1
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Li X, Zhao D, Wang Y, Huang H. Droplet-based cell-laden microgels for high-throughput analysis. Trends Biotechnol 2024; 42:397-401. [PMID: 37953082 DOI: 10.1016/j.tibtech.2023.10.010] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 10/21/2023] [Accepted: 10/24/2023] [Indexed: 11/14/2023]
Abstract
Cell-laden droplet microfluidics has revolutionized bulk biochemical analysis by offering compartmentalized microreactors for individual cells, but downstream operations of regular aqueous droplets are limited. Hydrogel matrix can provide a rigid scaffold for long-term culture of eukaryotic and prokaryotic cells, and can support several manipulations, facilitating subsequent high-throughput analysis of cellular heterogeneity.
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Affiliation(s)
- Xiang Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210046, China
| | - Danshan Zhao
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210046, China
| | - Yuetong Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210046, China.
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210046, China.
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2
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Kim MK, Park J, Tak S, Paek K, Bang G, Woo SM, Ravichandran NK, Hong WG, Kang HW, Kim H, Bae JY, Kim JA. A long-term storable gel-laden chip composite built in a multi-well plate enabling in situcell encapsulation for high-throughput liver model. Biofabrication 2024; 16:025020. [PMID: 38390723 DOI: 10.1088/1758-5090/ad28ef] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 02/13/2024] [Indexed: 02/24/2024]
Abstract
Hydrogels are widely used as scaffold materials for constructingin vitrothree-dimensional microphysiological systems. However, their high sensitivity to various external cues hinders the development of hydrogel-laden, microscale, and high-throughput chips. Here, we have developed a long-term storable gel-laden chip composite built in a multi-well plate, which enablesin situcell encapsulation and facilitates high-throughput analysis. Through optimized chemical crosslinking and freeze-drying method (C/FD), we have achieved a high-quality of gel-laden chip composite with excellent transparency, uniform porosity, and appropriate swelling and mechanical characteristics. Besides collagen, decellularized extracellular matrix with tissue-specific biochemical compound has been applied as chip composite. As a ready-to-use platform,in situcell encapsulation within the gel has been achieved through capillary force generated during gel reswelling. The liver-mimetic chip composite, comprising HepG2 cells or primary hepatocytes, has demonstrated favorable hepatic functionality and high sensitivity in drug testing. The developed fabrication process with improved stability of gels and storability allows chip composites to be stored at a wide range of temperatures for up to 28 d without any deformation, demonstrating off-the-shelf products. Consequently, this provides an exceptionally simple and long-term storable platform that can be utilized for an efficient tissue-specific modeling and various biomedical applications.
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Affiliation(s)
- Min Kyeong Kim
- Center for Scientific Instrumentation, Korea Basic Science Institute, Daejeon 34133, Republic of Korea
| | - Jubin Park
- Center for Scientific Instrumentation, Korea Basic Science Institute, Daejeon 34133, Republic of Korea
- Program in Biomicro System Technology, Korea University, Seoul 02841, Republic of Korea
| | - Sungho Tak
- Center for Bio-Imaging and Translational Research, Korea Basic Science Institute, Cheongju 28119, Chungbuk, Republic of Korea
| | - Kyurim Paek
- Center for Scientific Instrumentation, Korea Basic Science Institute, Daejeon 34133, Republic of Korea
- Program in Biomicro System Technology, Korea University, Seoul 02841, Republic of Korea
| | - Geul Bang
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju 28119, Chungbuk, Republic of Korea
| | - Sang-Mi Woo
- Center for Scientific Instrumentation, Korea Basic Science Institute, Daejeon 34133, Republic of Korea
| | - Naresh Kumar Ravichandran
- Center for Scientific Instrumentation, Korea Basic Science Institute, Daejeon 34133, Republic of Korea
| | - Won Gi Hong
- Research Center for Materials Analysis, Korea Basic Science Institute, Daejeon 34133, Republic of Korea
| | - Hyun-Wook Kang
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulju-gun 44919, Ulsan, Republic of Korea
| | - Hyang Kim
- Institute of New Horizon Regenerative Medicine, Myongji Hospital, Goyang 10475, Republic of Korea
| | - Ji Yong Bae
- Center for Scientific Instrumentation, Korea Basic Science Institute, Daejeon 34133, Republic of Korea
| | - Jeong Ah Kim
- Center for Scientific Instrumentation, Korea Basic Science Institute, Daejeon 34133, Republic of Korea
- Department of Bio-Analytical Science, University of Science and Technology, Daejeon 34113, Republic of Korea
- Chung-Ang University Hospital, Chung-Ang University College of Medicine, Seoul 06974, Republic of Korea
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3
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Park JY, Lee M, Jeong SH, Lee HK. Beagle: a near-edge X-ray absorption fine-structure spectroscopy data processing solution for beamline experiments at Pohang Accelerator Laboratory. J Synchrotron Radiat 2024; 31:202-207. [PMID: 37930256 PMCID: PMC10833428 DOI: 10.1107/s1600577523008755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 10/04/2023] [Indexed: 11/07/2023]
Abstract
Near-edge X-ray absorption fine-structure (NEXAFS) spectroscopy is a powerful tool for identifying chemical bonding states at synchrotron radiation facilities. Advances in new materials require researchers in both academia and industry to measure tens to hundreds of samples during the available beam time on a synchrotron beamline, which is typically allocated to users. Automated measurement methods, along with analysis software, have been developed for beamlines. Automated measurements facilitate high-throughput experiments and accumulate vast amounts of measured spectral data. The analysis software supports various functions for analyzing the experimental data; however, these analysis methods are complicated, and learning them can be time-consuming. To process large amounts of spectral data, a new analysis software, dedicated to NEXAFS spectroscopy, that is easy to use and can provide results in a short time is desired. Herein, the development of Beagle is described, software calculating molecular orientation from NEXAFS spectroscopy data that can report results in a short time comparable with that required to measure one sample at the beamline. It was designed to progress in a single sequence from data loading to the printing of the results with a `click of a button'. The functions of the software include recognizing the dataset, correcting the background, normalizing the plot, calculating the electron yield and determining the molecular orientation. The analysis results can be saved as {\tt{.txt}} files (spectral data), {\tt{.pdf}} files (graphic images) and Origin files (spectral data and graphic images).
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Affiliation(s)
- Jae Yeon Park
- Radiation Fusion Technology Research Division, Advanced Radiation Technology Institute (ARTI)/Korea Atomic Energy Research (KAERI), 29 Geum gu-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Minwoong Lee
- Radiation Fusion Technology Research Division, Advanced Radiation Technology Institute (ARTI)/Korea Atomic Energy Research (KAERI), 29 Geum gu-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Seong-Hoon Jeong
- Pohang Accelerator Laboratory, Pohang University of Science and Technology (POSTECH), 80 Jigok-ro 127 beon-gil, Nam-gu, Pohang-si, Gyeongsangbuk-do 37673, Republic of Korea
| | - Han-Koo Lee
- Pohang Accelerator Laboratory, Pohang University of Science and Technology (POSTECH), 80 Jigok-ro 127 beon-gil, Nam-gu, Pohang-si, Gyeongsangbuk-do 37673, Republic of Korea
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4
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Soma Nyansa M, Oronova A, Gora N, Geborkoff MR, Ostlund NR, Fritz DR, Werner T, Tanasova M. Turn-on Rhodamine Glycoconjugates Enable Real-Time GLUT Activity Monitoring in Live Cells and In Vivo. Chem Biomed Imaging 2023; 1:637-647. [PMID: 37873027 PMCID: PMC10593130 DOI: 10.1021/cbmi.3c00063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 08/14/2023] [Accepted: 08/16/2023] [Indexed: 10/25/2023]
Abstract
The direct relationship between facilitative glucose transporters (GLUTs) and metabolic diseases opens new avenues for sensing metabolic deregulations and drives the development of molecular probes for GLUT-targeted detection of metabolic diseases. Radiotracer-based molecular imaging probes have been effectively utilized in reporting alterations in sugar uptake as an indication of metabolic deregulations, cancer development, or inflammation. Progress in developing fluorophore-based tools facilitated GLUT-specific analyses using more accessible fluorescence-based instrumentation. However, restrictions on the emission range of fluorophores and the requirement for substantial post-treatments to reduce background fluorescence have brought to light the critical directions for improvement of the technology for broader use in screening applications. Here we present turn-on GLUT activity reporters activated upon cells' internalization. We demonstrate a specific delivery of a sizable rhodamine B fluorophore through GLUT5 and showcase a stringent requirement in conjugate structure for maintaining a GLUT-specific uptake. With the turn-on GLUT probes, we demonstrate the feasibility of high-throughput fluorescence microscopy and flow cytometry-based GLUT activity screening in live cells and the probes' applicability for assessing sugar uptake alterations in vivo.
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Affiliation(s)
- Monica
Mame Soma Nyansa
- Department
of Chemistry, Michigan Technological University,1400 Townsend Drive, Houghton, Michigan 49931, United States
| | - Adelina Oronova
- Department
of Chemistry, Michigan Technological University,1400 Townsend Drive, Houghton, Michigan 49931, United States
- Health
Research Institute, Michigan Technological
University, 1400 Townsend Drive, Houghton, Michigan 49931, United States
| | - Nazar Gora
- Department
of Chemistry, Michigan Technological University,1400 Townsend Drive, Houghton, Michigan 49931, United States
- Health
Research Institute, Michigan Technological
University, 1400 Townsend Drive, Houghton, Michigan 49931, United States
| | - Micaela Rayne Geborkoff
- Department
of Biological Sciences, Michigan Technological
University, 1400 Townsend Drive, Houghton, Michigan 49931, United States
| | - Nathan Randal Ostlund
- Department
of Biological Sciences, Michigan Technological
University, 1400 Townsend Drive, Houghton, Michigan 49931, United States
| | - Delaney Raine Fritz
- Department
of Biological Sciences, Michigan Technological
University, 1400 Townsend Drive, Houghton, Michigan 49931, United States
| | - Thomas Werner
- Department
of Biological Sciences, Michigan Technological
University, 1400 Townsend Drive, Houghton, Michigan 49931, United States
- Health
Research Institute, Michigan Technological
University, 1400 Townsend Drive, Houghton, Michigan 49931, United States
| | - Marina Tanasova
- Department
of Chemistry, Michigan Technological University,1400 Townsend Drive, Houghton, Michigan 49931, United States
- Health
Research Institute, Michigan Technological
University, 1400 Townsend Drive, Houghton, Michigan 49931, United States
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5
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Zhang J, Lin H, Xu J, Zhang M, Ge X, Zhang C, Huang WE, Cheng JX. High-throughput single-cell sorting by stimulated Raman-activated cell ejection. bioRxiv 2023:2023.10.16.562526. [PMID: 37904930 PMCID: PMC10614813 DOI: 10.1101/2023.10.16.562526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
Single-cell sorting is essential to explore cellular heterogeneity in biology and medicine. Recently developed Raman-activated cell sorting (RACS) circumvents the limitations of fluorescence-activated cell sorting, such as the cytotoxicity of labels. However, the sorting throughputs of all forms of RACS are limited by the intrinsically small cross-section of spontaneous Raman scattering. Here, we report a stimulated Raman-activated cell ejection (S-RACE) platform that enables high-throughput single-cell sorting based on high-resolution multi-channel stimulated Raman chemical imaging, in situ image decomposition, and laser-induced cell ejection. The performance of this platform was illustrated by sorting a mixture of 1 μm polymer beads, where 95% yield, 98% purity, and 14 events per second throughput were achieved. Notably, our platform allows live cell ejection, allowing for the growth of single colonies of bacteria and fungi after sorting. To further illustrate the chemical selectivity, lipid-rich Rhodotorula glutinis cells were successfully sorted from a mixture with Saccharomyces cerevisiae, confirmed by downstream quantitative PCR. Furthermore, by integrating a closed-loop feedback control circuit into the system, we realized real-time single-cell imaging and sorting, and applied this method to precisely eject regions of interest from a rat brain tissue section. The reported S-RACE platform opens exciting opportunities for a wide range of single-cell applications in biology and medicine.
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Affiliation(s)
- Jing Zhang
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
- Photonics Center, Boston University, Boston, MA 02215, USA
| | - Haonan Lin
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
- Photonics Center, Boston University, Boston, MA 02215, USA
| | - Jiabao Xu
- Division of Biomedical Engineering, James Watt School of Engineering, University of Glasgow, Glasgow, G12 8LT, UK
| | - Meng Zhang
- Photonics Center, Boston University, Boston, MA 02215, USA
- Department of Electrical and Computer Engineering, Boston University, Boston, MA 02215, USA
| | - Xiaowei Ge
- Photonics Center, Boston University, Boston, MA 02215, USA
- Department of Electrical and Computer Engineering, Boston University, Boston, MA 02215, USA
| | - Chi Zhang
- Department of Chemistry, Purdue University, 560 Oval Dr., West Lafayette, IN 47907, USA
| | - Wei E. Huang
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, UK
| | - Ji-Xin Cheng
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
- Photonics Center, Boston University, Boston, MA 02215, USA
- Department of Electrical and Computer Engineering, Boston University, Boston, MA 02215, USA
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6
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Abuhejail RM, Alzoman NZ, Darwish IA. Three Innovative Green and High-Throughput Microwell Spectrophotometric Methods for the Quantitation of Ceritinib, a Potent Drug for the Treatment of ALK-Positive Non-Small Cell Lung Cancer: An Application to the Analysis of Capsules and Drug Uniformity Testing. Molecules 2023; 28:7054. [PMID: 37894533 PMCID: PMC10609451 DOI: 10.3390/molecules28207054] [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: 09/26/2023] [Revised: 10/09/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
Ceritinib (CER) is a potent drug that has been recently approved by the Food and Drug Administration for the treatment of patients with non-small cell lung cancer harboring the anaplastic lymphoma kinase mutation gene. The existing methods for the quality control of CER are very limited and suffer from limited analytical throughput and do not meet the requirements of the green analytical principles. This study presented the first-ever development and validation of three innovative green and high-throughput microwell spectrophotometric methods (MW-SPMs) for the quality control of CER in its dosage form (Zykadia® capsules). These MW-SPMs were based on the formation of colored N-vinylamino-substituted haloquinone derivatives of CER upon its reactions with each of chloranil, bromanil, and 2,3-dichloro-1,4-naphthoquinone in the presence of acetaldehyde. The optimized procedures of the MW-SPMs were established, and their analytical performances were validated according to the ICH. The linear range of the MW-SPMs was 5-150 µg/mL, with limits of quantitation of 5.3-7.6 µg/mL. The accuracy and precision of the MW-SPMs were proved, as the average recovery values were 99.9-101.0%, and the relative standard deviations did not exceed 1.8%. The three methods were applied to the determination of CER content in Zykadia® capsules and drug content uniformity testing. The greenness of the MW-SPMs was proved using three different metric tools. In addition, these methods encompassed the advantage of high-throughput analysis. In conclusion, the three methods are valuable tools for convenient and reliable application in the pharmaceutical quality control units for CER-containing capsules.
