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Smith S, Sypabekova M, Kim S. Double-Sided Tape in Microfluidics: A Cost-Effective Method in Device Fabrication. BIOSENSORS 2024; 14:249. [PMID: 38785723 PMCID: PMC11118809 DOI: 10.3390/bios14050249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 04/17/2024] [Accepted: 05/09/2024] [Indexed: 05/25/2024]
Abstract
The demand for easy-to-use, affordable, accessible, and reliable technology is increasing in biological, chemical, and medical research. Microfluidic devices have the potential to meet these standards by offering cost-effective, highly sensitive, and highly specific diagnostic tests with rapid performance and minimal sample volumes. Traditional microfluidic device fabrication methods, such as photolithography and soft lithography, are time-consuming and require specialized equipment and expertise, making them costly and less accessible to researchers and clinicians and limiting the applicability and potential of microfluidic devices. To address this, researchers have turned to using new low-cost materials, such as double-sided tape for microfluidic device fabrication, which offers simple and low-cost processes. The innovation of low-cost and easy-to-make microfluidic devices improves the potential for more devices to be transitioned from laboratories to commercialized products found in stores, offices, and homes. This review serves as a comprehensive summary of the growing interest in and use of double-sided tape-based microfluidic devices in the last 20 years. It discusses the advantages of using double-sided tape, the fabrication techniques used to create and bond microfluidic devices, and the limitations of this approach in certain applications.
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Affiliation(s)
| | | | - Seunghyun Kim
- Department of Electrical & Computer Engineering, Baylor University, Waco, TX 76798, USA; (S.S.); (M.S.)
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Konanov DN, Babenko VV, Belova AM, Madan AG, Boldyreva DI, Glushenko OE, Butenko IO, Fedorov DE, Manolov AI, Krivonos DV, Lazarev VN, Govorun VM, Ilina EN. Snapper: high-sensitive detection of methylation motifs based on Oxford Nanopore reads. Bioinformatics 2023; 39:btad702. [PMID: 37982752 PMCID: PMC10689673 DOI: 10.1093/bioinformatics/btad702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 11/13/2023] [Accepted: 11/17/2023] [Indexed: 11/21/2023] Open
Abstract
MOTIVATION The Oxford Nanopore technology has a great potential for the analysis of methylated motifs in genomes, including whole-genome methylome profiling. However, we found that there are no methylation motifs detection algorithms, which would be sensitive enough and return deterministic results. Thus, the MEME suit does not extract all Helicobacter pylori methylation sites de novo even using the iterative approach implemented in the most up-to-date methylation analysis tool Nanodisco. RESULTS We present Snapper, a new highly sensitive approach, to extract methylation motif sequences based on a greedy motif selection algorithm. Snapper does not require manual control during the enrichment process and has enrichment sensitivity higher than MEME coupled with Tombo or Nanodisco instruments that was demonstrated on H.pylori strain J99 studied earlier by the PacBio technology and on four external datasets representing different bacterial species. We used Snapper to characterize the total methylome of a new H.pylori strain A45. At least four methylation sites that have not been described for H.pylori earlier were revealed. We experimentally confirmed the presence of a new CCAG-specific methyltransferase and inferred a gene encoding a new CCAAK-specific methyltransferase. AVAILABILITY AND IMPLEMENTATION Snapper is implemented using Python and is freely available as a pip package named "snapper-ont." Also, Snapper and the demo dataset are available in Zenodo (10.5281/zenodo.10117651).
