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Jeon E, Koo B, Kim S, Kim J, Yu Y, Jang H, Lee M, Kim SH, Kang T, Kim SK, Kwak R, Shin Y, Lee J. Publisher Correction: Biporous silica nanostructure-induced nanovortex in microfluidics for nucleic acid enrichment, isolation, and PCR-free detection. Nat Commun 2024; 15:1993. [PMID: 38443368 PMCID: PMC10915132 DOI: 10.1038/s41467-024-46401-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024] Open
Affiliation(s)
- Eunyoung Jeon
- Department of Chemistry, Hanyang University, Seoul, 04763, Republic of Korea
- Research Institute for Natural Science, Hanyang University, Seoul, 04763, Republic of Korea
- Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, 04763, Republic of Korea
| | - Bonhan Koo
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Suyeon Kim
- Department of Chemistry, Hanyang University, Seoul, 04763, Republic of Korea
- Research Institute for Natural Science, Hanyang University, Seoul, 04763, Republic of Korea
- Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, 04763, Republic of Korea
| | - Jieun Kim
- Department of Mechanical Convergence Engineering, Hanyang University, Seoul, 04763, Republic of Korea
| | - Yeonuk Yu
- Department of Mechanical Convergence Engineering, Hanyang University, Seoul, 04763, Republic of Korea
| | - Hyowon Jang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Minju Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Sung-Han Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - Taejoon Kang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Sang Kyung Kim
- Center for Augmented Safety Systems with Intelligence, Sensing and Tracking (ASSIST), Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea
| | - Rhokyun Kwak
- Department of Mechanical Convergence Engineering, Hanyang University, Seoul, 04763, Republic of Korea.
| | - Yong Shin
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea.
| | - Joonseok Lee
- Department of Chemistry, Hanyang University, Seoul, 04763, Republic of Korea.
- Research Institute for Natural Science, Hanyang University, Seoul, 04763, Republic of Korea.
- Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, 04763, Republic of Korea.
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Qiao Z, Zhang K, Liu H, Roh Y, Kim MG, Lee HJ, Koo B, Lee EY, Lee M, Park CO, Shin Y. CSMP: A Self-Assembled Plant Polysaccharide-Based Hydrofilm for Enhanced Wound Healing. Adv Healthc Mater 2024; 13:e2303244. [PMID: 37934913 DOI: 10.1002/adhm.202303244] [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: 10/15/2023] [Indexed: 11/09/2023]
Abstract
Wound management remains a critical healthcare issue due to the rising incidence of chronic diseases leading to persistent wounds. Traditional dressings have their limitations, such as potential for further damage during changing and suboptimal healing conditions. Recently, hydrogel-based dressings have gained attention due to their biocompatibility, biodegradability, and ability to fill wounds. Particularly, polysaccharide-based hydrogels have shown potential in various medical applications. This study focuses on the development of a novel hydrofilm wound dressing produced from a blend of chia seed mucilage (CSM) and polyvinyl alcohol (PVA), termed CSMP. While the individual properties of CSM and PVA are well-documented, their combined potential in wound management is largely unexplored. CSMP, coupled with sorbitol and glycerin, and cross-linked using ultraviolet light, results in a flexible, adhesive, and biocompatible hydrofilm demonstrating superior water absorption, moisturizing, and antibacterial properties. This hydrofilm promotes epithelial cell migration, enhanced collagen production, and outperforms existing commercial dressings in animal tests. The innovative CSMP hydrofilm offers a promising, cost-effective approach for improved wound care, bridging existing gaps in dressing performance and preparation simplicity. Future research can unlock further applications of such polysaccharide-based hydrofilm dressings.
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Affiliation(s)
- Zhen Qiao
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - KeLun Zhang
- Department of Dermatology, Severance, Hospital, Cutaneous Biology, Research Institute, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Huifang Liu
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Yeonjeong Roh
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Myoung Gyu Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Hyo Joo Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Bonhan Koo
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Eun Yeong Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Minju Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Chang Ook Park
- Department of Dermatology, Severance, Hospital, Cutaneous Biology, Research Institute, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Yong Shin
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
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Jeon E, Koo B, Kim S, Kim J, Yu Y, Jang H, Lee M, Kim SH, Kang T, Kim SK, Kwak R, Shin Y, Lee J. Biporous silica nanostructure-induced nanovortex in microfluidics for nucleic acid enrichment, isolation, and PCR-free detection. Nat Commun 2024; 15:1366. [PMID: 38355558 PMCID: PMC10866868 DOI: 10.1038/s41467-024-45467-w] [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: 09/29/2023] [Accepted: 01/24/2024] [Indexed: 02/16/2024] Open
Abstract
Efficient pathogen enrichment and nucleic acid isolation are critical for accurate and sensitive diagnosis of infectious diseases, especially those with low pathogen levels. Our study introduces a biporous silica nanofilms-embedded sample preparation chip for pathogen and nucleic acid enrichment/isolation. This chip features unique biporous nanostructures comprising large and small pore layers. Computational simulations confirm that these nanostructures enhance the surface area and promote the formation of nanovortex, resulting in improved capture efficiency. Notably, the chip demonstrates a 100-fold lower limit of detection compared to conventional methods used for nucleic acid detection. Clinical validations using patient samples corroborate the superior sensitivity of the chip when combined with the luminescence resonance energy transfer assay. The enhanced sample preparation efficiency of the chip, along with the facile and straightforward synthesis of the biporous nanostructures, offers a promising solution for polymer chain reaction-free detection of nucleic acids.
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Affiliation(s)
- Eunyoung Jeon
- Department of Chemistry, Hanyang University, Seoul, 04763, Republic of Korea
- Research Institute for Natural Science, Hanyang University, Seoul, 04763, Republic of Korea
- Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, 04763, Republic of Korea
| | - Bonhan Koo
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Suyeon Kim
- Department of Chemistry, Hanyang University, Seoul, 04763, Republic of Korea
- Research Institute for Natural Science, Hanyang University, Seoul, 04763, Republic of Korea
- Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, 04763, Republic of Korea
| | - Jieun Kim
- Department of Mechanical Convergence Engineering, Hanyang University, Seoul, 04763, Republic of Korea
| | - Yeonuk Yu
- Department of Mechanical Convergence Engineering, Hanyang University, Seoul, 04763, Republic of Korea
| | - Hyowon Jang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Minju Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Sung-Han Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - Taejoon Kang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Sang Kyung Kim
- Center for Augmented Safety Systems with Intelligence, Sensing and Tracking (ASSIST), Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea
| | - Rhokyun Kwak
- Department of Mechanical Convergence Engineering, Hanyang University, Seoul, 04763, Republic of Korea.
| | - Yong Shin
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea.
| | - Joonseok Lee
- Department of Chemistry, Hanyang University, Seoul, 04763, Republic of Korea.
- Research Institute for Natural Science, Hanyang University, Seoul, 04763, Republic of Korea.
- Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, 04763, Republic of Korea.
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Kim JY, Koo B, Lim SY, Cha HH, Kim MJ, Chong YP, Choi SH, Lee SO, Kim YS, Shin Y, Kim SH. A non-invasive, sensitive assay for active TB: combined cell-free DNA detection and FluoroSpot assays. Int J Tuberc Lung Dis 2023; 27:790-792. [PMID: 37749833 PMCID: PMC10519393 DOI: 10.5588/ijtld.23.0180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 06/18/2023] [Indexed: 09/27/2023] Open
Affiliation(s)
- J Y Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul
| | - B Koo
- Department of Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - S Y Lim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul
| | - H H Cha
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul
| | - M J Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul
| | - Y P Chong
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul
| | - S-H Choi
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul
| | - S-O Lee
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul
| | - Y S Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul
| | - Y Shin
- Department of Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - S-H Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul
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Kim MG, Jue M, Lee KH, Lee EY, Roh Y, Lee M, Lee HJ, Lee S, Liu H, Koo B, Jang YO, Kim EY, Zhen Q, Kim SH, Kim JK, Shin Y. Deep Learning Assisted Surface-Enhanced Raman Spectroscopy (SERS) for Rapid and Direct Nucleic Acid Amplification and Detection: Toward Enhanced Molecular Diagnostics. ACS Nano 2023; 17:18332-18345. [PMID: 37703463 DOI: 10.1021/acsnano.3c05633] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
Abstract
Surface-enhanced Raman scattering (SERS) has evolved into a robust analytical technique capable of detecting a variety of biomolecules despite challenges in securing a reliable Raman signal. Conventional SERS-based nucleic acid detection relies on hybridization assays, but reproducibility and signal strength issues have hindered research on directly amplifying nucleic acids on SERS surfaces. This study introduces a deep learning assisted ZnO-Au-SERS-based direct amplification (ZADA) system for rapid, sensitive molecular diagnostics. The system employs a SERS substrate fabricated by depositing gold on uniformly grown ZnO nanorods. These nanorods create hot spots for the amplification of the target nucleic acids directly on the SERS surface, eliminating the need for postamplification hybridization and Raman reporters. The limit of detection of the ZADA system was superior to those of the conventional amplification methods. Clinical validation of the ZADA system with coronavirus disease 2019 (COVID-19) samples from human patients yielded a sensitivity and specificity of 92.31% and 81.25%, respectively. The integration of a deep learning program further enhanced sensitivity and specificity to 100% and reduced SERS analysis time, showcasing the potential of the ZADA system for rapid, label-free disease diagnosis via direct nucleic acid amplification and detection within 20 min.
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Affiliation(s)
- Myoung Gyu Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei Ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Miyeon Jue
- Biomedical Engineering Research Center, Asan Medical Center, Seoul 05505, Republic of Korea
- Apollon, Inc., 68 Achasan-ro, Seongdong-gu, Seoul 05505, Republic of Korea
| | - Kwan Hee Lee
- Department of Medical Science, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Eun Yeong Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei Ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Yeonjeong Roh
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei Ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Minju Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei Ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Hyo Joo Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei Ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Sanghwa Lee
- Biomedical Engineering Research Center, Asan Medical Center, Seoul 05505, Republic of Korea
| | - Huifang Liu
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei Ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Bonhan Koo
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei Ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Yoon Ok Jang
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei Ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Eui Yeon Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei Ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Qiao Zhen
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei Ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Sung-Han Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Jun Ki Kim
- Biomedical Engineering Research Center, Asan Medical Center, Seoul 05505, Republic of Korea
- Department of Biomedical Engineering, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Yong Shin
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei Ro, Seodaemun-gu, Seoul 03722, Republic of Korea
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Jang YO, Kim NH, Roh Y, Koo B, Lee HJ, Kim JY, Kim SH, Shin Y. Self-directed molecular diagnostics (SdMDx) system for COVID-19 via one-pot processing. Sens Actuators B Chem 2023; 378:133193. [PMID: 36570722 PMCID: PMC9759472 DOI: 10.1016/j.snb.2022.133193] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/03/2022] [Accepted: 12/15/2022] [Indexed: 06/17/2023]
Abstract
Rapid, sensitive, and specific detection of the severe acute respiratory syndrome coronavirus (SARS-CoV)- 2 during early infection is pivotal in controlling the spread and pathological progression of Coronavirus Disease 2019 (COVID-19). Thus, highly accurate, affordable, and scalable point-of-care (POC) diagnostic technologies are necessary. Herein, we developed a rapid and efficient self-directed molecular diagnostic (SdMDx) system for SARS-CoV-2. This system combines the sample preparation step, including virus enrichment and extraction processes, which involve dimethyl suberimidate dihydrochloride and diatomaceous earth functionalized with 3-aminopropyl(diethoxy)methylsilane, and the detection step using loop-mediated isothermal amplification-lateral flow assay (LAMP-LFA). Using the SdMDx system, SARS-CoV-2 could be detected within 47 min by hand without the need for any larger instruments. The SdMDx system enabled detection as low as 0.05 PFU in the culture fluid of SARS-CoV-2-infected VeroE6 cells. We validated the accuracy of the SdMDx system on 38 clinical nasopharyngeal specimens. The clinical utility of the SdMDx system for targeting the S gene of SARS-CoV-2 showed 94.4% sensitivity and 100% specificity. This system is more sensitive than antigen and antibody assays, and it minimizes the use of complicated processes and reduces contamination risks. Accordingly, we demonstrated that the SdMDx system enables a rapid, accurate, simple, efficient, and inexpensive detection of SARS-CoV-2 at home, in emergency facilities, and in low-resource sites as a pre-screening platform and POC testing through self-operation and self-diagnosis.
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Affiliation(s)
- Yoon Ok Jang
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Nam Hun Kim
- INFUSIONTECH, 38 Heungan-daero, 427 beon-gil, Dongan-gu, Anyang-si 14059, Republic of Korea
| | - Yeonjeong Roh
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Bonhan Koo
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Hyo Joo Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Ji Yeun Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Songpa-gu, Seoul 05505, Republic of Korea
| | - Sung-Han Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Songpa-gu, Seoul 05505, Republic of Korea
| | - Yong Shin
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
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Jang YO, Ahn HS, Dao TNT, Hong J, Shin W, Lim YM, Chung SJ, Lee JH, Liu H, Koo B, Kim MG, Kim K, Lee EJ, Shin Y. Magnetic transferrin nanoparticles (MTNs) assay as a novel isolation approach for exosomal biomarkers in neurological diseases. Biomater Res 2023; 27:12. [PMID: 36797805 PMCID: PMC9936675 DOI: 10.1186/s40824-023-00353-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 02/05/2023] [Indexed: 02/18/2023] Open
Abstract
BACKGROUND Brain-derived exosomes released into the blood are considered a liquid biopsy to investigate the pathophysiological state, reflecting the aberrant heterogeneous pathways of pathological progression of the brain in neurological diseases. Brain-derived blood exosomes provide promising prospects for the diagnosis of neurological diseases, with exciting possibilities for the early and sensitive diagnosis of such diseases. However, the capability of traditional exosome isolation assays to specifically isolate blood exosomes and to characterize the brain-derived blood exosomal proteins by high-throughput proteomics for clinical specimens from patients with neurological diseases cannot be assured. We report a magnetic transferrin nanoparticles (MTNs) assay, which combined transferrin and magnetic nanoparticles to isolate brain-derived blood exosomes from clinical samples. METHODS The principle of the MTNs assay is a ligand-receptor interaction through transferrin on MTNs and transferrin receptor on exosomes, and electrostatic interaction via positively charged MTNs and negatively charged exosomes to isolate brain-derived blood exosomes. In addition, the MTNs assay is simple and rapid (< 35 min) and does not require any large instrument. We confirmed that the MTNs assay accurately and efficiently isolated exosomes from serum samples of humans with neurodegenerative diseases, such as dementia, Parkinson's disease (PD), and multiple sclerosis (MS). Moreover, we isolated exosomes from serum samples of 30 patients with three distinct neurodegenerative diseases and performed unbiased proteomic analysis to explore the pilot value of brain-derived blood protein profiles as biomarkers. RESULTS Using comparative statistical analysis, we found 21 candidate protein biomarkers that were significantly different among three groups of neurodegenerative diseases. CONCLUSION The MTNs assay is a convenient approach for the specific and affordable isolation of extracellular vesicles from body fluids for minimally-invasive diagnosis of neurological diseases.