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Affiliation(s)
| | | | - Ibrahim A. Darwish
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
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7
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Abuhejail RM, Alzoman NZ, Darwish IA. Development of Two Novel One-Step and Green Microwell Spectrophotometric Methods for High-Throughput Determination of Ceritinib, a Potent Drug for Treatment of Anaplastic Lymphoma Kinase-Positive Non-Small-Cell Lung Cancer. Medicina (Kaunas) 2023; 59:1813. [PMID: 37893531 PMCID: PMC10608039 DOI: 10.3390/medicina59101813] [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] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/01/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023]
Abstract
Background and Objectives: Ceritinib (CER) is a potent drug of the third-generation tyrosine kinase inhibitor class. CER has been approved for the treatment of patients with non-small-cell lung cancer (NSCLC) harboring the anaplastic lymphoma kinase (ALK) mutation gene. In the literature, there is no green and high-throughput analytical method for the quantitation of CER in its dosage form (Zykadia® capsules). This study describes, for the first time, the development and validation of two novel one-step and green microwell spectrophotometric methods (MW-SPMs) for the high-throughput quantitation of CER in Zykadia® capsules. Materials and Methods: These two methods were based on an in microwell formation of colored derivatives upon the reaction of CER with two different benzoquinone reagents via two different mechanisms. These reagents were ortho-benzoquinone (OBQ) and 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ), and their reactions proceeded via condensation and charge transfer reactions, respectively. The reactions were carried out in 96-well transparent plates, and the absorbances of the colored reaction products were measured with an absorbance microplate reader at 540 and 460 nm for reactions with OBQ and DDQ, respectively. The optimum conditions of reactions were established, their molar ratios were determined, and reaction mechanisms were postulated. Under the refined optimum reaction conditions, procedures of MW-SPMs were established and validated according to the guidelines of the International Council on Harmonization. Results: The limits of quantitation were 6.5 and 10.2 µg/well for methods involving reactions with OBQ and DDQ, respectively. Both methods were applied with great reliability to the determination of CER content in Zykadia® capsules and their drug uniformity. Greenness of the MW-SPMs was evaluated using three different metric tools, and the results proved that the two methods fulfil the requirements of green analytical approaches. In addition, the simultaneous handling of a large number of samples with microvolumes in the proposed methods gave them the advantage of a high-throughput analysis. Conclusions: The two methods are valuable tools for rapid routine application in pharmaceutical quality control units for the quantitation of CER.
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Affiliation(s)
| | | | - Ibrahim A. Darwish
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
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8
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Fuchs H, Jahn K, Hu X, Meister R, Binter M, Framme C. Breaking a Dogma: High-Throughput Live-Cell Imaging in Real-Time with Hoechst 33342. Adv Healthc Mater 2023; 12:e2300230. [PMID: 36934382 DOI: 10.1002/adhm.202300230] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 03/14/2023] [Indexed: 03/20/2023]
Abstract
Automated high-throughput live cell imaging (LCI) enables investigation of substance effects on cells in vitro. Usually, cell number is analyzed by phase-contrast imaging, which is reliable only for a few cell types. Therefore, an accurate cell counting method, such as staining the nuclei with Hoechst 33342 before LCI, will be desirable. However, since the mid-1980s, the dogma exists that Hoechst can only be used for endpoint analyses because of its cytotoxic properties and the potentially phototoxic effects of the excitation light. Since microscopic camera sensitivity has significantly improved, this study investigates whether this dogma is still justified. Therefore, exposure parameters are optimized using a 4× objective, and the minimum required Hoechst concentration is evaluated, allowing LCI at 30-min intervals over 5 days. Remarkably, a Hoechst concentration of only 57 × 10-9 m significantly inhibits proliferation and thus impairs cell viability. However, Hoechst concentrations between 7 × 10-9 and 28 × 10-9 m can be determined, which are neither cytotoxic nor impacting cell viability, proliferation, or signaling pathways. The method can be adapted to regular inverted fluorescence microscopes and allows, for example, to determine the cytotoxicity of a substance or the transduction efficiency, with the advantage that the analysis can be repeated at any desired time point.
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Affiliation(s)
- Heiko Fuchs
- Institute of Ophthalmology, University Eye Hospital, Hannover Medical School, Carl-Neuberg Strasse 1, 30625, Hannover, Germany
| | - Kirsten Jahn
- Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Carl-Neuberg Strasse 1, 30625, Hannover, Germany
| | - Xiaonan Hu
- Institute of Ophthalmology, University Eye Hospital, Hannover Medical School, Carl-Neuberg Strasse 1, 30625, Hannover, Germany
| | - Roland Meister
- Institute of Ophthalmology, University Eye Hospital, Hannover Medical School, Carl-Neuberg Strasse 1, 30625, Hannover, Germany
| | - Maximilian Binter
- Institute of Ophthalmology, University Eye Hospital, Hannover Medical School, Carl-Neuberg Strasse 1, 30625, Hannover, Germany
| | - Carsten Framme
- Institute of Ophthalmology, University Eye Hospital, Hannover Medical School, Carl-Neuberg Strasse 1, 30625, Hannover, Germany
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9
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Liu C. High-throughput MS for intact protein analysis. Bioanalysis 2023; 15:1017-1019. [PMID: 37584366 DOI: 10.4155/bio-2023-0139] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2023] Open
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10
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Robinson JP, Ostafe R, Iyengar SN, Rajwa B, Fischer R. Flow Cytometry: The Next Revolution. Cells 2023; 12:1875. [PMID: 37508539 PMCID: PMC10378642 DOI: 10.3390/cells12141875] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [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: 06/21/2023] [Revised: 07/06/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
Unmasking the subtleties of the immune system requires both a comprehensive knowledge base and the ability to interrogate that system with intimate sensitivity. That task, to a considerable extent, has been handled by an iterative expansion in flow cytometry methods, both in technological capability and also in accompanying advances in informatics. As the field of fluorescence-based cytomics matured, it reached a technological barrier at around 30 parameter analyses, which stalled the field until spectral flow cytometry created a fundamental transformation that will likely lead to the potential of 100 simultaneous parameter analyses within a few years. The simultaneous advance in informatics has now become a watershed moment for the field as it competes with mature systematic approaches such as genomics and proteomics, allowing cytomics to take a seat at the multi-omics table. In addition, recent technological advances try to combine the speed of flow systems with other detection methods, in addition to fluorescence alone, which will make flow-based instruments even more indispensable in any biological laboratory. This paper outlines current approaches in cell analysis and detection methods, discusses traditional and microfluidic sorting approaches as well as next-generation instruments, and provides an early look at future opportunities that are likely to arise.
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Affiliation(s)
- J Paul Robinson
- Department of Basic Medical Sciences, Purdue University, West Lafayette, IN 47907, USA
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Raluca Ostafe
- Molecular Evolution, Protein Engineering and Production Facility (PI4D), Purdue University, West Lafayette, IN 47907, USA
| | | | - Bartek Rajwa
- Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907, USA
| | - Rainer Fischer
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN 47907, USA
- Purdue Institute of Inflammation, Immunology and Infectious Diseases, Purdue University, West Lafayette, IN 47907, USA
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11
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Xiong Z, Yu Y, Chen H, Bai L. A coarse-grained study on mechanical behaviors of diamond-like carbon based on machine learning. Nanotechnology 2023; 34. [PMID: 37410425 DOI: 10.1088/1361-6528/acde5a] [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] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 06/13/2023] [Indexed: 07/07/2023]
Abstract
Diamond-like carbon (DLC) films have broad application potential due to their high hardness, high wear resistance, and self-lubricating properties. However, considering that DLC films are micron-scale, neither finite element methods nor macroscopic experiments can reveal their deformation and failure mechanisms. Here we propose a coarse-grained molecular dynamics (CGMD) approach which expands the capabilities of molecular dynamics simulations to uniaxial tensile behavior of DLC films at a higher scale. The Tersoff potential is modified by high-throughput screening calculations for CGMD. Given this circumstance, machine learning (ML) models are employed to reduce the high-throughput computational cost by 86%, greatly improving the efficiency of parameter optimization in second- and fourth-order CGMD. The final obtained coarse-grained tensile curves fit well with that of the all-atom curves, showing that the ML-based CGMD method can investigate DLC films at higher scales while saving a large number of computational resources, which is important for promoting the research and production of high-performance DLC films.
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Affiliation(s)
- Zhipeng Xiong
- Key Laboratory of Traffic Safety on Track (Central South University), Ministry of Education, School of Traffic & Transportation Engineering, Central South University, Changsha, 410075, People's Republic of China
| | - Yifeng Yu
- Department of Mechanics and Aerospace Engineering, Southern University of Science and Technology, Shenzhen, 518055, People's Republic of China
| | - Huan Chen
- Department of Materials Science and Engineering, City University of Hong Kong, Kowloon 999077, Hong Kong, People's Republic of China
| | - Lichun Bai
- Key Laboratory of Traffic Safety on Track (Central South University), Ministry of Education, School of Traffic & Transportation Engineering, Central South University, Changsha, 410075, People's Republic of China
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12
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An L, Ji F, Zhao E, Liu Y, Liu Y. Measuring cell deformation by microfluidics. Front Bioeng Biotechnol 2023; 11:1214544. [PMID: 37434754 PMCID: PMC10331473 DOI: 10.3389/fbioe.2023.1214544] [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: 04/30/2023] [Accepted: 06/14/2023] [Indexed: 07/13/2023] Open
Abstract
Microfluidics is an increasingly popular method for studying cell deformation, with various applications in fields such as cell biology, biophysics, and medical research. Characterizing cell deformation offers insights into fundamental cell processes, such as migration, division, and signaling. This review summarizes recent advances in microfluidic techniques for measuring cellular deformation, including the different types of microfluidic devices and methods used to induce cell deformation. Recent applications of microfluidics-based approaches for studying cell deformation are highlighted. Compared to traditional methods, microfluidic chips can control the direction and velocity of cell flow by establishing microfluidic channels and microcolumn arrays, enabling the measurement of cell shape changes. Overall, microfluidics-based approaches provide a powerful platform for studying cell deformation. It is expected that future developments will lead to more intelligent and diverse microfluidic chips, further promoting the application of microfluidics-based methods in biomedical research, providing more effective tools for disease diagnosis, drug screening, and treatment.
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Affiliation(s)
- Ling An
- School of Engineering, Dali University, Dali, Yunnan, China
| | - Fenglong Ji
- School of Textile Materials and Engineering, Wuyi University, Jiangmen, Guangdong, China
| | - Enming Zhao
- School of Engineering, Dali University, Dali, Yunnan, China
| | - Yi Liu
- School of Engineering, Dali University, Dali, Yunnan, China
| | - Yaling Liu
- Department of Bioengineering, Lehigh University, Bethlehem, PA, United States
- Department of Mechanical Engineering and Mechanics, Lehigh University, Bethlehem, PA, United States
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13
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Zhang Y, Tan Y, Dong Y, Dai L, Ren C, Zhang F, Zeng L, An F, Li C, Huang B, Zhong G, Li J. High-Throughput Scanning Second-Harmonic-Generation Microscopy for Polar Materials. Adv Mater 2023; 35:e2300348. [PMID: 36916868 DOI: 10.1002/adma.202300348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/06/2023] [Indexed: 05/12/2023]
Abstract
The Materials Genome Initiative aims to discover, develop, manufacture, and deploy advanced materials at twice the speed of conventional approaches. To achieve this, high-throughput characterization is essential for the rapid screening of candidate materials. In this study, a high-throughput scanning second-harmonic-generation microscope with automatic partitioning, accurate positioning, and fast scanning is developed that can rapidly probe and screen polar materials. Using this technique, typical ferroelectrics, including periodically poled lithium niobate crystals and PbZr0.2 Ti0.8 O3 (PZT) thin films are first investigated, whereby the microscopic domain structures are clearly revealed. This technique is then applied to a compositional-gradient (100-x)%BaTiO3 -x%SrTiO3 film and a thickness-gradient PZT film to demonstrate its high-throughput capabilities. Since the second-harmonic-generation signal is correlated with the macroscopic remnant polarization over the probed region determined by the laser spot, it is free of artifacts arising from leakage current and electrostatic interference, while materials' symmetries and domain structures must be carefully considered in the data analysis. It is believed that this work can help promote the high-throughput development of polar materials and contribute to the Materials Genome Initiative.
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Affiliation(s)
- Yuan Zhang
- Department of Materials Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, P. R. China
- Guangdong Provincial Key Laboratory of Functional Oxide Materials and Devices, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, P. R. China
| | - Yangchun Tan
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, 518055, P. R. China
| | - Yangda Dong
- Department of Materials Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, P. R. China
- Guangdong Provincial Key Laboratory of Functional Oxide Materials and Devices, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, P. R. China
| | - Liyufen Dai
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, 518055, P. R. China
| | - Chuanlai Ren
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, 518055, P. R. China
| | - Fengyuan Zhang
- Department of Materials Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, P. R. China
- Guangdong Provincial Key Laboratory of Functional Oxide Materials and Devices, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, P. R. China
| | - Lingping Zeng
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, 518055, P. R. China
| | - Feng An
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, 518055, P. R. China
| | - Changjian Li
- Department of Materials Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, P. R. China
- Guangdong Provincial Key Laboratory of Functional Oxide Materials and Devices, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, P. R. China
| | - Boyuan Huang
- Department of Materials Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, P. R. China
- Guangdong Provincial Key Laboratory of Functional Oxide Materials and Devices, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, P. R. China
| | - Gaokuo Zhong
- Guangdong Provincial Key Laboratory of Functional Oxide Materials and Devices, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, P. R. China
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, 518055, P. R. China
| | - Jiangyu Li
- Department of Materials Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, P. R. China
- Guangdong Provincial Key Laboratory of Functional Oxide Materials and Devices, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, P. R. China
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Darwish HW, Darwish IA, Ali AM, Almutairi HS. Charge Transfer Complex of Lorlatinib with Chloranilic Acid: Characterization and Application to the Development of a Novel 96-Microwell Spectrophotometric Assay with High Throughput. Molecules 2023; 28:molecules28093852. [PMID: 37175262 PMCID: PMC10179897 DOI: 10.3390/molecules28093852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/18/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
Lorlatinib (LRL) is the first drug of the third generation of anaplastic lymphoma kinase (ALK) inhibitors used a first-line treatment of non-small cell lung cancer (NSCLC). This study describes, for the first time, the investigations for the formation of a charge transfer complex (CTC) between LRL, as electron donor, with chloranilic acid (CLA), as a π-electron acceptor. The CTC was characterized by ultraviolet (UV)-visible spectrophotometry and computational calculations. The UV-visible spectrophotometry ascertained the formation of the CTC in methanol via formation of a new broad absorption band with maximum absorption peak (λmax) at 530 nm. The molar absorptivity (ε) of the complex was 0.55 × 103 L mol-1 cm-1 and its band gap energy was 2.3465 eV. The stoichiometric ratio of LRL/CLA was found to be 1:2. The association constant of the complex was 0.40 × 103 L mol-1, and its standard free energy was -0.15 × 102 J mole-1. The computational calculation for the atomic charges of an energy minimized LRL molecule was conducted, the sites of interaction on the LRL molecule were assigned, and the mechanism of the reaction was postulated. The reaction was adopted as a basis for developing a novel 96-microwell spectrophotometric method (MW-SPA) for LRL. The assay limits of detection and quantitation were 2.1 and 6.5 µg/well, respectively. The assay was validated, and all validation parameters were acceptable. The assay was implemented successfully with great precision and accuracy to the determination of LRL in its bulk form and pharmaceutical formulation (tablets). This assay is simple, economic, and more importantly has a high-throughput property. Therefore, the assay can be valuable for routine in quality control laboratories for analysis of LRL's bulk form and pharmaceutical tablets.
