716 DOI: 10.1016/j.aca.2023.341207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/07/2023] [Accepted: 04/10/2023] [Indexed: 05/02/2023]
Abstract
The state-of-the-art SARS-CoV-2 detection methods include qRT-PCR and antibody-based lateral flow assay (LFA) point-of-care tests. Despite the high sensitivity and selectivity, qRT-PCR is slow, expensive and needs well-trained operators. On the other extreme, LFA suffers from low sensitivity albeit its fast detection speed, low detection cost and ease of use. Therefore, the continuing COVID-19 pandemic calls for a SARS-CoV-2 detection method that is rapid, convenient and cost-effective without compromise in sensitivity. Here we provide a proof-of-principle demonstration of an optimized aptamer-based nanointerferometer that enables rapid and amplification-free detection of SARS-CoV-2 spike protein-coated pseudovirus directly from human saliva with the limit of detection (LOD) of about 400 copies per mL. This LOD is on par with that of qRT-PCR, making it 1000 to 100,000-fold more sensitive than commercial LFA tests. Using various combinations of negative selections during the screens for the aptamer targeting the receptor binding domain of the spike protein of SARS-CoV-2, we isolated two aptamers that can distinguish the Omicron and Delta variants. Integrating these two aptamers with LFA strips or the nanointerferometer sensors allows both detection and differentiation of the Omicron and Delta variants which has the potential to realize rapid triage of patients infected different SARS-CoV-2 variants.
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Affiliation(s)
- Changtian Chen
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China; Center for Life Sciences, Beijing, 100871, China
| | - Xiaohui Song
- State Key Laboratory of Protein and Plant Gene Research, And Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, China
| | - Yuanling Yu
- Changping Laboratory, Yard 28, Science Park Road, Changping District, Beijing, China
| | - Xingwei Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Hua Xu
- State Key Laboratory of Protein and Plant Gene Research, And Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, China
| | - Weiwei Ji
- College of Physics and Electronic Science, Hubei Normal University, Hubei, 435002, China
| | - Jingchen Ma
- School of Materials and Energy, Guangdong University of Technology, Guangzhou, 510006, China
| | - Chenyan Zhao
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, 102629, China
| | - Silu Feng
- School of Integrated Circuits, Guangdong University of Technology, Guangzhou, 510006, China.
| | - Youchun Wang
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, 102629, China; Changping Laboratory, Yard 28, Science Park Road, Changping District, Beijing, China.
| | - Xiao-Dong Su
- State Key Laboratory of Protein and Plant Gene Research, And Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, China.
| | - Wei Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China; Center for Life Sciences, Beijing, 100871, China.
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Tapp M, Dennis P, Naik RR, Milam VT. Competition-Enhanced Ligand Selection to Screen for DNA Aptamers for Spherical Gold Nanoparticles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:9043-9052. [PMID: 34279112 DOI: 10.1021/acs.langmuir.1c01053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The Competition-Enhanced Ligand Selection (CompELS) approach was used to identify aptamer candidates for spherical gold nanoparticles (AuNPs). This approach differs from conventional Systematic Evolution of Ligands by EXponential enrichment (SELEX)-based aptamer screening by eliminating repeated elution and polymerase chain reaction (PCR) amplification steps of bound candidate sequences between each selection round to continually enrich the candidate aptamer pool with oligonucleotides remaining from an earlier SELEX selection round. Instead, a new pool of unenriched oligonucleotides is added during each CompELS selection round to compete with existing target-bound oligonucleotides species for target binding sites. In this study, 24 aptamer candidates for AuNPs were identified using the CompELS approach and then compared to reveal similarities in their primary structures and their predicted secondary structures. No strong patterns in individual base identities (position-dependent) nor in segments of consecutive bases (independent of position) prevailed among the identified sequences. Motifs in predicted secondary structures, on the other hand, were shared among otherwise unrelated aptamer sequences. These motifs were revealed using a systematic classification and enumeration of distinct secondary structure elements, namely, hairpins, duplexes, single-stranded segments, interior loops, bulges, and multibranched loops.