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Affiliation(s)
- Dmitry N Konanov
- Research Institute for Systems Biology and Medicine, Moscow 117246, Russia
| | - Vladislav V Babenko
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow 119435, Russia
| | - Aleksandra M Belova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow 119435, Russia
| | - Arina G Madan
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow 119435, Russia
- Department of Molecular and Translational Medicine, Moscow Institute of Physics and Technology, State University, Dolgoprudny 141700, Russia
| | - Daria I Boldyreva
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow 119435, Russia
| | - Oksana E Glushenko
- Research Institute for Systems Biology and Medicine, Moscow 117246, Russia
| | - Ivan O Butenko
- Research Institute for Systems Biology and Medicine, Moscow 117246, Russia
| | - Dmitry E Fedorov
- Research Institute for Systems Biology and Medicine, Moscow 117246, Russia
| | | | - Danil V Krivonos
- Research Institute for Systems Biology and Medicine, Moscow 117246, Russia
- Department of Molecular and Translational Medicine, Moscow Institute of Physics and Technology, State University, Dolgoprudny 141700, Russia
| | - Vassilii N Lazarev
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow 119435, Russia
| | - Vadim M Govorun
- Research Institute for Systems Biology and Medicine, Moscow 117246, Russia
| | - Elena N Ilina
- Research Institute for Systems Biology and Medicine, Moscow 117246, Russia
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Jaradat H, Al-Hamry A, Ibbini M, Fourati N, Kanoun O. Novel Sensitive Electrochemical Immunosensor Development for the Selective Detection of HopQ H. pylori Bacteria Biomarker. BIOSENSORS 2023; 13:bios13050527. [PMID: 37232889 DOI: 10.3390/bios13050527] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/04/2023] [Accepted: 05/06/2023] [Indexed: 05/27/2023]
Abstract
Helicobacter pylori (H. pylori) is a highly contagious pathogenic bacterium that can cause gastrointestinal ulcers and may gradually lead to gastric cancer. H. pylori expresses the outer membrane HopQ protein at the earliest stages of infection. Therefore, HopQ is a highly reliable candidate as a biomarker for H. pylori detection in saliva samples. In this work, an H. pylori immunosensor is based on detecting HopQ as an H. pylori biomarker in saliva. The immunosensor was developed by surface modification of screen-printed carbon electrodes (SPCE) with MWCNT-COOH decorated with gold nanoparticles (AuNP) followed by HopQ capture antibody grafting on SPCE/MWCNT/AuNP surface using EDC/S-NHS chemistry. The sensor performance was investigated utilizing various methods, such as cyclic voltammetry (CV), electrochemical impedance spectroscopy (EIS), and scanning electron microscope (SEM) coupled with energy-dispersive X-ray spectroscopy (EDX). H. pylori detection performance in spiked saliva samples was evaluated by square wave voltammetry (SWV). The sensor is suitable for HopQ detection with excellent sensitivity and linearity in the 10 pg/mL-100 ng/mL range, with a 2.0 pg/mL limit of detection (LOD) and an 8.6 pg/mL limit of quantification (LOQ). The sensor was tested in saliva at 10 ng/mL, and recovery of 107.6% was obtained by SWV. From Hill's model, the dissociation constant Kd for HopQ/HopQ antibody interaction is estimated to be 4.60 × 10-10 mg/mL. The fabricated platform shows high selectivity, good stability, reproducibility, and cost-effectiveness for H. pylori early detection due to the proper choice of biomarker, the nanocomposite material utilization to boost the SPCE electrical performance, and the intrinsic selectivity of the antibody-antigen approach. Additionally, we provide insight into possible future aspects that researchers are recommended to focus on.