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Affiliation(s)
- Hany W Darwish
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
- Department of Analytical Chemistry, Faculty of Pharmacy, Cairo University, Kasr El-Aini St., Cairo 11562, Egypt
| | - Ibrahim A Darwish
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Awadh M Ali
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Halah S Almutairi
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
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15
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Darwish IA, Darwish HW, Ali AM, Almutairi HS. Spectrophotometric Investigations of Charge Transfer Complexes of Tyrosine Kinase Inhibitors with Iodine as a σ-Electron Acceptor: Application to Development of Universal High-Throughput Microwell Assay for Their Determination in Pharmaceutical Formulations. Medicina (Kaunas) 2023; 59:medicina59040775. [PMID: 37109733 PMCID: PMC10143458 DOI: 10.3390/medicina59040775] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 04/10/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023]
Abstract
Background and Objective: Tyrosine kinase inhibitors (TKIs) are used for the treatment of different types of cancers. The current study describes, for the first time, the ultraviolet-visible spectrophotometric investigation of charge transfer complexes (CTCs) of seven TKIs, as electron donors, and iodine, as σ-electron. Materials and Methods: The formation of CTCs was promoted in dichloromethane, among the other solvents used in the investigation. The molar absorptivity values, association constants, and free energy changes of the CTCs were determined. Stoichiometric ratio of TKI: iodine as well as TKIs site(s) of interaction were addressed. Reaction was the basis for constructing a novel simple and accurate 96-microwell spectrophotometric assay (MW-SPA) with high-throughput property for the quantitative determination of TKIs in their pharmaceutical formulations. Results: Beer's law, which relates CTC absorbances to TKI concentrations, was followed within the optimal range of 2 to 100 µg/well (r ranged from 0.9991 to 0.9998). Detection and quantification limits ranged from 0.91 to 3.60 and 2.76 to 10.92 g µmL-1, respectively. Relative standard deviations values for the intra- and inter-assay precisions of the proposed MW-SPA did not exceed 2.13 and 2.34%, respectively. Studies of recovery demonstrated MW-SPA accuracy, with results ranging from 98.9% to 102.4%. All TKIs, both in bulk form and in pharmaceutical formulations (tablets), were effectively determined using the suggested MW-SPA. Conclusions: The current MW-SPA involved a simple procedure and it was convenient as it could analyse all proposed TKIs utilizing a single assay system at once measuring wavelengths for all TKIs. In addition, the proposed MW-SPA has high throughput which enables the processing of a batch of huge samples' number in very short reasonable time period. In conclusion, TKIs can be routinely analysed in their dosage forms in quality control laboratories, and the assay can be highly valuable and helpful in this regard.
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Affiliation(s)
- Ibrahim A Darwish
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Hany W Darwish
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
- Department of Analytical Chemistry, Faculty of Pharmacy, Cairo University, Kasr El-Aini St., Cairo 11562, Egypt
| | - Awadh M Ali
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Halah S Almutairi
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
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16
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Spangenberg P, Hagemann N, Squire A, Förster N, Krauß SD, Qi Y, Mohamud Yusuf A, Wang J, Grüneboom A, Kowitz L, Korste S, Totzeck M, Cibir Z, Tuz AA, Singh V, Siemes D, Struensee L, Engel DR, Ludewig P, Martins Nascentes Melo L, Helfrich I, Chen J, Gunzer M, Hermann DM, Mosig A. Rapid and fully automated blood vasculature analysis in 3D light-sheet image volumes of different organs. Cell Rep Methods 2023; 3:100436. [PMID: 37056368 PMCID: PMC10088239 DOI: 10.1016/j.crmeth.2023.100436] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 09/15/2022] [Revised: 11/25/2022] [Accepted: 03/01/2023] [Indexed: 03/19/2023]
Abstract
Light-sheet fluorescence microscopy (LSFM) can produce high-resolution tomograms of tissue vasculature with high accuracy. However, data processing and analysis is laborious due to the size of the datasets. Here, we introduce VesselExpress, an automated software that reliably analyzes six characteristic vascular network parameters including vessel diameter in LSFM data on average computing hardware. VesselExpress is ∼100 times faster than other existing vessel analysis tools, requires no user interaction, and integrates batch processing and parallelization. Employing an innovative dual Frangi filter approach, we show that obesity induces a large-scale modulation of brain vasculature in mice and that seven other major organs differ strongly in their 3D vascular makeup. Hence, VesselExpress transforms LSFM from an observational to an analytical working tool.
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Affiliation(s)
- Philippa Spangenberg
- Department of Immunodynamics, Institute for Experimental Immunology and Imaging, University Hospital Essen, Essen, Germany
- Center for Protein Diagnostics (ProDi), Ruhr-University Bochum, Bochum, Germany
| | - Nina Hagemann
- Department of Neurology, University Hospital Essen, Essen, Germany
| | - Anthony Squire
- Institute for Experimental Immunology and Imaging, University Hospital Essen, Essen, Germany
| | - Nils Förster
- Center for Protein Diagnostics (ProDi), Ruhr-University Bochum, Bochum, Germany
- Bioinformatics Group, Faculty for Biology and Biotechnology, Ruhr-University Bochum, Germany
| | - Sascha D. Krauß
- Institute for Experimental Immunology and Imaging, University Hospital Essen, Essen, Germany
| | - Yachao Qi
- Department of Neurology, University Hospital Essen, Essen, Germany
| | | | - Jing Wang
- Department of Neurology, University Hospital Essen, Essen, Germany
| | - Anika Grüneboom
- Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V., Dortmund, Germany
| | - Lennart Kowitz
- Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V., Dortmund, Germany
| | - Sebastian Korste
- Department of Cardiology and Vascular Medicine, University Hospital Essen, Essen, Germany
| | - Matthias Totzeck
- Department of Cardiology and Vascular Medicine, University Hospital Essen, Essen, Germany
| | - Zülal Cibir
- Institute for Experimental Immunology and Imaging, University Hospital Essen, Essen, Germany
| | - Ali Ata Tuz
- Institute for Experimental Immunology and Imaging, University Hospital Essen, Essen, Germany
| | - Vikramjeet Singh
- Institute for Experimental Immunology and Imaging, University Hospital Essen, Essen, Germany
| | - Devon Siemes
- Department of Immunodynamics, Institute for Experimental Immunology and Imaging, University Hospital Essen, Essen, Germany
| | - Laura Struensee
- Center for Protein Diagnostics (ProDi), Ruhr-University Bochum, Bochum, Germany
| | - Daniel R. Engel
- Department of Immunodynamics, Institute for Experimental Immunology and Imaging, University Hospital Essen, Essen, Germany
| | - Peter Ludewig
- Department of Neurology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Iris Helfrich
- Clinic of Dermatology, University Hospital Essen, Essen, Germany
| | - Jianxu Chen
- Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V., Dortmund, Germany
| | - Matthias Gunzer
- Institute for Experimental Immunology and Imaging, University Hospital Essen, Essen, Germany
- Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V., Dortmund, Germany
| | - Dirk M. Hermann
- Department of Neurology, University Hospital Essen, Essen, Germany
| | - Axel Mosig
- Center for Protein Diagnostics (ProDi), Ruhr-University Bochum, Bochum, Germany
- Bioinformatics Group, Faculty for Biology and Biotechnology, Ruhr-University Bochum, Germany
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17
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Darwish IA, Darwish HW, Alzoman NZ, Ali AM. One-Step Microwell Plate-Based Spectrofluorimetric Assay for Direct Determination of Statins in Bulk Forms and Pharmaceutical Formulations: A Green Eco-Friendly and High-Throughput Analytical Approach. Molecules 2023; 28:molecules28062808. [PMID: 36985779 PMCID: PMC10051747 DOI: 10.3390/molecules28062808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/14/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
This study describes the development of a one-step microwell spectrofluorimetric assay (MW-SFA) with high sensitivity and throughput for the determination of four statins in their pharmaceutical and formulations (tablets). These statins were pitavastatin (PIT), fluvastatin (FLU), rosuvastatin (ROS) and atorvastatin (ATO). The MW-SFA involves the measurement of the native fluorescence of the statin aqueous solutions. The assay was conducted in white opaque 96-microwell plates, and the fluorescence intensities of the solutions were measured by using a fluorescence microplate reader. The optimum conditions of the assay were established; under which, linear relationships with good correlation coefficients (0.9991-0.9996) were found between the fluorescence intensity and the concentration of the statin drug in a range of 0.2-200 µg mL-1 with limits of detection in a range of 0.1-4.1 µg mL-1. The proposed MW-SFA showed high precision, as the values of the relative standard deviations did not exceed 2.5%. The accuracy of the assay was proven by recovery studies, as the recovery values were 99.5-101.4% (±1.4-2.1%). The assay was applied to the determination of the investigated statins in their tablets. The results were statistically compared with those obtained by a reference method and the results proved to have comparable accuracy and precision of both methods, as evidenced by the t- and F-tests, respectively. The green and eco-friendly feature of the proposed assay was assessed by four different metric tools, and all the results proved that the assay meets the requirements of green and eco-friendly analytical approaches. In addition, ever-increasing miniaturization as handling of large numbers of micro-volume samples simultaneously in the proposed assay gave it a high-throughput feature. Therefore, the assay is a valuable tool for the rapid routine application in the pharmaceutical quality control units for the determination of statins.
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Affiliation(s)
- Ibrahim A Darwish
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Hany W Darwish
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Nourah Z Alzoman
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Awadh M Ali
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
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18
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Boogaerts T, Quireyns M, Maes F, Laimou-Geraniou M, Van Wichelen N, Heath E, Pussig B, Aertgeerts B, Covaci A, van Nuijs ALN. Optimization, validation and application of a high-throughput 96-well elution protocol for the quantification of psychoactive substances in influent wastewater. Drug Test Anal 2023; 15:240-246. [PMID: 36260405 DOI: 10.1002/dta.3392] [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] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/06/2022] [Accepted: 10/17/2022] [Indexed: 11/11/2022]
Abstract
Wastewater-based epidemiology (WBE) is based on the analysis of human metabolic excretion products (biomarkers) of xenobiotics in wastewater, to gain information about various lifestyles and health aspects of a population in an evidence-based manner. Due to the complex wastewater matrix and trace level occurrence of human biomarkers in the sewage network, it is crucial to have sensitive analytical procedures available. Additionally, to improve the value of WBE as a complementary epidemiological source, there is increasing pressure on the analysis of more compounds, more locations and more samples. A high-throughput method based on 96-well Oasis MCX solid-phase extraction (SPE), requiring less influent wastewater (2 mL), was developed in accordance with the European Medicines Agency guidelines. Validation was successful for 28 parent drugs and metabolites of antidepressants, opioids and drugs of abuse. The selection of biomarkers and quantification limit was chosen to be relevant for WBE and was predominantly 10 ng/L or below. The final method was successfully applied to 24-h composite samples of October 2019 (n = 27), obtained from an urban wastewater treatment plant in Leuven (Belgium).
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Affiliation(s)
- Tim Boogaerts
- Toxicological Centre, University of Antwerp, Wilrijk, Belgium
| | | | - Florence Maes
- Toxicological Centre, University of Antwerp, Wilrijk, Belgium
| | - Maria Laimou-Geraniou
- Department of Environmental Sciences, Jožef Stefan Institute, Ljubljana, Slovenia.,Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
| | | | - Ester Heath
- Department of Environmental Sciences, Jožef Stefan Institute, Ljubljana, Slovenia.,Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
| | - Bram Pussig
- Academic Centre for General Practice, KU Leuven, Leuven, Belgium
| | - Bert Aertgeerts
- Academic Centre for General Practice, KU Leuven, Leuven, Belgium
| | - Adrian Covaci
- Toxicological Centre, University of Antwerp, Wilrijk, Belgium
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Wei H, Li X. Deep mutational scanning: A versatile tool in systematically mapping genotypes to phenotypes. Front Genet 2023; 14:1087267. [PMID: 36713072 PMCID: PMC9878224 DOI: 10.3389/fgene.2023.1087267] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [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: 11/02/2022] [Accepted: 01/02/2023] [Indexed: 01/13/2023] Open
Abstract
Unveiling how genetic variations lead to phenotypic variations is one of the key questions in evolutionary biology, genetics, and biomedical research. Deep mutational scanning (DMS) technology has allowed the mapping of tens of thousands of genetic variations to phenotypic variations efficiently and economically. Since its first systematic introduction about a decade ago, we have witnessed the use of deep mutational scanning in many research areas leading to scientific breakthroughs. Also, the methods in each step of deep mutational scanning have become much more versatile thanks to the oligo-synthesizing technology, high-throughput phenotyping methods and deep sequencing technology. However, each specific possible step of deep mutational scanning has its pros and cons, and some limitations still await further technological development. Here, we discuss recent scientific accomplishments achieved through the deep mutational scanning and describe widely used methods in each step of deep mutational scanning. We also compare these different methods and analyze their advantages and disadvantages, providing insight into how to design a deep mutational scanning study that best suits the aims of the readers' projects.
