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Li H, Zhang P, Hsieh K, Wang TH. Combinatorial nanodroplet platform for screening antibiotic combinations. LAB ON A CHIP 2022; 22:621-631. [PMID: 35015012 PMCID: PMC9035339 DOI: 10.1039/d1lc00865j] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The emergence and spread of multidrug resistant bacterial strains and concomitant dwindling of effective antibiotics pose worldwide healthcare challenges. To address these challenges, advanced engineering tools are developed to personalize antibiotic treatments by speeding up the diagnostics that is critical to prevent antibiotic misuse and overuse and make full use of existing antibiotics. Meanwhile, it is necessary to investigate novel antibiotic strategies. Recently, repurposing mono antibiotics into combinatorial antibiotic therapies has shown great potential for treatment of bacterial infections. However, widespread adoption of drug combinations has been hindered by the complexity of screening techniques and the cost of reagent consumptions in practice. In this study, we developed a combinatorial nanodroplet platform for automated and high-throughput screening of antibiotic combinations while consuming orders of magnitude lower reagents than the standard microtiter-based screening method. In particular, the proposed platform is capable of creating nanoliter droplets with multiple reagents in an automatic manner, tuning concentrations of each component, performing biochemical assays with high flexibility (e.g., temperature and duration), and achieving detection with high sensitivity. A biochemical assay, based on the reduction of resazurin by the metabolism of bacteria, has been characterized and employed to evaluate the combinatorial effects of the antibiotics of interest. In a pilot study, we successfully screened pairwise combinations between 4 antibiotics for a model Escherichia coli strain.
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Affiliation(s)
- Hui Li
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, USA.
| | - Pengfei Zhang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Kuangwen Hsieh
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, USA.
| | - Tza-Huei Wang
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, USA.
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
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Assays of CFTR Function In Vitro, Ex Vivo and In Vivo. Int J Mol Sci 2022; 23:ijms23031437. [PMID: 35163362 PMCID: PMC8836180 DOI: 10.3390/ijms23031437] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/12/2022] [Accepted: 01/21/2022] [Indexed: 12/22/2022] Open
Abstract
Cystic fibrosis, a multi-organ genetic disease, is characterized by abnormal function of the cystic fibrosis transmembrane conductance regulator (CFTR) protein, a chloride channel at the apical membrane of several epithelia. In recent years, therapeutic strategies have been developed to correct the CFTR defect. To evaluate CFTR function at baseline for diagnosis, or the efficacy of CFTR-restoring therapy, reliable tests are needed to measure CFTR function, in vitro, ex vivo and in vivo. In vitro techniques either directly or indirectly measure ion fluxes; direct measurement of ion fluxes and quenching of fluorescence in cell-based assays, change in transmembrane voltage or current in patch clamp or Ussing chamber, swelling of CFTR-containing organoids by secondary water influx upon CFTR activation. Several cell or tissue types can be used. Ex vivo and in vivo assays similarly evaluate current (intestinal current measurement) and membrane potential differences (nasal potential difference), on tissues from individual patients. In the sweat test, the most frequently used in vivo evaluation of CFTR function, chloride concentration or stimulated sweat rate can be directly measured. Here, we will describe the currently available bio-assays for quantitative evaluation of CFTR function, their indications, advantages and disadvantages, and correlation with clinical outcome measures.
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Ma Z, Zhao H, Shi L, Yu D, Guo X. Automatic medium exchange for micro-volume cell samples based on dielectrophoresis. Electrophoresis 2021; 42:1507-1515. [PMID: 33990980 DOI: 10.1002/elps.202000195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 03/27/2021] [Accepted: 04/20/2021] [Indexed: 11/06/2022]
Abstract
Cell medium exchange is a crucial step for life science and medicine. However, conventional cell medium exchange methods, including centrifuging and filtering, show limited ability for micro-volume cell samples such as circulating tumor cell (CTC) and circulating fetal cell (CFC). In this paper, we proposed an automatic medium exchange method for micro-volume cell samples based on dielectrophoresis (DEP) in microfluidic chip. Fresh medium and cell suspension were introduced into the microfluidic channel as the laminar flow. Plane stair-shaped interdigital electrodes were employed to drive the cells from the cell suspension to fresh media directly by DEP force. Additionally, we characterized and optimized the cell medium exchange according to both the theory and experiments. In the end, we achieved a 96.9% harvest rate of medium exchange for 0.3 μL samples containing micro-volume cells. For implementing an automatic continuous cell medium exchange, the proposed method can be integrated into the automatic cell processing system conveniently. Furthermore, the proposed method is a great candidate in micro-volume cell analysis and processing, cell electroporation, single cell sequencing, and other scenarios.