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Affiliation(s)
| | - Patrick Dennis
- Materials & Manufacturing Directorate, Soft Matter Materials Branch, Air Force Research Laboratory, Wright-Patterson AFB, Ohio 45433, United States
| | - Rajesh R Naik
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson AFB, Ohio 45433, United States
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Pavase TR, Lin H, Soomro MA, Zheng H, Li X, Wang K, Li Z. Visual detection of tropomyosin, a major shrimp allergenic protein using gold nanoparticles (AuNPs)-assisted colorimetric aptasensor. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:382-394. [PMID: 37073291 PMCID: PMC10077205 DOI: 10.1007/s42995-020-00085-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 11/05/2020] [Indexed: 05/03/2023]
Abstract
A gold nanoparticle-based label-free colorimetric assay was developed to detect the shrimp allergenic protein tropomyosin (TM), an important biomarker responsible for severe clinical reactivity to shellfish. In a gold nanoparticles (AuNPs)-tropomyosin-binding aptamer (TMBA) complex, the aptamer adsorbs onto the surface of AuNPs and dissociates in the presence of TM. In addition, AuNPs tend to aggregate in the presence of ionic salt, revealing a color change (i.e., wine-red to purple/blue) with a shift in the maximum absorption peak from 520 nm. In the presence of specific binding TM, the aptamer folds into a tertiary structure where it more efficiently stabilizes AuNPs toward the salt-induced aggregation with a hypsochromic shift in the absorption spectra compared to the stabilized AuNPs by aptamer alone. Based on the aggregation and sensitive spectral transformation principle, the AuNPs-based colorimetric aptasensor was successfully applied to detect TM with a range of 10-200 nmol/L and a low detection limit of 40 nmol/L in water samples. The reliability, selectivity, and sensitivity of the aptasensor was then tested with food samples spiked with TM. The observed detection limit was as low as 70 nmol/L in shrimp, 90 nmol/L in tofu, and 80 nmol/L in eggs, respectively. We anticipate the proposed AuNPs-based colorimetric aptasensor assay possesses a high potential for the easy and efficient visual colorimetric detection of TM. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-020-00085-5.
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Affiliation(s)
- Tushar Ramesh Pavase
- Food Safety Laboratory, Department of Food Science and Engineering, College of Food Science and Engineering, Ocean University of China, Qingdao, 266003 China
| | - Hong Lin
- Food Safety Laboratory, Department of Food Science and Engineering, College of Food Science and Engineering, Ocean University of China, Qingdao, 266003 China
| | - Maqsood Ahmed Soomro
- Fish Molecular Immunology Laboratory, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
| | - Hongwei Zheng
- Food Safety Laboratory, Department of Food Science and Engineering, College of Food Science and Engineering, Ocean University of China, Qingdao, 266003 China
| | - Xiaxia Li
- Food Safety Laboratory, Department of Food Science and Engineering, College of Food Science and Engineering, Ocean University of China, Qingdao, 266003 China
| | - Kexin Wang
- Food Safety Laboratory, Department of Food Science and Engineering, College of Food Science and Engineering, Ocean University of China, Qingdao, 266003 China
| | - Zhenxing Li
- Food Safety Laboratory, Department of Food Science and Engineering, College of Food Science and Engineering, Ocean University of China, Qingdao, 266003 China
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Ochoa S, Milam VT. Modified Nucleic Acids: Expanding the Capabilities of Functional Oligonucleotides. Molecules 2020; 25:E4659. [PMID: 33066073 PMCID: PMC7587394 DOI: 10.3390/molecules25204659] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/07/2020] [Accepted: 10/08/2020] [Indexed: 12/20/2022] Open
Abstract
In the last three decades, oligonucleotides have been extensively investigated as probes, molecular ligands and even catalysts within therapeutic and diagnostic applications. The narrow chemical repertoire of natural nucleic acids, however, imposes restrictions on the functional scope of oligonucleotides. Initial efforts to overcome this deficiency in chemical diversity included conservative modifications to the sugar-phosphate backbone or the pendant base groups and resulted in enhanced in vivo performance. More importantly, later work involving other modifications led to the realization of new functional characteristics beyond initial intended therapeutic and diagnostic prospects. These results have inspired the exploration of increasingly exotic chemistries highly divergent from the canonical nucleic acid chemical structure that possess unnatural physiochemical properties. In this review, the authors highlight recent developments in modified oligonucleotides and the thrust towards designing novel nucleic acid-based ligands and catalysts with specifically engineered functions inaccessible to natural oligonucleotides.