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Affiliation(s)
- Huijin Wei
- Zhejiang University—University of Edinburgh Institute, Zhejiang University, Haining, Zhejiang, China
| | - Xianghua Li
- Zhejiang University—University of Edinburgh Institute, Zhejiang University, Haining, Zhejiang, China,Deanery of Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom,The Second Affiliated Hospital of Zhejiang University, Hangzhou, Zhejiang, China,Biomedical and Health Translational Centre of Zhejiang Province, Haining, Zhejiang, China,*Correspondence: Xianghua Li,
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20
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Amin M, Sharif S, Akram S, Muhammad G, Amin S, Ashraf R, Mushtaq M. A dispersive liquid-liquid microextraction followed by reverse-phase high-performance liquid chromatography for QuEChERS determination of chlorogenic acid. Phytochem Anal 2023; 34:30-39. [PMID: 36151736 DOI: 10.1002/pca.3174] [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] [Received: 08/05/2022] [Revised: 08/30/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
INTRODUCTION The presence of chlorogenic acid (CGA) not only imparts a characteristic flavour to foods but also makes them useful against chronic diseases and metabolic syndromes, especially diabetes mellitus and asthma. OBJECTIVES The present study was designed to develop a quick, easy, cheap, effective, rugged, and safe (QuEChERS) and pragmatic method to analyse CGA in plant-based products by applying dispersive liquid-liquid microextraction (DLLME) followed by reverse-phase high-performance liquid chromatography under a diode array detector (RP-HPLC-DAD). METHODOLOGY The DLLME was carried out using Triton X-100 as a dispersant and ethanol as an extraction solvent, while method development and validation activities were performed on a Shimadzu 10-AT HPLC-DAD system equipped with C-18 columns as stationary phases. RESULTS The well-resolved peak for the standard CGA was observed at 2.92 min for the mobile phase comprising 0.1% aqueous formic acid-ethanol (22:78 v/v) of pH 3.0 programmed under an isocratic flow rate of 1.0 mL/min. The developed method was found to be linear (R2 = 0.9976) over 1-500 μg/mL of CGA concentration at 328 nm. Moreover, the assay was found to be repeatable with RSD ≤ 5.0, and the limit of detection (LOD) and limit of quantification (LOQ) were 0.0281 and 0.0853 μg/mL of CGA, respectively. The DLLME offered an overall recovery rate between 97.60% and 99.54% at an acceptable level of reproducibility [relative standard deviation (RSD) ≤ 5.0]. CONCLUSION The developed assay was found to be a QuEChERS and pragmatic choice for the high-throughput analysis of CGA in plant-based products/foods. Finally, the analysis revealed the presence of an ample level of CGA in guava fruit in addition to coffee beans and black tea.
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Affiliation(s)
- Mujahid Amin
- Department of Chemistry, Government College University, Lahore, Pakistan
| | - Shahzad Sharif
- Department of Chemistry, Government College University, Lahore, Pakistan
| | - Sumia Akram
- Division of Science and Technology, University of Education, Lahore, Pakistan
| | - Gulzar Muhammad
- Department of Chemistry, Government College University, Lahore, Pakistan
| | - Saqib Amin
- Department of Statistics, University of Oulu, Oulu, Finland
| | - Rizwan Ashraf
- Department of Chemistry, University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Mushtaq
- Department of Chemistry, Government College University, Lahore, Pakistan
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Okagawa T, Shimakura H, Konnai S, Saito M, Matsudaira T, Nao N, Yamada S, Murakami K, Maekawa N, Murata S, Ohashi K. Diagnosis and Early Prediction of Lymphoma Using High-Throughput Clonality Analysis of Bovine Leukemia Virus-Infected Cells. Microbiol Spectr 2022; 10:e0259522. [PMID: 36227090 DOI: 10.1128/spectrum.02595-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Bovine leukemia virus (BLV), a retrovirus, infects B cells of ruminants and is integrated into the host genome as a provirus for lifelong infection. After a long latent period, 1% to 5% of BLV-infected cattle develop aggressive lymphoma, enzootic bovine leukosis (EBL). Since the clonal expansion of BLV-infected cells is essential for the development of EBL, the clonality of proviral integration sites could be a molecular marker for diagnosis and early prediction of EBL. Recently, we developed Rapid Amplification of the Integration Site without Interference by Genomic DNA Contamination (RAISING) and an analysis software of clonality value (CLOVA) to analyze the clonality of transgene-integrated cells. RAISING-CLOVA is capable of assessing the risk of adult T-cell leukemia/lymphoma development in human T-cell leukemia virus-I-infected individuals through the clonality analysis of proviral integration sites. Thus, we herein examined the performance of RAISING-CLOVA for the clonality analysis of BLV-infected cells and conducted a comprehensive clonality analysis by RAISING-CLOVA in EBL and non-EBL cattle. RAISING-CLOVA targeting BLV was a highly accurate and reproducible method for measuring the clonality value. The comprehensive clonality analysis successfully distinguished EBL from non-EBL specimens with high sensitivity and specificity. A longitudinal clonality analysis in BLV-infected sheep, an experimental model of lymphoma, also confirmed the effectiveness of RAISING-CLOVA for early detection of EBL development. Therefore, our study emphasizes the usefulness of RAISING-CLOVA as a routine clinical test for monitoring virus-related cancers. IMPORTANCE Bovine leukemia virus (BLV) infection causes aggressive B-cell lymphoma in cattle and sheep. The virus has spread to farms around the world, causing significant economic damage to the livestock industry. Thus, the identification of high-risk asymptomatic cattle before they develop lymphoma can be effective in reducing the economic damage. Clonal expansion of BLV-infected cells is a promising marker for the development of lymphoma. Recently, we have developed a high-throughput method to amplify random integration sites of transgenes in host genomes and analyze their clonality, named as RAISING-CLOVA. As a new application of our technology, in this study, we demonstrate the value of the RAISING-CLOVA method for the diagnosis and early prediction of lymphoma development by BLV infection in cattle. RAISING-CLOVA is a reliable technology for monitoring the clonality of BLV-infected cells and would contribute to reduce the economic losses by EBL development.
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Wei W, Liu S, Han Y, Lu S, Yan G, Sun H, Wang X. Rapid identification of chemical components in Zhizi Baipi decoction by ultra performance liquid chromatography quadrupole time-of-flight mass spectrometry coupled with a novel informatics UNIFI platform. J Sep Sci 2022; 45:3679-3690. [PMID: 35943222 DOI: 10.1002/jssc.202200306] [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] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/14/2022] [Accepted: 07/25/2022] [Indexed: 11/10/2022]
Abstract
Zhizi Baipi Decoction is a classic traditional Chinese medicine formula for the treatment of jaundice and various liver diseases. The chemical components of Zhizi baipi decoction were not clear resulting from the paucity of relevant studies, which hindered the elucidation of the pharmacological mechanism, the comprehensive development and utilization of Zhizi baipi decoction in clinical. In this study, ultra performance liquid chromatography-quadrupole-time of flight mass spectrometry combined with UNIFI natural product information analysis platform was used to rapidly analyze and identify the chemical components in Zhizi baipi decoction. A total of 122 chemical components, including 53 flavonoids, 16 alkaloids, 25 terpenoids, 5 phenylpropanoids, 14 organic acids, and 7 others, were identified from Zhizi baipi decoction. These compounds may be the active components of Zhizi baipi decoction. The method established in this study can systematically, rapidly, and accurately resolve the chemical components in Zhizi baipi decoction, which lays the foundation for further establishment of the pharmacodynamic substance basis and quality control of Zhizi baipi decoction. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Wenfeng Wei
- National Chinmedomics Research Center, National TCM Key Laboratory of Serum Pharmacochemistry, Metabolomics Laboratory, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine, Heping Road 24, Harbin, 150040, China
| | - Shaobo Liu
- National Chinmedomics Research Center, National TCM Key Laboratory of Serum Pharmacochemistry, Metabolomics Laboratory, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine, Heping Road 24, Harbin, 150040, China
| | - Ying Han
- National Chinmedomics Research Center, National TCM Key Laboratory of Serum Pharmacochemistry, Metabolomics Laboratory, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine, Heping Road 24, Harbin, 150040, China
| | - Shengwen Lu
- National Chinmedomics Research Center, National TCM Key Laboratory of Serum Pharmacochemistry, Metabolomics Laboratory, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine, Heping Road 24, Harbin, 150040, China
| | - Guangli Yan
- National Chinmedomics Research Center, National TCM Key Laboratory of Serum Pharmacochemistry, Metabolomics Laboratory, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine, Heping Road 24, Harbin, 150040, China
| | - Hui Sun
- National Chinmedomics Research Center, National TCM Key Laboratory of Serum Pharmacochemistry, Metabolomics Laboratory, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine, Heping Road 24, Harbin, 150040, China
| | - Xijun Wang
- National Chinmedomics Research Center, National TCM Key Laboratory of Serum Pharmacochemistry, Metabolomics Laboratory, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine, Heping Road 24, Harbin, 150040, China.,State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau
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23
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Li J, Liu J, Wan Y, Wang J, Pi F. Routine analysis of pesticides in foodstuffs: Emerging ambient ionization mass spectrometry as an alternative strategy to be on your radar. Crit Rev Food Sci Nutr 2022; 63:7341-7356. [PMID: 35229702 DOI: 10.1080/10408398.2022.2045561] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Pesticides residues in foodstuffs are longstanding of great concern to consumers and governments, thus reliable evaluation techniques for these residues are necessary to ensure food safety. Emerging ambient ionization mass spectrometry (AIMS), a transformative technology in the field of analytical chemistry, is becoming a promising and solid evaluation technology due to its advantages of direct, real-time and in-situ ionization on samples without complex pretreatments. To provide useful guidance on the evaluation techniques in the field of food safety, we offered a comprehensive review on the AIMS technology and introduced their novel applications for the analysis of residual pesticides in foodstuffs under different testing scenarios (i.e., quantitative, screening, imaging, high-throughput detection and rapid on-site analysis). Meanwhile, the creative combination of AIMS with high-resolution mass analyzer (e.g., orbitrap and time-of-flight) was fundamentally mentioned based on recent studies about the detection and evaluation of multi-residual pesticides between 2015 and 2021. Finally, the technical challenges and prospects associated with AIMS operation in food industry were discussed.
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Affiliation(s)
- Jingkun Li
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, People's Republic of China
| | - Jinghan Liu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, People's Republic of China
| | - Yuqi Wan
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, People's Republic of China
| | - Jiahua Wang
- College of Food Science and Engineering, Wuhan Polytechnic University, Wuhan, People's Republic of China
| | - Fuwei Pi
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, People's Republic of China
- College of Food Science and Engineering, Wuhan Polytechnic University, Wuhan, People's Republic of China
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24
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Zorić L, Drinković N, Micek V, Frkanec L, Türeli AE, Günday-Türeli N, Vinković Vrček I, Frkanec R. High-Throughput Method for the Simultaneous Determination of Doxorubicin Metabolites in Rat Urine after Treatment with Different Drug Nanoformulations. Molecules 2022; 27:1177. [PMID: 35208967 DOI: 10.3390/molecules27041177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/28/2022] [Accepted: 02/06/2022] [Indexed: 11/23/2022]
Abstract
Doxorubicin (DOX) is one of the most effective cytotoxic agents against malignant diseases. However, the clinical application of DOX is limited, due to dose-related toxicity. The development of DOX nanoformulations that significantly reduce its toxicity and affect the metabolic pathway of the drug requires improved methods for the quantitative determination of DOX metabolites with high specificity and sensitivity. This study aimed to develop a high-throughput method based on high-performance liquid chromatography with fluorescence detection (HPLC-FD) for the quantification of DOX and its metabolites in the urine of laboratory animals after treatment with different DOX nanoformulations. The developed method was validated by examining its specificity and selectivity, linearity, accuracy, precision, limit of detection, and limit of quantification. The DOX and its metabolites, doxorubicinol (DOXol) and doxorubicinone (DOXon), were successfully separated and quantified using idarubicin (IDA) as an internal standard (IS). The linearity was obtained over a concentration range of 0.05–1.6 μg/mL. The lowest limit of detection and limit of quantitation were obtained for DOXon at 5.0 ng/mL and 15.0 ng/mL, respectively. For each level of quality control (QC) samples, the inter- and intra-assay precision was less than 5%. The accuracy was in the range of 95.08–104.69%, indicating acceptable accuracy and precision of the developed method. The method was applied to the quantitative determination of DOX and its metabolites in the urine of rats treated by novel nanoformulated poly(lactic-co-glycolic acid) (DOX-PLGA), and compared with a commercially available DOX solution for injection (DOX-IN) and liposomal-DOX (DOX-MY).
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25
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Harman-Ware AE, Happs RM, Macaya-Sanz D, Doeppke C, Muchero W, DiFazio SP. Abundance of Major Cell Wall Components in Natural Variants and Pedigrees of Populus trichocarpa. Front Plant Sci 2022; 13:757810. [PMID: 35185975 PMCID: PMC8850957 DOI: 10.3389/fpls.2022.757810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 01/04/2022] [Indexed: 06/14/2023]
Abstract
The rapid analysis of biopolymers including lignin and sugars in lignocellulosic biomass cell walls is essential for the analysis of the large sample populations needed for identifying heritable genetic variation in biomass feedstocks for biofuels and bioproducts. In this study, we reported the analysis of cell wall lignin content, syringyl/guaiacyl (S/G) ratio, as well as glucose and xylose content by high-throughput pyrolysis-molecular beam mass spectrometry (py-MBMS) for >3,600 samples derived from hundreds of accessions of Populus trichocarpa from natural populations, as well as pedigrees constructed from 14 parents (7 × 7). Partial Least Squares (PLS) regression models were built from the samples of known sugar composition previously determined by hydrolysis followed by nuclear magnetic resonance (NMR) analysis. Key spectral features positively correlated with glucose content consisted of m/z 126, 98, and 69, among others, deriving from pyrolyzates such as hydroxymethylfurfural, maltol, and other sugar-derived species. Xylose content positively correlated primarily with many lignin-derived ions and to a lesser degree with m/z 114, deriving from a lactone produced from xylose pyrolysis. Models were capable of predicting glucose and xylose contents with an average error of less than 4%, and accuracy was significantly improved over previously used methods. The differences in the models constructed from the two sample sets varied in training sample number, but the genetic and compositional uniformity of the pedigree set could be a potential driver in the slightly better performance of that model in comparison with the natural variants. Broad-sense heritability of glucose and xylose composition using these data was 0.32 and 0.34, respectively. In summary, we have demonstrated the use of a single high-throughput method to predict sugar and lignin composition in thousands of poplar samples to estimate the heritability and phenotypic plasticity of traits necessary to develop optimized feedstocks for bioenergy applications.