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Affiliation(s)
- Hussamaldeen Jaradat
- Measurement and Sensor Technology, Chemnitz University of Technology, 09126 Chemnitz, Germany
| | - Ammar Al-Hamry
- Measurement and Sensor Technology, Chemnitz University of Technology, 09126 Chemnitz, Germany
| | - Mohammed Ibbini
- Department of Biomedical Engineering, Jordan University of Science and Technology, Irbid 22110, Jordan
| | - Najla Fourati
- SATIE Laboratory, UMR CNRS 8029, Conservatoire National des Arts et Métiers, 75003 Paris, France
| | - Olfa Kanoun
- Measurement and Sensor Technology, Chemnitz University of Technology, 09126 Chemnitz, Germany
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Prusakov KA, Bagrov DV, Basmanov DV, Romanov SA, Klinov DV. Fluorescence imaging of cells using long-range electromagnetic surface waves for excitation. APPLIED OPTICS 2020; 59:4833-4838. [PMID: 32543477 DOI: 10.1364/ao.389120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 04/22/2020] [Indexed: 06/11/2023]
Abstract
We present a depth-localized illumination technique for wide-field fluorescence microscopy, based on long-range optical surface waves. This technique allows one to excite the fluorescence only in a thin near-substrate layer of the specimen. Our experimental setup is compatible with both upright and inverted microscopes. It provides fluorescent microscopic images, which are superior to the epifluorescence ones in signal-to-noise ratio, contrast, and detail. We demonstrate the applicability of our technique for imaging both bacterial and eukaryotic cells (E. coli and HeLa, respectively).
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Belova AM, Basmanov DV, Babenko VV, Podgorny OV, Mitko TV, Prusakov KA, Klinov DV, Lazarev VN. Two novel transcriptional reporter systems for monitoring Helicobacter pylori stress responses. Plasmid 2019; 106:102442. [PMID: 31669286 DOI: 10.1016/j.plasmid.2019.102442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 09/09/2019] [Accepted: 09/17/2019] [Indexed: 11/27/2022]
Abstract
Helicobacter pylori, a human pathogen linked to many stomach diseases, is well adapted to colonize aggressive gastric environments, and its virulence factors contribute this adaptation. Here, we report the construction of two novel H. pylori vectors, pSv2 and pSv4, carrying a reporter gene fused to the promoters of virulence factor genes for monitoring the response of single H. pylori cells to various stresses. H. pylori cryptic plasmids were modified by the introduction of the Escherichia coli origin of replication, chloramphenicol resistance cassette, and promoterless gfp gene to produce E. coli/H. pylori shuttle vectors. The promoter regions of vacA and ureA genes encoding well-characterized H. pylori virulence factors were fused to the promoterless gfp gene. Recording the GFP fluorescence signal from the genetically modified H. pylori cells immobilized in specifically designed microfluidic devices revealed the response of transcriptional reporter systems to osmotic stress, acidic stress, elevated Ni2+ concentration or iron chelation. Our observations validate the utility of the pSv2 and pSv4 vectors to monitor the regulation of virulence factor genes in diverse strains and clinical isolates of H. pylori.
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Affiliation(s)
- A M Belova
- Federal Research Clinical Center of Physical-Chemical Medicine, Federal Medical and Biological Agency of Russia, Moscow 119435, Russia.
| | - D V Basmanov
- Federal Research Clinical Center of Physical-Chemical Medicine, Federal Medical and Biological Agency of Russia, Moscow 119435, Russia
| | - V V Babenko
- Federal Research Clinical Center of Physical-Chemical Medicine, Federal Medical and Biological Agency of Russia, Moscow 119435, Russia
| | - O V Podgorny
- Federal Research Clinical Center of Physical-Chemical Medicine, Federal Medical and Biological Agency of Russia, Moscow 119435, Russia; Koltzov Institute of Developmental Biology of the Russian Academy of Sciences, Moscow 119334, Russia
| | - T V Mitko
- Federal Research Clinical Center of Physical-Chemical Medicine, Federal Medical and Biological Agency of Russia, Moscow 119435, Russia
| | - K A Prusakov
- Federal Research Clinical Center of Physical-Chemical Medicine, Federal Medical and Biological Agency of Russia, Moscow 119435, Russia
| | - D V Klinov
- Federal Research Clinical Center of Physical-Chemical Medicine, Federal Medical and Biological Agency of Russia, Moscow 119435, Russia
| | - V N Lazarev
- Federal Research Clinical Center of Physical-Chemical Medicine, Federal Medical and Biological Agency of Russia, Moscow 119435, Russia
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