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Affiliation(s)
- Yoon Ok Jang
- grid.15444.300000 0004 0470 5454Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722 Republic of Korea
| | - Hee-Sung Ahn
- grid.413967.e0000 0001 0842 2126Department of Convergence Medicine, Asan Medical Center, Seoul, 05505 Republic of Korea
| | - Thuy Nguyen Thi Dao
- grid.15444.300000 0004 0470 5454Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722 Republic of Korea
| | - JeongYeon Hong
- grid.413967.e0000 0001 0842 2126Asan Institute for Life Sciences, Asan Medical Center, Seoul, 05505 Republic of Korea ,grid.267370.70000 0004 0533 4667Department of Biomedical Sciences, University of Ulsan College of Medicine, Seoul, 05505 Republic of Korea
| | - Wangyong Shin
- grid.413967.e0000 0001 0842 2126Department of Neurology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505 Republic of Korea
| | - Young-Min Lim
- grid.413967.e0000 0001 0842 2126Department of Neurology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505 Republic of Korea
| | - Sun Ju Chung
- grid.413967.e0000 0001 0842 2126Department of Neurology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505 Republic of Korea
| | - Jae-Hong Lee
- grid.413967.e0000 0001 0842 2126Department of Neurology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505 Republic of Korea
| | - Huifang Liu
- grid.15444.300000 0004 0470 5454Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722 Republic of Korea
| | - Bonhan Koo
- grid.15444.300000 0004 0470 5454Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722 Republic of Korea
| | - Myoung Gyu Kim
- grid.15444.300000 0004 0470 5454Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722 Republic of Korea
| | - Kyunggon Kim
- Asan Institute for Life Sciences, Asan Medical Center, Seoul, 05505, Republic of Korea. .,Department of Biomedical Sciences, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea.
| | - Eun-Jae Lee
- Department of Neurology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea.
| | - Yong Shin
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea.
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Lee HJ, Kim NH, Lee EH, Yoon YS, Jeong YJ, Lee BC, Koo B, Jang YO, Kim SH, Kang YA, Lee SW, Shin Y. Multicenter Testing of a Simple Molecular Diagnostic System for the Diagnosis of Mycobacterium Tuberculosis. Biosensors (Basel) 2023; 13:259. [PMID: 36832025 PMCID: PMC9954000 DOI: 10.3390/bios13020259] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/04/2023] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
Mycobacterium tuberculosis (MTB) is a communicable disease and still remains a threat to common health. Thus, early diagnosis and treatment are required to prevent the spread of infection. Despite the recent advances in molecular diagnostic systems, the commonly used MTB diagnostic tools are laboratory-based assays, such as mycobacterial culture, MTB PCR, and Xpert MTB/RIF. To address this limitation, point-of-care testing (POCT)-based molecular diagnostic technologies capable of sensitive and accurate detection even in environments with limited sources are needed. In this study, we propose simple tuberculosis (TB) molecular diagnostic assay by combining sample preparation and DNA-detection steps. The sample preparation is performed using a syringe filter with amine-functionalized diatomaceous earth and homobifunctional imidoester. Subsequently, the target DNA is detected by quantitative PCR (polymerase chain reaction). The results can be obtained within 2 h from samples with large volumes, without any additional instruments. The limit of detection of this system is 10 times higher than those of conventional PCR assays. We validated the clinical utility of the proposed method in 88 sputum samples obtained from four hospitals in the Republic of Korea. Overall, the sensitivity of this system was superior to those of other assays. Therefore, the proposed system can be useful for MTB diagnosis in limited-resource settings.
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Affiliation(s)
- Hyo Joo Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Nam Hun Kim
- INFUSIONTECH, 38 Heungan-daero, 427 Beon-gil, Dongan-gu, Anyang-si 14059, Republic of Korea
| | - Eun Hye Lee
- Division of Pulmonology, Allergy and Critical Care Medicine, Department of Internal Medicine, Yongin Severance Hospital, Yonsei University College of Medicine, Yongin-si 06273, Republic of Korea
| | - Young Soon Yoon
- Division of Pulmonology and Critical Care Medicine, Department of Internal Medicine, Dongguk University Ilsan Hospital, Dongguk University College of Medicine, Goyang-si 10326, Republic of Korea
| | - Yun Jeong Jeong
- Division of Pulmonology and Critical Care Medicine, Department of Internal Medicine, Dongguk University Ilsan Hospital, Dongguk University College of Medicine, Goyang-si 10326, Republic of Korea
| | - Byung Chul Lee
- INFUSIONTECH, 38 Heungan-daero, 427 Beon-gil, Dongan-gu, Anyang-si 14059, Republic of Korea
| | - Bonhan Koo
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Yoon Ok Jang
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Sung-Han Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Songpa-gu, Seoul 05505, Republic of Korea
| | - Young Ae Kang
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Sei Won Lee
- Department of Pulmonary and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Yong Shin
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
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Liu H, Zhang K, Jang YO, Qiao Z, Jin J, Thi Dao TN, Koo B, Park CO, Shin Y. Homobifunctional imidoester-modified zinc nano-spindle attenuated hyphae growth of Aspergillus against hypersensitivity responses. iScience 2023; 26:105922. [PMID: 36866037 PMCID: PMC9971823 DOI: 10.1016/j.isci.2022.105922] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/05/2022] [Accepted: 12/30/2022] [Indexed: 01/13/2023] Open
Abstract
Fungi cause various forms of invasive fungal disease (IFD), and fungal sensitization can contribute to the development of asthma, asthma severity, and other hypersensitivity diseases, such as atopic dermatitis (AD). In this study, we introduce a facile and controllable approach, using homobifunctional imidoester-modified zinc nano-spindle (HINS), for attenuating hyphae growth of fungi and reducing the hypersensitivity response complications in fungi-infected mice. To extend the study of the specificity and immune mechanisms, we used HINS-cultured Aspergillus extract (HI-AsE) and common agar-cultured Aspergillus extract (Con-AsE) as the refined mouse models. HINS composites within the safe concentration range inhibited the hyphae growth of fungi but also reduce the number of fungal pathogens. Through the evaluation of lung and skin tissues from the mice, asthma pathogenesis (lung) and the hypersensitivity response (skin) to invasive aspergillosis were least severe in HI-AsE-infected mice. Therefore, HINS composites attenuate asthma and the hypersensitivity response to invasive aspergillosis.
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Affiliation(s)
- Huifang Liu
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - KeLun Zhang
- Department of Dermatology, Severance Hospital, Cutaneous Biology Research Institute, Yonsei University College of Medicine, Seoul, Korea,Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Yoon Ok Jang
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Zhen Qiao
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Jie Jin
- Department of Chemical and Biomolecular Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Thuy Nguyen Thi Dao
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Bonhan Koo
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Chang Ook Park
- Department of Dermatology, Severance Hospital, Cutaneous Biology Research Institute, Yonsei University College of Medicine, Seoul, Korea,Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea,Corresponding author
| | - Yong Shin
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea,Corresponding author
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10
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Belmonte M, Collet C, Nørgaard B, Otake H, Koo B, Andreini D, Mizukami T, Updegrove A, Barbato E, De Bruyne B, Leipsic J, Taylor C, Maeng M, Sonck J. 437 Accuracy Of The FFRCTPlanner In Coronary Calcific Lesions. J Cardiovasc Comput Tomogr 2022. [DOI: 10.1016/j.jcct.2022.06.042] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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11
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Kang YA, Koo B, Kim OH, Park JH, Kim HC, Lee HJ, Kim MG, Jang Y, Kim NH, Koo YS, Shin Y, Lee SW, Kim SH. Gene-Based Diagnosis of Tuberculosis from Oral Swabs with a New Generation Pathogen Enrichment Technique. Microbiol Spectr 2022; 10:e0020722. [PMID: 35587206 PMCID: PMC9241603 DOI: 10.1128/spectrum.00207-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 04/22/2022] [Indexed: 11/20/2022] Open
Abstract
A rapid and sensitive diagnosis is crucial for the management of tuberculosis (TB). A simple and label-free approach via homobifunctional imidoesters with a microfluidic platform (SLIM) assay showed a higher sensitivity than the Xpert MTB/RIF assay in the diagnosis of pulmonary TB (PTB). Here, we evaluated the efficacy of the SLIM assay for oral swab samples from cases of suspected PTB. Patients with clinically suspected PTB were prospectively enrolled and oral swab samples were processed using the SLIM assay and the attending physicians were blinded to the results of the SLIM assay. TB cases were defined as those treated with anti-TB chemotherapy for at least 6 months at the discretion of the specialists based on their clinical features and conventional laboratory results, including the Xpert assay. A total of 272 patients (with TB, n = 128 [47.1%]; without TB, n = 144 [52.9%]; mean age, 59.8 years) were enrolled. Overall, the sensitivity of the oral swab-based SLIM assay (65.6%) was higher than that of the sputum-based Xpert assay (43.4%; P = 0.001). Specifically, the SLIM oral swab assay showed a notably higher sensitivity in culture-negative TB cases compared with the Xpert assay (69.0% [95% CI: 49.2 to 84.7%] versus 7.4% [95% CI: 0.9 to 24.3%]; P = 0.001). The specificity of the SLIM and the Xpert assays was 86.1% (95% CI: 79.3 to 91.3%) and 100% (95% CI: 97.2 to 100%), respectively. When only culture-confirmed cases were analyzed, the SLIM oral swab was comparable to sputum Xpert in sensitivity (64.7% versus 54.3%, P = 0.26). The oral swab-based SLIM assay showed a superior sensitivity for TB diagnosis over the sputum-based Xpert assay, especially for culture-negative cases. IMPORTANCE The development of a rapid, accessible, and highly sensitive diagnostic tool is a major challenge in the control and management of tuberculosis. Gene-based diagnostics is recommended for the rapid diagnosis of pulmonary tuberculosis (PTB), but its sensitivity, such as Xpert MTB/RIF assay (Xpert), drops in cases with a low bacterial load. It can only be applied to sputum samples, and it is quite difficult for some patients to produce an adequate amount of sputum. We evaluated the clinical validity of an oral swab-based microfluidic system, i.e., the SLIM assay. The SLIM assay showed a significantly higher sensitivity than the Xpert assay, especially in smear-negative TB cases. This non-sputum-based SLIM assay can be a useful diagnostic test by overcoming the limitations of conventional sputum-based tests in pulmonary TB.
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Affiliation(s)
- Young Ae Kang
- Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine, College of Medicine, Yonsei University, Seoul, Republic of Korea
- Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine, Severance Hospital, Seoul, Republic of Korea
- Institute of Immunology and Immunological Disease, College of Medicine, Yonsei University, Seoul, Republic of Korea
| | - Bonhan Koo
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Ock-Hwa Kim
- Department of Pulmonary and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
- Division of Pulmonology and Critical Care Medicine, Department of Internal Medicine, Chungnam National University Sejong Hospital, Sejong, Republic of Korea
| | - Joung Ha Park
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Ho Cheol Kim
- Department of Pulmonary and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Hyo Joo Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Myoung Gyu Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Youngwon Jang
- Department of Pulmonary and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Na Hyun Kim
- Department of Pulmonary and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Yong Seo Koo
- Department of Neurology, Asan Medical Center, Seoul, Republic of Korea
| | - Yong Shin
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Sei Won Lee
- Department of Pulmonary and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Sung-Han Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
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12
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Koo B, Kim Y, Jang YO, Liu H, Kim MG, Lee HJ, Woo MK, Kim C, Shin Y. A novel platform using homobifunctional hydrazide for enrichment and isolation of urinary circulating RNAs. Bioeng Transl Med 2022; 8:e10348. [PMID: 36684108 PMCID: PMC9842063 DOI: 10.1002/btm2.10348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/22/2022] [Accepted: 05/06/2022] [Indexed: 01/25/2023] Open
Abstract
Changes in specific circulating RNA (circRNA) expressions can serve as diagnostic noninvasive biomarkers for prostate cancer (PCa). However, there are still unmet needs, such as unclear types and roles of circRNAs, PCa detection in benign prostatic hyperplasia (BPH) by unstandardized methods, and limitations of sample volume capacity and low circRNA concentrations. This study reports a simple and rapid circRNA enrichment and isolation technique named "HAZIS-CirR" for the analysis of urinary circRNAs. The method utilizes homobifunctional hydrazides with amine-modified zeolite and polyvinylidene fluoride (PVDF) syringe filtration for combining electrostatic and covalent coupling and size-based filtration, and it offers instrument-free isolation of circRNAs in 20 min without volume limitation, thermoregulation, and lysis. HAZIS-CirR has high capture efficiency (82.03%-92.38%) and a 10-fold more sensitive detection limit (20 fM) than before enrichment (200 fM). The clinical utility of HAZIS-CirR is confirmed by analyzing circulating mRNAs and circulating miRNAs in 89 urine samples. Furthermore, three miRNA panels that differentiate PCa from BPH and control, PCa from control, and BPH from control, respectively, are established by comparing miRNA levels. HAZIS-CirR will be used as an optimal and established method for the enrichment and isolation of circRNAs as diagnostic, prognostic, and predictive biomarkers in human cancers.
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Affiliation(s)
- Bonhan Koo
- Department of Biotechnology, College of Life Science and BiotechnologyYonsei UniversitySeodaemun‐gu, SeoulRepublic of Korea
| | - Yunlim Kim
- Department of Urology, Asan Medical CenterUniversity of Ulsan College of MedicineSongpa‐gu, SeoulRepublic of Korea
| | - Yoon Ok Jang
- Department of Biotechnology, College of Life Science and BiotechnologyYonsei UniversitySeodaemun‐gu, SeoulRepublic of Korea
| | - Huifang Liu
- Department of Biotechnology, College of Life Science and BiotechnologyYonsei UniversitySeodaemun‐gu, SeoulRepublic of Korea
| | - Myoung Gyu Kim
- Department of Biotechnology, College of Life Science and BiotechnologyYonsei UniversitySeodaemun‐gu, SeoulRepublic of Korea
| | - Hyo Joo Lee
- Department of Biotechnology, College of Life Science and BiotechnologyYonsei UniversitySeodaemun‐gu, SeoulRepublic of Korea
| | - Myung Kyun Woo
- Department of Biomedical EngineeringSchool of Electrical Engineering, University of UlsanNam‐gu, UlsanRepublic of Korea
| | - Choung‐Soo Kim
- Department of Urology, Asan Medical CenterUniversity of Ulsan College of MedicineSongpa‐gu, SeoulRepublic of Korea
- Department of UrologyEwha Womans University Mokdong HospitalYangcheon‐gu, SeoulRepublic of Korea
| | - Yong Shin
- Department of Biotechnology, College of Life Science and BiotechnologyYonsei UniversitySeodaemun‐gu, SeoulRepublic of Korea
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13
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Liu H, Zou Q, Kim MG, Qiao Z, Nguyen DTT, Koo B, Lee HJ, Jang YO, Kim JK, Shin Y. Homobifunctional Imidoester Combined Black Phosphorus Nanosheets Used as Cofactors for Nucleic Acid Extraction. BioChip J 2022. [DOI: 10.1007/s13206-022-00046-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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14
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Dao TNT, Kim MG, Koo B, Liu H, Jang YO, Lee HJ, Kim Y, Park Y, Kim HS, Kim C, Shin Y. Chimeric nanocomposites for the rapid and simple isolation of urinary extracellular vesicles. J Extracell Vesicles 2022; 11:e12195. [PMID: 35188341 PMCID: PMC8859916 DOI: 10.1002/jev2.12195] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 12/03/2021] [Accepted: 01/11/2022] [Indexed: 12/17/2022] Open
Abstract
Cancer cell-derived extracellular vesicles (EVs) are promising biomarkers for cancer diagnosis and prognosis. However, the lack of rapid and sensitive isolation techniques to obtain EVs from clinical samples at a sufficiently high yield limits their practicability. Chimeric nanocomposites of lactoferrin conjugated 2,2-bis(methylol)propionic acid dendrimer-modified magnetic nanoparticles (LF-bis-MPA-MNPs) are fabricated and used for simple and sensitive EV isolation from various biological samples via a combination of electrostatic interaction, physically absorption, and biorecognition between the surfaces of the EVs and the LF-bis-MPA-MNPs. The speed, efficiency, recovery rate, and purity of EV isolation by the LF-bis-MPA-MNPs are superior to those obtained by using established methods. The relative expressions of exosomal microRNAs (miRNAs) from isolated EVs in cancerous cell-derived exosomes are verified as significantly higher than those from noncancerous ones. Finally, the chimeric nanocomposites are used to assess urinary exosomal miRNAs from urine specimens from 20 prostate cancer (PCa), 10 benign prostatic hyperplasia (BPH), patients and 10 healthy controls. Significant up-regulation of miR-21 and miR-346 and down-regulation of miR-23a and miR-122-5p occurs in both groups compared to healthy controls. LF-bis-MPA-MNPs provide a rapid, simple, and high yield method for human excreta analysis in clinical applications.
