1
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Maimaiti Y, Su T, Zhang Z, Ma L, Zhang Y, Xu H. NOX4-mediated astrocyte ferroptosis in Alzheimer's disease. Cell Biosci 2024; 14:88. [PMID: 38956702 PMCID: PMC11218381 DOI: 10.1186/s13578-024-01266-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 06/19/2024] [Indexed: 07/04/2024] Open
Abstract
This study investigates NADPH oxidase 4 (NOX4) involvement in iron-mediated astrocyte cell death in Alzheimer's Disease (AD) using single-cell sequencing data and transcriptomes. We analyzed AD single-cell RNA sequencing data, identified astrocyte marker genes, and explored biological processes in astrocytes. We integrated AD-related chip data with ferroptosis-related genes, highlighting NOX4. We validated NOX4's role in ferroptosis and AD in vitro and in vivo. Astrocyte marker genes were enriched in AD, emphasizing their role. NOX4 emerged as a crucial player in astrocytic ferroptosis in AD. Silencing NOX4 mitigated ferroptosis, improved cognition, reduced Aβ and p-Tau levels, and alleviated mitochondrial abnormalities. NOX4 promotes astrocytic ferroptosis, underscoring its significance in AD progression.
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Affiliation(s)
- Yasenjiang Maimaiti
- Gerontology Center, People's Hospital of Xinjiang Uygur Autonomous Region, No.91 Tianchi Road, Urumqi, Xinjiang, China.
| | - Ting Su
- Gerontology Center, People's Hospital of Xinjiang Uygur Autonomous Region, No.91 Tianchi Road, Urumqi, Xinjiang, China
| | - Zhanying Zhang
- Gerontology Center, People's Hospital of Xinjiang Uygur Autonomous Region, No.91 Tianchi Road, Urumqi, Xinjiang, China
| | - Lingling Ma
- Gerontology Center, People's Hospital of Xinjiang Uygur Autonomous Region, No.91 Tianchi Road, Urumqi, Xinjiang, China
| | - Yuan Zhang
- Gerontology Center, People's Hospital of Xinjiang Uygur Autonomous Region, No.91 Tianchi Road, Urumqi, Xinjiang, China
| | - Hong Xu
- Gerontology Center, People's Hospital of Xinjiang Uygur Autonomous Region, No.91 Tianchi Road, Urumqi, Xinjiang, China.
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2
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Li G, Tian S, Sun X, Zhao M, Zhang F, Zhang JP, Cheng T, Zhang XB. Leveraging CRISPR-Cas9 for Accurate Detection of AAV-Neutralizing Antibodies: The AAV-HDR Method. Hum Gene Ther 2024; 35:490-505. [PMID: 38069573 DOI: 10.1089/hum.2023.129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024] Open
Affiliation(s)
- Guohua Li
- Department of Cell Biology, Tianjin Medical University, Tianjin, China
| | - Saining Tian
- Department of Cell Biology, Tianjin Medical University, Tianjin, China
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Xinyu Sun
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Mei Zhao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Feng Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Jian-Ping Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Tao Cheng
- Department of Cell Biology, Tianjin Medical University, Tianjin, China
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Xiao-Bing Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
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3
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Zwicklbauer K, von la Roche D, Krentz D, Kolberg L, Alberer M, Zablotski Y, Hartmann K, von Both U, Härtle S. Adapting the SMART tube technology for flow cytometry in feline full blood samples. Front Vet Sci 2024; 11:1377414. [PMID: 38988976 PMCID: PMC11234156 DOI: 10.3389/fvets.2024.1377414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 06/05/2024] [Indexed: 07/12/2024] Open
Abstract
Flow cytometry of blood samples is a very valuable clinical and research tool to monitor the immune response in human patients. Furthermore, it has been successfully applied in cats, such as for infections with feline immune deficiency virus (FIV). However, if cells are not isolated and frozen, analysis of anticoagulated blood samples requires mostly prompt processing following blood collection, making later analysis of stored full blood samples obtained in clinical studies often impossible. The SMART Tube system (SMART TUBE Inc., California, United States; SMT) allows fixation and long-term preservation of whole blood samples at -80°C. However, this system has so far only been applied to human biological samples. In the present study, a new flow cytometry SMART Tube protocol adapted for feline whole blood samples was successfully established allowing quantification of T-helper cells, cytotoxic T-cells, B-cells, monocytes, and neutrophils up to 2 years post sampling. Results obtained from frozen stabilized and fresh blood samples were compared for validation purposes and correlated to differential blood counts from a conventional hematology analyzer. Clinical applicability of the new technique was verified by using samples from a treatment study for feline infectious peritonitis (FIP). Using the new SMT protocol on retained samples, it could be demonstrated that long-term storage of these SMT tubes is also possible. In summary, the newly adapted SMT protocol proved suitable for performing flow cytometry analysis on stored feline whole blood samples, thus opening up new avenues for veterinary research on a variety of aspects of clinical interest.
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Affiliation(s)
- Katharina Zwicklbauer
- LMU Small Animal Clinic, Centre for Clinical Veterinary Medicine, LMU Munich, Munich, Germany
| | | | - Daniela Krentz
- LMU Small Animal Clinic, Centre for Clinical Veterinary Medicine, LMU Munich, Munich, Germany
| | - Laura Kolberg
- Division of Paediatric Infectious Diseases, Dr. von Hauner Children’s Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Martin Alberer
- Division of Paediatric Infectious Diseases, Dr. von Hauner Children’s Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Yury Zablotski
- LMU Small Animal Clinic, Centre for Clinical Veterinary Medicine, LMU Munich, Munich, Germany
| | - Katrin Hartmann
- LMU Small Animal Clinic, Centre for Clinical Veterinary Medicine, LMU Munich, Munich, Germany
| | - Ulrich von Both
- Division of Paediatric Infectious Diseases, Dr. von Hauner Children’s Hospital, University Hospital, LMU Munich, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Sonja Härtle
- Department of Veterinary Sciences, AG Immunology, LMU Munich, Planegg, Germany
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4
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Perez-Gonzalez A, Lopes T, Martinez L, Bispo C, Gardner R, Riddell A. Evaluation of Sort Recovery via Rmax. Curr Protoc 2024; 4:e986. [PMID: 38363042 DOI: 10.1002/cpz1.986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Cell sorting performance can be evaluated in regard to the purity and recovery of the sorted fractions. The purity provides checks on sample quality, acquisition settings, gating strategy, and the sort decisions made by the instrument, but alone it is not sufficient to evaluate sorting performance. Recovery, defined here as the number of target particles sorted relative to the number of original target particles to be sorted, is a key metric of sort fitness and performance but is often neglected due to difficulties in its measurement. Both purity and recovery require re-sampling of the sorted fraction, but unlike determining purity, calculating recovery calls for the absolute counting of particles in the sorted fraction that comes with large errors, and may not be feasible for rare populations or precious samples. Here, we describe a recently developed metric and method for calculating sort recovery called Rmax, representing the maximum expected recovery for a particular set of instrument settings. Rmax calculation avoids re-sampling of the total sorted fraction and absolute counting, being instead based on the ratios of target and non-target populations in the original pre-sort sample and in the waste stream or center stream catch. The Rmax method is ideal to evaluate and troubleshoot the optimum drop-charge delay of the sorter or any instrument-related failures that will affect sort performance. It can be used as a daily quality control check but can be particularly useful to assess instrument fitness before single-cell or rare population sorts. Because the sorted fraction is not perturbed, we can calculate Rmax during the sort run. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Evaluating sorter setup with Rmax Basic Protocol 2: Finding the maximum Rmax: scanning over the drop charge delay Alternate Protocol: Finding the maximum Rmax for cells: scanning over the drop charge delay Basic Protocol 3: Estimating sorted cell number with Rmax.
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Affiliation(s)
- Alexis Perez-Gonzalez
- Department of Microbiology and Immunology, The University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- Melbourne Cytometry Platform, The University of Melbourne, Parkville, Victoria, Australia
| | - Telma Lopes
- Roche Pharma Research and Early Development (pRED), Basel, Switzerland
| | - Lola Martinez
- Flow Cytometry Core Unit. Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Claudia Bispo
- Flow Cytometry Core Facility, AbbVie Biotherapeutics Inc., South San Francisco, California
| | - Rui Gardner
- Flow Cytometry Core Facility, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Andy Riddell
- Flow Cytometry Science and Technology Platform, The Francis Crick Institute, London, United Kingdom
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5
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Adel M, Allam A, Sayour AE, Ragai HF, Umezu S, Fath El-Bab AMR. Fabrication of Spiral Low-Cost Microchannel with Trapezoidal Cross Section for Cell Separation Using a Grayscale Approach. MICROMACHINES 2023; 14:1340. [PMID: 37512651 PMCID: PMC10384897 DOI: 10.3390/mi14071340] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 06/25/2023] [Accepted: 06/28/2023] [Indexed: 07/30/2023]
Abstract
Trapezoidal cross-sectional spiral microfluidic channels showed high resolution and throughput in cell separation in bio-applications. The main challenges are the complexity and high cost of the fabrication process of trapezoidal cross-sectional channels on the micro-scale. In this work, we present the application of grayscale in microfluidic channel design to overcome the complexity of the fabrication process. We also use direct engraving with a CO2 laser beam on polymethyl methacrylate (PMMA) material to drastically reduce the microfluidic chip's cost (to <30 cents) and fabrication time (to 20 min). The capability of the present fabrication methodology for cell sorting applications is demonstrated through experimental tests for the separation of white blood cells (WBCs) from whole blood at different dilution factors. The experimental results indicated that an 800 µL/min flow rate provided the optimal separation efficiency using the fabricated chip. A 90.14% separation efficiency at 1% hematocrit diluted blood sample was reported.
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Affiliation(s)
- Mohamed Adel
- Department of Mechatronics and Robotics Engineering, Egypt-Japan University of Science and Technology (E-JUST), Alexandria 21934, Egypt
- Mechanical Engineering Department, Helwan University, Cairo 11792, Egypt
| | - Ahmed Allam
- Department of Electronics and Communications Engineering, Egypt-Japan University of Science and Technology (E-JUST), Alexandria 21934, Egypt
| | - Ashraf E Sayour
- Molecular Biomimetics Research Group, Animal Health Research Institute, Agricultural Research Center, Giza 12618, Egypt
| | - Hani F Ragai
- Electronics and Communications Department, Faculty of Engineering, Ain Shams University, Cairo 11517, Egypt
| | - Shinjiro Umezu
- Department of Modern Mechanical Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Ahmed M R Fath El-Bab
- Department of Mechatronics and Robotics Engineering, Egypt-Japan University of Science and Technology (E-JUST), Alexandria 21934, Egypt
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6
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Huang C, Jiang Y, Li Y, Zhang H. Droplet Detection and Sorting System in Microfluidics: A Review. MICROMACHINES 2022; 14:mi14010103. [PMID: 36677164 PMCID: PMC9867185 DOI: 10.3390/mi14010103] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/23/2022] [Accepted: 12/26/2022] [Indexed: 05/26/2023]
Abstract
Since being invented, droplet microfluidic technologies have been proven to be perfect tools for high-throughput chemical and biological functional screening applications, and they have been heavily studied and improved through the past two decades. Each droplet can be used as one single bioreactor to compartmentalize a big material or biological population, so millions of droplets can be individually screened based on demand, while the sorting function could extract the droplets of interest to a separate pool from the main droplet library. In this paper, we reviewed droplet detection and active sorting methods that are currently still being widely used for high-through screening applications in microfluidic systems, including the latest updates regarding each technology. We analyze and summarize the merits and drawbacks of each presented technology and conclude, with our perspectives, on future direction of development.