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Affiliation(s)
- Anne E. Harman-Ware
- Renewable Resources and Enabling Sciences Center, Center for Bioenergy Innovation, National Renewable Energy Laboratory, Golden, CO, United States
| | - Renee M. Happs
- Renewable Resources and Enabling Sciences Center, Center for Bioenergy Innovation, National Renewable Energy Laboratory, Golden, CO, United States
| | - David Macaya-Sanz
- Department of Forest Ecology and Genetics, INIA-CIFOR, Madrid, Spain
- Department of Biology, West Virginia University, Morgantown, WV, United States
| | - Crissa Doeppke
- Renewable Resources and Enabling Sciences Center, Center for Bioenergy Innovation, National Renewable Energy Laboratory, Golden, CO, United States
| | - Wellington Muchero
- Biosciences Division, Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Stephen P. DiFazio
- Department of Biology, West Virginia University, Morgantown, WV, United States
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26
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Du XJ, Chen Y, Qin LY, Luo HQ, Li NB, Li BL. Plasmonic Gold Nanoparticles Stain Hydrogels for the Portable and High-Throughput Monitoring of Mercury Ions. Environ Sci Technol 2022; 56:1041-1052. [PMID: 34964603 DOI: 10.1021/acs.est.1c07217] [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] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The hybrid of l-cysteine and agarose can reduce HAuCl4 and support the rapid growth of plasmonic gold nanoparticles (Au NPs) in the hydrogel phase. The l-cysteine-doped agarose hydrogel (C-AGH) not only offers the substrate the capacity to reduce Au(III) ions but also stabilizes and precisely modulates the in situ grown Au NPs with high repeatability, easy operation, and anti-interference performance. Herein, before the incubation of HAuCl4, the improved hydrogel is preincubated in the aqueous solution containing mercury ions, and the cysteine can specifically conjugate with mercury via the thiol groups. Subsequently, the responsive allochroic bands from dark blue to red can be identified in the solid hydrogel after the incubation of HAuCl4, which is attributed to the formation of regulated Au-Hg nanoamalgams. As a proof-of-concept, toxic Hg2+ ions are exploited as targets for constructing novel sensing assays based on the improved C-AGH protocol. Based on naked-eye recognition, Hg2+ could be rapidly and simply measured. Additionally, the high-throughput and trace analysis with a low limit of detection (3.7 nM) is performed using a microplate reader. On the basis of the filtering technique and remodeling of hydrogels, C-AGH working as the filtering membrane can even achieve the integration of enrichment and measurement with enhanced sensitivity. Significantly, the strategy of using an allochroic hydrogel with the staining of Au NPs can promote the rapid and primary assessment of water quality in environmental analysis.
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Affiliation(s)
- Xiao Juan Du
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Yang Chen
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
- School of Architecture and Urban Planning, Chongqing University, Chongqing 400030, P. R. China
| | - Ling Yun Qin
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Hong Qun Luo
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Nian Bing Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Bang Lin Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
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27
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Li T, Zhang M, Tan Z, Miao J, He Y, Zhang A, Ou M, Huang D, Wu F, Wang X. Rapid characterization of the constituents in Jigucao capsule using ultra high performance liquid chromatography with quadrupole time-of-flight mass spectrometry. J Sep Sci 2021; 45:677-696. [PMID: 34822724 DOI: 10.1002/jssc.202100664] [Citation(s) in RCA: 6] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 11/09/2021] [Accepted: 11/18/2021] [Indexed: 12/12/2022]
Abstract
Jigucao capsule is a well-known Chinese patent medicine for the treatment of acute and chronic hepatitis and cholecystitis. The chemical components of Jigucao capsule were not clear resulting from the paucity of relevant studies, which hindered the research of the pharmacological mechanism, the comprehensive development, and utilization of Jigucao capsule in clinical studies. By establishing a high-throughput ultra-performance liquid chromatography quadrupole time of flight mass spectrometry in combination with intelligent UNIFI software data processing platform to automatically characterize and identify the chemical profile of Jigucao capsule, 144 compounds were determined rapidly, including 34 terpenoids, 25 flavonoids, 22 steroids, 21 phenylpropanoids, 10 glycosides, six alkaloids, 13 organic acids, and other 13 components. These compounds may be the active components of Jigucao capsule. In this study, a rapid and robust method for comprehensively analyzing the chemical composition of Jigucao capsule was described and established for the first time. The results will provide a reference for the quality control of Jigucao capsule and the establishment of a higher quality standard, as well as for the pharmacodynamic material basis research.
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Affiliation(s)
- Taiping Li
- National Engineering Laboratory for the Development of Southwestern Endangered, Medicinal Materials, Guangxi Botanical Garden of Medicinal Plants, Nanning, P. R. China.,National Chinmedomics Research Center, National TCM Key Laboratory of Serum Pharmacochemistry, Chinmedomics Research Center of State Administration of TCM, Laboratory of Metabolomics, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine, Harbin, P. R. China
| | - Mengli Zhang
- National Engineering Laboratory for the Development of Southwestern Endangered, Medicinal Materials, Guangxi Botanical Garden of Medicinal Plants, Nanning, P. R. China
| | - Zhien Tan
- National Engineering Laboratory for the Development of Southwestern Endangered, Medicinal Materials, Guangxi Botanical Garden of Medicinal Plants, Nanning, P. R. China
| | - Jianhua Miao
- National Engineering Laboratory for the Development of Southwestern Endangered, Medicinal Materials, Guangxi Botanical Garden of Medicinal Plants, Nanning, P. R. China
| | - Yanmei He
- National Chinmedomics Research Center, National TCM Key Laboratory of Serum Pharmacochemistry, Chinmedomics Research Center of State Administration of TCM, Laboratory of Metabolomics, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine, Harbin, P. R. China
| | - Aihua Zhang
- National Chinmedomics Research Center, National TCM Key Laboratory of Serum Pharmacochemistry, Chinmedomics Research Center of State Administration of TCM, Laboratory of Metabolomics, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine, Harbin, P. R. China
| | - Min Ou
- National Engineering Laboratory for the Development of Southwestern Endangered, Medicinal Materials, Guangxi Botanical Garden of Medicinal Plants, Nanning, P. R. China
| | - Danna Huang
- National Engineering Laboratory for the Development of Southwestern Endangered, Medicinal Materials, Guangxi Botanical Garden of Medicinal Plants, Nanning, P. R. China
| | - Fangfang Wu
- National Engineering Laboratory for the Development of Southwestern Endangered, Medicinal Materials, Guangxi Botanical Garden of Medicinal Plants, Nanning, P. R. China
| | - Xijun Wang
- National Engineering Laboratory for the Development of Southwestern Endangered, Medicinal Materials, Guangxi Botanical Garden of Medicinal Plants, Nanning, P. R. China.,National Chinmedomics Research Center, National TCM Key Laboratory of Serum Pharmacochemistry, Chinmedomics Research Center of State Administration of TCM, Laboratory of Metabolomics, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine, Harbin, P. R. China
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28
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Guo Y, Forbush M, Covey TR, Ghislain L, Liu C. High-Throughput Analysis from Complex Matrices: Acoustic Ejection Mass Spectrometry from Phase-Separated Fluid Samples. Metabolites 2021; 11:789. [PMID: 34822447 DOI: 10.3390/metabo11110789] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 11/17/2021] [Accepted: 11/17/2021] [Indexed: 11/17/2022] Open
Abstract
Acoustic ejection mass spectrometry is a novel high-throughput analytical technology that delivers high reproducibility without carryover observed. It eliminates the chromatography step used to separate analytes from matrix components. Fully-automated liquid–liquid extraction is widely used for sample cleanup, especially in high-throughput applications. We introduce a workflow for direct AEMS analysis from phase-separated liquid samples and explore high-throughput analysis from complex matrices. We demonstrate the quantitative determination of fentanyl from urine using this two-phase AEMS approach, with a LOD lower than 1 ng/mL, quantitation precision of 15%, and accuracy better than ±10% over the range of evaluation (1–100 ng/mL). This workflow offers simplified sample preparation and higher analytical throughput for some bioanalytical applications, in comparison to an LC-MS based approach.
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29
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Wilson JL, Wong M, Stepanov N, Petkovic D, Altman R. PhenClust, a standalone tool for identifying trends within sets of biological phenotypes using semantic similarity and the Unified Medical Language System metathesaurus. JAMIA Open 2021; 4:ooab079. [PMID: 34541463 PMCID: PMC8442701 DOI: 10.1093/jamiaopen/ooab079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 05/07/2021] [Revised: 08/12/2021] [Accepted: 09/02/2021] [Indexed: 11/13/2022] Open
Abstract
Objectives We sought to cluster biological phenotypes using semantic similarity and create an easy-to-install, stable, and reproducible tool. Materials and Methods We generated Phenotype Clustering (PhenClust)—a novel application of semantic similarity for interpreting biological phenotype associations—using the Unified Medical Language System (UMLS) metathesaurus, demonstrated the tool’s application, and developed Docker containers with stable installations of two UMLS versions. Results PhenClust identified disease clusters for drug network-associated phenotypes and a meta-analysis of drug target candidates. The Dockerized containers eliminated the requirement that the user install the UMLS metathesaurus. Discussion Clustering phenotypes summarized all phenotypes associated with a drug network and two drug candidates. Docker containers can support dissemination and reproducibility of tools that are otherwise limited due to insufficient software support. Conclusion PhenClust can improve interpretation of high-throughput biological analyses where many phenotypes are associated with a query and the Dockerized PhenClust achieved our objective of decreasing installation complexity.
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Affiliation(s)
- Jennifer L Wilson
- Department of Chemical and Systems Biology, Stanford University, Stanford, California, USA
| | - Mike Wong
- CoSE Computing for Life Science, San Francisco State University, San Francisco, California, USA
| | - Nicholas Stepanov
- Department of Computer Science, San Francisco State University, San Francisco, California, USA
| | - Dragutin Petkovic
- CoSE Computing for Life Science, San Francisco State University, San Francisco, California, USA.,Department of Computer Science, San Francisco State University, San Francisco, California, USA
| | - Russ Altman
- Department of Bioengineering, Stanford University, Stanford, California, USA.,Department of Genetics, Stanford University, Stanford, California, USA
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30
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Qi Y, Xin M, Zhang Y, Hao Y, Liu Q, Wang P, Guo Q. TTSurv: Exploring the Multi-Gene Prognosis in Thousands of Tumors. Front Oncol 2021; 11:691310. [PMID: 34113575 PMCID: PMC8186665 DOI: 10.3389/fonc.2021.691310] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 05/06/2021] [Indexed: 12/21/2022] Open
Abstract
Thoracic malignancies are a common type of cancer and area major global health problem. These complex diseases, including lung cancer, esophageal cancer, and breast cancer, etc. have attracted considerable attention from researchers. Potential gene-cancer associations can be explored by demonstrating the association between clinical data and gene expression data. Emerging evidence suggests that the transcriptome plays a particularly critical role as a diagnostic biomarker in pathology and histology studies. Thus, there is an urgent need to develop a platform that allows users to perform a comprehensive prognostic analysis of thoracic cancers. Here, we developed TTSurv, which aims to correlate coding and noncoding genes with cancers by combining high-throughput data with clinical prognosis. TTSurv focuses on the application of high-throughput data to detect ncRNAs, such as lncRNAs and microRNAs, as novel diagnostic and prognostic biomarkers. For a more comprehensive analysis, a large amount of public expression profile data with clinical follow-up information have been integrated into TTSurv. TTSurv also provides flexible methods such as a minimum p-value algorithm and unsupervised clustering methods that can classify thoracic cancer samples into different risk groups. TTSurv will expand our understanding of ncRNAs in thoracic malignancies and provide new insights into their application as potential prognostic/diagnostic biomarkers.
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Affiliation(s)
- Yue Qi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Mengyu Xin
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yuanfu Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yangyang Hao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Qian Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Peng Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Qiuyan Guo
- Department of Gynecology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
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31
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Nguyen TX, Su YH, Hattrick-Simpers J, Joress H, Nagata T, Chang KS, Sarker S, Mehta A, Ting JM. Exploring the First High-Entropy Thin Film Libraries: Composition Spread-Controlled Crystalline Structure. ACS Comb Sci 2020; 22:858-866. [PMID: 33146510 PMCID: PMC8415495 DOI: 10.1021/acscombsci.0c00159] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Thin films of two types of high-entropy oxides (HEOs) have been deposited on 76.2 mm Si wafers using combinatorial sputter deposition. In one type of the oxides, (MgZnMnCoNi)Ox, all the metals have a stable divalent oxidation state and similar cationic radii. In the second type of oxides, (CrFeMnCoNi)Ox, the metals are more diverse in the atomic radius and valence state, and have good solubility in their sub-binary and ternary oxide systems. The resulting HEO thin films were characterized using several high-throughput analytical techniques. The microstructure, composition, and electrical conductivity obtained on defined grid maps were obtained for the first time across large compositional ranges. The crystalline structure of the films was observed as a function of the metallic elements in the composition spreads, that is, the Mn and Zn in (MgZnMnCoNi)Ox and Mn and Ni in (CrFeMnCoNi)Ox. The (MgZnMnCoNi)Ox sample was observed to form two-phase structures, except single spinel structure was found in (MgZnMnCoNi)Ox over a range of Mn > 12 at. % and Zn < 44 at. %, while (CrFeMnCoNi)Ox was always observed to form two-phase structures. Composition-controlled crystalline structure is not only experimentally demonstrated but also supported by density function theory calculation.
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Affiliation(s)
- Thi Xuyen Nguyen
- Department of Materials Science and Engineering, National Cheng Kung University, Tainan 70101, Taiwan
| | - Yen-Hsun Su
- Department of Materials Science and Engineering, National Cheng Kung University, Tainan 70101, Taiwan
| | - Jason Hattrick-Simpers
- Materials Measurement Science Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Howie Joress
- Materials Measurement Science Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Takahiro Nagata
- Research Center for Functional Materials, National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
| | - Kao-Shuo Chang
- Department of Materials Science and Engineering, National Cheng Kung University, Tainan 70101, Taiwan
| | - Suchismita Sarker
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Apurva Mehta
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Jyh-Ming Ting
- Department of Materials Science and Engineering, National Cheng Kung University, Tainan 70101, Taiwan
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Holt CA, Cottyn B, Baumberger S, Kovacs-Schreiner K, Blacker AJ. High-Throughput Analysis of Lignin by Agarose Gel Electrophoresis. J Agric Food Chem 2020; 68:14297-14306. [PMID: 33200936 DOI: 10.1021/acs.jafc.0c06308] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 06/11/2023]
Abstract
A high-throughput agarose gel electrophoresis (AGE) analytical method has been developed to separate lignin fractions according to their molecular weight (Mw), charge, and shape. Operating conditions to effect separation of species have been evaluated along with imaging parameters. Kraft, soda (Protobind), and Organosolv lignins showed distinct differences in migration. Bands were cut, extracted, and cross-analyzed by gel permeation chromatography (GPC), 1H NMR, and pyrolysis GC/MS to confirm their identity as lignin. The band intensity was correlated with lignin concentration by running serially diluted samples and imaging each lane to produce a precise calibration curve. The AGE technique was used to monitor and compare enzymatic, bacterial, chemical, and hydrothermal lignin digestions. Each method showed changes in lignin migration and band intensities over time. Low Mw species were seen in samples collected from the anode buffer tank. Though requiring further development, the AGE method can provide structural information about the lignin and is accessible to biological and chemistry laboratories.