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Affiliation(s)
- Thuy Nguyen Thi Dao
- Department of BiotechnologyCollege of Life Science and BiotechnologyYonsei UniversitySeoulRepublic of Korea
| | - Myoung Gyu Kim
- Department of BiotechnologyCollege of Life Science and BiotechnologyYonsei UniversitySeoulRepublic of Korea
| | - Bonhan Koo
- Department of BiotechnologyCollege of Life Science and BiotechnologyYonsei UniversitySeoulRepublic of Korea
| | - Huifang Liu
- Department of BiotechnologyCollege of Life Science and BiotechnologyYonsei UniversitySeoulRepublic of Korea
| | - Yoon Ok Jang
- Department of BiotechnologyCollege of Life Science and BiotechnologyYonsei UniversitySeoulRepublic of Korea
| | - Hyo Joo Lee
- Department of BiotechnologyCollege of Life Science and BiotechnologyYonsei UniversitySeoulRepublic of Korea
| | - Yunlim Kim
- Department of UrologyAsan Medical CenterUniversity of Ulsan College of MedicineSeoulRepublic of Korea
| | - Yun‐Yong Park
- Department of Life ScienceChung‐Ang UniversitySeoulRepublic of Korea
| | - Hyun Soo Kim
- INFUSIONTECH38, Heungan‐daero 427 beon‐gilDongan‐guAnyang‐si14059Korea
- Department of Molecular Cell BiologySungkyunkwan University School of MedicineSuwon16419South Korea
| | - Choung‐Soo Kim
- Department of UrologyAsan Medical CenterUniversity of Ulsan College of MedicineSeoulRepublic of Korea
| | - Yong Shin
- Department of BiotechnologyCollege of Life Science and BiotechnologyYonsei UniversitySeoulRepublic of Korea
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15
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Jun E, Koo B, Kim EJ, Hwang DW, Lee JH, Song KB, Lee W, Park Y, Hong S, Shin Y, Kim SC. Analysis of KRAS Mutation Subtype in Tissue DNA and Cell-Free DNA Using Droplet Digital PCR and the Function of Cell-Free DNA as a Recurrence Predictive Marker in Pancreatic Cancer. Biomedicines 2021; 9:biomedicines9111599. [PMID: 34829828 PMCID: PMC8615414 DOI: 10.3390/biomedicines9111599] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/26/2021] [Accepted: 10/30/2021] [Indexed: 11/17/2022] Open
Abstract
KRAS mutation is a major regulator in the tumor progression of pancreatic cancer. Here, we compared the frequency and mutation burden of KRAS mutation subtypes with paired tumor tissue and blood in patients and examined their clinical significance. DNA from tumor tissues and cell-free DNA (cfDNA) from preoperative blood were obtained from 70 patients with pancreatic cancer. Subtypes and mutation burdens of KRAS G12D and G12V mutations were evaluated using droplet digital PCR. Comparing the presence of mutations in tissue, accumulative and simultaneous mutations of G12D or G12V were identified of 67 (95.7%), and 48 patients (68.6%). Conversely, in blood, they were only identified in 18 (25.7%) and four (5.7%) patients; respectively. Next, comparing the mutation burden in tissue, the mutation burden varied from less than 0.1 to more than five, whereas that of cfDNA in blood was mostly between one and five, as cases with a mutation burden lower than 0.1 and higher than five were rare. Finally, the presence of the G12V mutation alone in cfDNA and the combination of the G12V mutation with elevated CA 19-9 levels were associated with poor recurrence-free survival. These fundamental data on the KRAS mutation subtypes and their clinical significance could support their potential as predictive markers for postoperative recurrence.
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Affiliation(s)
- Eunsung Jun
- Department of Convergence Medicine, Asan Institute for Life Sciences, University of Ulsan College of Medicine and Asan Medical Center, Seoul 05505, Korea;
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Asan Medical Center, AMIST, University of Ulsan College of Medicine, Seoul 05505, Korea; (D.W.H.); (J.H.L.); (K.B.S.); (W.L.); (Y.P.); (S.H.)
- Correspondence: (E.J.); (Y.S.); (S.C.K.); Tel.: +82-2-3010-1696 (E.J.); +82-2-2123-2885 (Y.S.); +82-2-3010-3936 (S.C.K.); Fax: +82-2-474-9027 (E.J.); +82-2-362-7265 (Y.S.); +82-2-474-9027 (S.C.K.)
| | - Bonhan Koo
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea;
| | - Eo Jin Kim
- Department of Convergence Medicine, Asan Institute for Life Sciences, University of Ulsan College of Medicine and Asan Medical Center, Seoul 05505, Korea;
| | - Dae Wook Hwang
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Asan Medical Center, AMIST, University of Ulsan College of Medicine, Seoul 05505, Korea; (D.W.H.); (J.H.L.); (K.B.S.); (W.L.); (Y.P.); (S.H.)
| | - Jae Hoon Lee
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Asan Medical Center, AMIST, University of Ulsan College of Medicine, Seoul 05505, Korea; (D.W.H.); (J.H.L.); (K.B.S.); (W.L.); (Y.P.); (S.H.)
| | - Ki Byung Song
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Asan Medical Center, AMIST, University of Ulsan College of Medicine, Seoul 05505, Korea; (D.W.H.); (J.H.L.); (K.B.S.); (W.L.); (Y.P.); (S.H.)
| | - Woohyung Lee
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Asan Medical Center, AMIST, University of Ulsan College of Medicine, Seoul 05505, Korea; (D.W.H.); (J.H.L.); (K.B.S.); (W.L.); (Y.P.); (S.H.)
| | - Yejong Park
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Asan Medical Center, AMIST, University of Ulsan College of Medicine, Seoul 05505, Korea; (D.W.H.); (J.H.L.); (K.B.S.); (W.L.); (Y.P.); (S.H.)
| | - Sarang Hong
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Asan Medical Center, AMIST, University of Ulsan College of Medicine, Seoul 05505, Korea; (D.W.H.); (J.H.L.); (K.B.S.); (W.L.); (Y.P.); (S.H.)
| | - Yong Shin
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea;
- Correspondence: (E.J.); (Y.S.); (S.C.K.); Tel.: +82-2-3010-1696 (E.J.); +82-2-2123-2885 (Y.S.); +82-2-3010-3936 (S.C.K.); Fax: +82-2-474-9027 (E.J.); +82-2-362-7265 (Y.S.); +82-2-474-9027 (S.C.K.)
| | - Song Cheol Kim
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Asan Medical Center, AMIST, University of Ulsan College of Medicine, Seoul 05505, Korea; (D.W.H.); (J.H.L.); (K.B.S.); (W.L.); (Y.P.); (S.H.)
- Correspondence: (E.J.); (Y.S.); (S.C.K.); Tel.: +82-2-3010-1696 (E.J.); +82-2-2123-2885 (Y.S.); +82-2-3010-3936 (S.C.K.); Fax: +82-2-474-9027 (E.J.); +82-2-362-7265 (Y.S.); +82-2-474-9027 (S.C.K.)
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16
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Liu H, Qiao Z, Jang YO, Kim MG, Zou Q, Lee HJ, Koo B, Kim SH, Yun K, Kim HS, Shin Y. Diatomaceous earth/zinc oxide micro-composite assisted antibiotics in fungal therapy. Nano Converg 2021; 8:32. [PMID: 34694514 PMCID: PMC8542915 DOI: 10.1186/s40580-021-00283-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 10/05/2021] [Indexed: 05/27/2023]
Abstract
As the second wave of COVID-19 hits South Asia, an increasing deadly complication 'fungal infections (such as Mycosis, Candida and Aspergillus) outbreak' has been raised concern about the insufficient technologies and medicals for its diagnosis and therapy. Biosilica based nano-therapy can be used for therapeutic efficacy, yet their direct role as antibiotic agent with biocompatibility and stability remains unclear. Here, we report that a diatomaceous earth (DE) framework semiconductor composite conjugated DE and in-house synthesized zinc oxide (DE-ZnO), as an antibiotic agent for the enhancement of antibiotic efficacy and persistence. We found that the DE-ZnO composite had enhanced antibiotic activity against fungi (A. fumigatus) and Gram-negative bacteria (E. coli, S. enterica). The DE-ZnO composite provides enhancing large surface areas for enhancement of target pathogen binding affinity, as well as produces active ions including reactive oxygen species and metal ion for breaking the cellular network of fungi and Gram-negative bacteria. Additionally, the toxicity of DE-ZnO with 3 time less amount of dosage is 6 times lower than the commercial SiO2-ZnO. Finally, a synergistic effect of DE-ZnO and existing antifungal agents (Itraconazole and Amphotericin B) showed a better antifungal activity, which could be reduced the side effects due to the antifungal agents overdose, than a single antibiotic agent use. We envision that this DE-ZnO composite can be used to enhance antibiotic activity and its persistence, with less-toxicity, biocompatibility and high stability against fungi and Gram-negative bacteria which could be a valuable candidate in medical science and industrial engineering.
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Affiliation(s)
- Huifang Liu
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Zhen Qiao
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Yoon Ok Jang
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Myoung Gyu Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Qingshuang Zou
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Hyo Joo Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Bonhan Koo
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Sung-Han Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympicro-43gil, Songpa-gu, Seoul, 05505, Republic of Korea
| | - Kyusik Yun
- Department of Bionanotechnology, Gachon University, Gyeonggi-do, Seongnam, 13120, Republic of Korea
| | - Hyun-Soo Kim
- INFUSIONTECH, Gyeonggi-do, 427 beon-gil, Dongan-gu, Anyang-si 14059, Republic of Korea
| | - Yong Shin
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea.
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17
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Jang YO, Lee HJ, Koo B, Cha HH, Kwon JS, Kim JY, Kim MG, Kim HS, Kim SH, Shin Y. Rapid COVID-19 Molecular Diagnostic System Using Virus Enrichment Platform. Biosensors (Basel) 2021; 11:bios11100373. [PMID: 34677329 PMCID: PMC8534047 DOI: 10.3390/bios11100373] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/25/2021] [Accepted: 10/03/2021] [Indexed: 12/22/2022]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus (SARS-CoV)-2, is rapidly spreading and severely straining the capacities of public health communities and systems around the world. Therefore, accurate, rapid, and robust diagnostic tests for COVID-19 are crucial to prevent further spread of the infection, alleviate the burden on healthcare and diagnostic facilities, and ensure timely therapeutic intervention. To date, several detection methods based on nucleic acid amplification have been developed for the rapid and accurate detection of SARS-CoV-2. Despite the myriad of advancements in the detection methods for SARS-CoV-2, rapid sample preparation methods for RNA extraction from viruses have rarely been explored. Here, we report a rapid COVID-19 molecular diagnostic system that combines a self-powered sample preparation assay and loop-mediated isothermal amplification (LAMP) based naked-eye detection method for the rapid and sensitive detection of SARS-CoV-2. The self-powered sample preparation assay with a hydrophilic polyvinylidene fluoride filter and dimethyl pimelimidate can be operated by hand, without the use of any sophisticated instrumentation, similar to the reverse transcription (RT)-LAMP-based lateral flow assay for the naked-eye detection of SARS-CoV-2. The COVID-19 molecular diagnostic system enriches the virus population, extracts and amplifies the target RNA, and detects SARS-CoV-2 within 60 min. We validated the accuracy of the system by using 23 clinical nasopharyngeal specimens. We envision that this proposed system will enable simple, facile, efficient, and inexpensive diagnosis of COVID-19 at home and the clinic as a pre-screening platform to reduce the burden on the medical staff in this pandemic era.
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Affiliation(s)
- Yoon Ok Jang
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea; (Y.O.J.); (H.J.L.); (B.K.); (M.G.K.)
| | - Hyo Joo Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea; (Y.O.J.); (H.J.L.); (B.K.); (M.G.K.)
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Songpa-gu, Seoul 05505, Korea; (H.-H.C.); (J.-S.K.); (J.Y.K.)
| | - Bonhan Koo
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea; (Y.O.J.); (H.J.L.); (B.K.); (M.G.K.)
| | - Hye-Hee Cha
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Songpa-gu, Seoul 05505, Korea; (H.-H.C.); (J.-S.K.); (J.Y.K.)
| | - Ji-Soo Kwon
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Songpa-gu, Seoul 05505, Korea; (H.-H.C.); (J.-S.K.); (J.Y.K.)
| | - Ji Yeun Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Songpa-gu, Seoul 05505, Korea; (H.-H.C.); (J.-S.K.); (J.Y.K.)
| | - Myoung Gyu Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea; (Y.O.J.); (H.J.L.); (B.K.); (M.G.K.)
- Department of Convergence Medicine, Asan Medical Institute of Convergence Science and Technology (AMIST), University of Ulsan College of Medicine, Songpa-gu, Seoul 05505, Korea
| | - Hyun Soo Kim
- INFUSIONTECH, 38, Heungan-daero 427 beon-gil, Dongan-gu, Anyang-si 14059, Korea;
| | - Sung-Han Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Songpa-gu, Seoul 05505, Korea; (H.-H.C.); (J.-S.K.); (J.Y.K.)
- Correspondence: (S.-H.K.); (Y.S.)
| | - Yong Shin
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea; (Y.O.J.); (H.J.L.); (B.K.); (M.G.K.)
- Correspondence: (S.-H.K.); (Y.S.)
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Liu H, Zou Q, Qiao Z, Jang YO, Koo B, Kim MG, Lee HJ, Kim SH, Shin Y. Facile Homobifunctional Imidoester Modification of Advanced Nanomaterials for Enhanced Antibiotic Synergistic Effect. ACS Appl Mater Interfaces 2021; 13:40401-40414. [PMID: 34405670 DOI: 10.1021/acsami.1c12352] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Resistance to antibiotics because of misuse and overuse is one of the greatest public health challenges worldwide. Despite the introduction of advanced nanotechnology in the production of antibiotics, the choice of appropriate medicines is limited due to side effects such as blood coagulation, toxicity, low efficacy, and low biocompatibility; therefore, novel nanomaterial composites are required to counter these repercussions. We first introduce a facile method for synthesizing a homobifunctional imidoester-coated nanospindle (HINS) zinc oxide composite for enhancement of antibiotic efficacy and reduction of toxicity and blood coagulation. The antibiotic efficacy of the composites is twice that of commercialized zinc nanoparticles; in addition, they have good biocompatibility, have increased surface charge and solubility owing to the covalent acylation groups of HI, and produce a large number of Zn+ ions and defensive reactive oxygen species (ROS) that effectively kill bacteria and fungi. The synergistic effect of a combination therapy with the HINS composite and itraconazole shows more than 90% destruction of fungi in treatments with low dosage with no cytotoxicity or coagulation evident in intravenous administration in in vitro and in vivo experiments. Thus, HINS composites are useful in reducing the effect of misuse and overuse of antibiotics in the medical field.