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Affiliation(s)
- Can Huang
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77842, USA
| | - Yuqian Jiang
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Yuwen Li
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77842, USA
| | - Han Zhang
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77842, USA
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7
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Analysis of Tumor-Infiltrating T-Cell Transcriptomes Reveal a Unique Genetic Signature across Different Types of Cancer. Int J Mol Sci 2022; 23:ijms231911065. [PMID: 36232369 PMCID: PMC9569723 DOI: 10.3390/ijms231911065] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/09/2022] [Accepted: 08/16/2022] [Indexed: 11/16/2022] Open
Abstract
CD8+ and CD4+ T-cells play a key role in cellular immune responses against cancer by cytotoxic responses and effector lineages differentiation, respectively. These subsets have been found in different types of cancer; however, it is unclear whether tumor-infiltrating T-cell subsets exhibit similar transcriptome profiling across different types of cancer in comparison with healthy tissue-resident T-cells. Thus, we analyzed the single cell transcriptome of five tumor-infiltrating CD4-T, CD8-T and Treg cells obtained from different types of cancer to identify specific pathways for each subset in malignant environments. An in silico analysis was performed from single-cell RNA-sequencing data available in public repositories (Gene Expression Omnibus) including breast cancer, melanoma, colorectal cancer, lung cancer and head and neck cancer. After dimensionality reduction, clustering and selection of the different subpopulations from malignant and nonmalignant datasets, common genes across different types of cancer were identified and compared to nonmalignant genes for each T-cell subset to identify specific pathways. Exclusive pathways in CD4+ cells, CD8+ cells and Tregs, and common pathways for the tumor-infiltrating T-cell subsets were identified. Finally, the identified pathways were compared with RNAseq and proteomic data obtained from T-cell subsets cultured under malignant environments and we observed that cytokine signaling, especially Th2-type cytokine, was the top overrepresented pathway in Tregs from malignant samples.
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8
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Park S, Lee S, Kim HS, Choi HJ, Jeong OC, Lin R, Cho Y, Lee MH. Square microchannel enables to focus and orient ellipsoidal Euglena gracilis cells by two-dimensional acoustic standing wave. Mikrochim Acta 2022; 189:331. [PMID: 35969307 DOI: 10.1007/s00604-022-05439-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 07/31/2022] [Indexed: 11/26/2022]
Abstract
Flow cytometry has become an indispensable tool for counting, analyzing, and sorting large cell populations in biological research and medical practice. Unfortunately, it has limitations in the analysis of non-spherically shaped cells due to the variation of their alignment with respect to the flow direction and, hence, the optical interrogation axis, resulting in unreliable cell analysis. Here, we present a simple on-chip acoustofluidic method to fix the orientation of ellipsoidal cells and focus them into a single, aligned stream. Specifically, by generating acoustic standing waves inside a 100 ⋅ 100 µm square-shaped microchannel, we successfully aligned and focused up to 97.7% of a population of Euglena gracilis (an ellipsoidal shaped microalgal species) cells in the center of the microchannel with high precision at a volume rate of 25 to 200 µL min-1. Uniform positioning of ellipsoidal cells is essential for making flow cytometry applicable to the investigation of a greater variety of cell populations and is expected to be beneficial for ecological studies and aquaculture.
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Affiliation(s)
- Sungryul Park
- School of Integrative Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea
| | | | - Hyun Soo Kim
- Department of Electronic Engineering, Kwangwoon University, Seoul, 01897, Republic of Korea
| | - Hong Jin Choi
- Department of Digital Anti-Aging Health Care, Inje University, Gimhae-si, 50834, Republic of Korea
| | - Ok Chan Jeong
- Department of Biomedical Engineering, Inje University, Gimhae-si, 50834, Republic of Korea
| | - Ruixian Lin
- School of Integrative Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Younghak Cho
- Department of Mechanical Design and Robot Engineering, Seoul National University of Science & Technology, Seoul, 01811, Republic of Korea.
| | - Min-Ho Lee
- School of Integrative Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea.
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9
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Li Y, Cai S, Shen H, Chen Y, Ge Z, Yang W. Recent advances in acoustic microfluidics and its exemplary applications. BIOMICROFLUIDICS 2022; 16:031502. [PMID: 35712527 PMCID: PMC9197543 DOI: 10.1063/5.0089051] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 05/24/2022] [Indexed: 05/14/2023]
Abstract
Acoustic-based microfluidics has been widely used in recent years for fundamental research due to its simple device design, biocompatibility, and contactless operation. In this article, the basic theory, typical devices, and technical applications of acoustic microfluidics technology are summarized. First, the theory of acoustic microfluidics is introduced from the classification of acoustic waves, acoustic radiation force, and streaming flow. Then, various applications of acoustic microfluidics including sorting, mixing, atomization, trapping, patterning, and acoustothermal heating are reviewed. Finally, the development trends of acoustic microfluidics in the future were summarized and looked forward to.
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Affiliation(s)
- Yue Li
- School of Electromechanical and Automotive Engineering, Yantai University, Yantai 264005, China
| | - Shuxiang Cai
- School of Electromechanical and Automotive Engineering, Yantai University, Yantai 264005, China
| | - Honglin Shen
- School of Electromechanical and Automotive Engineering, Yantai University, Yantai 264005, China
| | - Yibao Chen
- School of Electromechanical and Automotive Engineering, Yantai University, Yantai 264005, China
| | - Zhixing Ge
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, China
| | - Wenguang Yang
- School of Electromechanical and Automotive Engineering, Yantai University, Yantai 264005, China
- Author to whom correspondence should be addressed:
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10
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Ogundero A, Vignola M, Connelly S, Sloan WT. Validating Flow Cytometry as a Method for Quantifying Bdellovibrio Predatory Bacteria and Its Prey for Microbial Ecology. Microbiol Spectr 2022; 10:e0103321. [PMID: 35196816 PMCID: PMC8865432 DOI: 10.1128/spectrum.01033-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 01/31/2022] [Indexed: 12/19/2022] Open
Abstract
Bdellovibrio bacteriovorus is a predatory, Gram-negative bacteria that feeds on many pathogenic bacteria and has been investigated as a possible solution for mitigating biofilms in different fields. The application depends on more fundamental ecological studies into the dynamics between Bdellovibrio and their prey. To do so requires an accurate, reliable, and, preferably rapid, way of enumerating the cells. Flow cytometry (FCM) is potentially a rapid, accurate, and inexpensive tool for this, but it has yet to be validated in the enumeration of Bdellovibrio. In this study, we developed a protocol to measure the number of Bdellovibrio in samples of various densities using FCM and compared the results with those of other methods: optical density (OD), PFU assay (PFU), and quantitative PCR (qPCR). We observed a strong correlation between values obtained using FCM and PFU (ρ = 0.923) and FCM and qPCR (ρ = 0.987). Compared to optical density there was a much weaker correlation (ρ = 0.784), which was to be expected given the well-documented uncertainty in converting optical density (OD) to cell numbers. The FCM protocol was further validated by demonstrating its ability to distinguish and count mixed populations of Bdellovibrio and the prey Pseudomonas. Thus, the accuracy of FCM as well as its speed and reproducibility make it a suitable alternative for measuring Bdellovibrio cell numbers, especially where many samples are required to capture the dynamics of predator-prey interactions. IMPORTANCE The rise of antibiotic resistance and the unwanted growth of bacteria is a universally growing problem. Predatory bacteria can be used as a biological alternative to antibiotics because they grow by feeding on other bacteria. To apply this effectively requires further study and a deeper understanding of the forces that drive a prey population to elimination. Initially, such studies require more reliable methods to count these cells. Flow cytometry (FCM) is potentially a rapid, accurate, and inexpensive tool for this, but it has yet to be validated for predatory bacteria. This study develops a protocol to count the predatory bacteria Bdellovibrio bacteriovorus and its Pseudomonas prey using FCM and compare the results with those of other methods, demonstrating its ability for studies into B. bacteriovorus predation dynamics. This could lead to the use of B. bacteriovorus for killing bacterial biofilms in fields, such as drinking water and agriculture.
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Affiliation(s)
- Ayo Ogundero
- Infrastructure and Environment, School of Engineering, University of Glasgow, Glasgow, UK
| | - Marta Vignola
- Infrastructure and Environment, School of Engineering, University of Glasgow, Glasgow, UK
| | - Stephanie Connelly
- Infrastructure and Environment, School of Engineering, University of Glasgow, Glasgow, UK
| | - William T. Sloan
- Infrastructure and Environment, School of Engineering, University of Glasgow, Glasgow, UK
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11
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Wang Y, Xue P, Cao M, Yu T, Lane ST, Zhao H. Directed Evolution: Methodologies and Applications. Chem Rev 2021; 121:12384-12444. [PMID: 34297541 DOI: 10.1021/acs.chemrev.1c00260] [Citation(s) in RCA: 184] [Impact Index Per Article: 61.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Directed evolution aims to expedite the natural evolution process of biological molecules and systems in a test tube through iterative rounds of gene diversifications and library screening/selection. It has become one of the most powerful and widespread tools for engineering improved or novel functions in proteins, metabolic pathways, and even whole genomes. This review describes the commonly used gene diversification strategies, screening/selection methods, and recently developed continuous evolution strategies for directed evolution. Moreover, we highlight some representative applications of directed evolution in engineering nucleic acids, proteins, pathways, genetic circuits, viruses, and whole cells. Finally, we discuss the challenges and future perspectives in directed evolution.