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Affiliation(s)
- Christopher A Holt
- Institute of Process Research and Development, School of Chemistry and School of Chemical and Process Engineering, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom
| | - Betty Cottyn
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles 78000, France
| | - Stephanie Baumberger
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles 78000, France
| | | | - A John Blacker
- Institute of Process Research and Development, School of Chemistry and School of Chemical and Process Engineering, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom
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Sobolevsky T, Ahrens B. High-throughput liquid chromatography tandem mass spectrometry assay as initial testing procedure for analysis of total urinary fraction. Drug Test Anal 2020; 13:283-298. [PMID: 32852861 DOI: 10.1002/dta.2917] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/16/2020] [Accepted: 08/17/2020] [Indexed: 12/14/2022]
Abstract
In the recent years, a lot of effort was put into the development of multiclass initial testing procedures (ITP) to streamline analytical workflow in antidoping laboratories. Here, a high-throughput assay based on liquid chromatography-triple quadrupole mass spectrometry suitable for use as initial testing procedure covering multiple classes of compounds prohibited in sports is described. Employing a 96-well plate packed with 10 mg of weak cation exchange polymeric sorbent, up to 94 urine samples and their associated positive and negative controls can be processed in less than 3 h with minimal labor. The assay requires a 0.5-ml urine aliquot, which is subjected to enzymatic hydrolysis followed by solid phase extraction, evaporation, and reconstitution in a 96-well collection plate. With a 10-min run time, more than 100 analytes can be detected using electrospray ionization with polarity switching. The assay can be run nearly 24/7 with minimal downtime for instrument maintenance while detecting picogram amounts for the majority of analytes. Having analyzed approximately 28,000 samples, nearly 400 adverse analytical findings were found of which only one tenth were at or above 50% of the minimum required performance level established by the World Anti-Doping Agency. Compounds most often identified were stanozolol, GW1516, ostarine, LGD4033, and clomiphene, with median estimated concentrations in the range of 0.02-0.09 ng/ml (either as parent drug or a metabolite). Our data demonstrate the importance of using a highly sensitive ITP to ensure efficient antidoping testing.
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Affiliation(s)
- Tim Sobolevsky
- UCLA Olympic Analytical Laboratory, Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, Los Angeles, California, USA
| | - Brian Ahrens
- UCLA Olympic Analytical Laboratory, Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, Los Angeles, California, USA
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34
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Gallagher MT, Cupples G, Ooi EH, Kirkman-Brown JC, Smith DJ. Rapid sperm capture: high-throughput flagellar waveform analysis. Hum Reprod 2020; 34:1173-1185. [PMID: 31170729 PMCID: PMC6613345 DOI: 10.1093/humrep/dez056] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [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: 02/13/2019] [Revised: 04/01/2019] [Indexed: 11/12/2022] Open
Abstract
STUDY QUESTION Can flagellar analyses be scaled up to provide automated tracking of motile sperm, and does knowledge of the flagellar waveform provide new insight not provided by routine head tracking? SUMMARY ANSWER High-throughput flagellar waveform tracking and analysis enable measurement of experimentally intractable quantities such as energy dissipation, disturbance of the surrounding medium and viscous stresses, which are not possible by tracking the sperm head alone. WHAT IS KNOWN ALREADY The clinical gold standard for sperm motility analysis comprises a manual analysis by a trained professional, with existing automated sperm diagnostics [computer-aided sperm analysis (CASA)] relying on tracking the sperm head and extrapolating measures. It is not currently possible with either of these approaches to track the sperm flagellar waveform for large numbers of cells in order to unlock the potential wealth of information enclosed within. STUDY DESIGN, SIZE, DURATION The software tool in this manuscript has been developed to enable high-throughput, repeatable, accurate and verifiable analysis of the sperm flagellar beat. PARTICIPANTS/MATERIALS, SETTING, METHODS Using the software tool [Flagellar Analysis and Sperm Tracking (FAST)] described in this manuscript, we have analysed 176 experimental microscopy videos and have tracked the head and flagellum of 205 progressive cells in diluted semen (DSM), 119 progressive cells in a high-viscosity medium (HVM) and 42 stuck cells in a low-viscosity medium. Unscreened donors were recruited at Birmingham Women's and Children's NHS Foundation Trust after giving informed consent. MAIN RESULTS AND THE ROLE OF CHANCE We describe fully automated tracking and analysis of flagellar movement for large cell numbers. The analysis is demonstrated on freely motile cells in low- and high-viscosity fluids and validated on published data of tethered cells undergoing pharmacological hyperactivation. Direct analysis of the flagellar beat reveals that the CASA measure 'beat cross frequency' does not measure beat frequency; attempting to fit a straight line between the two measures gives ${\mathrm{R}}^2$ values of 0.042 and 0.00054 for cells in DSM and HVM, respectively. A new measurement, track centroid speed, is validated as an accurate differentiator of progressive motility. Coupled with fluid mechanics codes, waveform data enable extraction of experimentally intractable quantities such as energy dissipation, disturbance of the surrounding medium and viscous stresses. We provide a powerful and accessible research tool, enabling connection of the mechanical activity of the sperm to its motility and effect on its environment. LARGE SCALE DATA The FAST software package and all documentation can be downloaded from www.flagellarCapture.com. LIMITATIONS, REASONS FOR CAUTION The FAST software package has only been tested for use with negative phase contrast microscopy. Other imaging modalities, with bright cells on a dark background, have not been tested but may work. FAST is not designed to analyse raw semen; it is specifically for precise analysis of flagellar kinematics, as that is the promising area for computer use. Flagellar capture will always require that cells are at a dilution where their paths do not frequently cross. WIDER IMPLICATIONS OF THE FINDINGS Combining tracked flagella with mathematical modelling has the potential to reveal new mechanistic insight. By providing the capability as a free-to-use software package, we hope that this ability to accurately quantify the flagellar waveform in large populations of motile cells will enable an abundant array of diagnostic, toxicological and therapeutic possibilities, as well as creating new opportunities for assessing and treating male subfertility. STUDY FUNDING/COMPETING INTEREST(S) M.T.G., G.C., J.C.K-B. and D.J.S. gratefully acknowledge funding from the Engineering and Physical Sciences Research Council, Healthcare Technologies Challenge Award (Rapid Sperm Capture EP/N021096/1). J.C.K-B. is funded by a National Institute of Health Research (NIHR) and Health Education England, Senior Clinical Lectureship Grant: The role of the human sperm in healthy live birth (NIHRDH-HCS SCL-2014-05-001). This article presents independent research funded in part by the NIHR and Health Education England. The views expressed are those of the authors and not necessarily those of the NHS, the NIHR or the Department of Health. The data for experimental set (2) were funded through a Wellcome Trust-University of Birmingham Value in People Fellowship Bridging Award (E.H.O.).The authors declare no competing interests.
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Affiliation(s)
- M T Gallagher
- School of Mathematics.,Institute for Metabolism and Systems Research, University of Birmingham, Birmingham, UK.,Centre for Human Reproductive Science, Birmingham Women's and Children's National Health Service Foundation Trust, Birmingham, UK
| | - G Cupples
- School of Mathematics.,Institute for Metabolism and Systems Research, University of Birmingham, Birmingham, UK.,Centre for Human Reproductive Science, Birmingham Women's and Children's National Health Service Foundation Trust, Birmingham, UK
| | - E H Ooi
- School of Engineering, Monash University Malaysia, Bandar Sunway, Malaysia
| | - J C Kirkman-Brown
- Institute for Metabolism and Systems Research, University of Birmingham, Birmingham, UK.,Centre for Human Reproductive Science, Birmingham Women's and Children's National Health Service Foundation Trust, Birmingham, UK
| | - D J Smith
- School of Mathematics.,Institute for Metabolism and Systems Research, University of Birmingham, Birmingham, UK.,Centre for Human Reproductive Science, Birmingham Women's and Children's National Health Service Foundation Trust, Birmingham, UK
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Abstract
Modern organic reaction discovery and development relies on the rapid assessment of large arrays of hypothesis-driven experiments. The time-intensive nature of reaction analysis presents the greatest practical barrier for the execution of this iterative process that underpins the development of new bioactive agents. Toward addressing this critical bottleneck, we report herein a high-throughput analysis (HTA) method of reaction mixtures by photocapture on a 384-spot diazirine-terminated self-assembled monolayer, and self-assembled monolayers for matrix-assisted laser desorption/ionization mass spectrometry (SAMDI-MS) analysis. This analytical platform has been applied to the identification of a single-electron-promoted reductive coupling of acyl azolium species.
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36
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Kresge GA, Grosse S, Zimmer A, Grinias KM, De Pra M, Wong JMT, Steiner F, Grinias JP. Strategies in developing high-throughput liquid chromatography protocols for method qualification of pharmacopeial monographs. J Sep Sci 2020; 43:2964-2970. [PMID: 32388922 DOI: 10.1002/jssc.202000403] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 04/08/2020] [Revised: 05/05/2020] [Accepted: 05/06/2020] [Indexed: 11/11/2022]
Abstract
Method qualification is a key step in the development of routine analytical monitoring of pharmaceutical products. However, when relying on published monographs that describe longer method times based on older high-performance liquid chromatography column and instrument technology, this can delay the overall analysis process for generated drug products. In this study, high-throughput ultrahigh pressure liquid chromatography techniques were implemented to decrease the amount of time needed to complete a 24-run sequence to identify linearity, recovery, and repeatability for both drug assay and impurity analysis in 16 min. Multiple experimental parameters were tested to identify a range of experimental settings that could be used for the sequence while still maintaining this fast analysis time. The full sequence was replicated on a different system and with different columns, further demonstrating its robustness.
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Affiliation(s)
- Glenn A Kresge
- Department of Chemistry & Biochemistry, Rowan University, Glassboro, NJ, USA
| | | | - Alexis Zimmer
- Department of Chemistry & Biochemistry, Rowan University, Glassboro, NJ, USA
| | - Kaitlin M Grinias
- Analytical Platforms & Platform Modernization , GlaxoSmithKline, Collegeville, PA, USA
| | | | | | | | - James P Grinias
- Department of Chemistry & Biochemistry, Rowan University, Glassboro, NJ, USA
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37
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Bee-DiGregorio MY, Feng H, Pan BS, Dokoozlian NK, Sacks GL. Polymeric Sorbent Sheets Coupled to Direct Analysis in Real Time Mass Spectrometry for Trace-Level Volatile Analysis-A Multi-Vineyard Evaluation Study. Foods 2020; 9:E409. [PMID: 32252228 DOI: 10.3390/foods9040409] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 03/19/2020] [Accepted: 03/21/2020] [Indexed: 11/17/2022] Open
Abstract
Etched polymeric sorbent sheets (solid-phase mesh-enhanced sorption from headspace (SPMESH) sheets) were recently described as an alternative to solid-phase microextraction (SPME) for rapid, parallel, multi-sample extraction and pre-concentration of headspace volatiles. In this report, a workflow was evaluated based on SPMESH sheet extraction followed by direct analysis in real time-mass spectrometry (DART-MS) using grape samples harvested from multiple commercial vineyards at different maturities. SPMESH sheet-DART-MS(-MS) was performed on two grape-derived odorants related to wine quality: 3-isobutyl-2-methoxypyrazine (IBMP) in Cabernet Sauvignon and Merlot grape homogenate (n = 86 samples) and linalool in Muscat-type grape juice samples (n = 18 samples). As part of the optimization process, an MS-MS method was developed for IBMP and an equilibration procedure prior to extraction was established for homogenate samples. Following optimization, we achieved good correlation between SPMESH sheet-DART-MS and SPME-GC-MS for both IBMP (range by GC-MS = < 2 ng/L to 28 ng/L, R2 = 0.70) and linalool (range by GC-MS = 135 to 415 μg/L, R2 = 0.66). The results indicate SPMESH sheet-DART-MS is suitable for rapid measurements of trace level volatiles in grapes.
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38
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Cerrato F, Sparago A, Ariani F, Brugnoletti F, Calzari L, Coppedè F, De Luca A, Gervasini C, Giardina E, Gurrieri F, Lo Nigro C, Merla G, Miozzo M, Russo S, Sangiorgi E, Sirchia SM, Squeo GM, Tabano S, Tabolacci E, Torrente I, Genuardi M, Neri G, Riccio A. DNA Methylation in the Diagnosis of Monogenic Diseases. Genes (Basel) 2020; 11:E355. [PMID: 32224912 DOI: 10.3390/genes11040355] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 03/13/2020] [Accepted: 03/24/2020] [Indexed: 02/08/2023] Open
Abstract
DNA methylation in the human genome is largely programmed and shaped by transcription factor binding and interaction between DNA methyltransferases and histone marks during gamete and embryo development. Normal methylation profiles can be modified at single or multiple loci, more frequently as consequences of genetic variants acting in cis or in trans, or in some cases stochastically or through interaction with environmental factors. For many developmental disorders, specific methylation patterns or signatures can be detected in blood DNA. The recent use of high-throughput assays investigating the whole genome has largely increased the number of diseases for which DNA methylation analysis provides information for their diagnosis. Here, we review the methylation abnormalities that have been associated with mono/oligogenic diseases, their relationship with genotype and phenotype and relevance for diagnosis, as well as the limitations in their use and interpretation of results.
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39
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Abstract
Background: One of the main challenges in developing phage therapy and manufacturing phage products is the reliable evaluation of their efficacy, performance, and quality. Since phage virulence is intrinsically difficult to fully capture, researchers have turned to rapid but partially inadequate methods for its evaluation. Materials and Methods: This study demonstrates a standardized quantitative method to assess phage virulence based on three parameters: the virulence index (VP )-quantifying the virulence of a phage against a host, the local virulence (vi )-assessing killing potential at given multiplicities of infection (MOIs), and MV50 -the MOI at which the phage achieves 50% of its maximum theoretical virulence. This was shown through comparative analysis of the virulence of phages T4, T5, and T7. Results: Under the conditions tested, phage T7 displayed the highest virulence, followed by phage T4 and, finally, by phage T5. The impact of parameters such as temperature and medium composition on virulence was shown for each phage. The use of the method to evaluate the virulence of combinations of phages-for example, for cocktail formulation-is also shown with phages T5 and T7. Conclusions: The method presented provides a platform for high-throughput quantitative assessment of phage virulence and quality control of phage products. It can also be applied to phage screening, evaluation of phage strains, phage mutants, infection conditions and/or the susceptibility of host strains, and the formulation of phage cocktails.