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Affiliation(s)
- Huifang Liu
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei Ro, Seodaemun-gu, Seoul 03722, Korea
| | - Qingshuang Zou
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei Ro, Seodaemun-gu, Seoul 03722, Korea
| | - Zhen Qiao
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei Ro, Seodaemun-gu, Seoul 03722, Korea
| | - Yoon Ok Jang
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei Ro, Seodaemun-gu, Seoul 03722, Korea
| | - Bonhan Koo
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei Ro, Seodaemun-gu, Seoul 03722, Korea
| | - Myoung Gyu Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei Ro, Seodaemun-gu, Seoul 03722, Korea
| | - Hyo Joo Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei Ro, Seodaemun-gu, Seoul 03722, Korea
| | - Sung-Han Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympicro-43gil, Songpa-gu, Seoul 05505, Korea
| | - Yong Shin
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei Ro, Seodaemun-gu, Seoul 03722, Korea
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19
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Park JH, Koo B, Kim MJ, Lee HJ, Cha HH, Kim JY, Lee SW, Shin Y, Kim SH. Utility of plasma cell-free DNA detection using homobifunctional imidoesters using a microfluidic system for diagnosing active tuberculosis. Infect Dis (Lond) 2021; 54:46-52. [PMID: 34405761 DOI: 10.1080/23744235.2021.1963839] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
BACKGROUND It is difficult to diagnose tuberculosis (TB), particularly sputum-scarce pulmonary TB and extrapulmonary TB, using conventional diagnostic tests. Since these cases require additional invasive procedures to obtain appropriate specimens, new non-invasive diagnostic tests are needed. Plasma cell-free DNA (cfDNA) detection has gained interest as a novel diagnostic test for TB as it is convenient and less invasive. Therefore, we investigated the performance of enriched cfDNA for diagnosing pulmonary TB and extrapulmonary TB. METHODS All patients suspected to have TB, who consented to the use of blood for detecting cfDNA, were prospectively enrolled from January 2019 to June 2020. We categorised the patients as confirmed, probable, possible TB, and not-TB. We compared the performance of cfDNA with those of conventional diagnostic tests. RESULTS Among the 96 patients enrolled, 40 (41.7%) had TB, including 34 with confirmed TB and six probable TB, and 41 (42.7%) did not have TB. Acid-fast bacilli microscopy, Xpert MTB/RIF, and mycobacterial culture results were positive in 12 (31.6%), 22 (61.1%), and 25 (65.8%) patients, respectively. The sensitivity and specificity of cfDNA were 80.0% and 78.1%, respectively. While the sensitivity and specificity of cfDNA were similar to those of interferon-gamma releasing assay (IGRA) (sensitivity 80.6% and specificity 71.4%), the combined sensitivity and specificity of the two assays were 94.4% and 64.3%, respectively, which can be used to rule out TB. CONCLUSIONS Plasma cfDNA assay seems to be a useful adjunct to the current tests for diagnosing TB, especially when used in combination with IGRA for ruling out TB.AbbreviationsTBtuberculosiscfDNAcell-free DNAPCRpolymerase chain reactionAFBacid-fast bacilliIGRAinterferon-gamma releasing assayCTcomputed tomographyHIVhuman immunodeficiency virus.
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Affiliation(s)
- Joung Ha Park
- Department of Infectious Diseases, Chung-Ang Medical Health Care System Hyundae Hospital, Seoul, South Korea.,Division of Infectious Diseases, Department of Internal Medicine, Chung-Ang University Hospital, Seoul, South Korea.,Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Bonhan Koo
- Department of Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Min Jae Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Hyo Joo Lee
- Department of Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Hye-Hee Cha
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Ji Yeun Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Sei Won Lee
- Department of Pulmonary and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Yong Shin
- Department of Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Sung-Han Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
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20
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Kundu S, Shahee A, Chakraborty A, Ranjith KM, Koo B, Sichelschmidt J, Telling MTF, Biswas PK, Baenitz M, Dasgupta I, Pujari S, Mahajan AV. Gapless Quantum Spin Liquid in the Triangular System Sr_{3}CuSb_{2}O_{9}. Phys Rev Lett 2020; 125:267202. [PMID: 33449718 DOI: 10.1103/physrevlett.125.267202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 12/01/2020] [Indexed: 06/12/2023]
Abstract
We report gapless quantum spin liquid behavior in the layered triangular Sr_{3}CuSb_{2}O_{9} system. X-ray diffraction shows superlattice reflections associated with atomic site ordering into triangular Cu planes well separated by Sb planes. Muon spin relaxation measurements show that the S=1/2 moments at the magnetically active Cu sites remain dynamic down to 65 mK in spite of a large antiferromagnetic exchange scale evidenced by a large Curie-Weiss temperature θ_{CW}≃-143 K as extracted from the bulk susceptibility. Specific heat measurements also show no sign of long-range order down to 0.35 K. The magnetic specific heat (C_{m}) below 5 K reveals a C_{m}=γT+αT^{2} behavior. The significant T^{2} contribution to the magnetic specific heat invites a phenomenology in terms of the so-called Dirac spinon excitations with a linear dispersion. From the low-T specific heat data, we estimate the dominant exchange scale to be ∼36 K using a Dirac spin liquid ansatz which is not far from the values inferred from microscopic density functional theory calculations (∼45 K) as well as high-temperature susceptibility analysis (∼70 K). The linear specific heat coefficient is about 18 mJ/mol K^{2} which is somewhat larger than for typical Fermi liquids.
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Affiliation(s)
- S Kundu
- Department of Physics, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Aga Shahee
- Department of Physics, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Atasi Chakraborty
- School of Physical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - K M Ranjith
- Max Planck Institute for Chemical Physics of Solids, 01187 Dresden, Germany
| | - B Koo
- Max Planck Institute for Chemical Physics of Solids, 01187 Dresden, Germany
| | - Jörg Sichelschmidt
- Max Planck Institute for Chemical Physics of Solids, 01187 Dresden, Germany
| | - Mark T F Telling
- ISIS Pulsed Neutron and Muon Source, STFC Rutherford Appleton Laboratory, Harwell Campus, Didcot, Oxfordshire OX110QX, United Kingdom
| | - P K Biswas
- ISIS Pulsed Neutron and Muon Source, STFC Rutherford Appleton Laboratory, Harwell Campus, Didcot, Oxfordshire OX110QX, United Kingdom
| | - M Baenitz
- Max Planck Institute for Chemical Physics of Solids, 01187 Dresden, Germany
| | - I Dasgupta
- School of Physical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Sumiran Pujari
- Department of Physics, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - A V Mahajan
- Department of Physics, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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21
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Hoshino M, Yang S, Sugiyama T, Zhang J, Kanaji Y, Yamaguchi M, Hada M, Sumino Y, Nogami K, Ueno H, Misawa T, Yonetsu T, Koo B, Kakuta T. Prognostic value of peri-coronary adipose tissue attenuation and whole vessel and lesion plaque quantification on Coronary Computed Tomography Angiography. Eur Heart J 2020. [DOI: 10.1093/ehjci/ehaa946.0155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
Peri-coronary adipose tissue attenuation expressed by fat attenuation index (FAI) on coronary CT angiography (CCTA) reflects peri-coronary inflammation and is associated with cardiac mortality. CCTA also provides two-dimensional and three-dimensional quantification of the individual component of atherosclerotic plaque and entire vessel. The atherosclerotic burden or disease extent in entire epicardial coronary arteries provides prognostic information in patients with coronary artery disease.
Purpose
This study sought to explore the prognostic significance of FAI values and whole vessel and lesion plaque quantification on CCTA in stable patients with intermediate epicardial stenosis evaluated by fractional flow reserve (FFR).
Methods
A total of 277 patients (277 lesions) with intermediate coronary stenosis who underwent FFR measurement and CCTA were studied. FAI was assessed by the crude analysis of the mean CT attenuation value (−190 to −30 Hounsfield units; higher values indicating inflammation) on CCTA. CT findings including whole vessel and lesion plaque quantification, and target vessel myocardial mass were investigated. Major adverse cardiovascular outcome (MACE) was defined as all cause death, cardiac death, myocardial infarction, unplanned revascularization, and heart failure requiring admission. Survivals from MACE were assessed.
Results
The mean FAI and the median FFR values were −71.6 and 0.77, respectively. FFR values were weakly albeit significantly correlated with FAI values. (r=−0.016, P=0.008.) MACE was occurred 43 (15.5%) patients during 5 years F-up. ROC analyses revealed that best cut-off value of FAI to predict MACE was −73.1. Kaplan-Meier analysis revealed that lesions with FAI ≥−73.1 had a significantly higher risk of MACE. (Chi-square 5.5, P=0.019) FFR values and the percutaneous coronary intervention were not predictive of MACE. Multivariate COX proportional hazards regression analysis revealed that age, remodeling index, and lesions with FAI ≥−73.1 were independent predictors of MACE.
Conclusion
The peri-coronary inflammation evaluated by FAI and CT remodeling index enhances cardiac risk prediction in chronic coronary syndrome patients with intermediate lesions. Non-invasive comprehensive CT assessment may help identify high risk patients of subsequent clinical events and provide enhanced patient management.
Funding Acknowledgement
Type of funding source: Foundation. Main funding source(s): This study was supported in part by an unrestricted research grant from St. Jude Medical (Abbot Vascular, Santa Clara, CA, USA). The company had no role in study design, conduct, data analysis or manuscript preparation.
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Affiliation(s)
- M Hoshino
- Tsuchiura Kyodo General Hospital, Tsuchiura, Japan
| | - S Yang
- Seoul National University Hospital, Seoul, Korea (Republic of)
| | - T Sugiyama
- Tsuchiura Kyodo General Hospital, Tsuchiura, Japan
| | - J Zhang
- Seoul National University Hospital, Seoul, Korea (Republic of)
| | - Y Kanaji
- Tsuchiura Kyodo General Hospital, Tsuchiura, Japan
| | - M Yamaguchi
- Tsuchiura Kyodo General Hospital, Tsuchiura, Japan
| | - M Hada
- Tsuchiura Kyodo General Hospital, Tsuchiura, Japan
| | - Y Sumino
- Tsuchiura Kyodo General Hospital, Tsuchiura, Japan
| | - K Nogami
- Tsuchiura Kyodo General Hospital, Tsuchiura, Japan
| | - H Ueno
- Tsuchiura Kyodo General Hospital, Tsuchiura, Japan
| | - T Misawa
- Tsuchiura Kyodo General Hospital, Tsuchiura, Japan
| | - T Yonetsu
- Tokyo Medical and Dental University, Tokyo, Japan
| | - B Koo
- Seoul National University Hospital, Seoul, Korea (Republic of)
| | - T Kakuta
- Tsuchiura Kyodo General Hospital, Tsuchiura, Japan
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22
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Hamaya R, Mittleman M, Hoshino M, Kanaji Y, Lee J, Hwang D, Zhang J, Chen S, Koo B, Kakuta T. Prognostic value of pre-revascularization fractional flow reserve mediated by the post-revascularization level: a causal mediation analysis. Eur Heart J 2020. [DOI: 10.1093/ehjci/ehaa946.1275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
The prognostic value of pre-percutaneous coronary intervention (PCI) fractional flow reserve (FFR) can depend on that of the post-PCI FFR and their interaction. To correctly interpret the prognostic value of pre-PCI FFR, it is essential to understand to what extent the relationship between pre-PCI FFR and clinical outcome is explained by pre-PCI FFR-related post-PCI FFR.
Purpose
The aim of this study is to investigate the extent to which post-PCI FFR mediates the relationship between pre-PCI FFR and vessel-related outcomes using a global, multicenter collaboration registry.
Methods
Patient data from 4 global FFR registries were pooled and 1488 patients with pre-PCI FFR ≤0.80 were analyzed. The primary outcome was target vessel failure (TVF) during 2-years of follow-up. We evaluated the extent to which post-PCI FFR <0.90 mediated the association between pre-PCI FFR <0.75 and TVF employing a causal mediation analysis in a counterfactual framework.
Results
Among 1488 patients, the mean (standard deviation) age was 63.5 (9.9) years and 78% (1161 patients) were male. The median (IQR) pre-PCI and post-PCI FFR were 0.71 (0.62–0.76) and 0.88 (0.83–0.92), respectively. The direct effect of low pre-PCI FFR (<0.75) on TVF was significantly elevated (OR: 1.81, 95% CI: 1.03–3.18, p=0.038), and was not mediated by post-PCI FFR<0.90 (indirect effect, OR: 1.01, 95% CI: 0.98–1.05, p=0.39). In the model, post-PCI FFR explained only 2.2% of the association between pre-PCI FFR and TVF. The subgroup analysis implicated that the prognostic information of pre-PCI FFR was mainly for diffuse lesions.
Conclusions
The prognostic information of pre-PCI FFR did not greatly depend on the results of PCI assessed by post-PCI FFR. Pre-PCI FFR, as a prognostic marker, may mainly reflect the global atherosclerotic burden of the artery, not the extent of the modifiable epicardial stenosis, thus providing independent information from post-PCI FFR.
Interpretation
Funding Acknowledgement
Type of funding source: None
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Affiliation(s)
- R Hamaya
- Harvard T.H. Chan School of Public Health, Epidemiology, Boston, United States of America
| | - M Mittleman
- Harvard T.H. Chan School of Public Health, Epidemiology, Boston, United States of America
| | - M Hoshino
- Tsuchiura Kyodo Hospital, cardiology, Tsuchiura, Japan
| | - Y Kanaji
- Tsuchiura Kyodo Hospital, cardiology, Tsuchiura, Japan
| | - J Lee
- Samsung Medical Center, Division of Cardiology, Seoul, Korea (Republic of)
| | - D Hwang
- Seoul National University Hospital, Department of Internal Medicine and Cardiovascular Center, Seoul, Korea (Republic of)
| | - J Zhang
- Seoul National University Hospital, Department of Internal Medicine and Cardiovascular Center, Seoul, Korea (Republic of)
| | - S Chen
- Nanjing Medical University, Cardiology, Nanjing, China
| | - B Koo
- Seoul National University Hospital, Department of Internal Medicine and Cardiovascular Center, Seoul, Korea (Republic of)
| | - T Kakuta
- Tsuchiura Kyodo Hospital, cardiology, Tsuchiura, Japan
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23
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Lee EY, Kim Y, Koo B, Noh GS, Lee H, Shin Y. A novel nucleic acid amplification system based on nano-gap embedded active disk resonators. Sens Actuators B Chem 2020. [PMID: 32501366 DOI: 10.1016/j.snb.2020.128358] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Recent advances in nucleic acid based testing using bio-optical sensor approaches have been introduced but most are based on hybridization between the optical sensor and the bio-molecule and not on an amplification mechanism. Direct nucleic acid amplification on an optical sensor has several technical limitations, such as the sensitivity of the temperature sensor, instrument complexity, and high background signal. We here describe a novel nucleic acid amplification method based on a whispering gallery mode active resonator and discuss its potential molecular diagnostic application. By implanting nanoclusters as active compounds, this active resonator operates without tapered fiber coupling and emits a strong photoluminescence signal with low background in the wavelength of low absorption in an aqueous environment that is typical of biosensors. Our method also offers an extremely low detection threshold down to a single copy within 10 min due to the strong light-matter interaction in a nano-gap structure. We envision that this active resonator provides a high refractive index contrast for tight mode confinement with simple alignment as well as the possibility of reducing the device size so that a point-of-care system with low-cost, high-sensitivity and simplicity.