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Affiliation(s)
- Yajie Wang
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Pu Xue
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Mingfeng Cao
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Tianhao Yu
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Stephan T Lane
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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12
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Feng X, Holzinger A, Permann C, Anderson D, Yin Y. Characterization of Two Zygnema Strains ( Zygnema circumcarinatum SAG 698-1a and SAG 698-1b) and a Rapid Method to Estimate Nuclear Genome Size of Zygnematophycean Green Algae. FRONTIERS IN PLANT SCIENCE 2021; 12:610381. [PMID: 33643345 PMCID: PMC7902510 DOI: 10.3389/fpls.2021.610381] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 01/15/2021] [Indexed: 05/07/2023]
Abstract
Zygnematophyceae green algae (ZGA) have been shown to be the closest relatives of land plants. Three nuclear genomes (Spirogloea muscicola, Mesotaenium endlicherianum, and Penium margaritaceum) of ZGA have been recently published, and more genomes are underway. Here we analyzed two Zygnema circumcarinatum strains SAG 698-1a (mating +) and SAG 698-1b (mating -) and found distinct cell sizes and other morphological differences. The molecular identities of the two strains were further investigated by sequencing their 18S rRNA, psaA and rbcL genes. These marker genes of SAG 698-1a were surprisingly much more similar to Z. cylindricum (SAG 698-2) than to SAG 698-1b. Phylogenies of these marker genes also showed that SAG 698-1a and SAG 698-1b were well separated into two different Zygnema clades, where SAG 698-1a was clustered with Z. cylindricum, while SAG 698-1b was clustered with Z. tunetanum. Additionally, physiological parameters like ETRmax values differed between SAG 698-1a and SAG 698-1b after 2 months of cultivation. The de-epoxidation state (DEPS) of the xanthophyll cycle pigments also showed significant differences. Surprisingly, the two strains could not conjugate, and significantly differed in the thickness of the mucilage layer. Additionally, ZGA cell walls are highly enriched with sticky and acidic polysaccharides, and therefore the widely used plant nuclear extraction protocols do not work well in ZGA. Here, we also report a fast and simple method, by mechanical chopping, for efficient nuclear extraction in the two SAG strains. More importantly, the extracted nuclei were further used for nuclear genome size estimation of the two SAG strains by flow cytometry (FC). To confirm the FC result, we have also used other experimental methods for nuclear genome size estimation of the two strains. Interestingly, the two strains were found to have very distinct nuclear genome sizes (313.2 ± 2.0 Mb in SAG 698-1a vs. 63.5 ± 0.5 Mb in SAG 698-1b). Our multiple lines of evidence strongly indicate that SAG 698-1a possibly had been confused with SAG 698-2 prior to 2005, and most likely represents Z. cylindricum or a closely related species.
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Affiliation(s)
- Xuehuan Feng
- Department of Food Science and Technology, Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, United States
| | | | | | - Dirk Anderson
- Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Yanbin Yin
- Department of Food Science and Technology, Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, United States
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13
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Leslie J, Robinson SM, Oakley F, Luli S. Non-invasive synchronous monitoring of neutrophil migration using whole body near-infrared fluorescence-based imaging. Sci Rep 2021; 11:1415. [PMID: 33446811 PMCID: PMC7809207 DOI: 10.1038/s41598-021-81097-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 12/30/2020] [Indexed: 12/20/2022] Open
Abstract
Advances in fluorescence imaging coupled with the generation of near infrared probes have significantly improved the capabilities of non-invasive, real-time imaging in whole animals. In this study we were able to overcome a limitation of in vivo fluorescence imaging and have established a dual cell tracking method where two different cell types can be monitored according to the spectral signature of the cell labelling fluorophore. Using a mouse model of acute liver injury, we have characterised the in vivo migration patterns of wild type and transgenic neutrophils with impaired chemotaxis. Here, we were able to demonstrate that IVIS provides a sensitive multiplexing technology to differentiate two different cell populations based on the spectral signature of the cell labelling fluorophores. This spectral unmixing methodology has the potential to uncover multidimensional cellular interactions involved in many diseases such as fibrosis and cancer. In vivo spectral un-mixing provides a useful tool for monitoring multiple biological process in real-time in the same animal.
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Affiliation(s)
- Jack Leslie
- Newcastle Fibrosis Research Group, Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Stuart M Robinson
- Newcastle Fibrosis Research Group, Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
- Department of Hepatobiliary Surgery, Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Fiona Oakley
- Newcastle Fibrosis Research Group, Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Saimir Luli
- Newcastle Fibrosis Research Group, Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK.
- Faculty of Medical Sciences, Preclinical In Vivo Imaging, Biosciences Institute, Newcastle University, 4th Floor, William Leech Building, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK.
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14
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An Overview of Flow Cytometry: Its Principles and Applications in Allergic Disease Research. Methods Mol Biol 2021; 2223:169-182. [PMID: 33226595 DOI: 10.1007/978-1-0716-1001-5_13] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Flow cytometry is a popular technique used for both clinical and research purposes. It involves laser-based technology to characterize cells based on size, shape, and complexity. Additionally, flow cytometers are equipped with the ability to take fluorescence measurements at multiple wavelengths. This capability makes the flow cytometer a practical resource in the utilization of fluorescently conjugated antibodies, fluorescent proteins, DNA binding dyes, viability dyes, and ion indicator dyes. As the technology advances, the number of parameters a flow cytometer can measure has increased tremendously, and now some has the capacity to analyze 30-50 or more parameters on a single cell. Here, we describe the basic principles involved in the mechanics and procedures of flow cytometry along with an insight into applications of flow cytometry techniques for biomedical and allergic disease research.
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15
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Bianchi M, Sivarajan R, Walles T, Hackenberg S, Steinke M. Susceptibility of primary human airway epithelial cells to Bordetella pertussis adenylate cyclase toxin in two- and three-dimensional culture conditions. Innate Immun 2020; 27:89-98. [PMID: 33317363 PMCID: PMC7780358 DOI: 10.1177/1753425920979354] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The human pathogen Bordetella pertussis targets the respiratory epithelium and causes whooping cough. Its virulence factor adenylate cyclase toxin (CyaA) plays an important role in the course of infection. Previous studies on the impact of CyaA on human epithelial cells have been carried out using cell lines derived from the airways or the intestinal tract. Here, we investigated the interaction of CyaA and its enzymatically inactive but fully pore-forming toxoid CyaA-AC– with primary human airway epithelial cells (hAEC) derived from different anatomical sites (nose and tracheo-bronchial region) in two-dimensional culture conditions. To assess possible differences between the response of primary hAEC and respiratory cell lines directly, we included HBEC3-KT in our studies. In comparative analyses, we studied the impact of both the toxin and the toxoid on cell viability, intracellular cAMP concentration and IL-6 secretion. We found that the selected hAEC, which lack CD11b, were differentially susceptible to both CyaA and CyaA-AC–. HBEC3-KT appeared not to be suitable for subsequent analyses. Since the nasal epithelium first gets in contact with airborne pathogens, we further studied the effect of CyaA and its toxoid on the innate immunity of three-dimensional tissue models of the human nasal mucosa. The present study reveals first insights in toxin–cell interaction using primary hAEC.
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Affiliation(s)
- Maria Bianchi
- Chair of Tissue Engineering and Regenerative Medicine, University Hospital Würzburg, Germany
| | - Rinu Sivarajan
- Chair of Tissue Engineering and Regenerative Medicine, University Hospital Würzburg, Germany
| | - Thorsten Walles
- Department of Thoracic Surgery, University Medicine Magdeburg, Germany
| | - Stephan Hackenberg
- Department of Oto-Rhino-Laryngology, Plastic, Aesthetic and Reconstructive Head and Neck Surgery, University Hospital Würzburg, Germany
| | - Maria Steinke
- Chair of Tissue Engineering and Regenerative Medicine, University Hospital Würzburg, Germany
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16
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Pfister G, Toor SM, Sasidharan Nair V, Elkord E. An evaluation of sorter induced cell stress (SICS) on peripheral blood mononuclear cells (PBMCs) after different sort conditions - Are your sorted cells getting SICS? J Immunol Methods 2020; 487:112902. [DOI: 10.1016/j.jim.2020.112902] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 09/10/2020] [Accepted: 10/13/2020] [Indexed: 01/02/2023]
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17
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Wongtawan T, Dararatana N, Thongkittidilok C, Kornmatitsuk S, Oonkhanond B. Enrichment of bovine X-sperm using microfluidic dielectrophoretic chip: A proof-of- concept study. Heliyon 2020; 6:e05483. [PMID: 33241151 PMCID: PMC7672294 DOI: 10.1016/j.heliyon.2020.e05483] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 09/07/2020] [Accepted: 11/06/2020] [Indexed: 11/30/2022] Open
Abstract
The microfluidic dielectrophoretic (MF-DEP) chip is a new, economical and readily-available technology that might be used to enrich X-sperm for increasing female offspring in dairy farms. In this study, we sought to develop an MF-DEP chip to enrich X bovine sperm. The MF-DEP chip was composed of an electrode attached to a glass slide and a microchannel made from polydimethylsiloxane. Sex-sorted sperm from flow cytometry were used to identify optimal electric field conditions while unsorted sperm were later tested for sorting efficiency. The results show that during dielectrophoresis some sperm attached to the electrode (called positive DEP; pDEP) whereas other moved away from the electrode (called negative DEP; nDEP). X and Y-sperm responded to dielectrophoresis differently depending on various factors such as buffers, voltages, and frequencies. We found that the condition 4 V 1 MHz significantly reduced (P < 0.05) the percentage of Y-sperm to nearly 30 and therefore enriched X-sperm. The sorting efficiency was dependent on buffer, bull, sorting cycle, flow rate, electrical voltage, and frequency. Notably, the best sorting buffer found in this experiment was the conducting buffer, but this buffer significantly reduced sperm viability and motility. Other sperm-friendly buffers, TRIS and mHTF, were also used, but could not enrich X-sperm. In conclusion, this is a proof of concept that the MF-DEP chip can be effectively used to enrich bovine X-sperm. However, more research must be performed particularly to find the best sorting buffer to effectively sex-sort sperm while providing high motility and sperm viability.
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Affiliation(s)
- Tuempong Wongtawan
- Akkhraratchakumari Veterinary College, Walailak University, Thai Buri Tha Sala, Nakhon Si Thammarat, 80160, Thailand
- Centre for One Health, Walailak University, Thai Buri Tha Sala, Nakhon Si Thammarat, 80160, Thailand
- Laboratory of Veterinary Biomedicine, Mahidol University, Salaya, Puttamonthon, Nakhon Pathom, 73170, Thailand
- Corresponding author.
| | - Naruphorn Dararatana
- Laboratory of Veterinary Biomedicine, Mahidol University, Salaya, Puttamonthon, Nakhon Pathom, 73170, Thailand
- Department of Biomedical Engineering, Faculty of Engineer, Mahidol University, Salaya, Puttamonthon, Nakhon Pathom, 73170, Thailand
| | - Chommanart Thongkittidilok
- Akkhraratchakumari Veterinary College, Walailak University, Thai Buri Tha Sala, Nakhon Si Thammarat, 80160, Thailand
- Centre for One Health, Walailak University, Thai Buri Tha Sala, Nakhon Si Thammarat, 80160, Thailand
| | - Sudsaijai Kornmatitsuk
- Laboratory of Veterinary Biomedicine, Mahidol University, Salaya, Puttamonthon, Nakhon Pathom, 73170, Thailand
- Department of Clinical Science and Public Health, Faculty of Veterinary Science, Mahidol University, Salaya, Puttamonthon, Nakhon Pathom, 73170, Thailand
| | - Bovornlak Oonkhanond
- Department of Biomedical Engineering, Faculty of Engineer, Mahidol University, Salaya, Puttamonthon, Nakhon Pathom, 73170, Thailand
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18
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Yamada S, Nomura S. Review of Single-Cell RNA Sequencing in the Heart. Int J Mol Sci 2020; 21:E8345. [PMID: 33172208 PMCID: PMC7664385 DOI: 10.3390/ijms21218345] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/25/2020] [Accepted: 11/05/2020] [Indexed: 02/07/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) technology is a powerful, rapidly developing tool for characterizing individual cells and elucidating biological mechanisms at the cellular level. Cardiovascular disease is one of the major causes of death worldwide and its precise pathology remains unclear. scRNA-seq has provided many novel insights into both healthy and pathological hearts. In this review, we summarize the various scRNA-seq platforms and describe the molecular mechanisms of cardiovascular development and disease revealed by scRNA-seq analysis. We then describe the latest technological advances in scRNA-seq. Finally, we discuss how to translate basic research into clinical medicine using scRNA-seq technology.