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Affiliation(s)
- Zhouyang Ma
- College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, P. R. China
| | - Hongwang Zhao
- School of Automobile and Traffic Engineering, Guilin University of Aerospace Technology, Guilin, Guangxi, P. R. China
| | - Liujia Shi
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, P. R. China
| | - Duli Yu
- College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, P. R. China.,Beijing Advance Innovation Center for Soft Matter Science and Engineering, Beijing, P. R. China
| | - Xiaoliang Guo
- College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, P. R. China
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Khalkhal E, Nobakht F, Haidari MH, Razaghi Z, Ghasemzad M, Sheikhan M, Rostami Nejad M. Evaluation of expression of common genes in the intestine and peripheral blood mononuclear cells (PBMC) associated with celiac disease. GASTROENTEROLOGY AND HEPATOLOGY FROM BED TO BENCH 2020; 13:S60-S67. [PMID: 33585005 PMCID: PMC7881404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
AIM this study was conducted to investigate expression of the genes associated with CD in the target tissue in order to estimate contribution of each single gene to development of immune response. Then, the same set of genes was evaluated in peripheral blood mononuclear cells (PBMCs). BACKGROUND Celiac disease (CD) is a chronic systemic autoimmune disease of the small intestine occurring in genetically-susceptible individuals. There are several genes related to immune response. METHODS For this purpose, the genes related to CD were extracted from public databases (documents of proteomics and microarray-based techniques) and were organized in a protein-protein interaction network using the search tool for retrieval of interacting genes/proteins (STRING) database as a plugin of Cytoscape software version 3.6.0. The main genes were introduced and enriched via ClueGO to find the related biochemical pathways. The network was analyzed, and the most important genes were introduced based on central indices. RESULTS Among 20 CD genes as hub and bottleneck nodes, there were 7 genes with common expression in blood and intestinal tissue (C-X-C motif chemokine 11(CXCL11), granzyme B (GZMB), interleukin 15(IL-15), interleukin 17(IL-17A), interleukin 23(IL-23A), t-box transcription factor 21(TBX21), and tumor necrosis factor alpha-induced protein 3(TNFAIP3)). CONCLUSION The enriched biological process related to the central nodes of celiac network indicated that most of hub-bottleneck genes are the well-known ones involved in different types of autoimmune and inflammatory diseases.
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Affiliation(s)
- Ensieh Khalkhal
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fatemeh Nobakht
- Chemical Injuries Research Center, Systems Biology and Poisoning Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mohammad Hossain Haidari
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zahra Razaghi
- Laser Application in Medical Sciences Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mahsa Ghasemzad
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Melika Sheikhan
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Rostami Nejad
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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3D Printed Lab-on-a-Chip Platform for Chemical Stimulation and Parallel Analysis of Ion Channel Function. MICROMACHINES 2019; 10:mi10080548. [PMID: 31430884 PMCID: PMC6722671 DOI: 10.3390/mi10080548] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/06/2019] [Accepted: 08/16/2019] [Indexed: 12/27/2022]
Abstract
Functional imaging has been a widely established method for the assessment of ion channel function in vitro. Conventional infrastructure used for in vitro functional analysis of ion channels is typically proprietary, non-customizable, expensive, and requires a high level of skill to use and maintain. 3D desktop printing, which is employed in the rapid prototyping field, allows for quick engineering of alternatives to conventional imaging infrastructure that are customizable, low cost, and user friendly. Here, we describe an ultra-low-cost microfluidic lab-on-a-chip (LOC) device manufactured using acrylonitrile butadiene styrene (ABS) for in vitro functional imaging of ion channels that can quickly and easily be reconstructed using three-dimensional (3D) desktop printing. The device is light weight (<5 g), small (20 mm × 49 mm), and extremely low cost (<EUR 1). We simulate fluidics within the printed channels and assess the suitability of the engineered chamber to generate homogeneous mixtures during solution exchange. We demonstrate the usability of the 3D printed microfluidic device in a case study using Fluo-4-loaded human embryonal kidney-derived (HEK293) cells, recombinantly expressing the capsaicin receptor, transient receptor potential vanilloid receptor type 1 (TRPV1), as a model system. In the case study, we confirm its applicability to solution exchange for chemical stimulation and parallel functional time-lapse fluorescence microscopy-based calcium imaging. We assess the suitability of ABS for culturing HEK293 cells inside the microfluidic LOC, based on qualitative analysis of microscopic transmission light images of ABS-exposed HEK293 cells and confirm the previously reported biocompatibility of ABS. To highlight the versatility of the 3D printed microfluidic device, we provide an example for multiplication of the shown concept within a 3D printed multichannel microfluidic LOC to be used, for example, in a higher throughput format for parallelized functional analysis of ion channels. While this work focusses on Ca2+ imaging with TRPV1 channels, the device may also be useful for application with other ion channel types and in vitro models.
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Rezaei Tavirani M, Bashash D, Tajik Rostami F, Rezaei Tavirani S, Nikzamir A, Rezaei Tavirani M, Haidary MH. Celiac disease microarray analysis based on System Biology Approach. GASTROENTEROLOGY AND HEPATOLOGY FROM BED TO BENCH 2018; 11:216-224. [PMID: 30013745 PMCID: PMC6040039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AIM Aim of this study is screen of the large numbers of related genes of CD to find the key ones. BACKGROUND Celiac disease (CD) is known as a gluten sensitive and immune system dependent disease. There are several high throughput investigations about CD but it is necessary to clarify new molecular aspects mechanism of celiac. METHODS Whole-genome profile (RNA) of the human peripheral blood mononuclear cells (PBMCs) as Gene expression profile GSE113469 was retrieved Gene Expression Omnibus (GEO) database. The significant genes were selected and analyzed via protein-protein interaction (PPI) network by Cytoscape software. The key genes were introduced and enriched via ClueGO to find the related biochemical pathways. RESULTS Among 250 significant genes 47 genes with expressed change above 2 fold change (FC) were interacted and the constructed network were analyzed. The network characterized by poor connections so it was promoted by addition 50 related nodes and 18 crucial nodes were introduced. Two clusters of biochemical pathways were identified and discussed. CONCLUSION There is an obvious conflict between microarray finding and the well-known related genes of CD. This problem can be solve by more attention to the interpretation of PPI ntwork analysis results.
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Affiliation(s)
- Mostafa Rezaei Tavirani
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Davood Bashash
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Sina Rezaei Tavirani
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Abdolrahim Nikzamir
- Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Mohammad Hossain Haidary
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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