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Affiliation(s)
- Eun Yeong Lee
- Department of Convergence Medicine, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - Yeseul Kim
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Bonhan Koo
- Department of Convergence Medicine, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - Geun Su Noh
- Department of Convergence Medicine, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - Hansuek Lee
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
- Graduate School of Nanoscience and Technology, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Yong Shin
- Department of Convergence Medicine, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
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24
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Lee EY, Kim Y, Koo B, Noh GS, Lee H, Shin Y. A novel nucleic acid amplification system based on nano-gap embedded active disk resonators. Sens Actuators B Chem 2020. [PMID: 32501366 DOI: 10.1016/j.snb.2020.128357] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Recent advances in nucleic acid based testing using bio-optical sensor approaches have been introduced but most are based on hybridization between the optical sensor and the bio-molecule and not on an amplification mechanism. Direct nucleic acid amplification on an optical sensor has several technical limitations, such as the sensitivity of the temperature sensor, instrument complexity, and high background signal. We here describe a novel nucleic acid amplification method based on a whispering gallery mode active resonator and discuss its potential molecular diagnostic application. By implanting nanoclusters as active compounds, this active resonator operates without tapered fiber coupling and emits a strong photoluminescence signal with low background in the wavelength of low absorption in an aqueous environment that is typical of biosensors. Our method also offers an extremely low detection threshold down to a single copy within 10 min due to the strong light-matter interaction in a nano-gap structure. We envision that this active resonator provides a high refractive index contrast for tight mode confinement with simple alignment as well as the possibility of reducing the device size so that a point-of-care system with low-cost, high-sensitivity and simplicity.
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Affiliation(s)
- Eun Yeong Lee
- Department of Convergence Medicine, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - Yeseul Kim
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Bonhan Koo
- Department of Convergence Medicine, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - Geun Su Noh
- Department of Convergence Medicine, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - Hansuek Lee
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
- Graduate School of Nanoscience and Technology, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Yong Shin
- Department of Convergence Medicine, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
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25
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Lee EY, Kim Y, Koo B, Noh GS, Lee H, Shin Y. A novel nucleic acid amplification system based on nano-gap embedded active disk resonators. Sens Actuators B Chem 2020; 320:128351. [PMID: 32501366 PMCID: PMC7250085 DOI: 10.1016/j.snb.2020.128351] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 05/15/2020] [Accepted: 05/21/2020] [Indexed: 06/11/2023]
Abstract
Recent advances in nucleic acid based testing using bio-optical sensor approaches have been introduced but most are based on hybridization between the optical sensor and the bio-molecule and not on an amplification mechanism. Direct nucleic acid amplification on an optical sensor has several technical limitations, such as the sensitivity of the temperature sensor, instrument complexity, and high background signal. We here describe a novel nucleic acid amplification method based on a whispering gallery mode active resonator and discuss its potential molecular diagnostic application. By implanting nanoclusters as active compounds, this active resonator operates without tapered fiber coupling and emits a strong photoluminescence signal with low background in the wavelength of low absorption in an aqueous environment that is typical of biosensors. Our method also offers an extremely low detection threshold down to a single copy within 10 min due to the strong light-matter interaction in a nano-gap structure. We envision that this active resonator provides a high refractive index contrast for tight mode confinement with simple alignment as well as the possibility of reducing the device size so that a point-of-care system with low-cost, high-sensitivity and simplicity.
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Affiliation(s)
- Eun Yeong Lee
- Department of Convergence Medicine, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - Yeseul Kim
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Bonhan Koo
- Department of Convergence Medicine, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - Geun Su Noh
- Department of Convergence Medicine, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - Hansuek Lee
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
- Graduate School of Nanoscience and Technology, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Yong Shin
- Department of Convergence Medicine, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
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Lee EY, Kim Y, Koo B, Noh GS, Lee H, Shin Y. A novel nucleic acid amplification system based on nano-gap embedded active disk resonators. Sens Actuators B Chem 2020; 320:128351. [PMID: 32501366 DOI: 10.1016/j.snb.2020.128391] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 05/15/2020] [Accepted: 05/21/2020] [Indexed: 05/28/2023]
Abstract
Recent advances in nucleic acid based testing using bio-optical sensor approaches have been introduced but most are based on hybridization between the optical sensor and the bio-molecule and not on an amplification mechanism. Direct nucleic acid amplification on an optical sensor has several technical limitations, such as the sensitivity of the temperature sensor, instrument complexity, and high background signal. We here describe a novel nucleic acid amplification method based on a whispering gallery mode active resonator and discuss its potential molecular diagnostic application. By implanting nanoclusters as active compounds, this active resonator operates without tapered fiber coupling and emits a strong photoluminescence signal with low background in the wavelength of low absorption in an aqueous environment that is typical of biosensors. Our method also offers an extremely low detection threshold down to a single copy within 10 min due to the strong light-matter interaction in a nano-gap structure. We envision that this active resonator provides a high refractive index contrast for tight mode confinement with simple alignment as well as the possibility of reducing the device size so that a point-of-care system with low-cost, high-sensitivity and simplicity.
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Affiliation(s)
- Eun Yeong Lee
- Department of Convergence Medicine, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - Yeseul Kim
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Bonhan Koo
- Department of Convergence Medicine, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - Geun Su Noh
- Department of Convergence Medicine, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - Hansuek Lee
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
- Graduate School of Nanoscience and Technology, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Yong Shin
- Department of Convergence Medicine, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
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Jang YO, Noh GS, Liu H, Koo B, Qiao Z, Shin Y. Dimethyl 3,3'-dithiobispropionimidate-functionalized diatomaceous earth particles for efficient biomolecule separation. Sci Rep 2020; 10:15592. [PMID: 32973156 PMCID: PMC7519118 DOI: 10.1038/s41598-020-72913-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 06/12/2020] [Accepted: 09/01/2020] [Indexed: 11/09/2022] Open
Abstract
The early diagnosis and monitoring of cancers are key factors in effective cancer treatment. Particularly, the separation of biomolecules is an essential step for both diagnostic and analytical purposes. However, the current techniques used to isolate biomolecules are intensive, laborious, and require multiple instruments as well as repeated sample preparations to separate each biomolecule. Thus, an efficient separation system that can simultaneously separate biomolecules from scarce samples is highly desirable. Hence, in this study, we developed a biosilica-based syringe filtration system for the efficient separation of biomolecules from cancer samples using amine-modified diatomaceous earth (AD) with dimethyl 3,3′-dithiobispropionimidate (DTBP). The syringe filter can be an efficient and rapid tool for use in various procedures without complex instruments. The DTBP-based AD system was combined with the syringe filter system for nucleic acid and protein separation from various cancer cells. We demonstrated the efficacy of the DTBP-based AD in a single-filter system for the efficient separation of DNA and proteins within 40 min. This DTBP-based AD syringe filter system showed good rapidity, efficiency, and affordability in the separation of biomolecules from single samples for the early diagnosis and clinical analysis of cancers.
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Affiliation(s)
- Yoon Ok Jang
- Department of Convergence Medicine, Asan Medical Institute of Convergence Science and Technology (AMIST), University of Ulsan College of Medicine, Biomedical Engineering Research Center, Asan Institute of Life Sciences, Asan Medical Center, 05505, Seoul, Republic of Korea
| | - Geun Su Noh
- Department of Convergence Medicine, Asan Medical Institute of Convergence Science and Technology (AMIST), University of Ulsan College of Medicine, Biomedical Engineering Research Center, Asan Institute of Life Sciences, Asan Medical Center, 05505, Seoul, Republic of Korea
| | - Huifang Liu
- Department of Convergence Medicine, Asan Medical Institute of Convergence Science and Technology (AMIST), University of Ulsan College of Medicine, Biomedical Engineering Research Center, Asan Institute of Life Sciences, Asan Medical Center, 05505, Seoul, Republic of Korea
| | - Bonhan Koo
- Department of Convergence Medicine, Asan Medical Institute of Convergence Science and Technology (AMIST), University of Ulsan College of Medicine, Biomedical Engineering Research Center, Asan Institute of Life Sciences, Asan Medical Center, 05505, Seoul, Republic of Korea
| | - Zhen Qiao
- Department of Convergence Medicine, Asan Medical Institute of Convergence Science and Technology (AMIST), University of Ulsan College of Medicine, Biomedical Engineering Research Center, Asan Institute of Life Sciences, Asan Medical Center, 05505, Seoul, Republic of Korea
| | - Yong Shin
- Department of Convergence Medicine, Asan Medical Institute of Convergence Science and Technology (AMIST), University of Ulsan College of Medicine, Biomedical Engineering Research Center, Asan Institute of Life Sciences, Asan Medical Center, 05505, Seoul, Republic of Korea.
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Koo B, Jun E, Liu H, Kim EJ, Park YY, Lim SB, Kim SC, Shin Y. A biocomposite-based rapid sampling assay for circulating cell-free DNA in liquid biopsy samples from human cancers. Sci Rep 2020; 10:14932. [PMID: 32913285 PMCID: PMC7484795 DOI: 10.1038/s41598-020-72163-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 08/12/2020] [Indexed: 12/18/2022] Open
Abstract
Cell-free nucleic acids (cfNAs) in liquid biopsy samples are emerging as important biomarkers for cancer diagnosis and monitoring, and for predicting treatment outcomes. Many cfNA isolation methods have been developed recently. However, most of these techniques are time-consuming, complex, require large equipment, and yield low-purity cfNAs because the genetic background of normal cells is amplified during cell lysis, which limits their clinical application. Here, we report a rapid and simple cfNA sampling platform that can overcome the limitations of conventional methods. We synthesised a biocomposite by combining amine-modified diatomaceous earth (DE) and cucurbituril (CB). The biocomposite platform showed high capture efficiency (86.78-90.26%) with genomic DNA and amplified DNA products (777, 525 and 150 bp). The biocomposite platform allowed the isolation of high purity and quantity cfDNAs from the plasma of 13 cancer patients (three colorectal cancer and ten pancreatic cancer samples) without requiring a lysis step or special equipment. The biocomposite platform may be useful to isolate cfNAs for the diagnosis and treatment of cancers in clinical applications.
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Affiliation(s)
- Bonhan Koo
- Department of Convergence Medicine, Asan Medical Center, Asan Medical Institute of Convergence Science and Technology, University of Ulsan College of Medicine, Seoul, Republic of Korea
- Biomedical Engineering Research Center, Asan Medical Center, Asan Institute of Life Science, Seoul, Republic of Korea
| | - Eunsung Jun
- Department of Convergence Medicine, Asan Medical Center, Asan Medical Institute of Convergence Science and Technology, University of Ulsan College of Medicine, Seoul, Republic of Korea
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Asan Medical Center, Asan Medical Institute of Convergence Science and Technology, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Huifang Liu
- Department of Convergence Medicine, Asan Medical Center, Asan Medical Institute of Convergence Science and Technology, University of Ulsan College of Medicine, Seoul, Republic of Korea
- Biomedical Engineering Research Center, Asan Medical Center, Asan Institute of Life Science, Seoul, Republic of Korea
| | - Eo Jin Kim
- Department of Convergence Medicine, Asan Medical Center, Asan Medical Institute of Convergence Science and Technology, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Yun-Yong Park
- Department of Convergence Medicine, Asan Medical Center, Asan Medical Institute of Convergence Science and Technology, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Seok-Byung Lim
- Division of Colon and Rectal Surgery, Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Song Cheol Kim
- Biomedical Engineering Research Center, Asan Medical Center, Asan Institute of Life Science, Seoul, Republic of Korea.
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Asan Medical Center, Asan Medical Institute of Convergence Science and Technology, University of Ulsan College of Medicine, Seoul, Republic of Korea.
| | - Yong Shin
- Department of Convergence Medicine, Asan Medical Center, Asan Medical Institute of Convergence Science and Technology, University of Ulsan College of Medicine, Seoul, Republic of Korea.
- Biomedical Engineering Research Center, Asan Medical Center, Asan Institute of Life Science, Seoul, Republic of Korea.
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Jin CE, Koo B, Lee HJ, Park IJ, Kim SH, Shin Y. Bis(sulfosuccinimidyl)suberate-Based Helix-Shaped Microchannels as Enhancers of Biomolecule Isolation from Liquid Biopsies. Anal Chem 2020; 92:11994-12001. [PMID: 32867489 DOI: 10.1021/acs.analchem.0c02503] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Most studies of ultrasensitive diagnosis of biomolecules from liquid specimens are limited by problems during sample preparation steps, including enrichment and isolation of biomolecules. Here we report a novel platform combining bis(sulfosuccinimidyl)suberate (BS3) and helix-shaped microchannels (BSH) to change the sample preparation paradigm. This BSH system is composed of BS3 for pathogen enrichment and nucleic acid isolation by electrostatic and covalent interaction, and helix-shaped microchannels to minimize sample loss and remove bubbles in large liquid specimens without pH change. The system detected Mycobacterium tuberculosis following enrichment and isolation of 10 mL of liquefied sputum from 11 patients with tuberculosis. Moreover, the system identified KRAS mutations following cell-free DNA isolation of blood plasma from 10 patients with colorectal cancer. This system allows ultrasensitive diagnosis in various disease applications with large volumes of liquid samples.
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Affiliation(s)
- Choong Eun Jin
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, Biomedical Engineering Research Center, Asan Institute of Life Sciences, Asan Medical Center, 88 Olympicro-43gil, Songpa-gu, Seoul, Republic of Korea
| | - Bonhan Koo
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, Biomedical Engineering Research Center, Asan Institute of Life Sciences, Asan Medical Center, 88 Olympicro-43gil, Songpa-gu, Seoul, Republic of Korea
| | - Hyo Joo Lee
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, Biomedical Engineering Research Center, Asan Institute of Life Sciences, Asan Medical Center, 88 Olympicro-43gil, Songpa-gu, Seoul, Republic of Korea
| | - In Ja Park
- Division of Colon & Rectal Surgery, Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympicro-43gil, Songpa-gu, Seoul, Republic of Korea
| | - Sung-Han Kim
- Department of Infectious Disease, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympicro-43gil, Songpa-gu, Seoul, Republic of Korea
| | - Yong Shin
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, Biomedical Engineering Research Center, Asan Institute of Life Sciences, Asan Medical Center, 88 Olympicro-43gil, Songpa-gu, Seoul, Republic of Korea
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Qiao Z, Liu H, Noh GS, Koo B, Zou Q, Yun K, Jang YO, Kim SH, Shin Y. A Simple and Rapid Fungal DNA Isolation Assay Based on ZnO Nanoparticles for the Diagnosis of Invasive Aspergillosis. Micromachines (Basel) 2020; 11:mi11050515. [PMID: 32438738 PMCID: PMC7281153 DOI: 10.3390/mi11050515] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/13/2020] [Accepted: 05/18/2020] [Indexed: 11/16/2022]
Abstract
Invasive aspergillosis (IA) is an important cause of morbidity and mortality among immunocompromised people. Imaging and specimen tests used in the clinical diagnosis of aspergillosis with weak and indistinct defects leads to delay in the treatment of early aspergillosis patients. The developing molecular techniques provide a new method for the aspergillosis diagnosis. However, the existing methods are complex, time-consuming and may even be potentially hazardous. In this study, we developed a simple and rapid Aspergillus fumigatus spores DNA isolation assay using synthesized zinc oxide (ZnO). ZnO nanoparticles were used to take the place of the traditional commercial lysis buffer. The quality and quantity of the extracted DNA were sufficient for further diagnostics with polymerase chain reaction (PCR) analysis. This method offers easy, green, and economic alternative DNA isolation for the diagnosis of invasive aspergillosis.