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Affiliation(s)
- Zachary J. Storms
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Canada
| | - Matthew R. Teel
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Canada
| | - Kevin Mercurio
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Canada
| | - Dominic Sauvageau
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Canada.,Address correspondence to: Dominic Sauvageau, PhD, Department of Chemical and Materials Engineering, University of Alberta, 9211-116 Street NW, Edmonton, AB T6G 1H9, Canada
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40
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Narisetti N, Neumann K, Röder MS, Gladilin E. Automated Spike Detection in Diverse European Wheat Plants Using Textural Features and the Frangi Filter in 2D Greenhouse Images. Front Plant Sci 2020; 11:666. [PMID: 32655586 PMCID: PMC7324796 DOI: 10.3389/fpls.2020.00666] [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] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 04/29/2020] [Indexed: 05/22/2023]
Abstract
Spike is one of the crop yield organs in wheat plants. Determination of the phenological stages, including heading time point (HTP), and area of spike from non-invasive phenotyping images provides the necessary information for the inference of growth-related traits. The algorithm previously developed by Qiongyan et al. for spike detection in 2-D images turns out to be less accurate when applied to the European cultivars that produce many more leaves. Therefore, we here present an improved and extended method where (i) wavelet amplitude is used as an input to the Laws texture energy-based neural network instead of original grayscale images and (ii) non-spike structures (e.g., leaves) are subsequently suppressed by combining the result of the neural network prediction with a Frangi-filtered image. Using this two-step approach, a 98.6% overall accuracy of neural network segmentation based on direct comparison with ground-truth data could be achieved. Moreover, the comparative error rate in spike HTP detection and growth correlation among the ground truth, the algorithm developed by Qiongyan et al., and the proposed algorithm are discussed in this paper. The proposed algorithm was also capable of significantly reducing the error rate of the HTP detection by 75% and improving the accuracy of spike area estimation by 50% in comparison with the Qionagyan et al. method. With these algorithmic improvements, HTP detection on a diverse set of 369 plants was performed in a high-throughput manner. This analysis demonstrated that the HTP of 104 plants (comprises of 57 genotypes) with lower biomass and tillering range (e.g., earlier-heading types) were correctly determined. However, fine-tuning or extension of the developed method is required for high biomass plants where spike emerges within green bushes. In conclusion, our proposed method allows significantly more reliable results for HTP detection and spike growth analysis to be achieved in application to European cultivars with earlier-heading types.
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Affiliation(s)
- Narendra Narisetti
- Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Kerstin Neumann
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Marion S. Röder
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Evgeny Gladilin
- Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- *Correspondence: Evgeny Gladilin
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41
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Millstead L, Jayakody H, Patel H, Kaura V, Petrie PR, Tomasetig F, Whitty M. Accelerating Automated Stomata Analysis Through Simplified Sample Collection and Imaging Techniques. Front Plant Sci 2020; 11:580389. [PMID: 33101348 PMCID: PMC7546325 DOI: 10.3389/fpls.2020.580389] [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: 07/06/2020] [Accepted: 09/10/2020] [Indexed: 05/13/2023]
Abstract
Digital image processing is commonly used in plant health and growth analysis, aiming to improve research efficiency and repeatability. One focus is analysing the morphology of stomata, with the aim to better understand the regulation of gas exchange, its link to photosynthesis and water use and how they are influenced by climatic conditions. Despite the key role played by these cells, their microscopic analysis is largely manual, requiring intricate sample collection, laborious microscope application and the manual operation of a graphical user interface to identify and measure stomata. This research proposes a simple, end-to-end solution which enables automatic analysis of stomata by introducing key changes to imaging techniques, stomata detection as well as stomatal pore area calculation. An optimal procedure was developed for sample collection and imaging by investigating the suitability of using an automatic microscope slide scanner to image nail polish imprints. The use of the slide scanner allows the rapid collection of high-quality images from entire samples with minimal manual effort. A convolutional neural network was used to automatically detect stomata in the input image, achieving average precision, recall and F-score values of 0.79, 0.85, and 0.82 across four plant species. A novel binary segmentation and stomatal cross section analysis method is developed to estimate the pore boundary and calculate the associated area. The pore estimation algorithm correctly identifies stomata pores 73.72% of the time. Ultimately, this research presents a fast and simplified method of stomatal assay generation requiring minimal human intervention, enhancing the speed of acquiring plant health information.
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Affiliation(s)
- Luke Millstead
- School of Mechanical and Manufacturing Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Hiranya Jayakody
- School of Mechanical and Manufacturing Engineering, University of New South Wales, Sydney, NSW, Australia
- *Correspondence: Hiranya Jayakody,
| | - Harsh Patel
- School of Mechanical and Manufacturing Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Vihaan Kaura
- School of Mechanical and Manufacturing Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Paul R. Petrie
- School of Mechanical and Manufacturing Engineering, University of New South Wales, Sydney, NSW, Australia
- Crop Sciences Division, South Australian Research and Development Institute, Waite Campus, Urrbrae, SA, Australia
| | - Florence Tomasetig
- Mark Wainwright Analytical Centre, University of New South Wales, Sydney, NSW, Australia
| | - Mark Whitty
- School of Mechanical and Manufacturing Engineering, University of New South Wales, Sydney, NSW, Australia
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42
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Abstract
Recent innovations of next-generation sequencing such as RNA-seq have generated an enormous amount of comparative transcriptome data, which have shed lights on our understanding of the complexity of transcriptional regulatory systems. Despite numerous RNA-seq analyses, statistical methods and computational tools designed for phylogenetic transcriptome analysis and evolution have not been well developed. In response to this need, we developed software TreeExp2 specifically for RNA-seq data. The R-package TreeExp2 has implemented a suite of advanced, recently developed methods for transcriptome evolutionary analysis. Its main functions include the ancestral transcriptome inference, estimation of the strength of expression conservation, new expression distance, and the relative expression rate test. TreeExp2 provides an integrated, statistically sound framework for phylogenetic transcriptome analysis. It will considerably enhance our analytical capability for exploring the evolution and selection at the transcriptome level. The current version of TreeExp2 is available under GPLv3 license at the Github developer site https://github.com/jingwyang/TreeExp; last accessed November 12, 2019, and its online tutorial which describes the biological theories in details and fully worked case studies with real data can be found at https://jingwyang.github.io/TreeExp-Tutorial; last accessed November 12, 2019.
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Affiliation(s)
- Jingwen Yang
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China.,Human Phenome Institute, Fudan University, Shanghai, China
| | - Hang Ruan
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston-McGovern Medical School
| | - Wenjie Xu
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Xun Gu
- Department of Genetics, Development and Cell Biology, Iowa State University
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43
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Suzuki Y. Development of Fluorescent Reagent Based on Ligand Exchange Reaction for the Highly Sensitive and Selective Detection of Dopamine in the Serum. Sensors (Basel) 2019; 19:E3928. [PMID: 31547244 PMCID: PMC6766910 DOI: 10.3390/s19183928] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 09/07/2019] [Accepted: 09/09/2019] [Indexed: 01/11/2023]
Abstract
A new fluorescent probe (BDP-Fe2+) was developed for targeting dopamine, with a boron-dipyrromethenyl (BDP) group as the fluorophore and a Fe2+ complex as the ligand exchange site. The free form of BDP-Fe2+ in solution displayed weak fluorescence emission, while it showed strong fluorescence emission after interaction with dopamine due to the release of Fe2+ from BDP-Fe2+, confirming the binding of Fe2+ to dopamine. The increase in fluorescence intensity was concentration-dependent, and a good linear relationship was observed between the fluorescence intensity and dopamine concentration. The detection limit of dopamine by BDP-Fe2+ was 1.1 nM, indicating a 20-fold higher sensitivity than that of previously reported compounds. The reaction of BDP-Fe2+ with dopamine was not affected by the presence of foreign substances, allowing the highly selective detection of dopamine in the human serum sample. The results of this study indicate that the novel compound BDP-Fe2+ is a reliable fluorescent molecular probe for the detection of dopamine and can be widely employed in diverse scientific areas.
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Affiliation(s)
- Yoshio Suzuki
- Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan.
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44
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Adamo A, Brandi J, Caligola S, Delfino P, Bazzoni R, Carusone R, Cecconi D, Giugno R, Manfredi M, Robotti E, Marengo E, Bassi G, Takam Kamga P, Dal Collo G, Gatti A, Mercuri A, Arigoni M, Olivero M, Calogero RA, Krampera M. Extracellular Vesicles Mediate Mesenchymal Stromal Cell-Dependent Regulation of B Cell PI3K-AKT Signaling Pathway and Actin Cytoskeleton. Front Immunol 2019; 10:446. [PMID: 30915084 PMCID: PMC6423067 DOI: 10.3389/fimmu.2019.00446] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [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: 11/29/2018] [Accepted: 02/19/2019] [Indexed: 12/11/2022] Open
Abstract
Mesenchymal stromal cells (MSCs) are adult, multipotent cells of mesodermal origin representing the progenitors of all stromal tissues. MSCs possess significant and broad immunomodulatory functions affecting both adaptive and innate immune responses once MSCs are primed by the inflammatory microenvironment. Recently, the role of extracellular vesicles (EVs) in mediating the therapeutic effects of MSCs has been recognized. Nevertheless, the molecular mechanisms responsible for the immunomodulatory properties of MSC-derived EVs (MSC-EVs) are still poorly characterized. Therefore, we carried out a molecular characterization of MSC-EV content by high-throughput approaches. We analyzed miRNA and protein expression profile in cellular and vesicular compartments both in normal and inflammatory conditions. We found several proteins and miRNAs involved in immunological processes, such as MOES, LG3BP, PTX3, and S10A6 proteins, miR-155-5p, and miR-497-5p. Different in silico approaches were also performed to correlate miRNA and protein expression profile and then to evaluate the putative molecules or pathways involved in immunoregulatory properties mediated by MSC-EVs. PI3K-AKT signaling pathway and the regulation of actin cytoskeleton were identified and functionally validated in vitro as key mediators of MSC/B cell communication mediated by MSC-EVs. In conclusion, we identified different molecules and pathways responsible for immunoregulatory properties mediated by MSC-EVs, thus identifying novel therapeutic targets as safer and more useful alternatives to cell or EV-based therapeutic approaches.
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Affiliation(s)
- Annalisa Adamo
- Stem Cell Research Laboratory, Section of Hematology, Department of Medicine, University of Verona, Verona, Italy
| | - Jessica Brandi
- Proteomics and Mass Spectrometry Laboratory, Department of Biotechnology, University of Verona, Verona, Italy
| | - Simone Caligola
- Department of Computer Science, University of Verona, Verona, Italy
| | - Pietro Delfino
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Riccardo Bazzoni
- Stem Cell Research Laboratory, Section of Hematology, Department of Medicine, University of Verona, Verona, Italy
| | - Roberta Carusone
- Stem Cell Research Laboratory, Section of Hematology, Department of Medicine, University of Verona, Verona, Italy
| | - Daniela Cecconi
- Proteomics and Mass Spectrometry Laboratory, Department of Biotechnology, University of Verona, Verona, Italy
| | - Rosalba Giugno
- Department of Computer Science, University of Verona, Verona, Italy
| | - Marcello Manfredi
- Department of Sciences and Technological Innovation, University of Piemonte Orientale, Alessandria, Italy.,Center for Translational Research on Autoimmune and Allergic Diseases (CAAD), Novara, Italy
| | - Elisa Robotti
- Department of Sciences and Technological Innovation, University of Piemonte Orientale, Alessandria, Italy
| | - Emilio Marengo
- Department of Sciences and Technological Innovation, University of Piemonte Orientale, Alessandria, Italy.,Center for Translational Research on Autoimmune and Allergic Diseases (CAAD), Novara, Italy
| | - Giulio Bassi
- Stem Cell Research Laboratory, Section of Hematology, Department of Medicine, University of Verona, Verona, Italy
| | - Paul Takam Kamga
- Stem Cell Research Laboratory, Section of Hematology, Department of Medicine, University of Verona, Verona, Italy
| | - Giada Dal Collo
- Stem Cell Research Laboratory, Section of Hematology, Department of Medicine, University of Verona, Verona, Italy
| | - Alessandro Gatti
- Stem Cell Research Laboratory, Section of Hematology, Department of Medicine, University of Verona, Verona, Italy
| | - Angela Mercuri
- Stem Cell Research Laboratory, Section of Hematology, Department of Medicine, University of Verona, Verona, Italy
| | - Maddalena Arigoni
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin, Italy
| | | | - Raffaele A Calogero
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin, Italy
| | - Mauro Krampera
- Stem Cell Research Laboratory, Section of Hematology, Department of Medicine, University of Verona, Verona, Italy
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45
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Pavlovic S, Kotur N, Stankovic B, Zukic B, Gasic V, Dokmanovic L. Pharmacogenomic and Pharmacotranscriptomic Profiling of Childhood Acute Lymphoblastic Leukemia: Paving the Way to Personalized Treatment. Genes (Basel) 2019; 10:E191. [PMID: 30832275 PMCID: PMC6471971 DOI: 10.3390/genes10030191] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [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: 02/04/2019] [Revised: 02/23/2019] [Accepted: 02/25/2019] [Indexed: 02/07/2023] Open
Abstract
Personalized medicine is focused on research disciplines which contribute to the individualization of therapy, like pharmacogenomics and pharmacotranscriptomics. Acute lymphoblastic leukemia (ALL) is the most common malignancy of childhood. It is one of the pediatric malignancies with the highest cure rate, but still a lethal outcome due to therapy accounts for 1%⁻3% of deaths. Further improvement of treatment protocols is needed through the implementation of pharmacogenomics and pharmacotranscriptomics. Emerging high-throughput technologies, including microarrays and next-generation sequencing, have provided an enormous amount of molecular data with the potential to be implemented in childhood ALL treatment protocols. In the current review, we summarized the contribution of these novel technologies to the pharmacogenomics and pharmacotranscriptomics of childhood ALL. We have presented data on molecular markers responsible for the efficacy, side effects, and toxicity of the drugs commonly used for childhood ALL treatment, i.e., glucocorticoids, vincristine, asparaginase, anthracyclines, thiopurines, and methotrexate. Big data was generated using high-throughput technologies, but their implementation in clinical practice is poor. Research efforts should be focused on data analysis and designing prediction models using machine learning algorithms. Bioinformatics tools and the implementation of artificial i Lack of association of the CEP72 rs924607 TT genotype with intelligence are expected to open the door wide for personalized medicine in the clinical practice of childhood ALL.
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Affiliation(s)
- Sonja Pavlovic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11000 Belgrade, Serbia.
| | - Nikola Kotur
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11000 Belgrade, Serbia.
| | - Biljana Stankovic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11000 Belgrade, Serbia.
| | - Branka Zukic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11000 Belgrade, Serbia.
| | - Vladimir Gasic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11000 Belgrade, Serbia.
| | - Lidija Dokmanovic
- University Children's Hospital, 11000 Belgrade, Serbia.
- University of Belgrade, Faculty of Medicine, 11000 Belgrade, Serbia.
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46
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Yang X, Huang H, Lu Q, Chen SH, Wang F, Huang OP, Hu B, Yang BC. High-throughput polymer tip-electrospray ionization mass spectrometry for enhanced detection of neopterin and biopterin in clinical urine samples. J Mass Spectrom 2019; 54:189-194. [PMID: 30597687 DOI: 10.1002/jms.4322] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 12/05/2018] [Accepted: 12/16/2018] [Indexed: 06/09/2023]
Abstract
Urinary biopterin (Bio) and neopterin (Neo) are important markers for clinical diagnosis of hyperphenylalaninemia. Herein, we developed a high-throughput analysis method based on electrospray ionization mass spectrometry (ESI-MS) with polymer tips for the rapid quantitative detection of Bio and Neo in clinical urine samples. Different polymer tips were investigated. It is found that the best detection sensitivity was achieved with hydrophobic polymer tip, ie, polyethylene tips. The high-throughput polymer tip-ESI-MS method allowed a rapid analysis speed at ~40 seconds per sample. The limits of quantification (LOQ) (S/N ≥ 10) for the detection of Bio and Neo were improved to be 5.0 ng/mL. Acceptable relative standard deviation (RSD) values for Neo and Bio were measured to be 12.2% and 13.4% for direct measurement of Bio and Neo in raw urine samples, respectively. Furthermore, Bio and Neo were directly quantified from 18 clinical urine samples by presented method. The ratios of urinary Bio-to-Neo were analyzed for diagnosis of hyperphenylalaninemia. The results demonstrated that the present polymer tip-ESI-MS method is a promising strategy for the rapid analysis of clinical samples.