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Affiliation(s)
- Shintaro Yamada
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8654, Japan
| | - Seitaro Nomura
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8654, Japan
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19
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Domenick TM, Gill EL, Vedam-Mai V, Yost RA. Mass Spectrometry-Based Cellular Metabolomics: Current Approaches, Applications, and Future Directions. Anal Chem 2020; 93:546-566. [PMID: 33146525 DOI: 10.1021/acs.analchem.0c04363] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Taylor M Domenick
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Emily L Gill
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104-4283, United States.,Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104-4283, United States
| | - Vinata Vedam-Mai
- Department of Neurology, University of Florida, Gainesville, Florida 32610, United States
| | - Richard A Yost
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
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20
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Maes E, Cools N, Willems H, Baggerman G. FACS-Based Proteomics Enables Profiling of Proteins in Rare Cell Populations. Int J Mol Sci 2020; 21:ijms21186557. [PMID: 32911660 PMCID: PMC7554798 DOI: 10.3390/ijms21186557] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/31/2020] [Accepted: 09/04/2020] [Indexed: 12/22/2022] Open
Abstract
Understanding disease pathology often does not require an overall proteomic analysis of clinical samples but rather the analysis of different, often rare, subpopulations of cells in a heterogeneous mixture of cell types. For the isolation of pre-specified cellular subtypes, fluorescence activated cell sorting (FACS) is commonly used for its ability to isolate the required cell populations with high purity, even of scarce cell types. The proteomic analysis of a limited number of FACS-sorted cells, however, is very challenging as both sample preparation inefficiencies and limits in terms of instrument sensitivity are present. In this study, we used CD14+CD15+ immune cells sorted out of peripheral blood mononuclear cells isolated from whole blood to improve and evaluate FACS-based proteomics. To optimize both the protein extraction protocol and the mass spectrometry (MS) data acquisition method, PBMCs as well as commercialized HeLa digest were used. To reflect the limited number of sorted cells in some clinical samples, different numbers of sorted cells (1000, 5000, 10,000, or 50,000) were used. This allowed comparing protein profiles across samples with limited protein material and provided further insights in the benefits and limitations of using a very limited numbers of cells.
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Affiliation(s)
- Evelyne Maes
- Food & Bio-Based Products, AgResearch Ltd., Lincoln 7674, New Zealand;
| | - Nathalie Cools
- Laboratory of Experimental Hematology, Faculty of Medicine and Health Sciences, Vaccine and Infectious Disease Institute (VaxInfectio), Antwerp University Hospital (UZA), University of Antwerp, 2020 Antwerpen, Belgium;
- Center for Cell Therapy and Regenerative Medicine, Antwerp University Hospital, 2650 Edegem, Belgium
| | - Hanny Willems
- Centre for Proteomics, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerpen, Belgium;
- Health Unit, Vlaamse Instelling voor Technologisch Onderzoek (VITO), Boeretang 200, 2400 Mol, Belgium
| | - Geert Baggerman
- Centre for Proteomics, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerpen, Belgium;
- Health Unit, Vlaamse Instelling voor Technologisch Onderzoek (VITO), Boeretang 200, 2400 Mol, Belgium
- Correspondence: ; Tel.: +32-476472918
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21
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Leal V, Ribeiro CF, Oliveiros B, António N, Silva S. Intrinsic Vascular Repair by Endothelial Progenitor Cells in Acute Coronary Syndromes: an Update Overview. Stem Cell Rev Rep 2020; 15:35-47. [PMID: 30345477 DOI: 10.1007/s12015-018-9857-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Bone marrow-derived endothelial progenitor cells (EPCs) play a key role in the maintenance of endothelial homeostasis and endothelial repair at areas of vascular damage. The quantification of EPCs in peripheral blood by flow cytometry is a strategy to assess this reparative capacity. The number of circulating EPCs is inversely correlated with the number of cardiovascular risk factors and to the occurrence of cardiovascular events. Therefore, monitoring EPCs levels may provide an accurate assessment of susceptibility to cardiovascular injury, greatly improving risk stratification of patients with high cardiovascular risk, such as those with an acute myocardial infarction. However, there are many issues in the field of EPC identification and quantification that remain unsolved. In fact, there have been conflicting protocols used to the phenotypic identification of EPCs and there is still no consensual immunophenotypical profile that corresponds exactly to EPCs. In this paper we aim to give an overview on EPCs-mediated vascular repair with special focus on acute coronary syndromes and to discuss the different phenotypic profiles that have been used to identify and quantify circulating EPCs in several clinical studies. Finally, we will synthesize evidence on the prognostic role of EPCs in patients with high cardiovascular risk.
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Affiliation(s)
- Vânia Leal
- Group of Pharmacology and Pharmaceutical Care, Faculty of Pharmacy, University of Coimbra, Pólo das Ciências da Saúde, Azinhaga de Santa Comba, 3000-548, Coimbra, Portugal.
| | - Carlos Fontes Ribeiro
- Institute of Pharmacology and Experimental Therapeutics, Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Bárbara Oliveiros
- Laboratory of Biostatistics and Medical Informatics, Faculty of Medicine, University of Coimbra, Coimbra, Portugal.,Coimbra Institute for Biomedical Imaging and Translational Research, University of Coimbra, Coimbra, Portugal.,Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Natália António
- Institute of Pharmacology and Experimental Therapeutics, Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, Coimbra, Portugal.,Cardiology Department, Coimbra Hospital and Universitary Centre, Coimbra, Portugal
| | - Sónia Silva
- Group of Pharmacology and Pharmaceutical Care, Faculty of Pharmacy, University of Coimbra, Pólo das Ciências da Saúde, Azinhaga de Santa Comba, 3000-548, Coimbra, Portugal.,Institute of Pharmacology and Experimental Therapeutics, Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, Coimbra, Portugal
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22
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Xie X, Nóbrega R, Pšenička M. Spermatogonial Stem Cells in Fish: Characterization, Isolation, Enrichment, and Recent Advances of In Vitro Culture Systems. Biomolecules 2020; 10:E644. [PMID: 32331205 PMCID: PMC7226347 DOI: 10.3390/biom10040644] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/13/2020] [Accepted: 04/14/2020] [Indexed: 12/14/2022] Open
Abstract
Spermatogenesis is a continuous and dynamic developmental process, in which a single diploid spermatogonial stem cell (SSC) proliferates and differentiates to form a mature spermatozoon. Herein, we summarize the accumulated knowledge of SSCs and their distribution in the testes of teleosts. We also reviewed the primary endocrine and paracrine influence on spermatogonium self-renewal vs. differentiation in fish. To provide insight into techniques and research related to SSCs, we review available protocols and advances in enriching undifferentiated spermatogonia based on their unique physiochemical and biochemical properties, such as size, density, and differential expression of specific surface markers. We summarize in vitro germ cell culture conditions developed to maintain proliferation and survival of spermatogonia in selected fish species. In traditional culture systems, sera and feeder cells were considered to be essential for SSC self-renewal, in contrast to recently developed systems with well-defined media and growth factors to induce either SSC self-renewal or differentiation in long-term cultures. The establishment of a germ cell culture contributes to efficient SSC propagation in rare, endangered, or commercially cultured fish species for use in biotechnological manipulation, such as cryopreservation and transplantation. Finally, we discuss organ culture and three-dimensional models for in vitro investigation of fish spermatogenesis.
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Affiliation(s)
- Xuan Xie
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in Ceske Budejovice, Zátiší 728/II, 389 25 Vodňany, Czech Republic;
| | - Rafael Nóbrega
- Reproductive and Molecular Biology Group, Department of Morphology, Institute of Biosciences, São Paulo State University, Botucatu, SP 18618-970, Brazil;
| | - Martin Pšenička
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in Ceske Budejovice, Zátiší 728/II, 389 25 Vodňany, Czech Republic;
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23
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Holler S, Hanczyc MM. Autoselective transport of mammalian cells with a chemotactic droplet. Sci Rep 2020; 10:5525. [PMID: 32218452 PMCID: PMC7099059 DOI: 10.1038/s41598-020-62325-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 03/11/2020] [Indexed: 11/17/2022] Open
Abstract
Liquid chemical droplets, as models of artificial life, when pushed away from equilibrium possess some life-like behaviors such as fission, fusion, movement and chemotaxis. Chemotaxis, directed motion in response to external gradients, is typically an important process in living systems, but certain artificial systems are also capable of this activity. Previously it was shown that droplet-based chemotactic systems when interfaced with biological systems can act as transporters to move cargo such as hydrogel alginate capsules containing living cells. Here the effectiveness of our system to transport different mammalian cell lines (H460, H1299, A549, HEK293T and HS68) was tested. It was discovered that some lung cancer cell lines release surfactants only when placed in the hydrogel capsules. These surfactants establish the interface between the encapsulated cells and the droplet and also support the chemotaxis of the droplet. Because of this, the droplet-mediated transport system is selective for living cells that produce biosurfactants. This is an example of how the integration of artificial life and biological life could be designed where the systems augment each other and function together as a unit. In this case the living system produces the surfactants that the droplet needs for cargo transport and the artificial system provides the transport for the otherwise sessile mammalian cells. Future applications of droplet-based cell handling that is able to distinguish between cells based not only on viability but cell type, developmental stage or other quantifiable traits are considered.
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Affiliation(s)
- Silvia Holler
- Laboratory for Artificial Biology, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123, Trento, Italy
| | - Martin M Hanczyc
- Laboratory for Artificial Biology, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123, Trento, Italy.
- Chemical and Biological Engineering, University of New Mexico, MSC01 1120, Albuquerque, NM, 87131-0001, USA.
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24
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Kreer C, Gruell H, Mora T, Walczak AM, Klein F. Exploiting B Cell Receptor Analyses to Inform on HIV-1 Vaccination Strategies. Vaccines (Basel) 2020; 8:vaccines8010013. [PMID: 31906351 PMCID: PMC7157687 DOI: 10.3390/vaccines8010013] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 12/23/2019] [Accepted: 12/24/2019] [Indexed: 12/22/2022] Open
Abstract
The human antibody repertoire is generated by the recombination of different gene segments as well as by processes of somatic mutation. Together these mechanisms result in a tremendous diversity of antibodies that are able to combat various pathogens including viruses and bacteria, or malignant cells. In this review, we summarize the opportunities and challenges that are associated with the analyses of the B cell receptor repertoire and the antigen-specific B cell response. We will discuss how recent advances have increased our understanding of the antibody response and how repertoire analyses can be exploited to inform on vaccine strategies, particularly against HIV-1.