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Affiliation(s)
- Zhen Qiao
- Department of Convergence Medicine, Asan Medical Institute of Convergence Science and Technology (AMIST), University of Ulsan College of Medicine, 88 Olympicro-43gil, Songpa-gu, Seoul 05505, Korea; (Z.Q.); (H.L.); (G.S.N.); (B.K.); (Q.Z.); (Y.O.J.)
| | - Huifang Liu
- Department of Convergence Medicine, Asan Medical Institute of Convergence Science and Technology (AMIST), University of Ulsan College of Medicine, 88 Olympicro-43gil, Songpa-gu, Seoul 05505, Korea; (Z.Q.); (H.L.); (G.S.N.); (B.K.); (Q.Z.); (Y.O.J.)
| | - Geun Su Noh
- Department of Convergence Medicine, Asan Medical Institute of Convergence Science and Technology (AMIST), University of Ulsan College of Medicine, 88 Olympicro-43gil, Songpa-gu, Seoul 05505, Korea; (Z.Q.); (H.L.); (G.S.N.); (B.K.); (Q.Z.); (Y.O.J.)
| | - Bonhan Koo
- Department of Convergence Medicine, Asan Medical Institute of Convergence Science and Technology (AMIST), University of Ulsan College of Medicine, 88 Olympicro-43gil, Songpa-gu, Seoul 05505, Korea; (Z.Q.); (H.L.); (G.S.N.); (B.K.); (Q.Z.); (Y.O.J.)
| | - Qingshuang Zou
- Department of Convergence Medicine, Asan Medical Institute of Convergence Science and Technology (AMIST), University of Ulsan College of Medicine, 88 Olympicro-43gil, Songpa-gu, Seoul 05505, Korea; (Z.Q.); (H.L.); (G.S.N.); (B.K.); (Q.Z.); (Y.O.J.)
| | - Kyusik Yun
- Department of Bionanotechnology, Gachon University, Gyeonggi-do 13120, Korea;
| | - Yoon Ok Jang
- Department of Convergence Medicine, Asan Medical Institute of Convergence Science and Technology (AMIST), University of Ulsan College of Medicine, 88 Olympicro-43gil, Songpa-gu, Seoul 05505, Korea; (Z.Q.); (H.L.); (G.S.N.); (B.K.); (Q.Z.); (Y.O.J.)
| | - Sung-Han Kim
- Department of Infectious Disease, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympicro-43gil, Songpa-gu, Seoul 05505, Korea
- Correspondence: (S.-H.K.); (Y.S.)
| | - Yong Shin
- Department of Convergence Medicine, Asan Medical Institute of Convergence Science and Technology (AMIST), University of Ulsan College of Medicine, 88 Olympicro-43gil, Songpa-gu, Seoul 05505, Korea; (Z.Q.); (H.L.); (G.S.N.); (B.K.); (Q.Z.); (Y.O.J.)
- Correspondence: (S.-H.K.); (Y.S.)
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Jang YO, Jin CE, Choi EH, Shin JH, Kweon J, Koo B, Lim SB, Lee SW, Shin Y. A homobifunctional imidoester-based microfluidic system for simultaneous DNA and protein isolation from solid or liquid biopsy samples. Lab Chip 2019; 19:2256-2264. [PMID: 31173022 DOI: 10.1039/c9lc00367c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The isolation of bio-molecules such as proteins and nucleic acids is a necessary step for both diagnostic and analytical processes in the broad fields of research and clinical applications. Although a myriad of isolation technologies have been developed, a method for simultaneous protein and nucleic acid isolation has not been explored for clinical use. Obtaining samples from certain cancers or rare diseases can be difficult. In addition, the heterogeneity of cancer tissues typically leads to inconsistent results when analyzing biomolecules. We here describe a homobifunctional imidoester (HI)-based microfluidic system for simultaneous DNA and protein isolation from either a solid or liquid single biopsy sample. An efficient and cost effective microfluidic design with less air bubbles was identified among several candidates using simulation and experimental results from the streamlining of isolation processing. HI groups were used as capture reagents for the simultaneous isolation of bio-molecules from a single specimen in a single microfluidic system. The clinical utility of this system for the simultaneous isolation of DNA and proteins within 40 min was validated in cancer cell lines and 23 tissue biopsies from colorectal cancer patients. The quantity of isolated protein and DNA was high using this system compared to the spin-column method. This HI-based microfluidic system shows good rapidity, affordability, and portability in the isolation of bio-molecules from limited samples for subsequent clinical analysis.
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Affiliation(s)
- Yoon Ok Jang
- Department of Convergence Medicine, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea.
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Liu H, Noh GS, Luan Y, Qiao Z, Koo B, Jang YO, Shin Y. A Sample Preparation Technique Using Biocompatible Composites for Biomedical Applications. Molecules 2019; 24:E1321. [PMID: 30987247 PMCID: PMC6479572 DOI: 10.3390/molecules24071321] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 04/02/2019] [Accepted: 04/03/2019] [Indexed: 12/12/2022] Open
Abstract
Infectious diseases, especially pathogenic infections, are a growing threat to public health worldwide. Since pathogenic bacteria usually exist in complex matrices at very low concentrations, the development of technology for rapid, convenient, and biocompatible sample enrichment is essential for sensitive diagnostics. In this study, a cucurbit[6]uril (CB) supermolecular decorated amine-functionalized diatom (DA) composite was fabricated to support efficient sample enrichment and in situ nucleic acid preparation from enriched pathogens and cells. CB was introduced to enhance the rate and effectiveness of pathogen absorption using the CB-DA composite. This novel CB-DA composite achieved a capture efficiency of approximately 90% at an Escherichia coli concentration of 10⁶ CFU/mL within 3 min. Real-time PCR analyses of DNA samples recovered using the CB-DA enrichment system showed a four-fold increase in the early amplification signal strength, and this effective method for capturing nucleic acid might be useful for preparing samples for diagnostic systems.
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Affiliation(s)
- Huifang Liu
- Department of Convergence Medicine, Asan Medical Institute of Convergence Science and Technology (AMIST), University of Ulsan College of Medicine, 88 Olympicro-43gil, Songpa-gu, Seoul 05505, Korea.
- Biomedical Engineering Research Center, Asan Institute of Life Sciences, Asan Medical Center, 88 Olympicro-43gil, Songpa-gu, Seoul 05505, Korea.
| | - Geun Su Noh
- Department of Convergence Medicine, Asan Medical Institute of Convergence Science and Technology (AMIST), University of Ulsan College of Medicine, 88 Olympicro-43gil, Songpa-gu, Seoul 05505, Korea.
- Biomedical Engineering Research Center, Asan Institute of Life Sciences, Asan Medical Center, 88 Olympicro-43gil, Songpa-gu, Seoul 05505, Korea.
| | - Yange Luan
- Department of Convergence Medicine, Asan Medical Institute of Convergence Science and Technology (AMIST), University of Ulsan College of Medicine, 88 Olympicro-43gil, Songpa-gu, Seoul 05505, Korea.
- Biomedical Engineering Research Center, Asan Institute of Life Sciences, Asan Medical Center, 88 Olympicro-43gil, Songpa-gu, Seoul 05505, Korea.
| | - Zhen Qiao
- Department of Convergence Medicine, Asan Medical Institute of Convergence Science and Technology (AMIST), University of Ulsan College of Medicine, 88 Olympicro-43gil, Songpa-gu, Seoul 05505, Korea.
- Biomedical Engineering Research Center, Asan Institute of Life Sciences, Asan Medical Center, 88 Olympicro-43gil, Songpa-gu, Seoul 05505, Korea.
| | - Bonhan Koo
- Department of Convergence Medicine, Asan Medical Institute of Convergence Science and Technology (AMIST), University of Ulsan College of Medicine, 88 Olympicro-43gil, Songpa-gu, Seoul 05505, Korea.
- Biomedical Engineering Research Center, Asan Institute of Life Sciences, Asan Medical Center, 88 Olympicro-43gil, Songpa-gu, Seoul 05505, Korea.
| | - Yoon Ok Jang
- Department of Convergence Medicine, Asan Medical Institute of Convergence Science and Technology (AMIST), University of Ulsan College of Medicine, 88 Olympicro-43gil, Songpa-gu, Seoul 05505, Korea.
- Biomedical Engineering Research Center, Asan Institute of Life Sciences, Asan Medical Center, 88 Olympicro-43gil, Songpa-gu, Seoul 05505, Korea.
| | - Yong Shin
- Department of Convergence Medicine, Asan Medical Institute of Convergence Science and Technology (AMIST), University of Ulsan College of Medicine, 88 Olympicro-43gil, Songpa-gu, Seoul 05505, Korea.
- Biomedical Engineering Research Center, Asan Institute of Life Sciences, Asan Medical Center, 88 Olympicro-43gil, Songpa-gu, Seoul 05505, Korea.
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Koo B, Bustamante-Garcia D, Nyachoti C. 353 Effects of Lactobacillus-fermented barley on intestinal morphology, cytokine gene expression, and fecal microbiota in weaned pigs challenged with Escherichia coli K88+. J Anim Sci 2018. [DOI: 10.1093/jas/sky404.383] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- B Koo
- Department of Animal Science, University of Manitoba, Winnipeg, MB, Canada, Winnipeg, MB, Canada
| | - D Bustamante-Garcia
- Department of Animal Science, University of Manitoba, Winnipeg, MB, Canada, Winnipeg, MB, Canada
| | - C Nyachoti
- Department of Animal Science, University of Manitoba, Winnipeg, MB, Canada, Winnipeg, MB, Canada
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Jayaraman B, Amarakoon S, Koo B, O K, Nyachoti C. PSIV-30 Effects of dietary supplementation with ground red-osier dogwood (Cornus stolonifera) on growth performance, blood profile, and ileal histomorphology in weaned pigs challenged with Escherichia coli K88+. J Anim Sci 2018. [DOI: 10.1093/jas/sky404.708] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- B Jayaraman
- Department of Animal Science, University of Manitoba, Winnipeg, MB, Canada
| | - S Amarakoon
- St. Boniface Hospital Research Centre, Winnipeg, MB, Canada
| | - B Koo
- Department of Animal Science, University of Manitoba, Winnipeg, MB, Canada
| | - K O
- St. Boniface Hospital Research Centre, Winnipeg, MB, Canada
| | - C Nyachoti
- Department of Animal Science, University of Manitoba, Winnipeg, MB, Canada
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Koo B, Amarakoon S, Jayaraman B, Siow Y, Prashar S, Shang Y, O K, Nyachoti C. 199 Effects of dietary supplementation with ground red-osier dogwood (Cornus stolonifera) on oxidative status in weaned pigs challenged with Escherichia coli K88+. J Anim Sci 2018. [DOI: 10.1093/jas/sky404.677] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- B Koo
- Department of Animal Science, University of Manitoba, Winnipeg, MB, Canada
| | - S Amarakoon
- St. Boniface Hospital Research Centre, Winnipeg, MB, Canada
| | - B Jayaraman
- Department of Animal Science, University of Manitoba, Winnipeg, MB, Canada
| | - Y Siow
- St. Boniface Hospital Research Centre, Winnipeg, MB, Canada
| | - S Prashar
- St. Boniface Hospital Research Centre, Winnipeg, MB, Canada
| | - Y Shang
- St. Boniface Hospital Research Centre, Winnipeg, MB, Canada
| | - K O
- St. Boniface Hospital Research Centre, Winnipeg, MB, Canada
| | - C Nyachoti
- Department of Animal Science, University of Manitoba, Winnipeg, MB, Canada
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Koo B, Kim DE, Kweon J, Jin CE, Kim SH, Kim Y, Shin Y. CRISPR/dCas9-mediated biosensor for detection of tick-borne diseases. Sens Actuators B Chem 2018; 273:316-321. [PMID: 32288252 PMCID: PMC7126152 DOI: 10.1016/j.snb.2018.06.069] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 05/23/2018] [Accepted: 06/14/2018] [Indexed: 05/18/2023]
Abstract
Rapid and highly sensitive detection of biomolecules is greatly needed for pathogen diagnosis in clinical samples, but the method needs to be significantly improved in terms of sensitivity and specificity for actual use in clinical settings. Here, we report the development of an improved molecular diagnostics tool that utilizes CRISPR/dCas9-mediated biosensor that couples a nuclease inactivated Cas9 (dCas9) and single microring resonator biosensor, enables label-free and real-time detection of pathogenic DNA and RNA. We addressed the clinical utility of this CRISPR/dCas9-mediated biosensor in tick-borne illnesses including scrub typhus (ST) and severe fever with thrombocytopenia syndrome (SFTS), whose clinical presentations are too similar to be easily differentiated. By using CRISPR/dCas9-mediated biosensor, we achieved single molecule sensitivity for the detection of ST (0.54 aM) and SFTS (0.63 aM); this detection sensitivity is 100 times more sensitive than that of RT-PCR assay. Finally, CRISPR/dCas9-mediated biosensor was able to clearly distinguish between ST and SFTS in serum samples within 20 min. We believe that CRISPR/dCas9-mediated biosensor will be useful for rapid and accurate molecular diagnostic tool that is suitable for immediate clinical applications.
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Affiliation(s)
- Bonhan Koo
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, 88 lympicro-43gil, Songpa-gu, Seoul, Republic of Korea
- Biomedical Engineering Research Center, Asan Institute for Life Sciences, Asan Medical Center, 88 lympicro-43gil, Songpa-gu, Seoul, Republic of Korea
| | - Da-eun Kim
- Department of Chemistry, Seoul National University, Gwanak-ro, Gwanak-gu, Seoul, Republic of Korea
- Center for Genome Engineering, Institute for Basic Science (IBS), Gwanak-ro, Gwanak-gu, Seoul, Republic of Korea
| | - Jiyeon Kweon
- Department of Biomedical Sciences, University of Ulsan College of Medicine, Asan Medical Center, 88 lympicro-43gil, Songpa-gu, Seoul, Republic of Korea
| | - Choong Eun Jin
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, 88 lympicro-43gil, Songpa-gu, Seoul, Republic of Korea
- Biomedical Engineering Research Center, Asan Institute for Life Sciences, Asan Medical Center, 88 lympicro-43gil, Songpa-gu, Seoul, Republic of Korea
| | - Sung-Han Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, 88 lympicro-43gil, Songpa-gu, Seoul, Republic of Korea
| | - Yongsub Kim
- Department of Biomedical Sciences, University of Ulsan College of Medicine, Asan Medical Center, 88 lympicro-43gil, Songpa-gu, Seoul, Republic of Korea
- Corresponding author.
| | - Yong Shin
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, 88 lympicro-43gil, Songpa-gu, Seoul, Republic of Korea
- Biomedical Engineering Research Center, Asan Institute for Life Sciences, Asan Medical Center, 88 lympicro-43gil, Songpa-gu, Seoul, Republic of Korea
- Corresponding author at: Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, 88 lympicro-43gil, Songpa-gu, Seoul, Republic of Korea.