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Affiliation(s)
- Xiao Yang
- Neonatal Disease Screening Center, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, 330006, China
| | - Huang Huang
- Department of Cardiac Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, China
| | - Qing Lu
- Neonatal Disease Screening Center, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, 330006, China
| | - Shao-Hong Chen
- Neonatal Disease Screening Center, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, 330006, China
| | - Feng Wang
- Neonatal Disease Screening Center, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, 330006, China
| | - Ou-Ping Huang
- Neonatal Disease Screening Center, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, 330006, China
| | - Bin Hu
- Institute of Mass Spectrometer and Atmospheric Environment, Jinan University, Guangzhou, 510632, China
- Guangdong Provincial Engineering Research Center for On-line Source Apportionment System of Air Pollution, Jinan University, Guangzhou, 510632, China
| | - Bi-Cheng Yang
- Neonatal Disease Screening Center, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, 330006, China
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47
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Zheng J, Wu M, Wang H, Li S, Wang X, Li Y, Wang D, Li S. Network Pharmacology to Unveil the Biological Basis of Health-Strengthening Herbal Medicine in Cancer Treatment. Cancers (Basel) 2018; 10:cancers10110461. [PMID: 30469422 PMCID: PMC6266222 DOI: 10.3390/cancers10110461] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [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: 09/12/2018] [Revised: 11/05/2018] [Accepted: 11/16/2018] [Indexed: 12/15/2022] Open
Abstract
Health-strengthening (Fu-Zheng) herbs is a representative type of traditional Chinese medicine (TCM) widely used for cancer treatment in China, which is in contrast to pathogen eliminating (Qu-Xie) herbs. However, the commonness in the biological basis of health-strengthening herbs remains to be holistically elucidated. In this study, an innovative high-throughput research strategy integrating computational and experimental methods of network pharmacology was proposed, and 22 health-strengthening herbs were selected for the investigation. Additionally, 25 pathogen-eliminating herbs were included for comparison. First, based on network-based, large-scale target prediction, we analyzed the target profiles of 1446 TCM compounds. Next, the actions of 166 compounds on 420 antitumor or immune-related genes were measured using a unique high-throughput screening strategy by high-throughput sequencing, referred to as HTS2. Furthermore, the structural information and the antitumor activity of the compounds in health-strengthening and pathogen-eliminating herbs were compared. Using network pharmacology analysis, we discovered that: (1) Functionally, the predicted targets of compounds from health strengthening herbs were enriched in both immune-related and antitumor pathways, similar to those of pathogen eliminating herbs. As a case study, galloylpaeoniflorin, a compound in a health strengthening herb Radix Paeoniae Alba (Bai Shao), was found to exert antitumor effects both in vivo and in vitro. Yet the inhibitory effects of the compounds from pathogen eliminating herbs on tumor cells proliferation as a whole were significantly stronger than those in health-strengthening herbs (p < 0.001). Moreover, the percentage of assay compounds in health-strengthening herbs with the predicted targets enriched in the immune-related pathways (e.g., natural killer cell mediated cytotoxicity and antigen processing and presentation) were significantly higher than that in pathogen-eliminating herbs (p < 0.05). This finding was supported by the immune-enhancing effects of a group of compounds from health-strengthening herbs indicated by differentially expressed genes in the HTS2 results. (2) Compounds in the same herb may exhibit the same or distinguished mechanisms in cancer treatment, which was demonstrated as the compounds influence pathway gene expressions in the same or opposite directions. For example, acetyl ursolic acid and specnuezhenide in a health-strengthening herb Fructus Ligustri lucidi (Nv Zhen Zi) both upregulated gene expressions in T cell receptor signaling pathway. Together, this study suggested greater potentials in tumor immune microenvironment regulation and tumor prevention than in direct killing tumor cells of health-strengthening herbs generally, and provided a systematic strategy for unveiling the commonness in the biological basis of health-strengthening herbs in cancer treatment.
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Affiliation(s)
- Jiahui Zheng
- MOE Key Laboratory of Bioinformatics; Bioinformatics Division Biology/Center for TCM-X, BNRist, TFIDT/Department of Automation, Tsinghua University, 100084 Beijing, China.
| | - Min Wu
- MOE Key Laboratory of Bioinformatics; Bioinformatics Division Biology/Center for TCM-X, BNRist, TFIDT/Department of Automation, Tsinghua University, 100084 Beijing, China.
| | - Haiyan Wang
- Department of Basic Medicine, School of Medicine, Tsinghua University, 100084 Beijing, China.
| | - Shasha Li
- Department of Basic Medicine, School of Medicine, Tsinghua University, 100084 Beijing, China.
| | - Xin Wang
- MOE Key Laboratory of Bioinformatics; Bioinformatics Division Biology/Center for TCM-X, BNRist, TFIDT/Department of Automation, Tsinghua University, 100084 Beijing, China.
| | - Yan Li
- State Key Laboratory of Bioactive Substances and Functions of Nature Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, 100730 Beijing, China.
| | - Dong Wang
- Department of Basic Medicine, School of Medicine, Tsinghua University, 100084 Beijing, China.
| | - Shao Li
- MOE Key Laboratory of Bioinformatics; Bioinformatics Division Biology/Center for TCM-X, BNRist, TFIDT/Department of Automation, Tsinghua University, 100084 Beijing, China.
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Xu P, Song Y, Feng B, Zeng Q, Shan B, Liu K, Su D. Multi-component profiles through the blood-brain barrier in rat after oral administration of over-the-counter drug Keke capsule by ultra-performance liquid chromatography/quadrupole- time-of-flight MS E method. Biomed Chromatogr 2018; 33:e4380. [PMID: 30178888 DOI: 10.1002/bmc.4380] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 08/18/2018] [Accepted: 08/30/2018] [Indexed: 01/10/2023]
Abstract
Keke capsule as a traditional Chinese medicine formulation is used to relieve cough, for analgesia and to reduce bronchial asthma. The multi-components are absorbed into the blood and brain after oral administration of Keke capsule, with no systematic investigation so far. A reliable and rapid UPLC-QTOF-MSE combined with a data processing software platform was used to characterize the components of Keke capsule and simultaneously identify bioactive components in blood and brain tissues in rat after oral administration. Consequently, a total of 41 components of Keke capsule, including alkaloids, flavone, flavonols, triterpene, lignanoid, organic acids, glycosides and coumarin were identified. Twenty-one components were found in plasma, including 18 prototypes and three metabolites; 15 components were found in brain tissues, including 10 prototypes and five metabolites. Alkaloids and flavonoids in Keke capsule were the main components which were absorbed into blood. The main alkaloids of Keke capsule can pass through the blood-brain barrier and show different distribution tendencies in brain tissues. The main components of keke capsule was simultaneously analyzed by throughput analysis, and the corresponding bioactive components were examined by blood-brain barrier in the rat after oral administration of the capsule.
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Affiliation(s)
- Pengfei Xu
- Jiangxi University of Traditional Chinese Medicine, Nanchang, China
| | - Yonggui Song
- Jiangxi University of Traditional Chinese Medicine, Nanchang, China
| | - Bingwei Feng
- Jiangxi University of Traditional Chinese Medicine, Nanchang, China
| | - Qiang Zeng
- Jiangxi University of Traditional Chinese Medicine, Nanchang, China
| | - Baixi Shan
- Jiangxi University of Traditional Chinese Medicine, Nanchang, China
| | - Kuangyi Liu
- SCIEX, Analytical Instrument Trading Co., Changning District, Shanghai, People's Republic of China
| | - Dan Su
- Jiangxi University of Traditional Chinese Medicine, Nanchang, China
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Chekmeneva E, Dos Santos Correia G, Gómez-Romero M, Stamler J, Chan Q, Elliott P, Nicholson JK, Holmes E. Ultra-Performance Liquid Chromatography-High-Resolution Mass Spectrometry and Direct Infusion-High-Resolution Mass Spectrometry for Combined Exploratory and Targeted Metabolic Profiling of Human Urine. J Proteome Res 2018; 17:3492-3502. [PMID: 30183320 PMCID: PMC6184476 DOI: 10.1021/acs.jproteome.8b00413] [Citation(s) in RCA: 12] [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] [Indexed: 02/07/2023]
Abstract
![]()
The
application of metabolic phenotyping to epidemiological studies
involving thousands of biofluid samples presents a challenge for the
selection of analytical platforms that meet the requirements of high-throughput
precision analysis and cost-effectiveness. Here direct infusion–nanoelectrospray
(DI–nESI) was compared with an ultra-performance liquid chromatography
(UPLC)–high-resolution mass spectrometry (HRMS) method for
metabolic profiling of an exemplary set of 132 human urine samples
from a large epidemiological cohort. Both methods were developed and
optimized to allow the simultaneous collection of high-resolution
urinary metabolic profiles and quantitative data for a selected panel
of 35 metabolites. The total run time for measuring the sample set
in both polarities by UPLC–HRMS was 5 days compared with 9
h by DI–nESI–HRMS. To compare the classification ability
of the two MS methods, we performed exploratory analysis of the full-scan
HRMS profiles to detect sex-related differences in biochemical composition.
Although metabolite identification is less specific in DI–nESI–HRMS,
the significant features responsible for discrimination between sexes
were mostly the same in both MS-based platforms. Using the quantitative
data, we showed that 10 metabolites have strong correlation (Pearson’s r > 0.9 and Passing–Bablok regression slope of 0.8–1.3)
and good agreement assessed by Bland–Altman plots between UPLC–HRMS
and DI–nESI–HRMS and thus can be measured using a cheaper
and less sample- and time-consuming method. A further twenty
metabolites showed acceptable correlation between the two methods
with only five metabolites showing weak correlation (Pearson’s r < 0.4) and poor agreement due to the overestimation
of the results by DI–nESI–HRMS.
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Affiliation(s)
- Elena Chekmeneva
- Division of Integrative Systems and Digestive Medicine, Department of Surgery and Cancer , Imperial College London , Sir Alexander Fleming Building, South Kensington Campus , London SW7 2AZ , United Kingdom.,NIHR-BRC Clinical Phenotyping Centre, Department of Surgery and Cancer , Imperial College London , Sir Alexander Fleming Building, South Kensington Campus , London SW7 2AZ , United Kingdom
| | - Gonçalo Dos Santos Correia
- Division of Integrative Systems and Digestive Medicine, Department of Surgery and Cancer , Imperial College London , Sir Alexander Fleming Building, South Kensington Campus , London SW7 2AZ , United Kingdom.,NIHR-BRC Clinical Phenotyping Centre, Department of Surgery and Cancer , Imperial College London , Sir Alexander Fleming Building, South Kensington Campus , London SW7 2AZ , United Kingdom
| | - María Gómez-Romero
- Division of Integrative Systems and Digestive Medicine, Department of Surgery and Cancer , Imperial College London , Sir Alexander Fleming Building, South Kensington Campus , London SW7 2AZ , United Kingdom.,NIHR-BRC Clinical Phenotyping Centre, Department of Surgery and Cancer , Imperial College London , Sir Alexander Fleming Building, South Kensington Campus , London SW7 2AZ , United Kingdom
| | - Jeremiah Stamler
- Department of Preventive Medicine, Feinberg School of Medicine , Northwestern University , Chicago , Illinois 60611 , United States
| | - Queenie Chan
- Department of Epidemiology and Biostatistics, School of Public Health , Imperial College London , St. Mary's Campus , London W2 1PG , United Kingdom.,MRC-PHE Centre for Environment and Health, School of Public Health , Imperial College London , St. Mary's Campus , London W2 1PG , United Kingdom
| | - Paul Elliott
- Department of Epidemiology and Biostatistics, School of Public Health , Imperial College London , St. Mary's Campus , London W2 1PG , United Kingdom.,MRC-PHE Centre for Environment and Health, School of Public Health , Imperial College London , St. Mary's Campus , London W2 1PG , United Kingdom
| | - Jeremy K Nicholson
- Division of Integrative Systems and Digestive Medicine, Department of Surgery and Cancer , Imperial College London , Sir Alexander Fleming Building, South Kensington Campus , London SW7 2AZ , United Kingdom.,NIHR-BRC Clinical Phenotyping Centre, Department of Surgery and Cancer , Imperial College London , Sir Alexander Fleming Building, South Kensington Campus , London SW7 2AZ , United Kingdom
| | - Elaine Holmes
- Division of Integrative Systems and Digestive Medicine, Department of Surgery and Cancer , Imperial College London , Sir Alexander Fleming Building, South Kensington Campus , London SW7 2AZ , United Kingdom.,MRC-PHE Centre for Environment and Health, School of Public Health , Imperial College London , St. Mary's Campus , London W2 1PG , United Kingdom
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50
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Berger D, Rakhamimova A, Pollack A, Loewy Z. Oral Biofilms: Development, Control, and Analysis. High Throughput 2018; 7:ht7030024. [PMID: 30200379 PMCID: PMC6163956 DOI: 10.3390/ht7030024] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 08/27/2018] [Accepted: 08/29/2018] [Indexed: 11/21/2022] Open
Abstract
The oral cavity harbors hundreds of microbial species that are present either as planktonic cells or incorporated into biofilms. The majority of the oral microbes are commensal organisms. Those that are pathogenic microbes can result in oral infections, and at times can initiate systemic diseases. Biofilms that contain pathogens are challenging to control. Many conventional antimicrobials have proven to be ineffective. Recent advances in science and technology are providing new approaches for pathogen control and containment and methods to characterize biofilms. This perspective provides (1) a general understanding of biofilm development; (2) a description of emerging chemical and biological methods to control oral biofilms; and (3) an overview of high-throughput analytical approaches to analyze biofilms.
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Affiliation(s)
- Daniela Berger
- Department of Pharmaceutical and Biomedical Sciences, Touro College of Pharmacy, New York, NY 10027, USA.
| | - Aviva Rakhamimova
- Department of Pharmaceutical and Biomedical Sciences, Touro College of Pharmacy, New York, NY 10027, USA.
| | - Andrew Pollack
- Department of Pharmaceutical and Biomedical Sciences, Touro College of Pharmacy, New York, NY 10027, USA.
| | - Zvi Loewy
- Department of Pharmaceutical and Biomedical Sciences, Touro College of Pharmacy, New York, NY 10027, USA.
- Department of Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA.
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