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Affiliation(s)
- Christoph Kreer
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; (C.K.); (H.G.)
| | - Henning Gruell
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; (C.K.); (H.G.)
- German Center for Infection Research, Partner Site Bonn-Cologne, 50931 Cologne, Germany
| | - Thierry Mora
- Laboratoire de Physique de l’École Normale Supérieure (PSL University), CNRS, Sorbonne Université, Université de Paris, 75005 Paris, France; (T.M.); (A.M.W.)
| | - Aleksandra M. Walczak
- Laboratoire de Physique de l’École Normale Supérieure (PSL University), CNRS, Sorbonne Université, Université de Paris, 75005 Paris, France; (T.M.); (A.M.W.)
| | - Florian Klein
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; (C.K.); (H.G.)
- German Center for Infection Research, Partner Site Bonn-Cologne, 50931 Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
- Correspondence:
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25
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Llopis-Lorente A, García-Fernández A, Murillo-Cremaes N, Hortelão AC, Patiño T, Villalonga R, Sancenón F, Martínez-Máñez R, Sánchez S. Enzyme-Powered Gated Mesoporous Silica Nanomotors for On-Command Intracellular Payload Delivery. ACS NANO 2019; 13:12171-12183. [PMID: 31580642 DOI: 10.1021/acsnano.9b06706] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The introduction of stimuli-responsive cargo release capabilities on self-propelled micro- and nanomotors holds enormous potential in a number of applications in the biomedical field. Herein, we report the preparation of mesoporous silica nanoparticles gated with pH-responsive supramolecular nanovalves and equipped with urease enzymes which act as chemical engines to power the nanomotors. The nanoparticles are loaded with different cargo molecules ([Ru(bpy)3]Cl2 (bpy = 2,2'-bipyridine) or doxorubicin), grafted with benzimidazole groups on the outer surface, and capped by the formation of inclusion complexes between benzimidazole and cyclodextrin-modified urease. The nanomotor exhibits enhanced Brownian motion in the presence of urea. Moreover, no cargo is released at neutral pH, even in the presence of the biofuel urea, due to the blockage of the pores by the bulky benzimidazole:cyclodextrin-urease caps. Cargo delivery is only triggered on-command at acidic pH due to the protonation of benzimidazole groups, the dethreading of the supramolecular nanovalves, and the subsequent uncapping of the nanoparticles. Studies with HeLa cells indicate that the presence of biofuel urea enhances nanoparticle internalization and both [Ru(bpy)3]Cl2 or doxorubicin intracellular release due to the acidity of lysosomal compartments. Gated enzyme-powered nanomotors shown here display some of the requirements for ideal drug delivery carriers such as the capacity to self-propel and the ability to "sense" the environment and deliver the payload on demand in response to predefined stimuli.
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Affiliation(s)
- Antoni Llopis-Lorente
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, Spain , Universitat Politècnica de València , Camino de Vera s/n , 46022 València , Spain
- Unidad Mixta UPV-CIPF de Investigación en Mecanismos de Enfermedades y Nanomedicina, Valencia , Universitat Politècnica de València, Centro de Investigación Príncipe Felipe , 46012 València , Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) , 28029 Madrid , Spain
| | - Alba García-Fernández
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, Spain , Universitat Politècnica de València , Camino de Vera s/n , 46022 València , Spain
- Unidad Mixta UPV-CIPF de Investigación en Mecanismos de Enfermedades y Nanomedicina, Valencia , Universitat Politècnica de València, Centro de Investigación Príncipe Felipe , 46012 València , Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) , 28029 Madrid , Spain
| | - Nerea Murillo-Cremaes
- Institute for Bioengineering of Catalonia (IBEC) , The Barcelona Institute of Science and Technology (BIST) , Baldiri Reixac 10-12 , 08028 Barcelona , Spain
| | - Ana C Hortelão
- Institute for Bioengineering of Catalonia (IBEC) , The Barcelona Institute of Science and Technology (BIST) , Baldiri Reixac 10-12 , 08028 Barcelona , Spain
| | - Tania Patiño
- Institute for Bioengineering of Catalonia (IBEC) , The Barcelona Institute of Science and Technology (BIST) , Baldiri Reixac 10-12 , 08028 Barcelona , Spain
| | - Reynaldo Villalonga
- Department of Analytical Chemistry, Faculty of Chemistry , Complutense University of Madrid , 28040 Madrid , Spain
| | - Félix Sancenón
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, Spain , Universitat Politècnica de València , Camino de Vera s/n , 46022 València , Spain
- Unidad Mixta UPV-CIPF de Investigación en Mecanismos de Enfermedades y Nanomedicina, Valencia , Universitat Politècnica de València, Centro de Investigación Príncipe Felipe , 46012 València , Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) , 28029 Madrid , Spain
| | - Ramón Martínez-Máñez
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, Spain , Universitat Politècnica de València , Camino de Vera s/n , 46022 València , Spain
- Unidad Mixta UPV-CIPF de Investigación en Mecanismos de Enfermedades y Nanomedicina, Valencia , Universitat Politècnica de València, Centro de Investigación Príncipe Felipe , 46012 València , Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) , 28029 Madrid , Spain
| | - Samuel Sánchez
- Institute for Bioengineering of Catalonia (IBEC) , The Barcelona Institute of Science and Technology (BIST) , Baldiri Reixac 10-12 , 08028 Barcelona , Spain
- Institució Catalana de Recerca i Estudies Avançats (ICREA) , Pg. Lluís Companys 23 , 08010 Barcelona , Spain
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Yao K, Rochman ND, Sun SX. Cell Type Classification and Unsupervised Morphological Phenotyping From Low-Resolution Images Using Deep Learning. Sci Rep 2019; 9:13467. [PMID: 31530889 PMCID: PMC6749053 DOI: 10.1038/s41598-019-50010-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 08/29/2019] [Indexed: 12/22/2022] Open
Abstract
Convolutional neural networks (ConvNets) have proven to be successful in both the classification and semantic segmentation of cell images. Here we establish a method for cell type classification utilizing images taken with a benchtop microscope directly from cell culture flasks, eliminating the need for a dedicated imaging platform. Significant flask-to-flask morphological heterogeneity was discovered and overcome to support network generalization to novel data. Cell density was found to be a prominent source of heterogeneity even when cells are not in contact. For the same cell types, expert classification was poor for single-cell images and better for multi-cell images, suggesting experts rely on the identification of characteristic phenotypes within subsets of each population. We also introduce Self-Label Clustering (SLC), an unsupervised clustering method relying on feature extraction from the hidden layers of a ConvNet, capable of cellular morphological phenotyping. This clustering approach is able to identify distinct morphological phenotypes within a cell type, some of which are observed to be cell density dependent. Finally, our cell classification algorithm was able to accurately identify cells in mixed populations, showing that ConvNet cell type classification can be a label-free alternative to traditional cell sorting and identification.
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Affiliation(s)
- Kai Yao
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America.,Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Nash D Rochman
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Sean X Sun
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America. .,Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland, United States of America. .,Physical Sciences in Oncology Center, Johns Hopkins University, Baltimore, Maryland, United States of America.
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27
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Abstract
Approximately 75% of all disease-relevant human proteins, including those involved in intracellular protein-protein interactions (PPIs), are undruggable with the current drug modalities (i.e., small molecules and biologics). Macrocyclic peptides provide a potential solution to these undruggable targets because their larger sizes (relative to conventional small molecules) endow them the capability of binding to flat PPI interfaces with antibody-like affinity and specificity. Powerful combinatorial library technologies have been developed to routinely identify cyclic peptides as potent, specific inhibitors against proteins including PPI targets. However, with the exception of a very small set of sequences, the vast majority of cyclic peptides are impermeable to the cell membrane, preventing their application against intracellular targets. This Review examines common structural features that render most cyclic peptides membrane impermeable, as well as the unique features that allow the minority of sequences to enter the cell interior by passive diffusion, endocytosis/endosomal escape, or other mechanisms. We also present the current state of knowledge about the molecular mechanisms of cell penetration, the various strategies for designing cell-permeable, biologically active cyclic peptides against intracellular targets, and the assay methods available to quantify their cell-permeability.
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Affiliation(s)
- Patrick G. Dougherty
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12 Avenue, Columbus, Ohio 43210, United States
| | - Ashweta Sahni
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12 Avenue, Columbus, Ohio 43210, United States
| | - Dehua Pei
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12 Avenue, Columbus, Ohio 43210, United States
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28
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Predicting Host Immune Cell Dynamics and Key Disease-Associated Genes Using Tissue Transcriptional Profiles. Processes (Basel) 2019. [DOI: 10.3390/pr7050301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Motivation: Immune cell dynamics is a critical factor of disease-associated pathology (immunopathology) that also impacts the levels of mRNAs in diseased tissue. Deconvolution algorithms attempt to infer cell quantities in a tissue/organ sample based on gene expression profiles and are often evaluated using artificial, non-complex samples. Their accuracy on estimating cell counts given temporal tissue gene expression data remains not well characterized and has never been characterized when using diseased lung. Further, how to remove the effects of cell migration on transcript counts to improve discovery of disease factors is an open question. Results: Four cell count inference (i.e., deconvolution) tools are evaluated using microarray data from influenza-infected lung sampled at several time points post-infection. The analysis finds that inferred cell quantities are accurate only for select cell types and there is a tendency for algorithms to have a good relative fit (R 2 ) but a poor absolute fit (normalized mean squared error; NMSE), which suggests systemic biases exist. Nonetheless, using cell fraction estimates to adjust gene expression data, we show that genes associated with influenza virus replication and increased infection pathology are more likely to be identified as significant than when applying traditional statistical tests.
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29
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Endothelial Microparticles in Uremia: Biomarkers and Potential Therapeutic Targets. Toxins (Basel) 2019; 11:toxins11050267. [PMID: 31086003 PMCID: PMC6563302 DOI: 10.3390/toxins11050267] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/05/2019] [Accepted: 05/08/2019] [Indexed: 12/26/2022] Open
Abstract
Endothelial microparticles (EMPs) are vesicles derived from cell membranes, which contain outsourced phosphatidylserine and express adhesion molecules, such as cadherin, intercellular cell adhesion molecule-1 (ICAM-1), E-selectin, and integrins. EMPs are expressed under physiological conditions and continue circulating in the plasma. However, in pathologic conditions their levels increase, and they assume a pro-inflammatory and pro-coagulant role via interactions with monocytes; these effects are related to the development of atherosclerosis. Chronic kidney dysfunction (CKD) characterizes this dysfunctional scenario through the accumulation of uremic solutes in the circulating plasma, whose toxicity is related to the development of cardiovascular diseases. Therefore, this review aims to discuss the formation of EMPs and their biological effects in the uremic environment. Data from previous research demonstrate that uremic toxins are closely associated with the activation of inflammatory biomarkers, cardiovascular dysfunction processes, and the release of EMPs. The impact of a decrease in circulating EMPs in clinical studies has not yet been evaluated. Thus, whether MPs are biochemical markers and/or therapeutic targets has yet to be established.