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Jin CE, Koo B, Lee TY, Han K, Lim SB, Park IJ, Shin Y. Simple and Low-Cost Sampling of Cell-Free Nucleic Acids from Blood Plasma for Rapid and Sensitive Detection of Circulating Tumor DNA. Adv Sci (Weinh) 2018; 5:1800614. [PMID: 30356899 PMCID: PMC6193143 DOI: 10.1002/advs.201800614] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Revised: 07/05/2018] [Indexed: 05/07/2023]
Abstract
Cell-free nucleic acids (cfNAs) are emerging diagnostic biomarkers for monitoring the treatment and recurrence of cancers. In particular, the biological role and clinical usefulness of cfNAs obtained from the plasma of patients with various cancers are popular and still intensely explored, yet most studies are limited by technical problems during cfNA isolation. A dimethyl dithiobispropionimidate (DTBP)-based microchannel platform that enables spontaneous cfNA capture in 15 min with minimal cellular background and no requirements for use of bulky instruments is reported first. This platform identified KRAS and BRAF hot-spot mutations following cfDNA isolation from the blood plasma and tissues obtained from 30 colorectal cancer patients. The correlation of mutations between the primary tissues and plasma from the patients was high using this platform with whole genome sequencing compared to the spin-column method. This platform can also be combined with various detection approaches (biooptical sensor, Sanger sequencing, and polymerase chain reaction (PCR)) for rapid, simple, low-cost, and sensitive circulating tumor DNA detection in blood plasma. The efficiency and versatility of this platform in isolating cfNAs from liquid biopsies has applications in cancer treatment and precision medicine.
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Affiliation(s)
- Choong Eun Jin
- Department of Convergence MedicineAsan Medical CenterUniversity of Ulsan College of Medicine88 Olympicro‐43gil, Songpa‐gu,05505SeoulRepublic of Korea
- Biomedical Engineering Research CenterAsan Institute of Life SciencesAsan Medical Center88 Olympicro‐43gil, Songpa‐gu,05505SeoulRepublic of Korea
| | - Bonhan Koo
- Department of Convergence MedicineAsan Medical CenterUniversity of Ulsan College of Medicine88 Olympicro‐43gil, Songpa‐gu,05505SeoulRepublic of Korea
- Biomedical Engineering Research CenterAsan Institute of Life SciencesAsan Medical Center88 Olympicro‐43gil, Songpa‐gu,05505SeoulRepublic of Korea
| | - Tae Yoon Lee
- Department of Technology Education and Department of Biomedical EngineeringChungnam National University99 Daehak‐ro, Yuseong‐guDaejeon34134Republic of Korea
| | - Kyudong Han
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative MedicineDankook UniversityCheonan31116Republic of Korea
| | - Seok Byung Lim
- Department of Colon & Rectal SurgeryAsan Medical CenterUniversity of Ulsan College of Medicine88 Olympicro‐43gil, Songpa‐gu,05505SeoulRepublic of Korea
| | - In Ja Park
- Department of Colon & Rectal SurgeryAsan Medical CenterUniversity of Ulsan College of Medicine88 Olympicro‐43gil, Songpa‐gu,05505SeoulRepublic of Korea
| | - Yong Shin
- Department of Convergence MedicineAsan Medical CenterUniversity of Ulsan College of Medicine88 Olympicro‐43gil, Songpa‐gu,05505SeoulRepublic of Korea
- Biomedical Engineering Research CenterAsan Institute of Life SciencesAsan Medical Center88 Olympicro‐43gil, Songpa‐gu,05505SeoulRepublic of Korea
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Kim JW, Koo B, Kim IH, Nyachoti CM. Effects of extrusion and microbial phytase on the apparent and standardized total tract digestibility of phosphorus in hemp hulls fed to growing pigs. J Anim Sci 2018; 96:1838-1845. [PMID: 29538763 PMCID: PMC6140985 DOI: 10.1093/jas/sky097] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 03/08/2018] [Indexed: 11/12/2022] Open
Abstract
An experiment was carried out to determine the apparent total tract digestibility (ATTD) and the standardized total tract digestibility (STTD) of P and the effects of extrusion and microbial phytase on ATTD and STTD of P in hemp hulls (HH). Thirty-six pigs (30.3 ± 2.7 kg) were randomly allotted to 1 of 6 experimental diets in a complete randomized design with 6 replicates per diet. A corn-soybean meal (SBM)-based basal diet was formulated. Two additional diets were formulated by replacing 40% of corn and SBM (on a 100% of total diet basis) with HH or extruded HH (EHH). The test ingredients, corn, and SBM were the only sources of P in the diets. Three additional diets were also prepared by supplementing 500 unit/kg of microbial phytase to the initial 3 diets (the corn-SBM basal diet and diets containing test ingredients). Pigs were fed experimental diets at 3 times the maintenance energy requirement (197 kcal ME/kg BW0.60). Results indicated that fecal P concentration and daily P output were reduced (P < 0.05) from pigs fed diets with dietary phytase compared with pigs fed diets without dietary phytase. The ATTD and STTD of P in experimental diets were not different. However, the ATTD and STTD of P in experimental diets supplemented with dietary phytase were increased (P < 0.05) compared with the diets without phytase. The ATTD and STTD of P in HH were 18.8% and 22.0%, respectively, whereas respective values for EHH were 22.5% and 26.3%. Extrusion had no effects on ATTD and STTD of P in HH. However, the ATTD and STTD of P in HH and EHH increased (P < 0.05) when dietary phytase was added to the diets. The concentration of Ca in feces and daily Ca output were reduced (P < 0.05) as a result of phytase supplementation. Addition of dietary phytase increased (P < 0.05) the ATTD of Ca in all experimental diets. In conclusion, the ATTD and STTD of P in HH fed to growing pigs were 18.8% and 22.0%, respectively. Respective values for EHH were 22.5% and 26.3%. Extrusion did not affect the ATTD and STTD of P in HH. However, the addition of microbial phytase to experimental diets increased the ATTD and STTD of P in diets and test ingredients and decreased fecal P output from pigs fed experimental diets. There was no interaction between extrusion and dietary phytase supplementation.
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Affiliation(s)
- J W Kim
- Department of Animal Science, University of Manitoba, Winnipeg, MB, Canada
| | - B Koo
- Department of Animal Science, University of Manitoba, Winnipeg, MB, Canada
| | - I H Kim
- Department of Animal Resource and Science, Dankook University, Cheonan, Chungnam, South Korea
| | - C M Nyachoti
- Department of Animal Science, University of Manitoba, Winnipeg, MB, Canada
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May AM, Koo B, Yaffe K, Leng Y, Cawthon PM, Redline S, Stone KL, Mehra R. 1015 Frequent Periodic Limb Movements During Sleep and Risk of Incident Stroke. Sleep 2018. [DOI: 10.1093/sleep/zsy061.1014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- A M May
- Louis Stokes Cleveland VA Medical Center, Cleveland, OH
| | - B Koo
- Yale School of Medicine, New Haven, CT
| | - K Yaffe
- University of California San Francisco, San Francisco, CA
| | - Y Leng
- University of California San Francisco, San Francisco, CA
| | - P M Cawthon
- California Pacific Medical Center Research Institute, San Francisco, CA
- University of California, San Francisco, San Francisco, CA
| | - S Redline
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
- Brigham and Women’s Hospitals, Harvard Medical School, Boston, MA
| | - K L Stone
- California Pacific Medical Center Research Institute, San Francisco, CA
| | - R Mehra
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH
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Kim JW, Koo B, Nyachoti CM. Net energy content of canola meal fed to growing pigs and effect of experimental methodology on energy values. J Anim Sci 2018; 96:1441-1452. [PMID: 29529226 PMCID: PMC6140956 DOI: 10.1093/jas/sky039] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 02/19/2018] [Indexed: 11/13/2022] Open
Abstract
An experiment was conducted to determine the digestible energy (DE), metabolizable energy (ME), and net energy (NE) contents of canola meal (CM) and to investigate the effects of basal diet [corn diet vs. corn-soybean meal (SBM) diet] and methodology (difference method vs. regression method) on energy values of CM. Thirty-six growing barrows (20.8 ± 1.0 kg initial body weight [BW]) were individually housed in metabolism crates and randomly allotted to one of six dietary treatments to give six replicates per treatment. The six experimental diets included a corn diet, a corn-SBM diet, a corn diet with 15 or 30% of CM, and a corn-SBM diet with 15 or 30% of CM. The DE, ME, and NE of CM were determined using the corn diet or the corn-SBM diet as a basal diet. In each basal diet, two additional diets containing 15 or 30% of CM were formulated to compare the determined energy values by the difference method and estimated energy values from the regression method. Feeding level was set at 550 kcal ME/kg BW0.6 per day. Pigs were fed experimental diets for 16 d including 10 d for adaptation and 6 d for total collection of feces and urine. Pigs were then moved into indirect calorimetry chambers to determine 24 h heat production (HP) and 12 h fasting HP. The DE, ME, and NE of CM determined by the difference method were within the 95% confidence intervals estimated for the DE, ME, and NE of CM by the regression method regardless of the basal diets used, which indicates that the difference and regression methods give equivalent DE, ME, and NE of CM. However, when the goodness of fit for the linear model was compared, the r2 of the regression analysis from the corn-SBM diet (0.78) was relatively greater than that from corn diet (0.40). The estimated NE of CM by the prediction equations generated by either the corn diet or corn-SBM diets were 2,096 kcal/kg and 1,960 kcal/kg (as-fed basis), respectively, whereas those values determined by the difference method were 2,233 kcal/kg and 2,106 kcal/kg (as-fed basis), respectively. In conclusion, the NE of CM determined in the current study was, on average, 2,099 kcal/kg (as-fed basis). The difference and regression methods do not give different NE value of CM fed to growing pigs. Although the NE values of CM determined using either the corn diet or the corn-SBM diet were not different, the greater r2 of the regression analysis from the corn-SBM diet than that from the corn diet suggests that the corn-SBM diet is a more appropriate basal diet for NE determination of ingredients.
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Affiliation(s)
- J W Kim
- Department of Animal Science, University of Manitoba, Winnipeg, MB, Canada
| | - B Koo
- Department of Animal Science, University of Manitoba, Winnipeg, MB, Canada
| | - C M Nyachoti
- Department of Animal Science, University of Manitoba, Winnipeg, MB, Canada
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Koo B, Bustamante-García D, Nyachoti CM. 155 The Energy Content of Diets Containing Lactobacillus-Fermented Barley or Wheat for Weaned Pigs. J Anim Sci 2018. [DOI: 10.1093/jas/sky073.152] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- B Koo
- Department of Animal Science, University of Manitoba, Winnipeg, MB, Canada
| | | | - C M Nyachoti
- Department of Animal Science, University of Manitoba, Winnipeg, MB, Canada
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Jin CE, Koo B, Lee EY, Kim JY, Kim SH, Shin Y. Simple and label-free pathogen enrichment via homobifunctional imidoesters using a microfluidic (SLIM) system for ultrasensitive pathogen detection in various clinical specimens. Biosens Bioelectron 2018; 111:66-73. [PMID: 29653418 PMCID: PMC7125596 DOI: 10.1016/j.bios.2018.04.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 03/16/2018] [Accepted: 04/01/2018] [Indexed: 01/12/2023]
Abstract
Diseases caused by pathogenic microorganisms including bacteria and viruses can cause serious medical issues including death and result in huge economic losses. Despite the myriad of recent advances in the rapid and accurate detection of pathogens, large volume clinical samples with a low concentration of pathogens continue to present challenges for diagnosis and surveillance. We here report a simple and label-free approach via homobifunctional imidoesters (HIs) with a microfluidic platform (SLIM) to efficiently enrich and extract pathogens at low concentrations from clinical samples. The SLIM system consists of an assembled double microfluidic chip for streamlining large volume processing and HIs for capturing pathogens and isolating nucleic acids by both electrostatic and covalent interaction without a chaotropic detergent or bulky instruments. The SLIM system significantly increases the enrichment and extraction rate of pathogens (up to 80% at 10 CFU (colony forming unit) in a 1 mL volume within 50 min). We demonstrated its clinical utility in large sample volumes from 46 clinical specimens including environmental swabs, saliva, and blood plasma. The SLIM system showed higher sensitivity with these samples and could detect pathogens that were below the threshold of detection with other methods. Finally, by combining our SLIM approach with an isothermal optical sensor, pathogens could be detected at a very high sensitivity in blood plasma samples within 80 min via enrichment, extraction and detection steps. Our SLIM system thus provides a simple, reliable, cost-effective and ultrasensitive pathogen diagnosis platform for use with large volume clinical samples and would thus have significant utility for various infectious diseases. SLIM system significantly increases the enrichment and extraction rate of pathogens. Demonstrated its clinical utility in large sample volumes from 46 clinical specimens. A simple, reliable, cost-effective and ultrasensitive pathogen diagnosis platform.
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Affiliation(s)
- Choong Eun Jin
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, Biomedical Engineering Research Center, Asan Institute of Life Sciences, Asan Medical Center, 88 Olympicro-43gil, Songpa-gu, Seoul, Republic of Korea
| | - Bonhan Koo
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, Biomedical Engineering Research Center, Asan Institute of Life Sciences, Asan Medical Center, 88 Olympicro-43gil, Songpa-gu, Seoul, Republic of Korea
| | - Eun Yeong Lee
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, Biomedical Engineering Research Center, Asan Institute of Life Sciences, Asan Medical Center, 88 Olympicro-43gil, Songpa-gu, Seoul, Republic of Korea
| | - Ji Yeun Kim
- Department of Infectious Disease, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Sung-Han Kim
- Department of Infectious Disease, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea.
| | - Yong Shin
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, Biomedical Engineering Research Center, Asan Institute of Life Sciences, Asan Medical Center, 88 Olympicro-43gil, Songpa-gu, Seoul, Republic of Korea.
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Koo B, Jin CE, Park SY, Lee TY, Nam J, Jang YR, Kim SM, Kim JY, Kim SH, Shin Y. A rapid bio-optical sensor for diagnosing Q fever in clinical specimens. J Biophotonics 2018; 11:e201700167. [PMID: 29024445 DOI: 10.1002/jbio.201700167] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 09/15/2017] [Accepted: 10/06/2017] [Indexed: 05/16/2023]
Abstract
Recent zoonotic outbreaks, such as Zika, Middle East respiratory syndrome and Ebola, have highlighted the need for rapid and accurate diagnostic assays that can be used to aid pathogen control. Q fever is a zoonotic disease caused by the transmission of Coxiella burnetii that can cause serious illness in humans through aerosols and is considered a potential bioterrorism agent. However, the existing assays are not suitable for the detection of this pathogen due to its low levels in real samples. We here describe a rapid bio-optical sensor for the accurate detection of Q fever and validate its clinical utility. By combining a bio-optical sensor, that transduces the presence of the target DNA based on binding-induced changes in the refractive index on the waveguide surface in a label-free and real-time manner, with isothermal DNA amplification, this new diagnostic tool offers a rapid (<20 min), 1-step DNA amplification/detection method. We confirmed the clinical sensitivity (>90%) of the bio-optical sensor by detecting C. burnetii in 11 formalin-fixed, paraffin-embedded liver biopsy samples from acute Q fever hepatitis patients and in 16 blood plasma samples from patients in which Q fever is the cause of fever of unknown origin.