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Affiliation(s)
- Steven Ochoa
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA;
| | - Valeria T. Milam
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA;
- Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
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7
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Amero P, Khatua S, Rodriguez-Aguayo C, Lopez-Berestein G. Aptamers: Novel Therapeutics and Potential Role in Neuro-Oncology. Cancers (Basel) 2020; 12:cancers12102889. [PMID: 33050158 PMCID: PMC7600320 DOI: 10.3390/cancers12102889] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/25/2020] [Accepted: 09/29/2020] [Indexed: 12/15/2022] Open
Abstract
A relatively new paradigm in cancer therapeutics is the use of cancer cell-specific aptamers, both as therapeutic agents and for targeted delivery of anticancer drugs. After the first therapeutic aptamer was described nearly 25 years ago, and the subsequent first aptamer drug approved, many efforts have been made to translate preclinical research into clinical oncology settings. Studies of aptamer-based technology have unveiled the vast potential of aptamers in therapeutic and diagnostic applications. Among pediatric solid cancers, brain tumors are the leading cause of death. Although a few aptamer-related translational studies have been performed in adult glioblastoma, the use of aptamers in pediatric neuro-oncology remains unexplored. This review will discuss the biology of aptamers, including mechanisms of targeting cell surface proteins, various modifications of aptamer structure to enhance therapeutic efficacy, the current state and challenges of aptamer use in neuro-oncology, and the potential therapeutic role of aptamers in pediatric brain tumors.
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Affiliation(s)
- Paola Amero
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA;
| | - Soumen Khatua
- Division of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Cristian Rodriguez-Aguayo
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA;
- Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
- Correspondence: (C.R.-A.); (G.L.-B.); Tel.: +1-713-563-6150 (C.R.-A.); +1-713-792-8140 (G.L.-B.)
| | - Gabriel Lopez-Berestein
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA;
- Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Correspondence: (C.R.-A.); (G.L.-B.); Tel.: +1-713-563-6150 (C.R.-A.); +1-713-792-8140 (G.L.-B.)
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Sullivan R, Adams MC, Naik RR, Milam VT. Analyzing Secondary Structure Patterns in DNA Aptamers Identified via CompELS. Molecules 2019; 24:molecules24081572. [PMID: 31010064 PMCID: PMC6515186 DOI: 10.3390/molecules24081572] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/09/2019] [Accepted: 04/15/2019] [Indexed: 12/12/2022] Open
Abstract
In contrast to sophisticated high-throughput sequencing tools for genomic DNA, analytical tools for comparing secondary structure features between multiple single-stranded DNA sequences are less developed. For single-stranded nucleic acid ligands called aptamers, secondary structure is widely thought to play a pivotal role in driving recognition-based binding activity between an aptamer sequence and its specific target. Here, we employ a competition-based aptamer screening platform called CompELS to identify DNA aptamers for a colloidal target. We then analyze predicted secondary structures of the aptamers and a large population of random sequences to identify sequence features and patterns. Our secondary structure analysis identifies patterns ranging from position-dependent score matrixes of individual structural elements to position-independent consensus domains resulting from global alignment.
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Affiliation(s)
- Richard Sullivan
- School of Materials Science and Engineering, Georgia Institute of Technology, 771 Ferst Dr. NW, Atlanta, GA 30332-0245, USA.
| | - Mary Catherine Adams
- School of Materials Science and Engineering, Georgia Institute of Technology, 771 Ferst Dr. NW, Atlanta, GA 30332-0245, USA.
| | - Rajesh R Naik
- 711 Human Performance Wing, Air Force Research Laboratory, Wright Patterson AFB, OH 45433, USA.
| | - Valeria T Milam
- School of Materials Science and Engineering, Georgia Institute of Technology, 771 Ferst Dr. NW, Atlanta, GA 30332-0245, USA.
- Wallace H. Coulter, Department of Biomedical Engineering, Georgia Institute of Technology, 313 Ferst Dr., Atlanta, GA 30332, USA.
- Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, 315 Ferst Dr., Atlanta, GA 30332-0363, USA.
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