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30
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Echeverri D, Romo J, Giraldo N, Atehortúa L. Microalgae protoplasts isolation and fusion for biotechnology research. REVISTA COLOMBIANA DE BIOTECNOLOGÍA 2019. [DOI: 10.15446/rev.colomb.biote.v21n1.80248] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Protoplasts are microbial or vegetable cells lacking a cell wall. These can be obtained from microalgae by an enzymatic hydrolysis process in the presence of an osmotic stabilizer. In general, protoplasts are experimentally useful in physiological, geneticand bio-chemical studies, so their acquisition and fusion will continue to be an active research area in modern biotechnology. The fusion of protoplasts in microalgae constitutes a tool for strain improvement because it allows both intra and interspecific genetic recombina-tion, resulting in organisms with new or improved characteristics of industrial interest. In this review we briefly describe themethod-ology for obtaining protoplasts, as well as fusion methods and the main applications of microalgal platforms.
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31
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Hermabessiere L, Himber C, Boricaud B, Kazour M, Amara R, Cassone AL, Laurentie M, Paul-Pont I, Soudant P, Dehaut A, Duflos G. Optimization, performance, and application of a pyrolysis-GC/MS method for the identification of microplastics. Anal Bioanal Chem 2018; 410:6663-6676. [PMID: 30051208 DOI: 10.1007/s00216-018-1279-0] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 06/26/2018] [Accepted: 07/17/2018] [Indexed: 12/01/2022]
Abstract
Plastics are found to be major debris composing marine litter; microplastics (MP, < 5 mm) are found in all marine compartments. The amount of MPs tends to increase with decreasing size leading to a potential misidentification when only visual identification is performed. These last years, pyrolysis coupled with gas chromatography/mass spectrometry (Py-GC/MS) has been used to get information on the composition of polymers with some applications on MP identification. The purpose of this work was to optimize and then validate a Py-GC/MS method, determine limit of detection (LOD) for eight common polymers, and apply this method on environmental MP. Optimization on multiple GC parameters was carried out using polyethylene (PE) and polystyrene (PS) microspheres. The optimized Py-GC/MS method require a pyrolysis temperature of 700 °C, a split ratio of 5 and 300 °C as injector temperature. Performance assessment was accomplished by performing repeatability and intermediate precision tests and calculating limit of detection (LOD) for common polymers. LODs were all below 1 μg. For performance assessment, identification remains accurate despite a decrease in signal over time. A comparison between identifications performed with Raman micro spectroscopy and with Py-GC/MS was assessed. Finally, the optimized method was applied to environmental samples, including plastics isolated from sea water surface, beach sediments, and organisms collected in the marine environment. The present method is complementary to μ-Raman spectroscopy as Py-GC/MS identified pigment containing particles as plastic. Moreover, some fibers and all particles from sediment and sea surface were identified as plastic. Graphical abstract ᅟ.
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Affiliation(s)
- Ludovic Hermabessiere
- ANSES, Laboratoire de Sécurité des Aliments, Boulevard du Bassin Napoléon, 62200, Boulogne, France
| | - Charlotte Himber
- ANSES, Laboratoire de Sécurité des Aliments, Boulevard du Bassin Napoléon, 62200, Boulogne, France
| | - Béatrice Boricaud
- ANSES, Laboratoire de Sécurité des Aliments, Boulevard du Bassin Napoléon, 62200, Boulogne, France
| | - Maria Kazour
- UMR 8187, LOG, Laboratoire d'Océanologie et de Géosciences, CNRS, University of Littoral Côte d'Opale, University of Lille, 32 Avenue Foch, 62930, Wimereux, France.,CNRS, National Centre for Marine Sciences, PO Box 534, Batroun, Lebanon
| | - Rachid Amara
- UMR 8187, LOG, Laboratoire d'Océanologie et de Géosciences, CNRS, University of Littoral Côte d'Opale, University of Lille, 32 Avenue Foch, 62930, Wimereux, France
| | - Anne-Laure Cassone
- Laboratoire des Sciences de l'Environnement Marin (LEMAR), UMR6539/UBO/CNRS/IRD/IFREMER, Technopôle Brest-Iroise, Institut Universitaire Européen de la Mer, rue Dumont d'Urville, 29280, Plouzané, France
| | - Michel Laurentie
- ANSES, Plateforme PAS, Laboratoire de Fougères, 10 B rue Claude Bourgelat, Javené, 35300, Fougères, France
| | - Ika Paul-Pont
- Laboratoire des Sciences de l'Environnement Marin (LEMAR), UMR6539/UBO/CNRS/IRD/IFREMER, Technopôle Brest-Iroise, Institut Universitaire Européen de la Mer, rue Dumont d'Urville, 29280, Plouzané, France
| | - Philippe Soudant
- Laboratoire des Sciences de l'Environnement Marin (LEMAR), UMR6539/UBO/CNRS/IRD/IFREMER, Technopôle Brest-Iroise, Institut Universitaire Européen de la Mer, rue Dumont d'Urville, 29280, Plouzané, France
| | - Alexandre Dehaut
- ANSES, Laboratoire de Sécurité des Aliments, Boulevard du Bassin Napoléon, 62200, Boulogne, France
| | - Guillaume Duflos
- ANSES, Laboratoire de Sécurité des Aliments, Boulevard du Bassin Napoléon, 62200, Boulogne, France.
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32
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Leme Silva AG, Nagai MH, Malnic B. Fluorescence-Activated Cell Sorting of Olfactory Sensory Neuron Subpopulations. Methods Mol Biol 2018; 1820:69-76. [PMID: 29884938 DOI: 10.1007/978-1-4939-8609-5_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The mouse olfactory epithelium is composed of a heterogeneous population of olfactory sensory neurons, where each neuron expresses one single type of odorant receptor gene, out of a repertoire of ~1000 different genes. Fluorescent-activated cell sorting (FACS) is a powerful technique, which can be used to isolate a cellular subpopulation from a heterogeneous tissue. The sorted neurons can then be used in gene expression studies, or analyzed for the presence of different DNA epigenetic modification marks. Here we describe a method to separate a subpopulation of olfactory sensory neurons expressing the odorant receptor Olfr17. In this method, the main olfactory epithelium from transgenic Olfr17-IRES-GFP mice is dissociated into single cells, followed by separation of the GFP positive cells by FACS.
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Affiliation(s)
- Artur G Leme Silva
- Department of Biochemistry, University of Sao Paulo, São Paulo, SP, Brazil
| | - Maíra H Nagai
- Department of Biochemistry, University of Sao Paulo, São Paulo, SP, Brazil
| | - Bettina Malnic
- Department of Biochemistry, University of Sao Paulo, São Paulo, SP, Brazil.
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33
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Sung HH, Seok DI, Jung YH, Kim DJ, Lee SJ. Experience of Reticulocytes Measurement at 720 nm Using Spectrophotometer. KOREAN JOURNAL OF CLINICAL LABORATORY SCIENCE 2017. [DOI: 10.15324/kjcls.2017.49.4.382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Hyun-Ho Sung
- Department of Clinical Laboratory Science, Dongnam Health University, Suwon, Korea
- Department of Biomedical Engineering, Seonam University, Namwon, Korea
| | - Dong-In Seok
- Department of Clinical Laboratory Science, Dongnam Health University, Suwon, Korea
- Department of U2BIO, Jangwon Incorporated Foundation, Seoul, Korea
| | - You-Hyun Jung
- Department of Clinical Laboratory Medicine, Dongsuwon General Hospital, Suwon, Korea
| | - Dae-Jung Kim
- Department of Clinical Laboratory Science, Dongnam Health University, Suwon, Korea
- Department of Clinical Laboratory Medicine, Bundang Jesaeng Hospital, Seongnam, Korea
| | - Seok-Jae Lee
- Department of Biomedical Engineering, Seonam University, Namwon, Korea
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34
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Cortesi M, Bandiera L, Pasini A, Bevilacqua A, Gherardi A, Furini S, Giordano E. Reliable measurement of E. coli single cell fluorescence distribution using a standard microscope set-up. J Biol Eng 2017; 11:8. [PMID: 28239411 PMCID: PMC5317050 DOI: 10.1186/s13036-017-0050-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 01/18/2017] [Indexed: 12/21/2022] Open
Abstract
Background Quantifying gene expression at single cell level is fundamental for the complete characterization of synthetic gene circuits, due to the significant impact of noise and inter-cellular variability on the system’s functionality. Commercial set-ups that allow the acquisition of fluorescent signal at single cell level (flow cytometers or quantitative microscopes) are expensive apparatuses that are hardly affordable by small laboratories. Methods A protocol that makes a standard optical microscope able to acquire quantitative, single cell, fluorescent data from a bacterial population transformed with synthetic gene circuitry is presented. Single cell fluorescence values, acquired with a microscope set-up and processed with custom-made software, are compared with results that were obtained with a flow cytometer in a bacterial population transformed with the same gene circuitry. Results The high correlation between data from the two experimental set-ups, with a correlation coefficient computed over the tested dynamic range > 0.99, proves that a standard optical microscope– when coupled with appropriate software for image processing– might be used for quantitative single-cell fluorescence measurements. The calibration of the set-up, together with its validation, is described. Conclusions The experimental protocol described in this paper makes quantitative measurement of single cell fluorescence accessible to laboratories equipped with standard optical microscope set-ups. Our method allows for an affordable measurement/quantification of intercellular variability, whose better understanding of this phenomenon will improve our comprehension of cellular behaviors and the design of synthetic gene circuits. All the required software is freely available to the synthetic biology community (MUSIQ Microscope flUorescence SIngle cell Quantification). Electronic supplementary material The online version of this article (doi:10.1186/s13036-017-0050-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marilisa Cortesi
- Department of Electrical, Laboratory of Cellular and Molecular Engineering "S.Cavalcanti", Electronic and Information Engineering "G.Marconi" (DEI), University of Bologna, Cesena, Italy
| | - Lucia Bandiera
- Department of Electrical, Laboratory of Cellular and Molecular Engineering "S.Cavalcanti", Electronic and Information Engineering "G.Marconi" (DEI), University of Bologna, Cesena, Italy.,Present address: SynthSys - Center for Synthetic and Systems Biology and School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Alice Pasini
- Department of Electrical, Laboratory of Cellular and Molecular Engineering "S.Cavalcanti", Electronic and Information Engineering "G.Marconi" (DEI), University of Bologna, Cesena, Italy.,Present address: Division of Respiratory Medicine, School of Medicine, University of Nottingham, Nottingham, UK
| | - Alessandro Bevilacqua
- Advanced Research Center on Electronic Systems for Information and Communication Technologies "E. De Castro" (ARCES), University of Bologna, Bologna, Italy.,Department of Computer Science and Engineering (DISI), University of Bologna, Bologna, Italy
| | - Alessandro Gherardi
- Advanced Research Center on Electronic Systems for Information and Communication Technologies "E. De Castro" (ARCES), University of Bologna, Bologna, Italy
| | - Simone Furini
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Emanuele Giordano
- Department of Electrical, Laboratory of Cellular and Molecular Engineering "S.Cavalcanti", Electronic and Information Engineering "G.Marconi" (DEI), University of Bologna, Cesena, Italy.,Advanced Research Center on Electronic Systems for Information and Communication Technologies "E. De Castro" (ARCES), University of Bologna, Bologna, Italy.,BioEngLab, Health Science and Technology, Interdepartmental Center for Industrial Research (HST-CIRI), University of Bologna, Ozzano Emilia, Italy
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Abstract
The rise of genomically targeted therapies and immunotherapy has revolutionized the practice of oncology in the last 10–15 years. At the same time, new technologies and the electronic health record (EHR) in particular have permeated the oncology clinic. Initially designed as billing and clinical documentation systems, EHR systems have not anticipated the complexity and variety of genomic information that needs to be reviewed, interpreted, and acted upon on a daily basis. Improved integration of cancer genomic data with EHR systems will help guide clinician decision making, support secondary uses, and ultimately improve patient care within oncology clinics. Some of the key factors relating to the challenge of integrating cancer genomic data into EHRs include: the bioinformatics pipelines that translate raw genomic data into meaningful, actionable results; the role of human curation in the interpretation of variant calls; and the need for consistent standards with regard to genomic and clinical data. Several emerging paradigms for integration are discussed in this review, including: non-standardized efforts between individual institutions and genomic testing laboratories; “middleware” products that portray genomic information, albeit outside of the clinical workflow; and application programming interfaces that have the potential to work within clinical workflow. The critical need for clinical-genomic knowledge bases, which can be independent or integrated into the aforementioned solutions, is also discussed.