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Affiliation(s)
- Bonhan Koo
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine and the Biomedical Engineering Research Center, Asan Institute of Life Sciences 88 Olympicro-43gil, Songpa-gu, Seoul, Republic of Korea
| | - Choong Eun Jin
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine and the Biomedical Engineering Research Center, Asan Institute of Life Sciences 88 Olympicro-43gil, Songpa-gu, Seoul, Republic of Korea
| | - Se Yoon Park
- Division of Infectious Diseases, Department of Internal Medicine, Soonchunhyang University College of Medicine 59 Daesangwan-ro, Yongsan-gu, Seoul, Republic of Korea
| | - Tae Yoon Lee
- Department of Technology Education, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Jeonghun Nam
- Department of Laboratory Medicine, School of Medicine, Korea University 145 Anam-ro, Seongbuk-gu, Seoul, Republic of Korea
| | - Young-Rock Jang
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine 88 Olympicro-43gil, Songpa-gu, Seoul, Republic of Korea
- Division of Infectious Disease, Department of Internal Medicine, Gil Medical Center, Gachon University College of Medicine, 21 Namdong-daero 774 beon-gil, Namdong-gu, Incheon, Republic of Korea
| | - Sun Mi Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine 88 Olympicro-43gil, Songpa-gu, Seoul, Republic of Korea
| | - Ji Yeun Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine 88 Olympicro-43gil, Songpa-gu, Seoul, Republic of Korea
| | - Sung-Han Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine 88 Olympicro-43gil, Songpa-gu, Seoul, Republic of Korea
| | - Yong Shin
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine and the Biomedical Engineering Research Center, Asan Institute of Life Sciences 88 Olympicro-43gil, Songpa-gu, Seoul, Republic of Korea
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Liu H, Zhao F, Jin CE, Koo B, Lee EY, Zhong L, Yun K, Shin Y. Large Instrument- and Detergent-Free Assay for Ultrasensitive Nucleic Acids Isolation via Binary Nanomaterial. Anal Chem 2018; 90:5108-5115. [PMID: 29561136 DOI: 10.1021/acs.analchem.7b05136] [Citation(s) in RCA: 18] [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: 02/08/2023]
Abstract
Nucleic acid-based diagnostics are widely used for clinical applications due to their powerful recognition of biomolecule properties. Isolation and purification of nucleic acids such as DNA and RNA in the diagnostic system have been severely hampered in point-of-care testing because of low recovery yields, degradation of nucleic acids due to the use of chaotropic detergent and high temperature, and the requirement of large instruments such as centrifuges and thermal controllers. Here, we report a novel large instrument- and detergent-free assay via binary nanomaterial for ultrasensitive nucleic acid isolation and detection from cells (eukaryotic and prokaryotic). This binary nanomaterial couples a zinc oxide nanomultigonal shuttle (ZnO NMS) for cell membrane rupture without detergent and temperature control and diatomaceous earth with dimethyl suberimidate complex (DDS) for the capture and isolation of nucleic acids (NA) from cells. The ZnO NMS was synthesized to a size of 500 nm to permit efficient cell lysis at room temperature within 2 min using the biological, chemical, and physical properties of the nanomaterial. By combining the ZnO NMS with the DDS and proteinase K, the nucleic acid extraction could be completed in 15 min with high quantity and quality. For bacterial cells, DNA isolation with the binary nanomaterial yielded 100 times more DNA, than a commercial spin column based reference kit, as determined by the NanoDrop spectrophotometer. We believe that this binary nanomaterial will be a useful tool for rapid and sensitive nucleic acid isolation and detection without large instruments and detergent in the field of molecular diagnostics.
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Affiliation(s)
- Huifang Liu
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine and Biomedical Engineering Research Center, Asan Institute of Life Sciences , Asan Medical Center , 88 Olympicro-43gil , Songpa-gu, Seoul 05505 , Republic of Korea
| | - Fei Zhao
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine and Biomedical Engineering Research Center, Asan Institute of Life Sciences , Asan Medical Center , 88 Olympicro-43gil , Songpa-gu, Seoul 05505 , Republic of Korea
| | - Choong Eun Jin
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine and Biomedical Engineering Research Center, Asan Institute of Life Sciences , Asan Medical Center , 88 Olympicro-43gil , Songpa-gu, Seoul 05505 , Republic of Korea
| | - Bonhan Koo
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine and Biomedical Engineering Research Center, Asan Institute of Life Sciences , Asan Medical Center , 88 Olympicro-43gil , Songpa-gu, Seoul 05505 , Republic of Korea
| | - Eun Yeong Lee
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine and Biomedical Engineering Research Center, Asan Institute of Life Sciences , Asan Medical Center , 88 Olympicro-43gil , Songpa-gu, Seoul 05505 , Republic of Korea
| | - Linlin Zhong
- Department of Bionanotechnology , Gachon University , Gyeonggi-do 13120 , Republic of Korea
| | - Kyusik Yun
- Department of Bionanotechnology , Gachon University , Gyeonggi-do 13120 , Republic of Korea
| | - Yong Shin
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine and Biomedical Engineering Research Center, Asan Institute of Life Sciences , Asan Medical Center , 88 Olympicro-43gil , Songpa-gu, Seoul 05505 , Republic of Korea
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Zhao F, Koo B, Liu H, Eun Jin C, Shin Y. A single-tube approach for in vitro diagnostics using diatomaceous earth and optical sensor. Biosens Bioelectron 2018; 99:443-449. [PMID: 28818785 PMCID: PMC7127695 DOI: 10.1016/j.bios.2017.08.027] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 08/03/2017] [Accepted: 08/11/2017] [Indexed: 12/20/2022]
Abstract
Versatile, simple and efficient sample preparation is desirable for point-of-care testing of emerging diseases such as zoonoses, but current sample preparation assays are insensitive, labour-intensive and time-consuming and require multiple instruments. We developed a single-tube sample preparation approach involving direct pathogen enrichment and extraction from human specimens using diatomaceous earth (DE). Amine-modified DE was used to directly enrich a zoonotic pathogen, Brucella, in a large sample volume. Next, a complex of amine-modified DE and dimethyl suberimidate was used for nucleic acid extraction from the enriched pathogen. Using our single-tube approach, the pathogen can be enriched and extracted within 60min at a level of 1 colony formation unit (CFU) from a 1ml sample volume in the same tube. The performance of this approach is 10-100 times better than that of a commercial kit (102 to 103CFU/ml) but does not require a large centrifuge. Finally, we combined the single-tube approach with a bio-optical sensor for rapid and accurate zoonotic pathogen detection in human urine samples. Using the combination system, Brucella in human urine can be efficiently enriched (~ 8-fold) and the detection limit is enhanced by up to 100 times (1CFU/ml bacteria in urine) compared with the commercial kit. This combined system is fast and highly sensitive and thus represents a promising approach for disease diagnosis in the clinical setting.
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Affiliation(s)
- Fei Zhao
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, and Biomedical Engineering Research Center, Asan Institute of Life Sciences, Asan Medical Center, 88 Olympicro-43gil, Songpa-gu, Seoul, Republic of Korea
| | - Bonhan Koo
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, and Biomedical Engineering Research Center, Asan Institute of Life Sciences, Asan Medical Center, 88 Olympicro-43gil, Songpa-gu, Seoul, Republic of Korea
| | - Huifang Liu
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, and Biomedical Engineering Research Center, Asan Institute of Life Sciences, Asan Medical Center, 88 Olympicro-43gil, Songpa-gu, Seoul, Republic of Korea
| | - Choong Eun Jin
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, and Biomedical Engineering Research Center, Asan Institute of Life Sciences, Asan Medical Center, 88 Olympicro-43gil, Songpa-gu, Seoul, Republic of Korea
| | - Yong Shin
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, and Biomedical Engineering Research Center, Asan Institute of Life Sciences, Asan Medical Center, 88 Olympicro-43gil, Songpa-gu, Seoul, Republic of Korea.
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Dao TNT, Lee EY, Koo B, Jin CE, Lee TY, Shin Y. A microfluidic enrichment platform with a recombinase polymerase amplification sensor for pathogen diagnosis. Anal Biochem 2017; 544:87-92. [PMID: 29289485 DOI: 10.1016/j.ab.2017.12.030] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 12/19/2017] [Accepted: 12/22/2017] [Indexed: 02/06/2023]
Abstract
Rapid and sensitive detection of low amounts of pathogen in large samples is needed for early diagnosis and treatment of patients and surveillance of pathogen. In this study, we report a microfluidic platform for detection of low pathogen levels in a large sample volume that couples an Magainin 1 based microfluidic platform for pathogen enrichment and a recombinase polymerase amplification (RPA) sensor for simultaneous pathogenic DNA amplification and detection in a label-free and real-time manner. Magainin 1 is used as a pathogen enrichment agent with a herringbone microfluidic chip. Using this enrichment platform, the detection limit was found to be 20 times more sensitive in 10 ml urine with Salmonella and 10 times more sensitive in 10 ml urine with Brucella than that of real-time PCR without the enrichment process. Furthermore, the combination system of the enrichment platform and an RPA sensor that based on an isothermal DNA amplification method with rapidity and sensitivity for detection can detect a pathogen at down to 50 CFU in 10 ml urine for Salmonella and 102 CFU in 10 ml urine for Brucella within 60 min. This system will be useful as it has the potential for better diagnosis of pathogens by increasing the capture efficiency of the pathogen in large samples, subsequently enhancing the detection limit of pathogenic DNA.
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Affiliation(s)
- Thuy Nguyen Thi Dao
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, Biomedical Engineering Research Center, Asan Institute of Life Sciences, Asan Medical Center, 88 Olympicro-43gil, Songpa-gu, Seoul 05505, Republic of Korea
| | - Eun Yeong Lee
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, Biomedical Engineering Research Center, Asan Institute of Life Sciences, Asan Medical Center, 88 Olympicro-43gil, Songpa-gu, Seoul 05505, Republic of Korea
| | - Bonhan Koo
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, Biomedical Engineering Research Center, Asan Institute of Life Sciences, Asan Medical Center, 88 Olympicro-43gil, Songpa-gu, Seoul 05505, Republic of Korea
| | - Choong Eun Jin
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, Biomedical Engineering Research Center, Asan Institute of Life Sciences, Asan Medical Center, 88 Olympicro-43gil, Songpa-gu, Seoul 05505, Republic of Korea
| | - Tae Yoon Lee
- Department of Technology Education and Department of Biomedical Engineering, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea.
| | - Yong Shin
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, Biomedical Engineering Research Center, Asan Institute of Life Sciences, Asan Medical Center, 88 Olympicro-43gil, Songpa-gu, Seoul 05505, Republic of Korea.
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Kim JY, Koo B, Jin CE, Kim MC, Chong YP, Lee SO, Choi SH, Kim YS, Woo JH, Shin Y, Kim SH. Rapid Diagnosis of Tick-Borne Illnesses by Use of One-Step Isothermal Nucleic Acid Amplification and Bio-Optical Sensor Detection. Clin Chem 2017; 64:556-565. [PMID: 29208659 DOI: 10.1373/clinchem.2017.280230] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 10/30/2017] [Indexed: 01/05/2023]
Abstract
BACKGROUND Scrub typhus and severe fever with thrombocytopenia syndrome (SFTS) are the most common tick-borne illnesses in South Korea. Early differentiation of SFTS from scrub typhus in emergency departments is essential but difficult because of their overlapping epidemiology, shared risk factors, and similar clinical manifestations. METHODS We compared the diagnostic performance of one-step isothermal nucleic acid amplification with bio-optical sensor detection (iNAD) under isothermal conditions, which is rapid (20-30 min), with that of real-time PCR, in patients with a confirmed tick-borne illness. Fifteen patients with confirmed SFTS who provided a total of 15 initial blood samples and 5 follow-up blood samples, and 21 patients with confirmed scrub typhus, were evaluated. RESULTS The clinical sensitivity of iNAD (100%; 95% CI, 83-100) for SFTS was significantly higher than that of real-time PCR (75%; 95% CI, 51-91; P = 0.047), while its clinical specificity (86%; 95% CI, 65-97) was similar to that of real-time PCR (95%; 95% CI, 77-99; P = 0.61). The clinical sensitivity of iNAD for scrub typhus (100%; 95% CI, 81-100) was significantly higher than that of real-time PCR for scrub typhus (67%; 95% CI, 43-85; P = 0.009), while its clinical specificity (90%; 95% CI, 67-98) was similar to that of real-time PCR (95%; 95% CI, 73-100; P > 0.99). CONCLUSIONS iNAD is a valuable, rapid method of detecting SFTS virus and Orientia tsutsugamushi with high clinical sensitivity and specificity.
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Affiliation(s)
- Ji Yeun Kim
- Departments of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Bonhan Koo
- Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Choong Eun Jin
- Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Min Chul Kim
- Departments of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Yong Pil Chong
- Departments of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Sang-Oh Lee
- Departments of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Sang-Ho Choi
- Departments of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Yang Soo Kim
- Departments of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Jun Hee Woo
- Departments of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Yong Shin
- Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea.
| | - Sung-Han Kim
- Departments of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea;
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Kim T, Jin CE, Sung H, Koo B, Park J, Kim SM, Kim JY, Chong YP, Lee SO, Choi SH, Kim YS, Woo JH, Lee JH, Lee JH, Lee KH, Shin Y, Kim SH. Molecular epidemiology and environmental contamination during an outbreak of parainfluenza virus 3 in a haematology ward. J Hosp Infect 2017; 97:403-413. [PMID: 28893615 PMCID: PMC7114920 DOI: 10.1016/j.jhin.2017.09.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 09/05/2017] [Indexed: 11/25/2022]
Abstract
Background Although fomites or contaminated surfaces have been considered as transmission routes, the role of environmental contamination by human parainfluenza virus type 3 (hPIV-3) in healthcare settings is not established. Aim To describe an hPIV-3 nosocomial outbreak and the results of environmental sampling to elucidate the source of nosocomial transmission and the role of environmental contamination. Methods During an hPIV-3 outbreak between May and June 2016, environmental surfaces in contact with clustered patients were swabbed and respiratory specimens used from infected patients and epidemiologically unlinked controls. The epidemiologic relatedness of hPIV-3 strains was investigated by sequencing of the haemagglutinin–neuraminidase and fusion protein genes. Findings Of 19 hPIV-3-infected patients, eight were haematopoietic stem cell recipients and one was a healthcare worker. In addition, four had upper and 12 had lower respiratory tract infections. Of the 19 patients, six (32%) were community-onset infections (symptom onset within <7 days of hospitalization) and 13 (68%) were hospital-onset infections (≥7 days of hospitalization). Phylogenetic analysis identified two major clusters: five patients, and three patients plus one healthcare worker. Therefore, seven (37%) were classified as nosocomial transmissions. hPIV-3 was detected in 21 (43%) of 49 environmental swabs up to 12 days after negative respiratory polymerase chain reaction conversion. Conclusion At least one-third of a peak season nosocomial hPIV-3 outbreak originated from nosocomial transmission, with multiple importations of hPIV-3 from the community, providing experimental evidence for extensive environmental hPIV-3 contamination. Direct contact with the contaminated surfaces and fomites or indirect transmission from infected healthcare workers could be responsible for nosocomial transmission.
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Affiliation(s)
- T Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea; Division of Infectious Diseases, Department of Internal Medicine, Gyeongsang National University Hospital, Republic of Korea
| | - C E Jin
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - H Sung
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - B Koo
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - J Park
- Department of Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - S-M Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - J Y Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Y P Chong
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - S-O Lee
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - S-H Choi
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Y S Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - J H Woo
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - J-H Lee
- Department of Hematology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - J-H Lee
- Department of Hematology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - K-H Lee
- Department of Hematology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Y Shin
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea.
| | - S-H Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea.
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Koo B, Kim JW, de Lange CFM, Hossain MM, Nyachoti CM. Effects of diet complexity and multicarbohydrase supplementation on growth performance, nutrient digestibility, blood profile, intestinal morphology, and fecal score in newly weaned pigs1. J Anim Sci 2017. [DOI: 10.2527/jas.2017.1760] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Kim JW, Koo B, Nyachoti CM. Digestible, metabolizable, and net energy of camelina cake fed to growing pigs and additivity of energy in mixed diets1,2. J Anim Sci 2017. [DOI: 10.2527/jas.2017.1759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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