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Affiliation(s)
- Jeremy L Warner
- Department of Medicine, Division of Hematology/Oncology, Vanderbilt University, Nashville, TN, USA. .,Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, 37232, USA. .,Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.
| | - Sandeep K Jain
- Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, 37232, USA.,Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Mia A Levy
- Department of Medicine, Division of Hematology/Oncology, Vanderbilt University, Nashville, TN, USA.,Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, 37232, USA.,Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
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Genomic amplification of 9p24.1 targeting JAK2, PD-L1, and PD-L2 is enriched in high-risk triple negative breast cancer. Oncotarget 2016; 6:26483-93. [PMID: 26317899 PMCID: PMC4694916 DOI: 10.18632/oncotarget.4494] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 06/22/2015] [Indexed: 12/16/2022] Open
Abstract
We used DNA content flow cytometry followed by oligonucleotide array based comparative genomic hybridization to survey the genomes of 326 tumors, including 41 untreated surgically resected triple negative breast cancers (TNBC). A high level (log2ratio ≥ 1) 9p24 amplicon was found in TNBC (12/41), glioblastomas (2/44), and colon carcinomas (2/68). The shortest region of overlap for the amplicon targets 9p24.1 and includes the loci for PD-L1, PD-L2, and JAK2 (PDJ amplicon). In contrast this amplicon was absent in ER+ (0/8) and HER2+ (0/15) breast tumors, and in pancreatic ductal adenocarcinomas (0/150). The PDJ amplicon in TNBCs was correlated with clinical outcomes in group comparisons by two-sample t-tests for continuous variables and chi-squared tests for categorical variables. TNBC patients with the PDJ amplicon had a worse outcome with worse disease-free and overall survival. Quantitative RT-PCR confirmed that the PDJ amplicon in TNBC is associated with elevated expression of JAK2 and of the PD-1 ligands. These initial findings demonstrate that the PDJ amplicon is enriched in TNBC, targets signaling pathways that activate the PD-1 mediated immune checkpoint, and identifies patients with a poor prognosis.
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Rahmanian N, Bozorgmehr M, Torabi M, Akbari A, Zarnani AH. Cell separation: Potentials and pitfalls. Prep Biochem Biotechnol 2016; 47:38-51. [PMID: 27045194 DOI: 10.1080/10826068.2016.1163579] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Cell separation techniques play an indispensable part in numerous basic biological studies and even clinical settings. Although various cell isolation methods with diverse applications have been devised so far, not all of them have been able to gain widespread popularity among researchers and clinicians. There is not a single method known to be advantageous over all cell isolation techniques, and in fact, it is the researcher's aim in performing a study that determines the most suitable method. A perfect method for one study might not be necessarily a proper choice for another and likewise, expensive and complex isolation methods might not always be the best choices. There are several criteria such as cell purity, viability, activation status, and frequency that need to be given serious thought before selecting an isolation technique. Moreover, time and cost are two of the key elements that should be taken into consideration before implementing a project. Hence, here we provide a succinct description of six more popular cell separation methods with respect to their principles, advantages, and disadvantages as well as their most common applications. We further provide several key features of each technique so that it helps the researchers to take the first step toward opting for the best method that fits well into their projects.
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Affiliation(s)
- Narges Rahmanian
- a Department of Molecular Medicine, School of Advanced Technologies in Medicine , Tehran University of Medical Sciences , Tehran , Iran
| | - Mohmood Bozorgmehr
- b Oncopathology Research Center , Iran University of Medical Sciences , Tehran , Iran
| | - Monir Torabi
- c Department of Pathology, Shariati Hospital , Tehran University of Medical Sciences , Tehran , Iran
| | - Abolfazl Akbari
- d Colorectal Research Center , Iran University of Medical Sciences , Tehran , Iran
| | - Amir-Hassan Zarnani
- e Department of Immunology , School of Public Health, Tehran University of Medical Sciences , Tehran , Iran.,f Immunology Research Center , Iran University of Medical Sciences , Tehran , Iran
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Busch DH, Fräßle SP, Sommermeyer D, Buchholz VR, Riddell SR. Role of memory T cell subsets for adoptive immunotherapy. Semin Immunol 2016; 28:28-34. [PMID: 26976826 DOI: 10.1016/j.smim.2016.02.001] [Citation(s) in RCA: 157] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 02/03/2016] [Accepted: 02/10/2016] [Indexed: 12/14/2022]
Abstract
Adoptive transfer of primary (unmodified) or genetically engineered antigen-specific T cells has demonstrated astonishing clinical results in the treatment of infections and some malignancies. Besides the definition of optimal targets and antigen receptors, the differentiation status of transferred T cells is emerging as a crucial parameter for generating cell products with optimal efficacy and safety profiles. Long-living memory T cells subdivide into phenotypically as well as functionally different subsets (e.g. central memory, effector memory, tissue-resident memory T cells). This diversification process is crucial for effective immune protection, with probably distinct dependencies on the presence of individual subsets dependent on the disease to which the immune response is directed as well as its organ location. Adoptive T cell therapy intends to therapeutically transfer defined T cell immunity into patients. Efficacy of this approach often requires long-term maintenance of transferred cells, which depends on the presence and persistence of memory T cells. However, engraftment and survival of highly differentiated memory T cell subsets upon adoptive transfer is still difficult to achieve. Therefore, the recent observation that a distinct subset of weakly differentiated memory T cells shows all characteristics of adult tissue stem cells and can reconstitute all types of effector and memory T cell subsets, became highly relevant. We here review our current understanding of memory subset formation and T cell subset purification, and its implications for adoptive immunotherapy.
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Affiliation(s)
- Dirk H Busch
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich 81675, Germany; Focus Group "Clinical Cell Processing and Purification", Institute for Advanced Study, TUM, Munich 81675, Germany; National Center for Infection Research (DZIF), Munich 81675, Germany.
| | - Simon P Fräßle
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich 81675, Germany; Focus Group "Clinical Cell Processing and Purification", Institute for Advanced Study, TUM, Munich 81675, Germany
| | - Daniel Sommermeyer
- Program in Immunology, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Veit R Buchholz
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich 81675, Germany
| | - Stanley R Riddell
- Focus Group "Clinical Cell Processing and Purification", Institute for Advanced Study, TUM, Munich 81675, Germany; Program in Immunology, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Medicine, University of Washington, Seattle, WA 98109, USA.
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41
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Nogales-Gadea G, Saxena A, Hoffmann C, Hounjet J, Coenen D, Molenaar P, Losen M, Martinez-Martinez P. Generation of Recombinant Human IgG Monoclonal Antibodies from Immortalized Sorted B Cells. J Vis Exp 2015:e52830. [PMID: 26132628 PMCID: PMC4545184 DOI: 10.3791/52830] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Finding new methods for generating human monoclonal antibodies is an active research field that is important for both basic and applied sciences, including the development of immunotherapeutics. However, the techniques to identify and produce such antibodies tend to be arduous and sometimes the heavy and light chain pair of the antibodies are dissociated. Here, we describe a relatively simple, straightforward protocol to produce human recombinant monoclonal antibodies from human peripheral blood mononuclear cells using immortalization with Epstein-Barr Virus (EBV) and Toll-like receptor 9 activation. With an adequate staining, B cells producing antibodies can be isolated for subsequent immortalization and clonal expansion. The antibody transcripts produced by the immortalized B cell clones can be amplified by PCR, sequenced as corresponding heavy and light chain pairs and cloned into immunoglobulin expression vectors. The antibodies obtained with this technique can be powerful tools to study relevant human immune responses, including autoimmunity, and create the basis for new therapeutics.
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Affiliation(s)
- Gisela Nogales-Gadea
- School for Mental Health and Neuroscience, Maastricht University; Department of Neurosciences, Institut d'Investigació Germans Trias i Pujol
| | - Abhishek Saxena
- School for Mental Health and Neuroscience, Maastricht University
| | - Carolin Hoffmann
- School for Mental Health and Neuroscience, Maastricht University
| | - Judith Hounjet
- School for Mental Health and Neuroscience, Maastricht University
| | - Daniëlle Coenen
- School for Mental Health and Neuroscience, Maastricht University
| | - Peter Molenaar
- School for Mental Health and Neuroscience, Maastricht University
| | - Mario Losen
- School for Mental Health and Neuroscience, Maastricht University
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Abstract
The increasing interest towards cellular heterogeneity within cell populations has pushed the development of new protocols to isolate and analyze single cells. PCR-based amplification techniques are widely used in this field. However, setting up an experiment and analyzing the results can sometimes be challenging. The aim of this chapter is to provide a general overview on single-cell PCR analysis focusing on the potential pitfalls and on the possible solutions to successfully perform the analysis.
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Altboum Z, Steuerman Y, David E, Barnett-Itzhaki Z, Valadarsky L, Keren-Shaul H, Meningher T, Mendelson E, Mandelboim M, Gat-Viks I, Amit I. Digital cell quantification identifies global immune cell dynamics during influenza infection. Mol Syst Biol 2014; 10:720. [PMID: 24586061 PMCID: PMC4023392 DOI: 10.1002/msb.134947] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Hundreds of immune cell types work in coordination to maintain tissue homeostasis. Upon infection, dramatic changes occur with the localization, migration, and proliferation of the immune cells to first alert the body of the danger, confine it to limit spreading, and finally extinguish the threat and bring the tissue back to homeostasis. Since current technologies can follow the dynamics of only a limited number of cell types, we have yet to grasp the full complexity of global in vivo cell dynamics in normal developmental processes and disease. Here, we devise a computational method, digital cell quantification (DCQ), which combines genome‐wide gene expression data with an immune cell compendium to infer in vivo changes in the quantities of 213 immune cell subpopulations. DCQ was applied to study global immune cell dynamics in mice lungs at ten time points during 7 days of flu infection. We find dramatic changes in quantities of 70 immune cell types, including various innate, adaptive, and progenitor immune cells. We focus on the previously unreported dynamics of four immune dendritic cell subtypes and suggest a specific role for CD103+CD11b−DCs in early stages of disease and CD8+pDC in late stages of flu infection.
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Affiliation(s)
- Zeev Altboum
- Department of Immunology, Weizmann Institute, Rehovot, Israel
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Wang H, Silva A, Ho CM. When Medicine Meets Engineering-Paradigm Shifts in Diagnostics and Therapeutics. Diagnostics (Basel) 2013; 3:126-54. [PMID: 26835672 PMCID: PMC4665584 DOI: 10.3390/diagnostics3010126] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 01/10/2013] [Accepted: 01/23/2013] [Indexed: 01/09/2023] Open
Abstract
During the last two decades, the manufacturing techniques of microfluidics-based devices have been phenomenally advanced, offering unlimited potential for bio-medical technologies. However, the direct applications of these technologies toward diagnostics and therapeutics are still far from maturity. The present challenges lay at the interfaces between the engineering systems and the biocomplex systems. A precisely designed engineering system with narrow dynamic range is hard to seamlessly integrate with the adaptive biological system in order to achieve the design goals. These differences remain as the roadblock between two fundamentally non-compatible systems. This paper will not extensively review the existing microfluidic sensors and actuators; rather, we will discuss the sources of the gaps for integration. We will also introduce system interface technologies for bridging the differences to lead toward paradigm shifts in diagnostics and therapeutics.
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Affiliation(s)
- Hann Wang
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Aleidy Silva
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Chih-Ming Ho
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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He Y, Mo Z, Xue Z, Fang Y. Establish a flow cytometric method for quantitative detection of Beclin-1 expression. Cytotechnology 2013; 65:481-9. [PMID: 23435577 DOI: 10.1007/s10616-012-9503-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Accepted: 09/22/2012] [Indexed: 12/18/2022] Open
Abstract
Flow cytometry is an advanced technology for efficient, rapid, specific and multi-parameter analysis of single cells in various basic research fields including cytobiology, immunology, genetic, hematology and other basic research. Beclin-1 protein is an important indicator in monitoring autophagic activity. However, quantitative flow cytometry had been rarely reported till now to be applied in the detection of Beclin-1 expression. The present study was aimed to establish a flow cytometric method for quantitative detection of Beclin-1 expression by employing the autophagy inhibitor 3-methyladenine as the control. A multi-parameter optimal method for Beclin-1 protein staining is as follows. 2 % bovine serum albumin in phosphate buffered saline was used for sample block. Concentration of primary antibody was 0.004 μg/μL. Samples were incubated at room temperature (25 °C) for 30 min. The prepared samples had better to be detected immediately or to be stored at 4 °C and detected within 6 h, otherwise the samples should be fixed in 1 % paraformaldehyde storing at 4 °C and detected within 3 d. Furthermore, we employed the immunohistochemistry to validate the method in vivo, the results confirmed flow cytometric method. The established flow cytometric analysis for Beclin-1 protein has the advantage of simpleness, speediness, sensitivity and reproducibility.
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Affiliation(s)
- Yuping He
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, 16, Jichang Road, Guangzhou, 510405, People's Republic of China
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Barrett MT, Lenkiewicz E, Evers L, Holley T, Ruiz C, Bubendorf L, Sekulic A, Ramanathan RK, Von Hoff DD. Clonal evolution and therapeutic resistance in solid tumors. Front Pharmacol 2013; 4:2. [PMID: 23372550 PMCID: PMC3556559 DOI: 10.3389/fphar.2013.00002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2012] [Accepted: 01/07/2013] [Indexed: 01/08/2023] Open
Abstract
Tumors frequently arise as a result of an acquired genomic instability and the subsequent evolution of neoplastic populations with variable genomes. A barrier to the study of the somatic genetics of human solid tumors in vivo is the presence of admixtures of non-neoplastic cells with normal genomes in patient samples. These can obscure the presence of somatic aberrations including mutations, homozygous deletions, and breakpoints in biopsies of interest. Furthermore, clinical samples frequently contain multiple neoplastic populations that cannot be distinguished by morphology. Consequently, it is difficult to determine whether mutations detected in a sample of interest are concurrent in a single clonal population or if they occur in distinct cell populations in the same sample. The advent of targeted therapies increases the selection for preexisting populations. However the asymmetric distribution of therapeutic targets in clonal populations provides a mechanism for the rapid evolution of resistant disease. Thus, there is a need to not only isolate tumor from normal cells, but to also enrich distinct populations of clonal neoplastic cells in order to apply genome technologies to identify clinically relevant genomic aberrations that drive disease in patients in vivo. To address this we have applied single and multiparameter DNA content based flow assays to the study of solid tumors. Our work has identified examples of clonal resistance to effective therapies. This includes androgen withdrawal in advanced prostate cancer. In addition we demonstrate examples of co-existing clonal populations with highly aberrant genomes and ploidies in a wide variety of solid tumors. We propose that clonal analysis of tumors, based on flow cytometry and high resolution genome analyses of purified neoplastic populations, provides a unique approach to the study of therapeutic responses and the evolution of resistance.
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Affiliation(s)
- Michael T Barrett
- The Translational Genomics Research Institute Scottsdale, AZ, USA ; Mayo Clinic Arizona Scottsdale, AZ, USA
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Abstract
Symbioses between microbes are likely widespread and functionally relevant in diverse biological systems; however, they are difficult to discover. Most microbes remain uncultivated, symbioses can be relatively rare or dynamic, and intercellular connections can be delicate. Thus, traditional methods such as microscopy are inadequate for efficient discovery and precise characterization of novel interactions, their metabolic basis, and the species involved. High-throughput metagenomic sequencing of entire microbial communities has revolutionized the field of microbial ecology; however, genomic signals from symbionts can get buried in sequences from abundant organisms and evidence for direct links between microbial species cannot be gained from bulk samples. Thus, a specialized approach to the characterization of symbioses between naturally occurring microbes is required. This chapter presents methods for combining fluorescence-activated cell sorting to isolate and separate uncultivated symbionts with molecular biology techniques for DNA amplification in order to characterize uncultivated symbionts through genomic and metagenomic techniques.
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Holley T, Lenkiewicz E, Evers L, Tembe W, Ruiz C, Gsponer JR, Rentsch CA, Bubendorf L, Stapleton M, Amorese D, Legendre C, Cunliffe HE, McCullough AE, Pockaj B, Craig D, Carpten J, Von Hoff D, Iacobuzio-Donahue C, Barrett MT. Deep clonal profiling of formalin fixed paraffin embedded clinical samples. PLoS One 2012; 7:e50586. [PMID: 23226320 PMCID: PMC3511535 DOI: 10.1371/journal.pone.0050586] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 10/23/2012] [Indexed: 01/15/2023] Open
Abstract
Formalin fixed paraffin embedded (FFPE) tissues are a vast resource of annotated clinical samples. As such, they represent highly desirable and informative materials for the application of high definition genomics for improved patient management and to advance the development of personalized therapeutics. However, a limitation of FFPE tissues is the variable quality of DNA extracted for analyses. Furthermore, admixtures of non-tumor and polyclonal neoplastic cell populations limit the number of biopsies that can be studied and make it difficult to define cancer genomes in patient samples. To exploit these valuable tissues we applied flow cytometry-based methods to isolate pure populations of tumor cell nuclei from FFPE tissues and developed a methodology compatible with oligonucleotide array CGH and whole exome sequencing analyses. These were used to profile a variety of tumors (breast, brain, bladder, ovarian and pancreas) including the genomes and exomes of matching fresh frozen and FFPE pancreatic adenocarcinoma samples.
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Affiliation(s)
- Tara Holley
- Clinical Translational Research Division, Translational Genomics Research Institute, Scottsdale, Arizona, United States of America
| | - Elizabeth Lenkiewicz
- Clinical Translational Research Division, Translational Genomics Research Institute, Scottsdale, Arizona, United States of America
| | - Lisa Evers
- Clinical Translational Research Division, Translational Genomics Research Institute, Scottsdale, Arizona, United States of America
| | - Waibhav Tembe
- Collaborative Bioinformatics Center, Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Christian Ruiz
- Institute for Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Joel R. Gsponer
- Institute for Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Cyrill A. Rentsch
- Institute for Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
- Department of Urology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Lukas Bubendorf
- Institute for Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | | | - Doug Amorese
- NuGEN, San Carlos, California, United States of America
| | - Christophe Legendre
- Collaborative Bioinformatics Center, Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Heather E. Cunliffe
- Computational Biology Division, Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Ann E. McCullough
- Department of Laboratory Medicine, Mayo Clinic, Scottsdale, Arizona, United States of America
| | - Barbara Pockaj
- Department of Surgery, Mayo Clinic, Scottsdale, Arizona, United States of America
| | - David Craig
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - John Carpten
- Integrated Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Daniel Von Hoff
- Clinical Translational Research Division, Translational Genomics Research Institute, Scottsdale, Arizona, United States of America
- Virginia G. Piper Cancer Center, Scottsdale Healthcare, Scottsdale, Arizona, United States of America
| | | | - Michael T. Barrett
- Clinical Translational Research Division, Translational Genomics Research Institute, Scottsdale, Arizona, United States of America
- * E-mail:
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Liu SV, Lenkiewicz E, Evers L, Holley T, Kiefer J, Ruiz C, Glatz K, Bubendorf L, Demeure MJ, Eng C, Ramanathan RK, Von Hoff DD, Barrett MT. Genomic analysis and selected molecular pathways in rare cancers. Phys Biol 2012. [DOI: 10.1088/1478-3975/9/6/065004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Abstract
The separation and or isolation of rare cells using magnetic forces are commonly used and growing in use ranging from simple sample prep for further studies to a FDA approved, clinical diagnostic test. This growth is the result of both the demand to obtain homogeneous rare cells for molecular analysis and the dramatic increases in the power of permanent magnets that even allow the separation of some unlabeled cells based on intrinsic magnetic moments, such as malaria parasite-infected red blood cells.
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Affiliation(s)
- Maciej Zborowski
- Department of Biomedical Engineering/ND-20, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, United States
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